cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8253367
title: Improving antibody language models with native pairing

description: Motivation. Existing large language models designed to predict antibody structure and function have been trained exclusively with unpaired antibody sequences. This is a substantial drawback, as each antibody represents a unique pairing of heavy and light chains that both contribute to antigen recognition. The cost of generating large datasets of natively paired antibody sequences is orders of magnitude higher than the cost of unpaired sequences, and the paucity of available paired antibody sequence datasets precludes training a state-of-the-art language model using only paired training data. Here, we sought to determine whether and to what extent natively paired training data improves model performance.


Results. Using a unique and recently reported dataset of approximately 1.6 x 106 natively paired human antibody sequences, we trained two baseline antibody language model (BALM) variants: BALM-paired and BALM-unpaired. We quantify the superiority of BALM-paired over BALM-unpaired, and we show that BALM-paired's improved performance can be attributed at least in part to its ability to learn cross-chain features that span natively paired heavy and light chains. Additionally, we fine-tuned the general protein language model ESM-2 using these paired antibody sequences and report that the fine-tuned model, but not base ESM-2, demonstrates a similar understanding of cross-chain features.


Files. The following files are included in this repository:



	
BALM-paired.tar.gz: Model weights for the BALM-paired model.
	
BALM-unpaired.tar.gz: Model weights for the BALM-unpaired model.
	
ESM2-650M_paired-fine-tuned.tar.gz: Model weights for the 650M-parameter ESM-2 model after fine-tuning with natively paired antibody sequences.
	
jaffe-paired-dataset_airr-annotation.tar.gz: All natively paired antibody sequences from the Jaffe dataset were annotated with abstar and subsequently filtered to remove duplicates or unproductive sequences. The annotated sequences are provided in an AIRR-compliant format.
	
train-test-eval_paired.tar.gz: Datasets used to train, test, and evaluate the BALM-paired model. Compressed folder containing three files: train.txt, test.txt, and eval.txt. Each file has one input sequence per line. This dataset was also used to fine-tune the 650M-parameter ESM-2 variant.
	
train-test-eval_unpaired.tar.gz: Datasets used to train, test, and evaluate the BALM-unpaired model. Compressed folder containing three files: train.txt, test.txt, and eval.txt. Each file has one input sequence per line.



Code: All code used for model training, testing, and figure generation is available under the MIT license on GitHub.
DOI: 10.34770/fwqx-xw53
title: STAT1-mediated interferon signaling in the hematopoietic system is essential for restricting Usutu virus infection in vivo

description: Usutu virus (USUV) is an emerging mosquito-borne flavivirus known to
 induce neuroinvasive disease in birds, mice, and humans in European and
 African countries. The mechanisms of infection and dissemination remain
 poorly understood. Elucidating how USUV spreads in a susceptible host is
 crucial for identifying therapeutic targets. To investigate host defenses
 against USUV, we generated an infectious clone of the TC508 isolate. After
 characterizing its replication dynamics in cultured cells from multiple
 species, we investigated its pathogenesis in an array of mice with genetic
 perturbations. Previous studies demonstrated that whole-body deletion of
 type I interferon (IFN) signaling led to widespread USUV infection and
 fatality in mice. Here, we observed the same lethal phenotype in
 STAT1-deficient mice and identified hematopoietic cells specifically as
 central to USUV pathogenesis in a mammalian host. Deletion of STAT1 in all
 hematopoietic subsets, but not hepatocytes, neurons, macrophages or
 conventional dendritic cells, was sufficient for systemic viral
 dissemination and ultimate fatality. Conversely, mice lacking functional
 B, T, and natural killer (NK) cells but with intact myeloid cells were
 resistant to USUV. Our findings provide new insights into the
 tissue-specific barriers that regulate USUV infection and underscore the
 importance of innate immunity in host defense for this important emerging
 flavivirus.
DOI: 10.5281/zenodo.15650870
title: Iridium L₃-edge XAS dataset of natural Ir-O phase, comprising IrO₂

description: This dataset contains Ir L₃-edge X-ray Absorption Spectroscopy (XAS) data supporting Figures 5–7 of the associated manuscript. It includes normalized XANES spectra (Figure 5), linear combination fitting (LCF) results (Figure 6), and background-subtracted k²-weighted EXAFS spectra with Fourier transforms and Artemis fit outputs (Figure 7) for Ir-bearing samples POI-I through POI-IV. Reference spectra (e.g., Ir@Ir, Ir@Pt, Ir@IrO₂) used in FDMNES simulations are also included. The dataset was collected at the BM23 beamline at ESRF and processed using Athena and Artemis software.
DOI: 10.5281/zenodo.15650871
title: Iridium L₃-edge XAS dataset of natural Ir-O phase, comprising IrO₂

description: This dataset contains Ir L₃-edge X-ray Absorption Spectroscopy (XAS) data supporting Figures 5–7 of the associated manuscript. It includes normalized XANES spectra (Figure 5), linear combination fitting (LCF) results (Figure 6), and background-subtracted k²-weighted EXAFS spectra with Fourier transforms and Artemis fit outputs (Figure 7) for Ir-bearing samples POI-I through POI-IV. Reference spectra (e.g., Ir@Ir, Ir@Pt, Ir@IrO₂) used in FDMNES simulations are also included. The dataset was collected at the BM23 beamline at ESRF and processed using Athena and Artemis software.
DOI: 10.15468/dl.epf2jq
title: Occurrence Download

description: A dataset containing 3831 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lasioglossum glabriusculum (Morawitz, 1872)"
 ]
}

 The dataset includes 3831 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039284-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.8237396
title: Improving antibody language models with native pairing

description: Motivation. Existing large language models designed to predict antibody structure and function have been trained exclusively with unpaired antibody sequences. This is a substantial drawback, as each antibody represents a unique pairing of heavy and light chains that both contribute to antigen recognition. The cost of generating large datasets of natively paired antibody sequences is orders of magnitude higher than the cost of unpaired sequences, and the paucity of available paired antibody sequence datasets precludes training a state-of-the-art language model using only paired training data. Here, we sought to determine whether and to what extent natively paired training data improves model performance.


Results. Using a unique and recently reported dataset of approximately 1.6 x 106 natively paired human antibody sequences, we trained two baseline antibody language model (BALM) variants: BALM-paired and BALM-unpaired. We quantify the superiority of BALM-paired over BALM-unpaired, and we show that BALM-paired's improved performance can be attributed at least in part to its ability to learn cross-chain features that span natively paired heavy and light chains. Additionally, we fine-tuned the general protein language model ESM-2 using these paired antibody sequences and report that the fine-tuned model, but not base ESM-2, demonstrates a similar understanding of cross-chain features.


Files. The following files are included in this repository:



	
BALM-paired.tar.gz: Model weights for the BALM-paired model.
	
BALM-unpaired.tar.gz: Model weights for the BALM-unpaired model.
	
ESM2-650M_paired-fine-tuned.tar.gz: Model weights for the 650M-parameter ESM-2 model after fine-tuning with natively paired antibody sequences.
	
jaffe-paired-dataset_airr-annotation.tar.gz: All natively paired antibody sequences from the Jaffe dataset were annotated with abstar and subsequently filtered to remove duplicates or unproductive sequences. The annotated sequences are provided in an AIRR-compliant format.
	
train-test-eval_paired.tar.gz: Datasets used to train, test, and evaluate the BALM-paired model. Compressed folder containing three files: train.txt, test.txt, and eval.txt. Each file has one input sequence per line. This dataset was also used to fine-tune the 650M-parameter ESM-2 variant.
	
train-test-eval_unpaired.tar.gz: Datasets used to train, test, and evaluate the BALM-unpaired model. Compressed folder containing three files: train.txt, test.txt, and eval.txt. Each file has one input sequence per line.



Code: All code used for model training, testing, and figure generation is available under the MIT license on GitHub.
DOI: 10.15468/dl.v4jzg3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nymphaea lotus L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((15.4784 -23.4046,15.4933 -24.0715,20.509 -24.0715,20.509 -24.0455,20.0952 -23.5072,19.9968 -23.017,19.7843 -22.5405,19.1988 -21.8785,18.5972 -21.5447,17.8859 -21.3993,17.1626 -21.4805,16.5332 -21.7596,16.1257 -22.0882,15.8234 -22.4662,15.606 -22.8993,15.4784 -23.4046))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039285-250525065834625/datasets/export for details.
DOI: 10.15468/dl.9cm6uk
title: Occurrence Download

description: A dataset containing 116 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paepalanthus Kunth"
 ]
}

 The dataset includes 116 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039286-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.smf4ug
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is University of Cincinnati, Margaret H. Fulford Herbarium - Lichens",
 "Country is Croatia"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039290-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4r3gwy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Frustulia copulata Kützing, 1833",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((27.1586 -33.5889,28.2048 -32.9007,25.5395 -32.9007,25.5395 -34.1098,25.6468 -34.1222,25.7787 -34.0734,25.7098 -33.9109,25.8639 -33.797,26.4806 -33.8473,27.1586 -33.5889))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039288-250525065834625/datasets/export for details.
DOI: 10.15468/dl.geu3a8
title: Occurrence Download

description: A dataset containing 540 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lasioglossum griseolum (Morawitz, 1872)"
 ]
}

 The dataset includes 540 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039291-250525065834625/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.29304905
title: Perguntas - Saúde Digital e Sociedade_ Percepção, Uso e Aceitação de Tecnologias no Cuidado com a Saúde no Recôncavo Baiano.pdf

description: Este estudo investiga a percepção, o uso e a aceitação de tecnologias de saúde digital pela população do Recôncavo Baiano, incluindo telemedicina, aplicativos de saúde e outras ferramentas digitais. Por meio de um questionário eletrônico com 12 perguntas, a pesquisa analisa fatores como frequência de uso, benefícios percebidos, desafios enfrentados e confiança nos serviços. Os resultados visam contribuir para reflexões acadêmicas e políticas públicas que promovam a inclusão digital e o acesso à saúde na região.
DOI: 10.6084/m9.figshare.29304905.v1
title: Perguntas - Saúde Digital e Sociedade_ Percepção, Uso e Aceitação de Tecnologias no Cuidado com a Saúde no Recôncavo Baiano.pdf

description: Este estudo investiga a percepção, o uso e a aceitação de tecnologias de saúde digital pela população do Recôncavo Baiano, incluindo telemedicina, aplicativos de saúde e outras ferramentas digitais. Por meio de um questionário eletrônico com 12 perguntas, a pesquisa analisa fatores como frequência de uso, benefícios percebidos, desafios enfrentados e confiança nos serviços. Os resultados visam contribuir para reflexões acadêmicas e políticas públicas que promovam a inclusão digital e o acesso à saúde na região.
DOI: 10.25345/c5125qn9z
title: MassIVE MSV000098162 - GNPS_U19_R01_MIND_Stool_Samples_Untargeted - Reuploaded
title: U19 Metabolomics samples from 600 brain cohort. Data set run on Q-Exactive Mass Spectrometer. Re-uploaded for U19.
DOI: 10.6084/m9.figshare.29304884
title: Respostas - Saúde Digital e Sociedade_ Percepção, Uso e Aceitação de Tecnologias no Cuidado com a Saúde no Recôncavo Baiano.pdf

description: Este estudo analisa as respostas de 228 participantes sobre a percepção, uso e aceitação de tecnologias de saúde digital no Recôncavo Baiano. Os resultados mostram que 75,4% já utilizaram serviços como teleconsultas e aplicativos de saúde, motivados principalmente por facilidade de acesso (76,8%) e economia de tempo (61,4%). Apesar disso, desafios como falta de confiança (24,6%) e dificuldade de acesso à internet (18,4%) foram relatados. A maioria (50,4%) acredita que essas tecnologias melhoram o acesso à saúde na região, embora parcialmente. Os dados destacam a relevância da saúde digital, mas apontam para barreiras que precisam ser superadas.
DOI: 10.6084/m9.figshare.29304884.v1
title: Respostas - Saúde Digital e Sociedade_ Percepção, Uso e Aceitação de Tecnologias no Cuidado com a Saúde no Recôncavo Baiano.pdf

description: Este estudo analisa as respostas de 228 participantes sobre a percepção, uso e aceitação de tecnologias de saúde digital no Recôncavo Baiano. Os resultados mostram que 75,4% já utilizaram serviços como teleconsultas e aplicativos de saúde, motivados principalmente por facilidade de acesso (76,8%) e economia de tempo (61,4%). Apesar disso, desafios como falta de confiança (24,6%) e dificuldade de acesso à internet (18,4%) foram relatados. A maioria (50,4%) acredita que essas tecnologias melhoram o acesso à saúde na região, embora parcialmente. Os dados destacam a relevância da saúde digital, mas apontam para barreiras que precisam ser superadas.
DOI: 10.15468/dl.n9k6bn
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Vascular plant collections of Tampere Museums (TMP)",
 "Country is Croatia"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039293-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n534gn
title: Occurrence Download

description: A dataset containing 372 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lasioglossum intermedium (Schenck, 1870)"
 ]
}

 The dataset includes 372 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039295-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ws2yr4
title: Occurrence Download

description: A dataset containing 131 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Natural History Museum Aarhus Freshwater Collection",
 "Country is Croatia"
 ]
}

 The dataset includes 131 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039294-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3bqy72
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nymphaea lotus L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((25.5395 -28.5786,20.509 -28.5786,20.509 -32.9007,25.5395 -32.9007,25.5395 -28.5786))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039296-250525065834625/datasets/export for details.
DOI: 10.6084/m9.figshare.29291387
title: Dataset for "Can You Feel the Closure? Consumer Neuroscience Evidence of Packaging Influence on Wine Tasting"

description: This dataset includes repeated-measures data from a neuromarketing study using EEG to examine how wine bottle closures (cork vs. screw cap) and sensory priming (auditory vs. visual) influence consumers' cognitive and emotional responses during wine tasting. Demographic data (age and gender) are also included.
DOI: 10.6084/m9.figshare.29291387.v1
title: Dataset for "Can You Feel the Closure? Consumer Neuroscience Evidence of Packaging Influence on Wine Tasting"

description: This dataset includes repeated-measures data from a neuromarketing study using EEG to examine how wine bottle closures (cork vs. screw cap) and sensory priming (auditory vs. visual) influence consumers' cognitive and emotional responses during wine tasting. Demographic data (age and gender) are also included.
DOI: 10.6084/m9.figshare.29291387.v2
title: Dataset for "Can You Feel the Closure? Consumer Neuroscience Evidence of Packaging Influence on Wine Tasting"

description: This dataset includes repeated-measures data from a neuromarketing study using EEG to examine how wine bottle closures (cork vs. screw cap) and sensory priming (auditory vs. visual) influence consumers' cognitive and emotional responses during wine tasting. Demographic data (age and gender) are also included.
DOI: 10.5519/qd.zj9m7gw7
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (621 records)
DOI: 10.15468/dl.djvwxv
title: Occurrence Download

description: A dataset containing 2899 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lasioglossum interruptum (Panzer, 1798)"
 ]
}

 The dataset includes 2899 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039297-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.beuq9q
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Frustulia copulata Kützing, 1833",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((18.2339 -32.5266,18.1411 -32.657,18.1007 -32.7021,18.0224 -32.6366,17.8923 -32.6419,17.754 -32.8255,17.7723 -32.9007,20.509 -32.9007,20.509 -28.5786,16.2782 -28.5786,16.4358 -28.7202,16.726 -29.1235,17.1957 -30.3752,17.6655 -31.1743,18.1322 -31.7679,18.2495 -32.2638,18.2339 -32.5266))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039298-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.15341664
title: Analyzing Generative AI's: A Comparative Study on Performance, Adaptability, and Precision

description: Dataset used of different AI models in the analysis, both files consist of Generative AI Models used and their respective URLs
DOI: 10.5281/zenodo.15650910
title: Analyzing Generative AI's: A Comparative Study on Performance, Adaptability, and Precision

description: Dataset used of different AI models in the analysis, both files consist of Generative AI Models used and their respective URLs
DOI: 10.15468/dl.z49sws
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Centre for Australian National Biodiversity Research (CANB) AVH data",
 "Country is Croatia"
 ]
}

 The dataset includes 39 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039299-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e232741
title: NCVAS State Summary Nebraska 2019-2021

description: Veterans as a Percent of County Population (FY2019)<br>VA Facilities (as of 3/30/2021)<br>VA Expenditures FY 2019<br>Veteran Population (as of 9/30/2019)<br>VA Healthcare and Benefits (as of 9/30/2020)<br>Veteran Population Projections
DOI: 10.5281/zenodo.15650923
title: THE REALITY OF LIFE, HISTORICAL TRUTH AND ARTISTIC PERCEPTION
DOI: 10.5281/zenodo.15650924
title: THE REALITY OF LIFE, HISTORICAL TRUTH AND ARTISTIC PERCEPTION
DOI: 10.3886/e232741v1
title: NCVAS State Summary Nebraska 2019-2021

description: Veterans as a Percent of County Population (FY2019)<br>VA Facilities (as of 3/30/2021)<br>VA Expenditures FY 2019<br>Veteran Population (as of 9/30/2019)<br>VA Healthcare and Benefits (as of 9/30/2020)<br>Veteran Population Projections
DOI: 10.15468/dl.khszge
title: Occurrence Download

description: A dataset containing 228 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lasioglossum laeve (Kirby, 1802)"
 ]
}

 The dataset includes 228 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039300-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n64hkf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nymphaea lotus L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.7576 -24.3688,20.529 -24.0715,20.509 -24.0715,20.509 -28.5786,25.5395 -28.5786,25.5395 -24.0715,25.1306 -24.0715,24.9333 -24.4571,23.8962 -24.2467,22.8065 -24.295,22.3719 -24.7207,22.2323 -25.547,22.0387 -25.7188,21.7833 -25.7784,21.5388 -25.7113,21.3553 -25.5415,20.7576 -24.3688))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039303-250525065834625/datasets/export for details.