cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30371484.v2
title: Genomic driver underlies clonal shift of methicillin-resistant <i>Staphylococcus aureus</i> in the healthcare setting

description: The epidemiology of healthcare-associated methicillin-resistant <i>Staphylococcus aureus</i> (HA-MRSA) has shifted in recent decades, with a notable decline in the lineage ST239 and continued dominance of ST5. The evolutionary mechanisms underlying these contrasting trends remain unclear. We conducted a longitudinal analysis of 3,410 clinical HA-MRSA isolates collected between 2005 and 2020 to assess clonal prevalence and genomic changes. Further phenotypic characteristics were evaluated through in vitro and in vivo experiments, including biofilm formation assays, antibiotic susceptibility testing, polymorphonuclear neutrophil leukocyte (PMN) killing assays, and mouse catheter infection models. The prevalence of ST239 declined markedly from 34.85% in 2005 to 0.52% in 2020, accompanied by reduced biofilm formation and increased susceptibility to vancomycin. Genomic analyses revealed a temporal accumulation of mutations in ST239 lineage, notably a specific <i>tarJ’</i> point mutation (C665T; Thr222Ile), whose detection frequency increased as ST239 prevalence declined, becoming fixed in 100% of ST239 isolates by 2020. This <i>tarJ’</i> mutation led to cell wall defects, decreased survival in acidic environments, reduction in biofilm formation, and attenuated persistence in mouse catheter models. In contrast, ST5 exhibited no comparable genomic deterioration and maintained phenotypic stability throughout the same period. The decline of ST239 HA-MRSA is driven by mutation-induced fitness trade-offs, particularly affecting cell wall integrity and persistent infection capacity. These findings highlight how evolutionary constraints and adaptive costs shape the population structure of bacterial pathogens.
DOI: 10.6084/m9.figshare.30371484.v1
title: Genomic driver underlies clonal shift of Methicillin-Resistant <i>Staphylococcus aureus</i> in the healthcare setting

description: The epidemiology of healthcare-associated methicillin-resistant <i>Staphylococcus aureus</i> (HA-MRSA) has shifted in recent decades, with a notable decline in the lineage ST239 and continued dominance of ST5. The evolutionary mechanisms underlying these contrasting trends remain unclear. We conducted a longitudinal analysis of 3,410 clinical HA-MRSA isolates collected between 2005 and 2020 to assess clonal prevalence and genomic changes. Further phenotypic characteristics were evaluated through in vitro and in vivo experiments, including biofilm formation assays, antibiotic susceptibility testing, polymorphonuclear neutrophil leukocyte (PMN) killing assays, and mouse catheter infection models. The prevalence of ST239 declined markedly from 34.85% in 2005 to 0.52% in 2020, accompanied by reduced biofilm formation and increased susceptibility to vancomycin. Genomic analyses revealed a temporal accumulation of mutations in ST239 lineage, notably a specific <i>tarJ’</i> point mutation (C665 T; Thr222Ile), whose detection frequency increased as ST239 prevalence declined, becoming fixed in 100% of ST239 isolates by 2020. This <i>tarJ’</i> mutation led to cell wall defects, decreased survival in acidic environments, reduction in biofilm formation, and attenuated persistence in mouse catheter models. In contrast, ST5 exhibited no comparable genomic deterioration and maintained phenotypic stability throughout the same period. The decline of ST239 HA-MRSA is driven by mutation-induced fitness trade-offs, particularly affecting cell wall integrity and persistent infection capacity. These findings highlight how evolutionary constraints and adaptive costs shape the population structure of bacterial pathogens.
DOI: 10.6084/m9.figshare.30373344
title: Enhanced replication of a contemporary avian influenza A H9N2 virus in human respiratory organoids

description: H9N2 is currently the second most common avian influenza A virus subtype infecting humans. Monitoring viral phenotypic and genotypic adaptation to humans is crucial for risk assessment. Here, we compared the replication of an H9N2 human isolate collected in 2024 (A/HK/2346/2024) to a human isolate collected in 1999 (A/HK/1073/1999). In Madin Darby canine kidney (MDCK) cells, A/HK/2346/2024 and A/HK/1073/1999 replicated to 8 and 5 log10 plaque-forming units (PFU) per ml, respectively. In both human nasal and lung organoids, A/HK/2346/2024 replicated to 6 log10 PFU/ml, but A/HK/1073/1999 failed to replicate in either organoid. The infection rates of both ciliated and non-ciliated cells and the ratios of infected 2,6/2,3 cells were higher for A/HK/2346/2024 than A/HK/1073/1999. Apart from the mammalian adaptive substitutions that were present in the nasopharyngeal specimen collected on day 1 post-symptom onset (pso) (HA-D183N/D190 T/Q192R/Q226L; NA-del62-64; PB2-A588V/K702R; PB1-I368V; PA-K356R/S409N; M1-R95K), the mammalian-adaptive substitution PB2-D253N emerged <i>de novo</i> on day 7 pso. Analysis of all human (n = 96) and avian influenza (<i>n</i> = 14,762) H9N2 deposited at GISAID showed the dominance of several human-adaptive substitutions in H9N2 strains collected from humans in recent years. In summary, we demonstrated that a recent H9N2 virus is more adapted to humans, and is able to replicate to high titres in both upper and lower human respiratory tract which may confer higher person-to-person transmissibility and virulence. Our study underscores the importance of human organoid-based phenotypic monitoring and inter/intrahost genotypic monitoring for assessing the zoonotic risk of avian influenza viruses.
DOI: 10.6084/m9.figshare.30373344.v2
title: Enhanced replication of a contemporary avian influenza A H9N2 virus in human respiratory organoids

description: H9N2 is currently the second most common avian influenza A virus subtype infecting humans. Monitoring viral phenotypic and genotypic adaptation to humans is crucial for risk assessment. Here, we compared the replication of an H9N2 human isolate collected in 2024 (A/HK/2346/2024) to a human isolate collected in 1999 (A/HK/1073/1999). In Madin Darby canine kidney (MDCK) cells, A/HK/2346/2024 and A/HK/1073/1999 replicated to 8 and 5 log10 plaque-forming units (PFU) per ml, respectively. In both human nasal and lung organoids, A/HK/2346/2024 replicated to 6 log10 PFU/ml, but A/HK/1073/1999 failed to replicate in either organoid. The infection rates of both ciliated and non-ciliated cells and the ratios of infected 2,6/2,3 cells were higher for A/HK/2346/2024 than A/HK/1073/1999. Apart from the mammalian adaptive substitutions that were present in the nasopharyngeal specimen collected on day 1 post-symptom onset (pso) (HA-D183N/D190 T/Q192R/Q226L; NA-del62-64; PB2-A588V/K702R; PB1-I368V; PA-K356R/S409N; M1-R95K), the mammalian-adaptive substitution PB2-D253N emerged <i>de novo</i> on day 7 pso. Analysis of all human (n = 96) and avian influenza (<i>n</i> = 14,762) H9N2 deposited at GISAID showed the dominance of several human-adaptive substitutions in H9N2 strains collected from humans in recent years. In summary, we demonstrated that a recent H9N2 virus is more adapted to humans, and is able to replicate to high titres in both upper and lower human respiratory tract which may confer higher person-to-person transmissibility and virulence. Our study underscores the importance of human organoid-based phenotypic monitoring and inter/intrahost genotypic monitoring for assessing the zoonotic risk of avian influenza viruses.
DOI: 10.6084/m9.figshare.30373344.v1
title: Enhanced replication of a contemporary avian influenza A H9N2 virus in human respiratory organoids

description: H9N2 is currently the second most common avian influenza A virus subtype infecting humans. Monitoring viral phenotypic and genotypic adaptation to humans is crucial for risk assessment. Here, we compared the replication of an H9N2 human isolate collected in 2024 (A/HK/2346/2024) to a historical human isolate collected in 1999 (A/HK/1073/1999). In Madin Darby canine kidney (MDCK) cells, A/HK/2346/2024 and A/HK/1073/1999 replicated to 8 log10 and 5 log10 plaque-forming units (PFU) per ml, respectively. In both human nasal and lung organoids, A/HK/2346/2024 replicated to 6 log10 PFU/ml, but A/HK/1073/1999 failed to replicate in either organoid. The infection rates of both ciliated and non-ciliated cells were higher for A/HK/2346/2024 than A/HK/1073/1999, and the ratios of infected 2,6/2,3 cells were also higher for A/HK/2346/2024. Apart from the mammalian adaptive substitutions that were present in the nasopharyngeal specimen collected on day 1 post-symptom onset (pso) (HA-D183N/D190 T/Q192R/Q226L; NA-del62-64; PB2-A588 V/K702R; PB1-I368 V; PA-K356R/S409N; M1-R95 K), the mammalian adaptive substitution PB2-D253N emerged de novo on day 7 pso. Analysis of all human (n = 96) and avian influenza (n = 14762) H9N2 deposited at GISAID showed the dominance of several human-adaptation substitutions in H9N2 strains collected from humans in recent years. In summary, we demonstrated that a recent H9N2 virus is more adapted to humans, and is able to replicate to high titers in both upper and lower human respiratory tract which may confer higher person-to-person transmissibility and virulence. Our study underscores the importance of human organoid-based phenotypic monitoring and inter/intrahost genotypic monitoring for assessing the zoonotic risk of avian influenza viruses.
DOI: 10.15468/dl.sazn6s
title: Occurrence Download

description: A dataset containing 2748 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0)",
 "TaxonKey is Meles"
 ]
}

 The dataset includes 2748 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013754-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17513941
title: Informing African agricultural health: Integrating human population dynamics and climate change into banana bunchy top disease risk assessment - model results and driver data.

description: Abstract

Banana bunchy top disease (BBTD) is a major emerging viral disease of banana plants in Africa, threatening food security and economies. BBTD has spread to numerous (sub-)tropical African countries, with new incursions in multiple countries confirmed even within the last few years. We assessed the continent-wide risk of BBTD, to provide an informative tool of large-scale risk areas of BBTD introduction, establishment and spread. These are the model outputs and underlying drivers of this assessment.

Data

The data include contemporary (contemporary_predictions_africa.tif) and future (future_predictions_africa.tif) predictions of BBTD presence, and the area-of-applicability (aoa), as well as the underlying driver dataset (drivers.tif). We also include the variables of importance ranking of the underlying model. Driver data includes subsets and regridded  data of 



CHELSA-BIOCLIM+ data (Brun et al., 2022)

WorldPop (WorldPop 2018, for year 2020)

CROPGRIDS (Tang et al., 2024)

MODIS EVI data (Didan, 2021)


References

Brun, P., Zimmermann, N.E., Hari, C., Pellisier, L., and Karger, D.N. (2022). Global climate-related predictors at kilometre resolution for the past and future. Earth System Science Data, 14(12), 5573-5603. doi:10.5194/essd-14-5573-2022

Didan, K. (2021). MODIS/Terra Vegetation Indices Monthly L3 Global 1km SIN Grid V061. NASA EOSDIS Land Processes Distributed Active Archive Center. Accessed 2024-06-11 from https://doi.org/10.5067/MODIS/MOD13A3.061.

Tang, F.H., Nguyen, T.H., Conchedda, G., Casse, L., Tubiello, F.N., and Maggi, F. (2024). CROPGRIDS: a global geo-referenced dataset of 173 crops. Scientific Data 11, 413. doi:10.1038/s41597-024-03247-7

WorldPop (www.worldpop.org - School of Geography and Environmental Science, University of Southampton; Department of Geography and Geosciences, University of Louisville; Departement de Geographie, Universite de Namur) and Center for International Earth Science Information Network (CIESIN), Columbia University (2018). Global High Resolution Population Denominators Project - Funded by The Bill and Melinda Gates Foundation (OPP1134076). doi:10.5258/SOTON/WP00674
DOI: 10.5281/zenodo.17513942
title: Informing African agricultural health: Integrating human population dynamics and climate change into banana bunchy top disease risk assessment - model results and driver data.

description: Abstract

Banana bunchy top disease (BBTD) is a major emerging viral disease of banana plants in Africa, threatening food security and economies. BBTD has spread to numerous (sub-)tropical African countries, with new incursions in multiple countries confirmed even within the last few years. We assessed the continent-wide risk of BBTD, to provide an informative tool of large-scale risk areas of BBTD introduction, establishment and spread. These are the model outputs and underlying drivers of this assessment.

Data

The data include contemporary (contemporary_predictions_africa.tif) and future (future_predictions_africa.tif) predictions of BBTD presence, and the area-of-applicability (aoa), as well as the underlying driver dataset (drivers.tif). We also include the variables of importance ranking of the underlying model. Driver data includes subsets and regridded  data of 



CHELSA-BIOCLIM+ data (Brun et al., 2022)

WorldPop (WorldPop 2018, for year 2020)

CROPGRIDS (Tang et al., 2024)

MODIS EVI data (Didan, 2021)


References

Brun, P., Zimmermann, N.E., Hari, C., Pellisier, L., and Karger, D.N. (2022). Global climate-related predictors at kilometre resolution for the past and future. Earth System Science Data, 14(12), 5573-5603. doi:10.5194/essd-14-5573-2022

Didan, K. (2021). MODIS/Terra Vegetation Indices Monthly L3 Global 1km SIN Grid V061. NASA EOSDIS Land Processes Distributed Active Archive Center. Accessed 2024-06-11 from https://doi.org/10.5067/MODIS/MOD13A3.061.

Tang, F.H., Nguyen, T.H., Conchedda, G., Casse, L., Tubiello, F.N., and Maggi, F. (2024). CROPGRIDS: a global geo-referenced dataset of 173 crops. Scientific Data 11, 413. doi:10.1038/s41597-024-03247-7

WorldPop (www.worldpop.org - School of Geography and Environmental Science, University of Southampton; Department of Geography and Geosciences, University of Louisville; Departement de Geographie, Universite de Namur) and Center for International Earth Science Information Network (CIESIN), Columbia University (2018). Global High Resolution Population Denominators Project - Funded by The Bill and Melinda Gates Foundation (OPP1134076). doi:10.5258/SOTON/WP00674
DOI: 10.5281/zenodo.16419669
title: Bipartite entanglement extracted from multimode squeezed light generated in lossy waveguides

description: This dataset includes the data on which the figures of the preprint "Bipartite entanglement extracted from multimode squeezed light generated in lossy waveguides" by Denis A. Kopylov, Torsten Meier,  and Polina R. Sharapova  (arXiv:2506.09587) are based. 

This work is supported by the “Photonic Quantum Computing” (PhoQC) project, funded by the Ministry for Culture and Science of the State of North-Rhine Westphalia. We acknowledge financial support of the Deutsche Forschungsgemeinschaft (DFG) via the Collaborative Research Center ”Tailored Nonlinear Photonics” TRR 142/3 (Project No. 231447078, Subproject No. C10).
DOI: 10.5281/zenodo.16419670
title: Bipartite entanglement extracted from multimode squeezed light generated in lossy waveguides

description: This dataset includes the data on which the figures of the preprint "Bipartite entanglement extracted from multimode squeezed light generated in lossy waveguides" by Denis A. Kopylov, Torsten Meier,  and Polina R. Sharapova  (arXiv:2506.09587) are based. 

This work is supported by the “Photonic Quantum Computing” (PhoQC) project, funded by the Ministry for Culture and Science of the State of North-Rhine Westphalia. We acknowledge financial support of the Deutsche Forschungsgemeinschaft (DFG) via the Collaborative Research Center ”Tailored Nonlinear Photonics” TRR 142/3 (Project No. 231447078, Subproject No. C10).
DOI: 10.15468/dl.2zaqb9
title: Occurrence Download

description: A dataset containing 7560072 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ardea cinerea"
 ]
}

 The dataset includes 7560072 records from 5141 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013702-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tbbxpk
title: Occurrence Download

description: A dataset containing 1101733 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Nepal",
 "DatasetKey is EOD – eBird Observation Dataset",
 "GadmGid is NPL",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1101733 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007043-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rm8b92
title: Occurrence Download

description: A dataset containing 47572 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Campephilus melanoleucos (J.F.Gmelin, 1788))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 47572 records from 152 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018670-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qszvvc
title: Occurrence Download

description: A dataset containing 196881 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amanita muscaria (L.) Lam."
 ]
}

 The dataset includes 196881 records from 434 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031790-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc112047410
title: Cuneiform Tablet 1913.14.0223, Spurlock 1913.14.0223

description: [Text Description:] Administrative tablet ❧ [Text or Publication Number Note:] Spurlock 1913.14.0223; CDLI P420605 ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Yellowish Gray (10YR 8.5/2) ❧ [Physical Object Note:] 2.8 x 2.7 x 2 cm (18g) ❧ [Physical Object Note:] Seal impressions
DOI: 10.15468/dl.sfjszs
title: Occurrence Download

description: A dataset listing the 65899 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((26.7542939189847 1.2186193716968,36.9991642472184 13.6345880476356,41.544901412726 10.038706409249,37.5419388341447 2.16847489881781,35.84576825 -7.80500813595271,36.2528491901947 -16.0144737632128,34.2174444892211 -16.5572483501391,27.5006089760084 -8.95840413317107,26.7542939189847 1.2186193716968))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset's 65899 records were derived from 1035 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027649-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc112047411
title: Cuneiform Tablet 1913.14.0223, Spurlock 1913.14.0223

description: [Text Description:] Administrative tablet ❧ [Text or Publication Number Note:] Spurlock 1913.14.0223; CDLI P420605 ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Yellowish Gray (10YR 8.5/2) ❧ [Physical Object Note:] 2.8 x 2.7 x 2 cm (18g) ❧ [Physical Object Note:] Seal impressions
DOI: 10.15468/dl.gsqr72
title: Occurrence Download

description: A dataset containing 3437143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Arundo donax L., Poa L., Acacia dealbata Link, Lantana camara L., Arum italicum Mill.)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3437143 records from 4289 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031789-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ej875a
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Dendroctonus approximatus"
 ]
}

 The dataset includes 16 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001994-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5kd2cg
title: Occurrence Download

description: A dataset containing 896 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus glaucoides)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 896 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001995-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/2zh-hm3-j3t
title: Megastomia conspicua (Alder, 1850)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c0z-zzc-rj4
title: Conus tinianus Hwass, 1792

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7f4-q9h-zbc
title: Pythia plicata (A. Férussac, 1821)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bk3-hl9-7ry
title: Fulgoraria cancellata Kuroda & Habe, 1950

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mwk-4g3-xz5
title: Pedipes pedipes (Bruguière, 1789)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jxn-4ax-n50
title: Agaronia hiatula (Gmelin, 1791)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/n4q-cew-3rf
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/06j-9ep-c20
title: Oliva reticulata (Röding, 1798)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6wt-dxl-nbk
title: Glabella faba (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9j6-e78-s6k
title: Oliva amethystina (Röding, 1798)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dw5-6jr-94n
title: Imbricaria verrucosa (Reeve, 1845)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pam-szp-n13
title: Goniofusus spectrum (A. Adams & Reeve, 1848)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wr0-wpc-86b
title: Africofusus ocelliferus (Lamarck, 1816)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/439-rfr-f5s
title: Prunum apicinum (Menke, 1828)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.