cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17185791
title: Multi-resolution confocal fluorescence microscopy of human dentin porosity

description: This is a collection of confocal fluorescence microscopy images of human dentin porosity acquired at different experimentally paired resolutions (typically HR, x2, x4, x8)

Images are provided as:



raw images at high- and low-resolution

registered low-resolution images against high-resolution

image patches of 128x128 pix2 classified by biological feature content: mostly tubules, mostly branches or both. This provides a useful classification for machine learning model training or testing IQA metrics. Patches were automatically classified based on histogram distributions of feature diameter maps of images. Each class has the exact same patch locations for each resolution (i.e. paired patches), with the same filename for of different resolutions.


The imaged teeth samples are histological slices stained with a fluorescent solution by infiltration; Imaging was performed using a confocal laser scanning microscope (see experimental description for each sample below).

-----

Sample01 – internal ref: THF_ 20230601_28y

28 year old female human 3rd molar.

Sample preparation:

Prepared on 2023-06-01 and imaged on 2024-01-25 at LIPhy.

Initial preparation: cleaned and disinfected with ChloramineT.

Fixation: Ethanol 70%

Cutting: approx. 300 um thick slices using a diamond saw (Struers E0D15 mounted on a Presi Mecatome T210) with water lubrication.

Extra: polished down to approx. 200 μm with 2000–4000 SiC abrasive paper (EU grade, Struers) and diamond polishing spray (DP-spray P, Struers) using aqueous lubricant oil (DP-lubricant red, Struers) from grain sizes of 3 μm down to 0.2 μm.

Dried in air at room temperature.

Staining: 0.02% weight Rhodamine B and glycerol solution infiltration.

Mounting: between glass slide and cover slip with staining solution.

Data acquisition:

Microscope: Leica SP8.

Objective: 40x/1.3NA with Leica immersion fluid (1.52).

Laser: λ = 561nm.

Detector: PMT detector with detection range of [565 – 700]nm

Multi-resolution:

Images were acquired at 4 different resolutions by changing the pixel size with the same objective.

High resolution (HR): 100 x 100nm2 pixel size with line average = 3

Low resolution: x2 (200 x 200nm2), x4 (400 x 400 nm2), x8 (800 x 800 nm2) pixel sizes.

All resolutions: 0.3µm step size, 200 x 200 x 5.1 µm3 field of view.

Image format: 8-bit greyscale tiff files

Folder structure:

>RawImages:

    >ROI1-6: 6 regions near the dentin-enamel junction (DEJ)

        >HR, x2, x4, x8: all resolution folders

>RegisteredImages: LR registered against HR using Antspy (Mutual information)

    >ROI1-6: 6 regions near the dentin-enamel junction (DEJ)

        >x2, x4, x8: all resolution folders

>ImagePatches128

    >Classified

        >Tubules, Branches, Both

            >HR, x2, x4, x8: all resolution folders
DOI: 10.15468/dl.gvxfe9
title: Occurrence Download

description: A dataset containing 15612 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lophura swinhoii",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 15612 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011199-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n5apcb
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aeschynomene indica",
 "Country is South Africa",
 "HasCoordinate is true"
 ]
}

 The dataset includes 44 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011203-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ra5uaz
title: Occurrence Download

description: A dataset containing 1476 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thevetia peruviana",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1476 records from 219 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011205-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zzmdru
title: Occurrence Download

description: A dataset containing 690 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Agrostis nebulosa)"
 ]
}

 The dataset includes 690 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011204-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dd.cefq9d
title: Dataset generated from Esri tool

description: Derived dataset generated by Esri geoprocessing tool using GBIF API
DOI: 10.15468/dl.6wkux5
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aeschynomene indica",
 "Country is Viet Nam",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011209-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.shczvh
title: Occurrence Download

description: A dataset containing 28668 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Geometry POLYGON((-61.9138 11.88953,-60.57762 11.88953,-60.57762 14.0853,-60.92897 14.15708,-61.9138 14.0853,-61.9138 11.88953))",
 "Geometry POLYGON((-63.63727 17.01546,-62.36471 17.01546,-62.36471 18.20836,-62.98043 18.36656,-63.63727 18.20836,-63.63727 17.01546))",
 "Geometry POLYGON((-66.85545 11.72121,-66.49496 11.72121,-66.49496 12.0039,-66.85545 12.0039,-66.85545 11.72121))",
 "Geometry POLYGON((-69.93009 12.25522,-68.00724 11.91368,-68.14524 12.39442,-70.15208 12.697,-69.93009 12.25522))",
 "Geometry POLYGON((-81.79444 12.43086,-81.65922 12.43796,-81.68167 12.66694,-81.79444 12.66112,-81.79444 12.43086))"
 ]
 },
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Porites astreoides, Montastraea cavernosa, Siderastrea siderea, Siderastrea radians, Agaricia agaricites, Stephanocoenia intersepta, Manicina areolata, Colpophyllia natans, Pseudodiploria strigosa, Diploria labyrinthiformis, Meandrina meandrites, Eusmilia fastigiata, Dichocoenia stokesii, Porites porites, Porites furcata, Orbicella annularis, Orbicella faveolata, Orbicella franksi, Pseudodiploria clivosa, Isophyllia sinuosa, Isophyllia rigida, Mycetophyllia aliciae, Mycetophyllia ferox, Mycetophyllia lamarckiana, Scolymia cubensis, Scolymia lacera, Agaricia tenuifolia, Agaricia lamarcki, Agaricia humilis, Porites divaricata, Madracis auretenra, Madracis decactis, Porites colonensis, Acropora palmata, Acropora cervicornis, Dendrogyra cylindrus, Meandrina jacksoni, Solenastrea bournoni, Solenastrea hyades, Favia fragum, Agaricia grahamae, Helioseris cucullata, Madracis carmabi, Porites branneri, Oculina diffusa)"
 ]
}

 The dataset includes 28668 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011207-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17189869
title: Mollusc-based proxies for the moisture and proximity of forest reconstruction (Data sets)

description: Mollusc-based proxies for the moisture and proximity of the forest used for regression models (Appendix S1).  List of shelled mollusc species categorised in ten ecological groups, according to Ložek (1964), with adjustments by Lisický (1991), Juřičková et al. (2014), Horsáková et al. (2018) and recent taxonomic and ecological updates (Appendix S2). Fossil mollusc and selected plant macrofossil data for two profiles used for verification of the new method (Appendix S3).
DOI: 10.5281/zenodo.17189870
title: Mollusc-based proxies for the moisture and proximity of forest reconstruction (Data sets)

description: Mollusc-based proxies for the moisture and proximity of the forest used for regression models (Appendix S1).  List of shelled mollusc species categorised in ten ecological groups, according to Ložek (1964), with adjustments by Lisický (1991), Juřičková et al. (2014), Horsáková et al. (2018) and recent taxonomic and ecological updates (Appendix S2). Fossil mollusc and selected plant macrofossil data for two profiles used for verification of the new method (Appendix S3).
DOI: 10.15468/dl.xd86j9
title: Occurrence Download

description: A dataset containing 36390 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thuja plicata",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 36390 records from 379 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011211-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nzqqjh
title: Occurrence Download

description: A dataset containing 685 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Aichryson villosum)"
 ]
}

 The dataset includes 685 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011213-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gxgy69
title: Occurrence Download

description: A dataset containing 28718 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phasianus colchicus",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 28718 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011210-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g2c97v
title: Occurrence Download

description: A dataset containing 387 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tachypleus tridentatus"
 ]
}

 The dataset includes 387 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011212-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qdayjt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Astragalus boeticus",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011214-250920141307145/datasets/export for details.
DOI: 10.21227/h1nt-2b80
title: "Apollo Go Autonomous Ride-Hailing User Reviews Dataset"

description: "Autonomous driving technology is increasingly regarded as a promising pathway to advance sustainable urban transportation. This study evaluates the societal impact of Baidu\u2019s Apollo Go autonomous ride-hailing platform in relation to the United Nations Sustainable Development Goal (SDG) 11, with particular emphasis on mobility, environmental sustainability, and inclusiveness. To capture public perception, user comments were collected from Xiaohongshu, Tencent News, and Toutiao, and analyzed using the BERTopic (Bidirectional Encoder Representations from Transformers Topic Modeling) method. The extracted topics reflect major public concerns, which were further assessed alongside operational indicators and third-party data on air quality, safety records, and service affordability. Results suggest that Apollo Go contributes positively to SDG 11.2 (transport accessibility), 11.6 (environmental impact), and 11.7 (inclusive public spaces), while limitations remain in equity and environmental performance. Subgroup analyses of comments from women and persons with disabilities provide additional insights into inclusivity and accessibility challenges. Overall, the findings indicate that Apollo Go demonstrates strong potential to promote sustainable urban mobility; however, continued refinement is required to ensure equitable service distribution and long-term environmental benefits. These insights can inform the deployment and regulation of autonomous ride-hailing services, while also guiding broader strategies aimed at enhancing transport equity, reducing environmental burdens, and fostering inclusive urban mobility systems."
DOI: 10.15468/dl.wxt73z
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Astragalus boeticus",
 "Country is Croatia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011215-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14260170
title: GEMS: Resolving Data Bias Improves Generalization in Binding Affinity Prediction

description: For fast reproduction of our results, we provide PyTorch datasets of precomputed interaction graphs for the entire PDBbind database on Zenodo. To enable quick establishment of leakage-free evaluation setups with PDBbind, we also provide pairwise similarity matrices for the entire PDBbind dataset on Zenodo.

Version 2 - Updated to improve the accuracy of Tanimoto Scores in the pairwise similarity matrices, which also caused minor changes in the composition of PDBbind CleanSplit.

Version 3 - Including pairwise similarity matrix for sequence identity (from TM-align)
DOI: 10.5281/zenodo.17190227
title: GEMS: Resolving Data Bias Improves Generalization in Binding Affinity Prediction

description: For fast reproduction of our results, we provide PyTorch datasets of precomputed interaction graphs for the entire PDBbind database on Zenodo. To enable quick establishment of leakage-free evaluation setups with PDBbind, we also provide pairwise similarity matrices for the entire PDBbind dataset on Zenodo.

Version 2 - Updated to improve the accuracy of Tanimoto Scores in the pairwise similarity matrices, which also caused minor changes in the composition of PDBbind CleanSplit.

Version 3 - Including pairwise similarity matrix for sequence identity (from TM-align)
DOI: 10.15468/dl.jsy76t
title: Occurrence Download

description: A dataset containing 269 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Tachypleus tridentatus"
 ]
}

 The dataset includes 269 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011217-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.68rnxr
title: Occurrence Download

description: A dataset containing 18574 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "HasCoordinate is true",
 "Year is 1907"
 ]
}

 The dataset includes 18574 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011206-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6bn5td
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Astragalus boeticus",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 20 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011218-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.auhj52
title: Occurrence Download

description: A dataset containing 10603 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-83.32694 11.94968,-84.24517 11.52157,-84.37635 10.53447,-83.28322 9.02637,-80.74715 8.33479,-78.38598 9.75973,-83.32694 11.94968))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Porites astreoides, Montastraea cavernosa, Siderastrea siderea, Siderastrea radians, Agaricia agaricites, Stephanocoenia intersepta, Manicina areolata, Colpophyllia natans, Pseudodiploria strigosa, Diploria labyrinthiformis, Meandrina meandrites, Eusmilia fastigiata, Dichocoenia stokesii, Porites porites, Porites furcata, Orbicella annularis, Orbicella faveolata, Orbicella franksi, Pseudodiploria clivosa, Isophyllia sinuosa, Isophyllia rigida, Mycetophyllia aliciae, Mycetophyllia ferox, Mycetophyllia lamarckiana, Scolymia cubensis, Scolymia lacera, Agaricia tenuifolia, Agaricia lamarcki, Agaricia humilis, Porites divaricata, Madracis auretenra, Madracis decactis, Porites colonensis, Acropora palmata, Acropora cervicornis, Dendrogyra cylindrus, Meandrina jacksoni, Solenastrea bournoni, Solenastrea hyades, Favia fragum, Agaricia grahamae, Helioseris cucullata, Madracis carmabi, Porites branneri, Oculina diffusa)"
 ]
}

 The dataset includes 10603 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011216-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hrjsde
title: Occurrence Download

description: A dataset containing 291 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tibouchina herbacea",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 291 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011219-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ny3d7w
title: Occurrence Download

description: A dataset containing 329 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Ajania pacifica)"
 ]
}

 The dataset includes 329 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011220-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/9j14ub
title: Data Lactuchelins.zip

description: Raw data LC-HRMS
DOI: 10.57745/5qgqpj
title: README.txt

description: :unav
DOI: 10.57745/cfu7fs
title: Lactuchelins: New lipopeptide siderophores from Pseudomonas lactucae inhibit Xanthomonas campestris pv. campestris 8004

description: Seeds harbor diverse microbial communities, including beneficial microbes that play a vital role in protecting plants from seed-borne pathogens. However, the molecular mechanisms underpinning intermicrobial competition within the seed microbiome remain poorly understood, limiting the development of effective seed inoculation strategies for biocontrol. In this study, we assessed the antagonistic interactions of 30 seed-borne bacterial strains against the phytopathogen Xanthomonas campestris pv. campestris 8004 (Xcc8004). We identified Pseudomonas lactucae CFBP 13502 as a potent inhibitor of Xcc8004, mediated by exometabolites, specifically induced by certain seed-borne strains. Transcriptomic analysis linked this inducible activity to the upregulation of a gene cluster encoding a lipopeptide siderophore. Targeted gene deletion in P. lactucae CFBP 13502 confirmed that this cluster is essential for antagonism against Xcc8004 Furthermore, iron supplementation abolished this inhibitory effect, strongly supporting iron chelation as the underlying mechanism. Through comparative metabolomics, we elucidated the structure of a novel family of lipopeptide siderophores, produced by P. lactucae CFBP 13502, which we named lactuchelins. Our findings provide the first molecular evidence of competitive exclusion mechanisms at the seed microbiome interface, highlighting lactuchelins as a promising avenue for the development of seed-based biocontrol strategies against seed-borne phytopathogens.
DOI: 10.15468/dl.qdrp65
title: Occurrence Download

description: A dataset containing 2297120 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Museum of Comparative Zoology, Harvard University"
 ]
}

 The dataset includes 2297120 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011197-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ps3sek
title: Occurrence Download

description: A dataset containing 90 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Synoicus chinensis",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 90 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011221-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mscjfu
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Astragalus cicer",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011223-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dgnmta
title: Occurrence Download

description: A dataset containing 2012 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Astragalus cicer",
 "Country is Canada",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2012 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011224-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.