cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/d8m-yyx-zcp
title: Trachelipus rathkii (Brandt 1833)

description: Digital Specimen for the physical specimen hosted at Senckenberg Research Institute and Natural History Museum Frankfurt/M.
DOI: 10.3535/y1p-w5c-hlp
title: Trachelipus rathkii (Brandt 1833)

description: Digital Specimen for the physical specimen hosted at Senckenberg Research Institute and Natural History Museum Frankfurt/M.
DOI: 10.15468/dl.5kdpf2
title: Occurrence Download

description: A dataset containing 673764 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Algeria, Bulgaria, Croatia, France, Germany, Greece, Hungary, Italy, Kazakhstan, Morocco, Netherlands, Russian Federation, Tunisia, Türkiye, Ukraine)",
 "Year is 2002",
 "TaxonKey is Aves",
 "HasCoordinate is true"
 ]
}

 The dataset includes 673764 records from 392 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032606-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y5btxz
title: Occurrence Download

description: A dataset containing 402 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aegilops columnaris Zhuk.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 402 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010664-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3asxgv
title: Occurrence Download

description: A dataset containing 301 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is MEX.10_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Pandionidae"
 ]
}

 The dataset includes 301 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010665-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a84qep
title: Occurrence Download

description: A dataset containing 1365 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Chile",
 "OccurrenceStatus is Present",
 "TaxonKey is Milvago chimango (Vieillot, 1816)"
 ]
}

 The dataset includes 1365 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010666-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10461659
title: Single-molecule imaging and molecular dynamics simulations reveal early activation of the MET receptor in situ

description: Data and analysis notebooks supporting:

Yunqing Li, Serena M. Arghittu, Marina S. Dietz, Gabriel J. Hella, Daniel Haße,  Davide M. Ferraris, Petra Freund, Hans-Dieter Barth, Hartmut H. Niemann, Roberto Covino, Mike Heilemann - "Single-molecule imaging and molecular dynamics simulations reveal early activation of the MET receptor in situ" (2024)
DOI: 10.5281/zenodo.10461660
title: Single-molecule FRET and molecular dynamics simulations reveal early activation steps of MET receptor by Listeria monocytogenes

description: Data and analysis notebooks supporting:

Yunqing Li, Serena M. Arghittu, Marina S. Dietz, Daniel Haße,  Davide M. Ferraris, Petra Freund, Hans-Dieter Barth, Hartmut H. Niemann, Roberto Covino, Mike Heilemann - "Single-molecule FRET and molecular dynamics simulations reveal early activation steps of MET receptor by Listeria monocytogenes" (2024)
DOI: 10.5281/zenodo.10978516
title: Single-molecule FRET and molecular dynamics simulations reveal early activation steps of MET receptor by Listeria monocytogenes

description: Data and analysis notebooks supporting:

Yunqing Li, Serena M. Arghittu, Marina S. Dietz, Daniel Haße,  Davide M. Ferraris, Petra Freund, Hans-Dieter Barth, Hartmut H. Niemann, Roberto Covino, Mike Heilemann - "Single-molecule FRET and molecular dynamics simulations reveal early activation steps of MET receptor by Listeria monocytogenes" (2024)
DOI: 10.5281/zenodo.11202330
title: Single-molecule imaging and molecular dynamics simulations reveal early activation of the MET receptor in situ

description: Data and analysis notebooks supporting:

Yunqing Li, Serena M. Arghittu, Marina S. Dietz,Gabriel J. Hella, Daniel Haße,  Davide M. Ferraris, Petra Freund, Hans-Dieter Barth, Hartmut H. Niemann, Roberto Covino, Mike Heilemann - "Single-molecule imaging and molecular dynamics simulations reveal early activation of the MET receptor in situ" (2024)
DOI: 10.5281/zenodo.13379187
title: Single-molecule imaging and molecular dynamics simulations reveal early activation of the MET receptor in situ

description: Data and analysis notebooks supporting:

Yunqing Li, Serena M. Arghittu, Marina S. Dietz, Gabriel J. Hella, Daniel Haße,  Davide M. Ferraris, Petra Freund, Hans-Dieter Barth, Hartmut H. Niemann, Roberto Covino, Mike Heilemann - "Single-molecule imaging and molecular dynamics simulations reveal early activation of the MET receptor in situ" (2024)
DOI: 10.5281/zenodo.13913751
title: Single-molecule imaging and molecular dynamics simulations reveal early activation of the MET receptor in situ

description: Data and analysis notebooks supporting:

Yunqing Li, Serena M. Arghittu, Marina S. Dietz, Gabriel J. Hella, Daniel Haße,  Davide M. Ferraris, Petra Freund, Hans-Dieter Barth, Hartmut H. Niemann, Roberto Covino, Mike Heilemann - "Single-molecule imaging and molecular dynamics simulations reveal early activation of the MET receptor in situ" (2024)
DOI: 10.15468/dl.cbp2be
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Xanthium cylindricum Millsp. & Sherff, Xanthium cylindricum Millsp. & Sherff, Xanthium cylindricum Millsp. & Sherff, Xanthium cylindricum Millsp. & Sherff, Xanthium cylindricum Millsp. & Sherff, Xanthium cylindricum Millsp. & Sherff, Xanthium cylindricum Millsp. & Sherff, Xanthium cylindricum Millsp. & Sherff, Xanthium cylindricum Millspaugh & Fernald, Xanthium cylindricum Millsp. & Sherff, 1918)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010667-241024112534372/datasets/export for details.
DOI: 10.15468/dl.hsd96h
title: Occurrence Download

description: A dataset containing 23708 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aegilops geniculata Roth",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 23708 records from 338 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010668-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14007620
title: Repeat-based holocentromeres of Luzula sylvatica

description: Abstract



Although the centromere is restricted to a single region of the chromosome in most studied eukaryotes, members of the rush family (Juncaceae) harbor either monocentric (Juncus) or holocentric (Luzula) chromosomes. This provides an opportunity to study the evolutionary mechanisms involved in the transition to holocentricity. Here by combining chromosome-scale genome assembly, epigenetic analyses, immuno-FISH, and super-resolution microscopy, we report the occurrence of repeat-based holocentromeres in L. sylvatica. We found an irregular distribution of genes, centromeric units, and most repeats along the chromosomes. We determined the centromere function predominantly associated with two satellite DNA repeats, Lusy1 and Lusy2 of 124- and 174-bp monomer length, respectively, while CENH3 also binds repeat-free gene-poor regions. Comparative repeat analysis revealed that Lusy1 is present in most Luzula species, suggesting a conserved centromere role of this repeat. Synteny between L. sylvatica (n = 6) and J. effusus (n = 21) genomes further evidenced a chromosome number reduction in Luzula derived from multiple chromosome fusions of ancestral J. effusus-like chromosomes. We propose that the transition to holocentricity in Luzula involves: (i) fusion of small chromosomes resembling Juncus-like centromeres; (ii) expansion of atypical centromeric units; and (iii) colonization of satellite DNA for centromere stabilization.

 

Description of the data and file structure

Chromosome-scale reference genome:

Luzula_sylvatica_asm.hic.chr.FINAL.fasta

Repeat annotation files:

Luzula_sylvatica_asm.hic.chr.FINAL.TE_domains_full_output.gff3

Luzula_sylvatica_asm.hic.chr.FINAL.LTR_retrotransposons_annotation.gff3

Luzula_sylvatica_asm.hic.chr.FINAL.TideCluster_tandem_repeats.gff3

DNA methylation files are coded as below:

6261_A*

R1 and R2 stands for forward (R1) and reverse (R2), respectively.

Code/Software

The original code used in this study is available on GitHub at https://github.com/437364/Repeat-based-holocentromeres-of-Luzula-sylvatica (opens in new window). Any additional information required to re-analyze the data reported in this paper is available from the corresponding author upon request.
DOI: 10.5281/zenodo.14007621
title: Repeat-based holocentromeres of Luzula sylvatica

description: Abstract



Although the centromere is restricted to a single region of the chromosome in most studied eukaryotes, members of the rush family (Juncaceae) harbor either monocentric (Juncus) or holocentric (Luzula) chromosomes. This provides an opportunity to study the evolutionary mechanisms involved in the transition to holocentricity. Here by combining chromosome-scale genome assembly, epigenetic analyses, immuno-FISH, and super-resolution microscopy, we report the occurrence of repeat-based holocentromeres in L. sylvatica. We found an irregular distribution of genes, centromeric units, and most repeats along the chromosomes. We determined the centromere function predominantly associated with two satellite DNA repeats, Lusy1 and Lusy2 of 124- and 174-bp monomer length, respectively, while CENH3 also binds repeat-free gene-poor regions. Comparative repeat analysis revealed that Lusy1 is present in most Luzula species, suggesting a conserved centromere role of this repeat. Synteny between L. sylvatica (n = 6) and J. effusus (n = 21) genomes further evidenced a chromosome number reduction in Luzula derived from multiple chromosome fusions of ancestral J. effusus-like chromosomes. We propose that the transition to holocentricity in Luzula involves: (i) fusion of small chromosomes resembling Juncus-like centromeres; (ii) expansion of atypical centromeric units; and (iii) colonization of satellite DNA for centromere stabilization.

 

Description of the data and file structure

Chromosome-scale reference genome:

Luzula_sylvatica_asm.hic.chr.FINAL.fasta

Repeat annotation files:

Luzula_sylvatica_asm.hic.chr.FINAL.TE_domains_full_output.gff3

Luzula_sylvatica_asm.hic.chr.FINAL.LTR_retrotransposons_annotation.gff3

Luzula_sylvatica_asm.hic.chr.FINAL.TideCluster_tandem_repeats.gff3

DNA methylation files are coded as below:

6261_A*

R1 and R2 stands for forward (R1) and reverse (R2), respectively.

Code/Software

The original code used in this study is available on GitHub at https://github.com/437364/Repeat-based-holocentromeres-of-Luzula-sylvatica (opens in new window). Any additional information required to re-analyze the data reported in this paper is available from the corresponding author upon request.
DOI: 10.5281/zenodo.14007788
title: Inje ANN and Data

description: This ANN model was created to conduct a comparison between openly available data to specific soil physical properties.
DOI: 10.5281/zenodo.14007789
title: Inje ANN and Data

description: This ANN model was created to conduct a comparison between openly available data to specific soil physical properties.
DOI: 10.15468/dl.z5hbbv
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Eriocheir sinensis H.Milne Edwards, 1853",
 "Year 1904-2024"
 ]
}

 The dataset's 2 records were derived from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010659-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zppydz
title: Occurrence Download

description: A dataset containing 12729 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aegilops neglecta Req. ex Bertol.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 12729 records from 266 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010669-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qd7sme
title: Occurrence Download

description: A dataset containing 528 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ophelimus maskelli (Ashmead, 1900)"
 ]
}

 The dataset includes 528 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010671-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5d99r9
title: Occurrence Download

description: A dataset containing 16765 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arachis hypogaea L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 16765 records from 249 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010672-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12738169
title: Data for: Antarctic wide subglacial hydrology modeling
DOI: 10.15468/dl.scqwqh
title: Occurrence Download

description: A dataset containing 89169 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Netherlands",
 "DatasetKey is The CPR Survey",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 89169 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010670-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13950340
title: MULTIPLIERS_WP3/4/5_Science learning project on Anti-microbial resistance_Public data_UCY_20241018_v1

description: This dataset contains the following data related to the science learning project on Anti-microbial resistance:



Summary of transcripts from interviews with teachers and students (Pseudo-/Anonymised)

Summary of transcripts from focus group discussions with students (Pseudo-/Anonymised)
DOI: 10.5281/zenodo.13950339
title: MULTIPLIERS_WP3/4/5_Science learning project on Anti-microbial resistance_Public data_UCY_20241018_v1

description: This dataset contains the following data related to the science learning project on Anti-microbial resistance:



Summary of transcripts from interviews with teachers and students (Pseudo-/Anonymised)

Summary of transcripts from focus group discussions with students (Pseudo-/Anonymised)
DOI: 10.15468/dl.8kpyq7
title: Occurrence Download

description: A dataset containing 90 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arachis monticola Krapov. & Rigoni",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 90 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010675-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nadxza
title: Occurrence Download

description: A dataset containing 78110 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.46_1",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Apidae, Andrenidae, Halictidae, Melittidae, Colletidae, Megachilidae)",
 "Year 1000-2023"
 ]
}

 The dataset includes 78110 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010674-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13383031
title: Data for "Nanoscale modification of MOC-based composites: The influence of alumina nanosheets on microstructure and material properties"
DOI: 10.5281/zenodo.13383032
title: Data for "Nanoscale modification of MOC-based composites: The influence of alumina nanosheets on microstructure and material properties"
DOI: 10.15468/dl.jpsxxe
title: Occurrence Download

description: A dataset containing 1346 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Asplenium appendiculatum var. appendiculatum",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1346 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010678-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13991030
title: MULTIPLIERS_WP3/4/5_Science learning project on Biodiversity and ecosystem services_Public data_UL_20241025_v1

description: This dataset contains the following data related to the science learning project on Biodiversity and ecosystem services:





Summary of transcripts from interviews with teachers, OSC members, and students (Pseudo-/Anonymised)


Summary of transcripts from focus group discussions with students (Pseudo-/Anonymised)
DOI: 10.5281/zenodo.13991031
title: MULTIPLIERS_WP3/4/5_Science learning project on Biodiversity and ecosystem services_Public data_UL_20241025_v1

description: This dataset contains the following data related to the science learning project on Biodiversity and ecosystem services:





Summary of transcripts from interviews with teachers, OSC members, and students (Pseudo-/Anonymised)


Summary of transcripts from focus group discussions with students (Pseudo-/Anonymised)
DOI: 10.15468/dl.e7zppu
title: Occurrence Download

description: A dataset containing 9342 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "GadmGid is USA.33.3_1",
 "Month is one of (January, February, March, April)",
 "TaxonKey is Piciformes",
 "Year 2016-2023"
 ]
}

 The dataset includes 9342 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010679-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5wu4qv
title: Occurrence Download

description: A dataset containing 28279 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "GadmGid is USA.33.3_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Piciformes",
 "Year 2015-2023"
 ]
}

 The dataset includes 28279 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010680-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pc9sbt
title: Occurrence Download

description: A dataset containing 468 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Censos de aves en los municipio de Fusagasugá y Sibaté (Cundinamarca) - BIO Alas, cantos y colores"
 ]
}

 The dataset includes 468 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010682-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3z97uj
title: Occurrence Download

description: A dataset containing 443 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Asplenium appendiculatum subsp. maritimum (Brownsey) Brownsey",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 443 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010681-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.7660423
title: Videos of Embryonic Wound Healing in Drosophila and Wound Segmentation

description: We collect a dataset of time-lapse sequences of Drosophila embryos healing after a laser-induced wound. Altogether we acquire 61 sequences, which we split into train, validation, and test sets of 44, 12, and 5 sequences, respectively. 
We use embryos expressing a GFP tagged myosin II (sqhGFP) imaged at stage 17. The embryos are collected after aging for 16 hours at 18°C. They are mounted on a coverslip covered with heptane glue for conventional confocal microscopy and
by mineral oil to prevent drying. Laser ablation is performed with a pulsed laser. The time-lapse sequences are acquired in vivo using an Olympus IXplore SpinSR10 at room temperature. The samples are illuminated by laser with \(488\,\textrm{nm} \) wavelength using a \(60\, \times \, 1.42 \) NA oil immersion objective.


The individual frames are taken once every minute. Each sequence captures the entire closure of the wound, resulting in an average length of 120 frames. Each frame has \(1152\times1152\) pixels and captures the whole embryo with \(4.6\, \mu \textrm{m/pixel}\) image resolution. A z-stack of the embryo is imaged at each time step with a z-step size of \(1\, \mu \textrm{m}\). 
The time-resolved z-stacks are max-projected along the z-axis, and registered by SIFT algorithm in Fiji. The wounds are segmented by a custom stable U-Net-like architecture and manually refined in napari. As each frame includes the entire embryo, it is cropped to a region of \(256\times 256\) pixels containing the wound and downsampled to \(128\times 128\) by bicubic interpolation.

The processed timelapse sequences are in the folder Video of the Dataset.zip, and their skeletonized segmentations in the folder Segmentations.