cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15184042
title: Dataset for "Growth history leaves a geometric trace in puzzle cells"

description: This record contains the datasets used in “Growth history leaves a geometric trace in puzzle cells”.

The datasets are organized into the following tar.gz files:

Contours.tar.gzCell contour data from various plant species used for analysis of puzzle cell shapes.   Drug treatments.tar.gzDescription: Data from pharmacological treatments of Arabidopsis thaliana cotyledons with oryzalin and latrunculin B.   LGO mutant analysis.tar.gzEpidermal cell data from leaves of mutants for LOSS OF GIANT CELLS FROM ORGANS (LGO) in Arabidopsis thaliana.

Maize data.tar.gzData from time-lapse experiments on leaf epidermis of maize (Zea mays) using the sequential replica method.    Miocene species analysis.tar.gzEpidermal cell data from Miocene plant fossils used for analysis of puzzle cell shapes in early plant species.

Models.tar.gzModel files, simulation data and parameter files. The file also includes two deb packages of the MorphoDynamX software for Ubuntu 22: MorphoDynamX_CUDA11_Ubuntu22.deb compiled with CUDA 11 support for systems with compatible NVIDIA graphics cards; MorphoDynamX_OMP_Ubuntu22.deb compiled with OpenMP support for systems without NVIDIA graphics cards or for running simulations on CPU only.   MT data and mass spring model.tar.gzData on microtubule orientation in epidermal pavement cells and files related to the mass-spring mechanical model simulations.   Mutants.tar.gzEpidermal cell data from Arabidopsis thaliana mutants with defects in puzzle cell shape formation (i.e., CA-ROP2, any1, ctr1).

Please extract the relevant tar.gz file(s) to access the datasets. 

For any questions or further information about the datasets, please contact the corresponding authors:Mateusz Majda (Mateusz.Majda@unil.ch) or Richard S. Smith (Richard.Smith@jic.ac.uk)

Please cite the related publication when using these datasets.
DOI: 10.5281/zenodo.15184043
title: Dataset for "Growth history leaves a geometric trace in puzzle cells"

description: This record contains the datasets used in “Growth history leaves a geometric trace in puzzle cells”.

The datasets are organized into the following tar.gz files:

Contours.tar.gzCell contour data from various plant species used for analysis of puzzle cell shapes.   Drug treatments.tar.gzDescription: Data from pharmacological treatments of Arabidopsis thaliana cotyledons with oryzalin and latrunculin B.   LGO mutant analysis.tar.gzEpidermal cell data from leaves of mutants for LOSS OF GIANT CELLS FROM ORGANS (LGO) in Arabidopsis thaliana.

Maize data.tar.gzData from time-lapse experiments on leaf epidermis of maize (Zea mays) using the sequential replica method.    Miocene species analysis.tar.gzEpidermal cell data from Miocene plant fossils used for analysis of puzzle cell shapes in early plant species.

Models.tar.gzModel files, simulation data and parameter files. The file also includes two deb packages of the MorphoDynamX software for Ubuntu 22: MorphoDynamX_CUDA11_Ubuntu22.deb compiled with CUDA 11 support for systems with compatible NVIDIA graphics cards; MorphoDynamX_OMP_Ubuntu22.deb compiled with OpenMP support for systems without NVIDIA graphics cards or for running simulations on CPU only.   MT data and mass spring model.tar.gzData on microtubule orientation in epidermal pavement cells and files related to the mass-spring mechanical model simulations.   Mutants.tar.gzEpidermal cell data from Arabidopsis thaliana mutants with defects in puzzle cell shape formation (i.e., CA-ROP2, any1, ctr1).

Please extract the relevant tar.gz file(s) to access the datasets. 

For any questions or further information about the datasets, please contact the corresponding authors:Mateusz Majda (Mateusz.Majda@unil.ch) or Richard S. Smith (Richard.Smith@jic.ac.uk)

Please cite the related publication when using these datasets.
DOI: 10.15468/dl.ku5jwx
title: Occurrence Download

description: A dataset containing 117 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Brassica juncea",
 "Year 1970-2000"
 ]
}

 The dataset includes 117 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073163-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4a99dp
title: Occurrence Download

description: A dataset containing 6674 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thecla betulae",
 "HasCoordinate is true",
 "CoordinateUncertaintyInMeters is less than or equal to 1000",
 "Year is greater than or equal to 1970",
 "Country is one of (Italy, Switzerland, Germany, Austria, Slovenia, France)"
 ]
}

 The dataset includes 6674 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073164-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rwr7bd
title: Occurrence Download

description: A dataset containing 73369 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Living Specimen, Occurrence evidence)",
 "OccurrenceStatus is Present",
 "TaxonKey is Elapidae",
 "Year 2009-2021"
 ]
}

 The dataset includes 73369 records from 223 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073113-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aac698
title: Occurrence Download

description: A dataset containing 5665 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ficedula zanthopygia)",
 "Country is one of (Philippines, Korea, Republic of, Japan, China, Chinese Taipei, Thailand, Viet Nam, Cambodia, Lao People’s Democratic Republic, Mongolia, Myanmar)",
 "Month is one of (May, June, July)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2024",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Human Observation, Observation)"
 ]
}

 The dataset includes 5665 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073165-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.43pz5k
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Hong Kong)",
 "OccurrenceStatus is Present",
 "TaxonKey is Myotis chinensis",
 "Year 1970-2024"
 ]
}

 The dataset includes 16 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073166-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kb5juj
title: Occurrence Download

description: A dataset containing 64 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Linum littorale)",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2025",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 64 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073169-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mggvv4
title: Occurrence Download

description: A dataset containing 6667 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Quercusia quercus",
 "HasCoordinate is true",
 "CoordinateUncertaintyInMeters is less than or equal to 1000",
 "Year is greater than or equal to 1970",
 "Country is one of (Italy, Switzerland, Germany, Austria, Slovenia, France)"
 ]
}

 The dataset includes 6667 records from 202 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073171-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xndwrw
title: Occurrence Download

description: A dataset containing 93 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Brassica rapa",
 "Year 1970-2000"
 ]
}

 The dataset includes 93 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073172-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sx65hs
title: Occurrence Download

description: A dataset containing 25911 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Spilopelia chinensis",
 "Year 2024-2026"
 ]
}

 The dataset includes 25911 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073174-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.am3wpr
title: Occurrence Download

description: A dataset containing 4400 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Emberiza elegans)",
 "Country is one of (Philippines, Korea, Republic of, Japan, China, Chinese Taipei, Thailand, Viet Nam, Cambodia, Lao People’s Democratic Republic, Mongolia, Myanmar)",
 "Month is one of (May, June, July)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2024",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Human Observation, Observation)"
 ]
}

 The dataset includes 4400 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073173-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16742748
title: 3D ED raw data for "Protecting Statuario white Carrara marble with organophosphorus salts: Case study of ammonium hydrogen phenylphosphonate"

description: 3D ED data for the crystal structure in the title publication (https://doi.org/10.1039/D5MA01116G). Data were collected using continuous rotation in selected area mode. The table below summarizes generic data collection parameters for the data collection.

 




Collection site
University of Southampton, NCS/NEDF


Sample label(s)
2024NCS0378


Crystal structure deposit
CSD 2473954


 
 


Instrumental
 


Instrument
Rigaku XtaLAB Synergy-ED, electron diffractometer


Radiation source
LaB6


Accelerating voltage [kV]
200


Wavelength [Å]
0.0251


Probe type
Parallel beam (SAED)


Beam convergence
Parallel beam


Detector
Rigaku HyPix-ED, hybrid pixel array detector


Number of pixels in the image
775 x 385


Pixel size [µm]
100


Hardware binning
1


 
 


Sample description
 


Name
Calcium phenylphosphonate dihydrate


Chemical composition
C6 H9 Ca O5 P


Sample source
Synthesis


Grid
holey carbon coated copper grid, 200 mesh (Agar Scientific)


Sample preparation
Sample ground between glass slides, grid dabbed, cryo transfer @ 175 K


Sample holder
GATAN Elsa cryo-transfer holder 698


 
 


Experimental
 


Data type
Electron diffraction data - 3D ED


Data collection method
Continuous rotation  - cRED


Collection temperature [K]
175


 
 


Software
 


Software used for the data collection
CrysAlisPro 1.171.44.90a


Software used for processing
CrysAlisPro 1.171.44.90a


 
 


Files and data formats
 


Image folders
./frames/xxx.rodhypix./frames/TIFF/xxx.tiff


Image format
.rodhypix.tiff (converted with CrysAlisPro)


Additional files


 

CrysAlisPro files:

./expinfo/./expinfo/exp_XXXX_datacoll.ini

./plots_dc.plots_dc/exp_XXX_hypix.dat.plots_dc/exp_XXX_Jeol_MicroED.dat.plots_dc/exp_XXX_primarybeam.dat.plots_dc/exp_XXX_primarybeam_0.jpg

./CrysalisExpSettings.ini./exp_XXX.par./exp_XXX.run./new.ccd

 

Grain snapshots files:

./exp_XXXX_microed_grain_snapshot.rodhypix./exp_XXXX_microed_grain_snapshot.tiff./exp_XXXX_microed_grain_snapshot.jpg
DOI: 10.5281/zenodo.16742747
title: 3D ED raw data for "Protecting Statuario white Carrara marble with organophosphorus salts: Case study of ammonium hydrogen phenylphosphonate"

description: 3D ED data for the crystal structure in the title publication (https://doi.org/10.1039/D5MA01116G). Data were collected using continuous rotation in selected area mode. The table below summarizes generic data collection parameters for the data collection.

 




Collection site
University of Southampton, NCS/NEDF


Sample label(s)
2024NCS0378


Crystal structure deposit
CSD 2473954


 
 


Instrumental
 


Instrument
Rigaku XtaLAB Synergy-ED, electron diffractometer


Radiation source
LaB6


Accelerating voltage [kV]
200


Wavelength [Å]
0.0251


Probe type
Parallel beam (SAED)


Beam convergence
Parallel beam


Detector
Rigaku HyPix-ED, hybrid pixel array detector


Number of pixels in the image
775 x 385


Pixel size [µm]
100


Hardware binning
1


 
 


Sample description
 


Name
Calcium phenylphosphonate dihydrate


Chemical composition
C6 H9 Ca O5 P


Sample source
Synthesis


Grid
holey carbon coated copper grid, 200 mesh (Agar Scientific)


Sample preparation
Sample ground between glass slides, grid dabbed, cryo transfer @ 175 K


Sample holder
GATAN Elsa cryo-transfer holder 698


 
 


Experimental
 


Data type
Electron diffraction data - 3D ED


Data collection method
Continuous rotation  - cRED


Collection temperature [K]
175


 
 


Software
 


Software used for the data collection
CrysAlisPro 1.171.44.90a


Software used for processing
CrysAlisPro 1.171.44.90a


 
 


Files and data formats
 


Image folders
./frames/xxx.rodhypix./frames/TIFF/xxx.tiff


Image format
.rodhypix.tiff (converted with CrysAlisPro)


Additional files


 

CrysAlisPro files:

./expinfo/./expinfo/exp_XXXX_datacoll.ini

./plots_dc.plots_dc/exp_XXX_hypix.dat.plots_dc/exp_XXX_Jeol_MicroED.dat.plots_dc/exp_XXX_primarybeam.dat.plots_dc/exp_XXX_primarybeam_0.jpg

./CrysalisExpSettings.ini./exp_XXX.par./exp_XXX.run./new.ccd

 

Grain snapshots files:

./exp_XXXX_microed_grain_snapshot.rodhypix./exp_XXXX_microed_grain_snapshot.tiff./exp_XXXX_microed_grain_snapshot.jpg
DOI: 10.15468/dl.6k7pm2
title: Occurrence Download

description: A dataset containing 728767 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (RUS, UKR.20_1, UKR.4_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta",
 "Year is 2025"
 ]
}

 The dataset includes 728767 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073151-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xau769
title: Occurrence Download

description: A dataset containing 678102 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lycaenidae",
 "HasCoordinate is true",
 "CoordinateUncertaintyInMeters is less than or equal to 1000",
 "Year is greater than or equal to 1970",
 "Country is one of (Italy, Switzerland, Germany, Austria, Slovenia, France)"
 ]
}

 The dataset includes 678102 records from 1082 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073159-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.frekgf
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Pakistan",
 "TaxonKey is Capra falconeri (Wagner, 1839)"
 ]
}

 The dataset includes 14 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009474-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2uxnf9
title: Occurrence Download

description: A dataset containing 23877 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is IND",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 23877 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0263895-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s01blt
title: Occurrence Download

description: A dataset containing 1771 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nicrophorus americanus A.G.Olivier, 1790"
 ]
}

 The dataset includes 1771 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009509-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z4hks2
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 },
 "TaxonKey is Gilmaniella G.L.Barron, 1964",
 "Year is greater than or equal to 1991"
 ]
}

 The dataset includes 12 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060163-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yfykqw
title: Occurrence Download

description: A dataset listing the 3888 species recorded in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Material citation",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Living Specimen",
 "BasisOfRecord is Occurrence evidence"
 ]
 },
 "Country is Cuba",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata"
 ]
}

 The dataset's 3888 records were derived from 265 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0416218-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.edkgcs
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((87.80273 21.05989,98.34961 21.05989,98.34961 29.77963,87.80273 29.77963,87.80273 21.05989))",
 "HasGeospatialIssue is false",
 "TaxonKey is Chromolaena odorata (L.) R.M.King & H.Rob."
 ]
}

 The dataset includes 39 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087718-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tthqkz
title: Occurrence Download

description: A dataset containing 5445 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "Geometry POLYGON((-0.63446 40.59508,4.67743 40.59508,4.67743 42.72094,-0.63446 42.72094,-0.63446 40.59508))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Senecio inaequidens DC."
 ]
}

 The dataset includes 5445 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087716-210914110416597/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.22823183
title: Plasmodium_falciparum

description: Gene, transcript, and intron level classification, by species
DOI: 10.6084/m9.figshare.22823183.v2
title: Plasmodium_falciparum

description: Gene, transcript, and intron level classification, by species
DOI: 10.6084/m9.figshare.22823183.v1
title: Plasmodium_falciparum

description: Gene, transcript, and intron level classification, by species
DOI: 10.15468/dl.56kzgz
title: Occurrence Download

description: A dataset containing 84 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "TaxonKey is Drypis spinosa L."
 ]
}

 The dataset includes 84 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0136745-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7ess4w
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ambulyx japonica, Ambulyx japonica, Ambulyx japonica Rothschild, 1894, Ambulyx japonica Rothschild, 1894, Ambulyx japonica Okono, 1959, 157922587, Ambulyx japonica Rothschild, 1894)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "Geometry POLYGON((102 17,117 17,117 26.5,102 26.5,102 17))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0181676-210914110416597/datasets/export for details.
DOI: 10.15468/dl.nxkfpx
title: Occurrence Download

description: A dataset containing 264 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spilogale gracilis Merriam, 1890",
 "HasCoordinate is True",
 "Country is United States of America",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2025",
 "Month is greater than or equal to January",
 "Month is less than or equal to December",
 "HasGeospatialIssue is False",
 "DecimalLatitude is greater than or equal to 18.00",
 "DecimalLatitude is less than or equal to 72.00",
 "DecimalLongitude is greater than or equal to -140.00",
 "DecimalLongitude is less than or equal to -68.00"
 ]
}

 The dataset includes 264 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0263161-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ugaksn
title: Occurrence Download

description: A dataset containing 252 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((-100.12327 22.23086,-99.88209 22.23086,-99.88209 22.33912,-100.12327 22.33912,-100.12327 22.23086))"
 ]
}

 The dataset includes 252 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029375-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.