cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.m58cc5
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cirsium congestissimum Kitam.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 34 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0201017-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n9kwc9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diospyros nigra (J.F.Gmel.) Perr.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0205547-220831081235567/datasets/export for details.
DOI: 10.15468/dl.ysd45w
title: Occurrence Download

description: A dataset containing 10840 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Taxonomic Checklist of the Dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae) of Sabah, Malaysia"
 ]
}

 The dataset includes 10840 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0283175-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4tc66f
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Semiarundinaria okuboi Makino",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0208146-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7kn3sp
title: Occurrence Download

description: A dataset containing 16868 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Priapulida"
 ]
}

 The dataset includes 16868 records from 170 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0238386-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8zss97
title: Occurrence Download

description: A dataset containing 1187 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helenium microcephalum DC."
 ]
}

 The dataset includes 1187 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0238384-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jt7q6n
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hystrix gracilis (Hook.f.) Allan"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0251893-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3bqabb
title: Occurrence Download

description: A dataset containing 87 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stenostachys laevis (Petrie) Connor"
 ]
}

 The dataset includes 87 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0251895-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4nem2w
title: Occurrence Download

description: A dataset containing 237 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Noccaea trinervia (DC.) Steud."
 ]
}

 The dataset includes 237 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0251902-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rer7gw
title: Occurrence Download

description: A dataset containing 2416 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Iberis aurosica Chaix"
 ]
}

 The dataset includes 2416 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0251906-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v47pq2
title: Occurrence Download

description: A dataset containing 119006 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "TaxonKey is Myopsida"
 ]
}

 The dataset includes 119006 records from 131 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0144478-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18739/a2pr7mw4n
title: Iron-Phosphorus sediment incubation experiment in Stordalen Mire, Abisko, Sweden (2019)

description: Phosphorus limits primary productivity in many (Sub-)Arctic ecosystems and may constrain biological carbon sequestration. Iron (III) oxides strongly bind phosphate in soils but can dissolve under flooded, reducing conditions induced by permafrost thaw and ground collapse. The ability for iron to regulate phosphate storage and solubility in thawing permafrost landscapes remains unclear. Here, iron-rich sediments containing iron oxides and organic-bound iron were incubated with or without added phosphate in soils along a permafrost thaw gradient to evaluate how iron-phosphate associations respond to thaw-induced redox shifts. Iron oxides partially dissolved and released sorbed phosphate when incubated in soils underlain by degraded permafrost. Iron complexed by organic matter remained stable but provided no phosphate binding capacity. Our study demonstrates that the capacity for iron oxides to immobilize and retain phosphate in permafrost peatlands decreases with permafrost thaw. This dataset includes soil redox potential measurements and soil water chemistry that provide the context for understanding iron mineral transformation and associations with phosphorus.
DOI: 10.21227/2cvj-bs21
title: Nurse Care Activity Recognition Challenge

description: In an aging population, the demand for nurse workers increases to care for elders. Helping nurse workers make their work more efficient, will help increase elders quality of life, as the nurses can focus their efforts on care activities instead of other activities such as documentation.
DOI: 10.22003/xfel.eu-data-003018-00
title: Photoactivation intermediates of a bacterial adenylate cyclase
DOI: 10.34677/1728-7936-2020-1-14-18
title: PARAMETERS AND OPERATION MODES OF ROTARY TILLAGE WITH SERRATED KNIVES

description: The authors have studied some ways of improving the technology of pre-planting tillage of lumpy soils using milling cutters with serrated profi les of the knife surface. This technology is certain to improve the cultivation quality and increase the agrotechnical indicators of soil cultivation. The study focused on the infl uence of the soil cultivation depth, the number of knives, the speed of the tiller rotor and the unit travel speed on the operation quality of a rotary tiller. The unit travel speed is characterized by the specifi c energy consumption of rotary tillage, the average size of lumps left on the fi eld after rotary tillage and the degree of soil crushing. The study applied the theory of experimental design. Taking into account the shape and size of a tuber bunch as applied to the actual conditions of potato cultivation, the authors have proposed methodological principles
for optimizing the parameters of formed ridges. When two cutters with a serrated blade are installed on the tiller rotor, an increase in the travel speed from 2.1 to 3.2 m/s results in a 2.5% increase in specifi c traction resistance, while that in the range between 3.2 and 4.3 m/s ensures a 3.0% increase. At an angular speed of the tiller rotor of 30 rad/s, when the depth of soil layer tillage increases from 100 to 120 mm, specifi c traction resistance increases by 2.0%, in case of an increase from 120 to 140 mm – by 2.5%. The study has proved the feasibility of using knives with serrated curved blades, as it ensures a reduction in the energy intensity of soil tillage and an increase in potato productivity by 20% as compared to the soil cultivation with the ФН-1.2 serial rotary tiller.
DOI: 10.48690/1527701
title: LandScan USA 2021

description: LandScan USA Population Database 2021 provides estimated population counts at 3 arc-second resolution for Nighttime and Daytime, for the contiguous United States, Hawaii, Alaska, American Samoa, Guam, Northern Mariana Islands, Puerto Rico, and the U.S. Virgin Islands. Residents, Prisoners, Workers, Students, and Shoppers are modeled. These are baseline population estimates, which do not include transitory populations such as business travelers and tourists.
DOI: 10.5281/zenodo.10480761
title: Model output for "Climate variability leads to multiple oxygenation episodes across the Great Oxidation Event"

description: This repository contains all the model output presented in Garduno et al. (2024). Climate variability leads to multiple oxygenation episodes across the Great Oxidation Event. Submitted to Geophysical Research Letters.

Model output organization

There are seven zip files containing the model output from different simulations described in the main manuscript. See the main manuscript and code repository for more details.:



`o2_flux_constant_1.8e12.zip`: model output for simulation in which the O2 input flux is kept constant at a value of 1.8e12 molecules/cm^2/s

`o2_flux_constant_2.2e12.zip`: model output for simulation in which the O2 input flux is kept constant at a value of 2.2e12 molecules/cm^2/s

`linear_o2_flux_increase.zip`:  model output for simulation in which the O2 input flux is linearly increased

`linear_o2_flux_increase_change_during_glaciations.zip`: model output for simulation in which the O2 input flux is linearly increased, superimposing a 60% decrease during glaciations and a 60% increase after glaciations.

`linear_ri_flux_decrease.zip`: model output for simulation in which the reductant input flux is linearly decreased and the O2 input flux is kept constant

`linear_ri_flux_decrease_change_during_glaciations.zip`: model output for simulation in which the reductant input flux is linearly decreased and the O2 input flux is kept constant with a 60% decrease during glaciations and a 60% increase after glaciations.

`stability_analysis.zip`: model output for stability analysis of steady states.


Each of these folders contains model output every 1e5 years. The files are numbered from 1 to 4998. `1` corresponds to the output at 1e5 years, `2` corresponds to the output at 2e5 years, and so on.

There are also files containing the O2 fluxes (`o2_flux.txt`) and reductant input (`ri_flux.txt`) used at each 1e5 output step.

Reading data

The data files are Fortran binary files. You can read the with the read_evolve_output function implemented in  PhotochemPy.

You can also use the Python functions provided in the paper's code repository: https://github.com/DanyIvan/climate_goe_over_time/blob/main/read_output.py

Names and units

The model output files contain the mixing ratios for all modeled species species. They also contain information about:

- 'T_time': temperature profile (K) at the output time step.- 'edd_time': eddy diffusivity profile (cm^2/s) at the output time step.- 'press_time': pressure profile (bar) at the output time step.- 'h2osat': saturation vapor pressure profile (bar) at the output time step.- 'time': time (s) at the output time step- 'den': air number density (molecules/cm^3)
DOI: 10.5281/zenodo.13137071
title: Data for Diamond et al. (2024), Testing Cloud Adjustment Hypotheses for the Maintenance of Earth's Hemispheric Albedo Symmetry With Natural Experiments, GRL
DOI: 10.5281/zenodo.13345944
title: InSAR coseismic deformation for the 2 April 2024, Mw 7.4, Hualien (Eastern Taiwan) earthquake

description: This dataset includes coseismic InSAR deformation for the 2024 Mw 7.4 Hualien (Eastern Taiwan) earthquake.
DOI: 10.5281/zenodo.13712504
title: 3D Coordinates of the isoxazole derivative 3a against FXR and hLIFR receptors

description: This repository contains the 3D Coordinates (Docking and Molecular Dynamics best cluster) in pdb extension of the isoxazole derivative 3a against FXR and hLIFR receptors.
DOI: 10.5281/zenodo.13851639
title: GRAVITY and CRIRES+ data for Gliese 229Bab

description: This Zenodo record contains the GRAVITY data and CRIRES+ RVs used in Xuan et al. 2024 to fit the orbit of the binary brown dwarf Gliese 229 BaBb. For the full author list and paper, please see https://www.nature.com/articles/s41586-024-08064-x

After unzipping, there will be one ipynb file and a folder for the five epochs of GRAVITY data. The CRIRES+ RVs are listed in the Jupyter notebook. The notebook will start an orbit fit. It is recommended that the code be run with multiple CPUs. 

The notebook is written in Julia, so users should install Julia first following resources provided in the notebook.
DOI: 10.5281/zenodo.13852023
title: Data and model output for "Evidence of subsurface control on the coevolution of hillslope morphology and runoff generation"

description: Data, model output, and scripts supporting the manuscript:

Litwin, D. G., & Harman, C. J. (2024) Evidence of subsurface control on the coevolution of hillslope morphology and runoff generation. Water Resources Research, 60, e2024WR037301. https://doi.org/10.1029/2024WR037301
DOI: 10.5281/zenodo.5195636
title: MARv3.10 outputs: What is the Surface Mass Balance of Antarctica? An Intercomparison of Regional Climate Model Estimates

description: MARv3.10 outputs used in: <em>Mottram, R., Hansen, N., Kittel, C., van Wessem, M., Agosta, C., Amory, C., Boberg, F., van de Berg, W. J., Fettweis, X., Gossart, A., van Lipzig, N. P. M., van Meijgaard, E., Orr, A., Phillips, T., Webster, S., Simonsen, S. B., and Souverijns, N.: What is the Surface Mass Balance of Antarctica? An Intercomparison of Regional Climate Model Estimates, The Cryosphere Discuss. [preprint], https://doi.org/10.5194/tc-2019-333, accepted, 2020.</em> MARv3.10 forced by ERA-Interim outputs with monthly values of SMB and components (kg m<sup>-2</sup> month<sup>-1</sup>), and (near-) surface temperature (°C) over the Antarctic ice sheet (1981--2018) Grid file used in MAR simulation Be carreful that the unit metadata in the netcdf files from SMB and its components are uncorrect. <strong>Values are in kg m<sup>-2</sup> month<sup>-1</sup></strong> instead of kg m<sup>-2</sup> day<sup>-1</sup>.<br> <br> If you need other variables or output frequencies from MAR, write me (c2kittel@gmail.com) and I will be glad to help you. I will also be happy to share the scripts I have developed to analyse the outputs and make the figures in this paper if needed. Please cite the paper if you use these MAR outputs. However, note that these outputs are now considered as deprecated since new outputs using a more recent model version (MARv3.11) and forcing (ERA5) have been published (see Kittel et al., 2021: https://tc.copernicus.org/articles/15/1215/2021/).<br> <br> Data usage notice: If you use any of these results, please acknowledge the work of the people involved in producing them. Acknowledgements should have language similar to the below that contained informations related to MAR. In order to document MAR scientific impact and enable ongoing support of the model, users are likely encouraged to contact C. Kittel and C. Agosta to add their works in the list of MAR-related publications. "We thank the MAR team which make available the model outputs, as well agencies (F.R.S - FNRS, CÉCI, and the Walloon Region) that provided computational resources for MAR simulations." You should also refer to and cite the following paper: <em>Mottram, R., Hansen, N., Kittel, C., van Wessem, M., Agosta, C., Amory, C., Boberg, F., van de Berg, W. J., Fettweis, X., Gossart, A., van Lipzig, N. P. M., van Meijgaard, E., Orr, A., Phillips, T., Webster, S., Simonsen, S. B., and Souverijns, N.: What is the Surface Mass Balance of Antarctica? An Intercomparison of Regional Climate Model Estimates, The Cryosphere Discuss. [preprint], https://doi.org/10.5194/tc-2019-333, accepted, 2020.</em>
description: {"references": ["Mottram et al. 2021: https://tc.copernicus.org/preprints/tc-2019-333/"]}
DOI: 10.5281/zenodo.5286019
title: Selected clear-sky FloX hyperspectral data

description: Zip - Folders containing calibrated reflectance, reflected radiance and incoming radiance retrieved from measurements with FloX field spectrometers over Alfalfa (2018 in Grosseto, Italy) and grass (2018 in Julich, Germany) during clear sky conditions. The incoming radiance is measured with optics of hemispherical (~180°) field of view and the reflected radiance with conical (~25°) field of view. The data is organized in sub-folders inside the zip-repositories which are named according to the date of recording, containing CSV-files which hold the hyperspecteral information. One file is associated to the integrated full-range (FULL) spectrometer between 340nm and 1000nm, and the fluorescence-range (FLUO) spectrometer between 650nm and 810nm, containing incoming radiance, reflected radiance or reflectance, respectively. The first collumn contains the associated central wavelengths, the first row the time of recording, each subsequent field of the table contains the calibrated radiance (in W m<sup>-2</sup> sr<sup>-1</sup> nm<sup>-1</sup>) or reflectance (unitless) values.
description: Supported by the European Space Agency in the frame of AtmoFLEX (4000122454/17/NL/FF).
DOI: 10.5281/zenodo.6962271
title: Supplementary files for the Xenoturbella bocki genome analysis

description: Supplementary files.


 


Abstract


The evolutionary origins of Bilateria remain enigmatic. One of the more enduring proposals highlights similarities between a
cnidarian-like planula larva and simple acoel-like flatworms. This idea is based in part on the view of the Xenacoelomorpha as an outgroup to all other bilaterians which are themselves designated the Nephrozoa (protostomes and deuterostomes). Genome data, which can help to elucidate phylogenetic relationships and provide important comparative data, remain sparse for early branching bilaterians. Here we assemble and analyse the genome of the simple, marine xenacoelomorph Xenoturbella bocki, a key species for our understanding of early bilaterian and deuterostome evolution. Our highly contiguous genome assembly of X. bocki has a size of ~110 Mbp in 18 chromosome like scaffolds, with repeat content, and intron, exon and intergenic space comparable to other bilaterian invertebrates. We find X. bocki to have a similar number of genes to other bilaterians and to have retained ancestral metazoan synteny. Key bilaterian signalling pathways are also largely complete and most bilaterian miRNAs are present. We conclude that X. bocki has a complex genome typical of bilaterians, in contrast to the apparent simplicity of its body plan. Overall, our data do not provide evidence supporting the idea that Xenacoelomorpha are a primitively simple outgroup to other bilaterians and gene presence/absence data support a relationship with Ambulacraria.
DOI: 10.5281/zenodo.7392545
title: Versatility of Cellulose Stimuli Responsive Membranes in the Detection of Dimethylamine

description: Data set for poster presented to 3rd commonwealth presentation held virtuallhttps://commonwealthchemistry.org/2022-winners-of-commonwealth-chemistry-posters/y
DOI: 10.5281/zenodo.7989843
title: Data and program codes to reproduce the results of seismic tomography for the Augustine Volcano (Alaska)

description: This file contains the files to reproduce the results presented in the article: by Ivan Koulakov, Saleh Ismail Quasi, and Pavel Izbekov (2023). Structure of shallow magma sources beneath Augustine Volcano (Alaska) inferred from local earthquake tomography, <em>Journal of Geophysical Research, Solid Earth</em>. This file includes: 1. The full folder with the LOTOS code for the passive-source seismic tomography (Koulakov, 2009, BSSA). 2. Folder with the dataset including arrival times of the P and S waves from local seismicity in the area of the Augustine Volcano in Alaska. 3. README_AUGUSTINE.PDF file with the description of the workflow on how to reproduce the tomography models based on experimental and synthetic data presented in the article. Koulakov, I., 2009, LOTOS code for local earthquake tomographic inversion: Benchmarks for testing tomographic algorithms: Bulletin of the Seismological Society of America, v. 99, p. 194–214, https://doi.org/10.1785/0120080013.
DOI: 10.6084/m9.figshare.27302328
title: Supplementary Material for: Implementation of machine learning algorithms to screen for advanced liver fibrosis in metabolic dysfunction-associated steatotic liver disease (MASLD): an in-depth explanatory analysis

description: Background 
This study aimed to train machine learning algorithms(MLAs) to detect advanced fibrosis(AF) in MASLD patients at the level of primary care setting and to explain the predictions to ensure responsible use by clinicians.
Methods
Readily available features of 618 MASLD patients followed up at a tertiary center were used to train five MLAs. AF was defined as liver stiffness≥9.3 kPa, measured via 2-dimension shear wave elastography(n=495) or liver biopsy≥F3(n=123). MLAs were compared to Fibrosis-4 index(FIB-4) and NAFLD fibrosis score(NFS) on 540 MASLD patients from the primary care setting as validation. Feature importance, partial dependence, and shapely additive explanations(SHAP) were utilized for explanation. 
Results
Extreme gradient boosting(XGBoost) achieved an AUC=0.91,outperforming FIB-4(AUC=0.78) and NFS(AUC=0.81, both p&lt;0.05) with specificity=76% vs. 59% and 48% for FIB-4≥1.3 and NFS≥-1.45, respectively(p&lt;0.05). Its sensitivity(91%) was superior to FIB-4(79%). XGBoost confidently excluded AF (negative predictive value=99%) with the highest positive predictive value (31%), superior to FIB-4 and NFS (all p&lt;0.05). The most important features were HbA1c and GGT with a steep increase in AF probability at HbA1c&gt;6.5%. The strongest interaction was between AST and age. XGBoost, but not logistic regression, extracted informative patterns from ALT, LDL-c,and ALP(p&lt;0.001). One quarter of the false positives (FP) were correctly reclassified with only one additional false negative based on the SHAP values of GGT, platelets, and ALT which were found to be associated with a FP classification.
Conclusions: 
An explainable XGBoost algorithm was demonstrated superior to FIB-4 and NFS for screening of AF in MASLD patients at the primary care setting. The algorithm also proved safe for use as clinicians can understand the predictions and flag FP classifications.
DOI: 10.7303/syn26707219
title: Endomapper dataset A complete endoscopy procedures dataset