cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15367402
title: Future Ocean Warming May Threaten Key Photosynthetic Microbes

description: Description

The datasets supporting the conclusions of this article, including field measurements of Prochlorococcus division rates, are available in this repository. 

The R code performs the following tasks:



Loads data from various sources, including lab experiments, dilution experiments, and in-situ measurements.

Calculates thermal norm predictions using different models (Eppley, Hinshelwood, Eppley-Norberg) to predict division rates based on temperature.

Generates figures to visualize the results, including latitudinal and temperature effects on division rates, model predictions compared with observed data, and changes in primary production under different emission scenarios.

Fits the Hinshelwood model to culture data and extracts best-fit parameters.

Performs bootstrapping to estimate uncertainty in the Hinshelwood model parameters.

Calculates confidence intervals for the bootstrapped parameters.


R Scripts



Ribalet_main.R: This script contains the main analysis code, including data loading, model fitting, figure generation, and bootstrapping.

Ribalet_fitting.R: This script defines functions for fitting different growth models to the data and estimating model parameters.


Requirements



R version 4.4.2 (2024-10-31)Platform: aarch64-apple-darwin20Running under: macOS Sequoia 15.1.1

Matrix products: defaultBLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

attached base packages:[1] parallel  stats     graphics  grDevices utils     datasets [7] methods   base     

other attached packages: [1] DEoptim_2.2-8   arrow_15.0.1    ggpubr_0.6.0    lubridate_1.9.3 [5] forcats_1.0.0   stringr_1.5.1   dplyr_1.1.4     purrr_1.0.2     [9] readr_2.1.5     tidyr_1.3.1     tibble_3.2.1    ggplot2_3.5.1  [13] tidyverse_2.0.0


Installation

Install the required R packages:



Code snippet





install.packages(c("tidyverse", "ggpubr", "arrow", "DEoptim"))





Usage

The scripts will generate figures and output files in the same directory.

Input Data

The code requires the following input data files:



culture.csv

dilution.csv

abundance.parquet

mpm.csv

model_results.parquet

bootstrap_projections.csv

modeled-thermal-traits.tsv

sst.parquet

culture_syn.csv


Please ensure that these files are present in the same directory as the R script files.

Output Data

The code generates the following output files:



Figures: Figure1.png, Figure2.png, Figure3.png, FigureS1.png, FigureS2.png, FigureS3.png, FigureS4.png, FigureS5.png, FigureS6.png, FigureS9.png, FigureS11.png, FigureS12.png, FigureS13.png, FigureS14.png, FigureS15.png

CSV files: bootstrap_parameters.csv, cultures_thermal_reactions.csv


License

This code is licensed under the MIT License.
DOI: 10.5281/zenodo.15485621
title: Future Ocean Warming May Threaten Key Photosynthetic Microbes

description: Description

The datasets supporting the conclusions of this article, including field measurements of Prochlorococcus division rates, are available in this repository. 

The R code performs the following tasks:



Loads data from various sources, including lab experiments, dilution experiments, and in-situ measurements.

Calculates thermal norm predictions using different models (Eppley, Hinshelwood, Eppley-Norberg) to predict division rates based on temperature.

Generates figures to visualize the results, including latitudinal and temperature effects on division rates, model predictions compared with observed data, and changes in primary production under different emission scenarios.

Fits the Hinshelwood model to culture data and extracts best-fit parameters.

Performs bootstrapping to estimate uncertainty in the Hinshelwood model parameters.

Calculates confidence intervals for the bootstrapped parameters.


R Scripts



Ribalet_main.R: This script contains the main analysis code, including data loading, model fitting, figure generation, and bootstrapping.

Ribalet_fitting.R: This script defines functions for fitting different growth models to the data and estimating model parameters.


Requirements



R version 4.4.2 (2024-10-31)Platform: aarch64-apple-darwin20Running under: macOS Sequoia 15.1.1

Matrix products: defaultBLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

attached base packages:[1] parallel  stats     graphics  grDevices utils     datasets [7] methods   base     

other attached packages: [1] DEoptim_2.2-8   arrow_15.0.1    ggpubr_0.6.0    lubridate_1.9.3 [5] forcats_1.0.0   stringr_1.5.1   dplyr_1.1.4     purrr_1.0.2     [9] readr_2.1.5     tidyr_1.3.1     tibble_3.2.1    ggplot2_3.5.1  [13] tidyverse_2.0.0


Installation

Install the required R packages:



Code snippet





install.packages(c("tidyverse", "ggpubr", "arrow", "DEoptim"))





Usage

The scripts will generate figures and output files in the same directory.

Input Data

The code requires the following input data files:



culture.csv

dilution.csv

abundance.csv

mpm.csv

model_results.parquet

bootstrap_projections.csv

modeled-thermal-traits.tsv

sst.parquet

culture_syn.csv


Please ensure that these files are present in the same directory as the R script files.

Output Data

The code generates the following output files:



Figures: Figure1.png, Figure2.png, Figure3.png, FigureS1.png, FigureS2.png, FigureS3.png, FigureS4.png, FigureS5.png, FigureS6.png, FigureS9.png, FigureS11.png, FigureS12.png, FigureS13.png, FigureS14.png, FigureS15.png

CSV files: bootstrap_parameters.csv, cultures_thermal_reactions.csv


License

This code is licensed under the MIT License.
DOI: 10.15468/dl.kjge2p
title: Occurrence Download

description: A dataset containing 73857 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Dichondra J.R.Forst. & G.Forst."
 ]
}

 The dataset includes 73857 records from 407 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031068-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sgpbsf
title: Occurrence Download

description: A dataset containing 542 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erythrina caffra Thunb."
 ]
}

 The dataset includes 542 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031075-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zh5jgt
title: Occurrence Download

description: A dataset listing the 1687 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((133.58203 -24.01378,134.25536 -24.01378,134.25536 -23.391,133.58203 -23.391,133.58203 -24.01378))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 1687 records were derived from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031066-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fagze2
title: Occurrence Download

description: A dataset containing 3317 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is North America",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is CC-BY 4.0",
 "OccurrenceStatus is Present",
 "TaxonKey is Crocodylia",
 "Year 2000-2025"
 ]
}

 The dataset includes 3317 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031077-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7939/r3-cp6y-5481
title: Laboratory Characterization and Experimental Data for Ultrasonic Experiments on Carbon Dioxide Saturated Porous Samples
title: Ultrasonic Wave Speeds and Attenuation for CO2 Saturated Porous Samples

description: These sample characterization and ultrasonic laboratory measurements were collected as part of the M.Sc. thesis of Helen Yam (Yam, H., CO2 Rock Physics: A Laboratory Study, M.Sc. Thesis, University of Alberta, https://doi.org/10.7939/R36704, 2011). Some of these data are presented and analyzed further in Schmitt, DR, G. Davila, H. Yam, G. Njiekak, and R. Kofman, Effects of CO2 Phase State on the Seismological Properties of Porous Materials: Implications for Seismic Monitoring of Volcanic Hazards and Sequestered Carbon submitted to the Geological Society of London Special Publication Enabling Secure Subsurface Storage in Future Energy Systems, 2022. Please refer to the README.txt file for additional information about the data and individual files.
DOI: 10.7939/r3-acrp-wd88
title: Data from a Magnetotelluric Survey Over the Southern Oklahoma Aulacogen
title: SOAMT

description: If you use this data, please cite either this portal or the journal article published using this data, which can be found here: https://doi.org/10.1029/2023JB026555 Please read the description below. Any questions can be emailed to bchase1@ualberta.ca This entry contains the data from 13 long-period magnetotelluric soundings collected over the Southern Oklahoma Aulacogen. Data files are in EDI format and contain unedited and unrotated transfer functions. The zip folder titled "TimeSeries" contains a series of subfolders named similarly to the EDI files. Each folder contains the raw time series data for each sounding. An Excel file that contains the metadata and survey notes for each sounding is also included.
DOI: 10.6084/m9.figshare.26798932
title: Finding-large-independent-sets-in-networks-using-competitive-dynamics

description: Many decision-making algorithms draw inspiration from the inner workings of individual biological systems. However, it remains unclear whether collective behaviour among biological species can also lead to solutions for computational tasks. By studying the coexistence of species that interact through simple rules on a network, we demonstrate that the underlying dynamical system can recover near-optimal solutions to the maximum independent set problem -- a fundamental, computationally hard problem in graph theory. Furthermore, we observe that the optimality of these solutions is improved when the competitive pressure in the system is gradually increased. We explain this phenomenon by showing that the cascade of bifurcation points, which occurs with increasing competitive pressure in our dynamical system, naturally gives rise to Katz centrality-based node removal in the network. The results are relevant for biology, economics, and analogue computing.
DOI: 10.18120/5qs2-s086
title: Simplified, Scalable 24-hour adaptive deep brain stimulation for Parkinson’s disease
DOI: 10.15468/dl.s8qzr9
title: Occurrence Download

description: A dataset containing 27215 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Celtis occidentalis L."
 ]
}

 The dataset includes 27215 records from 383 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031080-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.73br3w
title: Occurrence Download

description: A dataset containing 6780 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Dichopogon Kunth"
 ]
}

 The dataset includes 6780 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031081-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p5nq67
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Locality is one of (Gaualgeschein, les hauteuts près Bingen, Gaualgesheim, Gaualgesheim (Nassau), Gaualgesheim (near), Gaualgesheim près Bingen, Gaualgesheim\", Gaualgesheim, Felder, Gaualgesheim., Gaualgesheim. Oestrich (Nassau)., Gaualgesheim: Auf Tertiärkalk am Ockenheimer Hörnc, Gaualgesheim: Felder und Gebüsche der Tegelformati, Gaualgesheim; In sylvis, Gaualgesheimer \"Kopf\" bei Bingen., Gaualgesheimer Berg [=Gau-Algesheim], Gaualgesheimer Berges bei Bingen., Gaualgesheimer Kopf, Gaualgesheimer Kopf [Landkreis Mainz-Bingen], Gaualgesheimer Kopf bei Oestich, Gaualgesheimer Kopf, Oppenheimer Seite, Rheinhesse, Gaualgesheimer Kopf, Randzone des Waldes, Waldrand)",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 17 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031083-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4gsaax
title: Occurrence Download

description: A dataset containing 144875 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Troglodytes aedon Vieillot, 1809",
 "Country is Chile",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 144875 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031064-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bx9adb
title: Occurrence Download

description: A dataset containing 1746 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Juglans hindsii (Jeps.) Jeps. ex R.E.Sm."
 ]
}

 The dataset includes 1746 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031084-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15418499
title: Annexes for Management of Sustainable and secure Regional  Development
DOI: 10.5281/zenodo.15418500
title: Annexes for Management of Sustainable and secure Regional  Development
DOI: 10.15468/dl.r8fjm7
title: Occurrence Download

description: A dataset containing 153 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is LACM Vertebrate Collection",
 "TaxonKey is Urocyon littoralis (Baird, 1858)"
 ]
}

 The dataset includes 153 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031085-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7939/r3-ab89-qc85
title: Inuvik and Storm Hills Sites Data
DOI: 10.15468/dl.6snu8r
title: Occurrence Download

description: A dataset containing 1487 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Dichostemma Pierre"
 ]
}

 The dataset includes 1487 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031086-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60707/b64z-vb94
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.5281/zenodo.11458076
title: TIDMAD: Time Series Dataset for Discovering Dark Matter with AI Denoising

description: TIDMAD is the first dataset and benchmark from a dark matter physics experiment, providing ultra-long time series data and comprehensive tools that enable machine learning models to directly advance the fundamental physics search for dark matter.

This data is availble for download via download_data.py. Metadata for this dataset is specified in TIDMAD_croissant.json. The file names are listed in filelist.dat. For furhter information and publically available code, please see the associated GitHub repository. For more information on this dataset and benchmark, please reference our TIDMAD paper.
DOI: 10.60707/dec2-sc43
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.60707/wvgg-tr43
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.60707/hdmh-s451
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.60707/nk00-4k23
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.60707/v63z-6q79
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.60707/7byz-1130
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.15468/dl.bwvzqu
title: Occurrence Download

description: A dataset containing 1141 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acer ×freemanii A.E.Murray"
 ]
}

 The dataset includes 1141 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031087-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7nx59y
title: Occurrence Download

description: A dataset containing 7007 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Argentina",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Chiroptera"
 ]
}

 The dataset includes 7007 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031088-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11458075
title: TIDMAD: Time Series Dataset for Discovering Dark Matter with AI Denoising

description: TIDMAD is the first dataset and benchmark from a dark matter physics experiment, providing ultra-long time series data and comprehensive tools that enable machine learning models to directly advance the fundamental physics search for dark matter.

This data is availble for download via download_data.py. Metadata for this dataset is specified in TIDMAD_croissant.json. The file names are listed in filelist.dat. For furhter information and publically available code, please see the associated GitHub repository. For more information on this dataset and benchmark, please reference our TIDMAD paper.
DOI: 10.5281/zenodo.15418539
title: TIDMAD: Time Series Dataset for Discovering Dark Matter with AI Denoising

description: TIDMAD is the first dataset and benchmark from a dark matter physics experiment, providing ultra-long time series data and comprehensive tools that enable machine learning models to directly advance the fundamental physics search for dark matter.

This data is availble for download via download_data.py. Metadata for this dataset is specified in TIDMAD_croissant.json. The file names are listed in filelist.dat. For furhter information and publically available code, please see the associated GitHub repository. For more information on this dataset and benchmark, please reference our TIDMAD paper.
DOI: 10.15468/dl.4w5nz4
title: Occurrence Download

description: A dataset containing 2373 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is North America",
 "Country is Mexico",
 "License is CC-BY 4.0",
 "OccurrenceStatus is Present",
 "TaxonKey is Crocodylia",
 "Year 2005-2025"
 ]
}

 The dataset includes 2373 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031089-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4121/fd71c68f-ac6c-448a-98e7-f1017a0b4b7a.v1
title: Data underlying paper: Elucidation of Enhanced Lithium Conductivity in Nanoporous Ionogel Using Solid State NMR

description: Data supporting findings of paper https://doi.org/10.1002/admi.202201646<br>AbstractNanostructured solid composite electrolyte or nano-SCE, which is composed of an ionic liquid, nanoporous silica, and residuals of immobilized precursor components, shows promising synergistic properties. The ionic conductivity of nano-SCE is in the range of 2–5 mS cm<sup>−1</sup>, which exceeds the bulk ionic liquid conductivity at ambient temperature, while maintaining characteristics of a solid electrolyte such as having no leakage issues as the ionic liquid is confined, and lower flammability compared to conventional liquid electrolytes. In this study, the underlying mechanism of enhanced conductivity is investigated by using magic angle spinning NMR and NMR relaxometry analysis. Water, one of the volatile precursor molecules has shown to play a key role in the final conductivity and stability at the solid-electrolyte interface, as it enhances the temperature range in which the ionic liquid remains mobile. In line with previous studies, water with lowered mobility is found in the silicon matrix. The activation energies of lithium ion transfer probed by NMR relaxometry, however, do not change as function of water content. The increase in bulk mobility of lithium ions under ambient conditions compared to water-less nano-SCE is found to be the origin of the altered conductivity of this material.
DOI: 10.15468/dl.ag6k5f
title: Occurrence Download

description: A dataset containing 306 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Dichotomanthes Kurz"
 ]
}

 The dataset includes 306 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031093-250426092105405/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.24578905
title: Albin et al Data.

description: Activity and survial of spiders under controleld salinity conditions in the laboratory.
DOI: 10.15468/dl.4djuf8
title: Occurrence Download

description: A dataset listing the 1034 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((134.32495 -24.31761,135.42839 -24.31761,135.42839 -23.312,134.32495 -23.312,134.32495 -24.31761))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 1034 records were derived from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031079-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.