cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.982346
title: X-ray fluorescence (XRF) measurements of a Holocene sediment core from Limni Volvi, Greece

description: In 2020 and 2021, we retrieved six parallel sediment cores from Limni Volvi, northern Greece (coring location: 40°39′51.40″N, 23°32′30.70″E), at a water depth of 19.3 m using a UWITEC piston corer (6 cm diameter). Here, we present X-ray fluorescence (XRF), hyperspectral imaging (HSI) and magnetic susceptibility (MS) measurements made on the 19.65 m long composite core. The investigated time interval covers the entire Holocene. The core sequence was analysed to reconstruct the environmental history and palaeoclimatic changes in the area during the Holocene.MS was measured at the Institute of Plant Sciences of the University of Bern at a 5-mm resolution, using a Bartington MS2E sensor.Elemental analysis of the sediment half-cores was performed at the Swiss Federal Institute of Aquatic Science and Technology (Eawag) with an AVAATECH XRF core-scanner (AVAATECH XRF Technology, Dodewaard, The Netherlands) with a resolution of 5 mm. Low-energy elements from Al to Fe were measured at 10 kV with 1500 A and no filter, and exposed for 15s. Mid-energy elements Cu to Mo were acquired using 30 kV setting, 2000 A, with Pd thin filter at 40 s count time. The X-ray was sourced using Oxford 100 Watt with a rhodium anode. The scanner had a Canberra X − PIPS/DSA 1000 (MCA) detector.HSI scans were performed at the Institute of Geography of the University of Bern using a Specim PFD-xx-V10E hyperspectral single core scanning system. The following settings were used for all scans: field of view: 109.33 mm; resolution: 0.0833 mm; exposure: 160 ms; tray speed: 0.5 mm s−1; frame rate: 6 hz; aperture: 1.9.
DOI: 10.1594/pangaea.982564
title: Oxygen of bottom water samples from cruises conducted in 2020, 2021, and 2022 in Western Norwegian fjords

description: Bottom water samples were analysed in Bergen (Norway) using and ICP-OES Thermo Scientific iCAP 7600 to measure oxygen in seawater (umol/kg) from cruise conducted in 2020 (KB2020603), 2021 (KB2021605) and 2022 (KB2022602).
DOI: 10.1594/pangaea.982570
title: Bottom water oxygen values and mean oxygen from cruises conducted in 2020, 2021, and 2022 in Western Norwegian fjords

description: Bottom water samples were analysed in Bergen (Norway) to measure oxygen in seawater (umol/kg) and to calculate the oxygen mean values (2020-2022) from cruise KB2020603, KB2021605 and KB2022602.
DOI: 10.1594/pangaea.982575
title: Oxygen, trace elements (Mn, Ca, Mn/Ca ratio), oxygen saturation and apparent oxygen utilisation from water samples collected during cruises conducted in 2021, 2022 and 2023 in Western Norwegian fjords

description: Water samples at different depths were analysed in Bergen (Norway) to measure oxygen in seawater (umol/kg) and trace elements (Mn, Ca and Mn/Ca ratio) from cruise conducted in 2021 (KB2021620), 2022 (KB2022602) and 2023 (GS2023001003). We used oxygen from seawater to calculate oxygen saturation and the Apparent Oxygen Utilisation (AOU) using the gsw_O2sol toolkit for python.
DOI: 10.1594/pangaea.982586
title: Oxygen and trace elements (Mn/Ca ratio) collected in Anholt, Hano Bay and Gullmar fjord from Groeneveld et al., (2018) and Groeneveld and Filipsson (2013)

description: Oxygen (umol/kg) and trace elements (Mn/Ca ratio) from Groeneveld et al., (2018) and Groeneveld and Filipsson (2013). We used oxygen of seawater to calculate oxygen saturation and the Apparent Oxygen Utilisation (AOU) using the gsw_O2sol toolkit for python.
DOI: 10.15468/dl.ygvbuz
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amphora strigosa Hustedt, 1949",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((31.8862 -21.3285,30.5701 -20.3186,30.5701 -24.0715,35.5909 -24.0715,35.6007 -24.0157,35.6007 -23.8125,35.4969 -23.7035,35.6007 -23.165,35.6007 -22.9702,35.227 -22.2482,34.6862 -21.6944,34.013 -21.3095,33.5 -21.1593,32.9675 -21.1092,32.4352 -21.1612,31.8862 -21.3285))"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055714-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.npyg95
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "OccurrenceStatus is Present",
 "TaxonKey is Liolaemus huacahuasicus Laurent, 1985"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055715-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.3561112
title: Meta-analysis of multiple ion uptake kinetics in crop roots

description: This dataset collates measures of Michaelis-Menten root uptake parameters for several nutrients based on reported literature. The analysis appears in a review article by Marcus Griffiths (mdgriffiths at noble.org) and Larry York (lmyork at noble.org).


Please cite this repository and the review article if the data is reused.


Citation:


Griffiths, M. G., York, L. M. (In Press) Targeting root ion uptake kinetics to increase plant productivity and nutrient use efficiency. Plant Physiology. https://doi.org/10.1104/pp.19.01496


File descriptions and use


The R script assumes that all data files are in the working directory and that the "tidyverse" meta-package is installed.


Kinetics_metaanalysis_all_files_v2.zip - Contains all the files.

Kinetics_metaanalysis_column_definitions.txt  - Definitions of column names used in data files (not used by R script)

Kinetics_metaanalysis_csv.csv - Complete dataset in CSV format (used by R script)

Kinetics_metaanalysis_excel.xlsx - Complete dataset in Excel format (not used by R script)

Kinetics_metaanalysis_figure_subset.csv - Subset of total data used for figure generation (used by R script)

Kinetics_metaanalysis_figures_code.R - Required R script for statistical analysis 


Version 2 of this repository includes minor updates to include new papers and data.
DOI: 10.5281/zenodo.3653115
title: Meta-analysis of multiple ion uptake kinetics in crop roots

description: This dataset collates measures of Michaelis-Menten root uptake parameters for several nutrients based on reported literature. The analysis appears in a review article by Marcus Griffiths (mdgriffiths at noble.org) and Larry York (lmyork at noble.org).


Please cite this repository and the review article if the data is reused.


Citation:


Griffiths, M. G., York, L. M. (In Press) Targeting root ion uptake kinetics to increase plant productivity and nutrient use efficiency. Plant Physiology. https://doi.org/10.1104/pp.19.01496


File descriptions and use


The R script assumes that all data files are in the working directory and that the "tidyverse" meta-package is installed.


Kinetics_metaanalysis_all_files_v2.zip - Contains all the files.

Kinetics_metaanalysis_column_definitions.txt  - Definitions of column names used in data files (not used by R script)

Kinetics_metaanalysis_csv.csv - Complete dataset in CSV format (used by R script)

Kinetics_metaanalysis_excel.xlsx - Complete dataset in Excel format (not used by R script)

Kinetics_metaanalysis_figure_subset.csv - Subset of total data used for figure generation (used by R script)

Kinetics_metaanalysis_figures_code.R - Required R script for statistical analysis 


Version 2 of this repository includes minor updates to include new papers and data.
DOI: 10.15468/dl.4peqxz
title: Occurrence Download

description: A dataset containing 5149 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Parnara guttatus (Bremer & Grey, 1853)"
 ]
}

 The dataset includes 5149 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055717-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j9neu6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amphora strigosa Hustedt, 1949",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((27.1586 -33.5889,28.2048 -32.9007,25.5395 -32.9007,25.5395 -34.1098,25.6468 -34.1222,25.7787 -34.0734,25.7098 -33.9109,25.8639 -33.797,26.4806 -33.8473,27.1586 -33.5889))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055716-250525065834625/datasets/export for details.
DOI: 10.15468/dl.4f7u83
title: Occurrence Download

description: A dataset containing 24725 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "TaxonKey is Rhinella marina (Linnaeus, 1758)",
 "Year 2010-2025"
 ]
}

 The dataset includes 24725 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055718-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d4xjd4
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amphora strigosa Hustedt, 1949",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((18.2339 -32.5266,18.1411 -32.657,18.1007 -32.7021,18.0224 -32.6366,17.8923 -32.6419,17.754 -32.8255,17.7723 -32.9007,20.509 -32.9007,20.509 -28.5786,16.2782 -28.5786,16.4358 -28.7202,16.726 -29.1235,17.1957 -30.3752,17.6655 -31.1743,18.1322 -31.7679,18.2495 -32.2638,18.2339 -32.5266))"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055720-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.39akcv
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Liolaemus hugoi Bulacios-Arroyo, Semhan, Paz, Chafrat & Abdala, 2021, Liolaemus huayra Abdala, Quinteros & Espinoza, 2008)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055721-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w9eds3
title: Occurrence Download

description: A dataset containing 2139 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "TaxonKey is Didelphis albiventris Lund, 1840"
 ]
}

 The dataset includes 2139 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055722-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hh4668
title: Occurrence Download

description: A dataset containing 64 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Semiliquidambar cathayensis H.T.Chang"
 ]
}

 The dataset includes 64 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055724-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7z6dkf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amphora strigosa Hustedt, 1949",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((15.6372 -28.0032,16.2782 -28.5786,20.509 -28.5786,20.509 -24.0715,15.4933 -24.0715,15.4945 -24.1257,16.0509 -25.6631,15.6372 -28.0032))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055723-250525065834625/datasets/export for details.
DOI: 10.15468/dl.gwqm8t
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amphora strigosa Hustedt, 1949",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((15.4784 -23.4046,15.4933 -24.0715,20.509 -24.0715,20.509 -24.0455,20.0952 -23.5072,19.9968 -23.017,19.7843 -22.5405,19.1988 -21.8785,18.5972 -21.5447,17.8859 -21.3993,17.1626 -21.4805,16.5332 -21.7596,16.1257 -22.0882,15.8234 -22.4662,15.606 -22.8993,15.4784 -23.4046))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055725-250525065834625/datasets/export for details.
DOI: 10.15468/dl.kpaxvu
title: Occurrence Download

description: A dataset containing 10920 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Guadua angustifolia Kunth"
 ]
}

 The dataset includes 10920 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055726-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hesbuz
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amphora strigosa Hustedt, 1949",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((25.5395 -28.5786,20.509 -28.5786,20.509 -32.9007,25.5395 -32.9007,25.5395 -28.5786))"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055728-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3ee4w5
title: Occurrence Download

description: A dataset containing 344306 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Corydalis DC."
 ]
}

 The dataset includes 344306 records from 1330 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055699-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/9psr39bfmk
title: Mendeley Supplementary Table I

description: Taxonomy Codes Included Under Dermatology
DOI: 10.17632/9psr39bfmk.1
title: Mendeley Supplementary Table I

description: Taxonomy Codes Included Under Dermatology
DOI: 10.15468/dl.ny7y2v
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Maturnaria Metcalf, 1952"
 ]
}

 The dataset includes 43 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003044-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7f9y9t
title: Occurrence Download

description: A dataset containing 141522 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Vachellia Wight & Arn.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 141522 records from 744 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003032-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m45ere
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Country is one of (Brazil)",
 "Year is greater than or equal to 1905",
 "Year is less than or equal to 1945",
 "TaxonKey is Macrothelypteris torresiana (Gaudich.) Ching"
 ]
}

 The dataset includes 24 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003045-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/hjxtr5s8fg.1
title: Feedback effect from asthenospheric dynamics on lithospheric structure: insight from a combined geochemical and numerical modelling approach

description: This dataset includes the new and compiled whole-rock element and Sr-Nd-Pb isotopic compositions for the Middle Yangtze basaltic field
DOI: 10.17632/hjxtr5s8fg.2
title: Mantle dynamics of the long-lived Middle Yangtze basaltic field: insight from a combined geochemical and numerical modelling approach

description: This dataset includes the Supplementary Table S1-S3 for the manuscript titled "Mantle dynamics of the long-lived Middle Yangtze basaltic field: insight from a combined geochemical and numerical modelling approach", which was submitted to G-Cubed for consideration of publication. Table S1 contains the new and compiled whole-rock element and Sr-Nd-Pb isotopic compositions for the Middle Yangtze basaltic rocks. Table S2 and S3 show the uncertainties for the analyses of major- and trace-elements in the standards, respectively.
DOI: 10.17632/pbhrjcc3nx.1
title: Instances used in the paper: Edge downgrades in the Maximal Covering Location Problem

description: Instances used in the paper: Edge downgrades in the Maximal Covering Location Problem
---------------
Data structure:

num nodes num edges

RatleastOne RatLeast5Per RatLeast10Per

sum c_e*u_e

vector of nodes demands

adjacency matrix

vector of downgrading bounds

vector of downgrading costs
--------------
Data generation: 
The nodes were given by points whose coordinates followed a uniform distribution over [0,30]. We then built the complete graph, where the length of the edges is the Euclidean distance between the nodes rounded to two decimal places. These instances are called "graph" followed by n (the number of vertices); for example, "graph50" is a complete graph with 50 nodes and 1225 edges. 

The selection of parameters is outlined as follows. The number of facilities denoted as p was determined in proportion to the number of vertices, specifically, $p\in \{n/30, n/20, n/10\}$. The weights or demands assigned to nodes, denoted as $w_i$ for $i\in V$, were uniformly randomly generated integers from 1 to 100. We tested three different coverage radii, R, such that each node can cover at least one node, at least 5% of the number of nodes, and at least 10\% of the number of nodes, respectively. Downgrading costs, $c_e,$ for $e\in E,$ were uniformly randomly generated between 1 and 3 with two decimal places. The upper bounds $u_e$, for $e\in E,$ were uniformly randomly generated from $(0.5\ell_e, 1.5\ell_e),$ for $e\in E$ with two decimal places. 

Finally, the budget B was computed as follows. We calculated the maximum required budget for downgrading all the edges, $B_{max}=\sum_{e\in E} u_ec_e,$ selected $B_{per}\in \{0.1, 0.05, 0.025\},$ and computed B as: 

$B=\frac{B_{max}\cdot B_{per} \cdot p \cdot (p-1)}{n (n-1)} $ rounded to two decimal places. 

For each combination of parameters, five instances were generated with the same procedure, varying only the random seed for the generator.
DOI: 10.17632/pbhrjcc3nx.2
title: Instances used in the paper: Edge downgrades in the Maximal Covering Location Problem

description: Instances used in the paper: Edge downgrades in the Maximal Covering Location Problem
---------------
Data structure:

num nodes num edges

RatleastOne RatLeast5Per RatLeast10Per

sum c_e*u_e

vector of nodes demands

adjacency matrix

vector of downgrading bounds

vector of downgrading costs
--------------
Data generation: 
The nodes were given by points whose coordinates followed a uniform distribution over [0,30]. We then built the complete graph, where the length of the edges is the Euclidean distance between the nodes rounded to two decimal places. These instances are called "graph" followed by n (the number of vertices); for example, "graph50" is a complete graph with 50 nodes and 1225 edges. 

The selection of parameters is outlined as follows. The number of facilities denoted as p was determined in proportion to the number of vertices, specifically, $p\in \{n/30, n/20, n/10\}$. The weights or demands assigned to nodes, denoted as $w_i$ for $i\in V$, were uniformly randomly generated integers from 1 to 100. We tested three different coverage radii, R, such that each node can cover at least one node, at least 5% of the number of nodes, and at least 10\% of the number of nodes, respectively. Downgrading costs, $c_e,$ for $e\in E,$ were uniformly randomly generated between 1 and 3 with two decimal places. The upper bounds $u_e$, for $e\in E,$ were uniformly randomly generated from $(0.5\ell_e, 1.5\ell_e),$ for $e\in E$ with two decimal places. 

Finally, the budget B was computed as follows. We calculated the maximum required budget for downgrading all the edges, $B_{max}=\sum_{e\in E} u_ec_e,$ selected $B_{per}\in \{0.1, 0.05, 0.025\},$ and computed B as: 

$B=\frac{B_{max}\cdot B_{per} \cdot p \cdot (p-1)}{n (n-1)} $ rounded to two decimal places. 

For each combination of parameters, five instances were generated with the same procedure, varying only the random seed for the generator.
DOI: 10.15468/dl.bcmdvd
title: Occurrence Download

description: A dataset containing 4034 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Vasconcellea A.St.-Hil.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4034 records from 236 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003047-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.truvqe
title: Occurrence Download

description: A dataset containing 1094 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Vanda R.Br.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1094 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003046-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.