cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.uj9xk5
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-94.84684 28.61377,-88.7675 28.61377,-88.7675 33.68877,-94.84684 33.68877,-94.84684 28.61377))",
 "HasGeospatialIssue is false",
 "TaxonKey is Erythrina herbacea L."
 ]
}

 The dataset's 1 records were derived from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000719-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tew96k
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-94.77196 28.64392,-88.83088 28.64392,-88.83088 33.44608,-94.77196 33.44608,-94.77196 28.64392))",
 "HasGeospatialIssue is false",
 "TaxonKey is Styrax americanus Lam."
 ]
}

 The dataset's 2 records were derived from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000721-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dv8hdm
title: Occurrence Download

description: A dataset containing 95130 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Terathopius ecaudatus (Daudin, 1800))",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "OccurrenceStatus is Present",
 "DistanceFromCentroidInMeters is greater than or equal to 2000"
 ]
}

 The dataset includes 95130 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000724-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14586062
title: Data and code for "Ecosystem stability persists despite greater diversity loss under nitrogen inputs with higher inorganic components"

description: Atmospheric nitrogen (N) deposition consists of both inorganic N (IN) and organic N (ON). IN reduced species richness greater than ON, which likely induces lower ecosystem stability as species richness and ecosystem stability are usually positively related. However, whether IN decreased ecosystem stability greater than ON remains unknown. Here, we assessed the effects of IN:ON ratios (0:10, 3:7. 5:5, 7:3, and 10:0) at the rate of 10 g N m-2 yr-1 on the temporal stability of plant community productivity in a temperate meadow grassland with a 6-year N addition experiment. Species richness, species asynchrony, population stability, and dominant species stability were investigated to explore the mechanisms underlying changes in plant community stability. We found that IN:ON ratio showed no impact on community productivity stability although all N addition significantly reduced community stability. However, IN addition decreased species richness more intensely than ON. IN:ON ratio showed no impact on species asynchrony, population stability or dominant species stability. Species asynchrony and dominant species stability were both positively related to community stability, while population stability showed no significant association with community stability. It implies that species asynchrony and dominant species stability likely maintained plant community stability in fertilized plots across IN:ON ratios. Synthesis. Our study suggests that, although IN reduced species richness greater than ON, it might be reasonable to evaluate the effects of N deposition on ecosystem stability with either IN or ON addition due to the stable species asynchrony and dominant species stability.
DOI: 10.5281/zenodo.14586063
title: Data and code for "Ecosystem stability persists despite greater diversity loss under nitrogen inputs with higher inorganic components"

description: Atmospheric nitrogen (N) deposition consists of both inorganic N (IN) and organic N (ON). IN reduced species richness greater than ON, which likely induces lower ecosystem stability as species richness and ecosystem stability are usually positively related. However, whether IN decreased ecosystem stability greater than ON remains unknown. Here, we assessed the effects of IN:ON ratios (0:10, 3:7. 5:5, 7:3, and 10:0) at the rate of 10 g N m-2 yr-1 on the temporal stability of plant community productivity in a temperate meadow grassland with a 6-year N addition experiment. Species richness, species asynchrony, population stability, and dominant species stability were investigated to explore the mechanisms underlying changes in plant community stability. We found that IN:ON ratio showed no impact on community productivity stability although all N addition significantly reduced community stability. However, IN addition decreased species richness more intensely than ON. IN:ON ratio showed no impact on species asynchrony, population stability or dominant species stability. Species asynchrony and dominant species stability were both positively related to community stability, while population stability showed no significant association with community stability. It implies that species asynchrony and dominant species stability likely maintained plant community stability in fertilized plots across IN:ON ratios. Synthesis. Our study suggests that, although IN reduced species richness greater than ON, it might be reasonable to evaluate the effects of N deposition on ecosystem stability with either IN or ON addition due to the stable species asynchrony and dominant species stability.
DOI: 10.15468/dl.2wzgtg
title: Occurrence Download

description: A dataset containing 697 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-94.74999 28.7577,-88.81484 28.7577,-88.81484 33.40049,-94.74999 33.40049,-94.74999 28.7577))",
 "HasGeospatialIssue is false",
 "TaxonKey is Erythrina herbacea L."
 ]
}

 The dataset includes 697 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000726-250117142028555/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.28164461
title: <b>Arbuscular mycorrhizal fungi suffer from perfluoroalkyl substance pollution in soil but ameliorate negative effects on plant performance</b>

description: In this study, we assessed the effects of PFOA on AMF and onion plant growth under a laboratory condition. Our results showed that PFOA negatively impacted AMF colonization rate, arbuscules, and esicles, indicating the negative effects of PFOA on AMF-onion plant symbiosis relationships. In addition, the presence of PFOA negatively impacted all root traits we measured including root biomass, total length, average diameter, root tissue density, specific root length, and specific root surface area, and aboveground plant growth parameters such as leaf biomass and maximum height. While the inoculation of AMF mitigated the negative effects of PFOA on onion plant growth.
DOI: 10.15468/dl.sx3eaz
title: Occurrence Download

description: A dataset containing 1060 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Elephas maximus indicus Cuvier, 1798"
 ]
}

 The dataset includes 1060 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000728-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zjzk3f
title: Occurrence Download

description: A dataset containing 670063 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Egretta intermedia (Wagler, 1829))",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "OccurrenceStatus is Present",
 "DistanceFromCentroidInMeters is greater than or equal to 2000"
 ]
}

 The dataset includes 670063 records from 121 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000725-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/10505418
title: Supermarket-Superstore-Dataset-Bundle
DOI: 10.15468/dl.n93aa2
title: Occurrence Download

description: A dataset containing 2593837 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is 2023 Contributions of Plant Specimen Data inside China"
 ]
}

 The dataset includes 2593837 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000727-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zb5eaz
title: Occurrence Download

description: A dataset containing 1081590 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Limosa limosa (Linnaeus, 1758))",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "OccurrenceStatus is Present",
 "DistanceFromCentroidInMeters is greater than or equal to 2000"
 ]
}

 The dataset includes 1081590 records from 707 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000729-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nfre6e
title: Occurrence Download

description: A dataset containing 97 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "TaxonKey is Mustela erminea Linnaeus, 1758",
 "Year 2000-2025"
 ]
}

 The dataset includes 97 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000731-250117142028555/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.28233803
title: Monthly runoff and sediment flux data in the source region of the Yellow River. xlsx

description: Monthly runoff and sediment records from 1970 to 2020 at the Tangnaihai hydrological station (the outflow of the source region of the Yellow River).
DOI: 10.6084/m9.figshare.28233803.v2
title: Water and sediment flux.xlsx

description: Monthly water and sediment flux data in the source region of the Yellow River.
DOI: 10.15468/dl.mp8gcx
title: Occurrence Download

description: A dataset containing 104471 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pycnonotus capensis (Linnaeus, 1766))",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "OccurrenceStatus is Present",
 "DistanceFromCentroidInMeters is greater than or equal to 2000"
 ]
}

 The dataset includes 104471 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000732-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/10505515
title: World Weather Repository ( Daily Updating )
DOI: 10.15468/dl.6hph5c
title: Occurrence Download

description: A dataset containing 11767 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Indicator variegatus R.Lesson, 1830)",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "OccurrenceStatus is Present",
 "DistanceFromCentroidInMeters is greater than or equal to 2000"
 ]
}

 The dataset includes 11767 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000734-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y479n4
title: Occurrence Download

description: A dataset listing the 4019496 species recorded in GBIF matching the query:
{ }

 The dataset's 4019496 records were derived from 70536 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000730-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d7wmqf
title: Occurrence Download

description: A dataset containing 45994 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cisticola erythrops (Hartlaub, 1857))",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "OccurrenceStatus is Present",
 "DistanceFromCentroidInMeters is greater than or equal to 2000"
 ]
}

 The dataset includes 45994 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000736-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/10505535
title: World Stock Prices ( Daily Updating )
DOI: 10.15468/dl.rrse9u
title: Occurrence Download

description: A dataset containing 66564 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is FishBase Database",
 "Year 1984-2025"
 ]
}

 The dataset includes 66564 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000735-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eb74vb
title: Occurrence Download

description: A dataset containing 293210 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Microcarbo africanus (Gmelin, 1789))",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "OccurrenceStatus is Present",
 "DistanceFromCentroidInMeters is greater than or equal to 2000"
 ]
}

 The dataset includes 293210 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000737-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8vw4uh
title: Occurrence Download

description: A dataset containing 1660 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "TaxonKey is Euterpe edulis Mart."
 ]
}

 The dataset includes 1660 records from 156 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000739-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d8wwvr
title: Occurrence Download

description: A dataset containing 45639 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cecropis semirufa (Sundevall, 1850))",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "OccurrenceStatus is Present",
 "DistanceFromCentroidInMeters is greater than or equal to 2000"
 ]
}

 The dataset includes 45639 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000738-250117142028555/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.28233883
title: Code from Programming evolution of geometry in shape-morphing sheets via spatiotemporal activation

description: Code
DOI: 10.6084/m9.figshare.28233883.v1
title: Code from Programming evolution of geometry in shape-morphing sheets via spatiotemporal activation

description: Code
DOI: 10.5281/zenodo.13357569
title: Jupyter Notebook Activity Dataset (rsds-20241113)

description: List of data



rsds-20241113.zip: Collection of SQLite database files

image.tar.gz: Docker image provided in our data collection experiment

redspot-341ffa5.zip: Redspot source code (redspot@341ffa5)




Extended version of Section 2D of our paper
Redspot is a Jupyter extension (i.e., Python package) that records activity signals. However, it also offers interfaces to read recorded signals. The following shows the most basic usage of its command-line interface:

 

redspot replay <path-to-db>


This command generates snapshots (.ipynb files) restored from the signal records. Note that this command does not produce a snapshot for every signal. Since the change represented by a single signal is typically minimal (e.g., one keystroke), generating a snapshot for each signal results in a meaninglessly large number of snapshots. However, we want to obtain signal-level snapshots for some analyses. In such cases, one can analyze them using the application programming interfaces:


from redspot import database

from redspot.notebook import Notebook

nbk = Notebook()

for signal in database.get("path-to-db"):

    time, panel, kind, args = signal

    nbk.apply(kind, args) # apply change

    print(nbk) # print notebook


To record activities, one needs to run the Redspot command in the recording mode as follows:


redspot record


This command launches Jupyter Notebook with Redspot enabled. Activities made in the launched environment are stored in an SQLite file named ``redspot.db'' under the current path.


To launch the environment we provided to the participants, one first needs to download and import the image (image.tar.gz). One can then run the image with the following command:


docker run --rm -it -p8888:8888 <image-name>


Note that the SQLite file is generated in the running container. The file can be downloaded into the host machine via the file viewer of Jupyter Notebook.
DOI: 10.5281/zenodo.13357570
title: Jupyter Notebook Activity Dataset (rsds-20241113)

description: List of data



rsds-20241113.zip: Collection of SQLite database files

image.tar.gz: Docker image provided in our data collection experiment

redspot-341ffa5.zip: Redspot source code (redspot@341ffa5)




Extended version of Section 2D of our paper
Redspot is a Jupyter extension (i.e., Python package) that records activity signals. However, it also offers interfaces to read recorded signals. The following shows the most basic usage of its command-line interface:

 

redspot replay <path-to-db>


This command generates snapshots (.ipynb files) restored from the signal records. Note that this command does not produce a snapshot for every signal. Since the change represented by a single signal is typically minimal (e.g., one keystroke), generating a snapshot for each signal results in a meaninglessly large number of snapshots. However, we want to obtain signal-level snapshots for some analyses. In such cases, one can analyze them using the application programming interfaces:


from redspot import database

from redspot.notebook import Notebook

nbk = Notebook()

for signal in database.get("path-to-db"):

    time, panel, kind, args = signal

    nbk.apply(kind, args) # apply change

    print(nbk) # print notebook


To record activities, one needs to run the Redspot command in the recording mode as follows:


redspot record


This command launches Jupyter Notebook with Redspot enabled. Activities made in the launched environment are stored in an SQLite file named ``redspot.db'' under the current path.


To launch the environment we provided to the participants, one first needs to download and import the image (image.tar.gz). One can then run the image with the following command:


docker run --rm -it -p8888:8888 <image-name>


Note that the SQLite file is generated in the running container. The file can be downloaded into the host machine via the file viewer of Jupyter Notebook.
DOI: 10.15468/dl.egvgez
title: Occurrence Download

description: A dataset containing 1769297 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Motacilla flava Linnaeus, 1758)",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "OccurrenceStatus is Present",
 "DistanceFromCentroidInMeters is greater than or equal to 2000"
 ]
}

 The dataset includes 1769297 records from 2551 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000740-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uy57j4
title: Occurrence Download

description: A dataset containing 559 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "Country is Spain",
 "Geometry POLYGON((-0.62231 40.33785,6.68657 40.33785,6.68657 43.26490,-0.62231 43.26490,-0.62231 40.33785))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Senecio lividus L."
 ]
}

 The dataset includes 559 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085488-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hn52lq
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Japan",
 "TaxonKey is Goera japonica Banks, 1906"
 ]
}

 The dataset includes 39 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002740-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y67qnk
title: Occurrence Download

description: A dataset containing 15555 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Living Specimen",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Literature Occurrence",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Baeckea L."
 ]
}

 The dataset includes 15555 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0258632-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sekw8w
title: Occurrence Download

description: A dataset containing 2287 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Ibaraki Nature Museum, Mammals collection"
 ]
}

 The dataset includes 2287 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085507-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.