cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.knf8nz
title: Occurrence Download

description: A dataset containing 254 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Grampus griseus (G.Cuvier, 1812)",
 "Geometry POLYGON((-79.39 36.57,-79.39 39.74,-73.06 39.74,-73.06 36.57,-79.39 36.57))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 254 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002029-160118175350007/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uzyemz
title: Occurrence Download

description: A dataset containing 4761 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leopardus pardalis (Linnaeus, 1758)"
 ]
}

 The dataset includes 4761 records from 202 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0068694-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jt422w
title: Occurrence Download

description: A dataset containing 2115974 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mammalia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Material citation, Material sample, Living Specimen, Machine Observation, Observation, Specimen, Occurrence evidence)",
 "CoordinateUncertaintyInMeters is less than or equal to 10000",
 "Year is greater than or equal to 1876",
 "Elevation is less than or equal to 5000m",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 2115974 records from 1105 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0172619-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p3dewt
title: Occurrence Download

description: A dataset containing 2181 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Pimenta dioica (L.) Merr.)"
 ]
}

 The dataset includes 2181 records from 211 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014411-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uat9ks
title: Occurrence Download

description: A dataset containing 67927 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tetrastes bonasia (Linnaeus, 1758)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2011",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 67927 records from 135 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014410-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a9jnzb
title: Occurrence Download

description: A dataset containing 1380 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Pimenta racemosa (Mill.) J.W.Moore)"
 ]
}

 The dataset includes 1380 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014412-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4121/3bb2f535-59ec-426c-b69a-e113810543b2.v1
title: Supplementary data for the paper 'Using mobile devices for driving test assessment: A study of acceleration and GPS data'

description: There is a need to improve the validity of the driving test as a measure of an individual’s ability to drive safely. This paper explores the use of algorithms to analyze acceleration and GPS data from a smartphone and a GoPro to distinguish between different driving styles, as performed by experienced examiners portraying stereotypical driving test candidates. Measures from nine driving tests were analyzed, including (harsh) accelerations, jerk, mean speed, and speeding. Results showed that the type of car, instructed driving style, and driving route impacted the dependent measures. It is concluded that GPS and accelerometer data can effectively distinguish between cautious, normal, and aggressive driving. However, it is important to consider additional sensors, such as cameras, to allow for more context-aware assessments of driving behavior. Furthermore, we demonstrate methods to quantify variations in road conditions and provide suggestions for presenting the data to driving examiners.
DOI: 10.48668/x53ljm/f0qefs
title: Koleken data matrix.tnt

description: Phylogenetic data matrix
DOI: 10.48668/x53ljm/0cezzk
title: bremerRED.svg

description: Bremer support
DOI: 10.48668/x53ljm/izlkec
title: apolistREDCON.out

description: :unav
DOI: 10.48668/x53ljm/yire6j
title: iterpcr.out

description: :unav
DOI: 10.48668/x53ljm/okcmsg
title: List_of_characters.docx

description: List of characters
DOI: 10.48668/x53ljm/gevkiu
title: mpts.ctf

description: Most parsimonious trees
DOI: 10.48668/x53ljm/j0yy0a
title: pcrjak.out

description: :unav
DOI: 10.48668/x53ljm/bcavzj
title: chardata_pruned.nex

description: Nexus file with the character matrix subsampled to the stable taxa identified by the IterPCR analysis (32 taxa only) formatted for RevBayes.
DOI: 10.48668/x53ljm/b8xpra
title: starting_tree.tre

description: A Newick file with the tree used to initialize the final tip-dating analysis. The topology of the tree is identical to the maximum clade credibility tree from the topologically unconstrained nonclock analysis; the tip ages correspond to the midpoints of the corresponding priors; and the node ages were arbitrarily chosen to satisfy the requirement that ancestors predate descendants.
DOI: 10.6084/m9.figshare.25822948
title: <b>Pre-existing stem cell heterogeneity dictates clonal responses to acquisition of cancer driver mutations - RDS object and scripts</b>

description: This RDS object and the scripts are used for generating figures in our manuscript "Pre-existing stem cell heterogeneity dictates clonal responses to acquisition of cancer driver mutations". Markdown documents are provided for the figures. Additional details can be found in the accompanying scripts.
DOI: 10.6084/m9.figshare.25822948.v1
title: <b>Pre-existing stem cell heterogeneity dictates clonal responses to acquisition of cancer driver mutations - RDS object and scripts</b>

description: This RDS object and the scripts are used for generating figures in our manuscript "Pre-existing stem cell heterogeneity dictates clonal responses to acquisition of cancer driver mutations". Markdown documents are provided for the figures. Additional details can be found in the accompanying scripts.
DOI: 10.48668/x53ljm/few6m2
title: get_partition_specific_MCC_trees.sh

description: A shell script that runs TreeAnnotator on concatenated partition-specific `.trees` files, generated from the RevBayes output using the `concat.and.convert.trees()` and `write.beast.modified()` R functions defined in `Abelisauridae_tip-dating.Rmd`
DOI: 10.48668/x53ljm/pobstp
title: incompleteness_vs_instability.R

description: An R script used to (1) calculate the incompleteness of every taxon in the full character matrix (`chardata.nex`) and (2) perform logistic regression of taxon status (stable or unstable, according to IterPCR) on incompleteness as a predictor.
DOI: 10.48668/x53ljm/x8dseo
title: tipages.tsv

description: A tab-separated values (TSV) file used to set up tip age priors for the final tip-dating analysis. The values correspond to those from the `FADLAD` file used for the parsimony analyses.
DOI: 10.48668/x53ljm/7xq8hd
title: chardata_no_outgroups.nex

description: Nexus file with the character matrix used to run the tip-dating analysis, i.e., without outgroups (43 taxa only).
DOI: 10.48668/x53ljm/qq1708
title: white_noise_simulator.R

description: An R script to verify the validity of the branch rate reparameterization used to implement the white-noise relaxed clock in the tip-dating analyses.
DOI: 10.48668/x53ljm/4w3lfy
title: Supplementary Information.pdf

description: Supplement file containing supplementary figures and tables.
DOI: 10.48668/x53ljm/5o2wd1
title: Original_data.rar

description: :unav
DOI: 10.48668/x53ljm/8texu8
title: Parsimony.rar

description: :unav
DOI: 10.48668/x53ljm/xfgzvm
title: Abelisauridae_tip-dating.rar

description: Output of Abelisauridae_tip-dating.Rmd.
DOI: 10.48668/x53ljm/026guz
title: Strict_clock_fixed.rar

description: Contains the Rev script used to set up the fixed-topology strict-clock analysis (`Abelisauridae_strict_clock_fixed.Rev`), which was used to sample branch durations for the calculation of relaxed clock hyperpriors, as well as the corresponding output consisting of (1) `.log` files, which record the sampled values of scalar parameters; (2) `.trees` files, which record the sampled time trees; and (3) an `.mcc.tre` file, which records the maximum clade credibility (MCC) tree. The `.log` and `.trees` files have a suffix indicating the run that the samples were obtained from; in total, there were 2 runs numbered 1 and 2.
DOI: 10.48668/x53ljm/ek9ftl
title: Nonclock_pruned.rar

description: Contains the Rev script used to set up the nonclock analysis of the 32 taxa found to be stable by the IterPCR method (`Abelisauridae_nonclock_pruned.Rev`), as well as the corresponding output consisting of (1) `.log` files, which record the sampled values of scalar parameters; (2) `.trees` files, which record the sampled trees; and (3) an `.mcc.tre` file, which records the maximum clade credibility (MCC) tree. The `.log` and `.trees` files have a suffix indicating the run that the samples were obtained from; in total, there were 2 runs numbered 1 and 2.
DOI: 10.48668/x53ljm/ehvhfv
title: Nonclock.rar

description: Contains the Rev script used to set up the topologically unconstrained nonclock analysis of all 47 taxa (`Abelisauridae_nonclock.Rev`), as well as the corresponding output consisting of (1) `.log` files, which record the sampled values of scalar parameters; (2) `.trees` files, which record the sampled trees; and (3) an `.mcc.tre` file, which records the maximum clade credibility (MCC) tree. The `.log` and `.trees` files have a suffix indicating the run that the samples were obtained from; in total, there were 2 runs numbered 1 and 2.
DOI: 10.48668/x53ljm/rr0vwy
title: Nonclock_fixed.rar

description: Contains the Rev script used to set up the fixed-topology nonclock analysis (`Abelisauridae_nonclock_fixed.Rev`), which was used to sample branch lengths for the calculation of relaxed clock hyperpriors, as well as the corresponding output consisting of (1) `.log` files, which record the sampled values of scalar parameters; (2) `.trees` files, which record the sampled trees; and (3) an `.mcc.tre` file, which records the maximum clade credibility (MCC) tree. The `.log` and `.trees` files have a suffix indicating the run that the samples were obtained from; in total, there were 2 runs numbered 1 and 2.
DOI: 10.48668/x53ljm/vkdeqk
title: Relaxed_clocks_uniform_prior.rar

description: Contains the Rev script used to set up a sensitivity tip-dating analysis using the uniform rather than Fossilized Birth-Death branching process prior (`Abelisauridae_relaxed_clocks_uniform_prior.Rev`); the output of this analysis; and a tab-separated values file generated by Tracer, which records basic summary statistics for the posterior distributions of tip ages (`Tracer_summary_stats.tsv`). The output of the analysis consists of (1) `.log` files, which record the sampled values of scalar parameters; (2) modified `_NEW_HEADER.log` files in which the tip numbering scheme was changed to correspond to the indices used in the tree files; (3) `.trees` files, which record the sampled time trees; and (4) `.mcc.tre` files, which store the maximum clade credibility trees generated using TreeAnnotator. See above for the explanation of the suffixes of the individual output files. In total, there were 4 runs numbered 1 through 4.
DOI: 10.48668/x53ljm/nhluyq
title: Model_comparison.rar

description: Contains the Rev scripts used to set up marginal likelihood estimation for the two clock models (`Abelisauridae_multiple_relaxed_clocks.Rev`, `Abelisauridae_single_relaxed_clock.Rev`), as well as the corresponding output consisting of (1) `.log` files, which record the sampled values of scalar parameters; (2) `.trees` files, which record the sampled time trees; and (3) `.out` files, which record the sampled marginal likelihoods. All three types of output files have a suffix indicating the stone (i.e., power posterior) that the samples were obtained from; in total, there were 128 stones numbered 0 through 127.
DOI: 10.48668/x53ljm/kwnomf
title: Relaxed_clocks.rar

description: Contains the Rev script used to set up the final tip-dating analysis under the preferred clock model (`Abelisauridae_relaxed_clocks.Rev`); the output of this analysis; a tab-separated values file generated by Tracer, which records basic summary statistics for the posterior distributions of tip ages (`Tracer_summary_stats.tsv`); and a TNT output file recording the values of the MSM\* and GER stratigraphic congruence indices for all trees from the posterior (`MSM.OUT`). The output of the analysis consists of (1) `.log` files, which record the sampled values of scalar parameters; (2) `.trees` files, which record the sampled time trees; and (3) `.mcc.tre` files, which store the maximum clade credibility trees generated using TreeAnnotator. See above for the explanation of the suffixes of the individual output files. In total, there were 4 runs numbered 1 through 4.
DOI: 10.48668/x53ljm/flnozg
title: Relaxed_clocks_sampled_ancestors.rar

description: Contains the Rev script used to set up a sensitivity tip-dating analysis allowing for sampled ancestors (`Abelisauridae_relaxed_clocks_sampled_ancestors.Rev`); the output of this analysis; and a tab-separated values file generated by Tracer, which records basic summary statistics for the posterior distributions of tip ages (`Tracer_summary_stats.tsv`). The output of the analysis consists of (1) `.log` files, which record the sampled values of scalar parameters; (2) `.trees` files, which record the sampled time trees; and (3) `.mcc.tre` files, which store the maximum clade credibility trees generated using TreeAnnotator. See above for the explanation of the suffixes of the individual output files. In total, there were 8 runs numbered 1 through 8.
DOI: 10.48668/x53ljm/fgzvxk
title: Parsimony_Bayes_comparisons.rar

description: Contains the output of _evolrates_ and tip-dating analyses performed on fixed topologies to tease apart methodological vs. topological differences.
DOI: 10.48668/x53ljm/g9bfjx
title: evolrates..run

description: Custom TNT script to assess rates of morphological change based on the parsimony optimization of characters.
DOI: 10.48668/x53ljm/yjpgzq
title: Parsimony.rar

description: Contains the input data, TNT scripts, output files, and a visualization script for the parsimony analyses of tree topology and evolutionary rates.
DOI: 10.15784/601784
title: Constraining the Radiocarbon Reservoir Age for the Southern Ocean Using Whale Bones Salvaged from Early 20th Century Whaling Stations

description: Radiocarbon dating is arguably the most common method for dating Quaternary deposits. However, accurate age assignments using radiocarbon dating are dependent on knowing the radiocarbon reservoir. For the coastal waters across Antarctica, the radiocarbon reservoirs show significant variation, ranging from 700 to 6,000 years depending on the material dated and the period in question. In this study, we examine the radiocarbon reservoir age for the shallow waters of the Southern Ocean using 23 whale bones salvaged from whaling stations operating on or near the Western Antarctic Peninsula between 1904 and 1916. The species origin of the bones had been identified previously as humpback, fin, or blue whales using sequences of mitochondrial (mt)DNA. We find an average reservoir age of 1050 +/- 135 years for these 23 whale bones, with a &lt;100 year difference in the reservoir age value by species. A comparison between our results and other studies through the Holocene suggest that the Southern Ocean surface water radiocarbon reservoir age has not significantly changed for the last 14,000 years. Combining our new ages with existing data sets provides insight to the stability of the Southern Ocean marine radiocarbon reservoir age, enhancing our understanding of ocean ventilation and upwelling dynamics throughout the Holocene.
DOI: 10.5281/zenodo.11180648
title: Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7

description: Molecular dynamics simulation systems of publication "Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7" by Akseli Niemelä and Artturi Koivuniemi.
DOI: 10.5281/zenodo.11180649
title: Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7

description: Molecular dynamics simulation systems of publication "Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7" by Akseli Niemelä and Artturi Koivuniemi.
DOI: 10.5281/zenodo.11176732
title: LeafMachine2 D-3FAM Summary Images - Full Output - LM2 v-2-3

description: This version of D-3FAM was processed with LM2 v-2-3. It also contains ALL output files. This was processed with PCD=70%, so predictions for fruits/flowers is poorer than it would be at a lower threshold.

Nine PDFs containing summary images, for QC purposes, generated by LeafMachine2 for the D-3FAM dataset, which contains 831 images/species. These data were generated using LeafMachine2's default settings, notably, the PCD used a minimum threshold of 0.5 and segmented ideal and partial leaves. Ruler conversion validation images are on the right half of each PDF page.
DOI: 10.5281/zenodo.7763105
title: LeafMachine2 D-3FAM Summary Images - Full Output - LM2 v-2-3

description: This version of D-3FAM was processed with LM2 v-2-3. It also contains ALL output files. This was processed with PCD=70%, so predictions for fruits/flowers is poorer than it would be at a lower threshold.

Nine PDFs containing summary images, for QC purposes, generated by LeafMachine2 for the D-3FAM dataset, which contains 831 images/species. These data were generated using LeafMachine2's default settings, notably, the PCD used a minimum threshold of 0.5 and segmented ideal and partial leaves. Ruler conversion validation images are on the right half of each PDF page.
DOI: 10.15468/dl.65wvje
title: Occurrence Download

description: A dataset containing 5361 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Colección Ornitológica de la Universidad del Valle"
 ]
}

 The dataset includes 5361 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014415-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xq7zkt
title: Occurrence Download

description: A dataset containing 237 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Nicaragua",
 "TaxonKey is Lepidochelys Fitzinger, 1843"
 ]
}

 The dataset includes 237 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014416-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11043710
title: ELITE SLWR: global 1km 5-min SLUR at SIN Grid-Aqua (2011_350-365)

description: The Essential thermal Infrared remoTe sEnsing (ELITE) product suite currently has four types of products, including land surface temperature (LST: clear-sky and all-sky), emissivity (NBE: narrowband emissivity; BBE: broadband emissivity; and spectral emissivity), the component of surface radiation and energy budget (SLUR: surface longwave upwelling radiation; SLDR: surface longwave downward radiation SLDR; SLNR: surface longwave net radiation), and the component of Earth’s radiation budget (OLR; outgoing longwave radiation; RSR: reflected solar radiation). The spatial-temporal resolutions of the ELITE products are mainly determined by the employed satellite data sources. For more information about ELITE products, please refer to the website (https://elite.bnu.edu.cn).

This dataset is ELITE surface longwave upward radiation (SLUR) product at 1km spatial resolution and 5-min temporal resolution. It is provided on a Sinusoidal grid and ranges from 2000 to 2022 (continuously updated). This dataset was generated from the Moderate Resolution Imaging Spectrometer (MODIS) data using the algorithms developed by Cheng et al. (2016).

This is the ELITE SLUR product in 2011 (DOY: 350-365). Please click here to download the ELITE SLUR product in 2012 (DOY: 001-016).

Dataset Characteristics:



Spatial Coverage: Global

Temporal Coverage: 2011-12-16 ~ 2011-12-31

Spatial Resolution: 1 km

Temporal Resolution: 5-min

Data Format: h5

Projection: Sinusoidal

Scale: 0.05

Offset: -1000


Citation(Please cite these papers when using the data):



Cheng, J., & Liang, S. (2016). Global estimates for high spatial resolution clear-sky land surface upwelling longwave radiation from MODIS data. IEEE Transactions on Geoscience and Remote Sensing, 54, 4115-4129.


If you have any questions, please contact Prof. Jie Cheng (eliteqrs@126.com).
DOI: 10.5281/zenodo.11043711
title: ELITE SLWR: global 1km 5-min SLUR at SIN Grid-Aqua (2011_350-365)

description: The Essential thermal Infrared remoTe sEnsing (ELITE) product suite currently has four types of products, including land surface temperature (LST: clear-sky and all-sky), emissivity (NBE: narrowband emissivity; BBE: broadband emissivity; and spectral emissivity), the component of surface radiation and energy budget (SLUR: surface longwave upwelling radiation; SLDR: surface longwave downward radiation SLDR; SLNR: surface longwave net radiation), and the component of Earth’s radiation budget (OLR; outgoing longwave radiation; RSR: reflected solar radiation). The spatial-temporal resolutions of the ELITE products are mainly determined by the employed satellite data sources. For more information about ELITE products, please refer to the website (https://elite.bnu.edu.cn).

This dataset is ELITE surface longwave upward radiation (SLUR) product at 1km spatial resolution and 5-min temporal resolution. It is provided on a Sinusoidal grid and ranges from 2000 to 2022 (continuously updated). This dataset was generated from the Moderate Resolution Imaging Spectrometer (MODIS) data using the algorithms developed by Cheng et al. (2016).

This is the ELITE SLUR product in 2011 (DOY: 350-365). Please click here to download the ELITE SLUR product in 2012 (DOY: 001-016).

Dataset Characteristics:



Spatial Coverage: Global

Temporal Coverage: 2011-12-16 ~ 2011-12-31

Spatial Resolution: 1 km

Temporal Resolution: 5-min

Data Format: h5

Projection: Sinusoidal

Scale: 0.05

Offset: -1000


Citation(Please cite these papers when using the data):



Cheng, J., & Liang, S. (2016). Global estimates for high spatial resolution clear-sky land surface upwelling longwave radiation from MODIS data. IEEE Transactions on Geoscience and Remote Sensing, 54, 4115-4129.


If you have any questions, please contact Prof. Jie Cheng (eliteqrs@126.com).