cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8277126
title: Optimization procedure of low frequency vibration energy harvester based on magnetic levitation: Datasets and scripts

description: ****** Please view the README.txt file for detailed documentation of data. ******

 

Title: Optimization procedure of low frequency vibration energy harvester based on magnetic levitation: Datasets and scriptsVersion: 2.0Date of Release: 2023/08/23Identifier: doi:10.5281/zenodo.8317223Permalink: http://dx.doi.org/10.5281/zenodo.8317223

Associated publication: I. Royo-Silvestre, J. J. Beato-López, C. Gómez-Polo "Optimization procedure of low frequency vibration energy harvester  based on magnetic levitation", Applied Energy, Volume 360, 15 April 2024, 122778

Link to publication: https://doi.org/10.1016/j.apenergy.2024.122778

Suggested citation: Please reference the associated publication above when using any datasets or materials described in the README file.

 

Contact information: Isaac Royo Silvestre, Universidad Pública de Navarra, Pamplona, Spain., isaac.royo@unavarra.esCo-authors: juanjesus.beato@unavarra.es, gpolo@unavarra.es

 

Dates of data collection: 2023/03Geographic location: Pamplona, Spain

 

This directory contains the following datasets and scripts:

SCRIPTS

- harvester_op.m: Matlab script to automate the design and optimize a magnetic spring based vibration energy harvester (more information in the associated paper)

- harvester_op_par.m:     Matlab script, a version of harvester_op.m modified for parallel computing and shorter execution time in multicore computers (file added in v 2.0 of the data upload).

DATASETS- data.zip: Experimental data recorded by the datalogger as well as tabular data required to plot curves (compressed zip file) in csv format

 

Specific documentation of each file is described in readme files.

 

Refer to the original manuscript (see above) and the text of the Supplementary Materials published alongside this manuscript for additional information regarding the collection and generation of these data.
description: This work is funded by Spanish Agencia Estatal de Investigación and Ministerio de Ciencia e Innovación MCIN/AEI/ 10.13039/501100011033 and by "European Union NextGenerationEU/PRTR", project TED2021-130884B-I00.
Open access funding provided by Universidad Pública de Navarra.
DOI: 10.15468/dl.ukpm3d
title: Occurrence Download

description: A dataset containing 145 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Ramphastos vitellinus M.H.K.Lichtenstein, 1823)",
 "StateProvince is one of (santander)",
 "PublishingOrg is one of (04ce62dd-30ec-4d98-8b30-b09cafc3ac38)"
 ]
 }
 ]
}

 The dataset includes 145 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007900-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f6epsu
title: Occurrence Download

description: A dataset containing 231 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Canada",
 "Country is Canada"
 ]
 },
 "TaxonKey is one of (Veronica verna L.)"
 ]
}

 The dataset includes 231 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007901-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dpw2vb
title: Occurrence Download

description: A dataset containing 7855 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ateles geoffroyi Kuhl, 1820"
 ]
}

 The dataset includes 7855 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007902-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15467042
title: BPR_freshwater: v1.0.0

description: This dataset compiles biodiversity and environmental data from 81 freshwater datasets encompassing 36,195 study sites across lakes and rivers worldwide. The data include species abundance matrices, functional trait information, spatial coordinates, and total phosphorus (TP) concentrations, representing six major aquatic taxonomic groups: phytoplankton, benthic diatoms, aquatic plants, zooplankton, macroinvertebrates, and fish. For each site, both taxonomic diversity (species richness, Shannon diversity) and functional diversity (functional richness and dispersion) metrics were calculated. This dataset enables the examination of biodiversity–productivity relationships (BPRs) along nutrient gradients and facilitates cross-ecosystem comparisons of functional and taxonomic responses to environmental variation. It can support future studies on ecological forecasting, global change impacts, and freshwater biodiversity conservation. Data have been harmonized across datasets to ensure compatibility and reusability.
DOI: 10.5281/zenodo.15467043
title: BPR_freshwater: v1.0.0

description: This dataset compiles biodiversity and environmental data from 81 freshwater datasets encompassing 36,195 study sites across lakes and rivers worldwide. The data include species abundance matrices, functional trait information, spatial coordinates, and total phosphorus (TP) concentrations, representing six major aquatic taxonomic groups: phytoplankton, benthic diatoms, aquatic plants, zooplankton, macroinvertebrates, and fish. For each site, both taxonomic diversity (species richness, Shannon diversity) and functional diversity (functional richness and dispersion) metrics were calculated. This dataset enables the examination of biodiversity–productivity relationships (BPRs) along nutrient gradients and facilitates cross-ecosystem comparisons of functional and taxonomic responses to environmental variation. It can support future studies on ecological forecasting, global change impacts, and freshwater biodiversity conservation. Data have been harmonized across datasets to ensure compatibility and reusability.
DOI: 10.15468/dl.aw6wrn
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "TaxonKey is Listroderes costirostris Schoenherr, 1826"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007903-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15001926
title: Supplementary information and transcripts assembled by NIFFLR software for 92 GTEx long-read transcriptome sequencing samples

description: These data are associated with the manuscript titled: Assembly and quantification of transcripts from noisy long reads with NIFFLR

Abstract:

Long-read RNA sequencing technologies can produce complete or near-complete transcript sequences. Recently introduced methods for direct RNA and cDNA sequencing can provide a high-throughput strategy for the discovery of novel and rare gene isoforms. However, the high error rates in ONT sequences limit the ability to exactly pinpoint splice site boundaries when aligning reads to the genome. In this paper, we present a novel tool called NIFFLR (Novel IsoForm Finder using Long Reads) that identifies and quantifies both known and novel isoforms using long-read RNA sequencing data. We show that NIFFLR effectively recovers correct transcripts from simulated reads based on known transcript annotations, achieving higher sensitivity and precision compared to several previously-published tools. On real data, NIFFLR shows the high accuracy as measured by concordance of isoform counts to the counts computed from Illumina data for the same sample. We applied NIFFLR to a set of 92 GTEx long-read samples and produced transcript counts for both novel and known isoforms. In total, we identified and quantified 121,155 isoforms present in the RefSeq annotation of GRCh38 and 106,667 high-confidence novel isoforms across 32,875 genes present in two or more samples in these data, more than previous studies identified in this data set. NIFFLR is released under an open-source license and is available on GitHub at https://github.com/alguoo314/NIFFLR/releases.
DOI: 10.5281/zenodo.15001927
title: Transcripts assembled by NIFFLR software for 92 GTEx long-read transcriptome sequencing samples

description: These data are associated with the manuscript titled: Assembly and quantification of transcripts from noisy long reads with NIFFLR

Abstract:

Long-read RNA sequencing technologies can produce complete or near-complete transcript sequences. Recently introduced methods for direct RNA and cDNA sequencing can provide a high-throughput strategy for the discovery of novel and rare gene isoforms. However, the high error rates in ONT sequences limit the ability to exactly pinpoint splice site boundaries when aligning reads to the genome. In this paper, we present a novel tool called NIFFLR (Novel IsoForm Finder using Long Reads) that identifies and quantifies both known and novel isoforms using long-read RNA sequencing data. We show that NIFFLR effectively recovers correct transcripts from simulated reads based on known transcript annotations, achieving higher sensitivity and precision compared to several previously-published tools. On real data, NIFFLR shows the high accuracy as measured by concordance of isoform counts to the counts computed from Illumina data for the same sample. We applied NIFFLR to a set of 92 GTEx long-read samples and produced transcript counts for both novel and known isoforms. In total, we identified and quantified 121,155 isoforms present in the RefSeq annotation of GRCh38 and 106,667 high-confidence novel isoforms across 32,875 genes present in two or more samples in these data, more than previous studies identified in this data set. NIFFLR is released under an open-source license and is available on GitHub at https://github.com/alguoo314/NIFFLR/releases.
DOI: 10.5281/zenodo.15467129
title: Supplementary information and transcripts assembled by NIFFLR software for 92 GTEx long-read transcriptome sequencing samples

description: These data are associated with the manuscript titled: Assembly and quantification of transcripts from noisy long reads with NIFFLR

Abstract:

Long-read RNA sequencing technologies can produce complete or near-complete transcript sequences. Recently introduced methods for direct RNA and cDNA sequencing can provide a high-throughput strategy for the discovery of novel and rare gene isoforms. However, the high error rates in ONT sequences limit the ability to exactly pinpoint splice site boundaries when aligning reads to the genome. In this paper, we present a novel tool called NIFFLR (Novel IsoForm Finder using Long Reads) that identifies and quantifies both known and novel isoforms using long-read RNA sequencing data. We show that NIFFLR effectively recovers correct transcripts from simulated reads based on known transcript annotations, achieving higher sensitivity and precision compared to several previously-published tools. On real data, NIFFLR shows the high accuracy as measured by concordance of isoform counts to the counts computed from Illumina data for the same sample. We applied NIFFLR to a set of 92 GTEx long-read samples and produced transcript counts for both novel and known isoforms. In total, we identified and quantified 121,155 isoforms present in the RefSeq annotation of GRCh38 and 106,667 high-confidence novel isoforms across 32,875 genes present in two or more samples in these data, more than previous studies identified in this data set. NIFFLR is released under an open-source license and is available on GitHub at https://github.com/alguoo314/NIFFLR/releases.
DOI: 10.15468/dl.6kj8qv
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Tetracha floridana Leng & Mutchler, 1916",
 "Year is greater than or equal to 1950",
 {
 "or" : [
 "GadmGid is USA",
 "GadmGid is CAN",
 "GadmGid is MEX"
 ]
 }
 ]
}

 The dataset includes 14 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007904-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/8qgefz
title: Replication Data for: "Selective Attention? Human Rights Organizations and Anti-State Naming and Shaming, 1995-2018"

description: This Stata dataset was used for the analyses in the article "Selective Attention? Human Rights Organizations and Anti-State Naming and Shaming, 1995-2018," published in Social Problems. It is a cross-national dataset where the unit of analyses is the country-year.

The dependent variables in the study related to anti-state shaming were created using data from the Integrated Conflict Early Warning System (ICEWS) and transformed into cross-national data. The independent variables are gathered from various sources, such as the World Bank's World Development Indicators, Polity IV, the Cross-National Time-Series (CNTS) Data Archive, the Mass Mobilization Project, V-Dem, CIRIGHTS, and the Yearbook of International Associations (YIA).
description: Stata code to replicate regressions:

xtnbreg shameall ingos antigovprot csorepress intuse cellphones violrep masskill western antiwest population gdppc polity totalmedia
xtnbreg shameAI ingos antigovprot csorepress intuse cellphones violrep masskill western antiwest population gdppc polity totalmedia
xtnbreg shameHRW ingos antigovprot csorepress intuse cellphones violrep masskill western antiwest population gdppc polity totalmedia
xtnbreg shameothers ingos antigovprot csorepress intuse cellphones violrep masskill western antiwest population gdppc polity totalmedia
xtnbreg criticize ingos antigovprot csorepress intuse cellphones violrep masskill western antiwest population gdppc polity totalmedia
xtnbreg accusehr ingos antigovprot csorepress intuse cellphones violrep masskill western antiwest population gdppc polity totalmedia
xtnbreg demands ingos antigovprot csorepress intuse cellphones violrep masskill western antiwest population gdppc polity totalmedia
xtnbreg shamewest ingos antigovprot csorepress intuse cellphones violrep masskill western antiwest population gdppc polity totalmedia
xtnbreg shamewestcrit ingos antigovprot csorepress intuse cellphones violrep masskill western antiwest population gdppc polity totalmedia
DOI: 10.6084/m9.figshare.29104280
title: teste_EVSN

description: dados testes
DOI: 10.15468/dl.rp7qh7
title: Occurrence Download

description: A dataset containing 1961157 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Volatinia jacarina (Linnaeus, 1766), Brycon hilarii (Valenciennes, 1850), Ortalis canicollis (Wagler, 1830), Lonchophylla mordax Thomas, 1903, Chiroderma doriae Thomas, 1891, Monodelphis domestica (Wagner, 1842), Sporophila caerulescens (Vieillot, 1823), Brotogeris versicolurus (Statius Muller, 1776), Chelonoidis carbonarius (Spix, 1824), Cerradomys subflavus (Wagner, 1842), Ara chloropterus G.R.Gray, 1859, Leontopithecus rosalia (Linnaeus, 1766), Necromys lasiurus (Lund, 1841), Trachops cirrhosus (Spix, 1823), Euphractus sexcinctus (Linnaeus, 1758), Eucometis penicillata (Spix, 1825), Piaractus mesopotamicus (Holmberg, 1887), Alouatta caraya (Humboldt, 1812), Diopsittaca nobilis (Linnaeus, 1758), Rhea americana (Linnaeus, 1758), Aratinga aurea (Gmelin, 1788), Sapajus robustus (Kuhl, 1820), Manacus manacus (Linnaeus, 1766), Tonatia bidens (Spix, 1823), Saltator coerulescens Vieillot, 1817, Mylossoma duriventre (Cuvier, 1818), Tayassu pecari (Link, 1795), Sirystes sibilator (Vieillot, 1818), Dysithamnus mentalis (Temminck, 1823), Cerradomys scotti (Langguth & Bonvicino, 2002), Patagioenas speciosa (J.F.Gmelin, 1789), Hypsipyla grandella Zeller, 1848, Heuretes picticornis Grote & Robinson, 1868, Cotinga ridgwayi Ridgway, 1887, Platynota flavedana Clemens, 1860, Alouatta pigra Lawrence, 1933, Stilpnia larvata (Du Bus de Gisignies, 1846), Icterus pustulatus (Wagler, 1829), Euphonia affinis (Lesson, 1842), Caluromys derbianus (Waterhouse, 1841), Tangara chrysotis (Du Bus de Gisignies, 1846), Lophotriccus pileatus (Tschudi, 1844), Diglossa glauca P.L.Sclater & Salvin, 1876, Psarocolius atrovirens (Orbigny & Lafresnaye, 1838), Trogon personatus Gould, 1842, Elaenia pallatangae P.L.Sclater, 1862, Iridophanes pulcherrimus (P.L.Sclater, 1853), Pipreola intermedia Taczanowski, 1884, Diglossa caerulescens (P.L.Sclater, 1856), Zimmerius bolivianus (Orbigny, 1840))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1961157 records from 1052 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007878-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f8f5cy
title: Occurrence Download

description: A dataset containing 161 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Pasimachus marginatus (Fabricius, 1787)",
 "Year is greater than or equal to 1950",
 {
 "or" : [
 "GadmGid is USA",
 "GadmGid is CAN",
 "GadmGid is MEX"
 ]
 }
 ]
}

 The dataset includes 161 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007908-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fpz5jp
title: Occurrence Download

description: A dataset containing 981 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "OccurrenceStatus is Present",
 "TaxonKey is Freylinia Colla"
 ]
}

 The dataset includes 981 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007909-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14503843
title: Filtered and Annotated GBIF dataset for Wilcox et al 2025

description: These are GBIF data for land plants from 3 study areas in California: Marble Mountains, Mount Tamalpais, and Santa Monica Mountains. These data were cleaned, deduplicated, and taxon names were verified. In addition to the standard GBIF columns, we included the following columns:

place_name - name of each of the 3 study regions in which the record occurred

verifiedTaxon - indicating whether observation was congruent with that taxon’s reported geographic range in California and that nomenclatural synonyms were consistent.

keepWhenDeduplicating - indicating whether the record was retained in further analysis after deduplication.

Origin - native or naturalized according to Jepson eFlora.

Tip_SpeciesName - Crosswalk between our GBIF species list and the taxon list used by Thornhill et al. (2017). 

OTU - Operational taxonomic units (OTU) are the tip labels of the phylogenetic tree created by Thornhill et al. (2017), who's phylogeny we used in the phylogenetic diversity and bias analysis.

distance_to_nearest_trail - distance in meters to nearest OpenStreetMaps road to the record.

 

Citation: 

Thornhill, Andrew; Baldwin, Bruce; Freyman, William et al. (2017). Sequence matrix and tree files for Spatial phylogenetics of the native California flora (Thornhill et al. BMC Biology) [Dataset]. Dryad. https://doi.org/10.6078/D1VD4P
DOI: 10.5281/zenodo.14503844
title: Filtered GBIF dataset for Wilcox et al 2025

description: These are GBIF data from 3 study areas in California: Marble Mountains, Mount Tamalpais, and Santa Monica Mountains. These data were cleaned, deduplicated, and taxon names were verified. Also included is a column on origin, e.g. naturalized or historically native.
DOI: 10.5281/zenodo.15238775
title: Filtered GBIF dataset for Wilcox et al 2025

description: These are GBIF data for land plants from 3 study areas in California: Marble Mountains, Mount Tamalpais, and Santa Monica Mountains. These data were cleaned, deduplicated, and taxon names were verified. Also included is a column on origin, e.g. naturalized or historically native.
DOI: 10.5281/zenodo.15265921
title: Filtered and Annotated GBIF dataset for Wilcox et al 2025

description: These are GBIF data for land plants from 3 study areas in California: Marble Mountains, Mount Tamalpais, and Santa Monica Mountains. These data were cleaned, deduplicated, and taxon names were verified. In addition to the standard GBIF columns, we included the following columns:

place_name - name of each of the 3 study regions in which the record occurred

verifiedTaxon - indicating whether observation was congruent with that taxon’s reported geographic range in California and that nomenclatural synonyms were consistent.

keepWhenDeduplicating - indicating whether the record was retained in further analysis after deduplication.

Origin - native or naturalized according to Jepson eFlora.

Tip_SpeciesName - Crosswalk between our GBIF species list and the taxon list used by Thornhill et al. (2017). 

OTU - Operational taxonomic units (OTU) are the tip labels of the phylogenetic tree created by Thornhill et al. (2017), who's phylogeny we used in the phylogenetic diversity and bias analysis.

distance_to_nearest_trail - distance in meters to nearest OpenStreetMaps road to the record.

 

Citation: 

Thornhill, Andrew; Baldwin, Bruce; Freyman, William et al. (2017). Sequence matrix and tree files for Spatial phylogenetics of the native California flora (Thornhill et al. BMC Biology) [Dataset]. Dryad. https://doi.org/10.6078/D1VD4P
DOI: 10.15468/dl.m8ajs5
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Harpalus obliquus G.Horn, 1880",
 "Year is greater than or equal to 1950",
 {
 "or" : [
 "GadmGid is USA",
 "GadmGid is CAN",
 "GadmGid is MEX"
 ]
 }
 ]
}

 The dataset includes 52 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007912-250515123054153/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.29104295
title: Especificación del patrón de interacción en el requisito descrito en Confluence

description: Especificación del patrón de interacción en el requisito descrito en Confluence
DOI: 10.6084/m9.figshare.29104295.v1
title: Especificación del patrón de interacción en el requisito descrito en Confluence

description: Especificación del patrón de interacción en el requisito descrito en Confluence
DOI: 10.5281/zenodo.13968786
title: Dataset
DOI: 10.5281/zenodo.13968787
title: Datasets for TransFusion