cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.q37mw9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Palicourea sousae (Lorence & Dwyer) Lorence)",
 "BasisOfRecord is one of (Human Observation, Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017825-250127130748423/datasets/export for details.
DOI: 10.15468/dl.dw8z3d
title: Occurrence Download

description: A dataset containing 1062 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Cabo Verde",
 "DatasetKey is one of (CETUS: Cetacean monitoring surveys in the Eastern North Atlantic, Happywhale - Humpback whale in North Atlantic Ocean, Observation.org, Nature data from around the World, Cetacean sightings in Boa Vista, Cape Verde, iNaturalist Research-grade Observations, Seabird and cetacean sightings from Cruise SY002 of RV Shoyo Maru, Tropical Atlantic Ocean, Oct. 2000, NABU|naturgucker, Happywhale - Atlantic spotted dolphin in North Atlantic Ocean, Happywhale - Killer whale in North Atlantic Ocean)",
 "HasCoordinate is true",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "PublishingOrg is one of (67b2263f-6990-4d9d-b32b-20aa72ef4fbc, 2089ce96-4fb5-4a20-999c-3ccf45a27a4d, c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f, 28eb1a3f-1c15-4a95-931a-4af90ecb574d, bb646dff-a905-4403-a49b-6d378c2cf0d9)",
 "TaxonKey is Cetacea",
 "Year 2000-2025"
 ]
}

 The dataset includes 1062 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017827-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mbs5hg
title: Occurrence Download

description: A dataset containing 454 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Colección de semillas de variedades locales de la Alpujarra granadina"
 ]
}

 The dataset includes 454 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017829-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uhss7t
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Palicourea tetragona (Donn.Sm.) C.M.Taylor)",
 "BasisOfRecord is one of (Human Observation, Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 33 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017828-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25828/fs0p-tn17
title: South African Reconciliation Barometer 2017, Round 15
DOI: 10.15468/dl.3mss2d
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Palicourea triphylla DC.)",
 "BasisOfRecord is one of (Human Observation, Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 37 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017830-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wcd46e
title: Occurrence Download

description: A dataset containing 64501 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-77.09284 37.50194,-82.69372 31.2451,-96.06518 31.34602,-98.78993 26.24973,-96.72114 18.98372,-89.80834 15.30027,-78.50567 11.51589,-61.148 11.26359,-60.49204 37.45148,-77.09284 37.50194))",
 "LifeStage is one of (Juvenile, Subadult)",
 "Month is one of (February, March, April, May, June, July, August)",
 "Year 1990-2024"
 ]
}

 The dataset includes 64501 records from 157 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017826-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r3jyvt
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Laminatubus alvini Hove & Zibrowius, 1986"
 ]
}

 The dataset includes 70 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017831-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.52tfq5
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Mimosa bimucronata (DC.) Kuntze"
 ]
}

 The dataset includes 61 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017832-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zhutmk
title: Occurrence Download

description: A dataset containing 255299 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-35.70467 23.12994,98.70467 23.12994,98.70467 76.87006,-35.70467 76.87006,-35.70467 23.12994))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anacamptis pyramidalis (L.) Rich."
 ]
}

 The dataset includes 255299 records from 1633 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017779-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.75k5sv
title: Occurrence Download

description: A dataset containing 4702 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 Tesia olivea (McClelland, 1840)"
 ]
}

 The dataset includes 4702 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025878-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f1rib7
title: Occurrence Download

description: A dataset containing 1158 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Legume Collections of the Plant Genetic Resources Research Institute (CSIR-PGRRI),Ghana"
 ]
}

 The dataset includes 1158 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015931-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yxk9cj
title: Occurrence Download

description: A dataset containing 26785129 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 26785129 records from 3601 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025851-240314170635999/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.26552194
title: Additional file 8 of Improving the estimation of thermospheric neutral density via two-step assimilation of in situ neutral density into a numerical model

description: Additional file 8. Calibrated NRLMSIS 2.0 CHAMP.
DOI: 10.6084/m9.figshare.26552194.v1
title: Additional file 8 of Improving the estimation of thermospheric neutral density via two-step assimilation of in situ neutral density into a numerical model

description: Additional file 8. Calibrated NRLMSIS 2.0 CHAMP.
DOI: 10.6084/m9.figshare.26555828
title: Additional file 11 of In the battle of the disease: a transcriptomic analysis of European foulbrood-diseased larvae of the Western honey bee (Apis mellifera)

description: Additional file 11 : Table S9. Summary of read mapping for all samples performed with mapping-based mode and a transcriptome index in Salmon.
DOI: 10.6084/m9.figshare.26552200.v1
title: Additional file 10 of Improving the estimation of thermospheric neutral density via two-step assimilation of in situ neutral density into a numerical model

description: Additional file 10. Open loop simulation 3 CHAMP.
DOI: 10.6084/m9.figshare.26552137
title: Additional file 5 of Improving the estimation of thermospheric neutral density via two-step assimilation of in situ neutral density into a numerical model

description: Additional file 5. Calibrated NRLMSIS 2.0 GRACE.
DOI: 10.6084/m9.figshare.26552134.v1
title: Additional file 4 of Improving the estimation of thermospheric neutral density via two-step assimilation of in situ neutral density into a numerical model

description: Additional file 4. Accelerometer derived densities GRACE April 2010.
DOI: 10.15468/dl.2jm3xn
title: Occurrence Download

description: A dataset containing 310 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Occurrence evidence, Observation)",
 "TaxonKey is Manis pentadactyla Linnaeus, 1758"
 ]
}

 The dataset includes 310 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063804-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8uhtg2
title: Occurrence Download

description: A dataset listing the 130 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-29.78974 28.88059,188.61026 28.88059,188.61026 82.50706,-29.78974 82.50706,-29.78974 28.88059))",
 "TaxonKey is Onthophagus Latreille, 1802"
 ]
}

 The dataset's 130 records were derived from 588 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063767-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.huh79x
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.679422 -33.081151, 148.679422 -33.085643, 148.681668 -33.085643, 148.681668 -33.081151, 148.679422 -33.081151))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063805-240626123714530/datasets/export for details.
DOI: 10.15468/dl.3syd6r
title: Occurrence Download

description: A dataset containing 13802 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Electrona antarctica (Günther, 1878)"
 ]
}

 The dataset includes 13802 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063806-240626123714530/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.26555939.v1
title: Additional file 1 of DNA methylation patterns associated with konzo in Sub-Saharan Africa

description: Additional file 1: Table S1. Sample collection information. Sample IDs were relabeled with "Analysis ID" for improved readability on figures. Cohort specific information, location of sample collection, and age are also provided (average age = 13 years old). Table S2. Beta values of all konzo case and control samples. Beta values for individual konzo samples are labeled columns K1–K16; beta values for individual control samples are labeled C1–C16. Averages for both groups are labeled Average_Konzo_Bvalue and Average_Contrl_Bvalue. Mean for each group is labeled Average_Konzo_Bvalue_Total and Average_Contrl_Bvalue_Total. Table S3. DNA Methylation analysis tools, functions and references. Table S4. Output significantly differentially methylated probes from bioinformatic analysis. Threshold for significance: FDR p value &lt; 0.05, log2 fold-change of less than or equal to − 1 or greater than or equal to 1. Column headers include the Illumina ID (IlmnID), Chromosome Number (Chromosome) and location (Coordinate_start or Coordinate_end), positive or negative strand (Strand), gene name (Name), location of probe to CpG (Group), log2 fold-change value (logFC), and FDR adjusted p value (adj.P.Val). Table S5. Output significantly differentially methylated probes from bioinformatic analysis with immune cell fraction analysis. Threshold for significance: FDR p value &lt; 0.05, log2 fold-change of less than or equal to − 1 or greater than or equal to 1. Column headers include the Illumina ID (IlmnID), Chromosome Number (Chromosome) and location (Coordinate_start or Coordinate_end), positive or negative strand (Strand), gene name (Name), location of probe to CpG (Group), log2 fold-change value (logFC), and FDR adjusted p value (adj.P.Val). Table S6. Cell-type fraction means for Konzo cases and controls. Standard deviation (sd) was calculated for each mean. Column headers include: cell type (CellType), cohort specifics (Condition), mean (Mean), standard deviation (sd), and Upper (mean + sd) and Lower (mean-sd) bounds. Table S7. Output significantly enriched GO Terms. Threshold for significance: p value &lt; 0.05. Column headers include the GO ID (ID), GO Term Description (GO Description), absolute log10 p value (abs_log10_pval), log10 p value (log10_pval), p value (pval), and genes associated with GO ID (genes). Table S8. Targeted methylation analysis results. ProbeID: Illumina probe IDs; Genes: Associated genes; Transcripts: Associated transcripts; Chromosome: chromosomal position; Region: Regions in the chromosome that get affected; %MethylationDifference: Difference in methylation percentage; logFC: Difference in log (base 2) fold change; p value: associated p value.
DOI: 10.5281/zenodo.13306632
title: Role of energy migration in the efficiency of upconversion-based resonance energy transfer to organic acceptors

description: Graphs, data set and algorithms (in Matlab) for the article:

Kotulska, A. M., Prorok, K., Bezkrovnyi, O., Pilch-Wrobel, A., & Bednarkiewicz, A. (2024). Role of energy migration in the efficiency of upconversion-based resonance energy transfer to organic acceptors. Journal of Luminescence, 275, 120823. https://doi.org/10.1016/J.JLUMIN.2024.120823

(https://www.sciencedirect.com/science/article/pii/S0022231324003879)Abstract: Lanthanide (Ln)-doped upconverting nanocrystals (LnNPs) exhibit suitable features as energy donors for Förster resonance energy transfer (FRET). The sensitivity of biosensors can be improved by optically active materials with anti-Stokes emission, narrowband absorption and emission spectral lines, and long luminescence lifetimes. In contrast to energy reabsorption, energy transfer between the upconversion nanocrystals (UCNPs) and organic dyes attached to their surface can be observed through donor emission quenching and acceptor emission and decreases in the luminescence lifetimes of donors. Although the emission spectra confirmed that FRET occurred from the Er3+ ions to the Rose Bengal acceptor, the luminescence lifetimes were generally not affected by the presence of the acceptor. The Ln3+ dopant in LnNPs, which typically has 20–100 % Yb3+ sensitizer ions and 0.2–2% activator (Er3+/Tm3+/Ho3+) ions, results in hundreds to thousands of Ln3+ ions in a single UCNP. The interaction between multiple Ln3+ ions results in significant energy migration and storage in the Yb3+ sensitizer network, which is often recharged with the energy of the Er3+ ions when they emit and nonradiatively transfer their energy to acceptor species. However, the energy transfer mechanisms could not be unambiguously determined through spectroscopic data due to the nature the upconversion process. Studies confirmed that the energy migration distance was significantly shortened when the LnNP surface contained acceptors; this affected the energy storage and ‘recharging’ capability of the Yb3+ sensitizer network within the UCNPs. These results provide hints on the future use of LnNP as effective FRET probes, in which the highest possible absorption cross section and possibly lowest dopant concentration should be maintained.Keywords: Nanocrystals; Resonance energy transfer; FRET; Monte Carlo; Lanthanide ions
DOI: 10.5281/zenodo.13306633
title: Role of energy migration in the efficiency of upconversion-based resonance energy transfer to organic acceptors

description: Graphs, data set and algorithms (in Matlab) for the article:

Kotulska, A. M., Prorok, K., Bezkrovnyi, O., Pilch-Wrobel, A., & Bednarkiewicz, A. (2024). Role of energy migration in the efficiency of upconversion-based resonance energy transfer to organic acceptors. Journal of Luminescence, 275, 120823. https://doi.org/10.1016/J.JLUMIN.2024.120823

(https://www.sciencedirect.com/science/article/pii/S0022231324003879)Abstract: Lanthanide (Ln)-doped upconverting nanocrystals (LnNPs) exhibit suitable features as energy donors for Förster resonance energy transfer (FRET). The sensitivity of biosensors can be improved by optically active materials with anti-Stokes emission, narrowband absorption and emission spectral lines, and long luminescence lifetimes. In contrast to energy reabsorption, energy transfer between the upconversion nanocrystals (UCNPs) and organic dyes attached to their surface can be observed through donor emission quenching and acceptor emission and decreases in the luminescence lifetimes of donors. Although the emission spectra confirmed that FRET occurred from the Er3+ ions to the Rose Bengal acceptor, the luminescence lifetimes were generally not affected by the presence of the acceptor. The Ln3+ dopant in LnNPs, which typically has 20–100 % Yb3+ sensitizer ions and 0.2–2% activator (Er3+/Tm3+/Ho3+) ions, results in hundreds to thousands of Ln3+ ions in a single UCNP. The interaction between multiple Ln3+ ions results in significant energy migration and storage in the Yb3+ sensitizer network, which is often recharged with the energy of the Er3+ ions when they emit and nonradiatively transfer their energy to acceptor species. However, the energy transfer mechanisms could not be unambiguously determined through spectroscopic data due to the nature the upconversion process. Studies confirmed that the energy migration distance was significantly shortened when the LnNP surface contained acceptors; this affected the energy storage and ‘recharging’ capability of the Yb3+ sensitizer network within the UCNPs. These results provide hints on the future use of LnNP as effective FRET probes, in which the highest possible absorption cross section and possibly lowest dopant concentration should be maintained.Keywords: Nanocrystals; Resonance energy transfer; FRET; Monte Carlo; Lanthanide ions
DOI: 10.15468/dd.hv3w4j
title: Parametrization of biological assumptions to simulate growth of tree branching architectures

description: Summary of GBIF data used in [paper](https://doi.org10.1093/treephys/tpae045): 

We used some pictures of solitair tree and directly used the corresponding images from occurrence records with IDs: 3321164296; 3961477484; 4029227990; 4022155595; 2818760862; 574748831; 3860423420; 3407144501; 3407150608; 3407151530; 3407146945; 3407147089; 3407149256; 3407150769; 3407151629; 3873156180; 3112861866; 3112397813; 4006697428; 3355008845; 3859647129; 4028995995; 3455643027; 4015028487; 4014951478; 4029242554; 3428903329; 4028997432; 4018319381; 3698108157; 3407145657; 3407145834; 3407145957; 3407147824; 3407149772; 3407148357; 3407149164; 3407151876; 3407152407; 3407152707
DOI: 10.6084/m9.figshare.26552293.v1
title: Additional file 10 of Robust and rigorous identification of tissue-specific genes by statistically extending tau score

description: Additional file 10. Optimized thresholds and Z-scores for each dataset.
DOI: 10.6084/m9.figshare.26552287
title: Additional file 8 of Robust and rigorous identification of tissue-specific genes by statistically extending tau score

description: Additional file 8. Descriptive summary of all datasets.
DOI: 10.6084/m9.figshare.26552299
title: Additional file 12 of Robust and rigorous identification of tissue-specific genes by statistically extending tau score

description: Additional file 12. F-test results for each pair of datasets.
DOI: 10.15468/dl.t5knpp
title: Occurrence Download

description: A dataset containing 376 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((126.0076 38.54925,125.98024 37.98264,125.7489 33.01846,128.20655 33.28919,129.01498 34.55035,130.04978 35.71395,131.14926 37.5049,128.46525 38.72606,126.0076 38.54925))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Camellia japonica L.",
 "Year 1970-2024"
 ]
}

 The dataset includes 376 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063807-240626123714530/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.26552641
title: Additional file 3 of Publisher Correction: Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r

description: Additional file 3. supp file 3: accessions.csv.
DOI: 10.6084/m9.figshare.26552647.v1
title: Additional file 5 of Publisher Correction: Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r

description: Additional file 5. supp file 5: results-small-k.xlsx.
DOI: 10.6084/m9.figshare.26552299.v1
title: Additional file 12 of Robust and rigorous identification of tissue-specific genes by statistically extending tau score

description: Additional file 12. F-test results for each pair of datasets.
DOI: 10.6084/m9.figshare.26552293
title: Additional file 10 of Robust and rigorous identification of tissue-specific genes by statistically extending tau score

description: Additional file 10. Optimized thresholds and Z-scores for each dataset.
DOI: 10.6084/m9.figshare.26552653.v1
title: Additional file 7 of Publisher Correction: Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r

description: Additional file 7. supp file 7: results-subsamples.xlsx.
DOI: 10.6084/m9.figshare.26552638.v1
title: Additional file 2 of Publisher Correction: Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r

description: Additional file 2. supp file 2: results_sra.xlsx.
DOI: 10.6084/m9.figshare.26552662.v1
title: Additional file 10 of Publisher Correction: Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r

description: Additional file 10. supp file 10: accessions-CCLE.csv.
DOI: 10.6084/m9.figshare.26552296
title: Additional file 11 of Robust and rigorous identification of tissue-specific genes by statistically extending tau score

description: Additional file 11. Determining parent-child tissue relationship.