cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17764284
title: Polyploidy in Microsporidia

description: Supplementary material for "Polyploidy is widespread in Microsporidia" (https://doi.org/10.1128/spectrum.03669-23), with an additional ploidy estimation plot from "Microsporidia and invertebrate hosts: genome-informed taxonomy surrounding a new lineage of crayfish-infecting Nosema spp. (Nosematida)" (https://doi.org/10.1007/s13225-024-00543-w).

File_1 contains:



Table S1: SRA accession numbers, species name, and reason for exclusion of the SRA samples for which we were not able to reliably estimate ploidy in this study ("Polyploidy is widespread in Microsporidia").

Table S3: Ribosomal small subunit (SSU) sequences reconstructed from unassembled reads using PhyloFlash (with –emirge enabled).

Table S4: NCBI NT accession numbers of additional contextual species included in phylogenetic tree.

Text S1: Newick file format of generated phylogenetic tree.

Figure S1: Box plot of spore volume in diploid (n = 10) and tetraploid species (n = 6), calculated using data from Bojko et al. (2022).

Figure S2: Bar plot of habitats the diploid (n = 10) and tetraploid species (n = 6) identified in this study are found in according to Bojko et al. (2022).

Figure S3: Bar plot of different host groups the diploid (n = 10) and tetraploid species (n = 6) identified in this study occur in, according to Bojko et al. (2022).

Figure S4: Bar plot of different transmission modes the diploid (n = 10) and tetraploid species (n = 6) identified in this study possess, according to Bojko et al. (2022).

Figure S5: Box plot of average haploid genome size estimated for the diploid (n = 10) and tetraploid (n = 6) species identified in this study, using GenomeScope2.

Figure S6: Bar plot of number of nuclei in the spores of the diploid (n = 10) and tetraploid species (n = 6) identified in this study, according to Bojko et al. (2022).


File_2 contains:



Table S2: SRA accession numbers, species name, linear GenomeScope2 plots, transformed GenomeScope2 plots, and Smudgeplot plots of the 66 samples for which we were able to estimate ploidy in this study ("Polyploidy is widespread in Microsporidia").


Figure S7: (a) GenomeScope2 plot estimated a haploid genome size of ~6.6 Mbp for N. rusticus n. sp., with a tetraploidy model fit. (b) Smudgeplot indicates tetraploidy for N. rusticus. From "Microsporidia and invertebrate hosts: genome-informed taxonomy surrounding a new lineage of crayfish-infecting Nosema spp. (Nosematida)".
DOI: 10.5281/zenodo.17764285
title: Polyploidy in Microsporidia

description: Supplementary material for "Polyploidy is widespread in Microsporidia" (https://doi.org/10.1128/spectrum.03669-23), with an additional ploidy estimation plot from "Microsporidia and invertebrate hosts: genome-informed taxonomy surrounding a new lineage of crayfish-infecting Nosema spp. (Nosematida)" (https://doi.org/10.1007/s13225-024-00543-w).

File_1 contains:



Table S1: SRA accession numbers, species name, and reason for exclusion of the SRA samples for which we were not able to reliably estimate ploidy in this study ("Polyploidy is widespread in Microsporidia").

Table S3: Ribosomal small subunit (SSU) sequences reconstructed from unassembled reads using PhyloFlash (with –emirge enabled).

Table S4: NCBI NT accession numbers of additional contextual species included in phylogenetic tree.

Text S1: Newick file format of generated phylogenetic tree.

Figure S1: Box plot of spore volume in diploid (n = 10) and tetraploid species (n = 6), calculated using data from Bojko et al. (2022).

Figure S2: Bar plot of habitats the diploid (n = 10) and tetraploid species (n = 6) identified in this study are found in according to Bojko et al. (2022).

Figure S3: Bar plot of different host groups the diploid (n = 10) and tetraploid species (n = 6) identified in this study occur in, according to Bojko et al. (2022).

Figure S4: Bar plot of different transmission modes the diploid (n = 10) and tetraploid species (n = 6) identified in this study possess, according to Bojko et al. (2022).

Figure S5: Box plot of average haploid genome size estimated for the diploid (n = 10) and tetraploid (n = 6) species identified in this study, using GenomeScope2.

Figure S6: Bar plot of number of nuclei in the spores of the diploid (n = 10) and tetraploid species (n = 6) identified in this study, according to Bojko et al. (2022).


File_2 contains:



Table S2: SRA accession numbers, species name, linear GenomeScope2 plots, transformed GenomeScope2 plots, and Smudgeplot plots of the 66 samples for which we were able to estimate ploidy in this study ("Polyploidy is widespread in Microsporidia").


Figure S7: (a) GenomeScope2 plot estimated a haploid genome size of ~6.6 Mbp for N. rusticus n. sp., with a tetraploidy model fit. (b) Smudgeplot indicates tetraploidy for N. rusticus. From "Microsporidia and invertebrate hosts: genome-informed taxonomy surrounding a new lineage of crayfish-infecting Nosema spp. (Nosematida)".
DOI: 10.15468/dl.agwbvn
title: Occurrence Download

description: A dataset containing 119 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craugastor palenque"
 ]
}

 The dataset includes 119 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015892-251120083545085/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.30742568.v1
title: key processed objects (e.g., Seurat objects, DEG lists, trained ML model parameters)

description: key processed objects (e.g., Seurat objects, DEG lists, trained ML model parameters)
DOI: 10.15468/dl.9skgym
title: Occurrence Download

description: A dataset containing 506491 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nycticorax nycticorax, Oenanthe oenanthe, Oporornis agilis, Oxyura jamaicensis, Pandion haliaetus)",
 "Country is Canada",
 "OccurrenceStatus is Present",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON ((-84.76571 41.22334, -58.93394 41.22334, -58.93394 49.85477, -84.76571 49.85477, -84.76571 41.22334))",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 506491 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015872-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ft8fbq
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craugastor polymniae"
 ]
}

 The dataset includes 51 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015893-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kzbxxt
title: Occurrence Download

description: A dataset containing 375 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sclerotinia sclerotiorum",
 "HasCoordinate is true",
 "Year is greater than or equal to 2012"
 ]
}

 The dataset includes 375 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015894-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8beebp
title: Occurrence Download

description: A dataset containing 289 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craugastor punctariolus"
 ]
}

 The dataset includes 289 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015895-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8fsfmc
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craugastor rhyacobatrachus"
 ]
}

 The dataset includes 57 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015897-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17603/ds2-aak9-cq71
title: Seismic behavior of existing buildings with soft story and mitigation measures, in Evaluation of seismic vulnerability of Mexico City Buildings

description: This project focuses on the seismic behavior of existing buildings in Mexico City that were constructed under outdated seismic codes and exhibit soft-first-story irregularities. It also presents a proposed method to mitigate the associated vulnerabilities and improve their structural performance during earthquakes.

description: This project examines the seismic behavior of existing buildings in Mexico City, which were constructed under outdated seismic codes, with a particular focus on structures exhibiting soft-first-story irregularities. It also proposed a mitigation method aimed at improving their seismic performance
DOI: 10.15468/dl.7t5s7s
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craugastor saltuarius"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015899-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xsagqt
title: Occurrence Download

description: A dataset containing 222 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craugastor spatulatus"
 ]
}

 The dataset includes 222 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015900-251120083545085/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/13923515
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.ney5yc
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craugastor tabasarae"
 ]
}

 The dataset includes 68 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015901-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e4e5tu
title: Occurrence Download

description: A dataset containing 224 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Craugastor xucanebi"
 ]
}

 The dataset includes 224 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015903-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17764448
title: Magnetic field ( CRVD)

description: “In the CRVD framework, the magnetic field is nothing more than a

volumetric rearrangement of the electronic cloud surrounding the

nuclei of a material, such that this electronic volume is pushed

beyond the physical boundary of the host mass and occupies an

invisible spatial volume detached from the material itself.”
DOI: 10.5281/zenodo.17764447
title: Magnetic field ( CRVD)

description: “In the CRVD framework, the magnetic field is nothing more than a

volumetric rearrangement of the electronic cloud surrounding the

nuclei of a material, such that this electronic volume is pushed

beyond the physical boundary of the host mass and occupies an

invisible spatial volume detached from the material itself.”
DOI: 10.5281/zenodo.17267093
title: Alpha-Sigma Benchmark: O4 Gravitational-Wave Collapse Results (v1.1)

description: This dataset contains the summary results of a benchmarking analysis of 20 gravitational-wave (GW) events observed during the O4 run (May–Sept 2023).

Event-level χ_eff posteriors were examined, and the benchmarks show systematic reductions in scatter, with an average reduction of ~40% across the sample.

Included in this deposit are:





gw_baseline.xlsx – baseline scatter statistics,




gw_event_log.csv – event IDs and logged outcomes,




gw_individual_summary.txt – per-event summaries,




Documentation and licensing information.



Core analytic methods are withheld to protect intellectual property. Extended access may be available under NDA.
description: Dataset of 20 O4 gravitational-wave events (May–Sept 2023). Event-level χ_eff posteriors show systematic scatter reductions averaging ~40%. Includes baseline stats, event logs, and summaries. Core analytic methods withheld; extended access available under NDA.
DOI: 10.5281/zenodo.17267092
title: Alpha-Sigma Benchmark: O4 Gravitational-Wave Collapse Results (v1.1)

description: This dataset contains the summary results of a benchmarking analysis of 20 gravitational-wave (GW) events observed during the O4 run (May–Sept 2023).

Event-level χ_eff posteriors were examined, and the benchmarks show systematic reductions in scatter, with an average reduction of ~40% across the sample.

Included in this deposit are:





gw_baseline.xlsx – baseline scatter statistics,




gw_event_log.csv – event IDs and logged outcomes,




gw_individual_summary.txt – per-event summaries,




Documentation and licensing information.



Core analytic methods are withheld to protect intellectual property. Extended access may be available under NDA.
description: Dataset of 20 O4 gravitational-wave events (May–Sept 2023). Event-level χ_eff posteriors show systematic scatter reductions averaging ~40%. Includes baseline stats, event logs, and summaries. Core analytic methods withheld; extended access available under NDA.
DOI: 10.15468/dl.9zvpcm
title: Occurrence Download

description: A dataset containing 2474603349 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chordata",
 "Year 1814-2025"
 ]
}

 The dataset includes 2474603349 records from 29677 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015618-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7g5utj
title: Occurrence Download

description: A dataset containing 220 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 Sauromalus varius Dickerson, 1919"
 ]
}

 The dataset includes 220 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092961-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fnufrk
title: Occurrence Download

description: A dataset containing 9420 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Orthorhyncus cristatus (Linnaeus, 1758)"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 9420 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015883-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zgfjzv
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zingiber neotruncatum T.L.Wu, K.Larsen & Turland"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0138071-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6uz3fw
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "TaxonKey is Heringia latitarsis (Egger, 1865)"
 ]
}

 The dataset includes 37 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0222869-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n6edgp
title: Occurrence Download

description: A dataset containing 15449 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Pseudoeurycea Taylor, 1944"
 ]
}

 The dataset includes 15449 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001528-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t2gu68
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhamnaceae",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0138072-240321170329656/datasets/export for details.
DOI: 10.15468/dl.efqf62
title: Occurrence Download

description: A dataset containing 592593 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China"
 ]
}

 The dataset includes 592593 records from 311 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106611-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.su3c5a
title: Occurrence Download

description: A dataset listing the 599 species recorded in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((-121.10139 48.99266,-121.05005 48.99266,-121.05005 49.05825,-121.10139 49.05825,-121.10139 48.99266))"
 ]
}

 The dataset's 599 records were derived from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0137953-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2xycfx
title: Occurrence Download

description: A dataset containing 390447 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Bird Ringing Centre in Sweden (NRM)",
 "TaxonKey is Acrocephalus J.A.Naumann & J.F.Naumann, 1811"
 ]
}

 The dataset includes 390447 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015883-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dwatdq
title: Occurrence Download

description: A dataset containing 131502 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Mid-winter count of water birds and other bird species in Bulgaria"
 ]
}

 The dataset includes 131502 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092905-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jp2d55
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ageratina corylifolia (Griseb.) R.M.King & H.Rob."
 ]
}

 The dataset includes 11 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0138073-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y7kxy2
title: Occurrence Download

description: A dataset containing 151 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyclobalanopsis blakei (Skan) Schottky"
 ]
}

 The dataset includes 151 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106622-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qs5n9k
title: Occurrence Download

description: A dataset containing 21176 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Orthosia gracilis (Denis & Schiffermüller), 1775"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 21176 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015884-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6cu2u6
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Clerodendrum brunfelsiiflorum Hallier f."
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092940-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sggedm
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Xerophyta seinei Behnke, K.Kramer & E.Hummel"
 ]
}

 The dataset includes 6 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0138074-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ra8e3u
title: Occurrence Download

description: A dataset containing 122 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Prosopanche americana (R.Br.) Baill."
 ]
}

 The dataset includes 122 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106623-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.swh8vb
title: Occurrence Download

description: A dataset containing 61 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 Anolis pygmaeus Alvarez Del Toro & Smith, 1956"
 ]
}

 The dataset includes 61 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092971-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.