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

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:AAE8155"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014376-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16290039
title: SMT-LIB Catalog 2025

description: This artifact is a metadatadata database for the SMT-LIB benchmark library.

Effective use of this benchmark library often requires access to benchmark metadata, such as as the number of user defined symbols. This artifact is a comprehensive metadata catalog for the SMT-LIB benchmark library. It combines features extracted from the SMT-LIB benchmarks with the results of all past SMT-COMP competitions since 2005.

The catalog is implemented as a SQLite database.  We also provide a simple webapp that can be exectued locally to explore the database.
DOI: 10.5281/zenodo.16290040
title: SMT-LIB Catalog 2025

description: This artifact is a metadatadata database for the SMT-LIB benchmark library.

Effective use of this benchmark library often requires access to benchmark metadata, such as as the number of user defined symbols. This artifact is a comprehensive metadata catalog for the SMT-LIB benchmark library. It combines features extracted from the SMT-LIB benchmarks with the results of all past SMT-COMP competitions since 2005.

The catalog is implemented as a SQLite database.  We also provide a simple webapp that can be exectued locally to explore the database.
DOI: 10.15468/dl.5vrjq9
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ancistrus saudades)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 16 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014377-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48331/scielodata.4kh9yl/zapkls
title: Script Similaridade.R

description: In order to analyze the similarity of species richness among the conservation units in the Cerrado of Maranhão.
DOI: 10.48331/scielodata.4kh9yl/73ltuu
title: Planilha de presença e ausência_.txt

description: The raw data from the presence and absence used in the similarity.
DOI: 10.15468/dl.mdfhqu
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tapinoma melanocephalum",
 "Country is Barbados",
 "HasCoordinate is true"
 ]
}

 The dataset includes 38 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014378-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48331/scielodata.4kh9yl/id0apx
title: Readme.txt

description: Text file with information
DOI: 10.48331/scielodata.4kh9yl
title: Replication Data for: Diversity of bryophytes in the Mirador State Park and floristic similarity among conservation units in the Brazilian Cerrado in Maranhão

description: In order to analyze the similarity of species richness among the conservation units in the Cerrado of Maranhão, published data on the bryophyte flora were compiled (Table 1). Based on these data, a binary matrix of species presence (1) and absence (0) was created. Hierarchical cluster analysis was performed using the “eclust” function of the factoextra package in R software.
DOI: 10.15468/dl.gsv6sw
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tapinoma melanocephalum",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014379-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jxq9q7
title: Occurrence Download

description: A dataset containing 5425 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "HasCoordinate is TRUE",
 "TaxonKey is one of (Tabernaemontana divaricata, Tabernaemontana pauciflora, Tabernaemontana, Tabernaemontana sphaerocarpa, Tacca chantrieri, Tadehagi triquetrum, Tagetes erecta, Tarenna mollis, Teijsmanniodendron coriaceum, Tephrosia candida, Tephrosia hookeriana, Tephrosia noctiflora, Tephrosia purpurea, Ternstroemia aneura, Ternstroemia coriacea, Ternstroemia, Tetracera scandens, Tetradium trichotomum, Thunbergia alata, Thunbergia erecta, Timonius flavescens, Timonius, Timonius wallichianus, Tithonia diversifolia, Trachelospermum inflatum, Trema angustifolium, Trema cannabina, Trema orientalis, Trema tomentosum, Trichosanthes elmeri, Trichosanthes globosa, Trichosanthes, Trichosanthes montana, Trichosanthes quinquangulata, Trichosanthes rotundifolia, Trichosanthes tricuspidata, Trichosanthes wawraei, Trigonobalanus verticillata, Trigonostemon heteranthus, Trigonostemon verticillatus, Triphasia trifolia, Tristaniopsis, Tristaniopsis whiteana, Turpinia)"
 ]
}

 The dataset includes 5425 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014380-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nbju5m
title: Occurrence Download

description: A dataset containing 130 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tragopogon graminifolius",
 "Geometry POLYGON ((26.04335 1.226334, 135.0263 1.226334, 135.0263 55.38525, 26.04335 55.38525, 26.04335 1.226334))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 130 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014381-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n88uqv
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Spain, Portugal, Andorra)",
 "MediaType is Audio",
 "OccurrenceStatus is Present",
 "StartDayOfYear 105-259",
 "TaxonKey is Prunella modularis"
 ]
}

 The dataset includes 63 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014383-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u4bnqx
title: Occurrence Download

description: A dataset containing 167 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Muscicapa segregata)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 167 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014382-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wcnhe7
title: Occurrence Download

description: A dataset containing 31224606 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 PRINTF('%04d-%02d', "year", "month") yearmonth,
 GBIF_EQDGCODE(2, decimallatitude, decimallongitude, 0.0) eqdcellcode,
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, GBIF_EQDGCODE(2, decimallatitude, decimallongitude, 0.0), PRINTF('%04d-%02d', "year", "month"))) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, GBIF_EQDGCODE(2, decimallatitude, decimallongitude, 0.0), PRINTF('%04d-%02d', "year", "month"))) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, GBIF_EQDGCODE(2, decimallatitude, decimallongitude, 0.0), PRINTF('%04d-%02d', "year", "month"))) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, GBIF_EQDGCODE(2, decimallatitude, decimallongitude, 0.0), PRINTF('%04d-%02d', "year", "month"))) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, GBIF_EQDGCODE(2, decimallatitude, decimallongitude, 0.0), PRINTF('%04d-%02d', "year", "month"))) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, GBIF_EQDGCODE(2, decimallatitude, decimallongitude, 0.0), PRINTF('%04d-%02d', "year", "month"))) genuscount,
 COUNT(DISTINCT recordedby) distinctobservers,
 COUNT(*) occurrences
FROM
 occurrence
WHERE
 (occurrence.level0gid = 'AUS' OR occurrence.level1gid = 'AUS' OR occurrence.level2gid = 'AUS' OR occurrence.level3gid = 'AUS')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL AND occurrence."month" IS NOT NULL AND occurrence.hascoordinate = TRUE)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 PRINTF('%04d-%02d', occurrence."year", occurrence."month"),
 GBIF_EQDGCODE(2, occurrence.decimallatitude, occurrence.decimallongitude, 0.0)

 The dataset's 31224606 records were derived from 1354 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014353-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15256042
title: Temperature dependence of exchange stiffness and energy barrier in compensated ferrimagnets
DOI: 10.5281/zenodo.15256043
title: Temperature dependence of exchange stiffness and energy barrier in compensated ferrimagnets
DOI: 10.15468/dl.kequzf
title: Occurrence Download

description: A dataset containing 65375 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Eranthis Salisb."
 ]
}

 The dataset includes 65375 records from 261 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000373-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14230230
title: World constitutions: A Preliminary reading

description: This page describes a Distant Reader data set ("study carrel") called curated-world_constitutions-other -- a collection of world constitutions garnered from a site called Constitute.
description: I wrote the following missive almostd a year ago, and since then I learned the topic of our study was not "human rights" but "human values". That said, one still needs to get an understanding of ones content prior to in-depth analysis, and the following provides just that sort of context. Moreover, the computed summary page still has a great deal to offer.
description: All Distant Reader data sets ("study carrels") use the same method of creation. First, a set of narrative files of just about any type and any number are saved in a folder/directory. Second, the plain text is pulled from each file and saved. Third, feature extraction is done against the plain text to create tab-delimited indexes of bibliographics, email addresses, URLs, parts-of-speech, named-entities, and computed keywords. Fourth, all of the indexes are reduced to an SQLite database file. Finally, everything (the original files, the plain text files, the indexes, and SQLite database) is compressed into a zip file for distribution. The result is a platform- and network-independent data set that can be read and processed by any number of GUI applications, programming languages, or a Python module called the Distant Reader Toolbox.
DOI: 10.5281/zenodo.14230231
title: World constitutions: A Preliminary reading

description: This page describes a Distant Reader data set ("study carrel") called curated-world_constitutions-other -- a collection of world constitutions garnered from a site called Constitute.
description: I wrote the following missive almostd a year ago, and since then I learned the topic of our study was not "human rights" but "human values". That said, one still needs to get an understanding of ones content prior to in-depth analysis, and the following provides just that sort of context. Moreover, the computed summary page still has a great deal to offer.
description: All Distant Reader data sets ("study carrels") use the same method of creation. First, a set of narrative files of just about any type and any number are saved in a folder/directory. Second, the plain text is pulled from each file and saved. Third, feature extraction is done against the plain text to create tab-delimited indexes of bibliographics, email addresses, URLs, parts-of-speech, named-entities, and computed keywords. Fourth, all of the indexes are reduced to an SQLite database file. Finally, everything (the original files, the plain text files, the indexes, and SQLite database) is compressed into a zip file for distribution. The result is a platform- and network-independent data set that can be read and processed by any number of GUI applications, programming languages, or a Python module called the Distant Reader Toolbox.
DOI: 10.15468/dl.jrmfws
title: Occurrence Download

description: A dataset containing 10747 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Plantago asiatica L.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 10747 records from 156 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000386-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cbuw5h
title: Occurrence Download

description: A dataset containing 11666806 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Macaria colata (Grote, 1881), Arthropoda, Machaeranthera tanacetifolia (Kunth) Nees, Macrhybopsis storeriana (Kirtland, 1845), Macromia taeniolata Rambur, 1842, Makaira nigricans Lacepède, 1802, Malacoraja senta (Garman, 1885))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 },
 "Country is Canada",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 32000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 11666806 records from 607 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000378-250515123054153/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.28536455
title: Figure 1. Bacterial Feeding

description: <i>Hydroides elegans </i>RNAi
DOI: 10.6084/m9.figshare.28536455.v1
title: Figure 1. Bacterial Feeding

description: <i>Hydroides elegans </i>RNAi
DOI: 10.6084/m9.figshare.28536482
title: Figure 2. RNAi knockdown

description: <i>Hydroides elegans</i> RNAi
DOI: 10.6084/m9.figshare.28536491
title: Figure 3. MyD88 Knockdown

description: <i>Hydroides elegans </i>RNAi
DOI: 10.6084/m9.figshare.28536491.v1
title: Figure 3. MyD88 Knockdown

description: <i>Hydroides elegans </i>RNAi
DOI: 10.6084/m9.figshare.28536497
title: Figure 4. Downstream Genes

description: <i>Hydroides elegans</i> RNAi
DOI: 10.6084/m9.figshare.29069840
title: data for "Moist Energy Constraints on Surface Temperature Variance under Climate Warming"

description: The data for the paper <i>Moist Energy Constraints on Surface Temperature </i><i>Variance under Climate Warming</i>.
DOI: 10.57967/hf/5501
title: txt360_urls
DOI: 10.15468/dl.wq2gu2
title: Occurrence Download

description: A dataset containing 488 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Erblichia Seem."
 ]
}

 The dataset includes 488 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000388-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f37ht9
title: Occurrence Download

description: A dataset listing the 11 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Glossophaga soricina (Pallas, 1766)"
 ]
}

 The dataset's 11 records were derived from 332 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000384-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14847694
title: Programmable gene insertion in human cells with a laboratory-evolved CRISPR-associated transposase

description: Abstract

Programmable gene integration in human cells has the potential to enable mutation-agnostic treatments for loss-of-function genetic diseases and facilitate many applications in the life sciences. CRISPR-associated transposases (CASTs) catalyze RNA-guided DNA integration but thus far demonstrate minimal activity in human cells. Using phage-assisted continuous evolution (PACE), we identified CAST variants with ≥200-fold average improved integration activity. The evolved CAST system (evoCAST) achieves ~10-30% integration efficiencies of kilobase-size DNA cargoes in human cells across 14 tested genomic target sites, including safe harbor loci, sites used for immunotherapy, and genes implicated in loss-of-function diseases, with undetected indels and low levels of off-target integration. Collectively, our findings establish a platform for the laboratory evolution of CASTs and advance a versatile system for programmable gene integration in living systems.
description: Description of files uploaded

Off-target_ATAC_code.zip: Compressed folder of python/bash scripts used to calculate ATAC scores of off-target evoCAST integration events, and perform bootstrap analysis (fig. S25D)

HTS-IntegrationEfficiencyScript.zip: Compressed folder of script used to analyze integration efficiencies for CAST using HTS data, adapted from Lampe, et al. NBT 2023. Script also calculates distribution of T-RL insertion sites.

240111_1921_xSL0283.ncf: Raw flow-cytommetry data of TnsB-VP64 reporter assay (fig. S18, A and B). Example gating shown in Lampe, et al. NBT 2023.

240111_1921_xSL0283_Heat Map1.csv: CSV file of tdTomato MFI for TnsB-VP64 reporter assay (fig. S18, A and B). Example gating shown in Lampe, et al. NBT 2023.

220713_QCascade-structure-AF2.cxs: Chimera session of AlphaFold2-predicted PseQCascade (fig. S21A, C, and D).

PseTnsAB-STC.pse: PyMOL session of AlphaFold3-predicted PseTnsAB strand-transfer complex (Fig. 3E, figs. S16 and S18C).

PseTnsC7-DNA.pse: PyMOL session of AlphaFold3-predicted PseTnsC heptamer and target DNA (fig. S8).

PseTnsC7-TnsBhook.pse: PyMOL session of AlphaFold3-predicted PseTnsC heptamer in complex witih a PseTnsB C-terminal hook (Fig. 3F).

All ".ddpcrone" and "WellAnnotations.xlsx" files: Raw ddPCR files (.ddpcrone) for Fig. 5A and 5I, representative of ddPCR data throughout study. Well identities and efficiency calculations are in the ".xlsx" file. Figures S5 and S6 discuss ddPCR quantitation in depth.

ExampleGating-figS25H.ai and figS25H-flowquantitation.xlsx: Example flow cytometry gating (.ai) and % mCherry+ values (.xlsx) for off-target integration reporter assay (fig. S25H).

FigS18D_Western.jpg: Uncropped western blot image for fig. S18D.

UDiTaS analysis scripts are in the linked GitHub repository (https://github.com/sternberglab/Witte_Lampe_Eitzinger_et_al_2024)