cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.780381
title: (Table 5-3) Sulfate reduction rate and isotope compositions of sulfur in Atlantic bottom sediments of Poligon I near the Congo River mouth
DOI: 10.1594/pangaea.756823
title: Isotopic composition of various forms of sulfur in barite crusts from the Red Sea rift

description: Barite crusts were formed by an intermittent hydrothermal vent with output temperature from 85 to 465°C. Principal sources of supply of sulfate sulfur are sea water, evaporites, and tholeiitic basalts of the Red Sea rift. Sulfides and sulfates were formed in conditions of isotope disequilibrium with respect to sulfur because rate of precipitation of sulfur compounds from hydrothermal solution was high compared with rate of isotope exchange.
description: &lt;0.2% = traces.
description: Supplement to: Strizhov, Valentin P; Sval'nov, Vyacheslav N; Nikolaev, Sergey D; Zhabina, Nina N; Gurina, N V (1988): Isotope composition of sulfur in barite crusts of the Red Sea. Oceanology, 28(1), 83-85
DOI: 10.1594/pangaea.771457
title: (Table 8.3.16) Isotopic composition of carbon from carbonates and organic matter of deposits in the Haakon Mosby volcano

description: 0 = not found.
DOI: 10.1594/pangaea.774174
title: (Table T2) Sediment and pore water nitrogen and d15N concentrations of ODP Hole 202-1235A

description: Sediment depth is given in mcd.
DOI: 10.1594/pangaea.782402
title: (Table 4-2) Abundance of sulfate reducing bacteria, sulfate reduction rate and isotope compositions of sulfur in Atlantic bottom sediments of the Benguela upwelling area along 23°S
DOI: 10.1594/pangaea.770158
title: (Table 3.4.1) Distribution of primary production, bacteria, suspended matter, dissolved organic carbon, particulate organic carbon and its isotopic composition, and of CO2 dark assimilation rate in waters of the Chukchi Sea
DOI: 10.1594/pangaea.816375
title: (Table 2) Composition of sediment pore water at DSDP Hole 68-501 and Site 69-504
DOI: 10.1594/pangaea.816126
title: (Table 1) Concentration and isotope composition of sulphur in sediments at DSDP Site 70-506
DOI: 10.1594/pangaea.767648
title: (Table 1) Oxygen-18 distribution in waters of the Arctic Ocean in 1967 and 1969
DOI: 10.1594/pangaea.834252
title: (Table 2) Oxygen and silicon stable isotopes of diatom silica of sediment core MD01-2416
DOI: 10.1594/pangaea.770283
title: (Fig. 5) Stable oxygen isotopes of ice core VF79_core2 from the Vernagtferner
DOI: 10.1594/pangaea.818223
title: Planktonik δ¹⁸O and 13C of Globorotalia truncatulinoides sinistral from ODP Hole 172-1058C

description: DEPTH, sediment/rock = Depth (mcd)
DOI: 10.1594/pangaea.809819
title: (Table 1) Concentration and stable isotope ratios, pH and alkalinity, Blake Outer Ridge at DSDP Site 76-533
DOI: 10.1594/pangaea.755167
title: (Table 1) Oxygen isotope composition in planktonic foraminifers from surface sediments of the East Pacific

description: Oxygen isotope analysis of skeletal remains of planktonic foraminifers is being successfully used to solve paleoclimatic and stratigraphic problems. At middle latitudes, where considerable seasonal variations in environmental conditions of habitat are found, one has to use for analysis shells of an entire complex of planktonic foraminifera rather than those of individual species. At the same time, one must take into account to what average depths correspond obtained results. A study of variations of O18/O16 ratio in ocean water and in shells of recent foraminifera has made it possible to establish the average depth of habitat of their complexes. This depth is equal to about 200 m at middle, subtropical and tropical latitudes and 100-150 m in equatorial regions. These figures are confirmed by results of determination of average habitat depths by other methods.
description: Supplement to: Nikolaev, Vladimir I; Blyum, Natalia S; Nikolayev, Sergey D (1979): Average depth of habitat of planktonic foraminifera, according to oxygen isotope analysis. Oceanology, 19(6), 712-715
DOI: 10.1594/pangaea.785310
title: (Table 2) Rubidium and strontium contents and isotopic ratios in clay subfractions from formations of the Srednii Peninsula

description: U = untreated with ammonium acetate solution; E = acetate leachate; R = residue. Rb and Sr contents in leachates and residues are adjusted to untreated subfraction.
DOI: 10.1594/pangaea.788997
title: (Table 1c) Principal petrographic characteristics and K-Ar isotope-geochronological data on samples from the finishing of the Late Neopleistocene activity phase of the Keli Volcanic Highland
DOI: 10.1594/pangaea.775326
title: (Table 7) Isotopic compositions of oxygen and carbon from authigenic carbonates of bottom sediments from Northwest Pacific marginal seas
DOI: 10.15468/dl.xhscdx
title: Occurrence Download

description: A dataset containing 2718 species occurrences available in GBIF matching the query:
{
 "SpeciesKey" : [
 "is one of (Gracilaria vermiculophylla (Ohmi) Papenfuss)"
 ]
}

 The dataset includes 2718 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041172-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6vye4u
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pendulina harra (Forssk.) Willk."
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045961-220831081235567/datasets/export for details.
DOI: 10.15468/dl.qhm5rh
title: Occurrence Download

description: A dataset containing 2410 species occurrences available in GBIF matching the query:
{
 "SpeciesKey" : [
 "is one of (Euphorbia davidii Subils)"
 ]
}

 The dataset includes 2410 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041174-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdhr2s
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Jurinea moschus (Hablitz) Bobrov",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 126 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004468-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j5ckis
title: Occurrence Download

description: A dataset containing 3456 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paradoxornis webbianus (Gould, 1852)"
 ]
}

 The dataset includes 3456 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010524-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.34xs8f
title: Occurrence Download

description: A dataset containing 79 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "TaxonKey is Eunectes murinus (Linnaeus, 1758)"
 ]
}

 The dataset includes 79 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0197307-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eu2ru5
title: Occurrence Download

description: A dataset containing 1597 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Country is Germany",
 "DecimalLongitude is greater than or equal to 6.74442176392131",
 "DecimalLongitude is less than 6.7474813171057",
 "DecimalLatitude is greater than or equal to 47.27011",
 "DecimalLatitude is less than or equal to 55.05864"
 ]
}

 The dataset includes 1597 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003452-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bs4yyh
title: Occurrence Download

description: A dataset containing 14592 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is New Zealand",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Passeriformes"
 ]
}

 The dataset includes 14592 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017433-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ksvtxc
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "TaxonKey is Boronia granitica Maiden & Betche"
 ]
}

 The dataset's 1 records were derived from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0116249-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7qhkq4
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Crotalaria mahafalensis R.Vig."
 ]
}

 The dataset includes 38 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012426-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.srp2gs
title: Occurrence Download

description: A dataset containing 146502 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arum maculatum L."
 ]
}

 The dataset includes 146502 records from 373 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017390-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vfsg2u
title: Occurrence Download

description: A dataset containing 53901 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carex vaginata Tausch"
 ]
}

 The dataset includes 53901 records from 214 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0120813-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7m53nq
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Brillantaisia fulva Lindau"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076004-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3qmfbb
title: Occurrence Download

description: A dataset containing 1683 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "Geometry POLYGON((-100.46909 -7.69239,-54.53091 -7.69239,-54.53091 10.69239,-100.46909 10.69239,-100.46909 -7.69239))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tapirus pinchaque (Roulin, 1829)"
 ]
}

 The dataset includes 1683 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000594-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9s54ah
title: Occurrence Download

description: A dataset containing 408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tulipa greigii Regel",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 408 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000595-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14862163
title: Mathematica scripts for "From Matter Density to Deflection Angle and Gravitational Lensing Using Perturbative Method"

description: Here we have uploaded all the codes required for the computations in the paper. The calculations of the formulas and the generation of the figures in the paper were all carried out using these codes.

For the case that the matter distribution can extend to spatial infinity, all codes are in the folder named "Infinite_codes".

For the case that the matter exists only within a finite range, all codes are in the folder named "Finite_codes".

All figures used in our work are all in the folder named "Figures".
DOI: 10.5281/zenodo.14862162
title: Mathematica scripts for "From Matter Density to Deflection Angle and Gravitational Lensing Using Perturbative Method"

description: Here we have uploaded all the codes required for the computations in the paper. The calculations of the formulas and the generation of the figures in the paper were all carried out using these codes.

For the case that the matter distribution can extend to spatial infinity, all codes are in the folder named "Infinite_codes".

For the case that the matter exists only within a finite range, all codes are in the folder named "Finite_codes".

All figures used in our work are all in the folder named "Figures".
DOI: 10.5281/zenodo.14872932
title: Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining

description: # Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining


<https://www.biorxiv.org/content/10.1101/2024.08.27.610007v1>


Our simulated trees paired with lineage tracing data encompass a large number of lineage tracing regimes, which are used to assess the performance of our distance correction method.


## Description of the data and file structure


For each lineage tracing regime, 50 simulations are performed. All trees have exactly 400 leaves, and were simulated as described in the manuscript. The `default' regime consists of:


40 characters.


mutation rate adjusted to obtain an expected 50% mutated entries in the character matrix.


100 indel states.


20% missing data, with 10% coming from heritable epigenetic silencing and 10% coming from sequencing dropouts. (This does not include missing data further introduced by double-resection events, which we also simulate.)


Each lineage tracing regime is obtained by perturbing this 'default' lineage tracing regime by varying one of the above parameters. Specifically, we consider varying:


* number of characters (a.k.a. barcodes) in the set {10, 20, 40, 60, 90, 150} (with 40 being the default)

* number of states in the set {5, 10, 25, 50, 100, 500, 1000} (with 100 being the default)

* expected proportion mutated in the set {10%, 30%, 50%, 70%, 90%} (with 50 being the default)

* percent missing from epigenetic silencing and sequencing dropouts in the set {0%, 10%, 20%, 30%, 40%, 50%, 60%}, with the percent coming from sequencing dropouts fixed to 10% (except when the total is 0%, in which case it is set to 0%)


The data from each simulation is stored specifying the parameter that was varied, so for example the simulated data when the number of barcodes is 30 is stored under "trees/number_of_cassettes/30/" . In this directory, for each repetition, we have three files:


* tree_{repetition}_character_matrix.csv : Contains the lineage tracing data in csv format.

* tree_{repetition}_newick.txt : Contains the tree in newick format, with branch lengths.

* tree_{repetition}_CassiopeiaTree.pkl : Contains the pickled CassiopeiaTree object from the simulation, which in particular contains the fitness of different nodes in the tree, ancestral lineage tracing barcodes, etc.. It is not necessary for reproducing any of our results, but we provided in case it is convenient.


## Code/Software


We have additionally open-sourced a repository allowing seamless reproduction of all results in our paper, here:


https://github.com/songlab-cal/nj-theory
DOI: 10.5281/zenodo.14872933
title: Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining

description: # Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining


<https://www.biorxiv.org/content/10.1101/2024.08.27.610007v1>


Our simulated trees paired with lineage tracing data encompass a large number of lineage tracing regimes, which are used to assess the performance of our distance correction method.


## Description of the data and file structure


For each lineage tracing regime, 50 simulations are performed. All trees have exactly 400 leaves, and were simulated as described in the manuscript. The `default' regime consists of:


40 characters.


mutation rate adjusted to obtain an expected 50% mutated entries in the character matrix.


100 indel states.


20% missing data, with 10% coming from heritable epigenetic silencing and 10% coming from sequencing dropouts. (This does not include missing data further introduced by double-resection events, which we also simulate.)


Each lineage tracing regime is obtained by perturbing this 'default' lineage tracing regime by varying one of the above parameters. Specifically, we consider varying:


* number of characters (a.k.a. barcodes) in the set {10, 20, 40, 60, 90, 150} (with 40 being the default)

* number of states in the set {5, 10, 25, 50, 100, 500, 1000} (with 100 being the default)

* expected proportion mutated in the set {10%, 30%, 50%, 70%, 90%} (with 50 being the default)

* percent missing from epigenetic silencing and sequencing dropouts in the set {0%, 10%, 20%, 30%, 40%, 50%, 60%}, with the percent coming from sequencing dropouts fixed to 10% (except when the total is 0%, in which case it is set to 0%)


The data from each simulation is stored specifying the parameter that was varied, so for example the simulated data when the number of barcodes is 30 is stored under "trees/number_of_cassettes/30/" . In this directory, for each repetition, we have three files:


* tree_{repetition}_character_matrix.csv : Contains the lineage tracing data in csv format.

* tree_{repetition}_newick.txt : Contains the tree in newick format, with branch lengths.

* tree_{repetition}_CassiopeiaTree.pkl : Contains the pickled CassiopeiaTree object from the simulation, which in particular contains the fitness of different nodes in the tree, ancestral lineage tracing barcodes, etc.. It is not necessary for reproducing any of our results, but we provided in case it is convenient.


## Code/Software


We have additionally open-sourced a repository allowing seamless reproduction of all results in our paper, here:


https://github.com/songlab-cal/nj-theory
DOI: 10.5281/zenodo.14872926
title: SMS CSV

description: Este es una hoja de calculo que contiene los hallazgos del SMS Mapeo Sistemático de Herramientas y Plataforma para el Despliegue de Microservicios Web.
DOI: 10.5281/zenodo.14872927
title: SMS CSV

description: Este es una hoja de calculo que contiene los hallazgos del SMS Mapeo Sistemático de Herramientas y Plataforma para el Despliegue de Microservicios Web.
DOI: 10.5281/zenodo.14600231
title: Code and Loci for "Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins"

description: Scripts and genomic loci for "Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins"
DOI: 10.5281/zenodo.14600232
title: Code and Loci for "Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins"

description: Scripts and genomic loci for "Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins"
DOI: 10.15468/dl.ap92xy
title: Occurrence Download

description: A dataset containing 46954 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Herpetology Collection - Instituto Nacional de Pesquisas da Amazônia"
 ]
}

 The dataset includes 46954 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000596-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.98xmpa
title: Occurrence Download

description: A dataset containing 55247 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aedes aegypti (Linnaeus, 1762)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 55247 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000597-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e219462
title: HUD-USPS Census Tract Crosswalk

description: One of the many challenges that social science researchers and practitioners face is the difficulty of relating data between census tracts which are re-delineated with each decennial census. While some methods of harmonizing or crosswalking data between census tracts exist, to provide additional avenues for merging these data, PD&R has released the HUD-USPS Census Tract Crosswalk Files. These unique files are derived from the USPS Vacancy Data which are regularly updated by the USPS which makes them uniquely positioned to describe human settlements patterns between census tract delineations. These data use the locations of ZIP+4 centroids, an extremely granular level of geography, the number of addresses of various types (residential, business, other, and total), and do not rely on ancillary data to map where population or households might be located.<br><br>There are two types of HUD-USPS Census Tract Crosswalk Files to use. The first are used to crosswalk data from 2010 through 2019 in 2010 census tracts to 2020 census tracts. The second are used to crosswalk data from 2020 through 2023 in 2020 census tracts to 2010 census tracts. It is important to note that the relationship between the two types of crosswalk files is not perfectly inverse. That is to say, the 2010 to 2020 census tract crosswalk files cannot be used to crosswalk data from 2020 to 2010 census tracts and the inverse cannot be used, either.<br><br>In addition to the files, this collection also includes screenshots of the documentation and FAQ pages on HUD's distribution site.<br><br>