cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/y7vmt-xg023
title: Wild type control

description: Raw data files of Wild type control
description: <strong>Tilt Series Date:</strong> 2009-08-01</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, PEACH</p>
<strong>Collaborators and Roles:</strong> Experiments were done by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponential phase NA1000 cells.</p>
<strong>Sample Preparation:</strong> 10 nm gold </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-08-01-16/rawdata/</p>09aug01a_noaddctl1_016.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
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DOI: 10.15468/dl.utzwuq
title: Occurrence Download

description: A dataset containing 1246726 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 PRINTF('%04d-%02d-%02d', "year", "month", "day") yearmonthday,
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, PRINTF('%04d-%02d-%02d', "year", "month", "day"))) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, PRINTF('%04d-%02d-%02d', "year", "month", "day"))) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, PRINTF('%04d-%02d-%02d', "year", "month", "day"))) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, PRINTF('%04d-%02d-%02d', "year", "month", "day"))) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, PRINTF('%04d-%02d-%02d', "year", "month", "day"))) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, PRINTF('%04d-%02d-%02d', "year", "month", "day"))) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.datasetkey = '7a3679ef-5582-4aaa-81f0-8c2545cafc81'
 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.occurrencestatus = 'PRESENT'
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL AND occurrence."month" IS NOT NULL AND occurrence."day" IS NOT NULL)
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-%02d', "year", "month", "day")

 The dataset's 1246726 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006468-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/2vdxh-hxc54
title: Hyphomonas session10 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-28</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-28-37/rawdata/</p>09mar28a_bx60c_038.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
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DOI: 10.22002/b48wv-w5e83
title: 09may15a_grid4_016_modified

description: Raw data files of 09may15a_grid4_016_modified
description: <strong>Tilt Series Date:</strong> 2009-05-15</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Sphingopyxis alaskensis</p>
<strong>Strain:</strong> DSM No. 13593</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.5°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: 12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Reconstructed by Wesley</p>
<strong>Purification / Growth Conditions / Treatment:</strong> DSM 545 shaking at 28 C</p>
<strong>Sample Preparation:</strong> 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2009-05-15-14/3dimage_5981/</p>09may15a_grid4_016_modified.rec,  Reconstruction (Pixel Size 1.924 nm), 234.1 MB  
        
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DOI: 10.22002/8n7zg-zvp69
title: Hyphomonas session8 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-06</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 140.0 eV/Å²,  defocus: -8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media...</p>
<strong>Sample Preparation:</strong> C-flat grid, 5nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-06-41/rawdata/</p>09mar06a_20d_041.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
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DOI: 10.22002/cq7mh-6me54
title: IST1 N-terminal

description: IST1 N-terminal
description: <strong>Tilt Series Date:</strong> 2009-11-11</p>
<strong>Data Taken By:</strong> Megan Dobro</p>
<strong>Species / Specimen:</strong> IST1N tubes</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 1.0 eV/Å²,  defocus: -3.5 μm,  magnification: 41000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
<strong>Collaborators and Roles:</strong> purified by John McCullough, University of Utah</p>
<strong>Purification / Growth Conditions / Treatment:</strong> dialysis step upon receiving protein</p>
<strong>Sample Preparation:</strong> Vitrobot, varying blot times and offset, 100% humidity, 22 C, 10 nm gold</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2009-11-11-19/rawdata/</p>09nov11b_Box380grid2_021.mrc,  Tilt Series (Pixel Size 0.51 nm), 520.1 MB  
        
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DOI: 10.15468/dl.xfkq9w
title: Occurrence Download

description: A dataset containing 213023 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lonchura punctulata",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 213023 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006456-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/bqdms-xf389
title: Acidovorax

description: Acidovorax grown in NB
description: <strong>Tilt Series Date:</strong> 2009-04-01</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acidovorax sp.</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 0.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
<strong>Collaborators and Roles:</strong> grown by Bill Hickey at UW-Madison; data collected and processed by Elitza Tocheva</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in NB.</p>
<strong>Sample Preparation:</strong> 20nm gold, 2s blot, -2 offset</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-04-01-18/rawdata/</p>09mar31a_v_019.mrc,  Tilt Series (Pixel Size 0.962 nm), 1.0 GB  
        
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DOI: 10.22002/yxyeb-b8s91
title: Agro C58 22C liq

description: Raw data files of Agro C58 22C liq
description: <strong>Tilt Series Date:</strong> 2014-08-05</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Agrobacterium tumefaciens</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> C58 from Pat Zambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 22C liquid</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-08-05-90/rawdata/</p>test0001.mrc,  Tilt Series (Pixel Size 0.5 nm), 3.4 GB  
        
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DOI: 10.5281/zenodo.16991953
title: THE FREELANCE ERA: TRANSFORMING TRADITIONAL HUMAN RESOURCE MANAGEMENT
DOI: 10.5281/zenodo.16991954
title: THE FREELANCE ERA: TRANSFORMING TRADITIONAL HUMAN RESOURCE MANAGEMENT
DOI: 10.22002/09ks5-c5f67
title: Hyphomonas session10 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-28</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-28-1/rawdata/</p>09mar28a_bx60c_001.mrc,  Tilt Series (Pixel Size 0.632 nm), 570.4 MB  
        
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DOI: 10.22002/z0xv8-5s941
title: Streptococcus pneumoniae

description: wild type, no capsule
description: <strong>Tilt Series Date:</strong> 2013-09-08</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Streptococcus pneumoniae</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Andrew Camili</p>
<strong>Purification / Growth Conditions / Treatment:</strong> wt</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-09-08-2/rawdata/</p>wt0002.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
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DOI: 10.22002/s0rn3-7ev38
title: Agro_C58_22C_liq

description: Raw data files of Agro_C58_22C_liq
description: <strong>Tilt Series Date:</strong> 2014-09-05</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Agrobacterium tumefaciens</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> strain from Pat Zambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 22C liquid</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-09-05-32/rawdata/</p>c58_22_liq20005.mrc,  Tilt Series (Pixel Size 0.5 nm), 3.4 GB  
        
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DOI: 10.48425/4hwlfrdc
title: S_vegetation_vascular_plant_abundance

description: Abundance of vascular plants measured using point intercept frequency.

The datasets contains point frequency data (which can be converted to biomass estimates) of the following functional groups and species:

* Salix polaris
* Bistorta vivipara
* Dryas octopetala
* Grasses
* Oxyria digyna
* Sedges and rushes
* Small forbs
 
The dataset includes three different types of files and all files (except the readme) are saved as ;-separated txt-files:
One data file per year (_YEAR.txt).
One coordinate file with coordinates of all sites included in the dataset (_coordinates.txt).
One auxiliary file with information about which sites are included in the dataset and when (_aux.txt).
 
The dataset is under embargo, with new datasets uploaded on December 31st, two years after being collected. Older versions of the dataset are publicly available for download.

Note that from 2021, the vegetation type previously called dryas heath is now named dryas ridge.

This version will be published 31.12.2027, and includes data from 2019-2025
DOI: 10.22002/0fnmz-f5m90
title: Alongum

description: Alongum_periplasmiclayers
description: <strong>Tilt Series Date:</strong> 2012-05-20</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acetonema longum</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-30.0°, 30.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> WesleyChen helped remove layers</p>
<strong>Purification / Growth Conditions / Treatment:</strong> sporulation media</p>
<strong>Sample Preparation:</strong> quantifoil grid R2/2, 20nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-87/rawdata/</p>AlongProtK0006.mrc,  Tilt Series (Pixel Size 0.95 nm), 677.3 MB  
        
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DOI: 10.22002/0kv9m-kx807
title: JT5 on cellulose

description: JT5
description: <strong>Tilt Series Date:</strong> 2014-07-22</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacteroidetes</p>
<strong>Strain:</strong> JT5-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Eric Matson</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown on cellulose</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-07-22-10/rawdata/</p>JT5_cel10001.mrc,  Tilt Series (Pixel Size 0.5 nm), 3.4 GB  
        
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DOI: 10.22002/cajhc-4rd67
title: Agrobacterium tumefaciens

description: Agrobacterium_VirB8-GFP_deltaVirB8
description: <strong>Tilt Series Date:</strong> 2013-05-07</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Agrobacterium tumefaciens</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> strain from PatZambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Titan_K2</p>
<strong>Sample Preparation:</strong> quantifoil grid R2/2, 20nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-05-07-46/rawdata/</p>VirB_deltaVirB0016.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.4 GB  
        
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DOI: 10.48512/xcv8513389
title: Pollen Dataset, Tahcabo, Yucatán, Mexico

description: Abstract of associated paper: Sinkholes contributed to persistent human inhabitation of the northern Yucatán peninsula of Mexico for more than two millennia. Building on previous work on the use of sinkholes central to the town of Tahcabo and elsewhere in the Maya area, this study presents pollen, soil carbon isotope, radiocarbon, and artifactual evidence from four geomorphic features. They include the perennially wet cenote situated in the town center and three dry sinkholes (rejolladas) located in the commonly held lands (ejido) of the town. These features demonstrate striking variability in multispecies engagements with and within sinkholes, especially over the past 500 years, amid colonialism and more recent political contexts. Climate and political dynamics are implicated in the observed variability in agricultural practices. Community-engaged research often embraces a focus on persistent places, which can inspire contemporary people to reconnect with the past and with ancestors in ways that promote action to address challenges, such as adaptation to climate and other environmental change. Our research addresses long histories of sinkhole use to demonstrate the outcomes of variable cultivation strategies, such as increased biodiversity within towns and places of refuge, or conversely, production intensity and accelerated soil erosion into and mixing of sinkhole sediments.
DOI: 10.15468/d4k8cg
title: Earthworm (Lumbricidae) field occurrences from Central Kazakhstan

description: The dataset includes primary data from field surveys of earthworms (Lumbricidae) in forest habitats in Central Kazakhstan.