cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1001157.10fu
title: SH1001157.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1001158.10fu
title: SH1001158.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1001159.10fu
title: SH1001159.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1001160.10fu
title: SH1001160.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1001161.10fu
title: SH1001161.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1001162.10fu
title: SH1001162.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5281/zenodo.10038644
title: Ocean thermohaline clusters

description: This repository has the data sets containing temperature and salinity centroids, in addition to the location of the thermohaline, temperature and salinity clusters described in a scientific publication. The data set has the position of centroids of 2 to 50 clusters of Conservative Temperature, Absolute Salinity and Thermohaline, which allows delimiting coherent thermohaline structures in the global ocean at different spatial scales. The repository also contains demo notebooks of the use of these clusters and the procedures described in the manuscript.

If you use this repository, please include a reference to the following:

Romero, E., Portela, E., Tenorio-Fernandez, L., and Sánchez-Velasco, L.: Detection of coherent thermohaline structures over the global ocean using clustering. Deep Sea Research Part I: Oceanographic Research Papers, 209:104344, ISSN 09670637. doi: 10.1016/j.dsr.2024.104344. 2024.
DOI: 10.5281/zenodo.10038645
title: Ocean thermohaline clusters

description: This dataset contains the temperature and salinity centroids, in addition to the location of the thermohaline clusters described in a scientific publication that is currently under review. The data set has the position of centroids of 2 to 50 clusters of Conservative Temperature, Absolute Salinity and Thermohaline, which allows delimiting coherent thermohaline structures in the global ocean at different spatial scales. It also contains a Python implementation of Euclidean distance for using centroid datasets.
DOI: 10.5281/zenodo.11148337
title: Ocean thermohaline clusters

description: This repository has the data sets containing temperature and salinity centroids, in addition to the location of the thermohaline, temperature and salinity clusters described in a scientific publication. The data set has the position of centroids of 2 to 50 clusters of Conservative Temperature, Absolute Salinity and Thermohaline, which allows delimiting coherent thermohaline structures in the global ocean at different spatial scales. The repository also contains demo notebooks of the use of these clusters and the procedures described in the manuscript.
DOI: 10.5281/zenodo.12176247
title: Ocean thermohaline clusters

description: This repository has the data sets containing temperature and salinity centroids, in addition to the location of the thermohaline, temperature and salinity clusters described in a scientific publication. The data set has the position of centroids of 2 to 50 clusters of Conservative Temperature, Absolute Salinity and Thermohaline, which allows delimiting coherent thermohaline structures in the global ocean at different spatial scales. The repository also contains demo notebooks of the use of these clusters and the procedures described in the manuscript.

If you use this repository, please include a reference to the following:

Romero, E., Portela, E., Tenorio-Fernandez, L., and Sánchez-Velasco, L.: Detection of coherent thermohaline structures over the global ocean using clustering. Deep Sea Research Part I: Oceanographic Research Papers, 209:104344, ISSN 09670637. doi: 10.1016/j.dsr.2024.104344. 2024.
DOI: 10.22003/xfel.eu-data-900405-00
title: SASE3 Photon Beam Measurements
DOI: 10.22003/xfel.eu-data-006640-00
title: 1s3p RXES and Scattering to Probe the Excited State Dynamics of High Spin Fe(II) Polypyridine Complexes
DOI: 10.22003/xfel.eu-data-008376-00
title: Microbial rhodopsins at EuXFEL (retrieved from 5760)
DOI: 10.15468/dl.m28mhf
title: Occurrence Download

description: A dataset containing 49045 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "Geometry POLYGON((-104.45035 25.51188,-103.16442 25.51188,-103.16442 26.90392,-104.45035 26.90392,-104.45035 25.51188))",
 "OccurrenceStatus is Present",
 "StateProvince is Durango"
 ]
}

 The dataset includes 49045 records from 221 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109883-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21234/8v5d-rn16
title: Observation of high-energy neutrinos from the galactic plane

description: This data release accompanies results submitted to Science describing the observation of neutrinos from the galactic plane.
DOI: 10.6084/m9.figshare.3761562.v2618
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.5281/zenodo.8048802
title: anas_georgica_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.8048801
title: anas_georgica_zanfona_1.fasta.gz

description: .
DOI: 10.26093/cds/vizier.18980150
title: High-res. MIKE obs. of metal-poor stars

description: VizieR online Data Catalogue associated with article published in journal Astronomical Journal (AAS) with title 'The r-process alliance: first Magellan/MIKE release from the Southern search for r-process-enhanced stars.' (bibcode: 2020ApJ...898..150E)
DOI: 10.26093/cds/vizier.18990015
title: Parameters for the 58 {tau}HI(v) sightlines

description: VizieR online Data Catalogue associated with article published in journal Astronomical Journal (AAS) with title 'Extracting the Cold Neutral Medium from HI Emission with Deep Learning: Implications for Galactic Foregrounds at High Latitude' (bibcode: 2020ApJ...899...15M)
DOI: 10.26093/cds/vizier.19000004
title: Abundances and ages of stars in the Milky Way bulge

description: VizieR online Data Catalogue associated with article published in journal Astronomical Journal (AAS) with title 'The Age Distribution of Stars in the Milky Way Bulge.' (bibcode: 2020ApJ...900....4S)
DOI: 10.6084/m9.figshare.23535606
title: Untitled Item

description: This is an R data package. It provides the source data for a portion of the figures in the article <br> Buelow DR, Bhatnagar B, Orwick SJ, Jeon JY, Eisenmann ED, Stromatt JC, Pabla NS, Blachly JS, Baker SD, Blaser BW. BMX kinase mediates gilteritinib resistance in FLT3-mutated AML through microenvironmental factors. Blood Adv. 2022 Sep 13;6(17):5049-5060. doi: 10.1182/bloodadvances.2022007952. PMID: 35797240; PMCID: PMC9631628. <br> It is meant to be used with the companion analysis project which can be found at https://github.com/blaserlab/flt3_aml_bakerlab. <br> Instructions for installation and use of the data package can be found on the github site. All data objects are docuemented internally with standard R help manuals.
DOI: 10.6084/m9.figshare.20231931
title: roadkill_references

description: *.txt file with the references of the roadkill data collected for the paper [paper name].
DOI: 10.7303/syn51622714
title: Charney et al 2023 - Living Brain Project
DOI: 10.22002/b1wqa-rrt12
title: M. xanthus PilQ delete AA25-300

description: Grid box YWC126SA6808: delta-pilQ_AA25~300
description: <strong>Tilt Series Date:</strong> 2015-04-23</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</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: -6.0 μm,  magnification: 27500x. </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 form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 2 days in 220 rpm shaking CTT medium at 30 degrees without antibiotics. OD600=0.8</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-04-23-44</p>20150423_YWC126_10046.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-04-23-44/rawdata/20150423_YWC126_10046.mrc"
        > <i class="download icon"></i> Download </a></p>

        20150423_YWC126_10046_full.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-04-23-44/3dimage_54806/20150423_YWC126_10046_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/3j5pv-nzj59
title: PAOI delta aer2 pJN105-aer2

description: Pseudomonas aeruginosa strain PAOI delta aer2 pJN105-aer2
description: <strong>Tilt Series Date:</strong> 2015-02-12</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: 10.0 μm,  magnification: 34000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Batchruntomo</p>
<strong>Collaborators and Roles:</strong> Kylie Watts (Loma Linda)</p>
<strong>Purification / Growth Conditions / Treatment:</strong> induced pJN105-aer2, use 0.5% L-arabinoseStreak on LB plates and incubate overnight at 37°CInoculate 5 mL MOPS Minimal Media Limited Nitrogen (+ gentamicin for plasmid) from plate and grow at 30°C for ~24 hours</p>
description: Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-02-12-28</p>Pseudoaerplusinduced0031.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-02-12-28/rawdata/Pseudoaerplusinduced0031.mrc"
        > <i class="download icon"></i> Download </a></p>

        Pseudoaerplusinduced0031.rec,  Reconstruction (Pixel Size 1.28 nm), 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-02-12-28/3dimage_51874/Pseudoaerplusinduced0031.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/n9h5p-55t23
title: V. cholerae RT4236 (stationary)

description: Classical strain with ctxA deletion.Cell harbors pMT5 plasmid (inducible toxT).
description: <strong>Tilt Series Date:</strong> 2015-05-11</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O395-N1</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: -6.0 μm,  magnification: 27500x. </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 Ronald K. Taylor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Overnight cultures of Vibrio cholerae O395 NI pMT5 grown in LB pH 6.5, 1 mM IPTG and 100 ug/mL ampicilin</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 finder.</p>
description: Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-05-11-34</p>20150511_AK07_10034.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-05-11-34/rawdata/20150511_AK07_10034.mrc"
        > <i class="download icon"></i> Download </a></p>

        20150511_AK07_10034_full.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-05-11-34/3dimage_56424/20150511_AK07_10034_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/41vnk-qx639
title: JV5443

description: JV5443 Legionella (Super-deletion+CDHFG), no Thy
description: <strong>Tilt Series Date:</strong> 2016-08-09</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.50°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</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 sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal at Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate and cysteine hydrochloride  (no thymidine). Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV5443 strain at OD~3.2. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-09-75</p>JV5443a0042.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-09-75/rawdata/JV5443a0042.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV5443a0042_part81_5.rec,  Reconstruction (Pixel Size 1.68 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-09-75/3dimage_77722/JV5443a0042_part81_5.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/k5a0q-k8s36
title: LBculture_wt

description: This is a LB culture of wt from a flask grown into stationary phase. The purpose was to to check that there are no nanowires  and nothing was seen in sem, and when we do cryo-em to ensure we see flagellum. This would ensure that flagellum can't be seen in sem. But we did see long wires in sem. Sahand opined that is because we grew them into stationary phase. I imaged these to capture nanowires since they were present in sem
description: <strong>Tilt Series Date:</strong> 2015-07-25</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2.0°, constant angular increment, dosage: 150.0 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> Moh and Sahand</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Manual blotting Cu side glow discharged. Sample was put on opposite side and blotted. Similar to vitrobot</p>
description: Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-07-25-15</p>lbculture_nanowirepresent_atlas10014.mrc,  Tilt Series (Pixel Size 0.48 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-07-25-15/rawdata/lbculture_nanowirepresent_atlas10014.mrc"
        > <i class="download icon"></i> Download </a></p>

        lbculture_nanowirepresent_atlas10014_full.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-07-25-15/3dimage_59518/lbculture_nanowirepresent_atlas10014_full.rec"
        > <i class="download icon"></i> Download </a></p>