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

description: A dataset containing 1199 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lagopus muta",
 "Year is 2000",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 1199 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020106-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h8rhgd
title: Occurrence Download

description: A dataset containing 77 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Platyplectrurus madurensis"
 ]
}

 The dataset includes 77 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020107-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18299019
title: The C and N contents of bulk soil and aggregates
DOI: 10.5281/zenodo.18299018
title: The C and N contents of bulk soil and aggregates
DOI: 10.15468/dl.74txy7
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Carex arenaria, Carex arenaria, Carex arenaria, Carex arenaria, Carex arenaria, Carex arenaria, Carex arenaria, Carex arenaria, Carex arenaria)",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "Year is greater than or equal to 2010",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "CoordinateUncertaintyInMeters is less than or equal to 50",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020109-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h2k6fr
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Apatania sinensis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 43 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020110-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zauz9t
title: Occurrence Download

description: A dataset containing 111680 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alopecurus myosuroides"
 ]
}

 The dataset includes 111680 records from 1357 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020024-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/73xch-f5a05
title: BacillusSubtilis_328_4hr

description: Bacillus subtitles strain 328 overexpressing ymdB.
description: <strong>Tilt Series Date:</strong> 2020-02-26</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> AB328, ΔponA ΔymdB amyE::ymdB Δhag</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Samples were prepared with Ritesh and Amit from Ilan Rosenshine and Sigal ben Yehuda labs at . the Hebrew university. See tomograms mka2020-02-08-x.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Samples were prepared as mentioned in Bacillus subtitles tomograms taken on 8th of February . 2020.</p>
<strong>Sample Preparation:</strong> Samples were prepared as mentioned in Bacillus subtitles tomograms taken on 8th of February . 2020. See tomograms mka2020-02-08-x.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-26-47/rawdata/</p>Bsubtilis_328_028.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-26-47/rawdata/Bsubtilis_328_028.mrc"
        > <i class="download icon"></i> Download </a></p>

        Bsubtilis_328_028_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-26-47/3dimage_111823/Bsubtilis_328_028_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/yvkym-wve47
title: Hpylori_dFliF_FISE

description: These are H_pylori cells that are lacking FliP protein. In these cells, FliF protein was knocked out  .  to examine its relation to the hat-like complex.
description: <strong>Tilt Series Date:</strong> 2020-10-08</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The cells were prepared and sent by Carrie Schaffer from the university of Kentucky. The cells were grown at 37C with 5% CO2 on sheep blood agar plates for 2 days from a -80C. No growth was seen . on the plates after 24 hr therefore the plates were kept in the . incubator for another 24Hr.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100%  humidity. Cu grids. 10 nm . gold</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-449/rawdata/</p>Hpylori_DFliF_FISE_454.mrc,  Tilt Series (Pixel Size 0.452 nm), 1.9 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_454_full.rec,  Reconstruction (Pixel Size 1.808 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.7910/dvn/nfed5c
title: Replication Data for: Substitutes for Rule of Law? How BITs Deepen but Do Not Broaden U.S. Investment in Developing Countries

description: Replication for Yang & Bhandari (2025): Substitutes for Rule of Law? How BITs Deepen but Do Not Broaden U.S. Investment in Developing Countries
DOI: 10.22002/yswwj-kqb41
title: JV9082_Janelia42k

description: DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2018-08-29</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: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </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. Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV9082 strain (2x concentrated culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 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://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-34/rawdata/</p>JV9082_201808290062.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        JV9082_201808290062_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/r6ppc-e1644
title: JV9082_Janelia42k

description: DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2018-08-29</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: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </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. Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV9082 strain (2x concentrated culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 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://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-130/rawdata/</p>JV9082_201808290153.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        JV9082_201808290153_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.kstgsp
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Eichhornia crassipes",
 "Year 1965-1980"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048647-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/yc9nd-e6k93
title: Ecoli_EPEC_8612

description: These are E coli cells (EPEC 8612) obtained from Ritesh (Ilan Rosenshine lab at the Hebrew  .  university). The idea is to image bacterial nanotubes in these cells.
description: <strong>Tilt Series Date:</strong> 2020-02-09</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 8612, EPEC Δrof1-escLΔrof3-mpcΔescN-espFΔflhBAΔfliOPQRΔminCD</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> None</p>
<strong>Collaborators and Roles:</strong> These cells were prepared with Ritesh in Ilan Rosenshine lab at the Hebrew University.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The cells were incubated on grids on agar plates (DMEM agar plates for three hours) and then . on starvation medium agar plate for 1 hour Then washed with PBS and blotted and then plunge . frozen. Yuxi helped in sample preparation and data collection</p>
<strong>Sample Preparation:</strong> The cells were incubated on grids on agar plates (DMEM agar plates for three hours) and then . on starvation medium agar plate for 1 hour</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-09-8/rawdata/</p>EPEC_8612_tilt51.mrc,  Tilt Series (Pixel Size 0.449 nm), 576.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        EPEC_8612_tilt51.mrc.mdoc,  10.3 kB  
        
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DOI: 10.22002/rmgwc-wrs92
title: JV9082_K3_janelia

description: JV9082:DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2019-12-02</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: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 90.0 eV/Å²,  defocus: -2.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> SerialEM</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.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Data collected at Janelia Krios (K3 camera). Mag: 26000, pixel size: 2.61A. Defocus range -2 to -4 um.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-02-17/rawdata/</p>9082_Box1_No1_S124.mrc,  Tilt Series (Pixel Size 0.261 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        9082_Box1_No1_S124_full.rec,  Reconstruction (Pixel Size 1.044 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/a308a-kz778
title: P_aeruginosa_PA14_DfliF_Krios

description: Raw data files of P_aeruginosa_PA14_DfliF_Krios
description: <strong>Tilt Series Date:</strong> 2018-09-29</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (50.0°, -50.0°), step: 2°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -9.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> RAPTOR</p>
<strong>Collaborators and Roles:</strong> I (mohammed) obtained the cells from Shannon Park (Dianne Newman lab). The cells are available in their library of Pseudomonas aeruginosa PA14.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I inoculated one colony from an LB agar plate and grew the cells overnight in LB with 100 ug/ml of Gentamycin. Then I concentrated the cells three times and mixed them with gold nanoparticles and added 3 ul on to thick carbon R2 grids and blotted them and plunge froze them (force either 6 or 3, time either 3 or 2 seconds respectively, drain time 1 second).</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-09-29-18/rawdata/</p>Pseudomonas_DfliF12.mrc,  Tilt Series (Pixel Size 0.53 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Pseudomonas_DfliF12_full.rec,  Reconstruction (Pixel Size 2.12 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.4bhr78
title: Occurrence Download

description: A dataset containing 32137900 records in GBIF matching the query:
SELECT catalognumber, scientificname, publishingorgkey, institutioncode, datasetkey, gbifid, decimallatitude, decimallongitude, 
 recordedby, identifiedby, eventdate, kingdomkey, phylumkey, classkey, orderkey, familykey, genuskey, subgenuskey, specieskey,
 mediatype, v_associatedmedia
 FROM occurrence WHERE
 kingdomkey IN (2,3,4,5,7,8,0) 
 AND taxonomicstatus = 'ACCEPTED' //newly added 12Feb2025
 AND hascoordinate = 1
 AND hasgeospatialissues = 0
 AND specieskey IS NOT NULL
 AND occurrencestatus = 'PRESENT'
 -- AND (
 -- basisofrecord = 'HUMAN_OBSERVATION'
 -- OR basisofrecord = 'MACHINE_OBSERVATION'
 -- OR basisofrecord = 'OCCURRENCE'
 -- OR basisofrecord = 'LIVING_SPECIMEN'
 -- OR basisofrecord = 'MATERIAL_SAMPLE'
 -- )
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE') AND datasetkey NOT IN ('040c5662-da76-4782-a48e-cdea1892d14c') 

 The dataset's 32137900 records were derived from 8849 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011502-250415084134356/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.29105291
title: Applying borderline methods for setting standards in Objective Structured Clinical Examination: the first case in undergraduate medical program in Vietnam

description: <b>Abstract</b><b>Introduction:</b> Many medical schools in Vietnam have frequently used the arbitrary 50% score of checklist as passing scores in objective structured clinical examination (OSCE). As part of the competency-based education, we apply the borderline methods in this study to determine OSCE passing scores and to demonstrate whether cut-off scores of borderline methods significantly differ from the arbitrary 50% score.<b>Methods: </b>This descriptive study applied the Borderline Group Method (BGM) and Borderline Regression Method (BRM) to determine OSCE passing scores. Our OSCE exam consists of five stations and was administered to 406 second-year medical students in 2023. At each station, an examiner rated a checklist score and a global score. We use pair t-tests for the comparison of passing scores between scores of 50%, borderline group mean, borderline group median, and BRM scores.<b>Results:</b> The passing scores calculated according to the mean of BGM and BRM at 5 stations were 68-86.5 and 69.3-86.3, respectively. There was a statistically significant difference in passing scores between the 50% score and the mean/median of BGM as well as BRM (p=0.000) by pair t-test. There was no significant difference in passing scores between the mean or median of BGM and BRM (p=0.307 and p = 0.921).<b>Conclusion: </b>The passing scores determined by borderline methods were significantly higher than the arbitrary 50% score of checklist. Borderline methods can be used as appropriate standard-setting methods for OSCE in second-year medical students and should be considered for implementation in OSCE examinations for subsequent-year medical students at our university.
DOI: 10.15468/dl.rg7n34
title: Occurrence Download

description: A dataset containing 2725 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 Ottochloa Dandy"
 ]
}

 The dataset includes 2725 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008908-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ncj4gj
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-127.71239 -23.00610,-25.28761 -23.00610,-25.28761 18.00610,-127.71239 18.00610,-127.71239 -23.00610))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Coccoloba obovata Kunth"
 ]
}

 The dataset's 2 records were derived from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008896-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nrs5vh
title: Occurrence Download

description: A dataset containing 955 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coccoloba obovata Kunth"
 ]
}

 The dataset includes 955 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008907-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/fre4tv
title: Promises as commitments [Dataset]