cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/x0mtr-kb003
title: JV918 Legionella thyA ΔdotB

description: Legionella thyA ΔdotB. Lacks dotB ATPase.
description: <strong>Tilt Series Date:</strong> 2017-08-08</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: 2°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 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 sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal at F30, Caltech.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and 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. This time cell density was ~2.6.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for this strain at OD~2.9. 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://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-08-08-84/rawdata/</p>20170808_JV918b0087.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-08-08-84/rawdata/20170808_JV918b0087.mrc"
        > <i class="download icon"></i> Download </a></p>

        20170808_JV918b0087_part61_5.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-08-08-84/3dimage_87663/20170808_JV918b0087_part61_5.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.bpveba
title: Occurrence Download

description: A dataset containing 738 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Brienomyrus longianalis, Brycinus brevis, Brycinus carmesinus, Brycinus derhami, Brycinus grandisquamis, Brycinus leuciscus, Brycinus longipinnis, Brycinus luteus, Brycinus macrolepidotus, Brycinus poptae, Brycinus rhodopleura, Bryconaethiops boulengeri, Bryconaethiops macrops, Bryconaethiops microstoma, Bryconaethiops quinquesquamae, Bryconalestes derhami, Bryconalestes longipinnis, Bryconalestes tholloni, Buccochromis heterotaenia, Buccochromis lepturus, Buccochromis nototaenia, Buccochromis rhoadesii, Buccochromis spectabilis, Butis butis, Caecobarbus geertsii, Caffrogobius agulhensis, Callochromis macrops, Callochromis melanostigma, Callochromis pleurospilus, Callopanchax monroviae, Callopanchax occidentalis, Callopanchax toddi, Campylomormyrus alces, Campylomormyrus bredoi, Campylomormyrus cassaicus, Campylomormyrus christyi, Campylomormyrus curvirostris, Campylomormyrus elephas, Campylomormyrus luapulaensis, Campylomormyrus mirus, Campylomormyrus numenius, Campylomormyrus orycteropus, Campylomormyrus phantasticus, Campylomormyrus rhynchophorus, Campylomormyrus tamandua, Campylomormyrus tshokwe, Caprichromis liemi, Caprichromis orthognathus, Caranx sexfasciatus, Carasobarbus fritschii, Carasobarbus harterti, Carasobarbus moulouyensis, Carassius auratus, Carcharhinus leucas, Cardiopharynx schoutedeni, Carlarius latiscutatus, Carlarius parkii, Champsochromis caeruleus, Champsochromis spilorhynchus, Channa maculata, Channallabes alvarezi, Channallabes apus, Channallabes longicaudatus, Channallabes ogooensis, Channallabes sanghaensis, Channallabes teugelsi, Chanos chanos, Cheilochromis euchilus, Chelaethiops bibie, Chelaethiops congicus, Chelaethiops elongatus, Chelaethiops minutus, Chelaethiops rukwaensis, Chelidonichthys kumu, Chelon auratus, Chelon labrosus, Chelon melinopterus, Planiliza melinopterus, Chelon planiceps, Chelon ramada, Chelon saliens, Chelonodontops patoca, Chetia brevicauda, Chetia brevis, Chetia flaviventris, Chetia gracilis, Chetia mola, Chetia welwitschi, Chilochromis duponti, Chiloglanis angolensis, Chiloglanis anoterus, Chiloglanis asymetricaudalis, Chiloglanis batesii, Chiloglanis benuensis, Chiloglanis bifurcus, Chiloglanis brevibarbis, Chiloglanis camarabounyi, Chiloglanis cameronensis)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-16.8295 11.8376,-16.8618 11.7189,-16.8618 11.0599,-7.8618 11.0599,-7.8618 20.0599,-16.8618 20.0599,-16.8618 19.0648,-16.6653 18.7702,-16.5447 17.7591,-16.8618 16.9131,-16.8618 11.8636,-16.8295 11.8376))"
 ]
}

 The dataset includes 738 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006388-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16939443
title: meniscanData/KneeMRI-Meniscus-Dataset: MRI Meniscus Tear Dataset v1.0.0

description: This release contains the first public dataset for the task of automated recognition of meniscus tears in the knee joint based on MRI images.The source data were collected from patients between 2022 and 2024 at the National Scientific Center of Traumatology and Orthopedics named after Academician N.D. Batpenov (Astana, Kazakhstan).

Dataset characteristics:





Source file format: DICOM




Number of patients: 2,242




Age: 11 to 75 years




MRI scanners used: 1.5 T and 3.0 T from various manufacturers



Data classes:





0 — images without meniscus tear




1 — images with confirmed meniscus tear



Annotation:





Manually selected and annotated: 4,262 images




After expert verification: 2,000 images (1,000 without meniscus tear; 1,000 with confirmed meniscus tear)




Total number of objects (annotated menisci): 7,990



Clinical features:





The dataset includes only the horizontal tear type



Formats and data preparation:





Images exported to PNG using Weasis




Only slices visualizing the menisci were selected for analysis




MRI modes used: T1, T2, PD




Sequences used: SE, TSE, FSE, FatSat, FS




Main projections: coronal and sagittal



Link to the articlehttps://doi.org/10.3390/computers14080333

How to citeWhen using this dataset, please cite:





Dataset DOI: https://doi.org/10.5281/zenodo.16939444




Article DOI: https://doi.org/10.3390/computers14080333
DOI: 10.5281/zenodo.16939444
title: meniscanData/KneeMRI-Meniscus-Dataset: MRI Meniscus Tear Dataset v1.0.0

description: This release contains the first public dataset for the task of automated recognition of meniscus tears in the knee joint based on MRI images.The source data were collected from patients between 2022 and 2024 at the National Scientific Center of Traumatology and Orthopedics named after Academician N.D. Batpenov (Astana, Kazakhstan).

Dataset characteristics:





Source file format: DICOM




Number of patients: 2,242




Age: 11 to 75 years




MRI scanners used: 1.5 T and 3.0 T from various manufacturers



Data classes:





0 — images without meniscus tear




1 — images with confirmed meniscus tear



Annotation:





Manually selected and annotated: 4,262 images




After expert verification: 2,000 images (1,000 without meniscus tear; 1,000 with confirmed meniscus tear)




Total number of objects (annotated menisci): 7,990



Clinical features:





The dataset includes only the horizontal tear type



Formats and data preparation:





Images exported to PNG using Weasis




Only slices visualizing the menisci were selected for analysis




MRI modes used: T1, T2, PD




Sequences used: SE, TSE, FSE, FatSat, FS




Main projections: coronal and sagittal



Link to the articlehttps://doi.org/10.3390/computers14080333

How to citeWhen using this dataset, please cite:





Dataset DOI: https://doi.org/10.5281/zenodo.16939444




Article DOI: https://doi.org/10.3390/computers14080333
DOI: 10.15468/dl.qcx7av
title: Occurrence Download

description: A dataset containing 33901 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Holosteum umbellatum"
 ]
}

 The dataset includes 33901 records from 542 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006387-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/hwbs2-mqa87
title: H_pylori_dFliO_GC

description: These are fast tilt series taken by Georges Chreifi on the Krios for dFliO mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-10-25</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: 130.0 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> I received these cells from Carrie Schaffer from the university of Kentucky. These are wild . . type cells but they don't express complete FliP protein. Therefore, they don't assemble full . . flagella. We knocked out FliO protein of the flagellar motor to study the early assembly states . of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . . The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</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/mka2019-10-25-69/rawdata/</p>Hpylori_FliO_071_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-25-69/rawdata/Hpylori_FliO_071_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliO_071_af_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/mka2019-10-25-69/3dimage_107371/Hpylori_FliO_071_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/0vqy1-jd673
title: H-pylori_dFliM_GC

description: These are fast tilt series taken by Georges Chreifi on the Krios for dFliM mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-10-28</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: 130.0 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> I received these cells from Carrie Schaffer from the university of Kentucky. These are wild type cells but they . don't express complete FliP protein. Therefore, they don't assemble full flagella. We knocked out FliM protein . of the flagellar motor to study the early assembly states of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</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/mka2019-10-28-88/rawdata/</p>Hpylori_FliM_090_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-28-88/rawdata/Hpylori_FliM_090_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliM_090_af_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/mka2019-10-28-88/3dimage_107854/Hpylori_FliM_090_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/seezt-y0a39
title: Vibrio cholerae SAD2090

description: Vibrio, T4P, competence pilus
description: <strong>Tilt Series Date:</strong> 2020-09-09</p>
<strong>Data Taken By:</strong> Stefan Kreida</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> SAD2090</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -8.7 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> Strain from Ankur B Dalia, ankdalia@indiana.edu, PhD, Assistant Professor, Indiana University. . Cell growth & preparation, data collection and frame alignment by Stefan Kreida.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 100 uL O/N preculture used to inoculate 3 mL LB, 20 mM MgSO4, 10 mM CaCl2, 100 uM IPTG. . Cells were grown for 7 h (30C) on 170 rpm. 100 uL culture was then spun down at 5,000 x g (5') . and resuspended in 100 uL aquarium salt (Instant Ocean), 7 g/L. </p>
<strong>Sample Preparation:</strong> BSA/10 nm gold suspension: 1 mL 10 nm gold suspension mixed with 0.25 mL 5% BSA, spun . at 14,000 rpm (10'). Supernatant removed so that 35 uL remained, which was used to . resuspend the gold particles. 30 uL cells mixed with 5 uL gold suspension. 3 uL sample . applied in Vitrobot at 100% humidity. Grid: Quantifoil R2/2, Cu NH2, LotID 186865.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/skv2020-09-09-9/rawdata/</p>G12_SAD2090_TS18_ali.mrc,  Tilt Series (Pixel Size 0.33 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/skv2020-09-09-9/rawdata/G12_SAD2090_TS18_ali.mrc"
        > <i class="download icon"></i> Download </a></p>

        G12_SAD2090_TS18_ali_part61_9.rec,  Reconstruction (Pixel Size 1.32 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/zzzyg-a0m83
title: H-pylori_dFliM_GC

description: These are fast tilt series taken by Georges Chreifi on the Krios for dFliM mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-10-28</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: 130.0 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> I received these cells from Carrie Schaffer from the university of Kentucky. These are wild type cells but they . don't express complete FliP protein. Therefore, they don't assemble full flagella. We knocked out FliM protein . of the flagellar motor to study the early assembly states of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</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/mka2019-10-28-194/rawdata/</p>Hpylori_FliM_196_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-28-194/rawdata/Hpylori_FliM_196_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliM_196_af_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/mka2019-10-28-194/3dimage_108040/Hpylori_FliM_196_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/4mxrk-z9m56
title: H-pylori_dFliM_GC

description: These are fast tilt series taken by Georges Chreifi on the Krios for dFliM mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-10-28</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: 130.0 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> I received these cells from Carrie Schaffer from the university of Kentucky. These are wild type cells but they . don't express complete FliP protein. Therefore, they don't assemble full flagella. We knocked out FliM protein . of the flagellar motor to study the early assembly states of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</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/mka2019-10-28-47/rawdata/</p>Hpylori_FliM_049_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.9 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliM_049_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>