cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/70fpt-hx351
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/dga2019-12-02-65/rawdata/</p>9082_Box1_No1_S165.mrc,  Tilt Series (Pixel Size 0.261 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-02-65/rawdata/9082_Box1_No1_S165.mrc"
        > <i class="download icon"></i> Download </a></p>

        9082_Box1_No1_S165_full.rec,  Reconstruction (Pixel Size 1.044 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-02-65/3dimage_112609/9082_Box1_No1_S165_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/72kfg-9tj32
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/dga2018-08-29-50/rawdata/</p>JV9082_201808290070.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-50/rawdata/JV9082_201808290070.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_201808290070_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-50/3dimage_96422/JV9082_201808290070_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/n7tc0-rx350
title: Legionella IcmQ71::TevS 42C_On

description: Legionella IcmQ71::TevS 42C_On (HS004 E)
description: <strong>Tilt Series Date:</strong> 2019-05-31</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: (-51.0°, 51.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 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 Howard Shuman (University of Chicago). Data collected by Debnath Ghosal and Yuxi Liu.</p>
<strong>Sample Preparation:</strong> 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/dga2019-05-31-9/rawdata/</p>HS004E-area1-tomo0004.mrc,  Tilt Series (Pixel Size 0.26 nm), 996.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-31-9/rawdata/HS004E-area1-tomo0004.mrc"
        > <i class="download icon"></i> Download </a></p>

        HS004E-area1-tomo0004_part35_8.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-31-9/3dimage_103626/HS004E-area1-tomo0004_part35_8.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/zjxhp-dw354
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/dga2018-08-29-262/rawdata/</p>JV9082_20180901a0036.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-262/rawdata/JV9082_20180901a0036.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_20180901a0036_part37_2.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-262/3dimage_96939/JV9082_20180901a0036_part37_2.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.29493275
title: Case-Based Learning for Teaching Statistical Collaboration: Development, Application, and Evaluation

description: Case-based learning (CBL) is a highly effective approach in health professions education that remains underutilized in the field of statistics. To promote broader adoption, we have developed realistic cases designed to help learners practice critical thinking and devise appropriate solutions for complex scenarios. These cases, used in our graduate-level statistical collaboration course, incorporate social factors and real-world implications. The first case explores a newly graduated biostatistician navigating the challenges of meeting a client’s expectations. The second focuses on a junior biostatistician developing a statistical analysis plan for a client with limited statistical knowledge. The third case, inspired by the development of the American Statistical Association’s ethical guidelines, deliberates their need. Both training materials and fully developed cases are provided. We also discuss strategies for educators to create and facilitate similar cases. By engaging students in thoughtful consideration of these scenarios within a safe, structured environment, we encourage them to examine their assumptions and conclusions. This preparation equips them for real-world roles as consultants and team scientists. Additionally, student feedback from course evaluations and surveys indicates strong support for CBL, with the majority recommending its use in similar educational contexts.
DOI: 10.6084/m9.figshare.29493275.v2
title: Case-Based Learning for Teaching Statistical Collaboration: Development, Application, and Evaluation

description: Case-based learning (CBL) is a highly effective approach in health professions education that remains underutilized in the field of statistics. To promote broader adoption, we have developed realistic cases designed to help learners practice critical thinking and devise appropriate solutions for complex scenarios. These cases, used in our graduate-level statistical collaboration course, incorporate social factors and real-world implications. The first case explores a newly graduated biostatistician navigating the challenges of meeting a client’s expectations. The second focuses on a junior biostatistician developing a statistical analysis plan for a client with limited statistical knowledge. The third case, inspired by the development of the American Statistical Association’s ethical guidelines, deliberates their need. Both training materials and fully developed cases are provided. We also discuss strategies for educators to create and facilitate similar cases. By engaging students in thoughtful consideration of these scenarios within a safe, structured environment, we encourage them to examine their assumptions and conclusions. This preparation equips them for real-world roles as consultants and team scientists. Additionally, student feedback from course evaluations and surveys indicates strong support for CBL, with the majority recommending its use in similar educational contexts.
DOI: 10.6084/m9.figshare.29493275.v1
title: Case-Based Learning for Teaching Statistical Collaboration: Development, application, and evaluation

description: Case-based learning (CBL) is a highly effective approach in health professions education that remains underutilized in the field of statistics. To promote broader adoption, we have developed realistic cases designed to help learners practice critical thinking and devise appropriate solutions for complex scenarios. These cases, used in our graduate-level statistical collaboration course, incorporate social factors and real-world implications. The first case explores a newly graduated biostatistician navigating the challenges of meeting a client's expectations. The second focuses on a junior biostatistician developing a statistical analysis plan for a client with limited statistical knowledge. The third case, inspired by the development of the American Statistical Association's ethical guidelines, deliberates their need. Both training materials and fully developed cases are provided. We also discuss strategies for educators to create and facilitate similar cases. By engaging students in thoughtful consideration of these scenarios within a safe, structured environment, we encourage them to examine their assumptions and conclusions. This preparation equips them for real-world roles as consultants and team scientists. Additionally, student feedback from course evaluations and surveys indicates strong support for CBL, with the majority recommending its use in similar educational contexts.
DOI: 10.22002/1kf75-bp119
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/dga2019-12-02-21/rawdata/</p>9082_Box1_No1_S126.mrc,  Tilt Series (Pixel Size 0.261 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-02-21/rawdata/9082_Box1_No1_S126.mrc"
        > <i class="download icon"></i> Download </a></p>

        9082_Box1_No1_S126_full.rec,  Reconstruction (Pixel Size 1.044 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-02-21/3dimage_112492/9082_Box1_No1_S126_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.29546876
title: Doubly Adaptive Importance Sampling

description: We propose an adaptive importance sampling scheme for Gaussian approximations of intractable posteriors. Optimization-based approximations like variational inference can be too inaccurate while existing Monte Carlo methods can be too slow. Therefore, we propose a hybrid where, at each iteration, the Monte Carlo effective sample size can be guaranteed at a fixed computational cost by interpolating between natural-gradient variational inference and importance sampling. The amount of damping in the updates adapts to the posterior and guarantees the effective sample size. Gaussianity enables the use of Stein’s lemma to obtain gradient-based optimization in the highly damped variational inference regime and a reduction of Monte Carlo error for undamped adaptive importance sampling. The result is a generic, embarrassingly parallel and adaptive posterior approximation method. Numerical studies on simulated and real data show its competitiveness with other, less general methods. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.29546876.v1
title: Doubly Adaptive Importance Sampling

description: We propose an adaptive importance sampling scheme for Gaussian approximations of intractable posteriors. Optimization-based approximations like variational inference can be too inaccurate while existing Monte Carlo methods can be too slow. Therefore, we propose a hybrid where, at each iteration, the Monte Carlo effective sample size can be guaranteed at a fixed computational cost by interpolating between natural-gradient variational inference and importance sampling. The amount of damping in the updates adapts to the posterior and guarantees the effective sample size. Gaussianity enables the use of Stein’s lemma to obtain gradient-based optimization in the highly damped variational inference regime and a reduction of Monte Carlo error for undamped adaptive importance sampling. The result is a generic, embarrassingly parallel and adaptive posterior approximation method. Numerical studies on simulated and real data show its competitiveness with other, less general methods. Supplementary materials for this article are available online.
DOI: 10.22002/f9cxa-5re31
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/mka2020-02-26-84/rawdata/</p>Bsubtilis_328_084.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/mka2020-02-26-84/rawdata/Bsubtilis_328_084.mrc"
        > <i class="download icon"></i> Download </a></p>

        Bsubtilis_328_084_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/mka2020-02-26-84/3dimage_111896/Bsubtilis_328_084_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.34740/kaggle/dsv/12909223
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.vhctj5
title: Occurrence Download

description: A dataset containing 641 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tilia euchlora"
 ]
}

 The dataset includes 641 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007935-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/zdxtb-ty511
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/mka2020-10-08-259/rawdata/</p>Hpylori_DFliF_FISE_253.mrc,  Tilt Series (Pixel Size 0.452 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-259/rawdata/Hpylori_DFliF_FISE_253.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_253_full.rec,  Reconstruction (Pixel Size 1.808 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.6v3gkw
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Boana alemani"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007937-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.