cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/r82zr-f5266
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/dga2019-05-31-3/rawdata/</p>HS004E-area1-tomo0001.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/dga2019-05-31-3/rawdata/HS004E-area1-tomo0001.mrc"
        > <i class="download icon"></i> Download </a></p>

        HS004E-area1-tomo0001_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/dga2019-05-31-3/3dimage_103608/HS004E-area1-tomo0001_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.fh86ng
title: Occurrence Download

description: A dataset containing 2834 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Crocodylus acutus"
 ]
}

 The dataset includes 2834 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007204-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/3pvzm-6sk27
title: JV9082

description: DotF-GFP, defocus range -3 to 6
description: <strong>Tilt Series Date:</strong> 2019-12-05</p>
<strong>Data Taken By:</strong> Yuxi Liu</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°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -5.0 μm,  magnification: 33000x. </p>
<strong>Microscope:</strong> Janelia Titan</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 Joe Vogel lab</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Late exponential phase, early stationary phase</p>
<strong>Sample Preparation:</strong> 10nm gold, Quantifoil R2/2 copper mesh 200 Finder grid, Vitrobot 22 deg C, 100% humidity, blot . time 3 sec, blot force 6, drain 1 sec, wait 0 sec.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-12-05-56/rawdata/</p>9082_box1_No1_204.mrc,  Tilt Series (Pixel Size 0.2612 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-12-05-56/rawdata/9082_box1_No1_204.mrc"
        > <i class="download icon"></i> Download </a></p>

        9082_box1_No1_204_full.rec,  Reconstruction (Pixel Size 1.0448 nm), 516.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-12-05-56/3dimage_110164/9082_box1_No1_204_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.58053/mapbiomas/rdetdl
title: Deforestation statistics for special territories - AMACRO - MapBiomas Brazil Collection 10

description: Area data (hectares) of deforestation for AMACRO region from 1987 to 2024, based on MapBiomas Brazil Collection 10.
DOI: 10.22002/n6m6s-gfd10
title: JV9298

description: Legionella pneumophila JV9298 DotF-GFP DotB E191K
description: <strong>Tilt Series Date:</strong> 2020-04-23</p>
<strong>Data Taken By:</strong> Yuxi Liu</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°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -4.0 μm,  magnification: 33000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, tomo3d</p>
<strong>Collaborators and Roles:</strong> Sample preparation & data collection: Yuxi Liu Data processing: Phyllis Wang & Yuxi Liu</p>
<strong>Purification / Growth Conditions / Treatment:</strong> O.D. 2.5-3.0 in AYE</p>
<strong>Sample Preparation:</strong> Quantifoil R2/2 copper grid, 10nm gold, 100% humidity, 25deg C, 4uL of 2X concentrated cells Blotting: force 6, blot 3sec, wait 1sec</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-125/3dimage_123930/</p>JV9298_PD-1-3_494_SIRT_1k.mrc,  Reconstruction (Pixel Size 1.04 nm), 2.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-125/3dimage_123930/JV9298_PD-1-3_494_SIRT_1k.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9298_PD-1-3_494.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.7 GB  
        
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DOI: 10.15468/dl.3xtvm3
title: Occurrence Download

description: A dataset containing 19303 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Puma concolor"
 ]
}

 The dataset includes 19303 records from 332 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007202-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5255/ukda-sn-858021
title: Social Protection and The International Monetary Fund: Promise Versus Performance, 2021-2024

description: Countries in the Global South are currently facing momentous economic and social challenges, including major debt service problems. As in previous periods of global financial instability, a growing number of countries have turned to the International Monetary Fund (IMF) for financial assistance. The organization has a long track-record of advocating for extensive fiscal consolidation—commonly known as ‘austerity’—for its borrowers. However, in recent years, the IMF has announced major initiatives for ensuring that its loans support social spending, thus aiding countries in meeting their development targets and the Sustainable Development Goals. To assess this track record, we collected spending data on 21 loans signed in the 2020–2022 period, including from all their periodic reviews up to August 2023.

We find that austerity measures remain a core part of the organization’s mandated policies for its borrowers: 15 of the 21 countries studied here experience a decrease in fiscal space over the course of their IMF programs. Against this fiscal backdrop, social spending floors have failed to live up to their promise. There is no streamlined definition of these floors, thus rendering their application haphazard and inconsistent. But even on their own terms, these floors lack ambition: they often do not foresee trajectories of meaningful social spending increases over time, and, when they do, many of these gains are eaten up by soaring inflation. In addition, a third of social spending floors are not implemented—a much lower implementation rate from that for austerity conditions, which the IMF prioritizes. In several instances, where floors are implemented, they are not meaningfully exceeded, thus—in practice—acting as social spending ceilings.

The IMF’s lending programs are still heavily focused on austerity, and its strategy on social spending has not represented the sea-change that the organization advertised. At best, social spending floors act as damage control for the painful budget cuts: they are instruments of social amelioration, underpinned by principles of targeted assistance for highly disadvantaged groups. Alternative approaches rooted in principles of universalism can be employed to build up durable and resilient social protection systems.
DOI: 10.22002/52myv-39820
title: JV9298

description: Legionella pneumophila JV9298 DotF-GFP DotB E191K
description: <strong>Tilt Series Date:</strong> 2020-04-23</p>
<strong>Data Taken By:</strong> Yuxi Liu</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°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -4.0 μm,  magnification: 33000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, tomo3d</p>
<strong>Collaborators and Roles:</strong> Sample preparation & data collection: Yuxi Liu Data processing: Phyllis Wang & Yuxi Liu</p>
<strong>Purification / Growth Conditions / Treatment:</strong> O.D. 2.5-3.0 in AYE</p>
<strong>Sample Preparation:</strong> Quantifoil R2/2 copper grid, 10nm gold, 100% humidity, 25deg C, 4uL of 2X concentrated cells Blotting: force 6, blot 3sec, wait 1sec</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-277/3dimage_124216/</p>JV9298_PD-1-3_201_SIRT_1k.mrc,  Reconstruction (Pixel Size 1.04 nm), 2.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-277/3dimage_124216/JV9298_PD-1-3_201_SIRT_1k.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9298_PD-1-3_201.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.7 GB  
        
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DOI: 10.22002/z8ge8-rqs60
title: Legionella_JV9246

description: Legionella_JV9246: DotF-sfGFP fusion to the wild-type gene on the chromosome (thyA) and ΔdotO.
description: <strong>Tilt Series Date:</strong> 2019-05-28</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: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -4.0 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 by Debnath Ghosal and Yuxi Liu.</p>
<strong>Purification / Growth Conditions / Treatment:</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/dga2019-05-28-14/rawdata/</p>JV9246_area1_tomo0007.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-05-28-14/rawdata/JV9246_area1_tomo0007.mrc"
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        JV9246_area1_tomo0007_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.9dzmxd
title: Occurrence Download

description: A dataset containing 187075 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 187075 records from 238 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007122-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/vck1b-cqn59
title: JV9298

description: DotF-sfGFP DotB E191K
description: <strong>Tilt Series Date:</strong> 2019-10-14</p>
<strong>Data Taken By:</strong> Yuxi Liu</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°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -5.0 μm,  magnification: 33000x. </p>
<strong>Microscope:</strong> PNCC Krios 3</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 Joe Vogel</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Late exponential/Early stationary</p>
<strong>Sample Preparation:</strong> Quantifoil R2/2 copper. Vitrobot 22 deg C, 100% humidity, 4uL of 2X concentrated culture, blot force 6, blot time 3 sec, drain time 1 sec, wait time 0 sec.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-10-14-67/rawdata/</p>JV9298_105_A4.mrc,  Tilt Series (Pixel Size 0.1323 nm), 14.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-10-14-67/rawdata/JV9298_105_A4.mrc"
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        JV9298_105_A4_full.rec,  Reconstruction (Pixel Size 1.0584 nm), 737.3 MB  
        
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DOI: 10.22002/ddncf-aqf64
title: MEF cells - Septin2 knock down

description: Septin2 was knocked down using retroviral delivery of shRNA to study its role in Mitochondrial division. grid ID: DG4_grid4
description: <strong>Tilt Series Date:</strong> 2019-01-05</p>
<strong>Data Taken By:</strong> Shrawan kumar Mageswaran</p>
<strong>Species / Specimen:</strong> MEF cells</p>
<strong>Strain:</strong> </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: -8.0 μm,  magnification: 33000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD, tomo3D</p>
<strong>Collaborators and Roles:</strong> Chun-Shik from Chan lab helped design the shRNA against Septin2 and provided transduction protocol. Shrawan and Danielle Grotjahn created cell line. Danielle FIB-milled the cells and Shrawan performed ECT.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown on R2/2 quantifoil gold grids coated with 0.1 mg/mL fibronectin.</p>
<strong>Sample Preparation:</strong> Cells were treated with 10µM FCCP, plunge frozen and FIB-milled</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2019-01-05-8/rawdata/</p>TS1.mrc,  Tilt Series (Pixel Size 0.432 nm), 1.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2019-01-05-8/rawdata/TS1.mrc"
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        TS1_bin4_SIRT_rotx.rec,  Reconstruction (Pixel Size 0.0 nm), 890.9 MB  
        
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DOI: 10.22002/qacce-nf584
title: JV9298

description: Legionella pneumophila JV9298 DotF-GFP DotB E191K
description: <strong>Tilt Series Date:</strong> 2020-04-23</p>
<strong>Data Taken By:</strong> Yuxi Liu</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°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -4.0 μm,  magnification: 33000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, tomo3d</p>
<strong>Collaborators and Roles:</strong> Sample preparation & data collection: Yuxi Liu Data processing: Phyllis Wang & Yuxi Liu</p>
<strong>Purification / Growth Conditions / Treatment:</strong> O.D. 2.5-3.0 in AYE</p>
<strong>Sample Preparation:</strong> Quantifoil R2/2 copper grid, 10nm gold, 100% humidity, 25deg C, 4uL of 2X concentrated cells Blotting: force 6, blot 3sec, wait 1sec</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-04-23-261/3dimage_124190/</p>JV9298_PD-1-3_185_SIRT_1k.mrc,  Reconstruction (Pixel Size 1.04 nm), 2.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        JV9298_PD-1-3_185.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.7 GB  
        
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DOI: 10.6084/m9.figshare.29356876
title: Design-Based Causal Inference with Missing Outcomes: Missingness Mechanisms, Imputation-Assisted Randomization Tests, and Covariate Adjustment

description: Design-based causal inference, also known as randomization-based or finite-population causal inference, is one of the most widely used causal inference frameworks, largely due to the merit that its validity can be guaranteed by study design (e.g., randomized experiments) and does not require assuming specific outcome-generating distributions or super-population models. Despite its advantages, design-based causal inference can still suffer from other issues, among which outcome missingness is a prevalent and significant challenge. This work systematically studies the outcome missingness problem in design-based causal inference. First, we propose a general and flexible outcome missingness mechanism that can facilitate finite-population-exact randomization tests of no treatment effect. Second, under this general missingness mechanism, we propose a general framework called “imputation and re-imputation” for conducting randomization tests in design-based causal inference with missing outcomes. We prove that our framework can still ensure finite-population-exact Type-I error rate control even when the imputation model was misspecified or when unobserved covariates or interference exist in the missingness mechanism. Third, we extend our framework to conduct covariate adjustment in randomization tests and construct finite-population-valid confidence regions with missing outcomes. Our framework is evaluated via extensive simulation studies and applied to a large-scale randomized experiment. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.6084/m9.figshare.29356876.v1
title: Design-Based Causal Inference with Missing Outcomes: Missingness Mechanisms, Imputation-Assisted Randomization Tests, and Covariate Adjustment

description: Design-based causal inference, also known as randomization-based or finite-population causal inference, is one of the most widely used causal inference frameworks, largely due to the merit that its validity can be guaranteed by study design (e.g., randomized experiments) and does not require assuming specific outcome-generating distributions or super-population models. Despite its advantages, design-based causal inference can still suffer from other issues, among which outcome missingness is a prevalent and significant challenge. This work systematically studies the outcome missingness problem in design-based causal inference. First, we propose a general and flexible outcome missingness mechanism that can facilitate finite-population-exact randomization tests of no treatment effect. Second, under this general missingness mechanism, we propose a general framework called “imputation and re-imputation” for conducting randomization tests in design-based causal inference with missing outcomes. We prove that our framework can still ensure finite-population-exact Type-I error rate control even when the imputation model was misspecified or when unobserved covariates or interference exist in the missingness mechanism. Third, we extend our framework to conduct covariate adjustment in randomization tests and construct finite-population-valid confidence regions with missing outcomes. Our framework is evaluated via extensive simulation studies and applied to a large-scale randomized experiment. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.