cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/14edy-fca18
title: Salmonella typhimurium

description: Session notes: WT Salmonella minicell-producing strain Tilt series notes:  Tomogram notes: SIRT reconstruction
description: <strong>Tilt Series Date:</strong> 2011-03-24</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Salmonella typhimurium</p>
<strong>Strain:</strong> serovar Typhimurium str. LT2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-70.0°, 70.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-03-24-20/rawdata/</p>11mar24e_WTMini3hrs_041.st,  Tilt Series (Pixel Size 0.632 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        11mar24e_WTMini3hrs_041_SIRT.rec,  Reconstruction (Pixel Size 0.632 nm), 2.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/cykrn-4tp77
title: Campylobacter jejuni

description: Session notes: High magnification tomograms of whole WT Campylobacter cells. Tilt series notes: WT Campylobacter Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2011-02-16</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 5.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-02-16-50/rawdata/</p>11feb16a_WTCampy_152.mrc,  Tilt Series (Pixel Size 0.512 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-02-16-50/rawdata/11feb16a_WTCampy_152.mrc"
        > <i class="download icon"></i> Download </a></p>

        11feb16a_WTCampy_152_SIRT.rec,  Reconstruction (Pixel Size 0.512 nm), 171.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-02-16-50/3dimage_21461/11feb16a_WTCampy_152_SIRT.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.29974606
title: <b>Effects of Lifestyle and GLP-1RA based Interventions on Waist Circumference: A Systematic Review and Meta-Analysis</b>

description: This dataset and code package accompanies the systematic review and meta-analysis:<br><b>“Effects of Lifestyle and GLP-1RA Based Interventions on Waist Circumference: A Systematic Review and Meta-Analysis”</b> (INPLASY202580071).BackgroundVisceral adiposity, frequently indexed by waist circumference (WC), is a strong predictor of cardiometabolic risk. Lifestyle interventions (diet, exercise, diet+exercise) and glucagon-like peptide-1 receptor agonist therapies (GLP1RAs) are known to reduce body weight, but their comparative impact on WC has not been systematically synthesized.MethodsFollowing PRISMA guidelines, randomized controlled trials (RCTs) published between 2010–2025 were identified through PubMed, Embase, and Cochrane Library. A total of <b>36 RCTs (49 arms)</b> reporting visceral adipose tissue (VAT) outcomes were screened, with <b>21 RCTs (27 arms; n=2,839)</b> included in the primary analysis of WC change. Random-effects models were used to pool mean differences (MD) in WC; subgroup analyses and meta-regression examined baseline moderators (age, BMI, WC, body weight, type 2 diabetes prevalence). Prediction intervals (PIs) were calculated for pooled and category-level effects. Publication bias was evaluated via funnel plots and Egger’s regression.Results (summary)Overall, interventions significantly reduced WC (pooled MD −4.36 cm; 95% CI −4.97 to −3.74; PI −6.98 to −1.73). Subgroup analyses confirmed reductions with GLP1RAs, diet, and diet+exercise, while exercise alone was non-significant. Baseline BMI, WC, weight, and quadratic age significantly moderated the effect. Funnel plots suggested small-study effects.Contents of this repository<b>MasterDataset.xlsx</b> — tidy dataset combining baseline and intervention characteristics across 27 study arms, analysis-ready.<b>R scripts (00–06)</b> — reproducible code for primary, sensitivity, subgroup, and meta-regression analyses, forest plots, funnel plots, ROB2 templates, and prediction intervals.<b>Python script (05_correlation_python.py)</b> — scatter plot of WC vs. %VAT change (Pearson correlation).<b>README_Figshare.txt</b> — detailed instructions, package versions, and workflow.Software environmentR 4.4.3 (metafor ≥4.8-0, ggplot2, dplyr, cowplot, readxl)Python 3.11.9 (pandas, matplotlib 3.9.2, scipy)RegistrationProtocol registered with INPLASY: <b>INPLASY202580071</b> (DOI: 10.37766/inplasy2025.8.0071).
DOI: 10.6084/m9.figshare.29974606.v1
title: <b>Effects of Lifestyle and GLP-1RA based Interventions on Waist Circumference: A Systematic Review and Meta-Analysis</b>

description: This dataset and code package accompanies the systematic review and meta-analysis:<br><b>“Effects of Lifestyle and GLP-1RA Based Interventions on Waist Circumference: A Systematic Review and Meta-Analysis”</b> (INPLASY202580071).BackgroundVisceral adiposity, frequently indexed by waist circumference (WC), is a strong predictor of cardiometabolic risk. Lifestyle interventions (diet, exercise, diet+exercise) and glucagon-like peptide-1 receptor agonist therapies (GLP1RAs) are known to reduce body weight, but their comparative impact on WC has not been systematically synthesized.MethodsFollowing PRISMA guidelines, randomized controlled trials (RCTs) published between 2010–2025 were identified through PubMed, Embase, and Cochrane Library. A total of <b>36 RCTs (49 arms)</b> reporting visceral adipose tissue (VAT) outcomes were screened, with <b>21 RCTs (27 arms; n=2,839)</b> included in the primary analysis of WC change. Random-effects models were used to pool mean differences (MD) in WC; subgroup analyses and meta-regression examined baseline moderators (age, BMI, WC, body weight, type 2 diabetes prevalence). Prediction intervals (PIs) were calculated for pooled and category-level effects. Publication bias was evaluated via funnel plots and Egger’s regression.Results (summary)Overall, interventions significantly reduced WC (pooled MD −4.36 cm; 95% CI −4.97 to −3.74; PI −6.98 to −1.73). Subgroup analyses confirmed reductions with GLP1RAs, diet, and diet+exercise, while exercise alone was non-significant. Baseline BMI, WC, weight, and quadratic age significantly moderated the effect. Funnel plots suggested small-study effects.Contents of this repository<b>MasterDataset.xlsx</b> — tidy dataset combining baseline and intervention characteristics across 27 study arms, analysis-ready.<b>R scripts (00–06)</b> — reproducible code for primary, sensitivity, subgroup, and meta-regression analyses, forest plots, funnel plots, ROB2 templates, and prediction intervals.<b>Python script (05_correlation_python.py)</b> — scatter plot of WC vs. %VAT change (Pearson correlation).<b>README_Figshare.txt</b> — detailed instructions, package versions, and workflow.Software environmentR 4.4.3 (metafor ≥4.8-0, ggplot2, dplyr, cowplot, readxl)Python 3.11.9 (pandas, matplotlib 3.9.2, scipy)RegistrationProtocol registered with INPLASY: <b>INPLASY202580071</b> (DOI: 10.37766/inplasy2025.8.0071).
DOI: 10.22002/vcf44-mmk56
title: Campylobacter jejuni

description: Session notes: Campy motB mutant, filtered 0.28, 0.02 after binning 2x more (to ~5.5nm resolution) Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-01-13</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 15.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-01-13-30/rawdata/</p>12jan13a_motB_0003.st,  Tilt Series (Pixel Size 0.774 nm), 743.2 MB  
        
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        12jan13a_motB_0003.rec,  Reconstruction (Pixel Size 0.78 nm), 98.9 MB  
        
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DOI: 10.15468/dl.qkwp3m
title: Occurrence Download

description: A dataset containing 483 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paederia grandidieri"
 ]
}

 The dataset includes 483 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037852-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/6arqz-ced02
title: Campylobacter jejuni

description: Session notes: Medium magnification tomograms of whole FlgQ mutant Campylobacter cells. Tilt series notes: Nice horizontally-oriented cell Tomogram notes: Nice. One flagellum. Flagella:846,185,116 (FlgQ) Chemoreceptors:801,244,109 (Side view)
description: <strong>Tilt Series Date:</strong> 2010-08-29</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-59.0°, 64.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 15.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2010-08-29-2/rawdata/</p>10aug29b_Campy_FlgQ_005.st,  Tilt Series (Pixel Size 0.95 nm), 696.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        10aug29b_Campy_FlgQ_005.rec,  Reconstruction (Pixel Size 1.9 nm), 72.0 MB  
        
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DOI: 10.22002/y8gc2-as823
title: Salmonella typhimurium

description: Session notes: WT Salmonella minicells Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2011-08-01</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Salmonella typhimurium</p>
<strong>Strain:</strong> serovar Typhimurium str. LT2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: -1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor3</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-08-01-12/rawdata/</p>11aug01b_WT_0001.mrc,  Tilt Series (Pixel Size 0.632 nm), 726.8 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        11aug01b_WT_0001_bin1x_SIRT_trim.rec,  Reconstruction (Pixel Size 0.632 nm), 884.8 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/a211x-x8f56
title: Campylobacter jejuni

description: Session notes: Campylobacter cjj0996 cells, automatically reconstructed using SIRT, golds erased, binned 2x, filtered 0.28, 0.025 (to ~5.5nm resolution) Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-04-20</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 15.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-04-20-8/rawdata/</p>12apr20a_cjj0996_0012.st,  Tilt Series (Pixel Size 0.774 nm), 743.2 MB  
        
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        12apr20a_cjj0996_0012.rec,  Reconstruction (Pixel Size 1.56 nm), 10.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/c767s-t3a23
title: Salmonella typhimurium

description: Session notes: Salomella rabbit ears: 15min penicillin treatment with MgSO4 Tilt series notes: Seriously disrupted cell pole. Tomogram notes:  Pili:122,876,391 (Everywhere!)
description: <strong>Tilt Series Date:</strong> 2010-03-03</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Salmonella typhimurium</p>
<strong>Strain:</strong> serovar Typhimurium str. LT2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor3</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2010-03-03-2/rawdata/</p>10mar03b_rabbit_ears_gr4_003.mrc,  Tilt Series (Pixel Size 0.632 nm), 713.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        10mar03b_rabbit_ears_gr4_003_full.rec,  Reconstruction (Pixel Size 1.264 nm), 524.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.4cfh2d
title: Occurrence Download

description: A dataset containing 653 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Thunbergia coccinea"
 ]
}

 The dataset includes 653 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037851-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/14mrw-wf294
title: Vibrio fischeri

description: Session notes: Vibrio fischeri WT flagella, binned 4x total then filtered 0.28 (= 4.6nm resolution cutoff) Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2011-12-17</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Vibrio fischeri</p>
<strong>Strain:</strong> ES114</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: 10.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-12-17-19/rawdata/</p>11dec17c_WTVFischeri_0004.st,  Tilt Series (Pixel Size 0.632 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        11dec17c_WTVFischeri_0004.rec,  Reconstruction (Pixel Size 0.644 nm), 234.3 MB  
        
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DOI: 10.15468/dl.rnbpyb
title: Occurrence Download

description: A dataset containing 685 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bouteloua triaena"
 ]
}

 The dataset includes 685 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037850-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/fekyw-3pk63
title: Staphylococcus aureus

description: Session notes: Staphylococcus aureus PG&TA sacculi, 5 minute achromopeptidase digest Tilt series notes: Staphylococcus aureus sacculus in a grid hole. Tomogram notes: Flat sacculus seen end-on. Bands visible in PG.
description: <strong>Tilt Series Date:</strong> 2010-09-25</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Staphylococcus aureus</p>
<strong>Strain:</strong> subsp. aureus str. Newman</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 66.0°), step: 0.8°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2010-09-25-8/rawdata/</p>10sep25a_SA_PGTA_5min_004.st,  Tilt Series (Pixel Size 0.774 nm), 2.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        10sep25a_SA_PGTA_5min_004_median.rec,  Reconstruction (Pixel Size 1.548 nm), 211.2 MB  
        
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DOI: 10.15468/dl.9fsy5z
title: Occurrence Download

description: A dataset containing 243 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Artemisia abrotanum",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 243 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037854-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rf7qk7
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Artemisia abrotanum",
 "Country is Slovakia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 33 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037853-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/7jeq9-qr530
title: Campylobacter jejuni

description: Session notes: Campy flhBc cells, CTF-corrected then filtered at second zero (0.35, 0.05)... first zero should be around 0.14 Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2012-02-01</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Campylobacter jejuni</p>
<strong>Strain:</strong> subsp. jejuni 81116</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 1.5°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 15.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2012-02-01-14/rawdata/</p>12feb01a_flhBc_0022.st,  Tilt Series (Pixel Size 0.774 nm), 743.2 MB  
        
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        12feb01a_flhBc_0022.rec,  Reconstruction (Pixel Size 0.08667 nm), 539.7 MB  
        
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