cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/j17sv-bhg24
title: JV1644 Legionella thyA ΔdotO

description: JV1644 Legionella thyA ΔdotO. Lacks dotO ATPase.
description: <strong>Tilt Series Date:</strong> 2016-06-14</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: 1.5°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -6.0 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.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV1644 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/dga2016-06-14-27/rawdata/</p>DG1644_150620160027.mrc,  Tilt Series (Pixel Size 3.9 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-06-14-27/rawdata/DG1644_150620160027.mrc"
        > <i class="download icon"></i> Download </a></p>

        DG1644_150620160027.rec,  Reconstruction (Pixel Size 15.6 nm), 890.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-06-14-27/3dimage_75629/DG1644_150620160027.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/xp87d-xr938
title: JV5443

description: JV5443 Legionella (Super-deletion+CDHFG), no Thy
description: <strong>Tilt Series Date:</strong> 2016-08-09</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: 1.50°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </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 at Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate and cysteine hydrochloride  (no 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.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV5443 strain at OD~3.2. 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/dga2016-08-09-105/rawdata/</p>JV5443a0058.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-09-105/rawdata/JV5443a0058.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV5443a0058_full.rec,  Reconstruction (Pixel Size 1.68 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-09-105/3dimage_77780/JV5443a0058_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/yfv5p-hd644
title: JV7967

description: Legionella thyA ΔdotI ΔdotJ
description: <strong>Tilt Series Date:</strong> 2016-08-11</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: 1.50°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </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 at 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. 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.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV7967 strain at OD~3.3. 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/dga2016-08-11-5/rawdata/</p>7967-gridb-atlas3a0011.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-5/rawdata/7967-gridb-atlas3a0011.mrc"
        > <i class="download icon"></i> Download </a></p>

        7967-gridb-atlas3a0011_full.rec,  Reconstruction (Pixel Size 1.68 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-5/3dimage_77806/7967-gridb-atlas3a0011_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/f9waf-trt17
title: Caulobacter crescentus ftsE del

description: Caulobacter crescentus, ftsE, FtsZ, Long cell, PYE
description: <strong>Tilt Series Date:</strong> 2016-08-03</p>
<strong>Data Taken By:</strong> Qing Yao</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 190.0 eV/Å²,  defocus: -12.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFtomo</p>
<strong>Collaborators and Roles:</strong> Goley ED at Johns Hopkins University School of Medicine</p>
<strong>Purification / Growth Conditions / Treatment:</strong> C. crescentus was from Yi-Wei's cryo-stock and was grown in PYE medium overnight at 30°c 250 rpm. In the next days' morning, 1/20 subculture into the M2G medium. When OD600 reaches 0.30, 2 ml medium was spun down gently (3000 rpm for 3 min) and the resuspension was 100 ul for cryo-grid preparation.</p>
<strong>Sample Preparation:</strong> Glow discharged Quantifoil R2/R holey carbon film. 4 ul concentrated gold suspension was added to 16 ul bacteria and mix before plunge freezing. Plunge freezing condition: 6(force)-2(duration time)-1(dry time). Tilt Series Setting: single tilt. constant angular increment, step: 1. tilt range: (-60, 60). dosage: 180/A2. defocus: -10 um. magnification: 27500. Tilt Series Setting: single tilt. constant angular increment, step: 1.0. tilt range: (-60, 60).</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2016-08-03-28/rawdata/</p>square50005.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2016-08-03-28/rawdata/square50005.mrc"
        > <i class="download icon"></i> Download </a></p>

        square50005_full.rec,  Reconstruction (Pixel Size 1.92 nm), 311.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2016-08-03-28/3dimage_76585/square50005_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/2s0yh-43m78
title: JV7967

description: Legionella thyA ΔdotI ΔdotJ
description: <strong>Tilt Series Date:</strong> 2016-08-11</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: 1.50°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </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 at 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. 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.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV7967 strain at OD~3.3. 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/dga2016-08-11-31/rawdata/</p>7967-gridb-atlas3a0024.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-31/rawdata/7967-gridb-atlas3a0024.mrc"
        > <i class="download icon"></i> Download </a></p>

        7967-gridb-atlas3a0024_full.rec,  Reconstruction (Pixel Size 1.68 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-31/3dimage_77858/7967-gridb-atlas3a0024_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/48nhm-75s07
title: Agro_AD1484

description: Agro_AD1484 (AD1484:A348dB/pAD2079,virB on a multicopy plasmid).Cb resistance. Grown on induction plate pH5.8
description: <strong>Tilt Series Date:</strong> 2015-10-26</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Agrobacterium tumefaciens</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </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 constructed by Anath Das. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline. This data was collected at the Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Agro_AD1484 (AD1484:A348dB/pAD2079,virB on a multicopy plasmid). Cells were scraped off the induction plate (particularly from the immediate surface of the plate: this is to ensure that if something is happening on the real surface of the plate, we do not miss it), dissolved in induction media, spun for 15 min in a table top centrifuge, supernatant thrown away, cells redissolved in PBS. Add gold to this: 1ul of gold to 4 ul of cells and freeze.</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.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-10-26-54/3dimage_70927/</p>20151026_AD1484_20030_full.rec,  Reconstruction (Pixel Size 1.68 nm), 430.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-10-26-54/3dimage_70927/20151026_AD1484_20030_full.rec"
        > <i class="download icon"></i> Download </a></p>

        20151026_AD1484_20030.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-10-26-54/rawdata/20151026_AD1484_20030.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.30008662
title: Supplementary Material for: Creative arts therapies to improve health and well-being in obesity? A systematic literature review of current research

description: Introduction: The aim of this systematic literature review was to assess the effects of creative arts therapies on the health and well-being of overweight/obese patients. 
Methods: The database search was conducted in "American Search Ultimate, PsycINFO, PsycARTICLES, ERIC, MEDLINE (via PubMed), OpenDissertations, PSYNDEX Literature with PSYNDEX Test, SocINDEX, SocINDEX wih Full text", covering the period from 2000 to 2024. Studies with evidence level I-IV, subjects with a BMI &gt; 25 were included.
Results: 12 studies, including five controlled studies, were analysed. Significant results were achieved in self-esteem, quality of life, body awareness, dissatisfaction with one’s own body, social relationships, changes in health and eating behaviour; lower impact on body image, emotional eating, communication skills, dealing with your own body shape.
Discussion/Conclusion: Creative arts therapies can make a valuable contribution to health promotion for overweight individuals. Increased integration into weight reduction programmes would be a logical next step. Future research should place greater emphasis on increasing sample sizes, employing control group, specifying types of intervention and settings, and expanding the inclusion of children and adolescents as target groups to validate existing findings and to enhance the informative value of the results.
DOI: 10.6084/m9.figshare.30008662.v1
title: Supplementary Material for: Creative arts therapies to improve health and well-being in obesity? A systematic literature review of current research

description: Introduction: The aim of this systematic literature review was to assess the effects of creative arts therapies on the health and well-being of overweight/obese patients. 
Methods: The database search was conducted in "American Search Ultimate, PsycINFO, PsycARTICLES, ERIC, MEDLINE (via PubMed), OpenDissertations, PSYNDEX Literature with PSYNDEX Test, SocINDEX, SocINDEX wih Full text", covering the period from 2000 to 2024. Studies with evidence level I-IV, subjects with a BMI &gt; 25 were included.
Results: 12 studies, including five controlled studies, were analysed. Significant results were achieved in self-esteem, quality of life, body awareness, dissatisfaction with one’s own body, social relationships, changes in health and eating behaviour; lower impact on body image, emotional eating, communication skills, dealing with your own body shape.
Discussion/Conclusion: Creative arts therapies can make a valuable contribution to health promotion for overweight individuals. Increased integration into weight reduction programmes would be a logical next step. Future research should place greater emphasis on increasing sample sizes, employing control group, specifying types of intervention and settings, and expanding the inclusion of children and adolescents as target groups to validate existing findings and to enhance the informative value of the results.
DOI: 10.22002/8w1dk-yej84
title: JV3572

description: Legionella thyA ΔdotD
description: <strong>Tilt Series Date:</strong> 2016-04-02</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: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </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. 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</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV3572 strain (2x and 3x concentrated from OD-3 culture); 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/dga2016-04-02-90/rawdata/</p>dg20160331_3572_atlas20051.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-04-02-90/rawdata/dg20160331_3572_atlas20051.mrc"
        > <i class="download icon"></i> Download </a></p>

        dg20160331_3572_atlas20051_full.rec,  Reconstruction (Pixel Size 1.68 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-04-02-90/3dimage_74124/dg20160331_3572_atlas20051_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.30008665
title: Supplementary Material for: Epidemiology and Clinical Characteristics of Nummular Headache in Observational Studies: A systematic review and meta-analysis

description: Abstract
Introduction Nummular headache (NH) is a rare primary headache disorder which was first described in 2002. This meta-analysis aimed to evaluate the prevalence and relative frequencies of clinical features of NH.
Methods Pubmed, Embase, Medline and ScienceDirect were thoroughly searched for observational studies reporting the relevant data regarding NH diagnosed in accordance with ICHD-2, ICHD-3β, ICHD-3 or Pareja’s original study. Random-effects meta-analysis was performed in order to calculate the pooled prevalence estimates (PPE) and the I2 statistics was used to measure the between-study heterogeneity. The PRISMA guidelines were strictly followed by the study's structure. The Joanna Briggs Institute Checklist for Studies Reporting Prevalence Data was used to evaluate the risk of bias of included studies. 
Results Out of initial 2441 records, 17 studies met all of the inclusion criteria. The pooled mean age of onset of NH was 46.91 (95%CI: 43.85-49.96). The PPE of NH in adult patients evaluated for a headache in a clinic-based setting was 0.7% (95%CI: 0.2-2.4), with slight female predominance (females = 0.5%, 95%CI: 0.2-1.4 vs males = 0.3%, 95%CI: 0.1-0.8). The majority of patients (69.4%, 95%CI: 58.1-78.8) experience chronic course of NH. The shape of the headache was round/circular in 78.4% (95%CI: 71.9-83.7) and oval/elliptical in 21.6% (95%CI: 16.3-28.1) of patients. In 7.5% (95%CI: 2.7-19.0) of individuals pain had multifocal location and 59.1% (95%CI: 49.7-68.0) of NH patients experienced pain exacerbations. The pain was most prevalent in the strictly parietal region (43.0%, 95%CI: 37.4-48.7) of the cranium and had pressing quality (51.4%, 95%CI: 41.6-61.1). Migraine has been diagnosed in 29.3% (95%CI: 18.5-42.9) of patients prior to NH diagnosis and 42.4% (95%CI: 33.5-51.8) of patients experience a complete remission, with or without medication, of headache. 
Conclusion The results of our study showed that NH is a very distinct and relatively rare to encounter headache disorder. Due to its unique clinical phenotype, physicians need to be aware when a patient presents with a small, well-localized round/oval headache in the cranium region.