cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/k4prf-j9260
title: Hyphomonas 1st session 22.5kx

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2008-07-28</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 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> imod</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2008-07-28-37/rawdata/</p>08jul28b_box64_stack61.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        08jul28b_box64_stack61_1k.rec,  Reconstruction (Pixel Size 1.9 nm), 152.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2008-07-28-37/3dimage_5272/08jul28b_box64_stack61_1k.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.34740/kaggle/dsv/12907897
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.34aab4
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Japan",
 "InstitutionKey is 0e919a55-08d3-4bd2-aec1-200858fafd92",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Gyraulus, Gastropoda)",
 "TypeStatus is one of (Holotype, Lectotype)"
 ]
}

 The dataset includes 11 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007136-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/rn3ng-42b91
title: Pdb 110408 696

description: Prosthecobacter debontii, 08nov15a_b696_No1_041, filaments,
description: <strong>Tilt Series Date:</strong> 2008-11-15</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter debontii</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2008-11-15-37/rawdata/</p>08nov15a_b696_No1_041.mrc,  Tilt Series (Pixel Size 0.95 nm), 453.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        08nov15a_b696_No1_041_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2008-11-15-37/3dimage_13194/08nov15a_b696_No1_041_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/52g9q-jbc46
title: Two spores in one membrane

description: Raw data files of Two spores in one membrane
description: <strong>Tilt Series Date:</strong> 2008-02-05</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acetonema longum</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Eric Matson grew the cells.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Anaerobic growth on CO2</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2008-02-05-3/rawdata/</p>spore3.mrc,  Tilt Series (Pixel Size 0.961 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2008-02-05-3/rawdata/spore3.mrc"
        > <i class="download icon"></i> Download </a></p>

        spore3_full.rec,  Reconstruction (Pixel Size 1.922 nm), 367.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2008-02-05-3/3dimage_1394/spore3_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/28mcq-x8f51
title: Bdellovibrio attack-phase

description: Raw data files of Bdellovibrio attack-phase
description: <strong>Tilt Series Date:</strong> 2012-11-14</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Bdellovibrio bacteriovorus</p>
<strong>Strain:</strong> HD100</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 115.0 eV/Å²,  defocus: -10.0 μm,  magnification: 27500x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFTomo</p>
<strong>Collaborators and Roles:</strong> Strain from Liz Sockett</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown in S17-1 prey solution at 30 degrees. OD600=0.2</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 nm BSA treated gold. -3 offset, 4 sec blot time, no drain. Ethane/propane mix.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2012-11-14-19/rawdata/</p>Bdellovibrio_wt_20121114_0010004.mrc,  Tilt Series (Pixel Size 0.4 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Bdellovibrio_wt_20121114_0010004_full.rec,  Reconstruction (Pixel Size 1.6 nm), 441.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/4xavh-rht13
title: Hyphomonas session6 27.5KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2008-12-09</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 130.0 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>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2008-12-09-99/rawdata/</p>08dec09a_unk1c_105.mrc,  Tilt Series (Pixel Size 0.774 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2008-12-09-99/rawdata/08dec09a_unk1c_105.mrc"
        > <i class="download icon"></i> Download </a></p>

        08dec09a_unk1c_105_1k.rec,  Reconstruction (Pixel Size 1.548 nm), 129.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.8ka2xv
title: Occurrence Download

description: A dataset containing 761 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bertholletia excelsa)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 761 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007132-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/94b94-ywf92
title: Pdj 122708 634

description: Prosthecobacter dejongeii, 08dec28a_Pdj_739_w2_018,
description: <strong>Tilt Series Date:</strong> 2008-12-28</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter dejongeii</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2008-12-28-13/rawdata/</p>08dec28a_Pdj_739_w2_018.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        08dec28a_Pdj_739_w2_018_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/sxhp3-grn42
title: Pva 111908 921

description: Prosthecobacter vanneervenii, 08dec03a_pb_002,
description: <strong>Tilt Series Date:</strong> 2008-12-03</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter vanneervenii</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2008-12-03-2/rawdata/</p>08dec03a_pb_002.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2008-12-03-2/rawdata/08dec03a_pb_002.mrc"
        > <i class="download icon"></i> Download </a></p>

        08dec03a_pb_002_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2008-12-03-2/3dimage_13216/08dec03a_pb_002_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/x9j9d-9zp95
title: HIV capsid purified

description: 80 A/2 41000 3 defocus Box B search track 13500 ,slit in 20eV
description: <strong>Tilt Series Date:</strong> 2013-12-05</p>
<strong>Data Taken By:</strong> Stephen Carter</p>
<strong>Species / Specimen:</strong> HIV cores</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: -3.0 μm,  magnification: 41000x. </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> Wes Sundquist</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Purified HIV cores</p>
<strong>Sample Preparation:</strong> B box</p>
description: Files available via S3 at ://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2013-12-05-14/rawdata/</p>41000df3hiv-capsidatlas1_30014.mrc,  Tilt Series (Pixel Size 0.26 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        41000df3hiv-capsidatlas1_30014_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/z0ypc-nc685
title: Pseudomonas aeruginosa mut

description: Quadruple mutant for polyP synthesis
description: <strong>Tilt Series Date:</strong> 2014-02-09</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -8.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Lisa Racki</p>
<strong>Purification / Growth Conditions / Treatment:</strong> growth 3hours into starvation</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
  etl2014-02-09-10_slicer6798.jpg: Filament
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-09-10/rawdata/</p>quadmut_t3_30005.mrc,  Tilt Series (Pixel Size 0.4 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        quadmut_t3_30005_part121_23.rec,  Reconstruction (Pixel Size 0.0 nm), 356.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.9dwwz8
title: Occurrence Download

description: A dataset containing 15398 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Araucaria angustifolia"
 ]
}

 The dataset includes 15398 records from 229 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007135-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/0wcpc-7kn61
title: Agro pJW58

description: wild-type Agro with plasmid-borne VirC1-GFP translational fusion under control of the virB promoter.  Kanamycin-resistant (150 to 300 ug/mL)
description: <strong>Tilt Series Date:</strong> 2014-03-05</p>
<strong>Data Taken By:</strong> Elitza Tocheva</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: 1.0°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -8.0 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> Raptor</p>
<strong>Collaborators and Roles:</strong> Clay Fuqua</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AB medium</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-03-05-7/rawdata/</p>Agro_pJW580008.mrc,  Tilt Series (Pixel Size 0.4 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Agro_pJW580008_part121_14.rec,  Reconstruction (Pixel Size 1.6 nm), 356.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.7b4by2
title: Occurrence Download

description: A dataset containing 3090771 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Philippines",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 3090771 records from 1767 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007018-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29246441
title: Supplementary Material for: Unveiling the Hidden Burden: An Umbrella Review of Congenital Anomalies among Newborns in Low and Middle-Income Countries

description: Background: Congenital anomalies (CAs) are a major cause of newborn mortality and long-term disabilities, especially in developing countries. Research on CAs is limited and inconclusive. This umbrella review evaluates the pooled prevalence, patterns, and determinants of CAs among newborns in low- and middle-income countries.
Methods: We conducted a comprehensive search across databases, including PubMed and Cochrane Library, until 31 December 2024. Study quality was assessed using the AMSTAR checklist. Heterogeneity was measured with the I² test and Cochrane Q test, while publication bias was evaluated through funnel plots, Egger's, and Begg's tests. The pooled prevalence of CAs and determinants was calculated using the DerSimonian and Laird random-effects model.
Results: Seven studies revealed a pooled prevalence of CAs at 15 per 1,000 births (95% CI: 9.00, 21.00), with the highest rate in low-income countries at 18 per 1,000 (95% CI: 8.00, 27.00). Musculoskeletal and urogenital anomalies were the most prevalent, at 8 and 4 per 1,000 births, respectively. Key predictors include lack of folic acid supplementation (AOR 4.18, 95% CI: 2.35, 6.02), khat chewing (AOR 3.5, 95% CI: 2.97, 4.03), maternal illness (AOR 3.55, 95% CI: 3.37, 4.73), and drug use during pregnancy (AOR 4.37, 95% CI: 1.21, 7.54).
Conclusion: The pooled prevalence of CAs is significantly higher than WHO reports, with musculoskeletal and urogenital defects being the most common. Key risk factors include maternal illness, unidentified drug use, khat chewing, and lack of folic acid supplementation. Enhancing folic acid intake and targeting these risk factors are essential for policymakers.
Keywords: Associated factors, congenital anomalies, low and middle-income countries, prevalence, umbrella review
DOI: 10.6084/m9.figshare.29246441.v1
title: Supplementary Material for: Unveiling the Hidden Burden: An Umbrella Review of Congenital Anomalies among Newborns in Low and Middle-Income Countries

description: Background: Congenital anomalies (CAs) are a major cause of newborn mortality and long-term disabilities, especially in developing countries. Research on CAs is limited and inconclusive. This umbrella review evaluates the pooled prevalence, patterns, and determinants of CAs among newborns in low- and middle-income countries.
Methods: We conducted a comprehensive search across databases, including PubMed and Cochrane Library, until 31 December 2024. Study quality was assessed using the AMSTAR checklist. Heterogeneity was measured with the I² test and Cochrane Q test, while publication bias was evaluated through funnel plots, Egger's, and Begg's tests. The pooled prevalence of CAs and determinants was calculated using the DerSimonian and Laird random-effects model.
Results: Seven studies revealed a pooled prevalence of CAs at 15 per 1,000 births (95% CI: 9.00, 21.00), with the highest rate in low-income countries at 18 per 1,000 (95% CI: 8.00, 27.00). Musculoskeletal and urogenital anomalies were the most prevalent, at 8 and 4 per 1,000 births, respectively. Key predictors include lack of folic acid supplementation (AOR 4.18, 95% CI: 2.35, 6.02), khat chewing (AOR 3.5, 95% CI: 2.97, 4.03), maternal illness (AOR 3.55, 95% CI: 3.37, 4.73), and drug use during pregnancy (AOR 4.37, 95% CI: 1.21, 7.54).
Conclusion: The pooled prevalence of CAs is significantly higher than WHO reports, with musculoskeletal and urogenital defects being the most common. Key risk factors include maternal illness, unidentified drug use, khat chewing, and lack of folic acid supplementation. Enhancing folic acid intake and targeting these risk factors are essential for policymakers.
Keywords: Associated factors, congenital anomalies, low and middle-income countries, prevalence, umbrella review