cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25200803
title: Algorithmic assessment reveals functional implications of GABRD gene variants linked to idiopathic generalized epilepsy

description: The primary objective of this study is to address the challenge posed by the increasing number of variants of unknown clinical significance (VUS) within the GABRD gene, which encodes the δ subunit of γ-Aminobutyric acid type A receptors. The focus is on predicting the most pathogenic GABRD VUS to enhance precision medicine and improve our understanding of relevant pathophysiology. The study employs a combination of in silico algorithms to analyze 82 variants of unknown clinical significance of GABRD gene sourced from the ClinVar database. Initially, separate algorithms based on sequence homology are utilized to assess this variant set. Subsequently, consensus variants predicted as pathogenic undergo further evaluation through a web server employing an algorithm based on structural homology. The resulting 11 variants are then validated using in silico tools that assess variant effects based on genetic and molecular data. The evaluation includes consideration of disease association and protein stability due to amino acid substitutions. The study identifies specific variants (L111R, R114C, D123N, G150S, and L243P) in the coding region of the GABRD gene, which are predicted as deleterious by multiple algorithms. These variants are evolutionarily conserved, mapped onto the extracellular domain of the δ subunit, and associated with idiopathic generalized epilepsy. The findings suggest structural or functional consequences that lead to pathogenicity, offering valuable insights for wet-lab experimentation. Besides, the findings contribute to the validation of clinically significant genetic variants in the GABRD gene, which is critical for epilepsy precision medicine.
DOI: 10.6084/m9.figshare.25200803.v1
title: Algorithmic assessment reveals functional implications of GABRD gene variants linked to idiopathic generalized epilepsy

description: The primary objective of this study is to address the challenge posed by the increasing number of variants of unknown clinical significance (VUS) within the GABRD gene, which encodes the δ subunit of γ-Aminobutyric acid type A receptors. The focus is on predicting the most pathogenic GABRD VUS to enhance precision medicine and improve our understanding of relevant pathophysiology. The study employs a combination of in silico algorithms to analyze 82 variants of unknown clinical significance of GABRD gene sourced from the ClinVar database. Initially, separate algorithms based on sequence homology are utilized to assess this variant set. Subsequently, consensus variants predicted as pathogenic undergo further evaluation through a web server employing an algorithm based on structural homology. The resulting 11 variants are then validated using in silico tools that assess variant effects based on genetic and molecular data. The evaluation includes consideration of disease association and protein stability due to amino acid substitutions. The study identifies specific variants (L111R, R114C, D123N, G150S, and L243P) in the coding region of the GABRD gene, which are predicted as deleterious by multiple algorithms. These variants are evolutionarily conserved, mapped onto the extracellular domain of the δ subunit, and associated with idiopathic generalized epilepsy. The findings suggest structural or functional consequences that lead to pathogenicity, offering valuable insights for wet-lab experimentation. Besides, the findings contribute to the validation of clinically significant genetic variants in the GABRD gene, which is critical for epilepsy precision medicine.
DOI: 10.6084/m9.figshare.25375232
title: LncRNA PVT1 promotes neuroinflammation after intracerebral hemorrhage by regulating the miR-128-3p/TXNIP axis

description: Intracerebral hemorrhage (ICH) has significant morbidity and mortality. TXNIP and the competing endogenous RNA (ceRNA) regulatory mechanism involved in long non-coding RNA (lncRNA) play roles in ICH. We probed the upstream microRNAs (miRNAs)/lncRNAs that regulated TXNIP expression in the ceRNA mechanism. ICH mouse model was established, and ICH secondary injury was simulated in BV2 microglia by hemin treatment. TXNIP was silenced 48 h before ICH modeling. The ICH mouse brain water content (BWC) and brain lesion volume after ICH were recorded. Neuronal apoptosis and neurological deficits were evaluated by double staining of NeuN and TUNEL/modified Garcia/corner turn/forelimb placement tests. Iba1 + microglia number and tumor necrosis factor-α (TNF-α)/interleukin-1β (IL-1β)/IL-10/TXNIP/PVT1/miR-128-3p levels were assessed by immunohistochemistry, Western blot, ELISA, and RT-qPCR. Cell viability/death of BV2 cells conditioned medium-treated neuron HT22 cells were assessed by CCK-8/LDH assays. miRNA that had a targeted binding relationship with TXNIP was screened. The targeted bindings of miR-128-3p to TXNIP/PVT1 to miR-128-3p were verified by dual-luciferase reporter gene assay. TXNIP knockdown reduced post-ICH microglial activation/release of pro-inflammatory factors/brain edema/brain lesion volume/neurological deficits in mice and increased releases of anti-inflammatory factors. TXNIP/PVT1 knockdown inhibited hemin-induced inflammatory responses in BV2 cells and protected <i>in vitro</i> co-cultured HT22 cells. PVT1 was a sponge of miR-128-3p to repress TXNIP expression. miR-128-3p knockdown diminished PVT1 knockdown-inhibited hemin-induced BV2 cell inflammatory responses/neurotoxicity. PVT1 silencing reduced hemin-induced neuroinflammation and had a protective effect on neurons by increasing the targeted inhibition of TXNIP by miR-128-3p.
DOI: 10.6084/m9.figshare.25375232.v1
title: LncRNA PVT1 promotes neuroinflammation after intracerebral hemorrhage by regulating the miR-128-3p/TXNIP axis

description: Intracerebral hemorrhage (ICH) has significant morbidity and mortality. TXNIP and the competing endogenous RNA (ceRNA) regulatory mechanism involved in long non-coding RNA (lncRNA) play roles in ICH. We probed the upstream microRNAs (miRNAs)/lncRNAs that regulated TXNIP expression in the ceRNA mechanism. ICH mouse model was established, and ICH secondary injury was simulated in BV2 microglia by hemin treatment. TXNIP was silenced 48 h before ICH modeling. The ICH mouse brain water content (BWC) and brain lesion volume after ICH were recorded. Neuronal apoptosis and neurological deficits were evaluated by double staining of NeuN and TUNEL/modified Garcia/corner turn/forelimb placement tests. Iba1 + microglia number and tumor necrosis factor-α (TNF-α)/interleukin-1β (IL-1β)/IL-10/TXNIP/PVT1/miR-128-3p levels were assessed by immunohistochemistry, Western blot, ELISA, and RT-qPCR. Cell viability/death of BV2 cells conditioned medium-treated neuron HT22 cells were assessed by CCK-8/LDH assays. miRNA that had a targeted binding relationship with TXNIP was screened. The targeted bindings of miR-128-3p to TXNIP/PVT1 to miR-128-3p were verified by dual-luciferase reporter gene assay. TXNIP knockdown reduced post-ICH microglial activation/release of pro-inflammatory factors/brain edema/brain lesion volume/neurological deficits in mice and increased releases of anti-inflammatory factors. TXNIP/PVT1 knockdown inhibited hemin-induced inflammatory responses in BV2 cells and protected <i>in vitro</i> co-cultured HT22 cells. PVT1 was a sponge of miR-128-3p to repress TXNIP expression. miR-128-3p knockdown diminished PVT1 knockdown-inhibited hemin-induced BV2 cell inflammatory responses/neurotoxicity. PVT1 silencing reduced hemin-induced neuroinflammation and had a protective effect on neurons by increasing the targeted inhibition of TXNIP by miR-128-3p.
DOI: 10.15468/dl.wccszg
title: Occurrence Download

description: A dataset containing 568 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Azorella pedunculata (Spreng.) Mathias & Constance"
 ]
}

 The dataset includes 568 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013237-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/awndc-3e440
title: JV9264

description: Raw data files of JV9264
description: <strong>Tilt Series Date:</strong> 2018-09-06</p>
<strong>Data Taken By:</strong> Jun Zhang</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: 2°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 41000x. </p>
<strong>Microscope:</strong> Caltech Polara</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> Joseph</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 37 degree and OD 2.5-3.0</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jza2018-09-06-61/rawdata/</p>JV9264_B154.mrc,  Tilt Series (Pixel Size 0.2654 nm), 1.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jza2018-09-06-61/rawdata/JV9264_B154.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9264_B154_part55_1.rec,  Reconstruction (Pixel Size 1.0616 nm), 534.5 MB  
        
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DOI: 10.22002/0mbvh-nea48
title: U937 JV9298

description: Legionella pneumophila JV9298 DotF-GFP DotB E191K
description: <strong>Tilt Series Date:</strong> 2020-12-12</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: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -6.0 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 & processing: Yuxi Liu</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 1h infection, grids coated with 25ug/mL vitronectin</p>
<strong>Sample Preparation:</strong> Quantifoil R2/2 gold finder grid, 100% humidity, 22deg C, manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-12-12-8/3dimage_123624/</p>U937_9298_tomo_2_bin2_SIRT_1k.rec,  Reconstruction (Pixel Size 1.06 nm), 4.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        U937_9298_tomo_2_bin2.st,  Tilt Series (Pixel Size 0.53 nm), 436.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.w2jch8
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oxalis corniculata",
 "Country is Burundi",
 "HasCoordinate is true"
 ]
}

 The dataset includes 58 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045112-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/pvk75-p6n26
title: Caulobacter delta-CpaF

description: Raw data files of Caulobacter delta-CpaF
description: <strong>Tilt Series Date:</strong> 2019-01-08</p>
<strong>Data Taken By:</strong> Steven Wang</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: 183.0 eV/Å²,  defocus: -9.0 μm,  magnification: 42000x. </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> iMOD</p>
<strong>Collaborators and Roles:</strong> Patrick Viollier</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 28 degrees celsius</p>
<strong>Sample Preparation:</strong> plunge-freezing</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-01-08-66/rawdata/</p>targ30.mrc,  Tilt Series (Pixel Size 0.351 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-01-08-66/rawdata/targ30.mrc"
        > <i class="download icon"></i> Download </a></p>

        targ30_full.rec,  Reconstruction (Pixel Size 1.404 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-01-08-66/3dimage_100904/targ30_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/9xqsf-aqz18
title: Shewanella oneidensis dFlgH

description: Raw data files of Shewanella oneidensis dFlgH
description: <strong>Tilt Series Date:</strong> 2018-05-27</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </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> Jeff Granlick (Uni. of Minnesota) supplied the mutant cells.</p>
<strong>Sample Preparation:</strong> Samples were prepared from overnight LB culture</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-05-27-50/rawdata/</p>tilt55.mrc,  Tilt Series (Pixel Size 0.57 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-05-27-50/rawdata/tilt55.mrc"
        > <i class="download icon"></i> Download </a></p>

        tilt55_full.rec,  Reconstruction (Pixel Size 2.28 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-05-27-50/3dimage_93390/tilt55_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qydaj-ws163
title: Caulobacter crescentus

description: Raw data files of Caulobacter crescentus
description: <strong>Tilt Series Date:</strong> 2018-10-17</p>
<strong>Data Taken By:</strong> Lujia Zhang</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: 252.8 eV/Å²,  defocus: -10.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</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> For the research of pilus, Del E from Partick</p>
<strong>Purification / Growth Conditions / Treatment:</strong> swarmer cell, PVP</p>
<strong>Sample Preparation:</strong> force 4, time 6, humidity 100%, temp. 22</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lza2018-10-17-37/rawdata/</p>targ35.mrc,  Tilt Series (Pixel Size 0.3712 nm), 3.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lza2018-10-17-37/rawdata/targ35.mrc"
        > <i class="download icon"></i> Download </a></p>

        targ35_full.rec,  Reconstruction (Pixel Size 1.4848 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lza2018-10-17-37/3dimage_99605/targ35_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.a38uxd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oxalis corniculata",
 "Country is Burkina Faso",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045111-250811113504898/datasets/export for details.
DOI: 10.22002/24s36-0wq50
title: Legionella cells for the flagell

description: Raw data files of Legionella cells for the flagell
description: <strong>Tilt Series Date:</strong> 2018-03-13</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</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: 2°, constant angular increment, dosage: 90.0 eV/Å²,  defocus: -8.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> RAPTOR</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Samples were grown in LB overnight.</p>
<strong>Sample Preparation:</strong> Grids were prepared from an overnight LB culture.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-03-13-79/rawdata/</p>Legionella_flagella50.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-03-13-79/rawdata/Legionella_flagella50.mrc"
        > <i class="download icon"></i> Download </a></p>

        Legionella_flagella50_part53_5.rec,  Reconstruction (Pixel Size 1.56 nm), 444.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/h35wv-kwq70
title: Mycobacter smegmatis pneumonia

description: KP48s M. smegmatis Δ3877 (ΔeccD1)
description: <strong>Tilt Series Date:</strong> 2013-07-02</p>
<strong>Data Taken By:</strong> Alasdair McDowall</p>
<strong>Species / Specimen:</strong> Mycobacterium smegmatis</p>
<strong>Strain:</strong> 3877</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: -8.0 μm,  magnification: 26000x. </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> Koushik Paul /  Eric BrownGenentech, Inc.1 DNA WaySouth San Francisco, CA 94080(650) 225-6248Fax: (650) 225-1107</p>
<strong>Purification / Growth Conditions / Treatment:</strong> sauton media @ 37C</p>
<strong>Sample Preparation:</strong> 3ul + 10nm AuR2/2 quantifoils 4.5offset 1 blot 2s 1s drain</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/amw2013-07-02-14/rawdata/</p>KP48s0014.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/amw2013-07-02-14/rawdata/KP48s0014.mrc"
        > <i class="download icon"></i> Download </a></p>

        KP48s0014_full.rec,  Reconstruction (Pixel Size 1.68 nm), 602.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/amw2013-07-02-14/3dimage_27894/KP48s0014_full.rec"
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DOI: 10.22002/yvb8y-tpy42
title: Mycobacter smegmatis pneumonia

description: KP3wt  M. smegmatis mc2_155.Janelia Titan
description: <strong>Tilt Series Date:</strong> 2013-07-01</p>
<strong>Data Taken By:</strong> Alasdair McDowall</p>
<strong>Species / Specimen:</strong> Mycobacterium smegmatis</p>
<strong>Strain:</strong> mc2_155</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: -8.0 μm,  magnification: 26000x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor Janelia Titan</p>
<strong>Collaborators and Roles:</strong> Koushik Paul /  Eric BrownGenentech, Inc.1 DNA WaySouth San Francisco, CA 94080(650) 225-6248Fax: (650) 225-1107</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 7H9 media</p>
<strong>Sample Preparation:</strong> 3ul + 10nm AuR2/2 quantifoils 4.5offset 1 blot 2s 1s drain</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/amw2013-07-01-4/rawdata/</p>montage_0004.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/amw2013-07-01-4/rawdata/montage_0004.mrc"
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        montage_0004_full.rec,  Reconstruction (Pixel Size 1.68 nm), 602.8 MB  
        
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