cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30009058.v1
title: Supplementary Material for: Trends and Impact of Early Medical Complications in Acute Ischemic Stroke: Data from the Austrian Stroke Unit Registry

description: Introduction
Early medical complications following acute ischemic stroke (AIS) are common and might increase post-stroke morbidity and mortality. This study aimed to evaluate trends in the prevalence of early medical complications over almost two decades and their impact on three-month functional outcome and mortality.

Methods
A total of 181,704 AIS patients from the Austrian Stroke Unit Registry (2006-2024) were analyzed. Early medical complications included decompensated heart failure, cardiac arrythmia, sepsis, pneumonia, urinary tract infection (UTI), deep vein thrombosis, and pulmonary embolism. Functional outcomes were assessed using the modified Rankin Scale (mRS) after three-months, with favorable outcome defined as mRS ≤1. Associations between early medical complications and mRS were analyzed using multivariable Poisson regression models.

Results
Among all patients, 16,279 (9.0%) had early medical complications. Pneumonia (4.2%), UTI (2.9%), cardiac arrhythmia (1.4%), and decompensated heart failure (1.4%) were most common, with significant declines in prevalences over time. Admission NIHSS scores decreased, and the use of intravenous thrombolysis and mechanical thrombectomy increased. Decompensated heart failure (RR = 1.85, 95% CI 1.73-1.97, p &lt;0.001), sepsis (RR = 1.75, 95% CI 1.53-1.99, p &lt;0.001), pulmonary embolism (RR = 1.67, 95% CI 1.33-2.10, p &lt;0.001), and pneumonia (RR = 1.64, 95% CI 1.57-1.72, p &lt;0.001) were significantly associated with three-month mortality. Furthermore, the complications least associated with a favorable outcome were pneumonia (RR = 0.36, 95% CI 0.32-0.41, p &lt;0.001), decompensated heart failure (RR = 0.38, 95% CI 0.32-0.46, p &lt;0.001), and sepsis (RR = 0.59, 95% CI 0.45-0.77, p &lt;0.001). The effect sizes didn’t change significantly through the observed years.

Conclusions
This study observed a significant reduction in the prevalence of early medical complications after acute ischemic stroke. Especially decompensated heart failure, pneumonia, sepsis, and pulmonary embolism continue to substantially affect mortality and functional outcome in AIS patients.
DOI: 10.15468/dl.bu3e5x
title: Occurrence Download

description: A dataset containing 797 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Mergus squamatus",
 "Year 2000-2025"
 ]
}

 The dataset includes 797 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006568-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/bdf7m-t5z89
title: JV4404_delDot.Icm_Lp02

description: JV4404 is deletion of the Dot.Icm system. 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
description: <strong>Tilt Series Date:</strong> 2015-12-11</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: (-50.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 90.0 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, also manually processed 12 tomograms (and used SIRT) to check for presence of the T4SS basal-body</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. This data was collected at the Caltech Polara.</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. Added gold before freezing.</p>
<strong>Sample Preparation:</strong> 4 grids were frozen for JV4404 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/dga2015-12-11-6/3dimage_71332/</p>JV44040005.rec,  Reconstruction (Pixel Size 1.92 nm), 889.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-12-11-6/3dimage_71332/JV44040005.rec"
        > <i class="download icon"></i> Download </a></p>

        JV44040005.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-12-11-6/rawdata/JV44040005.mrc"
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DOI: 10.6084/m9.figshare.30009061
title: Supplementary Material for: SEEG-guided radiofrequency thermocoagulation of the epileptogenic networks: Its utility for both treatment and validation for localizing epileptogenic networks

description: Introduction: Stereoelectroencephalography-guided radio-frequency thermo coagulation (SEEG-RFTC) is a minimally invasive technique whereby radiofrequency-thermocoagulation is performed using SEEG electrodes, following recording and stimulation. It helps to disconnect/disrupt or ablate the epileptogenic networks, and provides both therapeutic and diagnostic abilities.
 Methods: Retrospective study (2016-2024). All underwent comprehensive epilepsy surgery workup (video EEG, MRI, ictal-SPECT, PET, and magnetoencephalography). SEEG was placed using robotic guidance. Recording of habitual seizure following stimulation (to produce seizures) was performed followed by SEEG-RFTC over the seizure onset zone(SOZ) was performed at the bedside, electrodes were then explanted. If seizures were still not, this was followed by surgery over SOZ.
Results: 61 patients underwent SEEG-RFTC, 41 males. Mean duration of seizures: 11 years; seizure frequency range 1-100/day. As per imaging, 5 had definite lesions, 12- dual substrates (either adjacent or distant), 5- doubtful lesions, 21- non-lesional on MRI, and 9-localization on SPECT/PET/MEG but MRI doubtful, 4-eloquent cortex and 5 had bilateral substrates. Seizure onset zone- frontal-18, temporal-35, insula-3, occipital-4, parietal-1. A total of 406 electrodes implanted, a mean 8.2+3.5/ patient. Mean follow up: 42 + 17.4 months.. About 72% (44/61) responded transiently (mean transient seizure free time- 95+19 days). Of these 29 underwent surgery; 48% had good outcomes (Class I & II). 22% (14/61) had good outcomes with SEEG-RFTC as stand-alone procedure (follow up 28+6.2 months, range 6-32 months). The Class I & I outcomes were 37% in MRI -ve and 53.8% in MRI +ve cases (p&lt;0.01). The transient time in our study did not correlate with good outcomes, but presence or absence of a substrate did. Temporal substrates had better outcomes than extra-temporal (57% vs 47% Class I & II, p&lt;0.01).
 Conclusion: SEEG-RFTC is a minimally invasive and effective adjuvant to SEEG recording and stimulation, may be done bedside under awake conditions and helps to disrupt/disconnect/ablate the abnormal networks. It may be therapeutic or can strengthen the hypothesis for a later surgical resection.
DOI: 10.6084/m9.figshare.30009061.v1
title: Supplementary Material for: SEEG-guided radiofrequency thermocoagulation of the epileptogenic networks: Its utility for both treatment and validation for localizing epileptogenic networks

description: Introduction: Stereoelectroencephalography-guided radio-frequency thermo coagulation (SEEG-RFTC) is a minimally invasive technique whereby radiofrequency-thermocoagulation is performed using SEEG electrodes, following recording and stimulation. It helps to disconnect/disrupt or ablate the epileptogenic networks, and provides both therapeutic and diagnostic abilities.
 Methods: Retrospective study (2016-2024). All underwent comprehensive epilepsy surgery workup (video EEG, MRI, ictal-SPECT, PET, and magnetoencephalography). SEEG was placed using robotic guidance. Recording of habitual seizure following stimulation (to produce seizures) was performed followed by SEEG-RFTC over the seizure onset zone(SOZ) was performed at the bedside, electrodes were then explanted. If seizures were still not, this was followed by surgery over SOZ.
Results: 61 patients underwent SEEG-RFTC, 41 males. Mean duration of seizures: 11 years; seizure frequency range 1-100/day. As per imaging, 5 had definite lesions, 12- dual substrates (either adjacent or distant), 5- doubtful lesions, 21- non-lesional on MRI, and 9-localization on SPECT/PET/MEG but MRI doubtful, 4-eloquent cortex and 5 had bilateral substrates. Seizure onset zone- frontal-18, temporal-35, insula-3, occipital-4, parietal-1. A total of 406 electrodes implanted, a mean 8.2+3.5/ patient. Mean follow up: 42 + 17.4 months.. About 72% (44/61) responded transiently (mean transient seizure free time- 95+19 days). Of these 29 underwent surgery; 48% had good outcomes (Class I & II). 22% (14/61) had good outcomes with SEEG-RFTC as stand-alone procedure (follow up 28+6.2 months, range 6-32 months). The Class I & I outcomes were 37% in MRI -ve and 53.8% in MRI +ve cases (p&lt;0.01). The transient time in our study did not correlate with good outcomes, but presence or absence of a substrate did. Temporal substrates had better outcomes than extra-temporal (57% vs 47% Class I & II, p&lt;0.01).
 Conclusion: SEEG-RFTC is a minimally invasive and effective adjuvant to SEEG recording and stimulation, may be done bedside under awake conditions and helps to disrupt/disconnect/ablate the abnormal networks. It may be therapeutic or can strengthen the hypothesis for a later surgical resection.
DOI: 10.22002/j82e9-ykt77
title: JV4404_delDot.Icm_Lp02

description: JV4404 is deletion of the Dot.Icm system. 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
description: <strong>Tilt Series Date:</strong> 2015-12-11</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: (-50.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 90.0 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, also manually processed 12 tomograms (and used SIRT) to check for presence of the T4SS basal-body</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. This data was collected at the Caltech Polara.</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. Added gold before freezing.</p>
<strong>Sample Preparation:</strong> 4 grids were frozen for JV4404 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/dga2015-12-11-31/3dimage_71381/</p>JV44040030_part111_1.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-12-11-31/3dimage_71381/JV44040030_part111_1.rec"
        > <i class="download icon"></i> Download </a></p>

        JV44040030.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-12-11-31/rawdata/JV44040030.mrc"
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DOI: 10.6084/m9.figshare.30009067
title: Supplementary Material for: Possible Treatment of Topical Steroid Withdrawal with methylene blue case report: implications for mitochondrial pathology

description: We present a case report of an 8-year-old girl with atopic dermatitis (AD) who was treated with topical corticosteroids (TCS) that included high potency agents. Her initial symptoms were limited to the chest and back. After approximately 3 months of treatment with escalating potency, the perceived lack of TCS efficacy prompted her parents to discontinue TCS while maintaining emollients. Four weeks later, the patient developed new symptoms consistent with topical steroid withdrawal (TSW) involving the face, neck, and legs. The family attempted alternative-medical treatments including turmeric, vitamin D3, and more without clinical response, before observing symptomatic relief with a self-initiated, low dose of methylene blue (MB). Although the merits of the case are anecdotal, existing literature suggests that TSW is associated with mitochondrial complex I dysfunction, which could explain the observed clinical benefit. Given that both TSW and AD have natural temporal variations, we cannot extrapolate conclusively based on a single report. However, our observations are consistent with the hypothesis that TSW is an induced, but targetable, defect in mitochondrial complex I function that warrants further investigation. At minimum, providers should be aware of the TSW patient community’s consideration of MB as an alternative therapy, especially given the lack of data on long-term safety.
DOI: 10.6084/m9.figshare.30009067.v1
title: Supplementary Material for: Possible Treatment of Topical Steroid Withdrawal with methylene blue case report: implications for mitochondrial pathology

description: We present a case report of an 8-year-old girl with atopic dermatitis (AD) who was treated with topical corticosteroids (TCS) that included high potency agents. Her initial symptoms were limited to the chest and back. After approximately 3 months of treatment with escalating potency, the perceived lack of TCS efficacy prompted her parents to discontinue TCS while maintaining emollients. Four weeks later, the patient developed new symptoms consistent with topical steroid withdrawal (TSW) involving the face, neck, and legs. The family attempted alternative-medical treatments including turmeric, vitamin D3, and more without clinical response, before observing symptomatic relief with a self-initiated, low dose of methylene blue (MB). Although the merits of the case are anecdotal, existing literature suggests that TSW is associated with mitochondrial complex I dysfunction, which could explain the observed clinical benefit. Given that both TSW and AD have natural temporal variations, we cannot extrapolate conclusively based on a single report. However, our observations are consistent with the hypothesis that TSW is an induced, but targetable, defect in mitochondrial complex I function that warrants further investigation. At minimum, providers should be aware of the TSW patient community’s consideration of MB as an alternative therapy, especially given the lack of data on long-term safety.
DOI: 10.22002/491yf-57b40
title: JV3588_ΔdotK

description: Legionella thyA JV3588_ΔdotK
description: <strong>Tilt Series Date:</strong> 2017-07-19</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: 2°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 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. This time cell density was ~2.8</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV3588 strain at OD~ 2.8, cell density was increased to 2x by centrifugation. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4 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/dga2017-07-19-4/rawdata/</p>20170719_JV35880003.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-07-19-4/rawdata/20170719_JV35880003.mrc"
        > <i class="download icon"></i> Download </a></p>

        20170719_JV35880003_part61_18.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
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DOI: 10.22002/ys38n-56d39
title: JV3559_Janelia

description: Legionella thyA ΔdotG.This is a single mutant that lacks DotG.
description: <strong>Tilt Series Date:</strong> 2017-01-08</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 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. This time cell density was ~3.4</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV3559 strain at OD~ 3.4, 4 grids at density x and another 4 at density 2x. 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/dga2017-01-08-97/3dimage_80429/</p>JV3559_20170108a_area20001_full.rec,  Reconstruction (Pixel Size 1.68 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        JV3559_20170108a_area20001.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
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