cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/chd76-46v13
title: Hpylori_dFliF_FISE

description: These are H_pylori cells that are lacking FliP protein. In these cells, FliF protein was knocked out  .  to examine its relation to the hat-like complex.
description: <strong>Tilt Series Date:</strong> 2020-10-08</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </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> The cells were prepared and sent by Carrie Schaffer from the university of Kentucky. The cells were grown at 37C with 5% CO2 on sheep blood agar plates for 2 days from a -80C. No growth was seen . on the plates after 24 hr therefore the plates were kept in the . incubator for another 24Hr.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100%  humidity. Cu grids. 10 nm . gold</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-210/rawdata/</p>Hpylori_DFliF_FISE_304.mrc,  Tilt Series (Pixel Size 0.452 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-210/rawdata/Hpylori_DFliF_FISE_304.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_304_full.rec,  Reconstruction (Pixel Size 1.808 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-210/3dimage_113908/Hpylori_DFliF_FISE_304_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/kn2b9-35890
title: JV9082_Janelia42k

description: DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2018-08-29</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: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </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.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV9082 strain (2x concentrated culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 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/dga2018-08-29-143/rawdata/</p>JV9082_201808290118.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-143/rawdata/JV9082_201808290118.mrc"
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        JV9082_201808290118_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-143/3dimage_96654/JV9082_201808290118_full.rec"
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DOI: 10.22002/fbsjc-3yb71
title: Hpylori_dFliF_FISE

description: These are H_pylori cells that are lacking FliP protein. In these cells, FliF protein was knocked out  .  to examine its relation to the hat-like complex.
description: <strong>Tilt Series Date:</strong> 2020-10-08</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </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> The cells were prepared and sent by Carrie Schaffer from the university of Kentucky. The cells were grown at 37C with 5% CO2 on sheep blood agar plates for 2 days from a -80C. No growth was seen . on the plates after 24 hr therefore the plates were kept in the . incubator for another 24Hr.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100%  humidity. Cu grids. 10 nm . gold</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-355/rawdata/</p>Hpylori_DFliF_FISE_360.mrc,  Tilt Series (Pixel Size 0.452 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-355/rawdata/Hpylori_DFliF_FISE_360.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_360_full.rec,  Reconstruction (Pixel Size 1.808 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-355/3dimage_114188/Hpylori_DFliF_FISE_360_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/7dknm-hzc09
title: Hpylori_dFliF_FISE

description: These are H_pylori cells that are lacking FliP protein. In these cells, FliF protein was knocked out  .  to examine its relation to the hat-like complex.
description: <strong>Tilt Series Date:</strong> 2020-10-08</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </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> The cells were prepared and sent by Carrie Schaffer from the university of Kentucky. The cells were grown at 37C with 5% CO2 on sheep blood agar plates for 2 days from a -80C. No growth was seen . on the plates after 24 hr therefore the plates were kept in the . incubator for another 24Hr.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100%  humidity. Cu grids. 10 nm . gold</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-420/rawdata/</p>Hpylori_DFliF_FISE_425.mrc,  Tilt Series (Pixel Size 0.452 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-420/rawdata/Hpylori_DFliF_FISE_425.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_425_full.rec,  Reconstruction (Pixel Size 1.808 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-420/3dimage_114316/Hpylori_DFliF_FISE_425_full.rec"
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DOI: 10.22002/cfx7b-j8h87
title: Myxococcus xanthus delta-pilC

description: grid box YWC060
description: <strong>Tilt Series Date:</strong> 2013-12-26</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 180.0 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 form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 48 hr in shaking CTT medium at 30 degrees without antibiotics. OD600=0.7</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. -4 offset, 4 sec blot time, 1s drain. Ethane/propane mix. Grid: Quantifoil Cu 2/2 Finder. 20 nm gold beads.</p>
  ycw2013-12-26-43_slicer9059.jpg: Myxococcus xanthus .  Filament bundle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-26-43/rawdata/</p>20131226_Janelia_YWC060_10030.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-26-43/rawdata/20131226_Janelia_YWC060_10030.mrc"
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        20131226_Janelia_YWC060_10030_full.rec,  Reconstruction (Pixel Size 1.68 nm), 688.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-26-43/3dimage_37128/20131226_Janelia_YWC060_10030_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.10685278
title: Datos limpios asociados a mensajes recabados en medios informativos españoles en X (Twitter), Facebook y Web, entre 2021 y 2022

description: Los datos recopilados corresponden a cinco medios informativos digitales, tomados como casos de estudio en el proyecto al que corresponde estos datos, tanto en la plataforma X, como en FB y en sus portales web; durante 2021-2022.

El proceso de recolección de estos datos fueron recolectados, a partir del procedimiento expuesto en:

Ruiz-Iniesta, Almudena; Blanco Valencia, Xiomara; Pérez, Daniel; De Gregorio Vicente, Oscar; José Cubillas, Juan; Julio Montero Díaz, https://orcid.org/0000-0002-4145-7424; et al. (2024). Informe final sobre el scrapeo de datos brutos obtenidos en medios informativos digitales españoles en X, FB y Web. figshare. Presentation. https://doi.org/10.6084/m9.figshare.25187591.v2

El proceso de limpieza de los datos recabados se hizo, a partir del procedimiento expuesto en: Pendiente.

El proceso de limpieza de los datos se puede conocer, ingresando en el siguiente informe: Pendiente

Los datos fueron recolectados con el apoyo de la empresa colaboradora: Possible Inc

Para más información del proyecto, ingresar en: https://www.hatemedia.es/

Si deseas tener acceso a estos datos, contactar con los IPs del proyecto, a traves de: elias.said@unir.net, en copia a julio.montero@unir.net
DOI: 10.5281/zenodo.15258978
title: Data from: Aberrant Striatal Firing Mediates Impulsive Decision-Making in a Mouse Model of Parkinson's Disease

description: Parkinson's disease (PD) is characterized by progressive neurodegeneration, which is associated with motor and non-motor symptoms. Dopamine replacement therapy can remediate motor symptoms, but can also cause impulse control disorder (ICD), characterized by pathological gambling, hypersexuality, and/or compulsive shopping. Approximately 14-40% of all medicated PD patients suffer from ICD. Despite the high prevalence of ICD in medicated PD patients, we know little of its mechanisms, and the main therapeutic strategy is reducing or eliminating dopamine agonist medication. Human imaging studies suggest that the input nucleus of the basal ganglia, the striatum, may be a critical site of circuit dysfunction in ICD. 

To explore the cellular and circuit mechanisms of ICD, we developed a mouse model in which we administered the dopamine D2/3 agonist pramipexole to parkinsonian and healthy control mice. ICD-like behavior was assessed using a delay discounting task. Delay discounting is a normal cognitive phenomenon, in which the value of a reward decreases according to the time needed to wait for it. Impulsivity is measured as the preference for immediate (small) over delayed (large) rewards. We combined this mouse model with chemogenetics and in vivo optically-identified single-unit recordings to examine how dopamine agonists act on vulnerable striatal circuitry to mediate impulsive decision-making.

We found that in parkinsonian mice, therapeutic doses of dopamine D2/3R or D1R agonists drove more pronounced delay discounting, reminiscent of what has been reported in PD/ICD patients on medication. In contrast, healthy mice did not become more impulsive when given the same dose of dopamine agonist. The clinically relevant dopamine D2/3R agonist pramipexole induced marked bidirectional changes in the firing of striatal direct and indirect pathway neurons in parkinsonian mice. Chronic pramipexole treatment potentiated these changes in striatal physiology and decision-making behavior. Furthermore, chemogenetic excitation of direct pathway striatal neurons or inhibition of indirect pathway neurons induced impulsive decision making in the absence of dopamine agonists. These findings indicate that abnormal striatal activity plays a causal role in mediating ICD-like behaviors. Together, they provide a robust mouse model and insights into ICD pathophysiology.
DOI: 10.5281/zenodo.8305248
title: Deliverable 2.2: Biodiversity indicator database for focus regions

description: To quantify human-driven impacts on biodiversity, we used advanced modeling techniques paired with a few key variables such as habitat quality, vegetation structure, climate, and topography to develop an innovative predictive model that estimates both 1) current biodiversity patterns and distributions and 2) a baseline model of biodiversity. By comparing both of these models, we are able to identify regions with significant human-driven reductions in species richness, endemism, and species composition across both of our focus regions, South America and Africa.


The files provided in this repository (1 km2 resolution) include:


1- Species richness (number of species).


2- Endemism (species rarity). For this metric, we used the corrected weight endemism index, which is the inverse of a species’ range size and effectively assigns higher scores to species with more restricted distributions. For this index, we used species ranges found within our study area (of South America and Africa).


3- Species composition of vertebrates, invertebrates, and plants (which species occur in a given location). This metric, also known as beta diversity, summarizes which sets of species occur at each location. For this, we used the Sorensen index metric, as it does not depend on species absence data.


These results provide a valuable first step in describing human-induced changes in vegetation and biodiversity patterns across both South America and Africa.
description: This project has received funding from the European Research Executive Agency under HORIZON Research and Innovation Actions, grant agreement no101060765
DOI: 10.5281/zenodo.16903052
title: STOPUP. WP1. Pollution risk characterization. Task1.2. Off-line measurements
DOI: 10.22002/6cx0c-9j527
title: SA5718_cryoPALM(20130220)

description: Cell with VipA-PA-GFP/ΔvipA.First imaged by cryoPALM.Grid dried up inside Polara column overtime.
description: <strong>Tilt Series Date:</strong> 2013-06-08</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-61.0°, 53.0°), step: 1.0°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -8.0 μm,  magnification: 22500x. </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 from Lotte Søgaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> (1) Cells grown 48 hr in CTT medium at 30 degrees without antibiotics to OD600~0.8. (2) 250 ul CTT with 20 % Dextran + 1 ul Invitrogen 200 nm orange fluosphere. (3) take 10 ul of the mixture and add into gold fiducial pellet. (4) add 10 ul cells prior to plunge freezing</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. -3 offset, 4 sec blot time, no drain. Ethane/propane mix. Grid: Quantifoil Au Finder.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-06-08-18/rawdata/</p>20130608_20130220_SA5718_cryoPALM_10018.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.3 GB  
        
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        20130608_20130220_SA5718_cryoPALM_10018_full.rec,  Reconstruction (Pixel Size 1.92 nm), 712.7 MB  
        
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DOI: 10.5281/zenodo.8322777
title: Dataset underpinning the development of a  PBK model for inhalation of TiO2 NPs in rats

description: This dataset contains concentration-time profiles (expressed as % of the initial dose) of 20 nm TiO2 nanoparticles following a 2-hour inhalation experiment in rats, with tissue and excreta samples taken over a period of 28 days post exposure. The data were extracted from the publication of Kreyling et al. (2019) (https://doi.org/10.1186/s12989-019-0303-7)
DOI: 10.5281/zenodo.8321246
title: Images of daphnids (control and exposed to NMs) over multiple generations, scored by experts as toxic or non-toxic and the resulting deepDaph predictions

description: Background


This study showcases a pioneering application of deep learning methodologies in ecotoxicology, aimed at facilitating hazard assessment and safer design of engineered nanomaterials (ENMs). The research hinges on a high-quality dataset comprising microscopic images of Daphnia magna exposed to various ENMs, collected systematically under controlled conditions.


The Dataset: A Cornerstone of Nanoinformatics


Our dataset, which will be openly accessible on Zenodo, serves as a foundational resource for the ecotoxicology community. It contains high-resolution images tagged with intricate details like malformations, tail lengths, lipid concentrations, and lipid deposit shapes. Researchers can use this exhaustive dataset to train a variety of predictive models for diverse applications.


Methodology


We employ two different deep learning architectures to process the dataset. These architectures automatically detect malformations and assess the impact of ENMs on D. magna by classifying various biological structures based on lipid densities.


Results and Validation


The developed models demonstrate high statistical validation, confirming their prediction accuracy on external D. magna images. Our dataset and the associated models not only accelerate manual procedures but also pave the way for automated, high-throughput analyses in ecotoxicology.


Future Prospects


The dataset holds the potential to extend investigations into predicting the impacts on future generations from parental exposures, thus reducing the time and cost of multi-generational toxicity assays.
DOI: 10.22002/d2sr4-63z74
title: Sulfolobus solfac.P2+STIV

description: STIV - infected Sulfolobus solfataricus, Sulfolobus turreted icosahedral virus, Taxonomy ID 269145, Sulfolobus solfataricus, thermophile, pyramid, intrapyramidal body, virus infection 2-4 hour post infection
description: <strong>Tilt Series Date:</strong> 2014-03-13</p>
<strong>Data Taken By:</strong> Rasika Ramdasi</p>
<strong>Species / Specimen:</strong> Sulfolobus solfataricus </p>
<strong>Strain:</strong> P2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-55.0°, 55.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 18000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSF TOMO</p>
<strong>Collaborators and Roles:</strong> With Jamie Snyder at MSU, Montana.</p>
<strong>Sample Preparation:</strong> S. solfataricus strain P2 cultures were infected with STIV as previously described (Ortmann et al., 2006). Sulfolobus were grown up from glycerol stock in media 182 (pH 3.5), 80°C and passage once. The cultures were passed second time to media 182 (pH 2.5) and infected with STIV at MOI ~10 at OD 650 nm ~0.2. At 2-4 hour Post infection, cells were concentrated ~20 fold by centrifugation.</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-03-13-10/rawdata/</p>stiv4hatlas10006.mrc,  Tilt Series (Pixel Size 0.63 nm), 3.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-03-13-10/rawdata/stiv4hatlas10006.mrc"
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        stiv4hatlas10006_full.rec,  Reconstruction (Pixel Size 2.52 nm), 623.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-03-13-10/3dimage_40126/stiv4hatlas10006_full.rec"
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