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700 results for “ex vivo”
Dataset of "Optical Signatures of Thermal Damage on ex-vivo Brain, Lung and Heart Tissues using Time-Domain Diffuse Optical Spectroscopy"
<p>Dataset for the article entitled "Optical Signatures of Thermal Damage on ex-vivo Brain, Lung and Heart Tissues using Time-Domain Diffuse Optical Spectroscopy" </p> <p> </p> <p>Abstract:</p> <p> </p> <p>Thermal Therapies treat tumors by means of heat, greatly reducing pain, post-operation complications, and cost as compared to traditional methods. Yet, effective tools to avoid under- or over-treatment are mostly needed, to guide surgeons in laparoscopic interventions.<br>In this work, we investigated the temperature-dependent optical signatures of ex-vivo calf brain, lung, and heart tissues, based on the reduced scattering and absorption coefficients in the near-infrared spectral range (657 to 1107 nm). These spectra were measured by time domain diffuse optics, applying a step-like spatially homogeneous thermal treatment at 43 °C, 60 °C, and 80 °C.<br>We found three main increases in scattering spectra, possibly due to the denaturation of collagen, myosin, and proteins secondary structure.<br>After 75 °C, we found the rise of two new peaks at 770 and 830 nm in the absorption spectra due to the formation of a new chromophore, possibly related to hemoglobin or myoglobin.<br>This research marks a significant step forward in controlling thermal therapies with diffuse optical techniques by identifying several key markers of thermal damage. This could enhance the ability to monitor and adjust treatment in real-time, promising improved outcomes in tumor therapy.</p> <p> </p> <p> </p> <p>Authors:</p> <p>ALESSANDRO BOSSI , LEONARDO BIANCHI , PAOLA SACCOMANDI , AND ANTONIO PIFFERI<br>Politecnico di Milano</p> <p> </p> <p> </p> <p><a href="https://opg.optica.org/boe/fulltext.cfm?uri=boe-15-4-2481&id=548108" target="_blank" rel="noopener">Link to the article</a></p>
Raman spectra from "Discrimination of immune cell activation using Raman micro-spectroscopy in an in-vitro & ex-vivo model"
<p>The uploaded files are data from Chaudhary et al, 2021 (Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Discrimination of immune cell activation using Raman micro-spectroscopy in an in-vitro & ex-vivo model, https://doi.org/10.1016/j.saa.2020.119118).</p> <p>There are two files in .mat format. In one (Preprocessed.mat) the data has been completely pre-processed according to the methods described in the paper.</p> <p>In the second (Unpreprocessed.mat) the data has been calibrated using the methods described in the paper, but has not received further pre-processing.</p> <p>Within both files there are datasets for the spectral measurement from each cell (‘spectra’), together with the treatment which was applied to each sample (‘treatment’) and the wavenumber at which the spectral measurements were made (‘wavenumber’).</p>
Dataset published in the article: "Electrospun poly(L-lactide-co-DL-lactide) nanofibrous scaffold as substrate for ex vivo limbal epithelial cell cultivation"
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Raw Data for the article: Klebsiella pneumoniae Lipopolysaccharides Serotype O2afg Induce Poor Inflammatory Immune Responses Ex Vivo
<p>Currently, <em>Klebsiella pneumoniae</em> is a pathogen of clinical relevance due to its plastic ability of acquiring resistance genes to multiple antibiotics. During <em>K. pneumoniae</em> infections, lipopolysaccharides (LPS) play an ambiguous role as they both activate immune responses but can also play a role in immune evasion. The LPS O2a and LPS O2afg serotypes are prevalent in most multidrug resistant <em>K. pneumoniae</em> strains. Thus, we sought to understand if those two particular LPS serotypes were involved in a mechanism of immune evasion. We have extracted LPS (serotypes O1, O2a and O2afg) from <em>K. pneumoniae</em> strains and, using human monocytes ex vivo, we assessed the ability of those LPS antigens to induce the production of pro-inflammatory cytokines and chemokines. We observed that, when human monocytes are incubated with LPS serotypes O1, O2a or O2afg strains, O2afg and, to a lesser extent, O2a but not O1 failed to elicit the production of pro-inflammatory cytokines and chemokines, which suggests a role in immune evasion. Our preliminary data also shows that nuclear translocation of NF-κB, a process which regulates an immune response against infections, occurs in monocytes incubated with LPS O1 and, to a smaller extent, with LPS O2a, but not with the LPS serotype O2afg. Our results indicate that multidrug resistant <em>K. pneumoniae</em> expressing LPS O2afg serotypes avoid an initial inflammatory immune response and, consequently, are able to systematically spread inside the host unharmed, which results in the several pathologies associated with this bacterium.</p>
Figure 1. Kaempferol-3-O in Analysis of the toxicological and pharmacokinetic profile of Kaempferol-3-O-β-D-(6"-E-p-coumaryl) glucopyranoside - Tiliroside: in silico, in vitro and ex vivo assay
Figure 1. Kaempferol-3-O-β-D-(6"-E-p-coumaryl) glucopyranoside – tiliroside.
Ex vivo modeling of precision immuno-oncology responses in lung cancer
<p>Single-cell RNA-sequencing (scRNA-seq) data from paired lung cancer organoids and immune cells. The experiment was performed using the Single Cell 5' solution of 10X Genomics. </p> <p>The dataset includes 15 samples from 4 multiplexed experiments. The multiplexing was performed using the Feature Barcoding technology of 10X Genomics.</p> <table> <tbody> <tr> <td><strong>Sample name</strong></td> <td><strong>Multiplexed experiment</strong></td> <td><strong>Donor<br></strong></td> <td><strong>Hashtag name</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>1-PBMCs_lung-19</td> <td>PBMCs_demux</td> <td>Lung-19</td> <td>Hashtag_1</td> <td>Untreated, baseline PBMCs for Lung-19</td> </tr> <tr> <td>2-PBMCs_lung-35</td> <td>PBMCs_demux</td> <td>Lung-35</td> <td>Hashtag_2</td> <td>Untreated, baseline PBMCs for Lung-35</td> </tr> <tr> <td>3-PBMCs_Lung-25</td> <td>PBMCs_demux</td> <td>Lung-25</td> <td>Hashtag_3</td> <td>Untreated, baseline PBMCs for Lung-25</td> </tr> <tr> <td>4-T_cells_Lung-19</td> <td>PBMCs_demux</td> <td>Lung-19</td> <td>Hashtag_4</td> <td>Tumor-stimulated immune cells for Lung-19</td> </tr> <tr> <td>5-T_cells_Lung-35</td> <td>PBMCs_demux</td> <td>Lung-35</td> <td>Hashtag_5</td> <td>Tumor-stimulated immune cells for Lung-35</td> </tr> <tr> <td>6-T_cells_Lung-25</td> <td>PBMCs_demux</td> <td>Lung-25</td> <td>Hashtag_6</td> <td>Tumor-stimulated immune cells for Lung-25</td> </tr> <tr> <td>1-Lung-19_tumor_cells</td> <td>Tumor_cells_1_demux</td> <td>Lung-19</td> <td>Hashtag_1</td> <td>Tumor cells alone for Lung-19</td> </tr> <tr> <td>2-Lung-35_T_tumor_cells</td> <td>Tumor_cells_1_demux</td> <td>Lung-35</td> <td>Hashtag_2</td> <td>Tumor cells alone for Lung-35</td> </tr> <tr> <td>3-Lung-25_tumor_cells</td> <td>Tumor_cells_1_demux</td> <td>Lung-25</td> <td>Hashtag_3</td> <td>Tumor cells alone for Lung-25</td> </tr> <tr> <td>1-Lung-19_tumor_cells_T_cells</td> <td>Tumor_cells_2_demux</td> <td>Lung-19</td> <td>Hashtag_7</td> <td>Tumor cells and ts-immune cells for Lung-19</td> </tr> <tr> <td>2-Lung-35_T_tumor_cells_T_cells</td> <td>Tumor_cells_2_demux</td> <td>Lung-35</td> <td>Hashtag_8</td> <td>Tumor cells and ts-immune cells for Lung-35</td> </tr> <tr> <td>3-Lung-25_tumor_cells_T_cells</td> <td>Tumor_cells_2_demux</td> <td>Lung-25</td> <td>Hashtag_9</td> <td>Tumor cells and ts-immune cells for Lung-25</td> </tr> <tr> <td>1-Lung-19_tumor_cells_T_cells_Nivolumab</td> <td>Tumor_cells_3_demux</td> <td>Lung-19</td> <td>Hashtag_10</td> <td>Tumor cells and ts-immune cells + Nivolumab for Lung-19</td> </tr> <tr> <td>2-Lung-35_T_tumor_cells_T_cells_Nivolumab</td> <td>Tumor_cells_3_demux</td> <td>Lung-35</td> <td>Hashtag_12</td> <td>Tumor cells and ts-immune cells + Nivolumab for Lung-35</td> </tr> <tr> <td>3-Lung-25_tumor_cells_T_cells_Nivolumab</td> <td>Tumor_cells_3_demux</td> <td>Lung-25</td> <td>Hashtag_13</td> <td>Tumor cells and ts-immune cells + Nivolumab for Lung-25</td> </tr> </tbody> </table> <p>This Zenodo repository provides:</p> <ul> <li>Processed RNA-seq and hashtag oligo sequencing (HTO-seq) data (<em>feature_bc_matrices.zip</em>)</li> <li>Hashtag names and sequences (<em>Custom_CMO_set.csv</em>), which are needed to rerun Cellranger</li> <li>Seurat v5 objects (<em>seurat_object_all_tumor_cells.rds, seurat_object_all_immune_cells.rds, seurat_object_PBMCs_demux.rds</em>)</li> </ul> <p>This Zenodo repository does <strong>not </strong>provide:</p> <ul> <li>Sensitive raw sequencing data</li> <li>Sensitive metadata</li> </ul> <p>The raw data generated from the scRNA sequencing is available at the European Genome-phenome Archive (EGA; <a href="https://ega-archive.org">https://ega-archive.org</a>) under accession number EGAD50000000845.</p> <div> <div> <p> </p> <p><strong>To cite our work</strong>:</p> </div> Bassel Alsaed <em>et al.</em> Ex vivo modeling of precision immuno-oncology responses in lung cancer.<em>Sci. Adv.</em><strong>10</strong>,eadq6830(2024).DOI:<a href="https://doi.org/10.1126/sciadv.adq6830">10.1126/sciadv.adq6830</a></div>
Ex vivo 100 μm isotropic diffusion MRI‐based tractography of connectivity changes in the end‐stage R6/2 mouse model of Huntington's disease
<div> <div> <div> <div> <p><strong>Background</strong>: Huntington's disease is a progressive neurodegenerative disorder. Brain atrophy, as measured by volumetric magnetic resonance imaging (MRI), is a downstream consequence of neurodegeneration, but microstructural changes within brain tissue are expected to precede this volumetric decline. The tissue microstructure can be assayed non-invasively using diffusion MRI, which also allows a tractographic analysis of brain connectivity.</p> <p><strong>Methods</strong>: We here used ex vivo diffusion MRI (11.7T) to measure microstructural changes in different brain regions of end‐stage (14 weeks of age) wild type and R6/2 mice (male and female) modeling Huntington's disease. To probe the microstructure of different brain regions, reduce partial volume effects and measure connectivity between different regions, a 100 μm isotropic voxel resolution was acquired.</p> <p><strong>Results</strong>: Although fractional anisotropy did not reveal any difference between wild‐type controls and R6/2 mice, mean, axial, and radial diffusivity were increased in female R6/2 mice and decreased in male R6/2 mice. Whole brain streamlines were only reduced in male R6/2 mice, but streamline density was increased. Region‐to‐region tractography indicated reductions in connectivity between the cortex, hippocampus, and thalamus with the striatum, as well as within the basal ganglia (striatum—globus pallidus—subthalamic nucleus—substantia nigra—thalamus).</p> <p><strong>Conclusions</strong>: Biological sex and left/right hemisphere affected tractographic results, potentially reflecting different stages of disease progression. This proof‐of‐principle study indicates that diffusion MRI and tractography potentially provide novel biomarkers that connect volumetric changes across different brain regions. In a translation setting, these measurements constitute a novel tool to assess the therapeutic impact of interventions such as neuroprotective agents in transgenic models, as well as patients with Huntington's disease.</p> </div> </div> </div> </div>
Long-term Follow-up of Subjects With Transfusion-Dependent β-Thalassemia (TDT) Treated With Ex Vivo Gene Therapy
ClinicalTrials.gov study NCT02633943. IPD Sharing: YES. Countries: 8. Publications: 3.
Transplantation of NiCord®, Umbilical Cord Blood-derived Ex Vivo Expanded Cells, in Patients With HM
ClinicalTrials.gov study NCT01816230. IPD Sharing: Not stated. Countries: 5. Publications: 1.
A Prospective Study of Remestemcel-L, Ex-vivo Cultured Adult Human Mesenchymal Stromal Cells, for the Treatment of Pediatric Participants Who Have Failed to Respond to Steroid Treatment for Acute Graf
ClinicalTrials.gov study NCT02336230. IPD Sharing: NO. Countries: 1. Publications: 1.
Allogeneic SCT of NiCord®, UCB-Derived Ex Vivo Expanded Stem and Progenitor Cells, in Patients With Hemoglobinopathies
ClinicalTrials.gov study NCT01590628. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Long-term Follow-up of Subjects with Sickle Cell Disease Treated with Ex Vivo Gene Therapy
ClinicalTrials.gov study NCT04628585. IPD Sharing: YES. Countries: 2. Publications: 1.
Autologous CD34+ Hematopoietic Stem Cells Transduced ex Vivo With Elongation Factor 1 Alpha Shortened (EFS) Lentiviral Vector Encoding for the Human ADA Gene
ClinicalTrials.gov study NCT01852071. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Evaluation of cCeLL-Ex Vivo Confocal Microscopy for Real-time Brain Tumor Diagnosis
ClinicalTrials.gov study NCT06098248. IPD Sharing: NO. Countries: 2. Publications: 6.
Ex-vivo Perfusion and Ventilation of Lungs Recovered From Non-Heart-Beating Donors to Assess Transplant Suitability
ClinicalTrials.gov study NCT01615484. IPD Sharing: UNDECIDED. Countries: 1. Publications: 11.
Ex vivo 100 μm isotropic diffusion MRI‐based tractography of connectivity changes in the end‐stage R6/2 mouse model of Huntington's disease
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Ex vivo Mesoscale human temporal lobe dataset
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Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"
<p>Phase-contrast CT of BDL rats liver-8 week</p>
Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"
<p>Phase-contrast CT of BDL rats liver-6 week</p>
Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"
<p>Phase-contrast CT of BDL rats liver-control group</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.