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4,004 results for “In vivo”
In Vivo Contactless Brain Nanothermometry
<p>Dataset accompanying figures published in the publication <a href="https://zenodo.org/record/3552591">https://zenodo.org/record/3552591</a></p>
Figure 3 in Embryonic development of the olive fruit fly, Bactrocera oleae Rossi (Diptera: Tephritidae), in vivo
Figure 3. Hatching of Bactrocera oleae egg by 66 h (A, B, C, and D).
Primary in vivo screen for MAPK/ERK pathway inhibitors among 433 annotated oncology related compounds
<p>The aim was to test if a C. elegans model could identify known MEK inhibitors in a blinded screen of 433 annotated oncology related compounds. Primary hits were further validated for pathway specificity. Please see the paper cross-reference for more details.</p> <p>We bought a chemical library (SciLife lab, Stockholm, Sweden) with 433 oncology-related compounds (see table S1 for the full list), where compounds had been acoustically dispensed from 10 mM stocks into 96-well plates. DMSO concentrations were adjusted to 0.5 % in all wells, including negative controls. Trametinib was used as a positive control at 7 muM. All chemicals were kept at -20 degrees C until use. The C. elegans strain ST65 was used. We dispensed 50 muL of worm culture into each well and incubated animals for 4-5 days at 20 degrees C until DMSO control animals reached early adulthood. Animals were then sedated for 30 minutes by adding 4 muL 20 mM levamisole per well before scoring.<br><br>Primary hit selection: 1) Wells were excluded if they contained progeny or fluorescent specles from drugs or bacteria, indicated by too many objects classified as vulvae. The cutoff was set to vulvae >2x the number of adults in the positive control. 2) Wells were excluded they contained < 30 % adults compared to the positive control, indicative of severely reduced larval growth. 3) Remaining compounds with vulvae/adult scores < 0.4 were considered primary hits. Scoring of the Muv phenotype in adult lin-1(e1777) mutants was done manually from ImageXpress images. See the paper cross-reference for more details.</p>
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>
In vivo optimization of the experimental conditions for the non-invasive optical assessment of breast density
<p>We applied time-domain diffuse optical spectroscopy over a broad spectral range (600-1100 nm) to estimate the breast composition in terms of water, lipids, collagen, oxy- and deoxy-hemoglobin concentrations, together with scattering parameters (scattering amplitude <em>a</em> and scattering power <em>b</em>). These optical parameters are correlated with the density of the breast, which is an important risk factor involved in the development of breast cancer. We performed <em>in vivo </em>measurement on 11 healthy volunteers, using a measurement protocol that involves reflectance and transmittance geometries, different positions of the subject and different measurement locations on the breast. This work has been pubblished in Scientific Reports: https://doi.org/10.1038/s41598-024-70099-x .</p> <p>This page contains the dataset generated during this work, togheter with some tools to read it and the analysis that we performed.</p>
In-vivo video microscopy of the rupturing process of thin blood vessels in transparent fish during contact with a blunt indenter
<p>To clarify the mechanism of bruise injuries caused by blunt impact, in vivo microscopy was performed. A flat ended indenter made of transparent acrylic was loaded onto the lateral side of the tail region of anesthetized fish. The process of the rupture of thin blood vessels was recorded in two specimens.</p> <p>This data set includes two types of files; (1) mp4 files of the in vivo microscopy; (2) pdf files to explain the mp4 files.</p> <p><span>The mp4 files are the original data of “Fujikawa, T., Yamada, Y. In vivo video microscopy of the rupturing process of thin blood vessels to clarify the mechanism of bruising caused by blunt impact: an animal study. BioMed Eng OnLine 23, 94 (2024). https://doi.org/10.1186/s12938-024-01284-2.”</span></p>
Computed tomography (CT) was used to study the interaction of NMs with the plant cell tissue in vivo using Zeiss Xradia 510 system on Arabidopsis thaliana leaf. T
<p>This work was supported by the National Research Facility for Lab X-ray CT (NXCT) at the µ-VIS X-ray Imaging Centre, University of Southampton, through EPSRC grant EP/T02593X.</p>
DAPI images, molecules and segmentation boundaries for: A Spatiotemporal Atlas of Mouse Gastrulation and Early Organogenesis to Explore Axial Patterning and Project In Vitro Models onto In Vivo Space
<div> </div> <p><strong>Data Description</strong></p> <ol> <li><strong>Stitched & rotated DAPI images</strong> - tiff file format filename indicates sample and optical z-slice position, i.e. embryo3_z5.tif is the DAPI image for embryo 3 in optical z-slice 5. Also provided in PNG format.</li> <li><strong>Detected molecules and cell segmentation in MoleculeExperiment objects</strong> - RDS files to read data using the MoleculeExperiment format in R/Bioconductor. Filename embryo3_z5.Rds indicates MoleculeExperiment RDS file for embryo 3 in optical z-slice 5. Coordinates are provided in microns. Note that z-slices 2 and 5 are only provided for embryos 1,2,3 as they were originally provided in Lohoff et al, Nature Biotechnology, 2023.</li> <li><strong>Pixels-to-microns conversion</strong> - pixelSize.R Simple R script/text to indicate the size of each pixel in the DAPI images, this is to align the coordinate systems between the DAPI images and molecules.<br><br> <div> <h4>Project Abstract</h4> </div> <p>At the onset of murine gastrulation, pluripotent epiblast cells migrate through the primitive streak, generating mesodermal and endodermal precursors, while the ectoderm arises from the remaining epiblast. Together, these germ layers establish the body plan, defining major body axes and initiating organogenesis. Although comprehensive single cell transcriptional atlases of dissociated mouse embryos across embryonic stages have provided valuable insights during gastrulation, the spatial context for cell differentiation and tissue patterning remain underexplored. In this study, we employed spatial transcriptomics to measure gene expression in mouse embryos at E6.5 and E7.5 and integrated these datasets with previously published E8.5 spatial transcriptomics and a scRNA-seq atlas spanning E6.5 to E9.5. This approach resulted in a comprehensive spatiotemporal atlas, comprising over 150,000 cells with 88 refined cell type annotations as well as genome-wide transcriptional imputation during mouse gastrulation and early organogenesis. The atlas facilitates exploration of gene expression dynamics along anterior-posterior and dorsal-ventral axes at cell type, tissue, and organismal scales, revealing insights into mesodermal fate decisions within the primitive streak. Moreover, we developed a bioinformatics pipeline to project additional scRNA-seq datasets into a spatiotemporal framework and demonstrate its utility by analysing cardiovascular models of gastrulation3. To maximise impact, the atlas is publicly accessible via a user-friendly web portal empowering the wider developmental and stem cell biology communities to explore mechanisms of early mouse development in a spatiotemporal context.</p> </li> </ol>
Artifacts for the FDL21 Paper: In-Vivo Stack Overflow Detection and Stack Size Estimation for Low-End Multithreaded Operating Systems using Virtual Prototypes
<p>Artifacts for the evaluation of the paper <em>In-Vivo Stack Overflow Detection and Stack Size Estimation for Low-End Multithreaded Operating Systems using Virtual Prototypes</em> which will be published as part of <a href="http://www.fdl-conference.org">FDL21</a>. The artifacts provided here use pre-compiled binaries and pre-generated stack usage databases. Based on these provided files, the stack size estimation and performance evaluation performed in the paper can be replicated. Various README.md files, which provide more information on individual artifacts, are also included.</p> <p>The software used in conjunction with these artifacts is also freely available on GitHub:</p> <ul> <li>https://github.com/agra-uni-bremen/fdl21-stackuse-vp</li> <li>https://github.com/agra-uni-bremen/stack-usage-db</li> </ul>
Data From: Fear conditioning potentiates the Hippocampal CA1 commissural pathway In vivo and increases awake phase sleep
<p>The hippocampus is essential for spatial learning and memory. To assess learning we used contextual fear conditioning (cFC), where animals learn to associate a place with aversive events like foot-shocks. Candidate memory mechanisms for cFC are long-term potentiation and long-term depression, but there is little direct evidence of them operating in the hippocampus in vivo following cFC. Also, little is known about the behavioral state changes induced by cFC. To address these issues, we recorded local field potentials in freely behaving mice by stimulating in the left dorsal CA1 region and recording in the right dorsal CA1 region. Synaptic strength in the commissural pathway was monitored by measuring field excitatory postsynaptic potentials (fEPSPs) before and after cFC. After cFC, the commissural pathway's synaptic strength was potentiated. Although recordings occurred during the wake phase of the light/dark cycle, the mice slept more in the post-conditioning period than in the pre-conditioning period. Relative to awake periods, in non-rapid eye movement (NREM) sleep the fEPSPs were larger in both pre- and post-conditioning periods. We also found a significant negative correlation between the animal's speed and fEPSP size. Therefore, to avoid confounds in the fEFSP potentiation estimates, we controlled for speed-related and sleep-related fEPSP changes and still found that cFC induced long-term potentiation, but no significant long-term depression. Synaptic strength changes were not found in the control group that simply explored the fear-conditioning chamber, indicating that exploration of the novel place did not produce the measurable effects caused by cFC. These results show that following cFC, the CA1 commissural pathway is potentiated, likely contributing to the functional integration of the left and right hippocampi in fear memory consolidation. In addition, the cFC paradigm produces significant changes in an animal's behavioral state, which are observable as proximal changes in sleep patterns.</p>
ARRIVE Questionnaire, CONSORT Check-list and Flow Diagram + TGO, TGP, HEMOGRAMA AND OSTEOREGENERATIVE DATA - Paper: "Biological performance of a bioabsorbable Poly (L-Lactic Acid) produced in polymerization unit: in vivo studies"
<p>The data in excel refer to 3 types of experimental analysis:</p> <p>1- Hepatocyte transaminase studies for animals at 6 and 9 months post implantation, implanted with PLLA and not implanted with PLLA.</p> <p>2- Hemogram studies for animals 6 and 9 months after implantation, implanted with PLLA and not implanted with PLLA. These data are divided in 2 files, one file for animals of 6 months and another file for animals of 9 months</p> <p>3- Bone lesion regeneration area study for animals 6 and 9 months after implantation, implanted with PLLA and not implanted with PLLA.</p> <p>4- File for CONSORT Checklist</p> <p>5- File for ARRIVE questionnaire</p> <p>6- File for Flow Diagram</p>
Supplementary datasets for the paper of "Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization"
<p>There are two eCLIP datasets (cell lines of K562 and HepG2). The eCLIP datasets were then divided into five categories for each cell line: low, medium 1, medium 2, high 1 and high 2 with peaks of >1,000 but <2,000, >2,000 but <4,000, >4,000 but <7,000, >7,000 but <10,000 and >10,000, respectively. </p>
Engineering gene overlaps to sustain genetic constructs in vivo
<p>Experimental data, simulation data, and code for data analysis and figure production for the paper "Engineering gene overlaps to sustain genetic constructs in vivo" (Decrulle, Frenoy, et al, PloS Computational Biology)</p>
Source data for - Bidirectional alterations in brain temperature profoundly modulate spatiotemporal neurovascular responses in-vivo: Implications for theragnostics
<p>Neurovascular coupling (NVC) is a mechanism that, amongst other known and latent critical functions, ensures activated brain regions are adequately supplied with oxygen and glucose. This biological phenomenon underpins non-invasive perfusion-related neuroimaging techniques, and recent reports have implicated NVC impairment in several neurodegenerative disorders. Yet, much remains unknown regarding NVC in health and disease, and only recently has there been burgeoning recognition of a close interplay with brain thermodynamics. Accordingly, we developed a novel multi-modal approach to systematically modulate cortical temperature and interrogate the spatiotemporal dynamics of sensory-evoked NVC. We show that changes in cortical temperature profoundly and intricately modulate NVC, with low temperatures associated with diminished oxygen delivery, and high temperatures inducing a distinct vascular oscillation. These observations provide novel insights into the relationship between NVC and brain thermodynamics, with important implications for brain-temperature-related therapies, functional biomarkers of elevated brain temperature, and in-vivo methods to study neurovascular coupling.</p>
A custom-made AAV1 variant (AAV1-T593K) enables efficient transduction of Japanese quail neurons in vitro and in vivo
<p><span>The widespread use of rodents in neuroscience has prompted the development of optimized viral variants for transduction of brain cells, <em>in vivo</em>. However, many of the viruses developed are less efficient in other model organisms, with birds being among the most resistant to transduction by current viral tools. Resultantly, the use of genetically-encoded tools and methods in avian species is markedly lower than in rodents; likely holding the field back. We sought to bridge this gap by developing custom viruses towards the transduction of brain cells of the Japanese quail. We first develop a protocol for culturing primary neurons and glia from quail embryos, followed by characterization of cultures via immunostaining, single-cell mRNA sequencing, patch clamp electrophysiology and calcium imaging. We then leverage the cultures for the rapid screening of various viruses, only to find that all yielded poor to no infection of cells <em>in vitro</em>. However, few infected neurons were obtained by AAV1 and AAV2. Scrutiny of the sequence of the AAV receptor found in quails led us to rationally design a custom-made AAV variant (AAV1-T593K; AAV1*) that exhibits improved transduction efficiencies <em>in vitro</em> and <em>in vivo</em> (eight- and five-fold, respectively). Together, we present a unique culturing method, transcriptomic profiles of quail's brain cells and a custom-tailored AAV1 for transduction of quail neurons <em>in vitro </em>and<em> in vivo.</em></span></p>
Data from "Artificial intelligence velocimetry reveals in vivo flow rates, pressure gradients, and shear stresses in murine perivascular flows"
<p>This is data from the paper "Artificial intelligence velocimetry reveals in vivo flow rates, pressure gradients, and shear stresses in murine perivascular flows" published in PNAS, 2023</p> <p>This is the raw imaging data from Mouse 1. The .raw file is the particle tracking video, and Geometry4.mat is a Matlab file containing the 3D z-stack and accompanying segmentation (pvs_smooth). Details regarding the subject and imaging can be found in the published paper.</p> <p>Additional codes and data used in the paper will be made available upon request.</p>
Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements
<p>A library of 50 enhancers, each tested in three different lengths and with two different promoters (300 combinations), was packaged into AAV9 and delivered to newborn mice. Enhancers were selected from the VISTA Enhancer Browser of transgenic reporter data, and included 25 candidates active in the embryonic myocardium and 25 negative control candidates active in embryonic endothelium but not in myocardium. In the heart, AAV9 selectively transduces cardiomyocytes. After collecting ventricles at P28, the reporter transcripts were sequenced, and the frequency of each barcode was compared to its frequency in the viral pool DNA.</p> <p>Here we provide fastq files for each sample, an Excel spreadsheet (MPRA-Metadata.xls) containing annotation, and an Excel spreadsheet (MPRA-counts.xlsx) containing extracted barcode counts for each enhancer, as well as additional annotation and calculated enhancer activity.</p>
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>
Cell tracking data from: Automated timelapse data segmentation reveals in vivo cell state dynamics
<p>Embryonic development proceeds as a series of orderly cell state transitions built upon noisy molecular processes. Here, we defined gene expression and cell motion states using single cell RNA sequencing data and in vivo timelapse cell tracking data of the zebrafish tailbud. We performed a parallel identification of these states using dimensional reduction methods and a change point detection algorithm. Both types of cell states were quantitatively mapped onto embryos, and we utilized the cell motion states to study the dynamics of biological state transitions over time. The time average pattern of cell motion states is reproducible among embryos. However, individual embryos exhibit transient deviations from the time average forming left-right asymmetries in collective cell motion. Thus, the reproducible pattern of cell states and bilateral symmetry arises from temporal averaging. In addition, collective cell behavior can be a source of asymmetry rather than a buffer against noisy individual cell behavior.</p>
The essential clathrin adaptor protein complex-2 is tumor suppressive specifically in vivo
<p>Full Immunoblots from publication</p>
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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.