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4,004 results for “In vivo”
In vivo imaging of retrovirus infection reveals a role for Siglec-1/CD169 in multiple routes of transmission
<p>Early events in retrovirus transmission are determined by interactions between incoming viruses and frontline cells near entry sites. Despite their importance for retroviral pathogenesis, very little is known about these events. We developed a bioluminescence imaging (BLI)-guided multiscale imaging approach to study these events <i>in vivo</i>. Engineered murine leukemia reporter viruses allowed us to monitor individual stages of retrovirus life cycle including virus particle flow, virus entry into cells, infection and spread for retroorbital, subcutaneous and oral routes. BLI permitted temporal tracking of orally administered retroviruses along the gastrointestinal tract as they traversed the lumen through Peyer's Patches to reach the draining mesenteric sac. Importantly, capture and acquisition of lymph-, blood- and milk-borne retroviruses spanning three routes, was promoted by a common host factor, the I-type lectin CD169, expressed on sentinel macrophages. These results highlight how retroviruses co-opt the immune surveillance function of tissue resident sentinel macrophages for establishing infection.</p>
Accurate In Vivo Nanothermometry through NIR-II Lanthanide Luminescence Lifetime
<p>Dataset of https://zenodo.org/record/5805844#.YcmOK2jMJPY</p>
Raw data for "A-Proof-of -Concept: In vivo Volatile Organic Compounds Secretion Monitoring as a Tool for Prediction of Natural Pest Control Ability"
<p>This upload refers to work entitled "A-Proof-of -Concept: In vivo Volatile Organic Compounds Secretion Monitoring as a Tool for Prediction of Natural Pest Control Ability" and contains the unprocessed data obtained during experiments perform. </p>
ACE2-IgG1 fusions with improved in vitro and in vivo activity against SARS-CoV-2
<p>These are raw data for figures in ACE2-IgG1 fusions with improved in vitro and in vivo activity against SARS-CoV-2, in iScience: PMID: 34957381</p>
Data from: In vivo human whole-brain Connectom diffusion MRI dataset at 760 µm isotropic resolution (PART I)
<p>This whole-brain in vivo diffusion MRI dataset was acquired at 760 µm isotropic resolution and sampled at 1260 q-space points across 9 two-hour sessions on a single healthy subject. It was acquired using state-of-the-art acquisition hardware and advanced reconstruction to achieve high SNR at such resolution, including a high-gradient-strength Connectom scanner, a custom-built 64-channel phased-array coil, a personalized motion-robust head stabilizer, a recently developed SNR-efficient dMRI acquisition, and parallel imaging reconstruction with advanced ghost reduction algorithms. With its unprecedented high resolution, SNR and image quality, it could help explore the fine-scale structures of in vivo human brain, and further advance the understanding of human brain connectivity. This dataset can also be used as a test bed for further technical development of new modeling, sub-sampling strategies, denoising and processing algorithms for in vivo high resolution dMRI. Whole brain anatomical T<sub>1</sub>-weighted and T<sub>2</sub>-weighted images at submillimeter scale, field maps and the code for preprocessing pipeline are also made available in the repository.</p>
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>
In vivo characterization of antibodies directed against TREAT-AD target proteins in mouse model of AD pathology
<p><em>In vivo </em>characterization of antibodies directed against TREAT-AD target proteins (Moesin, CD44, Midkine, and SFRP1) in the 5xFAD mouse model</p>
Understanding muscle function during perturbed in vivo locomotion using a muscle avatar approach
<p>To investigate in vivo mechanics of the guinea fowl lateral gastrocnemius (LG) muscle during obstacle negotiation while running on a treadmill, we used mouse extensor digitorum longus (EDL) muscles in ex vivo experiments with in vivo strain inputs from perturbed and steady strides obtained in a previous study. In vivo strain trajectories from a stride down from obstacle to treadmill, two strides up from treadmill to obstacle, and a level stride with no obstacle, as well as a sinusoidal strain trajectory at the same amplitude and frequency, were used as inputs in work loop experiments. With five strain trajectories and three activation patterns, each muscle was used in a total of 15 work loop experiments. EDL forces produced using in vivo strain trajectories were more similar to in vivo LG forces (<em>R<sup>2</sup></em> = 0.58 – 0.94) than to forces produced using the sinusoidal trajectory (average <em>R<sup>2</sup></em> = 0.045). Given the same activation, in vivo strain trajectories produced consistent work loops that showed a shift in muscle function from more positive work during strides up from treadmill to obstacle to less positive work in strides down from obstacle to treadmill. Activation, strain trajectory, and activation*strain trajectory interaction had significant effects on all work loop variables, with the interaction having the largest effect on peak force and work per cycle. These results support the hypothesis that muscle is an active material whose viscoelastic properties are tuned by activation, and which produces forces in response to deformations of length associated with time-varying loads.</p>
Overexpression of VEGF in dermal fibroblast cells accelerates the angiogenesis and wound healing function: in vitro and in vivo studies
<p>Human dermal fibroblasts (Hu02) were transfected by pcDNA3.1(-)-VEGF vector. Following selecting fibroblast cells with hygromycin, recombinant cells were investigated in terms of VEGF expression by quantifying method. We used Real-Time PCR assay to quantitate gene expression of vascular endothelial growth factor from manipulated cells and represented VEGF overexpression.</p> <p>Reverse transcription was performed from 1 μg of total RNA transcribed to complementary DNA (cDNA) through 1 μL of random hexamer primer. The reactions were incubated at 70°C for 5 minutes. After that, 5X RT-buffer, dNTP, and RT-enzyme were added, and the mixtures were incubated at 42°C for 60 minutes and 70°C for 10 minutes. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR was performed (Ampliqon, Denmark) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.</p> <p>The normalization and all the data analysis were performed according to RESR and Graph pad-Prism 8 software.<br> For the normalization, it uses the housekeeping gene: β-Actin.<br> Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].<br> </p>
A fast, precise, in-vivo method for micron-level 3D models of corals using dental scanners
<p>1. Several sampling and measurement strategies have been developed to assess biological forms in three dimensions (3D), including corals. However, the effectiveness (in speed and precision) of current 3D methods in scanning and model construction are challenging at small scales (μm – mm).</p> <p>2. In this paper, a practical 3D scanning and model construction tool using an intra-oral dental scanner was assessed to measure the surface area and volume of coral juveniles across multiple species. Intra-oral scanners using confocal imaging are fast, precise to the μm scale, and safe to use with live tissue, thereby eliminating the need to harm or kill the animals. The trial was conducted at the National Sea Simulator at the Australian Institute of Marine Science.</p> <p>3. High-quality 3D scans of individual coral juveniles were successfully generated and integrated automatically into high-resolution (μm) mesh from point clouds. The attained average scanning efficiency was < 2 min./individual, without a significant difference in speed given coral complexity or between live colonies or dead coral skeleton.</p> <p>4. Overall, this fast and precise system could become a promising tool for marine environmental surveys and restoration initiatives. This tool also removes the need to sacrifice animals for measurement analysis, thereby increasing conservation and animal welfare.</p>
Single-cell transcriptome analysis of the in vivo response to viral infection in the cave nectar bat Eonycteris spelaea
<p>Bats are reservoir hosts of many zoonotic viruses with pandemic potential in humans. Here, we<br> utilized single-cell transcriptome sequencing (scRNA-seq) to provide detailed comparative<br> analyses of the immune repertoire and the transcriptional responses in the bat lungs upon in<br> vivo infection with a double-stranded RNA virus, Pteropine orthoreovirus PRV3M. Neutrophils<br> were observed to have basally high IDO1 expression, uniquely amongst mammals currently<br> profiled by scRNA-seq. NK/T cells were the most abundant immune cell type in lung tissue, and<br> included three distinct CD8 + effector T cell populations delineated by the differential expression<br> of KLRB1, GFRA2 and DPP4. We identified NK/T clusters which up-regulated genes involved in<br> T-cell activation and effector function early after viral infection. Alveolar macrophages and<br> classical monocytes were key drivers of antiviral interferon signaling. Infection also resulted in<br> the expansion of a CSF1R + population expressing collagen-like genes, which became the<br> predominant myeloid cell type after infection. This work uncovers novel features relevant to viral<br> disease tolerance in bats, lays a foundation for future in vivo and in vitro experimental<br> investigations, and serves as a key resource for comparative immunology studies across bats<br> and other mammals.</p> <p> </p> <p>This upload is the transcriptome fasta file used for alignment for the dataset.</p>
An in vivo stable isotope labeling method to investigate individual matrix protein synthesis, ribosomal biogenesis, and chondrocyte proliferation in murine articular cartilage
<p>These experiments have used a stable-isotope method using <em>in vivo</em> deuterium oxide labeling and mass spectrometry to measure protein concentration, protein half-life, cell proliferation, and ribosomal biogenesis in a single sample of murine articular cartilage. We hypothesized that a 60-day labeling period would capture age-related declines in cartilage matrix protein content, protein synthesis rates, and chondrocyte proliferation. Knee cartilage was isolated from 25- and 90-week-old female C57BL/6J mice treated with deuterium oxide for 15, 30, 45 and 60 days. We measured protein abundance and half-lives using high resolution accurate mass spectrometry (HRAM) and d2ome data processing software. </p>
Fig. 1 Screening flow, testing 1600 FDA compounds against S in Assessment of FDA-approved drugs against StrongyloideS rAtti in vitro and in vivo to identify potentially active drugs against strongyloidiasis
Fig. 1 Screening flow, testing 1600 FDA compounds against S. ratti
Dataset: In-vivo characterization of magnetic inclusions in the subcortex from non-exponential transverse relaxation decay
<p>This repository includes the data used to compile the results presented in the scientific publication: "In-vivo characterization of magnetic inclusions in the subcortex from non-exponential transverse relaxation decay".</p> <p>Rita Oliveira, Antoine Lutti<br>Laboratory for Research in Neuroimaging (LREN)<br>Department of Clinical Neuroscience, Lausanne University Hospital and University of Lausanne<br>Mont-Paisible 16, CH-1011 Lausanne, Switzerland<br><br>Classically, the MRI transverse relaxation decay is analyzed by fitting the signal decay over echo time voxel-wise with a monoexponential function (Exp), for which a decay rate R<sub>2</sub><sup>∗</sup> is estimated. However, the presence of magnetic material within the tissue, such as iron-loaded cells, myelin, or blood vessels, introduces variations in the magnetic field, which can modify the exponential behaviour of the decay (1,2). In such inhomogeneous magnetic fields, the theory predicts a transient regime starting with a Gaussian behaviour at short echo times and approaching a monoexponential relaxation at long echo times (1,3–6).<br>We highlight three different analytical descriptions of the signal decay that account for the transient regime of the transverse relaxation decay: i) the Anderson and Weiss, 1953 model (AW); ii) the Jensen and Chandra, 2000 model/Sukstanskii and Yablonskiy, 2003 model (SY; in the article is called JC); iii) and following a Padé approximation (Padé) of the transition from Gaussian to exponential decay.<br>This repository includes transverse relaxation decay data that enables the observation of the non-exponential MRI transverse relaxation. The data was acquired from 5 healthy volunteers at 3T. AW, SY, Padé, and Exp are the different methods that we used to fit the data with. Here we focus on the analysis of subcortical brain regions: Substantia Nigra, Pallidum, Putamen, Caudate, and Thalamus.</p> <p><strong>Data Description</strong><br>The necessary files to compile the results presented in the scientific publication can be found in the ‘<em>multiecho</em>’ folder. There are three different folders corresponding to three repetitions of the acquisition (‘rep1’ to ‘rep3’). The data consists of:<br>• resc_den_ subject_name_N.nii: magnitude image file corresponding to echo N. These files were previously denoised and rescaled (resc_den). The description field of the header of the images contains the corresponding TE at which the image was acquired, which will be needed in the fitting routine. Since we focus on the analysis of subcortical brain regions (Substantia Nigra, Pallidum, Putamen, Caudate, and Thalamus), the multi-echo data is masked within this region.<br>• nf: value of the noise floor level. Corresponds to the noncentrality parameter of a Rician distribution fitted to the background signal.</p> <p>In the ‘<em>anat</em>’ folder the user has access to:<br>• MT: Magnetization Transfer map (MTsat) that serves as a reference anatomical image.<br>• ROI folder: contains masks of each of the 5 regions of interest analyzed in the scientific paper: Substantia Nigra, Pallidum, Putamen, Caudate, and Thalamus.</p> <p><br>The ‘<em>modelfits</em>’ folder contains pre-computed results for each subject analyzed. If the user uses the analysis code that comes along with this dataset (<a href="https://github.com/LREN-physics/TransverseRelaxation">https://github.com/LREN-physics/TransverseRelaxation</a>), this folder will be overwritten with the new results. For each method (‘AW’, ‘SY’, ‘Pade’, ‘Exp’) there is a folder containing the corresponding resulting maps. These maps are:<br>• R2s.nii: map of R<sub>2,micro</sub><sup>∗</sup> [ms<sup>-1</sup>] for ‘AW’, ‘SY’, and ‘Pade’ options. Map of R<sub>2</sub><sup>∗</sup> [ms<sup>-1</sup>] for ‘Exp’ fit.<br>• OmegaSq.nii: map of 〈\(\Omega^2\) [rad<sup>2</sup> ms<sup>-2</sup>]. Not available for ‘Exp’ fit.<br>• TE0signal.nii: map of the initial signal amplitude S<sub>0</sub>.<br>• T2mol.nii: map of the inverse of effective transverse relaxation rate resulting from processes on the nanoscale [ms]<br>• AIC.nii: map of Akaike information criterion regarding the fitting procedure.<br>• MSE.nii: maps of the mean square error of the fitting procedure.<br>• DataMatrix.mat: matrix containing the data used for the fitting procedure.<br>• VoxelIndices.mat: vector containing the indices of the voxels corresponding to the analyzed data, which is restricted to the subcortical regions.<br>• Params.mat: structure containing the parameters used for the analysis.<br>Inside ‘modelfits’ there are also two folders corresponding to two different regimes that can describe the transverse relaxation decay: static dephasing regime (‘SDR’) or diffusion narrowing regime (‘DNR’). Under the assumption of SDR, we computed:<br>• ki_ppm.nii: maps of 𝛥𝜒, which is the difference in susceptibility of the magnetic inclusions to the surrounding tissue [addimentional, in ppm and in SI units]<br>• zeta.nii: maps of 𝜁, which is the volume fraction of the magnetic inclusions [addimentional]<br>Under the assumption of DNR, we computed:<br>• alpha.nii: 𝛼=𝜏〈\(\sqrt{\Omega^2}\)〉 [addimentional]<br>• tau_ms.nii: maps of 𝜏, which is the time scale for water molecules to diffuse away from magnetic inclusions [ms]<br>Please refer to the corresponding article for a complete description of the methods and corresponding estimated parameters.</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.
Data from: Linking in vivo muscle dynamics to in situ force-length and force-velocity reveals that guinea fowl lateral gastrocnemius operates at shorter than optimal lengths
<p>Force-length (F-L) and force-velocity (F-V) properties characterize skeletal muscle's intrinsic properties under controlled conditions, and it is thought that these properties can inform and predict <em>in vivo</em> muscle function. Here, we map dynamic <em>in vivo</em> operating range and mechanical function during walking and running, to the measured <em>in situ</em> F-L and F-V characteristics of guinea fowl (<em>Numida meleagris</em>) lateral gastrocnemius (LG), a primary ankle extensor. We use <em>in vivo</em> patterns of muscle (tendon) force, fascicle length, and activation to test the hypothesis that muscle fascicles operate at optimal lengths and velocities to maximize force or power production during walking and running. Our findings only partly support our hypothesis: <em>in vivo</em> LG velocities are consistent with optimizing power during work production, and economy of force at higher loads. However, LG does not operate at lengths on the force plateau (±5% Fmax) during force production. LG length was near L<sub>0</sub> at the time of EMG onset but shortened rapidly such that force development during stance occurred almost entirely on the ascending limb of the F-L curve, at shorter than optimal lengths. These data suggest that muscle fascicles shorten across optimal lengths in late swing, to optimize the potential for rapid force development near the swing-stance transition. This may provide resistance against unexpected perturbations that require rapid force development at foot contact. We also found evidence of passive force rise (in absence of EMG activity) in late swing, at lengths where passive force is zero <em>in situ</em>, suggesting that history dependent and viscoelastic effects may contribute to <em>in vivo</em> force development. Direct comparison of<em> in vivo </em>work loops and physiological operating ranges to traditional measures of F-L and F-V properties suggests the need for new approaches to characterize dynamic muscle properties in controlled conditions that more closely resemble <em>in vivo </em>dynamics.</p>
Self-propagating wave drives noncanonical antidurotaxis of skull bones in vivo
<p>Cellular motion is a key feature of tissue morphogenesis and is often driven by migration. However, migration, need not explain cell motion in contexts where there is little free space or no obvious substrate such as those found during organogenesis of mesenchymal organs including the embryonic skull. Through <em>ex vivo</em> imaging, biophysical modeling, and perturbation experiments, we find that mechanical feedback between cell fate and stiffness drives bone expansion and controls bone size <em>in vivo</em>. This mechanical feedback system is sufficient to propagate a wave of differentiation that establishes a collagen gradient which we find sufficient to describe patterns of osteoblast motion. Our work provides a mechanism for coordinated motion that may not rely upon cell migration but on emergent properties of the mesenchymal collective. Identification of such alternative mechanisms of mechanochemical coupling between differentiation and morphogenesis will help in understanding how directed cellular motility arises in complex environments with inhomogeneous material properties.</p>
Proteomic analysis of Entamoeba histolytica in vivo assembled pre-mRNA splicing complexes
<p>Dataset for publication "Proteomic analysis of <em>Entamoeba histolytica</em> in vivo assembled pre-mRNA splicing complexes"</p>
In vivo characterisation of fluorescent proteins in budding yeast.
<p>Raw results of data of the paper 'In vivo characterisation of fluorescent proteins in budding yeast', including scripts to analyze and plot the data.</p>
Research data supporting "Renal clearable catalytic gold nanoclusters for in vivo disease monitoring"
<p>Raw research data suppoorting the publication:</p> <p>Loynachan C., et al., 2019, Nature Nanotechnology, DOI: https://doi.org/10.1038/s41565-019-0527-6</p>
ScienceDex guides
Understand access before you commit
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.