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395 results for “rat model”
Aligned bam files for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"
<p>Aligned bam files used for analysis in "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits".</p> <p>This is an accompanying dataset to Datasets and code for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits" (https://zenodo.org/record/7442105).</p>
Deciphering the scopolamine rat model by preclinical functional MRI
Open the record for dataset details and reuse information.
An assessment of the (anti)androgenic properties of hexachloronaphthalene (HxCN) using a model of immature male rats (Hershberger Bioassay)
<p>The persistent organic pollutants (POPs) include polychlorinated naphthalenes (PCNs); of these, the most toxic, abundant and found in human tissues are the hexachloronaphthalenes (HxCNs). The aim of this study was to evaluate the (anti)androgenic action of HxCN using the Hershberger Bioassay (OECD 441). Castrated male Wistar rats were exposed per os to HxCN at daily doses ranging from 0.3-3.0 mg*kg b.w.-1 for 10 days. Testosterone propionate (TP) was used as the reference androgen, and flutamide (FLU) as the reference antiandrogen. Five assessor sex tissues (ASTs) were weighed: ventral prostate, seminal vesicles, levator ani-bulbocavernosus muscle (LABC), glans penis and Cowper gland. In addition to determining the absolute weight of the ASTs, a number of other tests were performed on serum hormone levels (testosterone [T], triiodothyronine 99 [T3], thyroxine [T4], LH and FSH) and the histopathology of the ASTs. </p>
3D Nuclei annotations and StarDist 3D model(s) (rat brain)
<p><strong>Name</strong>: 3D Nuclei annotations and StarDist3D model(s) (rat brain)</p> <p><strong><em>Images: </em></strong>From a large tiling acquisition ( https://doi.org/10.5281/zenodo.6646128 ) individual Tile (xyz : 1024x1024x62) were downsampled and cropped (128x128x62). Four crops, from different tiles (./annotations_BIOP/images/) were manually annotated with ITK-SNAP (./annotations_BIOP/masks/)</p> <p>These four images, and their corresponding masks, were cropped into four quadrants (./crops_BIOP_v1/) in order to get 16 different images (64x64x62).</p> <p><strong><em>Conda environment</em></strong><em>: </em>A conda environment was created using the yml file <em>stardist0.8_TF1.15.yml</em></p> <p><strong><em>Training : </em></strong>Training was performed using the jupyter notebook <em>1-Training_notebook.ipynb</em>.<br> Three different trainings (with the same random seed, same anisotropy, patch size and grid) were performed and produced three different models (./models/)</p> <p>Validation images (from the random seed used) were exported to ease the visual inspection of the results(./val_rdm42/).</p> <p><strong><em>Validation: </em></strong>To save metrics in a csv file and compare predictions to the annotations the jupyter notebook <em>2-QC_notebook.ipynb </em>can be used on the validation folder.</p> <p><strong>Large images</strong>: To test the model on larger images one can use Whole_ds441.tif (or Crop_ds441.tif )<br> These images were obtained using the plugin <a href="https://imagej.net/plugins/bigstitcher/">BigSticher </a>on the raw data ( https://doi.org/10.5281/zenodo.6646128 ), resaved as h5 and exported the downsample by 4 version.</p> <p> </p> <p> </p>
Consensus models to predict oral rat acute toxicity and validation on a dataset coming from the industrial context
<p>We report predictive models of acute oral systemic toxicity representing a follow-up of our previous work in the framework of the NICEATM project. It includes the update of original models through the addition of new data and an external validation of the models using a dataset relevant for the chemical industry context. A regression model for LD50 and classification model for toxicity classes according to the Global Harmonized System categories were prepared. ISIDA descriptors were used to encode molecular structures. Machine learning algorithms included Support Vector Machine (SVM), Random Forest (RF) and Naïve Bayesian. Selected individual models were combined in consensus.</p> <p>The different datasets were compared using the Generative Topographic Mapping approach. It appeared that the NICEATM datasets were lacking some relevant chemotypes for chemical industry. The new models trained on enlarged data sets have applicability domain (AD) sufficiently large to accommodate industrial compounds. The fraction of compounds inside the models’ AD increased from 58 % (NICEATM model) to 94 % (new model). Yet, the increase of training sets only slightly improved of the models’ prediction performance: RMSE values decreased from 0.56 to 0.47 and balanced accuracies increased from 0.69 to 0.71 for NICEATM and new models, respectively.</p>
Neurometabolic changes in a rat pup model of type C HE - 1H MRS dataset (hippocampus)
<p>1H MRS in hippocampus was used to study longitudinally the effect of chronic liver disease (bile duct ligated rat model) in the brain (type C hepatic encephalopathy) of animals having developed disease a post natal day 15 (p15) corresponding to ~4 months old human brain. The dataset contains MR spectra and LCModel Quanifications from 7 bile duct ligated and 8 control animals at week 2, 4 and 6 after surgery.</p> <p>Please cite the following manuscript if you are using these data</p> <p><a href="https://pubmed.ncbi.nlm.nih.gov/37148431/">Neurometabolic changes in a rat pup model of type C hepatic encephalopathy depend on age at liver disease onset - PubMed (nih.gov)</a></p>
Calcium time series of cortex in a rat model of cortical dysplasia
<p>In vitro Calcium time series of rat (P30) primary motor cortex, were recorder by a CCD camera coupled to stereo-fluoerscence<br> microscope, with a fs = 300ms, following the next sequence: <strong>Basal, <em>Stimulus</em>, Rest.</strong></p> <p>All data is included in a compressed file named <strong>calcium_timeseries.tar.gz.</strong></p> <p>There are two groups of rats: <strong>Control</strong> (control animals), and <strong>BCNU</strong> (experimental animals using the BCNU/carmustine model of cortical dysplasia [1]).</p> <p>Time series are stored in .<strong>csv</strong> files with file names as <strong>R?Pilo-KCl.csv</strong> (where <strong>?</strong> indicates the rat ID). Each of these files holds the two recordings, one for each <em>Stimulus</em>, the first being <em>pilocarpine</em>, followd by <em>KCl</em> used as a control of cellular activity. (pilocarpine, KCl). recording session: The first 150 seconds of these time series correspond to basal activity, followed by 30 s of pilocarpine stimulus, and the rest of spontaneous activity after stimulation, for a total of 15 minutes for each <em>Stimulus</em>. The number of cells recorded varied between animals, as indicated by the number of columns in these .csv files. All of these files have the same number of rows (6000), with each row indicating a frame in the time series. The file <strong>dataEx.png</strong> illustrates this organization.</p> <p>Files named <strong>R?-Coor.csv</strong> (<strong>?</strong> indicates rat ID) show the <em>x</em> and <em>y</em> coordinates of every recorded cell, one for each row, ordered as<br> they appear in the calcium activity recordings. </p> <p><br> Authors:</p> <ul> <li>Ana Aquiles anaaquiles@ciencias.unam.mx</li> <li>Tatiana Fiordelisio tfiorde@ciencias.unam.mx</li> <li>Hiram Luna-Munguía hiram_luna@inb.unam.mx</li> <li>Luis Concha lconcha@unam.mx</li> </ul> <p> </p> <p>1. Benardete, E. A., & Kriegstein, A. R. (2002). Increased excitability and decreased sensitivity to GABA in an animal model of dysplastic cortex. <em>Epilepsia</em>, <em>43</em>(9), 970-982.</p>
Details of offspring and source data for analysis of metabolic health and dietary preference in a rat model of acute alcohol exposure.
<p>This Excel file contains information on the number of offspring used to examine each outcome and the raw data for each data Table and Figure within a manuscript submitted to Journal of Physiology. </p>
Data of PK/PD model of Reserpine-Induced Myalgia (RIM) model in rats
<p><span>This study aimed to establish a model that relates the pharmacokinetic and pharmacodynamic aspects of the reserpine-induced myalgia (RIM) model. To do this, measurements of reserpine in plasma and dopamine, norepinephrine, and serotonin in nervous tissue were carried out. </span></p>
3DAnatomicalRatModel: A printable version of a 3D anatomical rat model
<p>This is the version 1.0 of our static, 3D printable, anatomical rat model. The designed purpos is to provide a anatomical shaped phantom for medical imaging. The organs are constructed as hollow bodys, which can be filled with contrast agend suiteable for the technology of interest, e.g. iodine for CT, gadolinium for MRI or iron nanoparticles for MPI. Thus, it can be used as reference data or for experiment planing.</p> <p>In addition, it can be used for teaching purposes, for people making first steps in preclinical research.</p> <p>For best results, it is recommended to use the .form files to print the model in the optimized orientation on a Form2 or Form3 printer. On other printers the .stl files should be used.</p> <p>A publication using this phantom can be found here: <a href="https://doi.org/10.1515/cdbme-2019-0048">https://doi.org/10.1515/cdbme-2019-0048</a></p>
Raw data to "Blunting neuroinflammation with resolvin D1 prevents early pathology in a rat model of Parkinson's disease"
<p>Background: In vivo treatment of animals with anti-inflammatory and pro-resolving mediators (SPMs) could be counteracted by their limited in vivo bioavailability due to their unstable nature as lipids that can undergo oxidation or enzymatic degradation.</p> <p>Results: Thus, we performed a time course of RvD1 plasma levels over 36 hours after an initial intraperitonael injection of this lipid mediator at a concentration of 200 ng/animal. After a single injection the plasma concentration of RvD1 peaked at 1h (~360 pg/ml), stayed almost constant at 3h(~360 pg/ml), halved its levels after 6h (~180 pg/ml) and slowly returned close to the baseline after 36h (~30 pg/ml). These results indicate that RvD1 is rapidly distributed into the bloodstream and eliminated from the vascular compartment due to metabolism and/or diffusion into the blood–brain barrier.</p> <p>Conclusions: These findings are important to define route and timing of in vivo administration of SPMs in order to maintain sufficient levels to sustain biological activities both in the periphery and within the central nervous system.</p>
Quantification of stroke lesion volume using epidural EEG in a cerebral ischaemic rat model
<p>We have uploaded the dataset of rat EEG in response to the specific sound stimuli. The dataset includes rat EEG of normal subjects (n = 10), mild (n = 7), moderate (n = 7), and severe (n = 7) right auditory cortical infarction subjects. </p> <p>The dataset can be analyzed using MATLAB software. For power spectrum density (PSD) analysis of the data, we used the zero-phase forward and reverse Infinite Impulse Response Butterworth filter of 4th order. Further, we averaged the last 300 ms of the signal before stimulus onset as a baseline correction. Next, we down-sampled the data from 1,200 to 600 Hz. Subsequently, we conducted the PSD analysis using signals obtained from the target stimulus onset to 1 s using Welch’s method, which is one of the most widely used periodogram methods for determining the power density of EEG frequency components. The parameter was set to divide the EEG signals into eight sections of equal length, each with a 50% overlap based on the Hamming window. We defined the frequency range for each band as follows: Delta (1-4 Hz), theta (4-8 Hz), alpha (8-12 Hz), and beta (12-30 Hz). We calculated the relative power for each frequency band by summing all of the absolute PSD values across the four bands to compute the total power followed by dividing the absolute value for each frequency band with the total power. Finally, we calculated the DAR (delta/alpha ratio) and the DTABR ((delta + theta) / (alpha + beta) ratio), which were computed by the relative power of the relevant frequency bands. Further, we analysed AEPs in response to the target sound stimuli by averaging all of the epochs between 300 ms before the stimuli onset to 500 ms after it. The AEP amplitude was defined as the highest recorded voltage following the sound stimulus. The latency of the components of the AEPs was defined as the duration from stimulus onset to the peak amplitude.</p>
Developmental stress elicits preference for methamphetamine in the spontaneously hypertensive rat model of attention-deficit/hyperactivity disorder
<p>The raw data of the manuscript, "Developmental stress elicits preference for methamphetamine in the spontaneously hypertensive rat model of attention-deficit/hyperactivity disorder".</p>
Raw fMRI data from 12 rats used in the manuscript "Mapping of hemodynamic responses to the sensorymotor stimulation in a rodent model: a BOLD fMRI study" submitted to PlosOne for publication
<p>Raw data are from twelve male adult Wistar rats (Charles River Laboratories, Paris-France) weighing 300 ± 20g.</p> <p>Rats were initially anesthetized (induction) with 3% isoflurane and were maintained under 0,7-0.8% (sedation along with a muscle relaxation) during fMRI session. </p> <p>Each rat was submitted to two fMRI sessions: one with TE of 30 ms and and other with TE of 40 ms.</p> <p>For fMRI acquisition, electrodes were inserted subcutaneously in the palmar surface of the right hindpaw of each rat and electrical stimulation (current pulses with a 1.7 mA amplitude, 10 ms duration and 8 Hz frequency) was applied in a block-design starting with a resting period of 25s as a baseline followed by 25s stimulation, repeated 8 times.</p> <p>Ten 1-mm thick contiguous axial slices, from -6.36 mm to +2.64 mm to Bregma, were acquired with a two-shot gradient echo planar imaging (GE EPI) pulse sequence (2.56 cm2 FOV; 64x64 matrix size; a TR of 1000 ms; a flip angle of 50°) resulting in the pixel size of 0.4 mm.</p> <p>All imaging experiments were performed on a 4.7T Bruker (Biospec 47/40, Bruker, GmbH, Ettlingen,Germany) with a horizontal bore magnet equipped with a 12 cm gradient coil (Bruker BGA12, 400 mT/m) and interfaced to AVANCE III console. Two actively decoupled RF coils were used: a 7.2-cm diameter volume coil for transmission and a 2-cm diameter surface coil (Rapid Biomedical, Rimpar, Germany) positioned on the top of the animal's head for reception.</p>
Cognition-Associated Protein Structural Changes in a Rat Model of Aging are Related to Reduced Refolding Capacity – Peptide Quantifications
<p>Cognitive decline during aging represents a major societal burden, causing both personal and economic hardship in an increasingly aging population. There are a few well-known proteins that can misfold and aggregate in an age-dependent manner, such as amyloid β and α-synuclein. However, many studies have found that the proteostasis network, which functions to keep proteins properly folded, is impaired with age, suggesting that there may be many more proteins that incur structural alterations with age. Here, we used limited-proteolysis mass spectrometry (LiP-MS), a structural proteomic method, to globally interrogate protein conformational changes in a rat model of cognitive aging. Specifically, we compared soluble hippocampal proteins from aged rats with preserved cognition to those from aged rats with impaired cognition. We identified several hundred proteins as having undergone cognition-associated structural changes (CASCs). We report that CASC proteins are substantially more likely to be nonrefoldable than non-CASC proteins, meaning they typically cannot spontaneously refold to their native conformations after being chemically denatured. The potentially cofounding variable of post-translational modifications is systematically addressed, and we find that oxidation and phosphorylation cannot significantly explain the limited proteolysis signal. These findings suggest that noncovalent, conformational alterations may be general features in cognitive decline, and more broadly, that proteins need not form amyloids for their misfolded states to be relevant to age-related deterioration in cognitive abilities.</p> <p>This deposition provides processed peptide quantifications for all LC-MS/MS proteomics experiments conducted for this study.</p>
Neurochemical and cognitive changes precede structural abnormalities in the TgF344-AD rat model
<p>Raw data for manuscript accepted in Brain Communications, awaiting official publication. All datasets contain subject information and modality-specific data. Data was acquired longitudinally at four timepoints from hemizygous TgF344-AD rats (transgenic AD model bred on a Fischer 344 background) and wildtype littermates. </p> <p>1) Barnes Maze probe data. Probe data acquired 48 hours after last training trial. </p> <p>2) Magnetic Resonance Spectroscopy data: absolute concentrations are provided, as well as relative to total creatine. </p> <p>3) Magnetic Resonance Imaging data: absolute brain volumes generated from absolute jacobians. "Brain-size-corrected" volumes are referred to as "relative" volumes and are generated from relative jacobians. </p>
Characterization of NAD(P)H and FAD autofluorescence signatures in an isolated-perfused rat heart model
<p>Raw data concerning publication titled "Characterization of NAD(P)H and FAD autofluorescence signatures in an isolated-perfused rat heart model"</p> <p>Abstract</p> <p>Autofluorescence spectroscopy is a promising label-free approach to characterize biological samples with demonstrated potential to report structural and biochemical alterations in tissues in a number of clinical applications. We report a characterization of the ex vivo autofluorescence fingerprint of cardiac tissue, exploiting a Langendorff-perfused isolated rat heart model to induce physiological insults to the heart, with a view to understanding how metabolic alterations affect the autofluorescence signals. Changes in the autofluorescence intensity and lifetime signatures associated with reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavin adenine dinucleotide (FAD) were characterized during oxygen- or glucose-depletion protocols. Results suggest that both NAD(P)H and FAD autofluorescence intensity and lifetime parameters are sensitive to changes in the metabolic state of the heart owing to oxygen deprivation. We also observed changes in NAD(P)H fluorescence intensity and FAD lifetime parameter on reperfusion of oxygen, which might provide information on reperfusion injury, and permanent tissue damage or changes to the tissue during recovery from oxygen deprivation. We found that changes in the autofluorescence signature following glucose-depletion are, in general, less pronounced, and most clearly visible in NAD(P)H related parameters. Overall, the results reported in this investigation can serve as baseline for future investigations of cardiac tissue involving autofluorescence measurements.</p>
Endocrine profile of the vcd-induced perimenopausal model rat
<p>During the transition to menopause, women experience a variety of physical and psychological symptoms that are directly or indirectly linked to changes in hormone secretion. Establishing animal models with intact ovaries is essential for understanding these interactions and finding new therapeutic targets. In this study, we assessed the endocrine profile, as well as the estrous cycle, in the 4-vinylcyclohexene diepoxide (VCD)-induced follicular depletion rat model in 10-day intervals over 1 month to accurately establish the best period for studies of the transition period.</p>
Systemic inflammation accelerates neurodegeneration in a rat model of Parkinson's disease overexpressing human alpha synuclein
<p><span>Parkinson’s disease (PD) involves genetic and<span> </span>environmental risk factors. Increasing research efforts have been made to understand how they interact<span> </span>to<span> </span>impair<span> </span>homeostasis<span> </span>and<span> </span>elevate<span> </span>risk. Inflammation could be one unifying factor. In this study, <em>wild-type</em> (WT) and overexpressing human </span><span>α</span><span>-synuclein (<em>Snca</em><sup>+/+</sup>) rats <span>were intraperitoneally injected with a single dose of </span>lipopolysaccharide<span> </span>(LPS) or with saline (SAL). In these animals we assessed </span><span>the development of PD-like symptoms by immunohistology, high-dimensional flow cytometry, electrophysiology, and behavioral analyses. A single injection of LPS to both WT and <em>Snca<sup>+/+</sup> </em>rats triggered long-lasting increased activation of pro-inflammatory microglial markers, infiltrating monocytes and T-lymphocytes. However, only LPS <em>Snca</em><sup>+/+</sup> rats displayed dopaminergic neuronal loss in the <em>substantia<span> </span>nigra pars compacta<span> </span></em>(SNpc), associated with a reduction of evoked dopamine<span> release </span>in the striatum. No significant<span> </span>changes were observed in the behavioral domain. </span></p> <p><span> </span></p>
Blood glucose modulation and safety of efferent vagus nerve stimulation in a type 2 diabetic rat model
<p class="MsoNormal"><span>Vagus nerve stimulation is emerging as a promising treatment for type 2 diabetes. Here, we evaluated the ability of stimulation of the vagus nerve to reduce glycaemia in awake, freely moving metabolically compromised rats. A model of type 2 diabetes (n=10) was induced using a high-fat diet and low doses of streptozotocin. Stimulation of the abdominal vagus nerve was achieved by pairing 15 Hz pulses on a distal pair of electrodes </span><span>with high-frequency blocking stimulation (26 kHz, 4 mA) on a proximal pair of electrodes to preferentially produce efferent conducting activity </span><span>(eVNS)</span><span>. </span><span>Stimulation was well tolerated in awake, freely moving rats. During 1 hour of eVNS, glycaemia decreased in 90% of subjects (-1.25±1.25 mM·h, <em>P</em>=0.017), and 2 dB above neural threshold was established as the most effective 'dose' of eVNS (<em>P</em>=0.009). Following 5 weeks of implantation, eVNS was still effective, resulting in significantly decreased glycaemia (-1.7±0.6 mM·h, <em>P</em>=0.003) during 1 hour of eVNS. There were no overt changes in fascicle area or signs of histopathological damage observed in implanted vagal nerve tissue following chronic implantation and stimulation. </span><span>Demonstration of the biocompatability and safety of eVNS in awake, </span><span>metabolically compromised</span><span> animals is a critical first step to establishing this therapy for clinical use. With further development, </span><span>eVNS could be a promising novel therapy for treating type 2 diabetes.</span></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.