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4,483 results for “rat”
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>
Genetic Modulation of Protein Expression in Rat Brain
<p><span>Genetic variations in protein expression are implicated in a broad spectrum of common diseases and complex traits. However, the fundamental genetic architecture and variation of protein expression have received comparatively less attention than either mRNA or classical phenotypes. In this study, we systematically quantified proteins in the brains of a large family of rats using tandem mass tag (TMT)-based quantitative mass-spectrometry (MS) technology. We identified and quantified a comprehensive proteome of 8,119 proteins from Spontaneously Hypertensive (SHR/Olalpcv), Brown Norway with polydactyly-luxate (BN-Lx/Cub), and 29 of their fully inbred HXB/BXH progeny. Differential expression (DE) analysis identified 597 proteins with significant differences in expression between the parental strains (fold change > 2 and FDR < 0.01). We characterized 95 variant peptides by proteogenomics approach and discovered 464 proteins linked to strong <em>cis</em>-acting quantitative trait loci (pQTLs, FDR < 0.05). We also explored the linkage of pQTLs with behavioral phenotypes in rats and examined the sex-specific pQTLs to reveal both distinct and shared <em>cis</em>-pQTLs between sexes. Furthermore, by creating a novel view of the rat pangenome, we improved the ability to pinpoint candidate genes underlying pQTL. Finally, we explored the connection between the pQTLs in rat and human disorders, underscoring the translational potential of our findings. Collectively, this work demonstrates the value of large and systematic proteo-genetic datasets in understanding protein modulation in the brain and its functional linkage to complex central nervous system (CNS) traits.</span><span> </span></p>
Capacitance clamp demonstration in rat dentate gyrus granule cells
<p>Dataset for a demonstration of the capacitance clamp, a variant of the dynamic clamp technique, which allows to virtually modify the capacitance of a biological neuron (or any electrically excitable cell).</p> <p>Code for analysis and further explanations will be made available. </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>
Dataset provided for : Sensing Ultrasound Localization Microscopy reveals glomeruli in rats and humans
<p><strong>Abstract :</strong> Estimation of glomerular function is a key element in the diagnosis of kidney disease. However, the study of glomeruli in the clinic remains indirect through urine and blood tests. Recent imaging technique called Ultrasound Localization Microscopy (ULM) originated from the ability to record continuous movements of individual microbubbles in the bloodstream. Although it improved the resolution of vascular imaging up to tenfold, the imaging of the smallest vessels had yet to be reported.</p> <p>We acquired ultrasound sequences from living humans and rats and then applied filtering dividing the data set into slow-moving and fast-moving microbubbles. We performed a double tracking to highlight and characterize this new population of microbubbles with singular behaviors: we called this technique “sensing ULM” (sULM). We used post-mortem micro-CT for side-by-side confirmation in rats.</p> <p>In this study, we report the observation of microbubbles flowing in capillaries bundles, i.e. the glomeruli, in the kidney in living humans and rats. We introduce a set of analysis tools dedicated to extracting quantitative information from individual microbubbles, like the remanence time or the normalized distance.</p> <p>As glomeruli play a key role in kidney function, their observation could yield a deeper understanding of kidney diseases and provide a diagnostic tool for patients. More generally, it will bring imaging capabilities closer to the functional units of organs, which is one of the keys to understanding most diseases, like cancers, diabetes, or kidney failures. </p> <p><strong>Academic reference to be cited : </strong>Denis, Bodard, Hingot, Chavignon, Battaglia, Renault, Lager, Aissani, Hélénon, Correas, and Couture. <em>Sensing Ultrasound Localization Microscopy reveals glomeruli in rats and humans,</em> eBioMedicine, 2023.</p> <p><strong>Related scripts and software application</strong> : <a href="https://github.com/EngineerJB/akebia">https://github.com/EngineerJB/akebia</a></p> <p><strong>(New ! published in June 2024) Raw data :</strong> <a href="../records/11395562">https://zenodo.org/records/11395562</a></p> <p><strong>Corresponding authors : </strong></p> <ul> <li>Article : Louise Denis, <a href="mailto:louise.denis@sorbonne-universite.fr">louise.denis@sorbonne-universite.fr</a>, Sylvain Bodard, <a href="mailto:sylvain.bodard@aphp.fr">sylvain.bodard@aphp.fr</a></li> <li>Scripts, and codes : Louise Denis, <a href="mailto:louise.denis@sorbonne-universite.fr">louise.denis@sorbonne-universite.fr</a>, Jacques Battaglia, <a href="mailto:jacques.battaglia@sorbonne-universite.fr">jacques.battaglia@sorbonne-universite.fr</a></li> <li>Materials, collaborations, rights and others: Olivier Couture, <a href="mailto:olivier.couture@sorbonne-universite.fr">olivier.couture@sorbonne-universite.fr</a></li> </ul>
Prenatal diet programs the transgenerational inheritance of brain macro and microstructure defects, coding for anxiety-like behavior in male rats.
<p>T1-w 3DFLASH Preprocessed MRI images used for wistar rat used for the deformation-based morphological (DBM) model are released.</p> <p>Nifti files are duplicated. DBM used only mnc format.</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Data on the fleas of house mice and ship rats in the Orongorongo Valley, New Zealand
<p>Data on autopsies and fleas of individual rats and mice snap-trapped in 80 quarterly 3-day trapping sessions over 1971-1991 in the Orongorongo Valley, Wellington, New Zealand. The fleas are preserved as slides in the Pilgrim Collection of Te Papa Tongarewa Museum of New Zealand, Wellington. The data are analysed in a forthcoming paper by Fitzgerald, Efford and Karl.</p> <p>'Autopsy data.csv' is the main spreadsheet.</p> <p>'Data format.csv' defines columns and codes.</p> <p>The autopsy data are a subset of those reported by Fitzgerald, Efford<br> and Karl (2004) and Efford, Fitzgerald, Karl and Berben (2006), both<br> with respect to the sampling period (trapping continued after May 1991,<br> but rats and mice were not searched for fleas) and data columns<br> (some reproductive fields have been omitted).</p> <p>The autopsy data may be read from the csv file into R (R Core Team 2023)<br> with the statement:</p> <p>autopsyF <- read.csv(file = 'Orongorongo fleas 1971-1991 Autopsy data.csv')</p> <p>The resulting dataframe has 31 columns and 3006 rows:</p> <p>names(autopsyF)<br> [1] "Autopsy" "Line" "Date" "Analysis.Year" "Session" <br> [6] "Day" "Season" "Trap" "Traptype" "Alive.dead" <br> [11] "Species" "Sex" "Age" "Weight" "TotLth" <br> [16] "TailLth" "Fleas" "LsegnisM" "LsegnisF" "LsegnisU" <br> [21] "Lsegnis" "NfascM" "NfascF" "NfascU" "Nfasc" <br> [26] "Vagina" "Lact" "Uterus" "EmbryosT" "ScarCond" <br> [31] "Testes" <br> <br> nrow(autopsyF)<br> [1] 3006</p> <p>For completeness, the autopsy data include 64 hosts from these trapping sessions that were<br> not searched for fleas (coded as Fleas = 2).</p> <p>Quarterly indices of host density were tabulated by Fitzgerald et al. (2004; mice) and<br> Efford et al. (2006; rats).</p> <p>References</p> <p>Efford MG, Fitzgerald BM, Karl BJ, Berben PH. 2006. Population dynamics<br> of the ship rat <em>Rattus rattus</em> L. in the Orongorongo Valley, New Zealand.<br> New Zealand Journal of Zoology 33:273-297.</p> <p>Fitzgerald BM, Efford MG, Karl BJ. 2004. Breeding of house mice and the<br> mast seeding of southern beeches in the Orongorongo Valley, New Zealand.<br> New Zealand Journal of Zoology 31:167-184.</p> <p>Fitzgerald BM, Efford MG, Karl BJ. 2023. The fleas of house mice (<em>Mus musculus</em>)<br> and ship rats (<em>Rattus rattus</em>) in forest of the Orongorongo Valley, New Zealand.<br> For submission to New Zealand Journal of Zoology.</p> <p>R Core Team 2023. R: A Language and Environment for Statistical Computing.<br> R Foundation for Statistical Computing, Vienna, Austria.<br> https://www.R-project.org/</p>
Companion data for RAT 3.0: Global Database, Test data, Parameter files and Routing Script
<p><a href="https://depts.washington.edu/saswe/rat/">Reservoir Assessment Tool version 3.0</a> is a scalable and user-friendly software platform to mobilize the global water management community. RAT uses satellite remote sensing data to monitor water surface area and water level changes in artificial reservoirs. It uses this information, along with topographical information (either derived from satellite data, or in-situ topo maps) to estimate the Storage Change (∆S) in the reservoirs. Additionally, RAT models the Inflow (I) and the Evaporation (E) of each reservoir. Finally, RAT uses the modeled I, and E, and estimated ∆S, to estimate the Outflow (O) from reservoirs. The datasets and files provided here are used by RAT 3.0 as default inputs to make it easy to set up and execute RAT for first-time users.</p> <p><strong>global_data.zip</strong> - It includes <a href="https://rat-satellitedams.readthedocs.io/en/latest/RAT_Data/GlobalDatabase/">Global Database</a> encompassing global elevation data, global reservoir and dam data, major river basins in the world and the river networks, flow direction file, and geoid model. It is used by RAT 3.0 as default input for easy execution for first-time users.</p> <p><strong>global_vic_params.zip</strong> - It contains <a href="https://zenodo.org/record/3475602">global VIC soil and domain parameters</a> for executing the hydrological model within RAT 3.0. It is considered a part of the Global Database but is packaged separately.</p> <p><strong>params.zip</strong> - It consists of all the default parameter files used by RAT 3.0 to execute the hydrological model within it and to execute RAT itself. </p> <p><strong>routing.zip</strong> - It consists of the Fortran code for <a href="https://vic.readthedocs.io/en/vic.4.2.d/Documentation/Routing/RunRouting/">the Routing model</a> for easy installation for users. </p> <p><strong>test_data.zip</strong> - It consists of data used by RAT 3.0 to test whether it has been installed and initialized properly in a user's system.</p>
Invasive species and thermal squeeze: Distribution of two invasive predators and drivers of ship rat (Rattus rattus) invasion in mid-elevation Fuscospora forest
This data package is from a trapping network set up in Craigieburn Forest Park, New Zealand, in 2013. These are records of the stoats and rats caught in the traps each time the traps were checked by volunteers since 2013. Associated long term air temperature and seedfall data from the Craigieburn area is also provided. If the original trapping records (containing more mammalian catch information such as weasels and cats) are required please contact the data providers.
Invasive rat eradication effects on seedling counts on Palmyra Atoll, 2004-2016
In order to investigate the impacts of rat eradication on plant communities on the Palmyra Atoll, Line Islands, Central Pacific Ocean ecosystem, a study was conducted surveying the native and non-native tree and palm seedling abundance before and after an eradication event which took place in June 2011. The common plant species examined were P. grandis and C. nucifera, while the less-common species were B. asiatica, C. subcordata, H. sonora, G. speciosa, N. oppositifolium, and C. inophyllum. Data for common plant species were collected in 2007, 2011, 2012, 2014, and 2016, and for less-common species in 2004, 2011, 2012, 2014, and 2016. Data were collected via survey methods; 55 transect sites were examined for the common species, and between 49 to 55 sites were examined depending on the year, for the less-common species.
Effects of Kangaroo Rat Mounds on Seed Banks of Grass and Shrublands at the Sevilleta National Wildlife Refuge, New Mexico (2001)
Disturbance is a major factor in determining the spatial structure and temporal dynamics of ecological systems. Many studies have been conducted concerning the plant assemblages around Dipodmys spectabilis mounds compared to the off mound area. These studies have shown that annual plant cover is higher on the kangaroo rat mound compared to off the mound. However, no studies have addressed the effects of these rodents disturbance on the soil seed bank. Soil seed banks are an important component of the plant community particularly in arid environments. Annual plants have been known to create viable seeds that remain dormant in the soil for many years making their seed bank a persistent one. A persistent seed bank allows for future recruitment of plants given favorable conditions that could have a dramatic impact on the overall species diversity of the community. We studied the seed bank of eight forb taxa to ask the following questions: 1) Are there more seeds in the seed bank around kangaroo rat mounds compared to other microhabitats? 2) Does the seed composition differ among the different microhabitats? 3) If the seed composition does differ, do specific physical components of microhabitats predict seed populations?
CAMRI Rat Brain MRI Data
Open the record for dataset details and reuse information.
ParaVision Mouse, Rat, and Lemur Testing Data for SAMRI
<p>This is a testing data set encompassing mouse, rat, and lemur MRI data, acquired with diverse protocols, and stored in the Bruker ParaVision format. It serves as a demo and testing substrate for the SAMRI software package.</p>
Pterostilbene Protects Cochlea from Ototoxicity in Streptozotocin-Induced Diabetic Rats by Inhibiting Apoptosis
<p>Diabetes mellitus (DM) causes ototoxicity by inducing oxidative stress, microangiopathy, and apoptosis in the cochlear sensory hair cells. The natural anti-oxidant pterostilbene (PTS) (trans-3,5-dimethoxy-4-hydroxystylbene) has been reported to relieve oxidative stress and apoptosis in DM, but its role in diabetic-induced ototoxicity is unclear. This study aimed to investigate the effects of dose-dependent PTS on the cochlear cells of streptozotocin (STZ)-induced diabetic rats. The study included 30 albino male Wistar rats that were randomized into five groups: non-diabetic control (Control), diabetic control (DM), and diabetic rats treated with intraperitoneal PTS at 10, 20, or 40 mg/kg/day during the four-week experimental period (DM + PTS10, DM + PTS20, and DM + PTS40). Distortion product otoacoustic emission (DPOAE) tests were performed at the beginning and end of the study. At the end of the experimental period, apoptosis in the rat cochlea was investigated using caspase-8, cytochrome-c, and terminal deoxyribonucleotidyl transferase-mediated dUTP-biotin end labeling (TUNEL). Quantitative real-time polymerase chain reaction was used to assess the mRNA expression levels of the following genes: CASP-3, BCL-associated X protein (BAX), and BCL-2. Body weight, blood glucose, serum insulin, and malondialdehyde (MDA) levels in the rat groups were evaluated. The mean DPOAE amplitude in the DM group was significantly lower than the means of the other groups (0.9–8 kHz; P < 0.001 for all). A dose-dependent increase of the mean DPOAE amplitudes was observed with PTS treatment (P < 0.05 for all). The Caspase-8 and Cytochrome-c protein expressions and the number of TUNEL-positive cells in the hair cells of the Corti organs of the DM rat group were significantly higher than those of the PTS treatment and control groups (DM > DM + PTS10 > DM + PTS20 > DM + PTS40 > Control; P < 0.05 for all). PTS treatment also reduced cell apoptosis in a dose-dependent manner by increasing the mRNA expression of the anti-apoptosis BCL2 gene and by decreasing the mRNA expressions of both the pro-apoptosis BAX gene and its effector CASP-3 and the ratio of BAX/BCL-2 in a dose-dependent manner (P < 0.05 compared to DM for all). PTS treatment significantly improved the metabolic parameters of the diabetic rats, such as body weight, blood glucose, serum insulin, and MDA levels, consistent with our other findings (P < 0.05 compared to DM for all). PTS decreased the cochlear damage caused by diabetes, as confirmed by DPOAE, biochemical, histopathological, immunohistochemical, and molecular findings. This study reports the first in vivo findings to suggest that PTS may be a protective therapeutic agent against diabetes-induced ototoxicity.</p>
MR Spectra from rat hippocampus with LCModel quantification and the corresponding basis set
<p>This folder contains the LCModel quantifications of spectra acquired in hippocampus from 7 rats. The spectra were quntified using six different DKNTMN (spline stiffness) values (0.1, 0.25, 0.4, 0.5, 1, 5). In the folder Control_files_Basis_set you can find all the control files used in this quantification along with the corresponding basis set (metabolites/simulated using NMRScopeB from jMRUI and <em>in vivo </em>parameters + full MM spectrum).</p> <p>Please cite the following manuscript if you are using the data</p> <p><a href="https://pubmed.ncbi.nlm.nih.gov/34268821/">In vivo macromolecule signals in rat brain 1 H-MR spectra at 9.4T: Parametrization, spline baseline estimation, and T2 relaxation times - PubMed (nih.gov)</a><br> </p>
Data from: Using genetic relatedness to understand heterogeneous distributions of urban rat-associated pathogens
<p>Urban Norway rats (<i>Rattus norvegicus</i>) carry several pathogens transmissible to people. However, pathogen prevalence can vary across fine spatial scales (i.e., by city block). Using a population genomics approach, we sought to describe rat movement patterns across an urban landscape, and to evaluate whether these patterns align with pathogen distributions. We genotyped 605 rats from a single neighborhood in Vancouver, Canada and used 1,495 genome-wide single nucleotide polymorphisms to identify parent-offspring and sibling relationships using pedigree analysis. We resolved 1,246 pairs of relatives, of which only 1% of pairs were captured in different city blocks. Relatives were primarily caught within 33 meters of each other leading to a highly leptokurtic distribution of dispersal distances. Using binomial generalized linear mixed models we evaluated whether family relationships influenced rat pathogen status with the bacterial pathogens <i>Leptospira interrogans</i>, <i>Bartonella tribocorum</i>, and <i>Clostridium difficile</i>, and found that an individual's pathogen status was not predicted any better by including disease status of related rats. The spatial clustering of related rats and their pathogens lends support to the hypothesis that spatially restricted movement promotes the heterogeneous patterns of pathogen prevalence evidenced in this population. <span>Our findings also highlight the utility of evolutionary tools to understand movement and rat-associated health risks in urban landscapes.</span></p>
Fluorescent Microglia Images for Analyzing Morphological Changes due to Injury Duration in the Ischemic Rat Brain
<p>The image data included in this dataset are the confocal microscope images (converted from original .nd2 file to .tiff form) used for the publication: Joseph, A., Liao, R., Zhang, M., Helmbrecht, H., McKenna, M., Filteau, J. R., & Nance, E. (2020). Nanoparticle-microglial interaction in the ischemic brain is modulated by injury duration and treatment. <em>Bioengineering & translational medicine</em>, <em>5</em>(3), e10175. https://doi.org/10.1002/btm2.10175</p> <p>The data is organized by brain slice number, region, and image number. There is also an included excel file 'datadescriptions.xlsx' that provides more information about the metadata of the dataset. </p> <p> </p> <p>The data was procured and processed by the Disease Directed Engineering Lab, PI: Elizabeth Nance, at the University of Washington.</p>
A standardized method for the construction of tracer specific PET and SPECT rat brain templates: validation and implementation of a toolbox
<p>Data set used in "A standardized method for the construction of tracer specific PET and SPECT rat brain templates: validation and implementation of a toolbox"</p>
Circadian ontogenetic metabolomics atlas: an interactive resource with insights from rat plasma, tissues, and feces
<p>LC–MS instrumental files in mzXML format for metabolomics (HILICp, HILICn, HSST3p, HSST3n) and lipidomics platforms (LIPp, LIPn), including metadata for study samples, method blanks, quality control samples, and serial dilution samples. The instrumental files were acquired for each LC–MS platform as part of a study focused on creating a circadian ontogenetic metabolomics atlas of rat plasma, tissues, and feces. The original paper is accessible at http://doi.org/10.1007/s00018-025-05783-w</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.