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270 results for “Cerebellum”
Cerebellum Retinotopic Mapping
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Cerebellum spiking data during simulated saccade control
<p>This repository contains data generated by simulating the cerebellum spiking neural network for saccade motor control. Please refer to the article at https://doi.org/10.1101/2022.03.14.483471.</p> <p>Please check the journal of PLOS computational biology for the published version of this article (inpress).</p> <p>The python scripts will generate plots from the simulation datasets. In order to do so, please unzip the datasets and put each of the data subfolders into the current folder along with the plotting scripts.</p> <p>The spiking neuronal circuit datasets have been generated using the NEST spiking neural network library (https://www.nest-simulator.org/), in .gdf format. Users can refer to the presented python scripts to understand how to read from and plot the data. Additionally, for interested users, the trained PF-PC synaptic weights from saccade simulations are also available as EXCEL files in the same dataset folders.</p> <p>In case of queries or any problems, please email me at the email id given in the article linked above.</p>
Full summary statistics of mixQTL for GTEx v8 Brain_Cerebellum
The mixQTL method is described in paper doi.org/10.1101/2020.04.22.050666. Please cite the original paper if using the data.
Confocal dataset of Purkinjie cells from clarified cerebellum slices from L7GFP mouse
<div> <div> <h3><span><span>TITLE: Confocal dataset of Purkinjie cells from larified cerebellum slices from L7GFP mouse </span></span><span> </span></h3> </div> <div> <p><span><span> </span></span><strong><span><span>SUMMARY:</span></span> </strong><span> </span></p> </div> <div> <p><span><span>We have processed cerebellar material from transgenic mice expressing the green fluorescent protein (GFP). Specifically, in L7GFP mice, the expression of GFP in Purkinje is specifically driven by the Pcp-2 promoter (Zhang, X., Baader, S. L., Biang, F., Müller, W., and Oberdick, J. (2001). High level Purkinje cell specific expression of green fluorescent protein in transgenic mice. </span></span><span><span>Histochem</span><span>. Cell Biol</span></span><span><span>. 115, 455–464)</span><span>. </span><span>The sample were firstly clarified using the optimization of the CLARITY protocol developed by our group, and then </span><span>acquired</span><span> using a confocal microscope</span><span>. </span></span><span> </span></p> </div> <div> <p><strong><span><span> </span></span><span><span>EXPERIMENTAL METHODS AND MATERIALS:</span></span></strong> <span> </span></p> </div> <div> <p><span><span>Data contained in this folder belong to an adult male L7GFP mouse, processed as in Magliaro et al., 2016 </span></span><span><span>(</span></span><a href="https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2016.00179/full#h3" target="_blank" rel="noreferrer noopener"><span><span>https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2016.00179/full#h3</span></span></a><span><span>).</span></span><span> </span></p> </div> <div> <p><span> </span><span><span>Briefly, the L7GFP mouse was anesthetized with a lethal dose of 7% chloral hydrate and then perfused with 20 mL of Phosphate Buffered Saline and then 20 mL of a solution, containing 4% acrylamide, 0.05% bis-acrylamide and 0.25% VA-044 thermally triggered initiator at 4°C, as described in Chung et al. (2013) </span></span><span><span>(Chung, K., Wallace, J., Kim, S.-Y., Kalyanasundaram, S., </span><span>Andalman</span><span>, A. S., Davidson, T. J., et al. (2013). Structural and molecular interrogation of intact biological systems. </span></span><span><span>Nature</span></span><span><span> 497, 332–337. </span><span>doi</span><span>: 10.1038/nature12107)</span></span><span><span>. The brain was extracted and submerged in 20 mL hydrogel solution for 3 days at 4°C in a 50 mL Falcon tube to allow gel diffusion into the tissue. Then a vacuum was applied to the tube for 10 min to enable hydrogel formation. Hydrogel polymerization was thermally </span><span>initiated</span><span> by incubating the infused tissue overnight at 37°C. At this point, the mouse cerebellum was isolated and then cut into 1 mm-thick coronal slices using a Leica VT1200S vibratome. The cut settings were reported in Mattei et al., 2015 (</span></span><span><span>Mattei, G., Cristiani, I., Magliaro, C., and Ahluwalia, A. (2015). Profile analysis of hepatic porcine and murine brain tissue slices obtained with a vibratome. </span></span><span><span>PeerJ</span></span><span> <span>3:e</span><span>932. </span><span>doi</span><span>: 10.7717/peerj.932</span></span><span><span>). Each slice was finally placed in a 50 mL Falcon tube at 37°C with 20 mL of CLARITY clearing solution (200 mM Boric Acid and 4% Sodium Dodecyl Sulphate, pH adjusted to 8.5 by adding 1 M NaOH dropwise) for 5 days, as this is demonstrated to be the optimal clearing time in Magliaro et al., 2016</span></span><span><span> (</span></span><a href="https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2016.00179/full#h3" target="_blank" rel="noreferrer noopener"><span><span>https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2016.00179/full#h3</span></span></a><span><span>).</span></span><span> </span></p> </div> <div> </div> <div> <p><strong><span><span>Confocal microscopy data</span></span></strong> <span> </span></p> </div> <div> <p><span><span>Image stacks of samples were mounted on a glass slide with </span><span>FocusClear</span><span>™ (</span><span>Celexplorer</span><span> Labs Co., Hsinchu, Taiwan) and then </span><span>acquired</span><span> with a confocal microscope (Nikon A1). </span></span><span><span> The confocal settings were the following: 4.84 W laser power, emission and excitation wavelengths of 488 nm and 502 </span><span>nm</span><span> respectively.</span></span><span> Refer to metadata.xlsx file for detailed info.</span></p> </div> <div> <p> </p> </div> <div> <p><strong><span><span>Ethical approval</span></span><span> </span></strong></p> </div> <div> <p><span><span>The mouse was obtained from the Department of Translational Research, New Technologies in </span><span>Medicine</span><span> and Surgery of the University of Pisa (Italy). Mice were used to perform the experiments, which were conducted in conformity with the European Communities Council Directive of 24 November 1986 (86/609/EEC and 2010/63/UE) and in agreement with the Italian DM26/14. Experiments were approved by the Italian Ministry of Health and Ethical Committee of the University of Pisa.</span></span><span><span> </span></span><span> </span></p> </div> <div> <p><span><span> </span></span><span> </span></p> </div> </div>
FIG. 57. — Polysyncraton cerebellum n in Ascidians from the tropical western Pacific
FIG. 57. — Polysyncraton cerebellum n. sp.; A, B, thoraces; C, abdomen; D, larva. Scale bars: A, C, D, 0.5 mm; B, 0.1 mm.
Data for: The cerebellum regulates fear extinction through thalamo-prefrontal cortex interactions in male mice
<p>Fear extinction is a form of inhibitory learning that suppresses the expression of aversive memories and plays a key role in the recovery of anxiety and trauma-related disorders. Here, using male mice, we identify a cerebello-thalamo-cortical pathway regulating fear extinction. The cerebellar fastigial nucleus (FN) projects to the lateral subregion of the mediodorsal thalamic nucleus (MD), which is reciprocally connected with the dorsomedial prefrontal cortex (dmPFC). The inhibition of FN inputs to MD in male mice impairs fear extinction in animals with high fear responses and increases the bursting of MD neurons, a firing pattern known to prevent extinction learning. Indeed, this MD bursting is followed by high levels of the dmPFC 4 Hz oscillations causally associated with fear responses during fear extinction, and the inhibition of FN-MD neurons increases the coherence of MD bursts and oscillations with dmPFC 4 Hz oscillations. Overall, these findings reveal a regulation of fear-related thalamo-cortical dynamics by the cerebellum and its contribution to fear extinction.</p>
Data for: The cerebellum regulates fear extinction through thalamo-prefrontal cortex interactions in male mice
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A vector calculus for neural computation in the cerebellum
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Disrupted development of sensory systems and the cerebellum in a zebrafish ebf3a mutant
<p>Behavior and imaging data for the ebf3a mutant zebrafish line. Also, Supplementary Data S1, which contains additional RNA-seq analyses and code.</p>
Organization of reward and movement signals in the basal ganglia and cerebellum
<p>The basal ganglia and the cerebellum are major subcortical structures in the motor system. The basal ganglia have been cast as the reward center of the motor system, whereas the cerebellum is thought to be involved in adjusting sensorimotor parameters. Recent findings of reward signals in the cerebellum have challenged this dichotomous view. To compare the basal ganglia and the cerebellum directly, we recorded from oculomotor regions in both structures from the same monkeys. We partitioned the trial-by-trial variability of the neurons into reward and eye-movement signals to compare the coding across structures. Reward expectation and movement signals were the most pronounced in the output structure of the basal ganglia, intermediate in the cerebellum, and the smallest in the input structure of the basal ganglia. These findings suggest that reward and movement information is sharpened through the basal ganglia, resulting in a higher signal-to-noise ratio than in the cerebellum.</p>
IgLON5 immunoprecipitation files of binding partners in rat granullar cells of the cerebellum
<p class="MsoNormal"><span>Background: Anti-IgLON5 disease is a rare neurological disorder characterized by autoantibodies against IgLON5, and pathological evidence of neurodegeneration. IgLON5 is a cell adhesion molecule but its physiological function is unknown. Our aim was to investigate the IgLON5 interactome and to determine if IgLON5 antibodies (IgLON5-abs) affect these protein interactions.</span></p> <p class="MsoNormal"><span>Methods: IgLON5 interactome was investigated by mass spectrometry sequencing of proteins immunoprecipitated by IgLON5 autoantibodies using cultures of rat cerebellar granular neurons (CGNs). Shedding of IgLON5 was explored using HEK cells transfected with human IgLON5 plasmid and in CGNs. Interactions of IgLON5 with identified binding partners and IgLON5-abs effects were confirmed by immunofluorescence in transfected HEK cells and rat hippocampal neurons.</span></p> <p class="MsoNormal"><span>Results: Patients' IgLON5 antibodies co-precipitated all members of the IgLON family and three 3 additional surface proteins. IgLON5 predominantly establishes homomeric and heteromeric <em>cis</em> (within the cell) and <em>trans </em>(between cells)-interactions with other IgLON family members and undergoes spontaneous ectodomain shedding. Antibodies from patients with anti-IgLON5 disease prevent trans-interactions in hippocampal neurons independently of the IgLON5 IgG subclass distribution. </span></p> <p class="MsoNormal"><span>Conclusions: We show a potentially novel pathogenic mechanism of IgLON5-abs that consists in blocking IgLON5 interactions with its binding partners. These findings extend our knowledge about the physiological role of IgLON5 and pave the way to future understanding of the pathological mechanisms of anti-IgLON5 disease.</span></p>
Targeting Cerebellum to Treat Psychosis: a Transcranial Magnetic Stimulation (TMS) Study
ClinicalTrials.gov study NCT02642029. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Organization of reward and movement signals in the basal ganglia and cerebellum
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IgLON5 immunoprecipitation files of binding partners in rat granullar cells of the cerebellum
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Intrinsic and synaptic determinants of receptive field plasticity in Purkinje cells of the mouse cerebellum
<p>Here we provide the data for the paper "Intrinsic and synaptic determinants of receptive field plasticity in Purkinje cells of the mouse cerebellum". The dataset is saved as MAT-file (version 7.0). The source code for analysis is saved in github. Folder names indicate the contents corresponding to the specific figures in the paper.</p>
Golgi cell gap junction coupling in cerebellum cortex model WT and KO conditions
<p>Golgi cell gap junction coupling in cerebellum cortex model WT and KO conditions</p>
Oscillations in the granular layer of a cerebellum cortex model
<p>Oscillations in the granular layer of a cerebellum cortex model</p>
code for: The cerebellum computes frequency dynamics for motions with numerical precision and cross-individual uniformity
<p>MATLAB codes for data analyses performed in "The cerebellum computes frequency dynamics for motions with numerical precision and cross-individual uniformity".</p>
Data from: Encoding of locomotion kinematics in the mouse cerebellum
The cerebellum is involved in coordinating motor behaviour, but how the cerebellar network regulates locomotion is still not well understood. We characterised the activity of putative cerebellar Purkinje cells, Golgi cells and mossy fibres in awake mice engaged in an active locomotion task, using high-density silicon electrode arrays. Analysis of the activity of over 300 neurons in response to locomotion revealed that the majority of cells (53%) were significantly modulated by phase of the stepping cycle. However, in contrast to studies involving passive locomotion on a treadmill, we found that a high proportion of cells (45%) were tuned to the speed of locomotion, and 19% were tuned to yaw movements. The activity of neurons in the cerebellar vermis provided more information about future speed of locomotion than about past or present speed, suggesting a motor, rather than purely sensory, role. We were able to accurately decode the speed of locomotion with a simple linear algorithm, with only a relatively small number of well-chosen cells needed, irrespective of cell class. Our observations suggest that behavioural state modulates cerebellar sensorimotor integration, and advocate a role for the cerebellar vermis in control of high-level locomotor kinematic parameters such as speed and yaw.
Quantitative anatomy of the cerebellum on chickens and junglefowl
<p>Domestication is the process by which wild organisms become adapted for human use. Many phenotypic changes are associated with animal domestication, including decreases in brain and brain region sizes. In contrast to this pattern, the chicken has a larger cerebellum compared with the wild red junglefowl, but what neuroanatomical changes are responsible for this difference have yet to be investigated. Here, we quantified cell layer volumes, neuron numbers and neuron sizes in the cerebella of chickens and junglefowl. Chickens have larger, more folded cerebella with more and larger granule cells than junglefowl, but neuron numbers and cerebellar folding were proportional to cerebellum size. However, chickens do have relatively larger granule cell layer volumes and relatively larger granule cells than junglefowl. Thus, the chicken cerebellum can be considered a scaled-up version of the junglefowl cerebellum, but with enlarged granule cells. The combination of scaling neuron number and disproportionate enlargement of cell bodies partially supports a recent theory that domestication does not affect neuronal density within brain regions. Whether the neuroanatomical changes we observed are typical of domestication or not requires similar quantitative analyses in other domesticated species and across multiple brain regions.</p>
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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.