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36 results for “Cortical plasticity”
The gut microbiota of environmentally enriched mice regulates visual cortical plasticity
<p>ABSTRACT</p> <p>The complexity of brain circuits is sculpted both by innate genetic programs and environmental stimuli. Since the 1960s scientists have noticed that raising rodents in an enriched environment (EE) is able to improve all aspects of brain plasticity, from learning and memory to visual plasticity in adult and developing animals. Importantly, EE has also been shown to have beneficial effects on a variety of preclinical models of central nervous system diseases: Alzheimer’s and Parkinson’s disease, Rett syndrome, epilepsy etc, prompting intervention protocols in humans. However, the “enrichment derived key signals” through which this special environment performs its broad positive effects on brain health have not been completely elucidated yet. Here, we focused on signals coming from the body periphery and in particular on the gut microbiota. We found that the intestinal microbiota composition of EE mice is significantly different from the one of standard raised (ST) animals. Treatment of EE mice with an antibiotic cocktail completely prevented the EE-driven enhancement of OD plasticity. Strikingly, the fecal microbiota transplant from EE donors to adult ST mice was able to re-activate OD plasticity in the ST recipients. Thus, taken together our data suggest that experience-dependent changes in gut microbiota regulate brain plasticity.</p> <p>METHODS</p> <p>In the first dataset (Dataset1, files called zr2423) we report the raw data (.fastq) obtained from the sequencing of the fecal samples from C57BL/6J mice raised in EE or in ST from birth and collected at different time points during their lives.</p> <p>To analyze the composition of the microbiota of ST and EE mice at different ages, fresh faeces were collected longitudinally in the same subject at postnatal day (P)20 (n=6), P25 (n=6) and P90 (n=6). </p> <p>In the second dataset (Dataset2, files called zr2747) we report the raw data (.fastq) obtained from the sequencing of the fecal samples from C57BL/6J: adult donor mice living in EE (EE, n=8), adult recipient mice living in ST condition before the fecal transplantation (preFT, n=8) and 4 weeks after the fecal transplantation (postFT, n=8).</p> <p>For further details about the sample names see the “Explanation Table”.</p> <p>Bacterial DNA was extracted using a specific kit (QIAamp Powerfecal DNA kit, Qiagen) following the manufacturer's protocol. The 16S rRNA sequencing and analysis was performed by a service offered by Zymo Research (Irvine, CA, USA). </p> <p><em>Targeted Library Preparation</em>: The DNA samples were prepared for targeted sequencing with the Quick-16S™ NGS Library Prep Kit (Zymo Research). The primer sets used were Quick-16S™ Primer Set V3-V4 (Zymo Research). The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator™, then quantified with TapeStation® (Agilent Technologies, Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA). </p> <p><em>Sequencing:</em> The final library was sequenced on Illumina® MiSeq™ with a v3 reagent kit (600 cycles). The sequencing was performed with >10% PhiX spike-in.</p> <p> </p>
Assemblies, synapse clustering and network topology interact with plasticity to explain structure-function relationships of the cortical connectome
<p>Dataset linked to the article with the same title</p> <p>The model itself is very similar to its non-plastic counterpart under the following DOI: <a href="../record/7930275">10.5281/zenodo.7930275</a>, i.e. a 1.5 mm diameter cortical tissue comprising 211,712 neurons and their connectivity in the front limb and jaw subregions and the dysgranular zone of the Paxinos & Watson rat brain atlas. It's formatted in the open <a href="https://github.com/AllenInstitute/sonata">SONATA</a> standard and contains neuron locations and their properties (such as morphological types, cortical layer, etc.), their detailed morphologies, and synaptic connectivity (with all their anatomical and physiological parameters). The main difference from the non-plastic version is the addition of plasticity related parameters to <em>O1/S1nonbarrel_neurons__S1nonbarrel_neurons__chemical/edges.h5. </em>Extrinsic synaptic connections from the thalamus are included in this release, but for inputs from neurons in the remainder of non-barrel somatosensory cortex please see the non-plastic version of the circuit.</p> <p><strong>Analyzing the model</strong></p> <p>The model can be analyzed in terms of its anatomy, physiology and connectivity using the packages <a href="https://neurom.readthedocs.io/en/stable/">NeuroM</a>, <a href="https://bluebrainsnap.readthedocs.io/en/stable/">BlueBrain SNAP</a> and <a href="https://github.com/BlueBrain/ConnectomeUtilities">ConnectomeUtilities</a>. (see first Jupyter notebook)</p> <p><strong>Simulating the model</strong></p> <p>To simulate the model we'd recommend using out using our open-source simulator <a href="https://github.com/BlueBrain/neurodamus">Neurodamus</a>. The reference version is the branch <em>nbS1-2023</em>, which is archived under the following DOI: <a href="http://doi.org/10.5281/zenodo.8075202">10.5281/zenodo.8075202</a>. Instructions on how to use the simulator are provided on the GitHub page linked above. Briefly, you'll first have to <a href="https://github.com/BlueBrain/neurodamus#install-neurodamus">install Neurodamus</a>. Next, build a <em>"special"</em> executable that include compiled versions of ion channel and synapse models. To do that, follow <a href="https://github.com/BlueBrain/neurodamus#build-special-with-mod-files">these instructions</a>, where <em>mod-files-from-released-circuit </em>is replaced by the location of <em>O1/mods</em> on your system. Finally, <a href="https://github.com/BlueBrain/neurodamus#examples">run a simulation</a>. The specific simulation conditions and stimuli are specified in simulation configuration files. An exemplary simulation configuration is included in this release (<em>simulation_config.zip</em>).</p> <p><strong>Analyzing simulation results</strong></p> <p>Simulation results can be analyzed with <a href="https://bluebrainsnap.readthedocs.io/en/stable/">BlueBrain SNAP</a>, <a href="https://github.com/BlueBrain/ConnectomeUtilities">ConnectomeUtilities</a>, and <a href="https://github.com/BlueBrain/assemblyfire">assemblyfire</a>. Notebooks 2-5 go though these analysis and recreate some of the panels from our article. In most cases the notebooks can be run with the shared HDF5 files and don't require running any simulations.</p> <p><strong>Version 2</strong></p> <p>Bug fix in simulation_config.json and therefore new version of results (and corresponding notebooks). The underlying circuit model (O1.xz) did not change from v1.</p> <p>--</p> <p><em>The development of this dataset was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.</em></p>
All-trans retinoic acid induces synaptic plasticity in human cortical neurons
Open the record for dataset details and reuse information.
Data from: MRI-based visualization of rTMS-induced cortical plasticity in the primary motor cortex
<p>Repetitive transcranial magnetic stimulation (rTMS) induces changes in cortical excitability for minutes to hours after the end of intervention. However, it has not been precisely determined to what extent cortical plasticity prevails spatially in the cortex. Recent studies have shown that rTMS induces changes in "interhemispheric" functional connectivity, the resting-state functional connectivity between the stimulated region and the symmetrically corresponding region in the contralateral hemisphere. In the present study, quadripulse stimulation (QPS) was applied to the index finger representation in the left primary motor cortex (M1), while the position of the stimulation coil was constantly monitored by an online navigator. After QPS application, resting-state functional magnetic resonance imaging was performed, and the interhemispheric functional connectivity was compared with that before QPS. A cluster of connectivity changes was observed in the stimulated region in the central sulcus. The cluster was spatially extended approximately 10 mm from the center [half width at half maximum (HWHM): approximately 3 mm] and was extended approximately 20 mm long in depth (HWHM: approximately 7 mm). A localizer scan of the index finger motion confirmed that the cluster of interhemispheric connectivity changes overlapped spatially with the activation related to the index finger motion. These results indicate that cortical plasticity in M1 induced by rTMS was relatively restricted in space and suggest that rTMS can reveal functional dissociation associated with adjacent small areas by inducing neural plasticity in restricted cortical regions.</p>
Frequency-dependent cortical plasticity: evidence from psychophysics, functional imaging and computational modelling.
<p>fMRI data relating to the paper entitled 'Frequency-dependent cortical plasticity: evidence from psychophysics, functional imaging and computational modelling'. </p>
Cerebellum and Cortical Plasticity: the Case of Dystonia
ClinicalTrials.gov study NCT01272154. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Cortical Plasticity in a Complex Intervention for Endometriosis
ClinicalTrials.gov study NCT01321840. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Influence of Transcranial Direct Current Stimulation on Cortical Plasticity in Concussed Athletes
ClinicalTrials.gov study NCT01593956. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Cortical Plasticity After Motor Cortex Stimulation in Healthy Subject and Chronic Pain Patients
ClinicalTrials.gov study NCT02849834. IPD Sharing: NO. Countries: 1. Publications: 1.
Transcranial Direct Current Stimulation on Cortical Plasticity in Patients With Anti-NMDA Receptor Encephalitis
ClinicalTrials.gov study NCT01865578. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Cortical Plasticity of the Tactile Mirror System in Borderline Personality Disorder
ClinicalTrials.gov study NCT06702215. IPD Sharing: YES. Countries: 1. Publications: 1.
Data from: MRI-based visualization of rTMS-induced cortical plasticity in the primary motor cortex
Open the record for dataset details and reuse information.
A Study to Investigate Evoked Potentials as Markers of Ketamine-induced Cortical Plasticity in Patients With Major Depressive Disorder
ClinicalTrials.gov study NCT01957410. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Modulating Human Cortical Plasticity With Transcranial Electrical Stimulation
ClinicalTrials.gov study NCT03114488. IPD Sharing: NO. Countries: 1. Publications: 0.
Induction of Cortical Plasticity
ClinicalTrials.gov study NCT04553341. IPD Sharing: YES. Countries: 1. Publications: 0.
Interhemispheric Interaction of Parieto-Motor Cortico-Cortical Plasticity
ClinicalTrials.gov study NCT03253731. IPD Sharing: Not stated. Countries: 0. Publications: 3.
Repetitive transcranial magnetic stimulation induces cortical layer, brain region, and protocol dependent neural plasticity [Spatial transcriptomics]
GEO Series GSE259405. Mus musculus. 12 samples. Type: Other.
Integrative analysis of disease signatures shows inflammation disrupts juvenile experience-dependent cortical plasticity
GEO Series GSE89757. Mus musculus. 9 samples. Type: Expression profiling by array.
Influence of tDCS on Cortical Plasticity in Patients With Dementia of the Alzheimer Type
ClinicalTrials.gov study NCT01887899. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Cortical Pharyngeal Area: Excitability, Facilitation and Plasticity in Healthy Subjects
ClinicalTrials.gov study NCT00213382. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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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.