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25 results for “Cortical dysplasia”
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>
Multicenter Validated Detection of Focal Cortical Dysplasia using Deep Learning
<p>Lesional and non-lesional patches derived from 148 FCD patients is available as a HDF5 dataset (v1.0.0; doi: 10.5061/dryad.h70rxwdgm or 10.5281/zenodo.3239446). To create this dataset, for each of the 148 FCD patients, we sampled at most 1,000 (*_N1000.h5) or 1,500 (*_N1500.h5) cortical patches (or # voxels in the lesion, whichever is lower) of size 16×16×16 within the lesion.The same number of cortical patches were sampled randomly outside the lesion. The resulting lesional and non-lesional patches were concatenated, shuffled (to add another layer of randomization), and saved along with their binary labels (compressed HDF5 dataset).</p> <p>For axis=1, index 0 is T1 and 1 is FLAIR.</p>
Supplement: Multicenter validated detection of focal cortical dysplasia using deep learning
<p><span><b><span>Objective</span></b><span>. </span><span><span>To test the hypothesis that a multicenter-validated computer deep learning algorithm detects MRI-negative focal cortical dysplasia (FCD).</span></span></span></p> <p><span><b><span>Methods</span></b><span>. We used clinically acquired 3D T1-weighted and 3D FLAIR MRI of 148 patients (median age, 23 years [range, 2-55]; 47% female) with histologically verified FCD at nine centers to train a deep convolutional neural network (CNN) classifier. Images were initially deemed as MRI-negative in 51% of cases, in whom intracranial EEG determined the focus. For risk stratification, the CNN incorporated Bayesian uncertainty estimation as a measure of confidence. To evaluate performance, detection maps were compared to expert FCD manual labels. </span><span><span>We also tested sensitivity in an independent cohort of </span></span><span><span>23 FCD cases (13±10 years</span></span><span><span>).</span></span><span> Applying the algorithm to 38 healthy and 63 temporal lobe epilepsy disease controls tested specificity. </span></span></p> <p><span><b><span>Results.</span></b><span> Overall sensitivity was 93% (137/148 FCD detected) using a leave-one-site-out cross-validation, with an average of six false positives per patient. Sensitivity in MRI-negative FCD was 85%. In 73% of patients, the FCD was among the clusters with the highest confidence; in half it ranked the highest. </span><span><span>Sensitivity in the </span></span><span><span>independent cohort was </span></span><span><span>83% (19/23; average of five false positives per patient).</span></span><span> Specificity was 89% in healthy and disease controls.</span></span></p> <p><span><b><span>Conclusions</span></b><span>. This first multicenter-validated deep learning detection algorithm yields the highest sensitivity to date in MRI-negative FCD. By pairing predictions with risk stratification</span><span><span> this classifier may assist clinicians to adjust hypotheses relative to other tests, increasing </span></span><span>diagnostic confidence</span><span><span>.</span></span><span> Moreover, generalizability across age and MRI hardware </span><span><span>makes this approach ideal for pre-surgical evaluation of MRI-negative epilepsy. </span></span></span></p> <p><b><span>Classification of evidence</span></b><span>. This study provides Class III evidence that deep learning on multimodal MRI accurately identifies FCD in epilepsy patients initially diagnosed as MRI-negative.</span></p>
Supplement: Multicenter validated detection of focal cortical dysplasia using deep learning
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A Study Investigating the Anti-epileptic Efficacy of Afinitor (Everolimus) in Patients With Refractory Seizures Who Have Focal Cortical Dysplasia Type II (FCD II)
ClinicalTrials.gov study NCT03198949. IPD Sharing: NO. Countries: 1. Publications: 1.
Mos-FED (Mosaicism in Focal Epilepsy Cortical Dysplasia Tissue)
ClinicalTrials.gov study NCT06053671. IPD Sharing: YES. Countries: 1. Publications: 0.
Multimodal single-cell profiling reveals neuronal vulnerability and pathological cell states in focal cortical dysplasia
GEO Series GSE268807. Homo sapiens. 22 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Single-nucleus transcriptomics and chromatin accessibility of cell type-specific contributions to the epileptogenic cortex of focal cortical dysplasia type IIIa
GEO Series GSE266308. Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Single-nucleus transcriptomics and chromatin accessibility of cell type-specific contributions to the epileptogenic cortex of focal cortical dysplasia type IIIa [snATAC-seq]
GEO Series GSE266303. Homo sapiens. 7 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
CpG methylation analysis in Mesial temporal lobe epilepsy and Focal cortical dysplasia patients
GEO Series GSE96067. Homo sapiens. 9 samples. Type: Methylation profiling by genome tiling array.
The specific DNA methylation landscape in Focal Cortical Dysplasia ILAE Type 3D
GEO Series GSE227239. Homo sapiens. 7 samples. Type: Methylation profiling by genome tiling array.
Transcriptome analyses of the cortex and white matter of focal cortical dysplasia type II human samples: novel insights into disease mechanisms and contributions to tissue characterization
GEO Series GSE213488. Homo sapiens. 35 samples. Type: Expression profiling by high throughput sequencing.
Neuropsychological assessment and clinical evaluation in temporal lobeepilepsy with associated cortical dysplasia
<p>Temporal Lobe Epilepsy (TLE) is a chronic neurological disorder, often associated to cognitive deficits.Focal cortical dysplasia (FCD), frequently associated to high risk of epilepsy, can lead to abnormalitiesin cognition. The aim of this study was to explore neuropsychological performance and to identify poten-tial risk factors for cognitive impairment in TLE subjects with associated FCD. Our sample was composedby 46 TLE patients with FCD (37.76 ± 12.60 years; 29 females and 16 males) and 44 healthy controls (41.05 ± 9.74 years; 25 females and 19 males). All subjects performed a neuropsychological battery associ-ated to a measurement of depression and anxiety. Results showed a poor performance of all domainsof cognitive functioning and identified age of epilepsy onset as potential risk factor of cognitive impair-ment. These findings support the importance to focus on cognitive impairment in TLE patients with FCDto better clarify the impact of epilepsy features and FCD in therapeutic and everyday management</p>
Determining the Extent of Diffusion Tensor Abnormalities in Focal Cortical Dysplasia
ClinicalTrials.gov study NCT00687024. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Study of Predictive Biomarkers for Rational Management of Drug-resistant Epilepsy Associated With Focal Cortical Dysplasia
ClinicalTrials.gov study NCT03321240. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Safety, Tolerability, and Pharmacokinetics of SVG103 (Paxalisib) in Focal Cortical Dysplasia Type II (FCD-II), Tuberous Sclerosis Complex (TSC) or Hemimegalencephaly (HME)
ClinicalTrials.gov study NCT07287202. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Dysmorphic neurons express markers of inhibitory glycinergic signaling in focal cortical dysplasia
GEO Series GSE300645. Homo sapiens. 4 samples. Type: Other.
Single-nucleus transcriptomics and chromatin accessibility of cell type-specific contributions to the epileptogenic cortex of focal cortical dysplasia type IIIa [snRNA-seq]
GEO Series GSE266305. Homo sapiens. 7 samples. Type: Expression profiling by high throughput sequencing.
Modeling Focal Cortical Dysplasia (FCD) using cortical organoids
GEO Series GSE174605. Homo sapiens. 8 samples. Type: Expression profiling by array.
Gene expression analysis in human focal cortical dysplasia and tuberous sclerosis
GEO Series GSE62019. Homo sapiens. 11 samples. Type: Expression profiling by array.
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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.