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56 results for “neural pathways”
Deep learning models predicting gene functions and pathways using public DRKG knowledge graph and graph neural network
<p>The attached dataset contains pretrained link prediction models, as described in our paper 'Morphological Map of Under- and Over-Expression of Genes in Human Cells'.</p>
STM, locomotion and survival raw data for: A neural m6A/Ythdf pathway is required for learning and memory in Drosophila
<p>The files contain raw and summarized data files for the STM, locomotion and survival experiments published in the manuscript entitled " A neural m6A/Ythdf pathway is required for learning and memory in Drosophila". Instructions on how to process data and further information is found in the "summary" file.<br> </p>
Predicting the pathways of string-like motions in metallic glasses via path featurizing graph neural networks
<p>String-like motions (SLMs) cooperative, "snake"-like movements of particles—are crucial for dynamics in diverse glass formers. Despite their ubiquity, questions persist: do SLMs prefer specific paths? If so, can we predict these paths? Here, in Al-Sm glasses, our iso-configurational ensemble simulations reveal that SLMs indeed follow certain paths. By designing a graph neural network (GNN) to featurize the environment around directional paths, we achieve a high-fidelity prediction of likely SLM pathways solely based on the static structure. GNN gauges a structural measure to assess each path's propensity to engage in SLMs, akin to a "softness" metric, but for paths rather than for atoms. Our GNN interpretation reveals the critical role of the bottleneck zone along paths in steering SLMs. By monitoring "path-softness", we elucidate SLM-favored paths transit from fragmented to interconnected upon glass transition. Our findings reveal that, beyond atoms or clusters, glasses have another dimension of structural heterogeneity: "paths".</p>
Data from: Neural pathways of autonomic reflexes in familial autonomic ganglionopathy
<p><b>Objective: </b>We determined the molecular basis of a new monogenetic recessive disorder that results in familial neurogenic orthostatic hypotension (nOH) with impaired sympathetic (SNS) and parasympathetic (PNS) activity.<b> </b></p> <p><b>Methods:</b> Two adult siblings from one family (I-4, I-5) and an another subject from a second family (II-3) presented with severe nOH, poor compensatory increase in heart rate, small non-reactive pupils and constipation. All three affected members had low norepinephrine levels and diffuse autonomic failure.</p> <p><b>Results:</b> Whole exome sequencing of DNAs from subjects (I-4, I-5) showed compound heterozygosity for c.907_908delCT (p.L303Dfs*115) /c.688G>A (p.D230N) pathologic variants in the acetylcholine receptor, neuronal nicotinic, alpha 3 subunit (CHRNA3) gene. The II-3 from the second family was homozygous for the same frameshift(fs) variant (p.L303Dfs*115// p.L303Dfs*115). The CHRNA3 is a subunit of nicotinic acetylcholine receptors (nAChRs) that regulate SNS and PNS activity through fast synaptic transmission in the autonomic ganglia. The fs variant is obviously pathogenic and the p.D230N variant is predicted to be damaging (SIFT)/probably damaging (PolyPhen2). The p.D230N variant lies on the interface between CHRNA3 and other nAChR subunits based on structural modeling and is predicted to destabilize the nAChR pentameric complex.</p> <p><b>Conclusions:</b> We report a novel genetic disease that affected three individuals from two unrelated families who presented with nOH and diffuse autonomic failure. These subjects had rare pathologic variants in the CHRNA3 gene that co-segregate with and are predicted to be the likely cause of their SNS and PNS failure.</p>
Neural pathways and computations that achieve stable contrast processing tuned to natural scenes
<h1>Gur et al. 2024 database</h1> <p>Source data of the paper Gür et al. 2024, “Neural pathways and computations that achieve stable contrast processing tuned to natural scenes”, Nature Communications. This work contains an analysis of post-receptor luminance gain in the Drosophila visual system, focusing on the circuitry and algorithms for implementation of rapid luminance gain control.</p> <p>All data can be analyzed using the code provided in the Github repository: <a href="https://github.com/silieslab/Gur-etal-2024">https://github.com/silieslab/Gur-etal-2024</a>. Please go to the “Readme” file in the repository for how to use the code.</p> <h2>Raw data</h2> <p>All raw data is located in the folder “raw_data”. "Readme" file located in the code repository will guide you on how to analyze all data.</p> <h2>Processed data</h2> <p>All processed data is located in the folder “processed_data”. "Readme" file located in the code repository will guide you on how to analyze all data.</p> <p>- 2p_imaging_python_pickle: Processed data stored as .pickle files. <br>- Dm12_Figure7_Mat_files: Processed data for Dm12 imaging and optogenetics experiments presented in Figure 7 stored as .mat files.<br>- EM_data: Processed data for EM analysis done in Figure 7.<br>- Figure 6 Tm9 flpSTOP: tdTomato expression data for Figure 6 Tm9 flpSTOP experiments.<br>- Figure S5 Tm1 flpSTOP: tdTomato expression data for FigureS5 Tm1 flpSTOP experiments.</p>
TMS-fMRI for Neural Pathway in Smokers
ClinicalTrials.gov study NCT02665338. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Predicting the pathways of string-like motions in metallic glasses via path featurizing graph neural networks
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Data from: The transcription factor Pou3f1 promotes neural fate commitment via activation of neural lineage genes and inhibition of external signaling pathways
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Data from: Neural pathways of autonomic reflexes in familial autonomic ganglionopathy
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Topographic deep neural networks predict the functional organization of the primate ventral visual pathway
<p>Recording of presentation at the Neuroscience 2021 annual meeting (held virtually). The abstract follows:</p> <p> </p> <p>The primate ventral visual pathway is organized into functional maps, including pinwheel-like arrangements of orientation-tuned neurons in primary visual cortex (V1) and patches of category-selective neurons in higher visual cortex. While deep convolutional neural networks (DCNNs) trained for object recognition accurately predict neural representations throughout the ventral pathway, they have no spatial layout for features at a given retinotopic location and are thus unable to predict the rich topographic organization of visual cortex. Here, we close this gap by first assigning each DCNN unit a position in a 2D cortical sheet, then training the network to minimize a cost function with two components: one encouraging accurate object recognition, and another favoring correlated responses among nearby units in each model layer (Figure 1A, 1B). </p> <p>We find that training with this composite spatial loss produces brain-like topographic maps in both early and later model layers (Figure 1B). Early layers contain smooth orientation preference maps with pinwheels, clusters of units preferring the same spatial frequency, and color-preference domains resembling V1 “blobs”. In a later layer of the same model, we observe clusters of category-selective units, e.g., face patches, whose spatial organization largely matches that found in primate higher visual cortex. Our model thus leverages local response correlations, which have been linked to theories of wire-length minimization, to accurately predict neuron responses and functional organization throughout the ventral visual pathway. In support of the wire-length minimization hypothesis, we find that our topographic DCNN would require shorter connections than a standard DCNN to support connections between similarly-tuned neurons within early (38% reduction) and later (31% reduction) model layers (Figure 1D). These results suggest that the functional organization of visual cortex can be explained by two constraints: the need to perform object recognition and pressure for local populations of neurons to have correlated responses.</p>
Neural Conduction Along the Visual Pathways After Oral Treatment With Citicoline in Patients With Optic Nerve Diseases
ClinicalTrials.gov study NCT00404729. IPD Sharing: Not stated. Countries: 1. Publications: 1.
TBL1XR1 ensures balanced neural developmental through NCOR complex-mediated regulation of the MAPK pathway
GEO Series GSE162750. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
NAD+ Modulates the Proliferation and Differentiation of Adult Neural Stem/Progenitor Cells via Akt Signaling Pathway
GEO Series GSE200494. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
REST suppression mediates neural conversion of adult human fibroblasts via microRNA dependent and independent pathways
GEO Series GSE90068. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing.
Enterochromaffin cells are gut chemosensors that couple to sensory neural pathways
GEO Series GSE98794. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
The Hippo Pathway Prevents YAP/TAZ–Driven Hypertranscription and Controls Neural Progenitor Number
GEO Series GSE120016. Mus musculus. 23 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Expression profiling by array.
Identifying Altered Developmental Pathways in Induced Pluripotent Stem Cell-Derived Neural Stem Cells From a Patients with Globoid Cell Leukodystrophy Using Transcriptome Profiling
GEO Series GSE212512. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
STAT pathway activation limits the Ascl1-mediated chromatin remodeling required for neural regeneration from Müller glia in adult mouse retina
GEO Series GSE135414. Mus musculus. 7 samples. Type: Expression profiling by high throughput sequencing.
The influence of WWOX gene on cellular pathways in neuronal differentiation of human neural stem cells
GEO Series GSE126075. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Transcriptional reprogramming of neural stem cells by a PHF6/EphR signalling pathway [ChIP-Seq]
GEO Series GSE247836. Mus musculus. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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.