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Minimum embedding dimension analysis uncovers reduced network complexity during neuronal differentiation in autism spectrum disorder

ABSTRACT: Minimum embedding dimension analysis uncovers reduced network complexity during neuronal differentiation in autism spectrum disorder

PROVIDER: PRJNA514983 | ENA |

REPOSITORIES: ENA

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Minimum embedding dimension analysis uncovers reduced network complexity during neuronal differentiation in autism spectrum disorder

Project description:Background: Neuronal activity can be modeled as a nonlinear dynamical system to yield novel measures of neuronal state and dysfunction. We hypothesized that electrical activity during neuronal differentiation would be marked by a reduction in dynamical complexity in autism spectrum disorder (ASD). Methods: Electrical activity of induced pluripotent stem cell (iPSC)-derived neurons from ASD patients and controls were recorded using a multielectrode array (MEA). Minimum embedding dimension (MED) analysis was performed to characterize the complexity present in the electrical recordings of the neuronal cultures during differentiation. Gene expression changes with respect to the MED were analyzed, and gene ontology analysis and the BrainSpan Atlas were used to identify gene enrichments in specific biological pathways, brain regions, and developmental stages. Results: We found that the MED showed a statistically significant deficit in the ASD samples, suggesting that, compared to controls, network complexity is reduced in ASD during neuronal differentiation. MED was correlated to clinical endpoints such as nonverbal intelligence and was associated with 53 differentially expressed genes. These differentially expressed genes were overrepresented in ASD gene lists and pathways related to neurodevelopment, cell morphology, and cell migration. Spatiotemporal analysis also showed a prenatal temporal enrichment in cortical and deep brain structures. Conclusion: Reduced network complexity in ASD was observed by MED analysis during neuronal differentiation, indicating deficits in integrated and synchronized firing. The results present nonlinear dynamical analysis of iPSC-derived neuronal electrical recordings as a new paradigm for the investigation of aberrant brain activity in neurodevelopmental disorders.

2020-05-18 | GSE125020 | GEO

Low-melting point agarose as embedding medium for MALDI mass spectrometry imaging and laser-capture microdissection-based proteomics

Project description:We report an investigation of low-temperature embedding media in terms of their mechanical properties and embedding temperature, with the goal of determining a reliable embedding medium for the combination of MALDI MSI of lipids, laser-capture microdissection of tissue regions, and quantitative proteomics. We compared embedded and non-embedded tissues to ensure that the embedding media did not interfere with the analysis.

2024-01-26 | PXD045349 | Pride

Genetics and genomics of autism spectrum disorder: embracing complexity.

Project description: Not available

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Quantitative historical analysis uncovers a single dimension of complexity that structures global variation in human social organization.

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The Impact of Patient Complexity on Healthcare Utilization

Project description:Healthcare providers are routinely being assessed for metrics designed to assess the quality of the care they deliver. There is growing consensus that these measurements, which typically assess the percentage of patients meeting a specific standard of care, should be adjusted for the clinical complexity of the providers. This study will assess whether adjusting for the social complexity of the patient panel adds significantly to adjustment for clinical complexity in explaining apparent differences in quality of care provided by Primary care providers and clinics.

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Optimal Cutting Temperature Embedding Media Study

Project description:The goal of the Optimal Cutting Temperature (OCT) Embedding Media Study was to measure the effect of OCT embedding on peptide identification. One OCT embedded sample and one snap frozen sample were compared. Each sample was analyzed 3 times using label free proteomic profiling. The data sets below contain the raw data files for the 3 replicates, there were 15 fractions assayed per sample for a total of 45 raw data files. No effect has been identified thus far, so concern over OCT embedding of the TCGA samples has been diminished.<ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S014">https://cptac-data-portal.georgetown.edu/cptac/s/S014</a> on 11/02/18</li></ul>

2018-11-02 | MSV000083095 | MassIVE

Dynamical Electrical Complexity Is Reduced during Neuronal Differentiation in Autism Spectrum Disorder.

Project description: Not available

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Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid growth and maturation

Project description:While biochemical regulation has been extensively studied in cerebral organoid modeling protocols, the role of mechano-regulation in directing stem cell fate and organoid development has been relatively unexplored. Volumetric compression, a key aspect of natural brain development, is known to influence neuronal differentiation. However, stiff interpenetrating network compression fails to accurately replicate the dynamic organoid development observed in nature. In this study, we present a novel method of heterogeneous embedding using an alginate-shell-Matrigel-core system. This approach allows for cell-Matrigel remodeling by the inner layer and provides moderate normal compression through the soft alginate outer layer. Our results show significant improvements in cell proliferation and maturation of cerebral organoids, as evidenced by increased expression of neuronal markers such as neurofilament (NF) and microtubule-associated protein 2 (MAP2). Compared to non-alginate embedding and alginate compression groups, volume growth remains unimpeded. Our findings demonstrate the successful mechanical regulation of cerebral organoids, which not only mimics the mechanical environment of brain development but also exhibits a regular growth profile with enhanced maturation. These results highlight the importance and potential practical applications of mechano-regulation in the establishment of brain organoids.

2023-09-09 | GSE242715 | GEO

Principled approach to the selection of the embedding dimension of networks.

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Reduced structural complexity of the right cerebellar cortex in male children with autism spectrum disorder.

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