Dataset Information

Inferring a simple mechanism for alpha-blocking by fitting a neural population model to EEG spectra.

ABSTRACT: Alpha blocking, a phenomenon where the alpha rhythm is reduced by attention to a visual, auditory, tactile or cognitive stimulus, is one of the most prominent features of human electroencephalography (EEG) signals. Here we identify a simple physiological mechanism by which opening of the eyes causes attenuation of the alpha rhythm. We fit a neural population model to EEG spectra from 82 subjects, each showing a different degree of alpha blocking upon opening of their eyes. Though it has been notoriously difficult to estimate parameters by fitting such models, we show how, by regularizing the differences in parameter estimates between eyes-closed and eyes-open states, we can reduce the uncertainties in these differences without significantly compromising fit quality. From this emerges a parsimonious explanation for the spectral differences between states: Changes to just a single parameter, pei, corresponding to the strength of a tonic excitatory input to the inhibitory cortical population, are sufficient to explain the reduction in alpha rhythm upon opening of the eyes. We detect this by comparing the shift in each model parameter between eyes-closed and eyes-open states. Whereas changes in most parameters are weak or negligible and do not scale with the degree of alpha attenuation across subjects, the change in pei increases monotonically with the degree of alpha blocking observed. These results indicate that opening of the eyes reduces alpha activity by increasing external input to the inhibitory cortical population.

SUBMITTER: Hartoyo A

PROVIDER: S-EPMC7217488 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Inferring a simple mechanism for alpha-blocking by fitting a neural population model to EEG spectra.

Hartoyo Agus A Cadusch Peter J PJ Liley David T J DTJ Hicks Damien G DG

PLoS computational biology 20200430 4

Alpha blocking, a phenomenon where the alpha rhythm is reduced by attention to a visual, auditory, tactile or cognitive stimulus, is one of the most prominent features of human electroencephalography (EEG) signals. Here we identify a simple physiological mechanism by which opening of the eyes causes attenuation of the alpha rhythm. We fit a neural population model to EEG spectra from 82 subjects, each showing a different degree of alpha blocking upon opening of their eyes. Though it has been not ...[more]

PMID: 32352973

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Project description:BackgroundRNA viruses infecting a host usually exist as a set of closely related sequences, referred to as quasispecies. The genomic diversity of viral quasispecies is a subject of great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software was originally designed for single genome assembly and cannot be used to simultaneously assemble and estimate the abundance of multiple closely related quasispecies sequences.ResultsIn this paper, we introduce a new Viral Spectrum Assembler (ViSpA) method for quasispecies spectrum reconstruction and compare it with the state-of-the-art ShoRAH tool on both simulated and real 454 pyrosequencing shotgun reads from HCV and HIV quasispecies. Experimental results show that ViSpA outperforms ShoRAH on simulated error-free reads, correctly assembling 10 out of 10 quasispecies and 29 sequences out of 40 quasispecies. While ShoRAH has a significant advantage over ViSpA on reads simulated with sequencing errors due to its advanced error correction algorithm, ViSpA is better at assembling the simulated reads after they have been corrected by ShoRAH. ViSpA also outperforms ShoRAH on real 454 reads. Indeed, 7 most frequent sequences reconstructed by ViSpA from a real HCV dataset are viable (do not contain internal stop codons), and the most frequent sequence was within 1% of the actual open reading frame obtained by cloning and Sanger sequencing. In contrast, only one of the sequences reconstructed by ShoRAH is viable. On a real HIV dataset, ShoRAH correctly inferred only 2 quasispecies sequences with at most 4 mismatches whereas ViSpA correctly reconstructed 5 quasispecies with at most 2 mismatches, and 2 out of 5 sequences were inferred without any mismatches. ViSpA source code is available at http://alla.cs.gsu.edu/~software/VISPA/vispa.html.ConclusionsViSpA enables accurate viral quasispecies spectrum reconstruction from 454 pyrosequencing reads. We are currently exploring extensions applicable to the analysis of high-throughput sequencing data from bacterial metagenomic samples and ecological samples of eukaryote populations.

Dataset Information

Inferring a simple mechanism for alpha-blocking by fitting a neural population model to EEG spectra.

Publications

Inferring a simple mechanism for alpha-blocking by fitting a neural population model to EEG spectra.

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