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Spectral parameterization for studying neurodevelopment: How and why.

ABSTRACT: A growing body of literature suggests that the explicit parameterization of neural power spectra is important for the appropriate physiological interpretation of periodic and aperiodic electroencephalogram (EEG) activity. In this paper, we discuss why parameterization is an imperative step for developmental cognitive neuroscientists interested in cognition and behavior across the lifespan, as well as how parameterization can be readily accomplished with an automated spectral parameterization ("specparam") algorithm (Donoghue et al., 2020a). We provide annotated code for power spectral parameterization, via specparam, in Jupyter Notebook and R Studio. We then apply this algorithm to EEG data in childhood (N = 60; M_age = 9.97, SD = 0.95) to illustrate its utility for developmental cognitive neuroscientists. Ultimately, the explicit parameterization of EEG power spectra may help us refine our understanding of how dynamic neural communication contributes to normative and aberrant cognition across the lifespan. Data and annotated analysis code for this manuscript are available on GitHub as a supplement to the open-access specparam toolbox.

SUBMITTER: Ostlund B

PROVIDER: S-EPMC8792072 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

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Spectral parameterization for studying neurodevelopment: How and why.

Ostlund Brendan B Donoghue Thomas T Anaya Berenice B Gunther Kelley E KE Karalunas Sarah L SL Voytek Bradley B Pérez-Edgar Koraly E KE

Developmental cognitive neuroscience 20220115

A growing body of literature suggests that the explicit parameterization of neural power spectra is important for the appropriate physiological interpretation of periodic and aperiodic electroencephalogram (EEG) activity. In this paper, we discuss why parameterization is an imperative step for developmental cognitive neuroscientists interested in cognition and behavior across the lifespan, as well as how parameterization can be readily accomplished with an automated spectral parameterization ("s ...[more]

PMID: 35074579

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Project description:Accurate characterization of electrostatic interactions is crucial in molecular simulation. Various methods and programs have been developed to obtain electrostatic parameters for additive or polarizable models to replicate electrostatic properties obtained from experimental measurements or theoretical calculations. Electrostatic potentials (ESPs), a set of physically well-defined observables from quantum mechanical (QM) calculations, are well suited for optimization efforts due to the ease of collecting a large amount of conformation-dependent data. However, a reliable set of QM ESP computed at an appropriate level of theory and atomic basis set is necessary. In addition, despite the recent development of the PyRESP program for electrostatic parameterizations of induced dipole-polarizable models, the time-consuming and error-prone input file preparation process has limited the widespread use of these protocols. This work aims to comprehensively evaluate the quality of QM ESPs derived by eight methods, including wave function methods such as Hartree-Fock (HF), second-order Møller-Plesset (MP2), and coupled cluster-singles and doubles (CCSD), as well as five hybrid density functional theory (DFT) methods, used in conjunction with 13 different basis sets. The highest theory levels CCSD/aug-cc-pV5Z (a5z) and MP2/aug-cc-pV5Z (a5z) were selected as benchmark data over two homemade data sets. The results show that the hybrid DFT method, ωB97X-D, combined with the aug-cc-pVTZ (a3z) basis set, performs well in reproducing ESPs while taking both accuracy and efficiency into consideration. Moreover, a flexible and user-friendly program called PyRESP_GEN was developed to streamline input file preparation. The restraining strengths, along with strategies for polarizable Gaussian multipole (pGM) model parameterizations, were also optimized. These findings and the program presented in this work facilitate the development and application of induced dipole-polarizable models, such as pGM models, for molecular simulations of both chemical and biological significance.

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Spectral parameterization for studying neurodevelopment: How and why.

Publications

Spectral parameterization for studying neurodevelopment: How and why.

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