Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Realtime phase-amplitude coupling analysis of micro electrode recorded brain signals.

ABSTRACT: OBJECTIVE:To demonstrate a method to calculate phase amplitude coupling (PAC) quickly and robustly for realtime applications. METHODS:We designed and implemented a multirate PAC algorithm with efficient filter bank processing and efficient computation of PAC for many frequency-pair combinations. We tested the developed algorithm for computing PAC on simulated data and on intraoperative neural recording data obtained during deep brain stimulation (DBS) electrode implantation surgery. RESULTS:A combination of parallelized frequency-domain filtering and modulation index for PAC estimation provided robust results that could be calculated in real time on modest computing hardware. CONCLUSION:The standard methods for calculating PAC can be optimized for quick and robust performance. SIGNIFICANCE:These results demonstrated that PAC can be extracted in real time and is suitable for neurofeedback applications.

SUBMITTER: Lu DC

PROVIDER: S-EPMC6161890 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Realtime phase-amplitude coupling analysis of micro electrode recorded brain signals.

Lu David Chao-Chia DC Boulay Chadwick C Chan Adrian D C ADC Sachs Adam J AJ

PloS one 20180928 9

<h4>Objective</h4>To demonstrate a method to calculate phase amplitude coupling (PAC) quickly and robustly for realtime applications.<h4>Methods</h4>We designed and implemented a multirate PAC algorithm with efficient filter bank processing and efficient computation of PAC for many frequency-pair combinations. We tested the developed algorithm for computing PAC on simulated data and on intraoperative neural recording data obtained during deep brain stimulation (DBS) electrode implantation surger ...[more]

PMID: 30265705

Similar Datasets

Identifying Phase-Amplitude Coupling in Cyclic Alternating Pattern using Masking Signals.

Project description:Judiciously classifying phase-A subtypes in cyclic alternating pattern (CAP) is critical for investigating sleep dynamics. Phase-amplitude coupling (PAC), one of the representative forms of neural rhythmic interaction, is defined as the amplitude of high-frequency activities modulated by the phase of low-frequency oscillations. To examine PACs under more or less synchronized conditions, we propose a nonlinear approach, named the masking phase-amplitude coupling (MPAC), to quantify physiological interactions between high (?/low?) and low (?) frequency bands. The results reveal that the coupling intensity is generally the highest in subtype A1 and lowest in A3. MPACs among various physiological conditions/disorders (p?<?0.0001) and sleep stages (p?<?0.0001 except S4) are tested. MPACs are found significantly stronger in light sleep than deep sleep (p?<?0.0001). Physiological conditions/disorders show similar order in MPACs. Phase-amplitude dependence between ? and ?/low? oscillations are examined as well. ? phase tent to phase-locked to ?/low? amplitude in subtype A1 more than the rest. These results suggest that an elevated ?-?/low? MPACs can reflect some synchronization in CAP. Therefore, MPAC can be a potential tool to investigate neural interactions between different time scales, and ?-?/low? MPAC can serve as a feasible biomarker for sleep microstructure.

| S-EPMC5805690 | biostudies-literature

Tensorpac: An open-source Python toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals.

Project description:Despite being the focus of a thriving field of research, the biological mechanisms that underlie information integration in the brain are not yet fully understood. A theory that has gained a lot of traction in recent years suggests that multi-scale integration is regulated by a hierarchy of mutually interacting neural oscillations. In particular, there is accumulating evidence that phase-amplitude coupling (PAC), a specific form of cross-frequency interaction, plays a key role in numerous cognitive processes. Current research in the field is not only hampered by the absence of a gold standard for PAC analysis, but also by the computational costs of running exhaustive computations on large and high-dimensional electrophysiological brain signals. In addition, various signal properties and analyses parameters can lead to spurious PAC. Here, we present Tensorpac, an open-source Python toolbox dedicated to PAC analysis of neurophysiological data. The advantages of Tensorpac include (1) higher computational efficiency thanks to software design that combines tensor computations and parallel computing, (2) the implementation of all most widely used PAC methods in one package, (3) the statistical analysis of PAC measures, and (4) extended PAC visualization capabilities. Tensorpac is distributed under a BSD-3-Clause license and can be launched on any operating system (Linux, OSX and Windows). It can be installed directly via pip or downloaded from Github (https://github.com/EtienneCmb/tensorpac). By making Tensorpac available, we aim to enhance the reproducibility and quality of PAC research, and provide open tools that will accelerate future method development in neuroscience.

| S-EPMC7654762 | biostudies-literature

Empirical analysis of phase-amplitude coupling approaches.

Project description:Analysis of the coupling between the phases and amplitudes of oscillations within the same continuously sampled signal has provided interesting insights into the physiology of memory and other brain process, and, more recently, the pathophysiology of parkinsonism and other movement disorders. Technical aspects of the analysis have a significant impact on the results. We present an empirical exploration of a variety of analysis design choices that need to be considered when measuring phase-amplitude coupling (PAC). We studied three alternative filtering approaches to the commonly used Kullback-Leibler distance-based method of PAC analysis, including one method that uses wavelets, one that uses constant filter settings, and one in which filtering of the data is optimized for individual frequency bands. Additionally, we introduce a time-dependent PAC analysis technique that takes advantage of the inherent temporality of wavelets. We examined how the duration of the sampled data, the stability of oscillations, or the presence of artifacts affect the value of the "modulation index", a commonly used parameter describing the degree of PAC. We also studied the computational costs associated with calculating modulation indices by the three techniques. We found that wavelet-based PAC performs better with similar or less computational cost than the two other methods while also allowing to examine temporal changes of PAC. We also show that the reliability of PAC measurements strongly depends on the duration and stability of PAC, and the presence (or absence) of artifacts. The best parameters to be used for PAC analyses of long samples of data may differ, depending on data characteristics and analysis objectives. Prior to settling on a specific PAC analysis approach for a given set of data, it may be useful to conduct an initial analysis of the time-dependence of PAC using our time-resolved PAC analysis.

| S-EPMC6615623 | biostudies-literature

Spurious cross-frequency amplitude-amplitude coupling in nonstationary, nonlinear signals.

Project description:Recent studies of brain activities show that cross-frequency coupling (CFC) play an important role in memory and learning. Many measures have been proposed to investigate the CFC phenomenon, including the correlation between the amplitude envelopes of two brain waves at different frequencies - cross-frequency amplitude-amplitude coupling (AAC). In this short communication, we describe how nonstationary, nonlinear oscillatory signals may produce spurious cross-frequency AAC. Utilizing the empirical mode decomposition, we also propose a new method for assessment of AAC that can potentially reduce the effects of nonlinearity and nonstatonarity and, thus, help to avoid the detection of artificial AACs. We compare the performances of this new method and the traditional Fourier-based AAC method. We also discuss the strategies to identify potential spurious AACs.

| S-EPMC4834901 | biostudies-literature

Dissociated neuronal phase- and amplitude-coupling patterns in the human brain.

Project description:Coupling of neuronal oscillations may reflect and facilitate the communication between neuronal populations. Two primary neuronal coupling modes have been described: phase-coupling and amplitude-coupling. Theoretically, both coupling modes are independent, but so far, their neuronal relationship remains unclear. Here, we combined MEG, source-reconstruction and simulations to systematically compare cortical amplitude-coupling and phase-coupling patterns in the human brain. Importantly, we took into account a critical bias of amplitude-coupling measures due to phase-coupling. We found differences between both coupling modes across a broad frequency range and most of the cortex. Furthermore, by combining empirical measurements and simulations we ruled out that these results were caused by methodological biases, but instead reflected genuine neuronal amplitude coupling. Our results show that cortical phase- and amplitude-coupling patterns are non-redundant, which may reflect at least partly distinct neuronal mechanisms. Furthermore, our findings highlight and clarify the compound nature of amplitude coupling measures.

| S-EPMC7068703 | biostudies-literature

Therapeutic deep brain stimulation reduces cortical phase-amplitude coupling in Parkinson's disease.

Project description:Deep brain stimulation (DBS) is increasingly applied for the treatment of brain disorders, but its mechanism of action remains unknown. Here we evaluate the effect of basal ganglia DBS on cortical function using invasive cortical recordings in Parkinson's disease (PD) patients undergoing DBS implantation surgery. In the primary motor cortex of PD patients, neuronal population spiking is excessively synchronized to the phase of network oscillations. This manifests in brain surface recordings as exaggerated coupling between the phase of the beta rhythm and the amplitude of broadband activity. We show that acute therapeutic DBS reversibly reduces phase-amplitude interactions over a similar time course as that of the reduction in parkinsonian motor signs. We propose that DBS of the basal ganglia improves cortical function by alleviating excessive beta phase locking of motor cortex neurons.

| S-EPMC4414895 | biostudies-literature

Evaluation of Phase-Amplitude Coupling in Resting State Magnetoencephalographic Signals: Effect of Surrogates and Evaluation Approach.

Project description:Phase-amplitude coupling (PAC) plays an important role in neural communication and computation. Interestingly, recent studies have indicated the presence of ubiquitous PAC phenomenon even during the resting state. Despite the importance of PAC phenomenon, estimation of significant physiological PAC is challenging because of the lack of appropriate surrogate measures to control false positives caused by non-physiological PAC. Therefore, in the present study, we evaluated PAC phenomenon during resting-state magnetoencephalography (MEG) signal and considered various surrogate measures and computational approaches widely used in the literature in addition to proposing new ones. We evaluated PAC phenomenon over the entire length of the MEG signal and for multiple shorter time segments. The results indicate that the extent of PAC phenomenon mainly depends on the surrogate measures and PAC computational methods used, as well as the evaluation approach. After a careful and critical evaluation, we found that resting-state MEG signals failed to exhibit ubiquitous PAC phenomenon, contrary to what has been suggested previously.

| S-EPMC5122594 | biostudies-literature

Phase-Amplitude Coupling in Spontaneous Mouse Behavior.

Project description:The level of activity of many animals including humans rises and falls with a period of ~ 24 hours. The intrinsic biological oscillator that gives rise to this circadian oscillation is driven by a molecular feedback loop with an approximately 24 hour cycle period and is influenced by the environment, most notably the light:dark cycle. In addition to the circadian oscillations, behavior of many animals is influenced by multiple oscillations occurring at faster-ultradian-time scales. These ultradian oscillations are also thought to be driven by feedback loops. While many studies have focused on identifying such ultradian oscillations, less is known about how the ultradian behavioral oscillations interact with each other and with the circadian oscillation. Decoding the coupling among the various physiological oscillators may be important for understanding how they conspire together to regulate the normal activity levels, as well in disease states in which such rhythmic fluctuations in behavior may be disrupted. Here, we use a wavelet-based cross-frequency analysis to show that different oscillations identified in spontaneous mouse behavior are coupled such that the amplitude of oscillations occurring at higher frequencies are modulated by the phase of the slower oscillations. The patterns of these interactions are different among different individuals. Yet this variability is not random. Differences in the pattern of interactions are confined to a low dimensional subspace where different patterns of interactions form clusters. These clusters expose the differences among individuals-males and females are preferentially segregated into different clusters. These sex-specific features of spontaneous behavior were not apparent in the spectra. Thus, our methodology reveals novel aspects of the structure of spontaneous animal behavior that are not observable using conventional methodology.

| S-EPMC5025157 | biostudies-other

Thalamocortical control of propofol phase-amplitude coupling.

Project description:The anesthetic propofol elicits many different spectral properties on the EEG, including alpha oscillations (8-12 Hz), Slow Wave Oscillations (SWO, 0.1-1.5 Hz), and dose-dependent phase-amplitude coupling (PAC) between alpha and SWO. Propofol is known to increase GABAA inhibition and decrease H-current strength, but how it generates these rhythms and their interactions is still unknown. To investigate both generation of the alpha rhythm and its PAC to SWO, we simulate a Hodgkin-Huxley network model of a hyperpolarized thalamus and corticothalamic inputs. We find, for the first time, that the model thalamic network is capable of independently generating the sustained alpha seen in propofol, which may then be relayed to cortex and expressed on the EEG. This dose-dependent sustained alpha critically relies on propofol GABAA potentiation to alter the intrinsic spindling mechanisms of the thalamus. Furthermore, the H-current conductance and background excitation of these thalamic cells must be within specific ranges to exhibit any intrinsic oscillations, including sustained alpha. We also find that, under corticothalamic SWO UP and DOWN states, thalamocortical output can exhibit maximum alpha power at either the peak or trough of this SWO; this implies the thalamus may be the source of propofol-induced PAC. Hyperpolarization level is the main determinant of whether the thalamus exhibits trough-max PAC, which is associated with lower propofol dose, or peak-max PAC, associated with higher dose. These findings suggest: the thalamus generates a novel rhythm under GABAA potentiation such as under propofol, its hyperpolarization may determine whether a patient experiences trough-max or peak-max PAC, and the thalamus is a critical component of propofol-induced cortical spectral phenomena. Changes to the thalamus may be a critical part of how propofol accomplishes its effects, including unconsciousness.

| S-EPMC5739502 | biostudies-other

A Precise Annotation of Phase-Amplitude Coupling Intensity.

Project description:Neuronal information can be coded in different temporal and spatial scales. Cross-frequency coupling of neuronal oscillations, especially phase-amplitude coupling (PAC), plays a critical functional role in neuronal communication and large scale neuronal encoding. Several approaches have been developed to assess PAC intensity. It is generally agreed that the PAC intensity relates to the uneven distribution of the fast oscillation amplitude conditioned on the slow oscillation phase. However, it is still not clear what the PAC intensity exactly means. In the present study, it was found that there were three types of interferential signals taking part in PAC phenomenon. Based on the classification of interferential signals, the conception of PAC intensity is theoretically annotated as the proportion of slow or fast oscillation that is involved in a related PAC phenomenon. In order to make sure that the annotation is proper to some content, simulation data are constructed and then analyzed by three PAC approaches. These approaches are the mean vector length (MVL), the modulation index (MI), and a new permutation mutual information (PMI) method in which the permutation entropy and the information theory are applied. Results show positive correlations between PAC values derived from all three methods and the suggested intensity. Finally, the amplitude distributions, i.e. the phase-amplitude plots, obtained from different PAC intensities show that the annotation proposed in the study is in line with the previous understandings.

| S-EPMC5049761 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data