Inferring causality in biological oscillators

Motivation Fundamental to biological study is identifying regulatory interactions. The recent surge in time-series data collection in biology provides a unique opportunity to infer regulations computationally. However, when components oscillate, model-free inference methods, while easily implemented, struggle to distinguish periodic synchrony and causality. Alternatively, model-based methods test the reproducibility of time series given a specific model but require inefficient simulations and have limited applicability. Results We develop an inference method based on a general model of molecular, neuronal, and ecological oscillatory systems that merges the advantages of both model-based and model-free methods, namely accuracy, broad applicability, and usability. Our method successfully infers the positive and negative regulations within various oscillatory networks, e.g., the repressilator and a network of cofactors at the pS2 promoter, outperforming popular inference methods. Availability We provide a computational package, ION (Inferring Oscillatory Networks), that users can easily apply to noisy, oscillatory time series to uncover the mechanisms by which diverse systems generate oscillations. Accompanying MATLAB code under a BSD-style license and examples are available at ttps://github.com/Mathbiomed/ION. Additionally, the code is available under a CC-BY 4.0 License at https://doi.org/10.6084/m9.figshare.16431408.v1. Supplementary information Supplementary data are available at Bioinformatics online.

Identifying Oscillatory Hyperconnectivity and Hypoconnectivity Networks in Major Depression Using Coupled Tensor Decomposition

Previous researches demonstrate that major depression disorder (MDD) is associated with widespread network dysconnectivity, and the dynamics of functional connectivity networks are important to delineate the neural mechanisms of MDD. Cortical electroencephalography (EEG) oscillations act as coordinators to connect different brain regions, and various assemblies of oscillations can form different networks to support different cognitive tasks. Studies have demonstrated that the dysconnectivity of EEG oscillatory networks is related with MDD. In this study, we investigated the oscillatory hyperconnectivity and hypoconnectivity networks in MDD under a naturalistic and continuous stimuli condition of music listening. With the assumption that the healthy group and the MDD group share similar brain topology from the same stimuli and also retain individual brain topology for group differences, we applied the coupled nonnegative tensor decomposition algorithm on two adjacency tensors with the dimension of time × frequency × connectivity × subject, and imposed double-coupled constraints on spatial and spectral modes. The music-induced oscillatory networks were identified by a correlation analysis approach based on the permutation test between extracted temporal factors and musical features. We obtained three hyperconnectivity networks from the individual features of MDD and three hypoconnectivity networks from common features. The results demonstrated that the dysfunction of oscillation-modulated networks could affect the involvement in music perception for MDD patients. Those oscillatory dysconnectivity networks may provide promising references to reveal the pathoconnectomics of MDD and potential biomarkers for the diagnosis of MDD.

Blinking Networks of Memristor Oscillatory Circuits in the Flux-Charge Domain

Multistability phenomena and complex nonlinear dynamics in memristor oscillators pave the way to obtain efficient solutions to optimization problems by means of novel computational architectures based on the interconnection of single–device oscillators. It is well-known that topological properties of interconnections permit to control synchronization and spatio–temporal patterns in oscillatory networks. When the interconnections can change in time with a given probability to connect two oscillators, the whole network acts as a complex network with blinking couplings. The work of has shown that a particular class of blinking complex networks are able to completely synchronize in a faster fashion with respect to other coupling strategies. This work focuses on the specific class of blinking complex networks made of Memristor–based Oscillatory Circuits (MOCs). By exploiting the recent Flux–Charge Analysis Method, we make clear that synchronization phenomena in blinking networks of memristor oscillators having stochastic couplings, i.e., Blinking Memristor Oscillatory Networks (BMONs), correspond to global periodic oscillations on invariant manifolds and the effect of a blinking link is to shift the nonlinear dynamics through the infinite (invariant) manifolds. Numerical simulations performed on MOCs prove that synchronization phenomena can be controlled just by changing the coupling amongst them.

Inferring causality in biological oscillators

A fundamental goal of biological study is to identify regulatory interactions among components. The recent surge in time-series data collection in biology provides a unique opportunity to infer regulatory networks computationally. However, when the components oscillate, model-free inference methods, while easily implemented, struggle to distinguish periodic synchrony and causality. Alternatively, model-based methods test whether time series are reproducible with a specific model but require inefficient simulations and have limited applicability. Here, we develop an inference method based on a general model of molecular, neuronal, and ecological oscillatory systems that merges the advantages of both model-based and model-free methods, namely accuracy, broad applicability, and usability. Our method successfully infers the positive and negative regulations of various oscillatory networks, including the repressilator and a network of cofactors of pS2 promoter, outperforming popular inference methods. We also provide a computational package, ION (Inferring Oscillatory Networks), that users can easily apply to noisy, oscillatory time series to decipher the mechanisms by which diverse systems generate oscillations.

Neuronal Switching Between Single- and Dual-Network Activity via Modulation of Intrinsic Membrane Properties

Oscillatory networks underlie rhythmic behaviors (e.g. walking, chewing), and complex behaviors (e.g. memory formation, decision making). Flexibility of oscillatory networks includes neurons switching between single- and dual-network participation, even generating oscillations at two distinct frequencies. Modulation of synaptic strength can underlie this neuronal switching. Here we ask whether switching into dual-frequency oscillations can also result from modulation of intrinsic neuronal properties. The isolated stomatogastric nervous system of male Cancer borealis crabs contains two well-characterized rhythmic feeding-related networks (pyloric, ∼1 Hz; gastric mill, ∼0.1 Hz). The identified modulatory projection neuron MCN5 causes the pyloric-only LPG neuron to switch to dual pyloric/gastric mill bursting. Bath applying the MCN5 neuropeptide transmitter Gly1-SIFamide only partly mimics the LPG switch to dual activity, due to continued LP neuron inhibition of LPG. Here, we find that MCN5 uses a co-transmitter, glutamate, to inhibit LP, unlike Gly1-SIFamide excitation of LP. Thus, we modeled the MCN5-elicited LPG switching with Gly1-SIFamide application and LP photoinactivation. Using hyperpolarization of pyloric pacemaker neurons and gastric mill network neurons, we found that LPG pyloric-timed oscillations require rhythmic electrical synaptic input. However, LPG gastric mill-timed oscillations do not require any pyloric/gastric mill synaptic input and are voltage dependent. Thus, we identify modulation of intrinsic properties as an additional mechanism for switching a neuron into dual-frequency activity. Instead of synaptic modulation switching a neuron into a second network as a passive follower, modulation of intrinsic properties could enable a switching neuron to become an active contributor to rhythm generation in the second network.Significance StatementNeuromodulation of oscillatory networks can enable network neurons to switch from sing<bacle- to dual-network participation, even when two networks oscillate at distinct frequencies. We used small, well-characterized networks to determine whether modulation of synaptic strength, an identified mechanism for switching, is necessary for dual-network recruitment. We demonstrate that rhythmic electrical synaptic input is required for continued linkage with a “home” network, but that modulation of intrinsic properties is sufficient to switch a neuron into dual-frequency oscillations, linking it to a second network. Neuromodulator-induced switches in neuronal participation between networks occurs in motor, cognitive, and sensory networks. Our study highlights the importance of considering intrinsic properties as a pivotal target for enabling parallel participation of a neuron in two oscillatory networks.