A mean-field toolbox for spiking neuronal network model analysis

Mean-field theory of spiking neuronal networks has led to numerous advances in our analytical and intuitive understanding of the dynamics of neuronal network models during the past decades. But, the elaborate nature of many of the developed methods, as well as the difficulty of implementing them, may limit the wider neuroscientific community from taking maximal advantage of these tools. In order to make them more accessible, we implemented an extensible, easy-to-use open-source Python toolbox that collects a variety of mean-field methods for the widely used leaky integrate-and-fire neuron model. The Neuronal Network Mean-field Toolbox (NNMT) in its current state allows for estimating properties of large neuronal networks, such as firing rates, power spectra, and dynamical stability in mean-field and linear response approximation, without running simulations on high performance systems. In this article we describe how the toolbox is implemented, show how it is used to calculate neuronal network properties, and discuss different use-cases, such as extraction of network mechanisms, parameter space exploration, or hybrid modeling approaches. Although the initial version of the toolbox focuses on methods that are close to our own past and present research, its structure is designed to be open and extensible. It aims to provide a platform for collecting analytical methods for neuronal network model analysis and we discuss how interested scientists can share their own methods via this platform.

The connections of neocortical pyramidal cells can implement the learning of new categories, attractor memory, and top–down recall and attention

Neocortical pyramidal cells have three key classes of excitatory input: forward inputs from the previous cortical area (or thalamus); recurrent collateral synapses from nearby pyramidal cells; and backprojection inputs from the following cortical area. The neocortex performs three major types of computation: (1) unsupervised learning of new categories, by allocating neurons to respond to combinations of inputs from the preceding cortical stage, which can be performed using competitive learning; (2) short-term memory, which can be performed by an attractor network using the recurrent collaterals; and (3) recall of what has been learned by top–down backprojections from the following cortical area. There is only one type of excitatory neuron involved, pyramidal cells, with these three types of input. It is proposed, and tested by simulations of a neuronal network model, that pyramidal cells can implement all three types of learning simultaneously, and can subsequently usefully categorise the forward inputs; keep them active in short-term memory; and later recall the representations using the backprojection input. This provides a new approach to understanding how one type of excitatory neuron in the neocortex can implement these three major types of computation, and provides a conceptual advance in understanding how the cerebral neocortex may work.

Dynamic Transitions in Neuronal Network Firing Sustained by Abnormal Astrocyte Feedback

Astrocytes play a crucial role in neuronal firing activity. Their abnormal state may lead to the pathological transition of neuronal firing patterns and even induce seizures. However, there is still little evidence explaining how the astrocyte network modulates seizures caused by structural abnormalities, such as gliosis. To explore the role of gliosis of the astrocyte network in epileptic seizures, we first established a direct astrocyte feedback neuronal network model on the basis of the hippocampal CA3 neuron-astrocyte model to simulate the condition of gliosis when astrocyte processes swell and the feedback to neurons increases in an abnormal state. We analyzed the firing pattern transitions of the neuronal network when astrocyte feedback starts to change via increases in both astrocyte feedback intensity and the connection probability of astrocytes to neurons in the network. The results show that as the connection probability and astrocyte feedback intensity increase, neuronal firing transforms from a nonepileptic synchronous firing state to an asynchronous firing state, and when astrocyte feedback starts to become abnormal, seizure-like firing becomes more severe and synchronized; meanwhile, the synchronization area continues to expand and eventually transforms into long-term seizure-like synchronous firing. Therefore, our results prove that astrocyte feedback can regulate the firing of the neuronal network, and when the astrocyte network develops gliosis, there will be an increase in the induction rate of epileptic seizures.

Topographic Organization of Correlation Along the Longitudinal and Transverse Axes in Rat Hippocampal CA3 Due to Excitatory Afferents

The topographic organization of afferents to the hippocampal CA3 subfield are well-studied, but their role in influencing the spatiotemporal dynamics of population activity is not understood. Using a large-scale, computational neuronal network model of the entorhinal-dentate-CA3 system, the effects of the perforant path, mossy fibers, and associational system on the propagation and transformation of network spiking patterns were investigated. A correlation map was constructed to characterize the spatial structure and temporal evolution of pairwise correlations which underlie the emergent patterns found in the population activity. The topographic organization of the associational system gave rise to changes in the spatial correlation structure along the longitudinal and transverse axes of the CA3. The resulting gradients may provide a basis for the known functional organization observed in hippocampus.

A Computational Model to Investigate GABA-Activated Astrocyte Modulation of Neuronal Excitation

Gamma-aminobutyric acid (GABA) is critical for proper neural network function and can activate astrocytes to induce neuronal excitability; however, the mechanism by which astrocytes transform inhibitory signaling to excitatory enhancement remains unclear. Computational modeling can be a powerful tool to provide further understanding of how GABA-activated astrocytes modulate neuronal excitation. In the present study, we implemented a biophysical neuronal network model to investigate the effects of astrocytes on excitatory pre- and postsynaptic terminals following exposure to increasing concentrations of external GABA. The model completely describes the effects of GABA on astrocytes and excitatory presynaptic terminals within the framework of glutamatergic gliotransmission according to neurophysiological findings. Utilizing this model, our results show that astrocytes can rapidly respond to incoming GABA by inducing Ca2+ oscillations and subsequent gliotransmitter glutamate release. Elevation in GABA concentrations not only naturally decreases neuronal spikes but also enhances astrocytic glutamate release, which leads to an increase in astrocyte-mediated presynaptic release and postsynaptic slow inward currents. Neuronal excitation induced by GABA-activated astrocytes partly counteracts the inhibitory effect of GABA. Overall, the model helps to increase knowledge regarding the involvement of astrocytes in neuronal regulation using simulated bath perfusion of GABA, which may be useful for exploring the effects of GABA-type antiepileptic drugs.

From single neurons to behavior in the jellyfish Aurelia aurita

Jellyfish nerve nets provide insight into the origins of nervous systems, as both their taxonomic position and their evolutionary age imply that jellyfish resemble some of the earliest neuron-bearing, actively-swimming animals. Here, we develop the first neuronal network model for the nerve nets of jellyfish. Specifically, we focus on the moon jelly Aurelia aurita and the control of its energy-efficient swimming motion. The proposed single neuron model disentangles the contributions of different currents to a spike. The network model identifies factors ensuring non-pathological activity and suggests an optimization for the transmission of signals. After modeling the jellyfish’s muscle system and its bell in a hydrodynamic environment, we explore the swimming elicited by neural activity. We find that different delays between nerve net activations lead to well-controlled, differently directed movements. Our model bridges the scales from single neurons to behavior, allowing for a comprehensive understanding of jellyfish neural control of locomotion.