NetPyNE Implementation and Scaling of the Potjans-Diesmann Cortical Microcircuit Model.

The Potjans-Diesmann cortical microcircuit model is a widely used model originally implemented in NEST. Here, we reimplemented the model using NetPyNE, a high-level Python interface to the NEURON simulator, and reproduced the findings of the original publication. We also implemented a method for scaling the network size that preserves first- and second-order statistics, building on existing work on network theory. Our new implementation enabled the use of more detailed neuron models with multicompartmental morphologies and multiple biophysically realistic ion channels. This opens the model to new research, including the study of dendritic processing, the influence of individual channel parameters, the relation to local field potentials, and other multiscale interactions. The scaling method we used provides flexibility to increase or decrease the network size as needed when running these CPU-intensive detailed simulations. Finally, NetPyNE facilitates modifying or extending the model using its declarative language; optimizing model parameters; running efficient, large-scale parallelized simulations; and analyzing the model through built-in methods, including local field potential calculation and information flow measures.

Conductance-based models and the fragmentation problem: A case study based on hippocampal CA1 pyramidal cell models and epilepsy.

Epilepsy has been a central topic in computational neuroscience, and in silico models have shown to be excellent tools to integrate and evaluate findings from animal and clinical settings. Among the different languages and tools for computational modeling development, NEURON stands out as one of the most used and mature neurosimulators. However, despite the vast quantity of models developed with NEURON, a fragmentation problem is evident in the great majority of models related to the same type of cell or cell properties. This fragmentation causes a lack of interoperability between the models because of differences in parameters. The problem is not related to the neurosimulator, which is prepared to reuse elements of other models, but related to decisions made during the model development, when it is not uncommon to adjust parameter values according to the necessities of the study. Here, this problem is presented by studying computational models related to temporal lobe epilepsy and the definitions of hippocampal CA1 pyramidal cells. The current assessment aims to highlight the implications of fragmentation for reliable modeling and the need to adopt a framework that allows a better interoperability between different models. This article is part of the Special Issue "NEWroscience 2018".

Firing properties of ventral medullary respiratory neurons in sino-aortic denervated rats.

NEW FINDINGS: What is the central question of this study? After sino-aortic denervation (SAD), rats present normal levels of mean arterial pressure (MAP), high MAP variability and changes in breathing. However, mechanisms involved in SAD-induced respiratory changes and their impact on the modulation of sympathetic activity remain unclear. Herein, we characterized the firing frequency of medullary respiratory neurons after SAD. What is the main finding and its importance? Sino-aortic denervation-induced prolonged inspiration was associated with a reduced interburst frequency of pre-inspiratory/inspiratory neurons and an increased long-term variability of late inspiratory neurons, but no changes were observed in the ramp-inspiratory and post-inspiratory neurons. This imbalance in the respiratory network might contribute to the modulation of sympathetic activity after SAD. ABSTRACT: In previous studies, we documented that after sino-aortic denervation (SAD) in rats there are significant changes in the breathing pattern, but no significant changes in sympathetic activity and mean arterial pressure compared with sham-operated rats. However, the neural mechanisms involved in the respiratory changes after SAD and the extent to which they might contribute to the observed normal sympathetic activity and mean arterial pressure remain unclear. Here, we hypothesized that after SAD, rats present with changes in the firing frequency of the ventral medullary inspiratory and post-inspiratory neurons. To test this hypothesis, male Wistar rats underwent SAD or sham surgery and 3 days later were surgically prepared for an in situ experiment. The duration of inspiration significantly increased in SAD rats. During inspiration, the total firing frequency of ramp-inspiratory, pre-inspiratory/inspiratory and late-inspiratory neurons was not different between groups. During post-inspiration, the total firing frequency of post-inspiratory neurons was also not different between groups. Furthermore, the data demonstrate a reduced interburst frequency of pre-inspiratory/inspiratory neurons and an increased long-term variability of late-inspiratory neurons in SAD compared with sham-operated rats. These findings indicate that the SAD-induced prolongation of inspiration was not accompanied by alterations in the total firing frequency of the ventral medullary respiratory neurons, but it was associated with changes in the long-term variability of late-inspiratory neurons. We suggest that the timing imbalance in the respiratory network in SAD rats might contribute to the modulation of presympathetic neurons after removal of baroreceptor afferents.

Dynamics of spontaneous activity in random networks with multiple neuron subtypes and synaptic noise : Spontaneous activity in networks with synaptic noise.

Spontaneous cortical population activity exhibits a multitude of oscillatory patterns, which often display synchrony during slow-wave sleep or under certain anesthetics and stay asynchronous during quiet wakefulness. The mechanisms behind these cortical states and transitions among them are not completely understood. Here we study spontaneous population activity patterns in random networks of spiking neurons of mixed types modeled by Izhikevich equations. Neurons are coupled by conductance-based synapses subject to synaptic noise. We localize the population activity patterns on the parameter diagram spanned by the relative inhibitory synaptic strength and the magnitude of synaptic noise. In absence of noise, networks display transient activity patterns, either oscillatory or at constant level. The effect of noise is to turn transient patterns into persistent ones: for weak noise, all activity patterns are asynchronous non-oscillatory independently of synaptic strengths; for stronger noise, patterns have oscillatory and synchrony characteristics that depend on the relative inhibitory synaptic strength. In the region of parameter space where inhibitory synaptic strength exceeds the excitatory synaptic strength and for moderate noise magnitudes networks feature intermittent switches between oscillatory and quiescent states with characteristics similar to those of synchronous and asynchronous cortical states, respectively. We explain these oscillatory and quiescent patterns by combining a phenomenological global description of the network state with local descriptions of individual neurons in their partial phase spaces. Our results point to a bridge from events at the molecular scale of synapses to the cellular scale of individual neurons to the collective scale of neuronal populations.

A Negative Slope Conductance of the Persistent Sodium Current Prolongs Subthreshold Depolarizations.

Neuronal subthreshold voltage-dependent currents determine membrane properties such as the input resistance (Rin) and the membrane time constant (τm) in the subthreshold range. In contrast with classical cable theory predictions, the persistent sodium current (INaP), a non-inactivating mode of the voltage-dependent sodium current, paradoxically increases Rin and τm when activated. Furthermore, this current amplifies and prolongs synaptic currents in the subthreshold range. Here, using a computational neuronal model, we showed that the creation of a region of negative slope conductance by INaP activation is responsible for these effects and the ability of the negative slope conductance to amplify and prolong Rin and τm relies on the fast activation of INaP. Using dynamic clamp in hippocampal CA1 pyramidal neurons in brain slices, we showed that the effects of INaP on Rin and τm can be recovered by applying an artificial INaP after blocking endogenous INaP with tetrodotoxin. Furthermore, we showed that injection of a pure negative conductance is enough to reproduce the effects of INaP on Rin and τm and is also able to prolong artificial excitatory post synaptic currents. Since both the negative slope conductance and the almost instantaneous activation are critical for producing these effects, the INaP is an ideal current for boosting the amplitude and duration of excitatory post synaptic currents near the action potential threshold.

Combined role of seizure-induced dendritic morphology alterations and spine loss in newborn granule cells with mossy fiber sprouting on the hyperexcitability of a computer model of the dentate gyrus.

Temporal lobe epilepsy strongly affects hippocampal dentate gyrus granule cells morphology. These cells exhibit seizure-induced anatomical alterations including mossy fiber sprouting, changes in the apical and basal dendritic tree and suffer substantial dendritic spine loss. The effect of some of these changes on the hyperexcitability of the dentate gyrus has been widely studied. For example, mossy fiber sprouting increases the excitability of the circuit while dendritic spine loss may have the opposite effect. However, the effect of the interplay of these different morphological alterations on the hyperexcitability of the dentate gyrus is still unknown. Here we adapted an existing computational model of the dentate gyrus by replacing the reduced granule cell models with morphologically detailed models coming from three-dimensional reconstructions of mature cells. The model simulates a network with 10% of the mossy fiber sprouting observed in the pilocarpine (PILO) model of epilepsy. Different fractions of the mature granule cell models were replaced by morphologically reconstructed models of newborn dentate granule cells from animals with PILO-induced Status Epilepticus, which have apical dendritic alterations and spine loss, and control animals, which do not have these alterations. This complex arrangement of cells and processes allowed us to study the combined effect of mossy fiber sprouting, altered apical dendritic tree and dendritic spine loss in newborn granule cells on the excitability of the dentate gyrus model. Our simulations suggest that alterations in the apical dendritic tree and dendritic spine loss in newborn granule cells have opposing effects on the excitability of the dentate gyrus after Status Epilepticus. Apical dendritic alterations potentiate the increase of excitability provoked by mossy fiber sprouting while spine loss curtails this increase.

Computational models of dentate gyrus with epilepsy-induced morphological alterations in granule cells.

Temporal lobe epilepsy provokes a number of different morphological alterations in granule cells of the hippocampus dentate gyrus. These alterations may be associated with the hyperactivity and hypersynchrony found in the epileptic dentate gyrus, and their study requires the use of different kinds of approaches including computational modeling. Conductance-based models of both normal and epilepsy-induced morphologically altered granule cells have been used in the construction of network models of dentate gyrus to study the effects of these alterations on epilepsy. Here, we review these models and discuss their contributions to the understanding of the association between alterations in neuronal morphology and epilepsy in the dentate gyrus.

A Computational Model for the Simulation of Prepulse Inhibition and Its Modulation by Cortical and Subcortical Units.

The sensorimotor gating is a nervous system function that modulates the acoustic startle response (ASR). Prepulse inhibition (PPI) phenomenon is an operational measure of sensorimotor gating, defined as the reduction of ASR when a high intensity sound (pulse) is preceded in milliseconds by a weaker stimulus (prepulse). Brainstem nuclei are associated with the mediation of ASR and PPI, whereas cortical and subcortical regions are associated with their modulation. However, it is still unclear how the modulatory units can influence PPI. In the present work, we developed a computational model of a neural circuit involved in the mediation (brainstem units) and modulation (cortical and subcortical units) of ASR and PPI. The activities of all units were modeled by the leaky-integrator formalism for neural population. The model reproduces basic features of PPI observed in experiments, such as the effects of changes in interstimulus interval, prepulse intensity, and habituation of ASR. The simulation of GABAergic and dopaminergic drugs impaired PPI by their effects over subcortical units activity. The results show that subcortical units constitute a central hub for PPI modulation. The presented computational model offers a valuable tool to investigate the neurobiology associated with disorder-related impairments in PPI.

Binding of Filamentous Actin to CaMKII as Potential Regulation Mechanism of Bidirectional Synaptic Plasticity by ß CaMKII in Cerebellar Purkinje Cells.

Calcium-calmodulin dependent protein kinase II (CaMKII) regulates many forms of synaptic plasticity, but little is known about its functional role during plasticity induction in the cerebellum. Experiments have indicated that the ß isoform of CaMKII controls the bidirectional inversion of plasticity at parallel fibre (PF)-Purkinje cell (PC) synapses in cerebellar cortex. Because the cellular events that underlie these experimental findings are still poorly understood, we developed a simple computational model to investigate how ß CaMKII regulates the direction of plasticity in cerebellar PCs. We present the first model of AMPA receptor phosphorylation that simulates the induction of long-term depression (LTD) and potentiation (LTP) at the PF-PC synapse. Our simulation results suggest that the balance of CaMKII-mediated phosphorylation and protein phosphatase 2B (PP2B)-mediated dephosphorylation of AMPA receptors can determine whether LTD or LTP occurs in cerebellar PCs. The model replicates experimental observations that indicate that ß CaMKII controls the direction of plasticity at PF-PC synapses, and demonstrates that the binding of filamentous actin to CaMKII can enable the ß isoform of the kinase to regulate bidirectional plasticity at these synapses.

Optimal Interplay between Synaptic Strengths and Network Structure Enhances Activity Fluctuations and Information Propagation in Hierarchical Modular Networks.

In network models of spiking neurons, the joint impact of network structure and synaptic parameters on activity propagation is still an open problem. Here, we use an information-theoretical approach to investigate activity propagation in spiking networks with a hierarchical modular topology. We observe that optimized pairwise information propagation emerges due to the increase of either (i) the global synaptic strength parameter or (ii) the number of modules in the network, while the network size remains constant. At the population level, information propagation of activity among adjacent modules is enhanced as the number of modules increases until a maximum value is reached and then decreases, showing that there is an optimal interplay between synaptic strength and modularity for population information flow. This is in contrast to information propagation evaluated among pairs of neurons, which attains maximum value at the maximum values of these two parameter ranges. By examining the network behavior under the increase of synaptic strength and the number of modules, we find that these increases are associated with two different effects: (i) the increase of autocorrelations among individual neurons and (ii) the increase of cross-correlations among pairs of neurons. The second effect is associated with better information propagation in the network. Our results suggest roles that link topological features and synaptic strength levels to the transmission of information in cortical networks.

Goalkeeper Game: A New Assessment Tool for Prediction of Gait Performance Under Complex Condition in People With Parkinson's Disease.

Background: People with Parkinson's disease (PD) display poorer gait performance when walking under complex conditions than under simple conditions. Screening tests that evaluate gait performance changes under complex walking conditions may be valuable tools for early intervention, especially if allowing for massive data collection. Objectives: To investigate the use of the Goalkeeper Game (GG) to predict impairment in gait performance under complex conditions in people with Parkinson's disease (PPD) and compare its predictive power with the one of the Montreal Cognitive Assessment (MoCA) test. Methods: 74 PPD (HY stages: 23 in stage 1; 31 in stage 2; 20 in stage 3), without dementia (MoCA cut-off 21), tested in ON period with dopaminergic medication were submitted to single individual cognitive/motor evaluation sessions. MoCA and GG were used to assess cognition, and the dynamic gait index (DGI) test was used to assess gait performance under complex condition. GG test resulted in 9 measures extracted via a statistical model. The predictive power of the GG measures and the MoCA score with respect to gait performance, as assessed by DGI, were compared. Results: The predictive models based on GG obtained a better score of prediction (65%) then MoCA (56%) for DGI scores (at a 50% specificity). Conclusion: GG is a novel tool for noninvasive screening that showed a superior predictive power in assessing gait performance under complex condition in people with PD than the well-established MoCa test.

Interplay of activation kinetics and the derivative conductance determines resonance properties of neurons.

In a neuron with hyperpolarization activated current (I_{h}), the correct input frequency leads to an enhancement of the output response. This behavior is known as resonance and is well described by the neuronal impedance. In a simple neuron model we derive equations for the neuron's resonance and we link its frequency and existence with the biophysical properties of I_{h}. For a small voltage change, the component of the ratio of current change to voltage change (dI/dV) due to the voltage-dependent conductance change (dg/dV) is known as derivative conductance (G_{h}^{Der}). We show that both G_{h}^{Der} and the current activation kinetics (characterized by the activation time constant τ_{h}) are mainly responsible for controlling the frequency and existence of resonance. The increment of both factors (G_{h}^{Der} and τ_{h}) greatly contributes to the appearance of resonance. We also demonstrate that resonance is voltage dependent due to the voltage dependence of G_{h}^{Der}. Our results have important implications and can be used to predict and explain resonance properties of neurons with the I_{h} current.

Self-Consistent Scheme for Spike-Train Power Spectra in Heterogeneous Sparse Networks.

Recurrent networks of spiking neurons can be in an asynchronous state characterized by low or absent cross-correlations and spike statistics which resemble those of cortical neurons. Although spatial correlations are negligible in this state, neurons can show pronounced temporal correlations in their spike trains that can be quantified by the autocorrelation function or the spike-train power spectrum. Depending on cellular and network parameters, correlations display diverse patterns (ranging from simple refractory-period effects and stochastic oscillations to slow fluctuations) and it is generally not well-understood how these dependencies come about. Previous work has explored how the single-cell correlations in a homogeneous network (excitatory and inhibitory integrate-and-fire neurons with nearly balanced mean recurrent input) can be determined numerically from an iterative single-neuron simulation. Such a scheme is based on the fact that every neuron is driven by the network noise (i.e., the input currents from all its presynaptic partners) but also contributes to the network noise, leading to a self-consistency condition for the input and output spectra. Here we first extend this scheme to homogeneous networks with strong recurrent inhibition and a synaptic filter, in which instabilities of the previous scheme are avoided by an averaging procedure. We then extend the scheme to heterogeneous networks in which (i) different neural subpopulations (e.g., excitatory and inhibitory neurons) have different cellular or connectivity parameters; (ii) the number and strength of the input connections are random (Erdos-Rényi topology) and thus different among neurons. In all heterogeneous cases, neurons are lumped in different classes each of which is represented by a single neuron in the iterative scheme; in addition, we make a Gaussian approximation of the input current to the neuron. These approximations seem to be justified over a broad range of parameters as indicated by comparison with simulation results of large recurrent networks. Our method can help to elucidate how network heterogeneity shapes the asynchronous state in recurrent neural networks.

Non-Decaying postsynaptics potentials and delayed spikes in hippocampal pyramidal neurons generated by a zero slope conductance created by the persistent Na+ current.

The negative slope conductance created by the persistent sodium current (INaP) prolongs the decay phase of excitatory postsynaptic potentials (EPSPs). In a recent study, we demonstrated that this effect was due to an increase of the membrane time constant. When the negative slope conductance opposes completely the positive slope conductances of the other currents it creates a zero slope conductance region. In this region the membrane time constant is infinite and the decay phase of the EPSPs is virtually absent. Here we show that non-decaying EPSPs are present in CA1 hippocampal pyramidal cells in the zero slope conductance region, in the suprathreshold range of membrane potential. Na+ channel block with tetrodotoxin abolishes the non-decaying EPSPs. Interestingly, the non-decaying EPSPs are observed only in response to artificial excitatory postsynaptic currents (aEPSCs) of small amplitude, and not in response to aEPSCs of big amplitude. We also observed concomitantly delayed spikes with long latencies and high variability only in response to small amplitude aEPSCs. Our results showed that in CA1 pyramidal neurons INaP creates non-decaying EPSPs and delayed spikes in the subthreshold range of membrane potentials, which could potentiate synaptic integration of synaptic potentials coming from distal regions of the dendritic tree.

A non-expensive bidimensional kinematic balance assessment can detect early postural instability in people with Parkinson's disease.

Background: Postural instability is a debilitating cardinal symptom of Parkinson's disease (PD). Its onset marks a pivotal milestone in PD when balance impairment results in disability in many activities of daily living. Early detection of postural instability by non-expensive tools that can be widely used in clinical practice is a key factor in the prevention of falls in widespread population and their negative consequences. Objective: This study aimed to investigate the effectiveness of a two-dimensional balance assessment to identify the decline in postural control associated with PD progression. Methods: This study recruited 55 people with PD, of which 37 were men. Eleven participants were in stage I, twenty-three in stage II, and twenty-one in stage III. According to the Hoehn and Yahr (H&Y) rating scale, three clinical balance tests (Timed Up and Go test, Balance Evaluation Systems Test, and Push and Release test) were carried out in addition to a static stance test recorded by a two-dimensional movement analysis software. Based on kinematic variables generated by the software, a Postural Instability Index (PII) was created, allowing a comparison between its results and those obtained by clinical tests. Results: There were differences between sociodemographic variables directly related to PD evolution. Although all tests were correlated with H&Y stages, only the PII was able to differentiate the first three stages of disease evolution (H&Y I and II: p = 0.03; H&Y I and III: p = 0.00001; H&Y II and III: p = 0.02). Other clinical tests were able to differentiate only people in the moderate PD stage (H&Y III). Conclusion: Based on the PII index, it was possible to differentiate the postural control decline among the first three stages of PD evolution. This study offers a promising possibility of a low-cost, early identification of subtle changes in postural control in people with PD in clinical practice.

The role of negative conductances in neuronal subthreshold properties and synaptic integration.

Based on passive cable theory, an increase in membrane conductance produces a decrease in the membrane time constant and input resistance. Unlike the classical leak currents, voltage-dependent currents have a nonlinear behavior which can create regions of negative conductance, despite the increase in membrane conductance (permeability). This negative conductance opposes the effects of the passive membrane conductance on the membrane input resistance and time constant, increasing their values and thereby substantially affecting the amplitude and time course of postsynaptic potentials at the voltage range of the negative conductance. This paradoxical effect has been described for three types of voltage-dependent inward currents: persistent sodium currents, L- and T-type calcium currents and ligand-gated glutamatergic N-methyl-D-aspartate currents. In this review, we describe the impact of the creation of a negative conductance region by these currents on neuronal membrane properties and synaptic integration. We also discuss recent contributions of the quasi-active cable approximation, an extension of the passive cable theory that includes voltage-dependent currents, and its effects on neuronal subthreshold properties.

Corrigendum: Ih Equalizes Membrane Input Resistance in a Heterogeneous Population of Fusiform Neurons in the Dorsal Cochlear Nucleus.

[This corrects the article on p. 249 in vol. 10, PMID: 27833532.].

Modelling intracellular competition for calcium: kinetic and thermodynamic control of different molecular modes of signal decoding.

Frequently, a common chemical entity triggers opposite cellular processes, which implies that the components of signalling networks must detect signals not only through their chemical natures, but also through their dynamic properties. To gain insights on the mechanisms of discrimination of the dynamic properties of cellular signals, we developed a computational stochastic model and investigated how three calcium ion (Ca(2+))-dependent enzymes (adenylyl cyclase (AC), phosphodiesterase 1 (PDE1), and calcineurin (CaN)) differentially detect Ca(2+) transients in a hippocampal dendritic spine. The balance among AC, PDE1 and CaN might determine the occurrence of opposite Ca(2+)-induced forms of synaptic plasticity, long-term potentiation (LTP) and long-term depression (LTD). CaN is essential for LTD. AC and PDE1 regulate, indirectly, protein kinase A, which counteracts CaN during LTP. Stimulations of AC, PDE1 and CaN with artificial and physiological Ca(2+) signals demonstrated that AC and CaN have Ca(2+) requirements modulated dynamically by different properties of the signals used to stimulate them, because their interactions with Ca(2+) often occur under kinetic control. Contrarily, PDE1 responds to the immediate amplitude of different Ca(2+) transients and usually with the same Ca(2+) requirements observed under steady state. Therefore, AC, PDE1 and CaN decode different dynamic properties of Ca(2+) signals.

Mechanisms of Self-Sustained Oscillatory States in Hierarchical Modular Networks with Mixtures of Electrophysiological Cell Types.

In a network with a mixture of different electrophysiological types of neurons linked by excitatory and inhibitory connections, temporal evolution leads through repeated epochs of intensive global activity separated by intervals with low activity level. This behavior mimics "up" and "down" states, experimentally observed in cortical tissues in absence of external stimuli. We interpret global dynamical features in terms of individual dynamics of the neurons. In particular, we observe that the crucial role both in interruption and in resumption of global activity is played by distributions of the membrane recovery variable within the network. We also demonstrate that the behavior of neurons is more influenced by their presynaptic environment in the network than by their formal types, assigned in accordance with their response to constant current.

Ih Equalizes Membrane Input Resistance in a Heterogeneous Population of Fusiform Neurons in the Dorsal Cochlear Nucleus.

In a neuronal population, several combinations of its ionic conductances are used to attain a specific firing phenotype. Some neurons present heterogeneity in their firing, generally produced by expression of a specific conductance, but how additional conductances vary along in order to homeostatically regulate membrane excitability is less known. Dorsal cochlear nucleus principal neurons, fusiform neurons, display heterogeneous spontaneous action potential activity and thus represent an appropriate model to study the role of different conductances in establishing firing heterogeneity. Particularly, fusiform neurons are divided into quiet, with no spontaneous firing, or active neurons, presenting spontaneous, regular firing. These modes are determined by the expression levels of an intrinsic membrane conductance, an inwardly rectifying potassium current (IKir). In this work, we tested whether other subthreshold conductances vary homeostatically to maintain membrane excitability constant across the two subtypes. We found that Ih expression covaries specifically with IKir in order to maintain membrane resistance constant. The impact of Ih on membrane resistance is dependent on the level of IKir expression, being much smaller in quiet neurons with bigger IKir, but Ih variations are not relevant for creating the quiet and active phenotypes. Finally, we demonstrate that the individual proportion of each conductance, and not their absolute conductance, is relevant for determining the neuronal firing mode. We conclude that in fusiform neurons the variations of their different subthreshold conductances are limited to specific conductances in order to create firing heterogeneity and maintain membrane homeostasis.