Spikebench: An open benchmark for spike train time-series classification.

Modern well-performing approaches to neural decoding are based on machine learning models such as decision tree ensembles and deep neural networks. The wide range of algorithms that can be utilized to learn from neural spike trains, which are essentially time-series data, results in the need for diverse and challenging benchmarks for neural decoding, similar to the ones in the fields of computer vision and natural language processing. In this work, we propose a spike train classification benchmark, based on open-access neural activity datasets and consisting of several learning tasks such as stimulus type classification, animal's behavioral state prediction, and neuron type identification. We demonstrate that an approach based on hand-crafted time-series feature engineering establishes a strong baseline performing on par with state-of-the-art deep learning-based models for neural decoding. We release the code allowing to reproduce the reported results.

Enhanced motor cortex output and disinhibition in asymptomatic female mice with C9orf72 genetic expansion.

Information and action coding by cortical circuits relies on a balanced dialogue between excitation and inhibition. Circuit hyperexcitability is considered a potential pathophysiological mechanism in various brain disorders, but the underlying deficits, especially at early disease stages, remain largely unknown. We report that asymptomatic female mice carrying the chromosome 9 open reading frame 72 (C9orf72) repeat expansion, which represents a high-prevalence genetic abnormality for human amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) spectrum disorder, exhibit abnormal motor cortex output. The number of primary motor cortex (M1) layer 5 pyramidal neurons is reduced in asymptomatic mice, with the surviving neurons receiving a decreased inhibitory drive that results in a higher M1 output, specifically during high-speed animal locomotion. Importantly, using deep-learning algorithms revealed that speed-dependent M1 output predicts the likelihood of C9orf72 genetic expansion. Our data link early circuit abnormalities with a gene mutation in asymptomatic ALS/FTLD carriers.

Cholinergic modulation of hierarchical inhibitory control over cortical resting state dynamics: Local circuit modeling of schizophrenia-related hypofrontality.

Nicotinic acetylcholine receptors (nAChRs) modulate the cholinergic drive to a hierarchy of inhibitory neurons in the superficial layers of the PFC, critical to cognitive processes. It has been shown that genetic deletions of the various types of nAChRs impact the properties of ultra-slow transitions between high and low PFC activity states in mice during quiet wakefulness. The impact characteristics depend on specific interneuron populations expressing the manipulated receptor subtype. In addition, recent data indicate that a genetic mutation of the α5 nAChR subunit, located on vasoactive intestinal polypeptide (VIP) inhibitory neurons, the rs16969968 single nucleotide polymorphism (α5 SNP), plays a key role in the hypofrontality observed in schizophrenia patients carrying the SNP. Data also indicate that chronic nicotine application to α5 SNP mice relieves the hypofrontality. We developed a computational model to show that the activity patterns recorded in the genetically modified mice can be explained by changes in the dynamics of the local PFC circuit. Notably, our model shows that these altered PFC circuit dynamics are due to changes in the stability structure of the activity states. We identify how this stability structure is differentially modulated by cholinergic inputs to the parvalbumin (PV), somatostatin (SOM) or the VIP inhibitory populations. Our model uncovers that a change in amplitude, but not duration of the high activity states can account for the lowered pyramidal (PYR) population firing rates recorded in α5 SNP mice. We demonstrate how nicotine-induced desensitization and upregulation of the ß2 nAChRs located on SOM interneurons, as opposed to the activation of α5 nAChRs located on VIP interneurons, is sufficient to explain the nicotine-induced activity normalization in α5 SNP mice. The model further implies that subsequent nicotine withdrawal may exacerbate the hypofrontality over and beyond one caused by the SNP mutation.

Activity-dependent switches between dynamic regimes of extracellular matrix expression.

Experimental studies highlight the important role of the extracellular matrix (ECM) in the regulation of neuronal excitability and synaptic connectivity in the nervous system. In its turn, the neural ECM is formed in an activity-dependent manner. Its maturation closes the so-called critical period of neural development, stabilizing the efficient configurations of neural networks in the brain. ECM is locally remodeled by proteases secreted and activated in an activity-dependent manner into the extracellular space and this process is important for physiological synaptic plasticity. We ask if ECM remodeling may be exaggerated under pathological conditions and enable activity-dependent switches between different regimes of ECM expression. We consider an analytical model based on known mechanisms of interaction between neuronal activity and expression of ECM, ECM receptors and ECM degrading proteases. We demonstrate that either inhibitory or excitatory influence of ECM on neuronal activity may lead to the bistability of ECM expression, so two stable stationary states are observed. Noteworthy, only in the case when ECM has predominant inhibitory influence on neurons, the bistability is dependent on the activity of proteases. Excitatory ECM-neuron feedback influences may also result in spontaneous oscillations of ECM expression, which may coexist with a stable stationary state. Thus, ECM-neuronal interactions support switches between distinct dynamic regimes of ECM expression, possibly representing transitions into disease states associated with remodeling of brain ECM.

Mechanisms of Supralinear Calcium Integration in Dendrites of Hippocampal CA1 Fast-Spiking Cells.

In fast-spiking (FS), parvalbumin-expressing interneurons of the CA1 hippocampus, activation of the GluA2-lacking Ca2+-permeable AMPA receptors (CP-AMPARs) in basal dendrites is coupled to Ca2+-induced Ca2+-release (CICR), and can result in a supralinear summation of postsynaptic Ca2+-transients (post-CaTs). While this mechanism is important in controlling the direction of long-term plasticity, it is still unknown whether it can operate at all excitatory synapses converging onto FS cells or at a set of synapses receiving a particular input. Using a combination of patch-clamp recordings and two-photon Ca2+ imaging in acute mouse hippocampal slices with computational simulations, here we compared the generation of supralinear post-CaTs between apical and basal dendrites of FS cells. We found that, similar to basal dendrites, apical post-CaTs summated supralinearly and relied mainly on the activation of the CP-AMPARs, with a variable contribution of other Ca2+ sources, such as NMDA receptors, L-type voltage-gated Ca2+-channels and Ca2+ release. In addition, supralinear post-CaTs generated in apical dendrites had a slower decay time and a larger cumulative charge than those in basal, and were associated with a stronger level of somatic depolarization. The model predicted that modulation of ryanodine receptors and of the Ca2+ extrusion mechanisms, such as the Na+/Ca2+-exchanger and SERCA pump, had a major impact on the magnitude of supralinear post-CaTs. These data reveal that supralinear Ca2+ summation is a common mechanism of Ca2+ signaling at CP-AMPAR-containing synapses. Shaped in a location-specific manner through modulation of ryanodine receptors and Ca2+ extrusion mechanisms, CP-AMPAR/CICR signaling is suitable for synapse-specific bidirectional modification of incoming inputs in the absence of active dendritic conductances.

Dendritic signal transmission induced by intracellular charge inhomogeneities.

Signal propagation in neuronal dendrites represents the basis for interneuron communication and information processing in the brain. Here we take into account charge inhomogeneities arising in the vicinity of ion channels in cytoplasm and obtain a modified cable equation. We show that charge inhomogeneities acting on a millisecond time scale can lead to the appearance of propagating waves with wavelengths of hundreds of micrometers. They correspond to a certain frequency band predicting the appearance of resonant properties in brain neuron signaling. We also show that membrane potential in spiny dendrites obeys the modified cable equation suggesting a crucial role of the spines in dendritic subthreshold resonance.