Models that contain the Model Concept : Sensory coding

(The pattern(s) of neuronal signals that represent the sensing of stimulation(s).)
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    Models   Description
1.  A two-layer biophysical olfactory bulb model of cholinergic neuromodulation (Li and Cleland 2013)
This is a two-layer biophysical olfactory bulb (OB) network model to study cholinergic neuromodulation. Simulations show that nicotinic receptor activation sharpens mitral cell receptive field, while muscarinic receptor activation enhances network synchrony and gamma oscillations. This general model suggests that the roles of nicotinic and muscarinic receptors in OB are both distinct and complementary to one another, together regulating the effects of ascending cholinergic inputs on olfactory bulb transformations.
2.  Ambiguous Encoding and Distorted Perception (Carlson and Kawasaki 2006)
"... In the weakly electric fish Eigenmannia, P- and T-type primary afferent fibers are specialized for encoding the amplitude and phase, respectively, of electrosensory stimuli. We used a stimulus estimation technique to quantify the ability of P- and T-units to encode random modulations in amplitude and phase. As expected, P-units exhibited a clear preference for encoding amplitude modulations, whereas T-units exhibited a clear preference for encoding phase modulations. Surprisingly, both types of afferents also encoded their nonpreferred stimulus attribute when it was presented in isolation or when the preferred stimulus attribute was sufficiently weak. Because afferent activity can be affected by modulations in either amplitude or phase, it is not possible to unambiguously distinguish between these two stimulus attributes by observing the activity of a single afferent fiber. Simple model neurons with a preference for encoding either amplitude or phase also encoded their nonpreferred stimulus attribute when it was presented in isolation, suggesting that such ambiguity is unavoidable. ... " See paper for more and details.
3.  Dynamics of Spike Initiation (Prescott et al. 2008)
"Transduction of graded synaptic input into trains of all-or-none action potentials (spikes) is a crucial step in neural coding. Hodgkin identified three classes of neurons with qualitatively different analog-to-digital transduction properties. Despite widespread use of this classification scheme, a generalizable explanation of its biophysical basis has not been described. We recorded from spinal sensory neurons representing each class and reproduced their transduction properties in a minimal model. With phase plane and bifurcation analysis, each class of excitability was shown to derive from distinct spike initiating dynamics. Excitability could be converted between all three classes by varying single parameters; moreover, several parameters, when varied one at a time, had functionally equivalent effects on excitability. From this, we conclude that the spike-initiating dynamics associated with each of Hodgkin’s classes represent different outcomes in a nonlinear competition between oppositely directed, kinetically mismatched currents. ..."
4.  Function and energy constrain neuronal biophysics in coincidence detection (Remme et al 2018)
" ... We use models of conductance-based neurons constrained by experimentally observed characteristics with parameters varied within a physiologically realistic range. Our study shows that neuronal design of MSO cells does not compromise on function, but favors energetically less costly cell properties where possible without interfering with function."
5.  Microsaccades and synchrony coding in the retina (Masquelier et al. 2016)
We show that microsaccades (MS) enable efficient synchrony-based coding among the primate retinal ganglion cells (RGC). We find that each MS causes certain RGCs to fire synchronously, namely those whose receptive fields contain contrast edges after the MS. The emitted synchronous spike volley thus rapidly transmits the most salient edges of the stimulus. We demonstrate that the readout could be done rapidly by simple coincidence-detector neurons, and that the required connectivity could emerge spontaneously with spike timing-dependent plasticity.
6.  Mitral cell activity gating by respiration and inhibition in an olfactory bulb NN (Short et al 2016)
To explore interactions between respiration, inhibition, and olfaction, experiments using light to active channel rhodopsin in sensory neurons expressing Olfactory Marker Protein were performed in mice and modeled in silico. This archive contains NEURON models that were run on parallel computers to explore the interactions between varying strengths of respiratory activity and olfactory sensory neuron input and the roles of periglomerular, granule, and external tufted cells in shaping mitral cell responses.
7.  Olfactory bulb microcircuits model with dual-layer inhibition (Gilra & Bhalla 2015)
A detailed network model of the dual-layer dendro-dendritic inhibitory microcircuits in the rat olfactory bulb comprising compartmental mitral, granule and PG cells developed by Aditya Gilra, Upinder S. Bhalla (2015). All cell morphologies and network connections are in NeuroML v1.8.0. PG and granule cell channels and synapses are also in NeuroML v1.8.0. Mitral cell channels and synapses are in native python.
8.  Parallel odor processing by mitral and middle tufted cells in the OB (Cavarretta et al 2016, 2018)
"[...] experimental findings suggest that MC and mTC may encode parallel and complementary odor representations. We have analyzed the functional roles of these pathways by using a morphologically and physiologically realistic three-dimensional model to explore the MC and mTC microcircuits in the glomerular layer and deeper plexiform layers. [...]"
9.  Role of Ih in firing patterns of cold thermoreceptors (Orio et al., 2012)
" ... Here we investigated the role of Ih in cold-sensitive (CS) nerve endings, where cold sensory transduction actually takes place. Corneal CS nerve endings in mice show a rhythmic spiking activity at neutral skin temperature that switches to bursting mode when the temperature is lowered. ... Mathematical modeling shows that the firing phenotype of CS nerve endings from HCN1-/- mice can be reproduced by replacing HCN1 channels with the slower HCN2 channels rather than by abolishing Ih. We propose that Ih carried by HCN1 channels helps tune the frequency of the oscillation and the length of bursts underlying regular spiking in cold thermoreceptors, having important implications for neural coding of cold sensation. "
10.  Thalamocortical Relay cell under current clamp in high-conductance state (Zeldenrust et al 2018)
Mammalian thalamocortical relay (TCR) neurons switch their firing activity between a tonic spiking and a bursting regime. In a combined experimental and computational study, we investigated the features in the input signal that single spikes and bursts in the output spike train represent and how this code is influenced by the membrane voltage state of the neuron. Identical frozen Gaussian noise current traces were injected into TCR neurons in rat brain slices to adjust, fine-tune and validate a three-compartment TCR model cell (Destexhe et al. 1998, accession number 279). Three currents were added: an h-current (Destexhe et al. 1993,1996, accession number 3343), a high-threshold calcium current and a calcium- activated potassium current (Huguenard & McCormick 1994, accession number 3808). The information content carried by the various types of events in the signal as well as by the whole signal was calculated. Bursts phase-lock to and transfer information at lower frequencies than single spikes. On depolarization the neuron transits smoothly from the predominantly bursting regime to a spiking regime, in which it is more sensitive to high-frequency fluctuations. Finally, the model was used to in the more realistic “high-conductance state” (Destexhe et al. 2001, accession number 8115), while being stimulated with a Poisson input (Brette et al. 2007, Vogels & Abbott 2005, accession number 83319), where fluctuations are caused by (synaptic) conductance changes instead of current injection. Under “standard” conditions bursts are difficult to initiate, given the high degree of inactivation of the T-type calcium current. Strong and/or precisely timed inhibitory currents were able to remove this inactivation.
11.  TRPM8-dependent dynamic response in cold thermoreceptors (Olivares et al. 2015)
This model reproduces the dynamic response of cold thermoreceptors, transiently changing the firing rate upon heating or cooling. It also displays the 'static' or adapted firing patterns observed in these receptors.

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