Months-long tracking of neuronal ensembles spanning multiple brain areas with Ultra-Flexible Tentacle Electrodes.

We introduce Ultra-Flexible Tentacle Electrodes (UFTEs), packing many independent fibers with the smallest possible footprint without limitation in recording depth using a combination of mechanical and chemical tethering for insertion. We demonstrate a scheme to implant UFTEs simultaneously into many brain areas at arbitrary locations without angle-of-insertion limitations, and a 512-channel wireless logger. Immunostaining reveals no detectable chronic tissue damage even after several months. Mean spike signal-to-noise ratios are 1.5-3x compared to the state-of-the-art, while the highest signal-to-noise ratios reach 89, and average cortical unit yields are ~1.75/channel. UFTEs can track the same neurons across sessions for at least 10 months (longest duration tested). We tracked inter- and intra-areal neuronal ensembles (neurons repeatedly co-activated within 25 ms) simultaneously from hippocampus, retrosplenial cortex, and medial prefrontal cortex in freely moving rodents. Average ensemble lifetimes were shorter than the durations over which we can track individual neurons. We identify two distinct classes of ensembles. Those tuned to sharp-wave ripples display the shortest lifetimes, and the ensemble members are mostly hippocampal. Yet, inter-areal ensembles with members from both hippocampus and cortex have weak tuning to sharp wave ripples, and some have unusual months-long lifetimes. Such inter-areal ensembles occasionally remain inactive for weeks before re-emerging.

Deviance Distraction and Stimulus-Specific Adaptation in the Somatosensory Cortex Reduce with Experience.

Automatic detection of a surprising change in the sensory input is a central element of exogenous attentional control. Stimulus-specific adaptation (SSA) is a potential neuronal mechanism detecting such changes and has been robustly described across sensory modalities and different instances of the ascending sensory pathways. However, little is known about the relationship of SSA to perception. To assess how deviating stimuli influence target signal detection, we used a behavioral cross-modal paradigm in mice and combined it with extracellular recordings from the primary somatosensory whisker cortex. In this paradigm, male mice performed a visual detection task while task-irrelevant whisker stimuli were either presented as repetitive "standard" or as rare deviant stimuli. We found a deviance distraction effect on the animals' performance: Faster reaction times but worsened target detection was observed in the presence of a deviant stimulus. Multiunit activity and local field potentials exhibited enhanced neuronal responses to deviant compared with standard whisker stimuli across all cortical layers, as a result of SSA. The deviant-triggered behavioral distraction correlated with these enhanced neuronal deviant responses only in the deeper cortical layers. However, the layer-specific effect of SSA on perception reduced with increasing task experience as a result of statistical distractor learning. These results demonstrate a layer-specific involvement of SSA on perception that is susceptible to modulation over time.SIGNIFICANCE STATEMENT Detecting sudden changes in our immediate environment is behaviorally relevant and important for efficient perceptual processing. However, the connection between the underpinnings of cortical deviance detection and perception remains unknown. Here, we investigate how the cortical representation of deviant whisker stimuli impacts visual target detection by recording local field potential and multiunit activity in the primary somatosensory cortex of mice engaged in a cross-modal visual detection task. We find that deviant whisker stimuli distract animals in their task performance, which correlates with enhanced neuronal responses for deviants in a layer-specific manner. Interestingly, this effect reduces with the increased experience of the animal as a result of distractor learning on statistical regularities.

Modelling novelty detection in the thalamocortical loop.

In complex natural environments, sensory systems are constantly exposed to a large stream of inputs. Novel or rare stimuli, which are often associated with behaviorally important events, are typically processed differently than the steady sensory background, which has less relevance. Neural signatures of such differential processing, commonly referred to as novelty detection, have been identified on the level of EEG recordings as mismatch negativity (MMN) and on the level of single neurons as stimulus-specific adaptation (SSA). Here, we propose a multi-scale recurrent network with synaptic depression to explain how novelty detection can arise in the whisker-related part of the somatosensory thalamocortical loop. The "minimalistic" architecture and dynamics of the model presume that neurons in cortical layer 6 adapt, via synaptic depression, specifically to a frequently presented stimulus, resulting in reduced population activity in the corresponding cortical column when compared with the population activity evoked by a rare stimulus. This difference in population activity is then projected from the cortex to the thalamus and amplified through the interaction between neurons of the primary and reticular nuclei of the thalamus, resulting in rhythmic oscillations. These differentially activated thalamic oscillations are forwarded to cortical layer 4 as a late secondary response that is specific to rare stimuli that violate a particular stimulus pattern. Model results show a strong analogy between this late single neuron activity and EEG-based mismatch negativity in terms of their common sensitivity to presentation context and timescales of response latency, as observed experimentally. Our results indicate that adaptation in L6 can establish the thalamocortical dynamics that produce signatures of SSA and MMN and suggest a mechanistic model of novelty detection that could generalize to other sensory modalities.

Bayesian surprise shapes neural responses in somatosensory cortical circuits.

Numerous psychophysical studies show that Bayesian inference governs sensory decision-making; however, the specific neural circuitry underlying this probabilistic mechanism remains unclear. We record extracellular neural activity along the somatosensory pathway of mice while delivering sensory stimulation paradigms designed to isolate the response to the surprise generated by Bayesian inference. Our results demonstrate that laminar cortical circuits in early sensory areas encode Bayesian surprise. Systematic sensitivity to surprise is not identified in the somatosensory thalamus, rather emerging in the primary (S1) and secondary (S2) somatosensory cortices. Multiunit spiking activity and evoked potentials in layer 6 of these regions exhibit the highest sensitivity to surprise. Gamma power in S1 layer 2/3 exhibits an NMDAR-dependent scaling with surprise, as does alpha power in layers 2/3 and 6 of S2. These results show a precise spatiotemporal neural representation of Bayesian surprise and suggest that Bayesian inference is a fundamental component of cortical processing.

Machine learning reveals interhemispheric somatosensory coherence as indicator of anesthetic depth.

The goal of this study was to identify features in mouse electrocorticogram recordings that indicate the depth of anesthesia as approximated by the administered anesthetic dosage. Anesthetic depth in laboratory animals must be precisely monitored and controlled. However, for the most common lab species (mice) few indicators useful for monitoring anesthetic depth have been established. We used electrocorticogram recordings in mice, coupled with peripheral stimulation, in order to identify features of brain activity modulated by isoflurane anesthesia and explored their usefulness in monitoring anesthetic depth through machine learning techniques. Using a gradient boosting regressor framework we identified interhemispheric somatosensory coherence as the most informative and reliable electrocorticogram feature for determining anesthetic depth, yielding good generalization and performance over many subjects. Knowing that interhemispheric somatosensory coherence indicates the effectively administered isoflurane concentration is an important step for establishing better anesthetic monitoring protocols and closed-loop systems for animal surgeries.

Deep-learning based identification, tracking, pose estimation, and behavior classification of interacting primates and mice in complex environments.

The quantification of behaviors of interest from video data is commonly used to study brain function, the effects of pharmacological interventions, and genetic alterations. Existing approaches lack the capability to analyze the behavior of groups of animals in complex environments. We present a novel deep learning architecture for classifying individual and social animal behavior, even in complex environments directly from raw video frames, while requiring no intervention after initial human supervision. Our behavioral classifier is embedded in a pipeline (SIPEC) that performs segmentation, identification, pose-estimation, and classification of complex behavior, outperforming the state of the art. SIPEC successfully recognizes multiple behaviors of freely moving individual mice as well as socially interacting non-human primates in 3D, using data only from simple mono-vision cameras in home-cage setups.

A robust model of Stimulus-Specific Adaptation validated on neuromorphic hardware.

Stimulus-Specific Adaptation (SSA) to repetitive stimulation is a phenomenon that has been observed across many different species and in several brain sensory areas. It has been proposed as a computational mechanism, responsible for separating behaviorally relevant information from the continuous stream of sensory information. Although SSA can be induced and measured reliably in a wide variety of conditions, the network details and intracellular mechanisms giving rise to SSA still remain unclear. Recent computational studies proposed that SSA could be associated with a fast and synchronous neuronal firing phenomenon called Population Spikes (PS). Here, we test this hypothesis using a mean-field rate model and corroborate it using a neuromorphic hardware. As the neuromorphic circuits used in this study operate in real-time with biologically realistic time constants, they can reproduce the same dynamics observed in biological systems, together with the exploration of different connectivity schemes, with complete control of the system parameter settings. Besides, the hardware permits the iteration of multiple experiments over many trials, for extended amounts of time and without losing the networks and individual neural processes being studied. Following this "neuromorphic engineering" approach, we therefore study the PS hypothesis in a biophysically inspired recurrent networks of spiking neurons and evaluate the role of different linear and non-linear dynamic computational primitives such as spike-frequency adaptation or short-term depression (STD). We compare both the theoretical mean-field model of SSA and PS to previously obtained experimental results in the area of novelty detection and observe its behavior on its neuromorphic physical equivalent model. We show how the approach proposed can be extended to other computational neuroscience modelling efforts for understanding high-level phenomena in mechanistic models.

Non-invasive molecularly-specific millimeter-resolution manipulation of brain circuits by ultrasound-mediated aggregation and uncaging of drug carriers.

Non-invasive, molecularly-specific, focal modulation of brain circuits with low off-target effects can lead to breakthroughs in treatments of brain disorders. We systemically inject engineered ultrasound-controllable drug carriers and subsequently apply a novel two-component Aggregation and Uncaging Focused Ultrasound Sequence (AU-FUS) at the desired targets inside the brain. The first sequence aggregates drug carriers with millimeter-precision by orders of magnitude. The second sequence uncages the carrier's cargo locally to achieve high target specificity without compromising the blood-brain barrier (BBB). Upon release from the carriers, drugs locally cross the intact BBB. We show circuit-specific manipulation of sensory signaling in motor cortex in rats by locally concentrating and releasing a GABAA receptor agonist from ultrasound-controlled carriers. Our approach uses orders of magnitude (1300x) less drug than is otherwise required by systemic injection and requires very low ultrasound pressures (20-fold below FDA safety limits for diagnostic imaging). We show that the BBB remains intact using passive cavitation detection (PCD), MRI-contrast agents and, importantly, also by sensitive fluorescent dye extravasation and immunohistochemistry.

Evoked Response Strength in Primary Auditory Cortex Predicts Performance in a Spectro-Spatial Discrimination Task in Rats.

The extent to which the primary auditory cortex (A1) participates in instructing animal behavior remains debated. Although multiple studies have shown A1 activity to correlate with animals' perceptual judgments (Jaramillo and Zador, 2011; Bizley et al., 2013; Rodgers and DeWeese, 2014), others have found no relationship between A1 responses and reported auditory percepts (Lemus et al., 2009; Dong et al., 2011). To address this ambiguity, we performed chronic recordings of evoked local field potentials (eLFPs) in A1 of head-fixed female rats performing a two-alternative forced-choice auditory discrimination task. Rats were presented with two interleaved sequences of pure tones from opposite sides and had to indicate the side from which the higher-frequency target stimulus was played. Animal performance closely correlated (rrm = 0.68) with the difference between the target and distractor eLFP responses: the more the target response exceeded the distractor response, the better the animals were at identifying the side of the target frequency. Reducing the evoked response of either frequency through stimulus-specific adaptation affected performance in the expected way: target localization accuracy was degraded when the target frequency was adapted and improved when the distractor frequency was adapted. Target frequency eLFPs were stronger on hit trials than on error trials. Our results suggest that the degree to which one stimulus stands out over others within A1 activity may determine its perceptual saliency for the animals and accordingly bias their behavioral choices.SIGNIFICANCE STATEMENT The brain must continuously calibrate the saliency of sensory percepts against their relevance to the current behavioral goal. The inability to ignore irrelevant distractors characterizes a spectrum of human attentional disorders. Meanwhile, the connection between the neural underpinnings of stimulus saliency and sensory decisions remains elusive. Here, we record local field potentials in the primary auditory cortex of rats engaged in auditory discrimination to investigate how the cortical representation of target and distractor stimuli impacts behavior. We find that the amplitude difference between target- and distractor-evoked activity predicts discrimination performance (rrm = 0.68). Specific adaptation of target or distractor shifts performance either below or above chance, respectively. It appears that recent auditory history profoundly influences stimulus saliency, biasing animals toward diametrically-opposed decisions.

Deviant Processing in the Primary Somatosensory Cortex.

Stimulus-specific adaptation (SSA) to repetitive stimulation has been proposed to separate behaviorally relevant features from a stream of continuous sensory information. However, the exact mechanisms giving rise to SSA and cortical deviance detection are not well understood. We therefore used an oddball paradigm and multicontact electrodes to characterize single-neuron and local field potential responses to various deviant stimuli across the rat somatosensory cortex. Changing different single-whisker stimulus features evoked robust SSA in individual cortical neurons over a wide range of stimulus repetition rates (0.25-80 Hz). Notably, SSA was weakest in the granular input layer and significantly stronger in the supra- and infragranular layers, suggesting that a major part of SSA is generated within cortex. Moreover, we found a small subset of neurons in the granular layer with a deviant-specific late response, occurring roughly 200 ms after stimulus offset. This late deviant response exhibited true-deviance detection properties that were not explained by depression of sensory inputs. Our results show that deviant responses are actively amplified within cortex and contain an additional late component that is sensitive for context-specific sensory deviations. This strongly implicates deviance detection as a feature of intracortical stimulus processing beyond simple sensory input depression.

Tactile frequency discrimination is enhanced by circumventing neocortical adaptation.

Neocortical responses typically adapt to repeated sensory stimulation, improving sensitivity to stimulus changes, but possibly also imposing limitations on perception. For example, it is unclear whether information about stimulus frequency is perturbed by adaptation or encoded by precise response timing. We addressed this question in rat barrel cortex by comparing performance in behavioral tasks with either whisker stimulation, which causes frequency-dependent adaptation, or optical activation of cortically expressed channelrhodopsin-2, which elicits non-adapting neural responses. Circumventing adaption by optical activation substantially improved cross-hemispheric discrimination of stimulus frequency. This improvement persisted when temporal precision of optically evoked spikes was reduced. We were able to replicate whisker-driven behavior only by applying adaptation rules mimicking sensory-evoked responses to optical stimuli. Conversely, in a change-detection task, animals performed better with whisker than optical stimulation. Our results directly demonstrate that sensory adaptation critically governs the perception of stimulus patterns, decreasing fidelity under steady-state conditions in favor of change detection.

Animal models of subjective tinnitus.

Tinnitus is one of the major audiological diseases, affecting a significant portion of the ageing society. Despite its huge personal and presumed economic impact there are only limited therapeutic options available. The reason for this deficiency lies in the very nature of the disease as it is deeply connected to elementary plasticity of auditory processing in the central nervous system. Understanding these mechanisms is essential for developing a therapy that reverses the plastic changes underlying the pathogenesis of tinnitus. This requires experiments that address individual neurons and small networks, something usually not feasible in human patients. However, in animals such invasive experiments on the level of single neurons with high spatial and temporal resolution are possible. Therefore, animal models are a very critical element in the combined efforts for engineering new therapies. This review provides an overview over the most important features of animal models of tinnitus: which laboratory species are suitable, how to induce tinnitus, and how to characterize the perceived tinnitus by behavioral means. In particular, these aspects of tinnitus animal models are discussed in the light of transferability to the human patients.

Stimulus-specific adaptation in field potentials and neuronal responses to frequency-modulated tones in the primary auditory cortex.

In order to structure the sensory environment our brain needs to detect changes in the surrounding that might indicate events of presumed behavioral relevance. A characteristic brain response presumably related to the detection of such novel stimuli is termed mismatch negativity (MMN) observable in human scalp recordings. A candidate mechanism underlying MMN at the neuronal level is stimulus-specific adaptation (SSA) which has several characteristics in common. SSA is the specific decrease in the response to a frequent stimulus, which does not generalize to an interleaved rare stimulus in a sequence of events. SSA was so far mainly described for changes in the response to simple pure tone stimuli differing in tone frequency. In this study we provide data from the awake rat auditory cortex on adaptation in the responses to frequency-modulated tones (FM) with the deviating feature being the direction of FM modulation. Adaptation of cortical neurons to the direction of FM modulation was stronger for slow modulation than for faster modulation. In contrast to pure tone SSA which showed no stimulus preference, FM adaptation in neuronal data differed sometimes between upward and downward FM. This, however, was not the case in the local field potential data recorded simultaneously. Our findings support the role of the auditory cortex as the source for change-related activity induced by FM stimuli by showing that dynamic stimulus features such as FM modulation can evoke SSA in the rat in a way very similar to FM-induced MMN in the human auditory cortex.

Novel two-alternative forced choice paradigm for bilateral vibrotactile whisker frequency discrimination in head-fixed mice and rats.

Rats and mice receive a constant bilateral stream of tactile information with their large mystacial vibrissae when navigating in their environment. In a two-alternative forced choice paradigm (2-AFC), head-fixed rats and mice learned to discriminate vibrotactile frequencies applied simultaneously to individual whiskers on the left and right sides of the snout. Mice and rats discriminated 90-Hz pulsatile stimuli from pulsatile stimuli with lower repetition frequencies (10-80 Hz) but with identical kinematic properties in each pulse. Psychometric curves displayed an average perceptual threshold of 50.6-Hz and 53.0-Hz frequency difference corresponding to Weber fractions of 0.56 and 0.58 in mice and rats, respectively. Both species performed >400 trials a day (>200 trials per session, 2 sessions/day), with a peak performance of >90% correct responses. In general, rats and mice trained in the identical task showed comparable psychometric curves. Behavioral readouts, such as reaction times, learning rates, trial omissions, and impulsivity, were also very similar in the two species. Furthermore, whisking of the animals before stimulus presentation reduced task performance. This behavioral paradigm, combined with whisker position tracking, allows precise stimulus control in the 2-AFC task for head-fixed rodents. It is compatible with state-of-the-art neurophysiological recording techniques, such as electrophysiology and two-photon imaging, and therefore represents a valuable framework for neurophysiological investigations of perceptual decision-making.

Stimulus-specific adaptation in the gerbil primary auditory thalamus is the result of a fast frequency-specific habituation and is regulated by the corticofugal system.

The detection of novel and therefore potentially behavioral relevant stimuli is of fundamental importance for animals. In the auditory system, stimulus-specific adaptation (SSA) resulting in stronger responses to rare compared with frequent stimuli was proposed as such a novelty detection mechanism. SSA is a now well established phenomenon found at different levels along the mammalian auditory pathway. It depends on various stimulus features, such as deviant probability, and may be an essential mechanism underlying perception of changes in sound statistics. We recorded neuronal responses from the ventral part of the medial geniculate body (vMGB) in Mongolian gerbils to determine details of the adaptation process that might indicate underlying neuronal mechanisms. Neurons in the vMGB exhibited a median spike rate change of 15.4% attributable to a fast habituation to the frequently presented standard stimulus. Accordingly, the main habituation effect could also be induced by the repetition of a few uniform tonal stimuli. The degree of habituation was frequency-specific, and comparison across simultaneously recorded units indicated that adaptation effects were apparently topographically organized. At the population level, stronger habituation effects were on average associated with the border regions of the frequency response areas. Finally, the pharmacological inactivation of the auditory cortex demonstrated that SSA in the vMGB is mainly regulated by the corticofugal system. Hence, these results indicate a more general function of SSA in the processing and analysis of auditory information than the term novelty detection suggests.

Correlating stimulus-specific adaptation of cortical neurons and local field potentials in the awake rat.

Changes in the sensory environment are good indicators for behaviorally relevant events and strong triggers for the reallocation of attention. In the auditory domain, violations of a pattern of repetitive stimuli precipitate in the event-related potentials as mismatch negativity (MMN). Stimulus-specific adaptation (SSA) of single neurons in the auditory cortex has been proposed to be the cellular substrate of MMN (Nelken and Ulanovsky, 2007). However, until now, the existence of SSA in the awake auditory cortex has not been shown. In the present study, we recorded single and multiunits in parallel with evoked local field potentials (eLFPs) in the primary auditory cortex of the awake rat. Both neurons and eLFPs in the awake animal adapted in a stimulus-specific manner, and SSA was controlled by stimulus probability and frequency separation. SSA of isolated units was significant during the first stimulus-evoked "on" response but not in the following inhibition and rebound of activity. The eLFPs exhibited SSA in the first negative deflection and, to a lesser degree, in a slower positive deflection but no MMN. Spike adaptation correlated closely with adaptation of the fast negative deflection but not the positive deflection. Therefore, we conclude that single neurons in the auditory cortex of the awake rat adapt in a stimulus-specific manner and contribute to corresponding changes in eLFP but do not generate a late deviant response component directly equivalent to the human MMN. Nevertheless, the described effect may reflect a certain part of the process needed for sound discrimination.

Discrimination of direction in fast frequency-modulated tones by rats.

Fast frequency modulations (FM) are an essential part of species-specific auditory signals in animals as well as in human speech. Major parameters characterizing non-periodic frequency modulations are the direction of frequency change in the FM sweep (upward/downward) and the sweep speed, i.e., the speed of frequency change. While it is well established that both parameters are represented in the mammalian central auditory pathway, their importance at the perceptual level in animals is unclear. We determined the ability of rats to discriminate between upward and downward modulated FM-tones as a function of sweep speed in a two-alternative-forced-choice-paradigm. Directional discrimination in logarithmic FM-sweeps was reduced with increasing sweep speed between 20 and 1,000 octaves/s following a psychometric function. Average threshold sweep speed for FM directional discrimination was 96 octaves/s. This upper limit of perceptual FM discrimination fits well the upper limit of preferred sweep speeds in auditory neurons and the upper limit of neuronal direction selectivity in the rat auditory cortex and midbrain, as it is found in the literature. Influences of additional stimulus parameters on FM discrimination were determined using an adaptive testing-procedure for efficient threshold estimation based on a maximum likelihood approach. Directional discrimination improved with extended FM sweep range between two and five octaves. Discrimination performance declined with increasing lower frequency boundary of FM sweeps, showing an especially strong deterioration when the boundary was raised from 2 to 4 kHz. This deterioration corresponds to a frequency-dependent decline in direction selectivity of FM-encoding neurons in the rat auditory cortex, as described in the literature. Taken together, by investigating directional discrimination of FM sweeps in the rat we found characteristics at the perceptual level that can be related to several aspects of FM encoding in the central auditory pathway.

Transient calretinin expression defines early postmitotic step of neuronal differentiation in adult hippocampal neurogenesis of mice.

We here show that the early postmitotic stage of granule cell development during adult hippocampal neurogenesis is characterized by the transient expression of calretinin (CR). CR expression was detected as early as 1 day after labeling dividing cells with bromodeoxyuridine (BrdU), but not before. Staining for Ki-67 confirmed that no CR-expressing cells were in cell cycle. Early after BrdU, CR colocalized with immature neuronal marker doublecortin; and later with persisting neuronal marker NeuN. BrdU/CR-labeled cells were negative for GABA and GABAA1 receptor, but early on expressed granule cell marker Prox-1. After 6 weeks, no new neurons expressed CR, but all contained calbindin. Stimuli inducing adult neurogenesis have limited (enriched environment), strong (voluntary wheel running), and very strong effects on cell proliferation (kainate-induced seizures). In these models the induction of cell proliferation was paralleled by an increase of CR-positive cells, indicating the stimulus-dependent progression from cell division to a postmitotic stage.