Automated registration-based skull stripping procedure for feline neuroimaging.

Skull stripping is a fundamental preprocessing step in modern neuroimaging analyses that consists of removing non-brain voxels from structural images. When performed entirely manually, this laborious step can be rate-limiting for analyses, with the potential to influence the population size chosen. This emphasizes the need for a fully- or semi-automated masking procedure to decrease man-hours without an associated decline in accuracy. These algorithms are plentiful in human neuroimaging but are relatively lacking for the plethora of animal species used in research. Unfortunately, software designed for humans cannot be easily transformed for animal use due to the high amount of tailoring required to accurately account for the considerable degree of variation within the highly folded human cortex. As most animals have a relatively less complex cerebral morphology, intersubject variability is consequently decreased, presenting the possibility to simply warp the brain mask of a template image into subject space for the purpose of skull stripping. This study presents the use of the Cat Automated Registration-based Skull Stripper (CARSS) tool on feline structural images. Validation metrics revealed that this method was able to perform on par with manual raters on >90 % of scans tested, and that its consistency across multiple runs was superior to that of masking performed by two independent raters. Additionally, CARSS outperformed three well-known skull stripping programs on the validation dataset. Despite a handful of manual interventions required, the presented tool reduced the man-hours required to skull strip 60 feline images over tenfold when compared to a fully manual approach, proving to be invaluable for feline neuroimaging studies, particularly those with large population sizes.

Gray matter volume of the feline cerebral cortex and structural plasticity following perinatal deafness.

In response to sensory deprivation, the brain adapts according to contemporary demands to efficiently navigate a modified perceptual environment. This reorganization may result in improved processing of the remaining senses-a phenomenon referred to as compensatory crossmodal plasticity. One approach to explore this neuroplasticity is to consider the macrostructural changes in neural tissue that mirror this functional optimization. The current study is the first of its kind to measure MRI-derived gray matter (GM) volumes of control felines (n=30), while additionally identifying volumetric differences in response to perinatal deafness (30 ototoxically-deafened cats). To accomplish this purpose, regional and morphometric methods were performed in parallel. The regional analysis evaluated volumetric alterations of global GM, as well as the volumes of 146 regions of interest (ROIs) and 12 functional subgroupings of these ROIs. Results revealed whole-brain GM preservation; however, somatosensory and visual cortices exhibited an overall increase in volume. On a smaller scale, this analysis uncovered two auditory ROIs (second auditory cortex, A2, and ventral auditory field, VAF) that decreased in volume alongside two visual regions (anteromedial lateral suprasylvian area, AMLS and splenial visual area, SVA) that increased-all localized within the right hemisphere. Comparatively, the findings of tensor-based morphometry (TBM) generally aligned with those of the ROI-based method, as this voxel-wise approach demonstrated clusters of expansion coincident with visual- and somatosensory-related loci; although, it failed to detect any GM reductions following deafness. As distinct differences were identified in each analysis, the current study highlights the importance of employing multiple methods when exploring MRI volumetry. Overall, this study proposes that volumetric alterations within sensory loci allude to a redistribution of cortical space arising from modified perceptual demands following auditory deprivation.

Visual modulation of auditory evoked potentials in the cat.

Visual modulation of the auditory system is not only a neural substrate for multisensory processing, but also serves as a backup input underlying cross-modal plasticity in deaf individuals. Event-related potential (ERP) studies in humans have provided evidence of a multiple-stage audiovisual interactions, ranging from tens to hundreds of milliseconds after the presentation of stimuli. However, it is still unknown if the temporal course of visual modulation in the auditory ERPs can be characterized in animal models. EEG signals were recorded in sedated cats from subdermal needle electrodes. The auditory stimuli (clicks) and visual stimuli (flashes) were timed by two independent Poison processes and were presented either simultaneously or alone. The visual-only ERPs were subtracted from audiovisual ERPs before being compared to the auditory-only ERPs. N1 amplitude showed a trend of transiting from suppression-to-facilitation with a disruption at ~ 100-ms flash-to-click delay. We concluded that visual modulation as a function of SOA with extended range is more complex than previously characterized with short SOAs and its periodic pattern can be interpreted with "phase resetting" hypothesis.

Connectome alterations following perinatal deafness in the cat.

Following sensory deprivation, areas and networks in the brain may adapt and reorganize to compensate for the loss of input. These adaptations are manifestations of compensatory crossmodal plasticity, which has been documented in both human and animal models of deafness-including the domestic cat. Although there are abundant examples of structural plasticity in deaf felines from retrograde tracer-based studies, there is a lack of diffusion-based knowledge involving this model compared to the current breadth of human research. The purpose of this study was to explore white matter structural adaptations in the perinatally-deafened cat via tractography, increasing the methodological overlap between species. Plasticity was examined by identifying unique group connections and assessing altered connectional strength throughout the entirety of the brain. Results revealed a largely preserved connectome containing a limited number of group-specific or altered connections focused within and between sensory networks, which is generally corroborated by deaf feline anatomical tracer literature. Furthermore, five hubs of cortical plasticity and altered communication following perinatal deafness were observed. The limited differences found in the present study suggest that deafness-induced crossmodal plasticity is largely built upon intrinsic structural connections, with limited remodeling of underlying white matter.

Resilience of FEF neuronal saccade code to V4 perturbations.

The frontal eye field (FEF) plays a key role in initiating rapid eye movements known as saccades. Accumulation models have been proposed to explain the dynamic of these neurons and how they may enable the initiation of saccades. To update the scope of the viability of this model, we studied single neurons recorded from the FEF of two rhesus monkeys while they performed a memory-guided saccade task. We evaluated the degree to which each type of FEF neuron complied with these models by quantifying how precisely their discharge predicted an imminent saccade based on their immediate presaccadic activity. We found that decoders trained on single neurons with a stronger motor component performed better than decoders trained on neurons with a stronger visual component in predicting the saccade. Importantly, despite a dramatic effect on the reaction times, the perturbations delivered to the FEF neurons via area V4 did not impact their saccade predictability. Our results demonstrate a high degree of resilience of the FEF neuronal presaccadic discharge patterns, fulfilling the predictions of accumulation models.NEW & NOTEWORTHY We studied neurons in the brain's frontal eye field (FEF) to understand how these neurons predict swift eye shifts called saccades. We found that neurons with more movement-related activity were better at predicting saccades than those with sensory-related activity. Interestingly, electrical disruptions of this region strongly impacted saccade onset times but did not affect the individual neuron's saccade predictability, consistent with models suggesting that a specific threshold in neural activity triggers the saccade.

Deafness induces complete crossmodal plasticity in a belt region of dorsal auditory cortex.

Many neural areas, where patterned activity is lost following deafness, have the capacity to become activated by the remaining sensory systems. This crossmodal plasticity can be measured at perceptual/behavioural as well as physiological levels. The dorsal zone (DZ) of auditory cortex of deaf cats is involved in supranormal visual motion detection, but its physiological level of crossmodal reorganisation is not well understood. The present study of early-deaf DZ (and hearing controls) used multiple single-channel recording methods to examine neuronal responses to visual, auditory, somatosensory and combined stimulation. In early-deaf DZ, no auditory activation was observed, but 100% of the neurons were responsive to visual cues of which 21% were also influenced by somatosensory stimulation. Visual and somatosensory responses were not anatomically organised as they are in hearing cats, and fewer multisensory neurons were present in the deaf condition. These crossmodal physiological results closely correspond with and support the perceptual/behavioural enhancements that occur following hearing loss.

Applying machine learning techniques to detect the deployment of spatial working memory from the spiking activity of MT neurons.

Neural signatures of working memory have been frequently identified in the spiking activity of different brain areas. However, some studies reported no memory-related change in the spiking activity of the middle temporal (MT) area in the visual cortex. However, recently it was shown that the content of working memory is reflected as an increase in the dimensionality of the average spiking activity of the MT neurons. This study aimed to find the features that can reveal memory-related changes with the help of machine-learning algorithms. In this regard, different linear and nonlinear features were obtained from the neuronal spiking activity during the presence and absence of working memory. To select the optimum features, the Genetic algorithm, Particle Swarm Optimization, and Ant Colony Optimization methods were employed. The classification was performed using the Support Vector Machine (SVM) and the K-Nearest Neighbor (KNN) classifiers. Our results suggest that the deployment of spatial working memory can be perfectly detected from spiking patterns of MT neurons with an accuracy of 99.65±0.12 using the KNN and 99.50±0.26 using the SVM classifiers.

Higuchi fractal dimension is a unique indicator of working memory content represented in spiking activity of visual neurons in extrastriate cortex.

Working memory has been identified as a top-down modulation of the average spiking activity in different brain parts. However, such modification has not yet been reported in the middle temporal (MT) cortex. A recent study showed that the dimensionality of the spiking activity of MT neurons increases after deployment of spatial working memory. This study is devoted to analyzing the ability of nonlinear and classical features to capture the content of the working memory from the spiking activity of MT neurons. The results suggest that only the Higuchi fractal dimension can be considered as a unique indicator of working memory while the Margaos-Sun fractal dimension, Shannon entropy, corrected conditional entropy, and skewness are perhaps indicators of other cognitive factors such as vigilance, awareness, and arousal as well as working memory.

Visually evoked potentials (VEPs) across the visual field in hearing and deaf cats.

Introduction: Congenitally deaf cats perform better on visual localization tasks than hearing cats, and this advantage has been attributed to the posterior auditory field. Successful visual localization requires both visual processing of the target and timely generation of an action to approach the target. Activation of auditory cortex in deaf subjects during visual localization in the peripheral visual field can occur either via bottom-up stimulus-driven and/or top-down goal-directed pathways. Methods: In this study, we recorded visually evoked potentials (VEPs) in response to a reversing checkerboard stimulus presented in the hemifield contralateral to the recorded hemisphere in both hearing and deaf cats under light anesthesia. Results: Although VEP amplitudes and latencies were systematically modulated by stimulus eccentricity, we found little evidence of changes in VEP in deaf cats that can explain their behavioral advantage. A statistical trend was observed, showing larger peak amplitudes and shorter peak latencies in deaf subjects for stimuli in the near- and mid-peripheral field. Additionally, latency of the P1 wave component had a larger inter-sweep variation in deaf subjects. Discussion: Our results suggested that cross-modal plasticity following deafness does not play a major part in cortical processing of the peripheral visual field when the "vision for action" system is not recruited.

Hybrid feature engineering of medical data via variational autoencoders with triplet loss: a COVID-19 prognosis study.

Medical machine learning frameworks have received much attention in recent years. The recent COVID-19 pandemic was also accompanied by a surge in proposed machine learning algorithms for tasks such as diagnosis and mortality prognosis. Machine learning frameworks can be helpful medical assistants by extracting data patterns that are otherwise hard to detect by humans. Efficient feature engineering and dimensionality reduction are major challenges in most medical machine learning frameworks. Autoencoders are novel unsupervised tools that can perform data-driven dimensionality reduction with minimum prior assumptions. This study, in a novel approach, investigated the predictive power of latent representations obtained from a hybrid autoencoder (HAE) framework combining variational autoencoder (VAE) characteristics with mean squared error (MSE) and triplet loss for forecasting COVID-19 patients with high mortality risk in a retrospective framework. Electronic laboratory and clinical data of 1474 patients were used in the study. Logistic regression with elastic net regularization (EN) and random forest (RF) models were used as final classifiers. Moreover, we also investigated the contribution of utilized features towards latent representations via mutual information analysis. HAE Latent representations model achieved decent performance with an area under ROC curve of 0.921 (±0.027) and 0.910 (±0.036) with EN and RF predictors, respectively, over the hold-out data in comparison with the raw (AUC EN: 0.913 (±0.022); RF: 0.903 (±0.020)) models. The study aims to provide an interpretable feature engineering framework for the medical environment with the potential to integrate imaging data for efficient feature engineering in rapid triage and other clinical predictive models.

A comparison of multisensory features of two auditory cortical areas: primary (A1) and higher-order dorsal zone (DZ).

From myriads of ongoing stimuli, the brain creates a fused percept of the environment. This process, which culminates in perceptual binding, is presumed to occur through the operations of multisensory neurons that occur throughout the brain. However, because different brain areas receive different inputs and have different cytoarchitechtonics, it would be expected that local multisensory features would also vary across regions. The present study investigated that hypothesis using multiple single-unit recordings from anesthetized cats in response to controlled, electronically-generated separate and combined auditory, visual, and somatosensory stimulation. These results were used to compare the multisensory features of neurons in cat primary auditory cortex (A1) with those identified in the nearby higher-order auditory region, the Dorsal Zone (DZ). Both regions exhibited the same forms of multisensory neurons, albeit in different proportions. Multisensory neurons exhibiting excitatory or inhibitory properties occurred in similar proportions in both areas. Also, multisensory neurons in both areas expressed similar levels of multisensory integration. Because responses to auditory cues alone were so similar to those that included non-auditory stimuli, it is proposed that this effect represents a mechanism by which multisensory neurons subserve the process of perceptual binding.

The gradient in gray matter thickness across auditory cortex and differential cortical thickness changes following perinatal deafness.

In the absence of hearing during development, the brain adapts and repurposes what was destined to become auditory cortex. As cortical thickness is commonly used as a proxy to identify cortical regions that have undergone plastic changes, the purpose of this investigation was to compare cortical thickness patterns between hearing and deaf cats. In this study, normal hearing (n = 29) and deaf (n = 26) cats were scanned to examine cortical thickness in hearing controls, as well as differential changes in thickness as a consequence of deafness. In hearing cats, a gradient in cortical thickness was identified across auditory cortex in which it is thinner in more dorsal regions and thicker in more ventral regions. Compared with hearing controls, differential thickening and thinning was observed in specific regions of deaf auditory cortex. More dorsal regions were found to be bilaterally thicker in the deaf group, while more ventral regions in the left hemisphere were thinner. The location and nature of these changes creates a gradient along the dorsoventral axis, wherein dorsal auditory cortical fields are thicker, whereas more ventral fields are thinner in deaf animals compared with hearing controls.

Do blind people hear better?

For centuries, anecdotal evidence such as the perfect pitch of the blind piano tuner or blind musician has supported the notion that individuals who have lost their sight early in life have superior hearing abilities compared with sighted people. Recently, auditory psychophysical and functional imaging studies have identified that specific auditory enhancements in the early blind can be linked to activation in extrastriate visual cortex, suggesting crossmodal plasticity. Furthermore, the nature of the sensory reorganization in occipital cortex supports the concept of a task-based functional cartography for the cerebral cortex rather than a sensory-based organization. In total, studies of early-blind individuals provide valuable insights into mechanisms of cortical plasticity and principles of cerebral organization.

Multisensory responses in a belt region of the dorsal auditory cortical pathway.

A basic function of the cerebral cortex is to receive and integrate information from different sensory modalities into a comprehensive percept of the environment. Neurons that demonstrate multisensory convergence occur across the necortex but are especially prevalent in higher order association areas. However, a recent study of a cat higher order auditory area, the dorsal zone (DZ) of auditory cortex, did not observe any multisensory features. Therefore, the goal of the present investigation was to address this conflict using recording and testing methodologies that are established for exposing and studying multisensory neuronal processing. Among the 482 neurons studied, we found that 76.6% were influenced by non-auditory stimuli. Of these neurons, 99% were affected by visual stimulation, but only 11% by somatosensory. Furthermore, a large proportion of the multisensory neurons showed integrated responses to multisensory stimulation, constituted a majority of the excitatory and inhibitory neurons encountered (as identified by the duration of their waveshape) and exhibited a distinct spatial distribution within DZ. These findings demonstrate that the DZ of auditory cortex robustly exhibits multisensory properties and that the proportions of multisensory neurons encountered are consistent with those identified in other higher order cortices.

Transient deactivation of dorsal premotor cortex or parietal area 5 impairs feedback control of the limb in macaques.

We can generate goal-directed motor corrections with surprising speed, but their neural basis is poorly understood. Here, we show that temporary cooling of dorsal premotor cortex (PMd) impaired both spatial accuracy and the speed of corrective responses, whereas cooling parietal area 5 (A5) impaired only spatial accuracy. Simulations based on optimal feedback control (OFC) models demonstrated that "deactivation" of the control policy (reduction in feedback gain) and state estimation (reduction in Kalman gain) caused impairments similar to that observed for PMd and A5 cooling, respectively. Furthermore, combined deactivation of both cortical regions led to additive impairments of individual deactivations, whereas reducing the amount of cooling to PMd led to impairments in response speed but not spatial accuracy, both also predicted by OFC models. These results provide causal support that frontoparietal circuits beyond primary somatosensory and motor cortices are involved in generating goal-directed motor corrections.

Early hearing loss induces plasticity within extra-striate visual cortex.

Supranormal perceptual performance has been observed within the intact senses of early-deaf or blind humans and animals. For cortical areas deprived of their normal sensory input, numerous studies have shown that the lesioned modality is replaced by that of the intact sensory modalities through a process termed crossmodal plasticity. In contrast, little is known about the effects of loss of a particular sensory modality on the cortical representations of the remaining, intact sensory modalities. In the present study, an area of extrastriate visual cortex from early-deaf adult cats was examined for features of dendritic plasticity known to occur after early-deafness. Using light-microscopy of Golgi-stained pyramidal neurons from the posterolateral lateral suprasylvian (PLLS) cortex, dendritic spine density significantly increased (~19%), while spine head size was slightly but significantly decreased (~9%) following early hearing loss. Curiously, these changes were not localized to regions of the visual PLLS known to receive auditory inputs, but instead showed a broad pattern more reflective of the distribution of the area's visual features. Whereas hearing loss results in crossmodal plasticity in auditory cortices, the same peripheral lesion can also induce intramodal plasticity within representations of the intact sensory systems that may also contribute to supranormal performance.

Frontal eye field inactivation alters the readout of superior colliculus activity for saccade generation in a task-dependent manner.

Saccades require a spatiotemporal transformation of activity between the intermediate layers of the superior colliculus (iSC) and downstream brainstem burst generator. The dynamic linear ensemble-coding model (Goossens and Van Opstal 2006) proposes that each iSC spike contributes a fixed mini-vector to saccade displacement. Although biologically-plausible, this model assumes cortical areas like the frontal eye fields (FEF) simply provide the saccadic goal to be executed by the iSC and brainstem burst generator. However, the FEF and iSC operate in unison during saccades, and a pathway from the FEF to the brainstem burst generator that bypasses the iSC exists. Here, we investigate the impact of large yet reversible inactivation of the FEF on iSC activity in the context of the model across four saccade tasks. We exploit the overlap of saccade vectors generated when the FEF is inactivated or not, comparing the number of iSC spikes for metrically-matched saccades. We found that the iSC emits fewer spikes for metrically-matched saccades during FEF inactivation. The decrease in spike count is task-dependent, with a greater decrease accompanying more cognitively-demanding saccades. Our results show that FEF integrity influences the readout of iSC activity in a task-dependent manner. We propose that the dynamic linear ensemble-coding model be modified so that FEF inactivation increases the gain of a readout parameter, effectively increasing the influence of a single iSC spike. We speculate that this modification could be instantiated by FEF and iSC pathways to the cerebellum that could modulate the excitability of the brainstem burst generator.

The limited capacity of visual temporal integration in cats.

It has been long known that prolonging stimulus duration may increase the perceived brightness of a visual stimulus. The interaction between intensity and duration generally follows a rule, such as that described in Bloch's law. This visual temporal integration relationship has been identified in human subjects and in non-human primates. However, although auditory temporal integration has been extensively studied in the cat, visual temporal integration has not. Therefore, the goal of this study was to examine visual temporal integration in the cat. We trained five cats to respond when a brief luminance change was detected in a fixation dot. After training, we measured the success rate of detecting the luminance change with varying durations at threshold, subthreshold, and suprathreshold luminance levels. Psychometric functions showed that prolonging stimulus duration improved task performance, more noticeably for stimuli below 100 ms than beyond. Most psychometric functions were better fit to an exponential model than to a linear model. The gradually saturated performance observed here, as in previous studies, can be explained by the "leaky integrator" hypothesis, that is, temporal integration is only valid below a critical duration. Overall, we developed a task whereby visual temporal integration was successfully demonstrated in the cat. The effect of stimulus duration on detection success rate displayed a pattern generally consistent with previous human and non-human primate findings on visual temporal integration.

Impairment but not abolishment of express saccades after unilateral or bilateral inactivation of the frontal eye fields.

Express saccades are a manifestation of a visual grasp reflex triggered when visual information arrives in the intermediate layers of the superior colliculus (SCi), which in turn orchestrates the lower level brainstem saccade generator to evoke a saccade with a very short latency (~100 ms or less). A prominent theory regarding express saccades generation is that they are facilitated by preparatory signals, presumably from cortical areas, which prime the SCi before the arrival of visual information. Here, we test this theory by reversibly inactivating a key cortical input to the SCi, the frontal eye fields (FEF), while monkeys perform an oculomotor task that promotes express saccades. Across three tasks with a different combination of potential target locations and unilateral or bilateral FEF inactivation, we found a spared ability for monkeys to generate express saccades, despite decreases in express saccade frequency during FEF inactivation. This result is consistent with the FEF having a facilitatory but not critical role in express saccade generation, likely because other cortical areas compensate for the loss of preparatory input to the SCi. However, we also found decreases in the accuracy and peak velocity of express saccades generated during FEF inactivation, which argues for an influence of the FEF on the saccadic burst generator even during express saccades. Overall, our results shed further light on the role of the FEF in the shortest-latency visually-guided eye movements.NEW & NOTEWORTHY Express saccades are the shortest-latency saccade. The frontal eye fields (FEF) are thought to promote express saccades by presetting the superior colliculus. Here, by reversibly inactivating the FEF either unilaterally or bilaterally via cortical cooling, we support this by showing that the FEF plays a facilitative but not critical role in express saccade generation. We also found that FEF inactivation lowered express saccade peak velocity, emphasizing a contribution of the FEF to express saccade kinematics.

Parietal Cortex Regulates Visual Salience and Salience-Driven Behavior.

Unique stimuli stand out. Despite an abundance of competing sensory stimuli, the detection of the most salient ones occurs without effort, and that detection contributes to the guidance of adaptive behavior. Neurons sensitive to the salience of visual stimuli are widespread throughout the primate visual system and are thought to shape the selection of visual targets. However, a neural source of salience remains elusive. In an attempt to identify a source of visual salience, we reversibly inactivated parietal cortex and simultaneously recorded salience signals in prefrontal cortex. Inactivation of parietal cortex not only caused pronounced and selective reductions of salience signals in prefrontal cortex but also diminished the influence of salience on visually guided behavior. These observations demonstrate a causal role of parietal cortex in regulating salience signals within the brain and in controlling salience-driven behavior.