A Tradeoff in the Neural Code across Regions and Species.

Many evolutionary years separate humans and macaques, and although the amygdala and cingulate cortex evolved to enable emotion and cognition in both, an evident functional gap exists. Although they were traditionally attributed to differential neuroanatomy, functional differences might also arise from coding mechanisms. Here we find that human neurons better utilize information capacity (efficient coding) than macaque neurons in both regions, and that cingulate neurons are more efficient than amygdala neurons in both species. In contrast, we find more overlap in the neural vocabulary and more synchronized activity (robustness coding) in monkeys in both regions and in the amygdala of both species. Our findings demonstrate a tradeoff between robustness and efficiency across species and regions. We suggest that this tradeoff can contribute to differential cognitive functions between species and underlie the complementary roles of the amygdala and the cingulate cortex. In turn, it can contribute to fragility underlying human psychopathologies.

Peeling the Onion of Brain Representations.

The brain's function is to enable adaptive behavior in the world. To this end, the brain processes information about the world. The concept of representation links the information processed by the brain back to the world and enables us to understand what the brain does at a functional level. The appeal of making the connection between brain activity and what it represents has been irresistible to neuroscience, despite the fact that representational interpretations pose several challenges: We must define which aspects of brain activity matter, how the code works, and how it supports computations that contribute to adaptive behavior. It has been suggested that we might drop representational language altogether and seek to understand the brain, more simply, as a dynamical system. In this review, we argue that the concept of representation provides a useful link between dynamics and computational function and ask which aspects of brain activity should be analyzed to achieve a representational understanding. We peel the onion of brain representations in search of the layers (the aspects of brain activity) that matter to computation. The article provides an introduction to the motivation and mathematics of representational models, a critical discussion of their assumptions and limitations, and a preview of future directions in this area.

Oculo-retinal dynamics can explain the perception of minimal recognizable configurations.

Natural vision is a dynamic and continuous process. Under natural conditions, visual object recognition typically involves continuous interactions between ocular motion and visual contrasts, resulting in dynamic retinal activations. In order to identify the dynamic variables that participate in this process and are relevant for image recognition, we used a set of images that are just above and below the human recognition threshold and whose recognition typically requires >2 s of viewing. We recorded eye movements of participants while attempting to recognize these images within trials lasting 3 s. We then assessed the activation dynamics of retinal ganglion cells resulting from ocular dynamics using a computational model. We found that while the saccadic rate was similar between recognized and unrecognized trials, the fixational ocular speed was significantly larger for unrecognized trials. Interestingly, however, retinal activation level was significantly lower during these unrecognized trials. We used retinal activation patterns and oculomotor parameters of each fixation to train a binary classifier, classifying recognized from unrecognized trials. Only retinal activation patterns could predict recognition, reaching 80% correct classifications on the fourth fixation (on average, ∼2.5 s from trial onset). We thus conclude that the information that is relevant for visual perception is embedded in the dynamic interactions between the oculomotor sequence and the image. Hence, our results suggest that ocular dynamics play an important role in recognition and that understanding the dynamics of retinal activation is crucial for understanding natural vision.

Neural activity temporal pattern dictates long-range propagation targets.

Brain possesses a complex spatiotemporal architecture for efficient information processing and computing. However, it remains unknown how neural signal propagates to its intended targets brain-wide. Using optogenetics and functional MRI, we arbitrarily initiated various discrete neural activity pulse trains with different temporal patterns and revealed their distinct long-range propagation targets within the well-defined, topographically organized somatosensory thalamo-cortical circuit. We further observed that such neural activity propagation over long range could modulate brain-wide sensory functions. Electrophysiological analysis indicated that distinct propagation pathways arose from system level neural adaptation and facilitation in response to the neural activity temporal characteristics. Together, our findings provide fundamental insights into the long-range information transfer and processing. They directly support that temporal coding underpins the whole brain functional architecture in presence of the vast and relatively static anatomical architecture.

Effects of receptor density on the tactile perception of roughness: implications for neural mechanisms of texture perception.

Aim of the study: The purpose of this study was to investigate the effects of receptor density in the glabrous skin of the hand on the perception of the roughness of a textured surface.Materials and methods: This was done by having observers make magnitude estimates of the perceived roughness of raised-dot surfaces at the fingertip, with its high receptor density, and the thenar eminence, with its much lower receptor density.Results: Judgments of perceived roughness averaged over the inter-dot spacings (0.8-5.9 mm) employed in the study did not differ significantly between the two sites, which suggested that roughness perception is not exclusively dependent upon a neural code involving variation in the activity levels of the nerve fibers of spatially distributed receptors, as is the case in spatial discrimination tasks such as spatial-gap detection, grove-orientation discrimination and letter recognition. This hypothesis was further supported by the finding that the elimination of temporal cues by preventing movement of the skin over the raised-dot surface drastically impaired judgments of perceived roughness at the thenar but had little effect on judgments of perceived roughness at the fingertip.Conclusion: These findings suggested that the neural code for perceived roughness at the fingertip is mediated primarily by spatial variation in the activity levels of spatially distributed receptors whereas the neural code for perceived roughness at the thenar is mediated primarily by temporal variation in the activity levels of individual receptors.

Predictive processing: Is the future just a memory?

Predictive processing seems like a radical departure from traditional theories of information processing in the brain, but a broader view of predictions highlights many similarities with standard frameworks. Predictive processing is memory and competitive bias in a new outlook-and we should use this correspondence to advance research on both fronts.

Spiking time-dependent plasticity leads to efficient coding of predictions.

Latency reduction in postsynaptic spikes is a well-known effect of spiking time-dependent plasticity. We expand this notion for long postsynaptic spike trains on single neurons, showing that, for a fixed input spike train, STDP reduces the number of postsynaptic spikes and concentrates the remaining ones. Then, we study the consequences of this phenomena in terms of coding, finding that this mechanism improves the neural code by increasing the signal-to-noise ratio and lowering the metabolic costs of frequent stimuli. Finally, we illustrate that the reduction in postsynaptic latencies can lead to the emergence of predictions.

Unstructured network topology begets order-based representation by privileged neurons.

How spiking activity reverberates through neuronal networks, how evoked and spontaneous activity interacts and blends, and how the combined activities represent external stimulation are pivotal questions in neuroscience. We simulated minimal models of unstructured spiking networks in silico, asking whether and how gentle external stimulation might be subsequently reflected in spontaneous activity fluctuations. Consistent with earlier findings in silico and in vitro, we observe a privileged subpopulation of 'pioneer neurons' that, by their firing order, reliably encode previous external stimulation. We also confirm that pioneer neurons are 'sensitive' in that they are recruited by small fluctuations of population activity. We show that order-based representations rely on a 'chain' of pioneer neurons with different degrees of sensitivity and thus constitute an emergent property of collective dynamics. The forming of such representations is greatly favoured by a broadly heterogeneous connection topology-a broad 'middle class' in degree of connectedness. In conclusion, we offer a minimal model for the representational role of pioneer neurons, as observed experimentally in vitro. In addition, we show that broadly heterogeneous connectivity enhances the representational capacity of unstructured networks.

The Case for Algebraic Biology: from Research to Education.

Though it goes without saying that linear algebra is fundamental to mathematical biology, polynomial algebra is less visible. In this article, we will give a brief tour of four diverse biological problems where multivariate polynomials play a central role-a subfield that is sometimes called algebraic biology. Namely, these topics include biochemical reaction networks, Boolean models of gene regulatory networks, algebraic statistics and genomics, and place fields in neuroscience. After that, we will summarize the history of discrete and algebraic structures in mathematical biology, from their early appearances in the late 1960s to the current day. Finally, we will discuss the role of algebraic biology in the modern classroom and curriculum, including resources in the literature and relevant software. Our goal is to make this article widely accessible, reaching the mathematical biologist who knows no algebra, the algebraist who knows no biology, and especially the interested student who is curious about the synergy between these two seemingly unrelated fields.

Temporal coding of reward-guided choice in the posterior parietal cortex.

Making a decision involves computations across distributed cortical and subcortical networks. How such distributed processing is performed remains unclear. We test how the encoding of choice in a key decision-making node, the posterior parietal cortex (PPC), depends on the temporal structure of the surrounding population activity. We recorded spiking and local field potential (LFP) activity in the PPC while two rhesus macaques performed a decision-making task. We quantified the mutual information that neurons carried about an upcoming choice and its dependence on LFP activity. The spiking of PPC neurons was correlated with LFP phases at three distinct time scales in the theta, beta, and gamma frequency bands. Importantly, activity at these time scales encoded upcoming decisions differently. Choice information contained in neural firing varied with the phase of beta and gamma activity. For gamma activity, maximum choice information occurred at the same phase as the maximum spike count. However, for beta activity, choice information and spike count were greatest at different phases. In contrast, theta activity did not modulate the encoding properties of PPC units directly but was correlated with beta and gamma activity through cross-frequency coupling. We propose that the relative timing of local spiking and choice information reveals temporal reference frames for computations in either local or large-scale decision networks. Differences between the timing of task information and activity patterns may be a general signature of distributed processing across large-scale networks.

Neural representations of time-linked memory.

Many cognitive processes, such as episodic memory and decision making, rely on the ability to form associations between two events that occur separately in time. The formation of such temporal associations depends on neural representations of three types of information: what has been presented (trace holding), what will follow (temporal expectation), and when the following event will occur (explicit timing). The present review seeks to link these representations with firing patterns of single neurons recorded while rodents and non-human primates associate stimuli, outcomes, and motor responses over time intervals. Across these studies, two distinct firing patterns were observed in the hippocampus, neocortex, and striatum: some neurons change firing rates during or shortly after the stimulus presentation and sustain the firing rate stably or sidlingly during the subsequent intervals (tonic firings). Other neurons transiently change firing rates during a specific moment within the time intervals (phasic firings), and as a group, they form a sequential firing pattern that covers the entire interval. Clever task designs used in some of these studies collectively provide evidence that both tonic and phasic firing responses represent trace holding, temporal expectation, and explicit timing. Subsequently, we applied machine-learning based classification approaches to the two firing patterns within the same dataset collected from rat medial prefrontal cortex during trace eyeblink conditioning. This quantitative analysis revealed that phasic-firing patterns showed greater selectivity for stimulus identity and temporal position than tonic-firing patterns. Our summary illuminates distributed neural representations of temporal association in the forebrain and generates several ideas for future investigations.

Information-Theoretical Analysis of the Neural Code in the Rodent Temporal Lobe.

In the study of the neural code, information-theoretical methods have the advantage of making no assumptions about the probabilistic mapping between stimuli and responses. In the sensory domain, several methods have been developed to quantify the amount of information encoded in neural activity, without necessarily identifying the specific stimulus or response features that instantiate the code. As a proof of concept, here we extend those methods to the encoding of kinematic information in a navigating rodent. We estimate the information encoded in two well-characterized codes, mediated by the firing rate of neurons, and by the phase-of-firing with respect to the theta-filtered local field potential. In addition, we also consider a novel code, mediated by the delta-filtered local field potential. We find that all three codes transmit significant amounts of kinematic information, and informative neurons tend to employ a combination of codes. Cells tend to encode conjunctions of kinematic features, so that most of the informative neurons fall outside the traditional cell types employed to classify spatially-selective units. We conclude that a broad perspective on the candidate stimulus and response features expands the repertoire of strategies with which kinematic information is encoded.

Assessing the Relevance of Specific Response Features in the Neural Code.

The study of the neural code aims at deciphering how the nervous system maps external stimuli into neural activity-the encoding phase-and subsequently transforms such activity into adequate responses to the original stimuli-the decoding phase. Several information-theoretical methods have been proposed to assess the relevance of individual response features, as for example, the spike count of a given neuron, or the amount of correlation in the activity of two cells. These methods work under the premise that the relevance of a feature is reflected in the information loss that is induced by eliminating the feature from the response. The alternative methods differ in the procedure by which the tested feature is removed, and the algorithm with which the lost information is calculated. Here we compare these methods, and show that more often than not, each method assigns a different relevance to the tested feature. We demonstrate that the differences are both quantitative and qualitative, and connect them with the method employed to remove the tested feature, as well as the procedure to calculate the lost information. By studying a collection of carefully designed examples, and working on analytic derivations, we identify the conditions under which the relevance of features diagnosed by different methods can be ranked, or sometimes even equated. The condition for equality involves both the amount and the type of information contributed by the tested feature. We conclude that the quest for relevant response features is more delicate than previously thought, and may yield to multiple answers depending on methodological subtleties.

Advances in two photon scanning and scanless microscopy technologies for functional neural circuit imaging.

Recent years have seen substantial developments in technology for imaging neural circuits, raising the prospect of large scale imaging studies of neural populations involved in information processing, with the potential to lead to step changes in our understanding of brain function and dysfunction. In this article we will review some key recent advances: improved fluorophores for single cell resolution functional neuroimaging using a two photon microscope; improved approaches to the problem of scanning active circuits; and the prospect of scanless microscopes which overcome some of the bandwidth limitations of current imaging techniques. These advances in technology for experimental neuroscience have in themselves led to technical challenges, such as the need for the development of novel signal processing and data analysis tools in order to make the most of the new experimental tools. We review recent work in some active topics, such as region of interest segmentation algorithms capable of demixing overlapping signals, and new highly accurate algorithms for calcium transient detection. These advances motivate the development of new data analysis tools capable of dealing with spatial or spatiotemporal patterns of neural activity, that scale well with pattern size.

A Neural Substrate for Rapid Timbre Recognition? Neural and Behavioral Discrimination of Very Brief Acoustic Vowels.

The timbre of a sound plays an important role in our ability to discriminate between behaviorally relevant auditory categories, such as different vowels in speech. Here, we investigated, in the primary auditory cortex (A1) of anesthetized guinea pigs, the neural representation of vowels with impoverished timbre cues. Five different vowels were presented with durations ranging from 2 to 128 ms. A psychophysical experiment involving human listeners showed that identification performance was near ceiling for the longer durations and degraded close to chance level for the shortest durations. This was likely due to spectral splatter, which reduced the contrast between the spectral profiles of the vowels at short durations. Effects of vowel duration on cortical responses were well predicted by the linear frequency responses of A1 neurons. Using mutual information, we found that auditory cortical neurons in the guinea pig could be used to reliably identify several vowels for all durations. Information carried by each cortical site was low on average, but the population code was accurate even for durations where human behavioral performance was poor. These results suggest that a place population code is available at the level of A1 to encode spectral profile cues for even very short sounds.

Delayed and Temporally Imprecise Neurotransmission in Reorganizing Cortical Microcircuits.

Synaptic neurotransmission is modified at cortical connections throughout life. Varying the amplitude of the postsynaptic response is one mechanism that generates flexible signaling in neural circuits. The timing of the synaptic response may also play a role. Here, we investigated whether weakening and loss of an entire connection between excitatory cortical neurons was foreshadowed in the timing of the postsynaptic response. We made electrophysiological recordings in rat primary somatosensory cortex that was undergoing experience-dependent loss of complete local excitatory connections. The synaptic latency of pyramid-pyramid connections, which typically comprise multiple synapses, was longer and more variable. Connection strength and latency were not correlated. Instead, prolonged latency was more closely related to progression of connection loss. The action potential waveform and axonal conduction velocity were unaffected, suggesting that the altered timing of neurotransmission was attributable to a synaptic mechanism. Modeling studies indicated that increasing the latency and jitter at a subset of synapses reduced the number of action potentials fired by a postsynaptic neuron. We propose that prolonged synaptic latency and diminished temporal precision of neurotransmission are hallmarks of impending loss of a cortical connection.

Multiple neural representations of elementary logical connectives.

A defining trait of human cognition is the capacity to form compounds out of simple thoughts. This ability relies on the logical connectives AND, OR and IF. Simple propositions, e.g., 'There is a fork' and 'There is a knife', can be combined in alternative ways using logical connectives: e.g., 'There is a fork AND there is a knife', 'There is a fork OR there is a knife', 'IF there is a fork, there is a knife'. How does the brain represent compounds based on different logical connectives, and how are compounds evaluated in relation to new facts? In the present study, participants had to maintain and evaluate conjunctive (AND), disjunctive (OR) or conditional (IF) compounds while undergoing functional MRI. Our results suggest that, during maintenance, the left posterior inferior frontal gyrus (pIFG, BA44, or Broca's area) represents the surface form of compounds. During evaluation, the left pIFG switches to processing the full logical meaning of compounds, and two additional areas are recruited: the left anterior inferior frontal gyrus (aIFG, BA47) and the left intraparietal sulcus (IPS, BA40). The aIFG shows a pattern of activation similar to pIFG, and compatible with processing the full logical meaning of compounds, whereas activations in IPS differ with alternative interpretations of conditionals: logical vs conjunctive. These results uncover the functions of a basic cortical network underlying human compositional thought, and provide a shared neural foundation for the cognitive science of language and reasoning.

Signal switching may enhance processing power of the brain.

Our ability to perceive multiple objects is mysterious. Sensory neurons are broadly tuned, producing potential overlap in the populations of neurons activated by each object in a scene. This overlap raises questions about how distinct information is retained about each item. We present a novel signal switching theory of neural representation, which posits that neural signals may interleave representations of individual items across time. Evidence for this theory comes from new statistical tools that overcome the limitations inherent to standard time-and-trial-pooled assessments of neural signals. Our theory has implications for diverse domains of neuroscience, including attention, figure binding/scene segregation, oscillations, and divisive normalization. The general concept of switching between functions could also lend explanatory power to theories of grounded cognition.

Absence of paresthesia during high-rate spinal cord stimulation reveals importance of synchrony for sensations evoked by electrical stimulation.

Electrically activating mechanoreceptive afferents inhibits pain. However, paresthesia evoked by spinal cord stimulation (SCS) at 40-60 Hz becomes uncomfortable at high pulse amplitudes, limiting SCS "dosage." Kilohertz-frequency SCS produces analgesia without paresthesia and is thought, therefore, not to activate afferent axons. We show that paresthesia is absent not because axons do not spike but because they spike asynchronously. In a pain patient, selectively increasing SCS frequency abolished paresthesia and epidurally recorded evoked compound action potentials (ECAPs). Dependence of ECAP amplitude on SCS frequency was reproduced in pigs, rats, and computer simulations and is explained by overdrive desynchronization: spikes desychronize when axons are stimulated faster than their refractory period. Unlike synchronous spikes, asynchronous spikes fail to produce paresthesia because their transmission to somatosensory cortex is blocked by feedforward inhibition. Our results demonstrate how stimulation frequency impacts synchrony based on axon properties and how synchrony impacts sensation based on circuit properties.

Neural Fluctuation Contrast as a Code for Complex Sounds: The Role and Control of Peripheral Nonlinearities.

The nonlinearities of the inner ear are often considered to be obstacles that the central nervous system has to overcome to decode neural responses to sounds. This review describes how peripheral nonlinearities, such as saturation of the inner-hair-cell response and of the IHC-auditory-nerve synapse, are instead beneficial to the neural encoding of complex sounds such as speech. These nonlinearities set up contrast in the depth of neural-fluctuations in auditory-nerve responses along the tonotopic axis, referred to here as neural fluctuation contrast (NFC). Physiological support for the NFC coding hypothesis is reviewed, and predictions of several psychophysical phenomena, including masked detection and speech intelligibility, are presented. Lastly, a framework based on the NFC code for understanding how the medial olivocochlear (MOC) efferent system contributes to the coding of complex sounds is presented. By modulating cochlear gain control in response to both sound energy and fluctuations in neural responses, the MOC system is hypothesized to function not as a simple feedback gain-control device, but rather as a mechanism for enhancing NFC along the tonotopic axis, enabling robust encoding of complex sounds across a wide range of sound levels and in the presence of background noise. Effects of sensorineural hearing loss on the NFC code and on the MOC feedback system are presented and discussed.