Cognition as a Window into Neuronal Population Space.

Understanding how cognitive processes affect the responses of sensory neurons may clarify the relationship between neuronal population activity and behavior. However, tools for analyzing neuronal activity have not kept up with technological advances in recording from large neuronal populations. Here, we describe prevalent hypotheses of how cognitive processes affect sensory neurons, driven largely by a model based on the activity of single neurons or pools of neurons as the units of computation. We then use simple simulations to expand this model to a new conceptual framework that focuses on subspaces of population activity as the relevant units of computation, uses comparisons between brain areas or to behavior to guide analyses of these subspaces, and suggests that population activity is optimized to decode the large variety of stimuli and tasks that animals encounter in natural behavior. This framework provides new ways of understanding the ever-growing quantity of recorded population activity data.

Topological insights into the neural basis of flexible behavior.

It is widely accepted that there is an inextricable link between neural computations, biological mechanisms, and behavior, but it is challenging to simultaneously relate all three. Here, we show that topological data analysis (TDA) provides an important bridge between these approaches to studying how brains mediate behavior. We demonstrate that cognitive processes change the topological description of the shared activity of populations of visual neurons. These topological changes constrain and distinguish between competing mechanistic models, are connected to subjects' performance on a visual change detection task, and, via a link with network control theory, reveal a tradeoff between improving sensitivity to subtle visual stimulus changes and increasing the chance that the subject will stray off task. These connections provide a blueprint for using TDA to uncover the biological and computational mechanisms by which cognition affects behavior in health and disease.

Methylphenidate as a causal test of translational and basic neural coding hypotheses.

Most systems neuroscience studies fall into one of two categories: basic science work aimed at understanding the relationship between neurons and behavior, or translational work aimed at developing treatments for neuropsychiatric disorders. Here we use these two approaches to inform and enhance each other. Our study both tests hypotheses about basic science neural coding principles and elucidates the neuronal mechanisms underlying clinically relevant behavioral effects of systemically administered methylphenidate (Ritalin). We discovered that orally administered methylphenidate, used clinically to treat attention deficit hyperactivity disorder (ADHD) and generally to enhance cognition, increases spatially selective visual attention, enhancing visual performance at only the attended location. Further, we found that this causal manipulation enhances vision in rhesus macaques specifically when it decreases the mean correlated variability of neurons in visual area V4. Our findings demonstrate that the visual system is a platform for understanding the neural underpinnings of both complex cognitive processes (basic science) and neuropsychiatric disorders (translation). Addressing basic science hypotheses, our results are consistent with a scenario in which methylphenidate has cognitively specific effects by working through naturally selective cognitive mechanisms. Clinically, our findings suggest that the often staggeringly specific symptoms of neuropsychiatric disorders may be caused and treated by leveraging general mechanisms.

Cigarette Smoke Exposure and Acute Respiratory Distress Syndrome in Sepsis: Epidemiology, Clinical Features, and Biologic Markers.

Rationale: Cigarette smoke exposure is associated with an increased risk of developing acute respiratory distress syndrome (ARDS) in trauma, transfusion, and nonpulmonary sepsis. It is unknown whether this relationship exists in the general sepsis population. Furthermore, it is unknown if patients with ARDS have differences in underlying biology based on smoking status. Objectives: To assess the relationship between cigarette smoke exposure and ARDS in sepsis and identify tobacco-related biomarkers of lung injury. Methods: We studied a prospective cohort of 592 patients with sepsis from 2009 to 2017. Plasma cotinine and urine NNAL [urine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol] were measured to categorize smoking status. Plasma biomarkers of inflammation and lung injury were measured, including in a smaller cohort of trauma patients with ARDS to increase generalizability. Measurements and Main Results: Passive and active smoking were associated with increased odds of developing ARDS in patients with sepsis. Among patients with sepsis and ARDS, active cigarette smokers were younger and had lower severity of illness than nonsmokers. Patients with ARDS with cigarette smoke exposure had lower plasma levels of IL-8 (P = 0.01) and sTNFR-1 (soluble tumor necrosis factor 1; P = 0.01) compared with those without exposure. Similar biomarker patterns were observed in blunt trauma patients with ARDS. Conclusions: Passive and active smoking are associated with an increased risk of developing ARDS in patients with pulmonary and nonpulmonary sepsis. Among patients with ARDS, those with cigarette smoke exposure have less systemic inflammation, while active smokers also have lower severity of illness compared with nonsmokers, suggesting that smoking contributes to biological heterogeneity in ARDS.

Neuronal Effects of Spatial and Feature Attention Differ Due to Normalization.

Although spatial and feature attention have differing effects on neuronal responses in visual cortex, it remains unclear why. Response normalization has been implicated in both types of attention (Carandini and Heeger, 2011), and single-unit studies have demonstrated that the magnitude of spatial attention effects on neuronal responses covaries with the magnitude of normalization effects. However, the relationship between feature attention and normalization remains largely unexplored. We recorded from individual neurons in the middle temporal area of rhesus monkeys using a task that allowed us to isolate the effects of feature attention, spatial attention, and normalization on the responses of each neuron. We found that the magnitudes of neuronal response modulations due to spatial attention and feature attention are correlated; however, whereas modulations due to spatial attention are correlated with normalization strength, those due to feature attention are not. Additionally, spatial attention modulations are stronger with multiple stimuli in the receptive field, whereas feature attention modulations are not. These findings are captured by a model in which spatial and feature attention share common top-down attention signals that nonetheless result in differing sensory neuron response modulations because of a spatially tuned sensory normalization mechanism. This model explains previously reported commonalities and differences between these two types of attention by clarifying the relationship between top-down attention signals and sensory normalization. We conclude that similar top-down signals to visual cortex can have distinct effects on neuronal responses due to distinct interactions with sensory mechanisms.SIGNIFICANCE STATEMENT Subjects use attention to improve their visual perception in several ways, including by attending to a location in space or to a visual feature. Prior studies have found both commonalities and differences between the effects of spatial and feature attention on neuronal responses in visual cortex, although it is unclear what mechanisms could explain this range of effects. Normalization, a computation by which neuronal responses are modified by stimulus context, has been implicated in many neuronal mechanisms throughout the brain. Here we propose that normalization provides a simple explanation for how spatial and feature attention could share common top-down attention signals that still affect sensory neuron responses differently.

Spatially tuned normalization explains attention modulation variance within neurons.

Spatial attention improves perception of attended parts of a scene, a behavioral enhancement accompanied by modulations of neuronal firing rates. These modulations vary in size across neurons in the same brain area. Models of normalization explain much of this variance in attention modulation with differences in tuned normalization across neurons (Lee J, Maunsell JHR. PLoS One 4: e4651, 2009; Ni AM, Ray S, Maunsell JHR. Neuron 73: 803-813, 2012). However, recent studies suggest that normalization tuning varies with spatial location both across and within neurons (Ruff DA, Alberts JJ, Cohen MR. J Neurophysiol 116: 1375-1386, 2016; Verhoef BE, Maunsell JHR. eLife 5: e17256, 2016). Here we show directly that attention modulation and normalization tuning do in fact covary within individual neurons, in addition to across neurons as previously demonstrated. We recorded the activity of isolated neurons in the middle temporal area of two rhesus monkeys as they performed a change-detection task that controlled the focus of spatial attention. Using the same two drifting Gabor stimuli and the same two receptive field locations for each neuron, we found that switching which stimulus was presented at which location affected both attention modulation and normalization in a correlated way within neurons. We present an equal-maximum-suppression spatially tuned normalization model that explains this covariance both across and within neurons: each stimulus generates equally strong suppression of its own excitatory drive, but its suppression of distant stimuli is typically less. This new model specifies how the tuned normalization associated with each stimulus location varies across space both within and across neurons, changing our understanding of the normalization mechanism and how attention modulations depend on this mechanism.NEW & NOTEWORTHY Tuned normalization studies have demonstrated that the variance in attention modulation size seen across neurons from the same cortical area can be largely explained by between-neuron differences in normalization strength. Here we demonstrate that attention modulation size varies within neurons as well and that this variance is largely explained by within-neuron differences in normalization strength. We provide a new spatially tuned normalization model that explains this broad range of observed normalization and attention effects.

Strategies for targeting primate neural circuits with viral vectors.

Understanding how the brain works requires understanding how different types of neurons contribute to circuit function and organism behavior. Progress on this front has been accelerated by optogenetics and chemogenetics, which provide an unprecedented level of control over distinct neuronal types in small animals. In primates, however, targeting specific types of neurons with these tools remains challenging. In this review, we discuss existing and emerging strategies for directing genetic manipulations to targeted neurons in the adult primate central nervous system. We review the literature on viral vectors for gene delivery to neurons, focusing on adeno-associated viral vectors and lentiviral vectors, their tropism for different cell types, and prospects for new variants with improved efficacy and selectivity. We discuss two projection targeting approaches for probing neural circuits: anterograde projection targeting and retrograde transport of viral vectors. We conclude with an analysis of cell type-specific promoters and other nucleotide sequences that can be used in viral vectors to target neuronal types at the transcriptional level.

Strength of gamma rhythm depends on normalization.

Neuronal assemblies often exhibit stimulus-induced rhythmic activity in the gamma range (30-80 Hz), whose magnitude depends on the attentional load. This has led to the suggestion that gamma rhythms form dynamic communication channels across cortical areas processing the features of behaviorally relevant stimuli. Recently, attention has been linked to a normalization mechanism, in which the response of a neuron is suppressed (normalized) by the overall activity of a large pool of neighboring neurons. In this model, attention increases the excitatory drive received by the neuron, which in turn also increases the strength of normalization, thereby changing the balance of excitation and inhibition. Recent studies have shown that gamma power also depends on such excitatory-inhibitory interactions. Could modulation in gamma power during an attention task be a reflection of the changes in the underlying excitation-inhibition interactions? By manipulating the normalization strength independent of attentional load in macaque monkeys, we show that gamma power increases with increasing normalization, even when the attentional load is fixed. Further, manipulations of attention that increase normalization increase gamma power, even when they decrease the firing rate. Thus, gamma rhythms could be a reflection of changes in the relative strengths of excitation and normalization rather than playing a functional role in communication or control.

Orthogonal neural representations support perceptual judgements of natural stimuli.

In natural behavior, observers must separate relevant information from a barrage of irrelevant information. Many studies have investigated the neural underpinnings of this ability using artificial stimuli presented on simple backgrounds. Natural viewing, however, carries a set of challenges that are inaccessible using artificial stimuli, including neural responses to background objects that are task-irrelevant. An emerging body of evidence suggests that the visual abilities of humans and animals can be modeled through the linear decoding of task-relevant information from visual cortex. This idea suggests the hypothesis that irrelevant features of a natural scene should impair performance on a visual task only if their neural representations intrude on the linear readout of the task relevant feature, as would occur if the representations of task-relevant and irrelevant features are not orthogonal in the underlying neural population. We tested this hypothesis using human psychophysics and monkey neurophysiology, in response to parametrically variable naturalistic stimuli. We demonstrate that 1) the neural representation of one feature (the position of a central object) in visual area V4 is orthogonal to those of several background features, 2) the ability of human observers to precisely judge object position was largely unaffected by task-irrelevant variation in those background features, and 3) many features of the object and the background are orthogonally represented by V4 neural responses. Our observations are consistent with the hypothesis that orthogonal neural representations can support stable perception of objects and features despite the tremendous richness of natural visual scenes.

A general decoding strategy explains the relationship between behavior and correlated variability.

Improvements in perception are frequently accompanied by decreases in correlated variability in sensory cortex. This relationship is puzzling because overall changes in correlated variability should minimally affect optimal information coding. We hypothesize that this relationship arises because instead of using optimal strategies for decoding the specific stimuli at hand, observers prioritize generality: a single set of neuronal weights to decode any stimuli. We tested this using a combination of multineuron recordings in the visual cortex of behaving rhesus monkeys and a cortical circuit model. We found that general decoders optimized for broad rather than narrow sets of visual stimuli better matched the animals' decoding strategy, and that their performance was more related to the magnitude of correlated variability. In conclusion, the inverse relationship between perceptual performance and correlated variability can be explained by observers using a general decoding strategy, capable of decoding neuronal responses to the variety of stimuli encountered in natural vision.

Rapid remodeling of airway vascular architecture at birth.

Recent advances have documented the development of lung vasculature before and after birth, but less is known of the growth and maturation of airway vasculature. We sought to determine whether airway vasculature changes during the perinatal period and when the typical adult pattern develops. On embryonic day 16.5 mouse tracheas had a primitive vascular plexus unlike the adult airway vasculature, but instead resembling the yolk sac vasculature. Soon after birth (P0), the primitive vascular plexus underwent abrupt and extensive remodeling. Blood vessels overlying tracheal cartilage rings regressed from P1 to P3 but regrew from P4 to P7 to form the hierarchical, segmented, ladder-like adult pattern. Hypoxia and HIF-1α were present in tracheal epithelium over vessels that survived but not where they regressed. These findings reveal the plasticity of airway vasculature after birth and show that these vessels can be used to elucidate factors that promote postnatal vascular remodeling and maturation.

Capillary defects and exaggerated inflammatory response in the airways of EphA2-deficient mice.

Both Eph receptors and ephrin ligands have been implicated in blood vessel and neuronal development. Recent studies suggested that EphA2 inhibition reduces tumor angiogenesis, but its role in blood vessel development and inflammation is unclear. We examined these issues using either airways of pathogen-free, EphA2-deficient mice at various ages or EphA2-deficient mice whose airways were inflamed by either Mycoplasma pulmonis infection or ovalbumin sensitization and challenge. EphA2-deficient mice had fewer capillaries, a greater number of endothelial sprouts, and greater capillary diameters than age-matched, wild-type control mice. Moreover, capillaries in EphA2-deficient mice had significantly less pericyte coverage, suggesting abnormal interactions between endothelial cells and pericytes. These differences were apparent in early postnatal life but decreased during progression into adulthood. In inflamed airways, significantly more angiogenesis and lymphangiogenesis, a greater number of infiltrating leukocytes, and higher expression levels of inflammatory cytokine mRNA were present in EphA2-deficient mice after M. pulmonis infection. Additionally, in allergic airway inflammation with ovalbumin sensitization and challenge, a greater number of lymphatic sprouts and infiltrating leukocytes, higher mRNA expression levels of TH2 cytokines and chemokines related to allergic airway inflammation, and enhanced airway hyper-responsiveness were present in EphA2-deficient mice. We conclude that defective pericyte coverage causes capillary defects, abundant endothelial sprouts, and thick capillary diameters in EphA2-deficient mice, indicating that these animals have exaggerated responses to airway inflammation.

alpha5beta1 Integrin blockade inhibits lymphangiogenesis in airway inflammation.

The integrin alpha5beta1 has been previously implicated in tumor angiogenesis, but its role in the remodeling of both blood vessels and lymphatics during inflammation is at an early stage of understanding. We examined this issue using a selective, small-molecule inhibitor of alpha5beta1 integrin, 2-aroylamino-3-{4-[(pyridin-2-ylaminomethyl)heterocyclyl]phenyl}propionic acid (JSM8757), in a model of sustained airway inflammation in mice with Mycoplasma pulmonis infection, which is known to be accompanied by robust blood vessel remodeling and lymphangiogenesis. The inhibitor significantly decreased the proliferation of lymphatic endothelial cells in culture and the number of lymphatic sprouts and new lymphatics in airways of mice infected for 2 weeks but did not reduce remodeling of blood vessels in the same airways. In inflamed airways, alpha5 integrin immunoreactivity was present on lymphatic sprouts, but not on collecting lymphatics or blood vessels, and was not found on any lymphatics of normal airways. Macrophages, potential targets of the inhibitor, did not have alpha5 integrin immunoreactivity in inflamed airways. In addition, macrophage recruitment, assessed in infected airways by quantitative reverse transcription-polymerase chain reaction measurements of expression of the marker protein ionized calcium-binding adapter molecule 1 (Iba1), was not reduced by JSM8757. We conclude that inhibition of the alpha5beta1 integrin reduces lymphangiogenesis in inflamed airways after M. pulmonis infection because expression of the integrin is selectively increased on lymphatic sprouts and plays an essential role in lymphatic growth.

Electrical Microstimulation of Visual Cerebral Cortex Elevates Psychophysical Detection Thresholds.

Sensory prostheses can restore aspects of natural sensation by delivering electrical current directly into sensory circuits. An effective sensory prosthetic should be capable of generating reliable real-time perceptual signals for hours each day over many years. However, we still know little regarding the stability of percepts produced by electrical microstimulation of cerebral sensory cortex when stimulation is delivered repeatedly over long periods. Developing methods that yield highly sensitive and reliable assessments of a subject's sensitivity to stimulation is important for developing prosthetic devices that can mimic the constant stream of information inherent in daily experience. Here, we trained rhesus monkeys to report electrical microstimulation of their primary visual cortex (V1) and measured how repeated stimulation affected the minimal electrical current needed to generate a percept (behavioral detection threshold). Using adaptive staircase procedures with a two-alternative forced-choice (2AFC) detection task, we obtained highly reliable detection threshold measures with as few as 100 trials. Using either chronically implanted or acutely inserted microelectrodes, we found that repeated electrical microstimulation elevated detection thresholds, with effects persisting between daily testing sessions. Our results demonstrate task designs that can support rapid and reliable measurements of detection thresholds, and point to the need for validation that detection thresholds in targeted structures will be sufficiently stable in the face of the amount of chronic stimulation that will be required for effective sensory prosthetics.

Object-centered shifts of receptive field positions in monkey primary visual cortex.

Stimuli that project the same retinal visual angle can appear to occupy very different proportions of the visual field if they are perceived to be at different distances [1-8]. Previous research shows that perceived angular size alters the spatial distribution of activity in early retinotopic visual cortex [7, 9-11]. For example, a sphere superimposed on the far end of a corridor scene appears to occupy a larger visual angle and activates a larger region of primary visual cortex (V1) compared with the same sphere superimposed on the near end of the corridor [7]. These previous results, however, were obtained from human subjects using psychophysics and fMRI, a fact that fundamentally limits our understanding of the underlying neuronal mechanisms. Here, we present an animal model that allows for a finer examination of size perception at the level of single neurons. We first show that macaque monkeys perceive a size-distance illusion similarly to humans. Then, using extracellular recordings, we test the specific hypothesis [12] that neurons in V1 shift the position of their receptive fields (RFs) in response to complex monocular depth cues. Consistent with this hypothesis, we found that when ring-shaped stimuli appeared at the back of the corridor, RFs of V1 neurons shifted toward the center of the rings. When the same stimuli appeared at the front of the corridor, RFs shifted outward. Thus, our results show for the first time that V1 RFs can shift, potentially serving as the neural basis for the perception of angular size.

Insights into cortical mechanisms of behavior from microstimulation experiments.

Even the simplest behaviors depend on a large number of neurons that are distributed across many brain regions. Because electrical microstimulation can change the activity of localized subsets of neurons, it has provided valuable evidence that specific neurons contribute to particular behaviors. Here we review what has been learned about cortical function from behavioral studies using microstimulation in animals and humans. Experiments that examine how microstimulation affects the perception of stimuli have shown that the effects of microstimulation are usually highly specific and can be related to the stimuli preferred by neurons at the stimulated site. Experiments that ask subjects to detect cortical microstimulation in the absence of other stimuli have provided further insights. Although subjects typically can detect microstimulation of primary sensory or motor cortex, they are generally unable to detect stimulation of most of cortex without extensive practice. With practice, however, stimulation of any part of cortex can become detected. These training effects suggest that some patterns of cortical activity cannot be readily accessed to guide behavior, but that the adult brain retains enough plasticity to learn to process novel patterns of neuronal activity arising anywhere in cortex.

Tuned normalization explains the size of attention modulations.

The effect of attention on firing rates varies considerably within a single cortical area. The firing rate of some neurons is greatly modulated by attention while others are hardly affected. The reason for this variability across neurons is unknown. We found that the variability in attention modulation across neurons in area MT of macaques can be well explained by variability in the strength of tuned normalization across neurons. The presence of tuned normalization also explains a striking asymmetry in attention effects within neurons: when two stimuli are in a neuron's receptive field, directing attention to the preferred stimulus modulates firing rates more than directing attention to the nonpreferred stimulus. These findings show that much of the neuron-to-neuron variability in modulation of responses by attention depends on variability in the way the neurons process multiple stimuli, rather than differences in the influence of top-down signals related to attention.

Microstimulation reveals limits in detecting different signals from a local cortical region.

Behavioral performance depends on the activity of neurons in sensory cortex, but little is known about the brain's capacity to access specific neuronal signals to guide behavior. Even the individual sensory neurons that are most sensitive to a relevant stimulus are only weakly correlated with behavior, suggesting that behavioral decisions are based on the combined activity of groups of neurons with sensitivities well matched to task demands. To explore how flexibly different patterns of activity can be accessed from a given cortical region, we trained animals to detect electrical microstimulation of local V1 sites. By allowing the animals to become expert at the detection of microstimulation of specific V1 sites that corresponded to particular retinotopic locations, we could measure the effects of that training on the ability of those sites to support the detection of visual stimuli. Training to detect electrical activation caused a large, reversible, retinotopically localized impairment of thresholds for detecting visual stimuli. Retraining on visual detection restored normal thresholds and in turn impaired thresholds for detecting microstimulation. These results suggest that there are substantial limits to the types of signals for which a local cortical region can be simultaneously optimized.