A robust platform for integrative spatial multi-omics analysis to map immune responses to SARS-CoV-2 infection in lung tissues.

The SARS-CoV-2 (COVID-19) virus has caused a devastating global pandemic of respiratory illness. To understand viral pathogenesis, methods are available for studying dissociated cells in blood, nasal samples, bronchoalveolar lavage fluid and similar, but a robust platform for deep tissue characterization of molecular and cellular responses to virus infection in the lungs is still lacking. We developed an innovative spatial multi-omics platform to investigate COVID-19-infected lung tissues. Five tissue-profiling technologies were combined by a novel computational mapping methodology to comprehensively characterize and compare the transcriptome and targeted proteome of virus infected and uninfected tissues. By integrating spatial transcriptomics data (Visium, GeoMx and RNAScope) and proteomics data (CODEX and PhenoImager HT) at different cellular resolutions across lung tissues, we found strong evidence for macrophage infiltration and defined the broader microenvironment surrounding these cells. By comparing infected and uninfected samples, we found an increase in cytokine signalling and interferon responses at different sites in the lung and showed spatial heterogeneity in the expression level of these pathways. These data demonstrate that integrative spatial multi-omics platforms can be broadly applied to gain a deeper understanding of viral effects on cellular environments at the site of infection and to increase our understanding of the impact of SARS-CoV-2 on the lungs.

Nonlinear Spatial Integration Underlies the Diversity of Retinal Ganglion Cell Responses to Natural Images.

How neurons encode natural stimuli is a fundamental question for sensory neuroscience. In the early visual system, standard encoding models assume that neurons linearly filter incoming stimuli through their receptive fields, but artificial stimuli, such as contrast-reversing gratings, often reveal nonlinear spatial processing. We investigated to what extent such nonlinear processing is relevant for the encoding of natural images in retinal ganglion cells in mice of either sex. We found that standard linear receptive field models yielded good predictions of responses to flashed natural images for a subset of cells but failed to capture the spiking activity for many others. Cells with poor model performance displayed pronounced sensitivity to fine spatial contrast and local signal rectification as the dominant nonlinearity. By contrast, sensitivity to high-frequency contrast-reversing gratings, a classical test for nonlinear spatial integration, was not a good predictor of model performance and thus did not capture the variability of nonlinear spatial integration under natural images. In addition, we also observed a class of nonlinear ganglion cells with inverse tuning for spatial contrast, responding more strongly to spatially homogeneous than to spatially structured stimuli. These findings highlight the diversity of receptive field nonlinearities as a crucial component for understanding early sensory encoding in the context of natural stimuli.SIGNIFICANCE STATEMENT Experiments with artificial visual stimuli have revealed that many types of retinal ganglion cells pool spatial input signals nonlinearly. However, it is still unclear how relevant this nonlinear spatial integration is when the input signals are natural images. Here we analyze retinal responses to natural scenes in large populations of mouse ganglion cells. We show that nonlinear spatial integration strongly influences responses to natural images for some ganglion cells, but not for others. Cells with nonlinear spatial integration were sensitive to spatial structure inside their receptive fields, and a small group of cells displayed a surprising sensitivity to spatially homogeneous stimuli. Traditional analyses with contrast-reversing gratings did not predict this variability of nonlinear spatial integration under natural images.

Linkage between retinal ganglion cell density and the nonuniform spatial integration across the visual field.

The ability to integrate visual information over space is a fundamental component of human pattern vision. Regardless of whether it is for detecting luminance contrast or for recognizing objects in a cluttered scene, the position of the target in the visual field governs the size of a window within which visual information is integrated. Here we analyze the relationship between the topographic distribution of ganglion cell density and the nonuniform spatial integration across the visual field. The extent of spatial integration for luminance detection (Ricco's area) and object recognition (crowding zone) are measured at various target locations. The number of retinal ganglion cells (RGCs) underlying Ricco's area or crowding zone is estimated by computing the product of Ricco's area (or crowding zone) and RGC density for a given target location. We find a quantitative agreement between the behavioral data and the RGC density: The variation in the sampling density of RGCs across the human retina is closely matched to the variation in the extent of spatial integration required for either luminance detection or object recognition. Our empirical data combined with the simulation results of computational models suggest that a fixed number of RGCs subserves spatial integration of visual input, independent of the visual-field location.

Ecological infrastructure planning of large river basin to promote nature conservation and ecosystem functions.

Ecological infrastructure (EI) planning can promote regional nature conservation efficiency and enhance ecosystem functions. Watershed-scale EI research is a research hotspot in landscape ecology. This study proposed a method framework to develop EI planning in large river basins based on the connectivity of ecological processes and the integrity of ecosystems in the whole basin, as well as the typical ecological problems in each sub-basin. The framework included three parts: determining the protective EI i.e. the spatial range of the watershed ecological networks; quantifying and mapping the functional EI i.e. the typical ecosystem functions within each sub-basin; and integrating ecological networks and key ecosystem function area into an EI planning based on their spatial overlap and functional synergy. The method framework was applied in the Yellow River Basin. Results showed that spatial range of ecological networks of the basin accounted for 35.8% of the study area. Key ecosystem function area including ecosystem function important area and ecosystem function improvement area accounted for 35.6%. Spatial overlay analysis of ecological networks and key ecosystem function areas showed that they overlap spatially and have synergistic effects functionally, but core habitats existed less human activities compared to key ecosystem function area. By integrating ecological networks and key ecosystem function areas, EI planning including four spatial types: water system, core habitat area, important area for ecological function maintenance, priority area for ecological function improvement. The corresponding protection and development measures were formulated. In addition, along with the improvement of ecosystem function in the basin, sediment content, sand transport and other indicators in Yellow River has been obviously improved. It indicated that the EI construction in the basin had positive significance for river governance. Results showed that the EI planning method could improve both the spatial accuracy of nature conservation in the watershed and promote the specific ecosystem functions. It is also applicable to river management and watershed territorial spatial planning in other large river basins.

Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics.

Single-cell technologies allow measuring chromatin accessibility and gene expression in each cell, but jointly utilizing both layers to map bona fide gene regulatory networks and enhancers remains challenging. Here, we generate independent single-cell RNA-seq and single-cell ATAC-seq atlases of the Drosophila eye-antennal disc and spatially integrate the data into a virtual latent space that mimics the organization of the 2D tissue using ScoMAP (Single-Cell Omics Mapping into spatial Axes using Pseudotime ordering). To validate spatially predicted enhancers, we use a large collection of enhancer-reporter lines and identify ~ 85% of enhancers in which chromatin accessibility and enhancer activity are coupled. Next, we infer enhancer-to-gene relationships in the virtual space, finding that genes are mostly regulated by multiple, often redundant, enhancers. Exploiting cell type-specific enhancers, we deconvolute cell type-specific effects of bulk-derived chromatin accessibility QTLs. Finally, we discover that Prospero drives neuronal differentiation through the binding of a GGG motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue.

Potential downside of high initial visual acuity.

Children who are treated for congenital cataracts later exhibit impairments in configural face analysis. This has been explained in terms of a critical period for the acquisition of normal face processing. Here, we consider a more parsimonious account according to which deficits in configural analysis result from the abnormally high initial retinal acuity that children treated for cataracts experience, relative to typical newborns. According to this proposal, the initial period of low retinal acuity characteristic of normal visual development induces extended spatial processing in the cortex that is important for configural face judgments. As a computational test of this hypothesis, we examined the effects of training with high-resolution or blurred images, and staged combinations, on the receptive fields and performance of a convolutional neural network. The results show that commencing training with blurred images creates receptive fields that integrate information across larger image areas and leads to improved performance and better generalization across a range of resolutions. These findings offer an explanation for the observed face recognition impairments after late treatment of congenital blindness, suggest an adaptive function for the acuity trajectory in normal development, and provide a scheme for improving the performance of computational face recognition systems.

Crowding and Binding: Not All Feature Dimensions Behave in the Same Way.

Humans often fail to identify a target because of nearby flankers. The nature and stages at which this crowding occurs are unclear, and whether crowding operates via a common mechanism across visual dimensions is unknown. Using a dual-estimation report (N = 42), we quantitatively assessed the processing of features alone and in conjunction with another feature both within and between dimensions. Under crowding, observers misreported colors and orientations (i.e., reported a flanker value instead of the target's value) but averaged the target's and flankers' spatial frequencies (SFs). Interestingly, whereas orientation and color errors were independent, orientation and SF errors were interdependent. These qualitative differences of errors across dimensions revealed a tight link between crowding and feature binding, which is contingent on the type of feature dimension. These results and a computational model suggest that crowding and misbinding are due to pooling across a joint coding of orientations and SFs but not of colors.

The optomotor response of the praying mantis is driven predominantly by the central visual field.

The optomotor response has been widely used to investigate insect sensitivity to contrast and motion. Several studies have revealed the sensitivity of this response to frequency and contrast, but we know less about the spatial integration underlying this response. Specifically, few studies have investigated how the horizontal angular extent of stimuli influences the optomotor response. We presented mantises with moving gratings of varying horizontal extents at three different contrasts in the central or peripheral regions of their visual fields. We assessed the relative effectivity of different regions to elicit the optomotor response and modelled the dependency of the response on the angular extent subtended by stimuli at these different regions. Our results show that the optomotor response is governed by stimuli in the central visual field and not in the periphery. The model also shows that in the central region, the probability of response increases linearly with increase in horizontal extent up to a saturation point. Furthermore, the dependency of the optomotor response on the angular extent of the stimulus is modulated by contrast. We discuss the implications of our results for different modes of stimulus presentation and for models of the underlying mechanisms of motion detection in the mantis.

Perception of wide-expanse symmetric patterns.

Humans are remarkably proficient at the task of distinguishing between symmetric and non-symmetric visual patterns. The neural mechanisms underlying this ability are still unclear. Here we examine symmetry perception along a dimension that can help place some constraints on the nature of these mechanisms. Specifically, we study whether and how human performance on the task of classifying patterns as bilaterally symmetric versus non-symmetric changes as a function of the spatial separation between the flanks. Working with briefly flashed stimuli that embody flank separations of 6 degrees to 54 degrees, we find that classification performance declines significantly with increasing inter-flank distance, but remains well above chance even at the largest separations. Response time registers a progressive increase as the space between the flanks expands. Baseline studies show that these performance changes cannot be attributed solely to reduced acuity in the visual periphery, or increased conduction times for relaying information from those locations. The findings argue for the need to adapt current feedforward models of symmetry perception to be more consistent with the empirical data, and also point to the possible involvement of recurrent processing, as suggested by recent computational results.

Constraints on integration of orthographic information across multiple stimuli: effects of contiguity, eccentricity, and attentional span.

Five flanked lexical decision experiments investigated the integration of information across spatially distinct letter strings. Experiment 1 found no significant difference between quadrigram flankers (e.g., CKRO ROCK CKRO) and double bigram flankers (e.g., CK RO ROCK CK RO). Experiment 2 varied the eccentricity of single bigram flankers and found that closer flankers generated greater effects. A combined analysis of these experiments revealed that the double bigram condition (Experiment 1) was less effective than the close single bigram condition (Experiment 2). Experiment 3 tested one explanation for this pattern - that the outer bigrams in the double bigram condition interfered with processing the inner bigrams, and that spatial integration only operates across adjacent stimuli. In Experiment 3, outer bigrams were now a repeat of the inner bigram (e.g., RO RO ROCK CK CK), and this repeated bigram condition was still found to be significantly less effective than single bigrams. Experiments 4 and 5 tested an alternative explanation whereby the addition of spatially distinct flanking stimuli increases the spread of spatial attention, hence reducing the impact of proximal flankers. In line with this explanation, we found no significant difference between repeated bigram flankers and a condition where only the inner bigram was related to the target (e.g., CA RO ROCK CK SH). We conclude that spatial integration processes only operate across the central target and proximal flankers, and that these effects are diluted by the increased spread of spatial attention caused by additional spatially distinct flankers.

Spatial integration of dendrites in fast-spiking basket cells.

Dendrites of fast-spiking basket cells (FS BCs) impact neural circuit functions in brain with both supralinear and sublinear integration strategies. Diverse spatial synaptic inputs and active properties of dendrites lead to distinct neuronal firing patterns. How the FS BCs with this bi-modal dendritic integration respond to different spatial dispersion of synaptic inputs remains unclear. In this study, we construct a multi-compartmental model of FS BC and analyze neuronal firings following simulated synaptic protocols from fully clustered to fully dispersed. Under these stimulation protocols, we find that supralinear dendrites dominate somatic firing of FS BC, while the preference for dispersing is due to sublinear dendrites. Moreover, we find that dendritic diameter and Ca2+-permeable AMPA conductance play an important role in it, while A-type K+ channel and NMDA conductance have little effect. The obtained results may give some implications for understanding dendritic computation.

The role of awareness in shaping responses in human visual cortex.

The visual cortex contains information about stimuli even when they are not consciously perceived. However, it remains unknown whether the visual system integrates local features into global objects without awareness. Here, we tested this by measuring brain activity in human observers viewing fragmented shapes that were either visible or rendered invisible by fast counterphase flicker. We then projected measured neural responses to these stimuli back into visual space. Visible stimuli caused robust responses reflecting the positions of their component fragments. Their neural representations also strongly resembled one another regardless of local features. By contrast, representations of invisible stimuli differed from one another and, crucially, also from visible stimuli. Our results demonstrate that even the early visual cortex encodes unconscious visual information differently from conscious information, presumably by only encoding local features. This could explain previous conflicting behavioural findings on unconscious visual processing.

Feature representation under crowding in macaque V1 and V4 neuronal populations.

Visual perception depends strongly on spatial context. A profound example is visual crowding, whereby the presence of nearby stimuli impairs the discriminability of object features. Despite extensive work on perceptual crowding and the spatial integrative properties of visual cortical neurons, the link between these two aspects of visual processing remains unclear. To understand better the neural basis of crowding, we recorded activity simultaneously from neuronal populations in V1 and V4 of fixating macaque monkeys. We assessed the information available from the measured responses about the orientation of a visual target both for targets presented in isolation and amid distractors. Both single neuron and population responses had less information about target orientation when distractors were present. Information loss was moderate in V1 and more substantial in V4. Information loss could be traced to systematic divisive and additive changes in neuronal tuning. Additive and multiplicative changes in tuning were more severe in V4; in addition, tuning exhibited other, non-affine transformations that were greater in V4, further restricting the ability of a fixed sensory readout strategy to extract accurate feature information across displays. Our results provide a direct test of crowding effects at different stages of the visual hierarchy. They reveal how crowded visual environments alter the spiking activity of cortical populations by which sensory stimuli are encoded and connect these changes to established mechanisms of neuronal spatial integration.

Cascaded normalizations for spatial integration in the primary visual cortex of primates.

Spatial integration of visual information is an important function in the brain. However, neural computation for spatial integration in the visual cortex remains unclear. In this study, we recorded laminar responses in V1 of awake monkeys driven by visual stimuli with grating patches and annuli of different sizes. We find three important response properties related to spatial integration that are significantly different between input and output layers: neurons in output layers have stronger surround suppression, smaller receptive field (RF), and higher sensitivity to grating annuli partially covering their RFs. These interlaminar differences can be explained by a descriptive model composed of two global divisions (normalization) and a local subtraction. Our results suggest suppressions with cascaded normalizations (CNs) are essential for spatial integration and laminar processing in the visual cortex. Interestingly, the features of spatial integration in convolutional neural networks, especially in lower layers, are different from our findings in V1.

Numerosity Perception in Peripheral Vision.

Peripheral vision has different functional priorities for mammals than foveal vision. One of its roles is to monitor the environment while central vision is focused on the current task. Becoming distracted too easily would be counterproductive in this perspective, so the brain should react to behaviourally relevant changes. Gist processing is good for this purpose, and it is therefore not surprising that evidence from both functional brain imaging and behavioural research suggests a tendency to generalize and blend information in the periphery. This may be caused by the balance of perceptual influence in the periphery between bottom-up (i.e., sensory information) and top-down (i.e., prior or contextual information) processing channels. Here, we investigated this interaction behaviourally using a peripheral numerosity discrimination task with top-down and bottom-up manipulations. Participants compared numerosity between the left and right peripheries of a screen. Each periphery was divided into a centre and a surrounding area, only one of which was a task relevant target region. Our top-down task modulation was the instruction which area to attend - centre or surround. We varied the signal strength by altering the stimuli durations i.e., the amount of information presented/processed (as a combined bottom-up and recurrent top-down feedback factor). We found that numerosity perceived in target regions was affected by contextual information in neighbouring (but irrelevant) areas. This effect appeared as soon as stimulus duration allowed the task to be reliably performed and persisted even at the longest duration (1 s). We compared the pattern of results with an ideal-observer model and found a qualitative difference in the way centre and surround areas interacted perceptually in the periphery. When participants reported on the central area, the irrelevant surround would affect the response as a weighted combination - consistent with the idea of a receptive field focused in the target area to which irrelevant surround stimulation leaks in. When participants report on surround, we can best describe the response with a model in which occasionally the attention switches from task relevant surround to task irrelevant centre - consistent with a selection model of two competing streams of information. Overall our results show that the influence of spatial context in the periphery is mandatory but task dependent.

Space-luminance crossmodal correspondences in domestic chicks.

Crossmodal correspondences are spontaneous associations of non-redundant information across different modalities. Infants and some non-human animals (i.e., chimpanzees, rhesus monkeys, and dogs) showed crossmodal correspondences like adult humans, suggesting a shared origin (at least among mammals) of such a phenomenon. Here we investigate visual-spatial crossmodal correspondences in a precocial avian species, i.e., the domestic chicken. Three-day-old chicks (n = 40) were presented with two (one in the left and one in the right hemispace of an arena) identical panels, either dyed black (low luminance) or white (high luminance). Chicks could circumnavigate either panel to obtain a food reward. Akin to humans, they preferentially chose the left side when presented with black panels and the right side when presented with white panels. The control group (n = 39), tested with grey panels, showed no spatial preference. In light of our results, we discuss crossmodal correspondences in terms of an early available mechanism widespread across different species.

Contrast adaptation improves spatial integration.

The effects of contrast adaptation and contrast area summation (spatial integration) were investigated using a contrast discrimination task. The task consisted of a target of variable size, and a pedestal with a fixed base contrast. Discrimination performance was examined for a condition in which the pedestal size was fixed, equal to the largest target size, and for a condition in which the pedestal size matched the target size and thus varied with it. Repeated performance of the task produced rapid within-session improvements for both conditions. For stimuli with a matching size of target and pedestal, the performance improved only for the larger targets, indicating the development of spatial integration, which was initially absent for these stimuli. However, the improvements were mostly temporary, and were not fully retained between subsequent daily sessions. The temporary nature of the sensitivity gains implies that they resulted, at least in part, from rapid adaptation to the stimulus contrast. We suggest that adaptation decorrelates and thus reduces the spatial noise generated by a high-contrast pedestal, leading to improved spatial integration (area summation) and better contrast sensitivity. A decorrelation model successfully predicted our experimental results.

A Skin-Inspired Artificial Mechanoreceptor for Tactile Enhancement and Integration.

Mechanoreceptors endow humans with the sense of touch by translating the external stimuli into coded spikes, inspiring the rise of artificial mechanoreceptor systems. However, to incorporate slow adaptive receptors-like pressure sensors with artificial neurons remains a challenge. Here we demonstrate an artificial mechanoreceptor by rationally integrating a polypyrrole-based resistive pressure sensor with a volatile NbOx memristor, to mimic the tactile sensation and perception in natural skin, respectively. The artificial mechanoreceptor enables the tactile sensory coding by converting the external mechanical stimuli into strength-modulated electrical spikes. Also, tactile sensation enhancement is achieved by processing the spike frequency characteristics with the pulse coupled neural network. Furthermore, the artificial mechanoreceptor can integrate signals from parallel sensor channels and encode them into unified electrical spikes, resembling the coding of intensity in tactile neural processing. These results provide simple and efficient strategies for constructing future bio-inspired electronic systems.

Higher-Order Conditioning in the Spatial Domain.

Spatial learning and memory, the processes through which a wide range of living organisms encode, compute, and retrieve information from their environment to perform goal-directed navigation, has been systematically investigated since the early twentieth century to unravel behavioral and neural mechanisms of learning and memory. Early theories about learning to navigate space considered that animals learn through trial and error and develop responses to stimuli that guide them to a goal place. According to a trial-and error learning view, organisms can learn a sequence of motor actions that lead to a goal place, a strategy referred to as response learning, which contrasts with place learning where animals learn locations with respect to an allocentric framework. Place learning has been proposed to produce a mental representation of the environment and the cartesian relations between stimuli within it-which Tolman coined the cognitive map. We propose to revisit some of the best empirical evidence of spatial inference in animals, and then discuss recent attempts to account for spatial inferences within an associative framework as opposed to the traditional cognitive map framework. We will first show how higher-order conditioning can successfully account for inferential goal-directed navigation in a variety of situations and then how vectors derived from path integration can be integrated via higher-order conditioning, resulting in the generation of higher-order vectors that explain novel route taking. Finally, implications to cognitive map theories will be discussed.

Nonlinear spatial integration in retinal bipolar cells shapes the encoding of artificial and natural stimuli.

The retina dissects the visual scene into parallel information channels, which extract specific visual features through nonlinear processing. The first nonlinear stage is typically considered to occur at the output of bipolar cells, resulting from nonlinear transmitter release from synaptic terminals. In contrast, we show here that bipolar cells themselves can act as nonlinear processing elements at the level of their somatic membrane potential. Intracellular recordings from bipolar cells in the salamander retina revealed frequent nonlinear integration of visual signals within bipolar cell receptive field centers, affecting the encoding of artificial and natural stimuli. These nonlinearities provide sensitivity to spatial structure below the scale of bipolar cell receptive fields in both bipolar and downstream ganglion cells and appear to arise at the excitatory input into bipolar cells. Thus, our data suggest that nonlinear signal pooling starts earlier than previously thought: that is, at the input stage of bipolar cells.