Biology subjects

Brainard, D.

Publications and source records attributed to Brainard, D..

5 recordsLinked to original sources

bioRxiv2020

What we talk about when we talk about color

Names for colors vary widely across languages, but color categories are remarkably consistent (Berlin & Kay, 1969). Shared mechanisms of color perception help explain consistent partitions of visible light into discrete color vocabularies (Regier et al., 2007). But the mappings from colors to words are not identical across languages, which may reflect communicative needs - how often speakers must refer to objects of different color (Gibson et al., 2017). Here we quantify the communicative needs of colors in 130 different languages by means of a novel inference algorithm. We find that communicative needs are not uniform: some regions of color space exhibit 30-fold greater demand for communication than other regions. The regions of greatest demand correlate with the colors of salient objects, including ripe fruits in primate diets. Our analysis also reveals a hidden diversity in the communicative needs of colors across different languages, which is partly explained by differences in geographic location and the local biogeography of linguistic communities. Accounting for language-specific, non-uniform communicative needs improves predictions for how a language maps colors to words, and how these mappings vary across languages. Our account closes an important gap in the compression theory of color naming, while opening new directions to study cross-cultural variation in the need to communicate different colors and its impact on the cultural evolution of color categories.

animal behavior and cognition↗

bioRxiv2018

Pervasive adaptation of hepatitis C virus to interferon lambda polymorphism across multiple genotypes

Genetic polymorphism in the interferon lambda (IFN-{lambda}) region is associated with spontaneous clearance of hepatitis C virus (HCV) infection and with response to interferon-based antiviral treatment. Here, we evaluate the associations between IFN- {lambda} polymorphism and HCV variation through a genome-to-genome analysis in 8,729 patients from diverse ancestral backgrounds infected with various HCV genotypes. We searched for associations between rs12979860 genotype, a tag for IFN-{lambda} haplotypes, and amino acid variants in the NS3, NS4A, NS5A and NS5B HCV proteins. We report multiple associations between host and pathogen variants in the full cohort as well as in subgroups defined by viral genotype and human ancestry. We also assess the combined impact of human and HCV variation on pre-treatment viral load. By demonstrating that IFN-{lambda} genetic variation leaves a large footprint in the viral genome, this study provides strong evidence of pervasive viral adaptation to host innate immune pressure during chronic HCV infection.

genomics↗

bioRxiv2018

The relative contribution of color and material in object selection

Information about color, material, texture and shape guide how we interact with objects. We developed a paradigm that quantifies how two object properties (color and material) combine in object selection. On each experimental trial, observers viewed three blob-shaped objects -- the target and two tests -- and selected the test that was more similar to the target. Across trials the target was fixed while the tests varied in color and material. We present a novel observer model that allows us to describe observers selection data in terms of (1) the underlying perceptual stimulus representation and (2) a color-material weight, which quantifies the relative importance of color vs. material in selection. We document large individual differences in the color-material weight. Furthermore, our analyses reveal limits on how precisely selection data simultaneously constrain perceptual representations and the color-material weight. These limits should guide future efforts towards understanding the multidimensional nature of object perception.

neuroscience↗

bioRxiv2018

Computational-Observer Analysis of Illumination Discrimination

The spectral properties of the ambient illumination provide useful information about time of day and weather. We study the perceptual representation of illumination by analyzing measurements of how well people discriminate between illuminations across scene configurations. More specifically, we compare human performance to a computational-observer analysis that evaluates the information available in the isomerizations of the cones in a model human photoreceptor mosaic. Some patterns of human performance are predicted by the computational observer, other aspects are not. The analysis clarifies which aspects of performance require additional explanation in terms of the action of visual mechanisms beyond the isomerization of light by the cones.

neuroscience↗

bioRxiv2017

Simulating retinal encoding: factors influencing Vernier acuity

Humans resolve the spatial alignment between two visual stimuli at a resolution that is substantially finer than the spacing between the foveal cones. In this paper, we analyze the factors that limit the information at the cone photoreceptors that is available to make these acuity judgments (Vernier acuity). We use open-source software, ISETBIO1 to quantify the stimulus and encoding stages in the front-end of the human visual system, starting with a description of the stimulus spectral radiance and a computational model that includes the physiological optics, inert ocular pigments, eye movements, photoreceptor sampling and absorptions. The simulations suggest that the visual system extracts the information available within the spatiotemporal pattern of photoreceptor absorptions within a small spatial (0.12 deg) and temporal (200 ms) regime. At typical display luminance levels, the variance arising from the Poisson absorptions and small eye movements (tremors and microsaccades) both appear to be critical limiting factors for Vernier acuity.

neuroscience↗