Biology subjects

Schmid, A. C.

Publications and source records attributed to Schmid, A. C..

4 recordsLinked to original sources

bioRxiv2020

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and their intriguing patterns of site specificity amidst the lack of dispersal limitation. Yet, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among the taxa that belong to recently discovered branches of microbial life. Here we assembled metagenomes from daily tongue and dental plaque samples from multiple individuals and reconstructed 790 non-redundant genomes, 43 of which resolved to TM7 that formed six monophyletic clades distinctly associated either with plaque or with tongue. Both pangenomic and phylogenomic analyses grouped tongue-specific TM7 clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 grouped together with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and the mobilome of the cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of human associated microbes. Additionally, we report that prophages are widespread amongst oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment.

microbiology↗

bioRxiv2020

Dynamic dot displays reveal material motion network in the human brain

There is growing research interest in the neural mechanisms underlying the recognition of material categories and properties. This research field, however, is relatively more recent and limited compared to investigations of the neural mechanisms underlying object and scene category recognition. Motion is particularly important for the perception of non-rigid materials, but the neural basis of non-rigid material motion remains unexplored. Using fMRI, we investigated which brain regions respond preferentially to material motion versus other types of motion. We introduce a new database of stimuli - dynamic dot materials - that are animations of moving dots that induce vivid percepts of various materials in motion, e.g. flapping cloth, liquid waves, wobbling jelly. Control stimuli were scrambled versions of these same animations and rigid three-dimensional rotating dots. Results showed that isolating material motion properties with dynamic dots (in contrast with other kinds of motion) activates a network of cortical regions in both ventral and dorsal visual pathways, including areas normally associated with the processing of surface properties and shape, and extending to somatosensory and premotor cortices. We suggest that such a widespread preference for material motion is due to strong associations between stimulus properties. For example viewing dots moving in a specific pattern not only elicits percepts of material motion; one perceives a flexible, non-rigid shape, identifies the object as a cloth flapping in the wind, infers the objects weight under gravity, and anticipates how it would feel to reach out and touch the material. These results are a first important step in mapping out the cortical architecture and dynamics in material-related motion processing.

neuroscience↗

bioRxiv2020

Material category determined by specular reflection structure mediates the processing of image features for perceived gloss

Recognising materials and their properties from visual information is vital for successful interactions with our environment, from avoiding slippery floors to handling fragile objects. Yet there is no simple mapping of retinal image intensities to the physical properties that define materials. While studies have investigated how material properties like surface gloss are perceived from regularities in image structure, such as the size, sharpness, contrast, and position of bright patches caused by specular reflections, little is known how this translates to the recognition of different material classes like plastic, pearl, satin, or steel, and the underlying mechanisms involved. We investigated this by collecting human psychophysical judgments about complex glossy objects rendered in natural illumination fields. We found that variations in specular image structure - produced either by different reflectance properties or direct manipulation of image features - caused categorical shifts in material appearance, suggesting that specular reflections provide diagnostic information about a wide range of material classes, including many that should be defined by more complex scattering functions. Moreover, differences in material category were predicted by, but also appeared to mediate, cues for surface gloss, providing evidence against a traditional feedforward view of neural processing that assumes combinations of mid-level properties mediate our holistic, categorical impressions. Instead, our results suggest that the image structure that triggers our perception of surface gloss plays a direct role in visual categorisation and, importantly, that the perception and neural processing of stimulus properties should not be studied in isolation but rather in the context of recognition.

neuroscience↗

bioRxiv2019

Visual perception of surprising materials in dynamic scenes

Many objects that we encounter have typical material qualities: spoons are hard, pillows are soft, and jell-O dessert is wobbly. Over a lifetime of experiences, strong associations between an object and its typical material properties may be formed, and these associations not only include how glossy, rough or pink an object is, but also how it behaves under force: we expect knocked over vases to shatter, popped bike tires to deflate, and gooey grilled cheese to hang between two slices of bread when pulled apart. Here we ask how such rich visual priors affect the visual perception of material qualities and present a particularly striking example of expectation violation. In a cue conflict design, we pair computer-rendered familiar objects with surprising material behaviors (a linen curtain shattering, a porcelain teacup wrinkling, etc.) and find that material qualities are not solely estimated from the objects kinematics (i.e. its physical (atypical) motion while shattering, wrinkling, wobbling etc.); rather, material appearance is sometimes "pulled" towards the "native" motion, shape, and optical properties that are associated with this object. Our results, in addition to patterns we find in response time data, suggest that visual priors about materials can set up high-level expectations about complex future states of an object and show how these priors modulate material appearance.

neuroscience↗