Bala, K. | bioRxiv Science

bioRxiv2022

SARS-CoV-2 Omicron Variant Wave in India: Advent, Phylogeny and Evolution

SARS-CoV-2 evolution has continued to generate variants, responsible for new pandemic waves locally and globally. Varying disease presentation and severity has been ascribed to inherent variant characteristics and vaccine immunity. This study analyzed genomic data from 305 whole genome sequences from SARS-CoV-2 patients before and through the third wave in India. Delta variant was responsible for disease in patients without comorbidity(97%), while Omicron BA.2 caused disease primarily in those with comorbidity(77%). Tissue adaptation studies brought forth higher propensity of Omicron variants to bronchial tissue than lung, contrary to observation in Delta variants from Delhi. Study of codon usage pattern distinguished the prevalent variants, clustering them separately, Omicron BA.2 isolated in February grouped away from December strains, and all BA.2 after December acquired a new mutation S959P in ORF1b (44.3% of BA.2 in the study) indicating ongoing evolution. Loss of critical spike mutations in Omicron BA.2 and gain of immune evasion mutations including G142D, reported in Delta but absent in BA.1, and S371F instead of S371L in BA.1 could possibly be due to evolutionary trade-off and explain very brief period of BA.1 in December 2021, followed by complete replacement by BA.2.

genomics↗

bioRxiv2019

Effect of Geometric Sharpness on Translucent Material Perception

When judging optical properties of a translucent object, humans often look at sharp geometric features such as edges and thin parts. Analysis of the physics of light transport shows that these sharp geometries are necessary for scientific imaging systems to be able to accurately measure the underlying material optical properties. In this paper, we examine whether human perception of translucency is likewise affected by the presence of sharp geometry, by confounding our perceptual inferences about an objects optical properties. We employ physically accurate simulations to create visual stimuli of translucent materials with varying shapes and optical properties under different illuminations. We then use these stimuli in psychophysical experiments, where human observers are asked to match an image of a target object by adjusting the material parameters of a match object with different geometric sharpness, lighting geometry, and 3D geometry. We find that the level of geometric sharpness significantly affects perceived translucency by the observers. These findings generalize across a few illuminations and object shapes. Our results suggest that the perceived translucency of an object depends on both the underlying material optical parameters and 3D shape. We also conduct analyses using computational metrics including (luminance-normalized) L2, structural similarity index (SSIM), and Michelson contrast. We find that these image metrics cannot predict perceptual results, suggesting low level image cues are not sufficient to explain our results.

neuroscience↗