Biology subjects

Yakovleva, A.

Publications and source records attributed to Yakovleva, A..

5 recordsLinked to original sources

bioRxiv2024

Visual field asymmetries in responses to ON and OFF pathway biasing stimuli

Recent reports suggest the ON and OFF pathways are differentially susceptible to selective vision loss in glaucoma. Thus, perimetric assessment of ON- and OFF-pathway function may serve as a useful diagnostic. However, this necessitates a developed understanding of normal ON/OFF pathway function around the visual field and as a function of input intensity. Here, using electroencephalography, we measured ON- and OFF-pathway biased contrast response functions in the upper and lower visual fields. Using the steady-state visually evoked potential paradigm, we flickered achromatic luminance probes according to a saw-tooth waveform, the fast-phase of which biased responses towards the ON or OFF pathways. Neural responses from the upper and lower visual fields were simultaneously measured using frequency tagging - probes in the upper visual field modulated at 3.75Hz, while those in the lower visual field modulated at 3Hz. We find that responses to OFF/decrements are larger than ON/increments, especially in the lower visual field. In the lower visual field, both ON and OFF responses were well described by a sigmoidal non-linearity. In the upper visual field, the ON pathway function was very similar to that of the lower, but the OFF pathway function showed reduced saturation and more cross-subject variability. Overall, this demonstrates that the relationship between the ON and OFF pathways depends on the visual field location and contrast level, potentially reflective of natural scene statistics.

neuroscience↗

bioRxiv2021

Neural Sources Underlying Visual Word Form Processing as Revealed by Steady State Visual Evoked Potentials (SSVEP)

EEG has been central to investigations of the time course of various neural functions underpinning visual word recognition. Recently the steady-state visual evoked potential (SSVEP) paradigm has been increasingly adopted for word recognition studies due to its high signal-to-noise ratio. Such studies, however, have been typically framed around a single source in the left ventral occipitotemporal cortex (vOT). Here, we combine SSVEP recorded from 16 adult native English speakers with a data-driven spatial filtering approach--Reliable Components Analysis (RCA)--to elucidate distinct functional sources with overlapping yet separable time courses and topographies that emerge when contrasting words with pseudofont visual controls. The first component topography was maximal over left vOT regions with an early latency (approximately 180 msec). A second component was maximal over more dorsal parietal regions with a longer latency (approximately 260 msec). Both components consistently emerged across a range of parameter manipulations including changes in the spatial overlap between successive stimuli, and changes in both base and deviation frequency. We then contrasted word-in-nonword and word-in-pseudoword to test the hierarchical processing mechanisms underlying visual word recognition. Results suggest that these hierarchical contrasts fail to evoke a unitary component that might be reasonably associated with lexical access.

neuroscience↗

bioRxiv2020

Patterns of within-host genetic diversity in SARS-CoV-2

Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1,181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within and between host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.

genomics↗

bioRxiv2018

Dynamics of contrast decrement and increment responses in human visual cortex

The goal of the present experiments was to determine whether electrophysiological response properties of the ON and OFF visual pathways observed in animal experimental models can be observed in human. Visual Evoked Potentials (VEPs) were recorded in response to equivalent magnitude contrast increments and decrements presented using sawtooth temporal waveforms at a temporal frequency of 2.73 Hz. VEP response waveforms and response spectra for incremental and decremental stimuli were analyzed as a function of stimulus size and visual field location in 68 healthy adult participants. VEP response were larger in amplitude and shorter in latency for contrast decrements than for contrast increments. The spatial tuning was narrower for contrast decrements than for contrast increments and responses were larger for displays that were scaled for cortical magnification. VEPs recorded at the scalp differ between contrast decrements and increments of equal Weber contrast in a fashion that parallels results from the early visual system of cats and monkeys. Because our assay allows differential detection of ON and OFF pathway activity in human, the approach may be useful in future work on disease detection and treatment monitoring.

neuroscience↗

bioRxiv2018

The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens.

The Network of Cancer Genes (NCG) is a manually curated repository of 2,372 genes whose somatic modifications have a known or predicted cancer driver role. These genes were collected from 275 publications, including two sources of known cancer genes and 273 cancer sequencing screens of 119 cancer types in 31 primary sites from 34,905 cancer donors. This represents a more than 1.5-fold increase in content as compared to the previous version. NCG also annotates properties of cancer genes, such as duplicability, evolutionary origin, RNA and protein expression, miRNA and protein interactions, protein function and essentiality. NCG is accessible at http://ncg.kcl.ac.uk/.

cancer biology↗