Biology subjects

Carrasco, C. D.

Publications and source records attributed to Carrasco, C. D..

3 recordsLinked to original sources

bioRxiv2024

Enhanced Working Memory Representations for Rare Events

Rare events (oddballs) produce a variety of enhanced physiological responses relative to frequent events (standards), including the P3b component of the event-related potential (ERP) waveform. Previous research has suggested that the P3b is related to working memory, which implies that working memory representations will be enhanced for rare stimuli. To test this hypothesis, we devised a modified oddball paradigm where a target disk was presented at one of 16 different locations, which were divided into rare and frequent sets. Participants made a binary response on each trial to report whether the target appeared in the rare set or the frequent set. As expected, the P3b was much larger for stimuli appearing at a location within the rare set. We also included occasional probe trials in which the subject reported the exact location of the target. Accuracy was higher for rare than frequent locations. In addition, memory reports on rare trials were more accurate in participants with larger P3b amplitudes on rare trials (although reports were not more accurate for trials with larger P3b amplitudes within participants). We also applied multivariate pattern analysis to the ERP data to "decode" the remembered location of the target. Decoding accuracy was greater for locations within the rare set than for locations within the frequent set. We then replicated and extended our behavioral findings in a follow-up experiment. These behavioral and electrophysiological results demonstrate that although both frequent and rare events are stored in working memory, working memory performance is enhanced for rare oddball events. Impact StatementFor many decades, researchers have observed that rare events elicit a broad range of physiological responses, and there has been much speculation about the functional significance of these responses. One such response is the P3b component, which is a large voltage deflection in scalp EEG recordings. Over 40 years ago, the P3b was hypothesized to reflect "context updating" (now often called "working memory updating"). However, there has been no direct evidence that working memory is actually enhanced for rare, P3b-eliciting events. In the present study, we found that both behavioral and electrophysiological measures of working memory were enhanced for rare events. However, it is not clear that the increased P3b-related brain activity actually caused the enhancement of working memory.

neuroscience↗

bioRxiv2023

Using Multivariate Pattern Analysis to Increase Effect Sizes for Event-Related Potential Analyses

Multivariate pattern analysis approaches can be applied to the topographic distribution of event-related potential (ERP) signals to decode subtly different stimulus classes, such as different faces or different orientations. These approaches are extremely sensitive, and it seems possible that they could also be used to increase effect sizes and statistical power in traditional paradigms that ask whether an ERP component differs in amplitude across conditions. To assess this possibility, we leveraged the open-source ERP CORE dataset and compared the effect sizes resulting from conventional univariate analyses of mean amplitude with two multivariate pattern analysis approaches (support vector machine decoding and the cross-validated Mahalanobis distance, both of which are easy to compute using open-source software). We assessed these approaches across seven widely studied ERP components (N170, N400, N2pc, P3b, lateral readiness potential, error related negativity, and mismatch negativity). Across all components, we found that multivariate approaches yielded effect sizes that were as large or larger than the effect sizes produced by univariate approaches. These results indicate that researchers could obtain larger effect sizes, and therefore greater statistical power, by using multivariate analysis of topographic voltage patterns instead of traditional univariate analyses in many ERP studies.

neuroscience↗

bioRxiv2023

An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster

Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive success, founder effects, and rapid genetic drift, but is important to retain adaptive potential and avoid inbreeding depression. To support broodstock management and selective breeding in cultured Pacific oysters (Crassostrea (Magallana) gigas), we developed an amplicon panel targeting 592 genomic regions and SNP variants with an average of 50 amplicons per chromosome. Target SNPs were selected based on elevated observed heterozygosity or differentiation in Pacific oyster populations in British Columbia (BC), Canada. The use of the panel for parentage applications was evaluated by genotyping three generations of oysters from a breeding program in BC (n = 181) and a set of families that were selected for Ostreid herpesvirus-1 (OSHV-1) resistance from the Molluscan Broodstock Program, a Pacific oyster breeding program in Oregon, USA (n = 136). Population characterization was evaluated using collections of wild, naturalized, farmed, or hatchery oysters sampled throughout the Northern Hemisphere (n = 190). Technical replicate samples showed high genotype concordance (97.5%; n = 68 replicates). Initial parentage analysis found instances of suspected pedigree and sample handling errors, demonstrating the panels value for quality control in breeding programs. Suspected null alleles were identified in parentage datasets and were found to reduce assignment success. Null alleles were largely population dependent, suggesting population-specific variation impacts target amplification. By taking an iterative approach, null alleles were identified using existing data without the need for pedigree information, and once null alleles were removed, assignments increased to 93.0% and 86.0% of possible assignments in the two breeding program datasets. A pipeline for analyzing the amplicon sequence data from sequencer output, amplitools, is also provided.

genetics↗