Dataset Information

Exaggerated groups: amplification in ensemble coding of temporal and spatial features.

ABSTRACT: The human visual system represents summary statistical information (e.g. average) along many visual dimensions efficiently. While studies have indicated that approximately the square root of the number of items in a set are effectively integrated through this ensemble coding, how those samples are determined is still unknown. Here, we report that salient items are preferentially weighted over the other less salient items, by demonstrating that the perceived means of spatial (i.e. size) and temporal (i.e. flickering temporal frequency (TF)) features of the group of items are positively biased as the number of items in the group increases. This illusory 'amplification effect' was not the product of decision bias but of perceptual bias. Moreover, our visual search experiments with similar stimuli suggested that this amplification effect was due to attraction of visual attention to the salient items (i.e. large or high TF items). These results support the idea that summary statistical information is extracted from sets with an implicit preferential weighting towards salient items. Our study suggests that this saliency-based weighting may reflect a more optimal and efficient integration strategy for the extraction of spatio-temporal statistical information from the environment, and may thus be a basic principle of ensemble coding.

SUBMITTER: Kanaya S

PROVIDER: S-EPMC5998104 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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Publications

Exaggerated groups: amplification in ensemble coding of temporal and spatial features.

Kanaya Shoko S Hayashi Masamichi J MJ Whitney David D

Proceedings. Biological sciences 20180501 1879

The human visual system represents summary statistical information (e.g. average) along many visual dimensions efficiently. While studies have indicated that approximately the square root of the number of items in a set are effectively integrated through this ensemble coding, how those samples are determined is still unknown. Here, we report that salient items are preferentially weighted over the other less salient items, by demonstrating that the perceived means of spatial (i.e. size) and tempo ...[more]

PMID: 29794039

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Project description:BACKGROUND: Ensemble attribute profile clustering is a novel, text-based strategy for analyzing a user-defined list of genes and/or proteins. The strategy exploits annotation data present in gene-centered corpora and utilizes ideas from statistical information retrieval to discover and characterize properties shared by subsets of the list. The practical utility of this method is demonstrated by employing it in a retrospective study of two non-overlapping sets of genes defined by a published investigation as markers for normal human breast luminal epithelial cells and myoepithelial cells. RESULTS: Each genetic locus was characterized using a finite set of biological properties and represented as a vector of features indicating attributes associated with the locus (a gene attribute profile). In this study, the vector space models for a pre-defined list of genes were constructed from the Gene Ontology (GO) terms and the Conserved Domain Database (CDD) protein domain terms assigned to the loci by the gene-centered corpus LocusLink. This data set of GO- and CDD-based gene attribute profiles, vectors of binary random variables, was used to estimate multiple finite mixture models and each ensuing model utilized to partition the profiles into clusters. The resultant partitionings were combined using a unanimous voting scheme to produce consensus clusters, sets of profiles that co-occurred consistently in the same cluster. Attributes that were important in defining the genes assigned to a consensus cluster were identified. The clusters and their attributes were inspected to ascertain the GO and CDD terms most associated with subsets of genes and in conjunction with external knowledge such as chromosomal location, used to gain functional insights into human breast biology. The 52 luminal epithelial cell markers and 89 myoepithelial cell markers are disjoint sets of genes. Ensemble attribute profile clustering-based analysis indicated that both lists contained groups of genes with the functional properties of membrane receptor biology/signal transduction and nucleic acid binding/transcription. A subset of the luminal markers was associated with metabolic and oxidoreductase activities, whereas a subset of myoepithelial markers was associated with protein hydrolase activity. CONCLUSION: Given a set of genes and/or proteins associated with a phenomenon, process or system of interest, ensemble attribute profile clustering provides a simple method for collating and sythesizing the annotation data pertaining to them that are present in text-based, gene-centered corpora. The results provide information about properties common and unique to subsets of the list and hence insights into the biology of the problem under investigation.

Project description:UnlabelledWhen viruses infect their host cells, they can make defective virus-like particles along with intact virus. Cells coinfected with virus and defective particles often exhibit interference with virus growth caused by the competition for resources by defective genomes. Recent reports of the coexistence and cotransmission of such defective interfering particles (DIPs) in vivo, across epidemiological length and time scales, suggest a role in viral pathogenesis, but it is not known how DIPs impact infection spread, even under controlled culture conditions. Using fluorescence microscopy, we quantified coinfections of vesicular stomatitis virus (VSV) expressing a fluorescent reporter protein and its DIPs on BHK-21 host cell monolayers. We found that viral gene expression was more delayed, infections spread more slowly, and patterns of spread became more "patchy" with higher DIP inputs to the initial cell. To examine how infection spread might depend on the behavior of the initial coinfected cell, we built a computational model, adapting a cellular automaton (CA) approach to incorporate kinetic data on virus growth for the first time. Specifically, changes in observed patterns of infection spread could be directly linked to previous high-throughput single-cell measures of virus-DIP coinfection. The CA model also provided testable hypotheses on the spatial-temporal distribution of the DIPs, which remain governed by their predator-prey interaction. More generally, this work offers a data-driven computational modeling approach for better understanding of how single infected cells impact the multiround spread of virus infections across cell populations.ImportanceDefective interfering particles (DIPs) compete with intact virus, depleting host cell resources that are essential for virus growth and infection spread. However, it is not known how such competition, strong or weak, ultimately affects the way in which infections spread and cause disease. In this study, we address this unmet need by developing an integrated experimental-computational approach, which sheds new light on how infections spread. We anticipate that our approach will also be useful in the development of DIPs as therapeutic agents to manage the spread of viral infections.

Dataset Information

Exaggerated groups: amplification in ensemble coding of temporal and spatial features.

Publications

Exaggerated groups: amplification in ensemble coding of temporal and spatial features.

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