Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cell groups reveal structure of stimulus space.

ABSTRACT: An important task of the brain is to represent the outside world. It is unclear how the brain may do this, however, as it can only rely on neural responses and has no independent access to external stimuli in order to "decode" what those responses mean. We investigate what can be learned about a space of stimuli using only the action potentials (spikes) of cells with stereotyped -- but unknown -- receptive fields. Using hippocampal place cells as a model system, we show that one can (1) extract global features of the environment and (2) construct an accurate representation of space, up to an overall scale factor, that can be used to track the animal's position. Unlike previous approaches to reconstructing position from place cell activity, this information is derived without knowing place fields or any other functions relating neural responses to position. We find that simply knowing which groups of cells fire together reveals a surprising amount of structure in the underlying stimulus space; this may enable the brain to construct its own internal representations.

SUBMITTER: Curto C

PROVIDER: S-EPMC2565599 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Maps of protein structure space reveal a fundamental relationship between protein structure and function.

Project description:To study the protein structure-function relationship, we propose a method to efficiently create three-dimensional maps of structure space using a very large dataset of > 30,000 Structural Classification of Proteins (SCOP) domains. In our maps, each domain is represented by a point, and the distance between any two points approximates the structural distance between their corresponding domains. We use these maps to study the spatial distributions of properties of proteins, and in particular those of local vicinities in structure space such as structural density and functional diversity. These maps provide a unique broad view of protein space and thus reveal previously undescribed fundamental properties thereof. At the same time, the maps are consistent with previous knowledge (e.g., domains cluster by their SCOP class) and organize in a unified, coherent representation previous observation concerning specific protein folds. To investigate the function-structure relationship, we measure the functional diversity (using the Gene Ontology controlled vocabulary) in local structural vicinities. Our most striking finding is that functional diversity varies considerably across structure space: The space has a highly diverse region, and diversity abates when moving away from it. Interestingly, the domains in this region are mostly alpha/beta structures, which are known to be the most ancient proteins. We believe that our unique perspective of structure space will open previously undescribed ways of studying proteins, their evolution, and the relationship between their structure and function.

| S-EPMC3145735 | biostudies-literature

Structure and topology of band structures in the 1651 magnetic space groups.

Project description:The properties of electrons in magnetically ordered crystals are of interest both from the viewpoint of realizing novel topological phases, such as magnetic Weyl semimetals, and from the application perspective of creating energy-efficient memories. A systematic study of symmetry and topology in magnetic materials has been challenging given that there are 1651 magnetic space groups (MSGs). By using an efficient representation of allowed band structures, we obtain a systematic description of several basic properties of free electrons in all MSGs in three dimensions, as well as in the 528 magnetic layer groups relevant to two-dimensional magnetic materials. We compute constraints on electron fillings and band connectivity compatible with insulating behavior. In addition, by contrasting with atomic insulators, we identify band topology entailed by the symmetry transformation of bands, as determined by the MSG alone. We provide an application of our results to identifying topological semimetals arising in periodic arrangements of hedgehog-like magnetic textures.

| S-EPMC6070365 | biostudies-other

Combinatorial Neural Inhibition for Stimulus Selection across Space.

Project description:The ability to select the most salient among competing stimuli is essential for animal behavior and operates no matter which spatial locations stimuli happen to occupy. We provide evidence that the brain employs a combinatorially optimized inhibition strategy for selection across all pairs of stimulus locations. With experiments in a key inhibitory nucleus in the vertebrate midbrain selection network, called isthmi pars magnocellularis (Imc) in owls, we discovered that Imc neurons encode visual space with receptive fields that have multiple excitatory hot spots ("lobes"). Such multilobed encoding is necessitated by scarcity of Imc neurons. Although distributed seemingly randomly, the locations of these lobes are optimized across the high-firing Imc neurons, allowing them to combinatorially solve selection across space. This strategy minimizes metabolic and wiring costs, a principle that also accounts for observed asymmetries between azimuthal and elevational coding. Combinatorially optimized inhibition may be a general neural principle for efficient stimulus selection.

| S-EPMC6331182 | biostudies-literature

Snapshots of nascent RNA reveal cell- and stimulus-specific responses to acute kidney injury.

Project description:The current strategy to detect acute injury of kidney tubular cells relies on changes in serum levels of creatinine. Yet serum creatinine (sCr) is a marker of both functional and pathological processes and does not adequately assay tubular injury. In addition, sCr may require days to reach diagnostic thresholds, yet tubular cells respond with programs of damage and repair within minutes or hours. To detect acute responses to clinically relevant stimuli, we created mice expressing Rosa26-floxed-stop uracil phosphoribosyltransferase (Uprt) and inoculated 4-thiouracil (4-TU) to tag nascent RNA at selected time points. Cre-driven 4-TU-tagged RNA was isolated from intact kidneys and demonstrated that volume depletion and ischemia induced different genetic programs in collecting ducts and intercalated cells. Even lineage-related cell types expressed different genes in response to the 2 stressors. TU tagging also demonstrated the transient nature of the responses. Because we placed Uprt in the ubiquitously active Rosa26 locus, nascent RNAs from many cell types can be tagged in vivo and their roles interrogated under various conditions. In short, 4-TU labeling identifies stimulus-specific, cell-specific, and time-dependent acute responses that are otherwise difficult to detect with other technologies and are entirely obscured when sCr is the sole metric of kidney damage.

| S-EPMC8986083 | biostudies-literature

3D Chromosome Structure Can Reveal Stem Cell Signatures

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-01-20 | GSE126014 | GEO

Populations of auditory cortical neurons can accurately encode acoustic space across stimulus intensity.

Project description:The auditory cortex is critical for perceiving a sound's location. However, there is no topographic representation of acoustic space, and individual auditory cortical neurons are often broadly tuned to stimulus location. It thus remains unclear how acoustic space is represented in the mammalian cerebral cortex and how it could contribute to sound localization. This report tests whether the firing rates of populations of neurons in different auditory cortical fields in the macaque monkey carry sufficient information to account for horizontal sound localization ability. We applied an optimal neural decoding technique, based on maximum likelihood estimation, to populations of neurons from 6 different cortical fields encompassing core and belt areas. We found that the firing rate of neurons in the caudolateral area contain enough information to account for sound localization ability, but neurons in other tested core and belt cortical areas do not. These results provide a detailed and plausible population model of how acoustic space could be represented in the primate cerebral cortex and support a dual stream processing model of auditory cortical processing.

| S-EPMC2667094 | biostudies-literature

Adaptation to stimulus statistics in the perception and neural representation of auditory space.

Project description:Sensory systems are known to adapt their coding strategies to the statistics of their environment, but little is still known about the perceptual implications of such adjustments. We investigated how auditory spatial processing adapts to stimulus statistics by presenting human listeners and anesthetized ferrets with noise sequences in which interaural level differences (ILD) rapidly fluctuated according to a Gaussian distribution. The mean of the distribution biased the perceived laterality of a subsequent stimulus, whereas the distribution's variance changed the listeners' spatial sensitivity. The responses of neurons in the inferior colliculus changed in line with these perceptual phenomena. Their ILD preference adjusted to match the stimulus distribution mean, resulting in large shifts in rate-ILD functions, while their gain adapted to the stimulus variance, producing pronounced changes in neural sensitivity. Our findings suggest that processing of auditory space is geared toward emphasizing relative spatial differences rather than the accurate representation of absolute position.

| S-EPMC2938477 | biostudies-literature

Refined symmetry indicators for topological superconductors in all space groups.

Project description:Topological superconductors are exotic phases of matter featuring robust surface states that could be leveraged for topological quantum computation. A useful guiding principle for the search of topological superconductors is to relate the topological invariants with the behavior of the pairing order parameter on the normal-state Fermi surfaces. The existing formulas, however, become inadequate for the prediction of the recently proposed classes of topological crystalline superconductors. In this work, we advance the theory of symmetry indicators for topological (crystalline) superconductors to cover all space groups. Our main result is the exhaustive computation of the indicator groups for superconductors under a variety of symmetry settings. We further illustrate the power of this approach by analyzing fourfold symmetric superconductors with or without inversion symmetry and show that the indicators can diagnose topological superconductors with surface states of different dimensionalities or dictate gaplessness in the bulk excitation spectrum.

| S-EPMC7195178 | biostudies-literature

Emergence of spatial structure in cell groups and the evolution of cooperation.

Project description:On its own, a single cell cannot exert more than a microscopic influence on its immediate surroundings. However, via strength in numbers and the expression of cooperative phenotypes, such cells can enormously impact their environments. Simple cooperative phenotypes appear to abound in the microbial world, but explaining their evolution is challenging because they are often subject to exploitation by rapidly growing, non-cooperative cell lines. Population spatial structure may be critical for this problem because it influences the extent of interaction between cooperative and non-cooperative individuals. It is difficult for cooperative cells to succeed in competition if they become mixed with non-cooperative cells, which can exploit the public good without themselves paying a cost. However, if cooperative cells are segregated in space and preferentially interact with each other, they may prevail. Here we use a multi-agent computational model to study the origin of spatial structure within growing cell groups. Our simulations reveal that the spatial distribution of genetic lineages within these groups is linked to a small number of physical and biological parameters, including cell growth rate, nutrient availability, and nutrient diffusivity. Realistic changes in these parameters qualitatively alter the emergent structure of cell groups, and thereby determine whether cells with cooperative phenotypes can locally and globally outcompete exploitative cells. We argue that cooperative and exploitative cell lineages will spontaneously segregate in space under a wide range of conditions and, therefore, that cellular cooperation may evolve more readily than naively expected.

| S-EPMC2841614 | biostudies-literature

Symmetry-based indicators of band topology in the 230 space groups.

Project description:The interplay between symmetry and topology leads to a rich variety of electronic topological phases, protecting states such as the topological insulators and Dirac semimetals. Previous results, like the Fu-Kane parity criterion for inversion-symmetric topological insulators, demonstrate that symmetry labels can sometimes unambiguously indicate underlying band topology. Here we develop a systematic approach to expose all such symmetry-based indicators of band topology in all the 230 space groups. This is achieved by first developing an efficient way to represent band structures in terms of elementary basis states, and then isolating the topological ones by removing the subset of atomic insulators, defined by the existence of localized symmetric Wannier functions. Aside from encompassing all earlier results on such indicators, including in particular the notion of filling-enforced quantum band insulators, our theory identifies symmetry settings with previously hidden forms of band topology, and can be applied to the search for topological materials.Understanding the role of topology in determining electronic structure can lead to the discovery, or appreciation, of materials with exotic properties such as protected surface states. Here, the authors present a framework for identifying topologically distinct band-structures for all 3D space groups.

| S-EPMC5493703 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data