Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Basilar membrane responses to noise at a basal site of the chinchilla cochlea: quasi-linear filtering.

ABSTRACT: Basilar membrane responses to clicks and to white noise were recorded using laser velocimetry at basal sites of the chinchilla cochlea with characteristic frequencies near 10 kHz. Responses to noise grew at compressive rates and their instantaneous frequencies decreased with increasing stimulus level. First-order Wiener kernels were computed by cross-correlation of the noise stimuli and the responses. For linear systems, first-order Wiener kernels are identical to unit impulse responses. In the case of basilar membrane responses, first-order Wiener kernels and responses to clicks measured at the same sites were similar but not identical. Both consisted of transient oscillations with onset frequencies which increased rapidly, over about 0.5 ms, from 4-5 kHz to the characteristic frequency. Both first-order Wiener kernels and responses to clicks were more highly damped, exhibited slower frequency modulation, and grew at compressive rates with increasing stimulus levels. Responses to clicks had longer durations than the Wiener kernels. The statistical distribution of basilar membrane responses to Gaussian white noise is also Gaussian and the envelopes of the responses are Rayleigh distributed, as they should be for Gaussian noise passing through a linear band-pass filter. Accordingly, basilar membrane responses were accurately predicted by linear filters specified by the first-order Wiener kernels of responses to noise presented at the same level. Overall, the results indicate that cochlear nonlinearity is not instantaneous and resembles automatic gain control.

SUBMITTER: Recio-Spinoso A

PROVIDER: S-EPMC2774406 | biostudies-other | 2009 Dec

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Responses to sound of the basilar membrane of the mammalian cochlea.

Project description:Recent evidence shows that the frequency-specific non-linear properties of auditory nerve and inner hair cell responses to sound, including their sharp frequency tuning, are fully established in the vibration of the basilar membrane. In turn, the sensitivity, frequency selectivity and non-linear properties of basilar membrane responses probably result from an influence of the outer hair cells.

| S-EPMC3579517 | biostudies-literature

Molecular circuits for dynamic noise filtering.

Project description:The invention of the Kalman filter is a crowning achievement of filtering theory-one that has revolutionized technology in countless ways. By dealing effectively with noise, the Kalman filter has enabled various applications in positioning, navigation, control, and telecommunications. In the emerging field of synthetic biology, noise and context dependency are among the key challenges facing the successful implementation of reliable, complex, and scalable synthetic circuits. Although substantial further advancement in the field may very well rely on effectively addressing these issues, a principled protocol to deal with noise-as provided by the Kalman filter-remains completely missing. Here we develop an optimal filtering theory that is suitable for noisy biochemical networks. We show how the resulting filters can be implemented at the molecular level and provide various simulations related to estimation, system identification, and noise cancellation problems. We demonstrate our approach in vitro using DNA strand displacement cascades as well as in vivo using flow cytometry measurements of a light-inducible circuit in Escherichia coli.

| S-EPMC4855548 | biostudies-literature

Quasi noise-free digital holography.

Project description:One of the main drawbacks of Digital Holography (DH) is the coherent nature of the light source, which severely corrupts the quality of holographic reconstructions. Although numerous techniques to reduce noise in DH have provided good results, holographic noise suppression remains a challenging task. We propose a novel framework that combines the concepts of encoding multiple uncorrelated digital holograms, block grouping and collaborative filtering to achieve quasi noise-free DH reconstructions. The optimized joint action of these different image-denoising methods permits the removal of up to 98% of the noise while preserving the image contrast. The resulting quality of the hologram reconstructions is comparable to the quality achievable with non-coherent techniques and far beyond the current state of art in DH. Experimental validation is provided for both single-wavelength and multi-wavelength DH, and a comparison with the most used holographic denoising methods is performed.

| S-EPMC6059929 | biostudies-literature

Conserved role of Sonic Hedgehog in tonotopic organization of the avian basilar papilla and mammalian cochlea.

Project description:Sound frequency discrimination begins at the organ of Corti in mammals and the basilar papilla in birds. Both of these hearing organs are tonotopically organized such that sensory hair cells at the basal (proximal) end respond to high frequency sound, whereas their counterparts at the apex (distal) respond to low frequencies. Sonic hedgehog (Shh) secreted by the developing notochord and floor plate is required for cochlear formation in both species. In mice, the apical region of the developing cochlea, closer to the ventral midline source of Shh, requires higher levels of Shh signaling than the basal cochlea farther away from the midline. Here, gain-of-function experiments using Shh-soaked beads in ovo or a mouse model expressing constitutively activated Smoothened (transducer of Shh signaling) show up-regulation of apical genes in the basal cochlea, even though these regionally expressed genes are not necessarily conserved between the two species. In chicken, these altered gene expression patterns precede morphological and physiological changes in sensory hair cells that are typically associated with tonotopy such as the total number of stereocilia per hair cell and gene expression of an inward rectifier potassium channel, IRK1, which is a bona fide feature of apical hair cells in the basilar papilla. Furthermore, our results suggest that this conserved role of Shh in establishing cochlear tonotopy is initiated early in development by Shh emanating from the notochord and floor plate.

| S-EPMC4378437 | biostudies-literature

Direction of wave propagation in the cochlea for internally excited basilar membrane.

Project description:Otoacoustic emissions are an indicator of a normally functioning cochlea and as such are a useful tool for non-invasive diagnosis as well as for understanding cochlear function. While these emitted waves are hypothesized to arise from active processes and exit through the cochlear fluids, neither the precise mechanism by which these emissions are generated nor the transmission pathway is completely known. With regard to the acoustic pathway, two competing hypotheses exist to explain the dominant mode of emission. One hypothesis, the backward-traveling wave hypothesis, posits that the emitted wave propagates as a coupled fluid-structure wave while the alternate hypothesis implicates a fast, compressional wave in the fluid as the main mechanism of energy transfer. In this paper, we study the acoustic pathway for transmission of energy from the inside of the cochlea to the outside through a physiologically-based theoretical model. Using a well-defined, compact source of internal excitation, we predict that the emission is dominated by a backward traveling fluid-structure wave. However, in an active model of the cochlea, a forward traveling wave basal to the location of the force is possible in a limited region around the best place. Finally, the model does predict the dominance of compressional waves under a different excitation, such as an apical excitation.

| S-EPMC3386980 | biostudies-other

Inner-ear sound pressures near the base of the cochlea in chinchilla: further investigation.

Project description:The middle-ear pressure gain GMEP, the ratio of sound pressure in the cochlear vestibule PV to sound pressure at the tympanic membrane PTM, is a descriptor of middle-ear sound transfer and the cochlear input for a given stimulus in the ear canal. GMEP and the cochlear partition differential pressure near the cochlear base ΔPCP, which determines the stimulus for cochlear partition motion and has been linked to hearing ability, were computed from simultaneous measurements of PV, PTM, and the sound pressure in scala tympani near the round window PST in chinchilla. GMEP magnitude was approximately 30 dB between 0.1 and 10 kHz and decreased sharply above 20 kHz, which is not consistent with an ideal transformer or a lossless transmission line. The GMEP phase was consistent with a roughly 50-μs delay between PV and PTM. GMEP was little affected by the inner-ear modifications necessary to measure PST. GMEP is a good predictor of ΔPCP at low and moderate frequencies where PV >> PST but overestimates ΔPCP above a few kilohertz where PV ≈ PST. The ratio of PST to PV provides insight into the distribution of sound pressure within the cochlear scalae.

| S-EPMC3631268 | biostudies-other

High internal noise and poor external noise filtering characterize perception in autism spectrum disorder.

Project description:An emerging hypothesis postulates that internal noise is a key factor influencing perceptual abilities in autism spectrum disorder (ASD). Given fundamental and inescapable effects of noise on nearly all aspects of neural processing, this could be a critical abnormality with broad implications for perception, behavior, and cognition. However, this proposal has been challenged by both theoretical and empirical studies. A crucial question is whether and how internal noise limits perception in ASD, independently from other sources of perceptual inefficiency, such as the ability to filter out external noise. Here, we separately estimated internal noise and external noise filtering in ASD. In children and adolescents with and without ASD, we computationally modeled individuals' visual orientation discrimination in the presence of varying levels of external noise. The results revealed increased internal noise and worse external noise filtering in individuals with ASD. For both factors, we also observed high inter-individual variability in ASD, with only the internal noise estimates significantly correlating with severity of ASD symptoms. We provide evidence for reduced perceptual efficiency in ASD that is due to both increased internal noise and worse external noise filtering, while highlighting internal noise as a possible contributing factor to variability in ASD symptoms.

| S-EPMC5730555 | biostudies-literature

Operating regimes of signaling cycles: statics, dynamics, and noise filtering.

Project description:A ubiquitous building block of signaling pathways is a cycle of covalent modification (e.g., phosphorylation and dephosphorylation in MAPK cascades). Our paper explores the kind of information processing and filtering that can be accomplished by this simple biochemical circuit. Signaling cycles are particularly known for exhibiting a highly sigmoidal (ultrasensitive) input-output characteristic in a certain steady-state regime. Here, we systematically study the cycle's steady-state behavior and its response to time-varying stimuli. We demonstrate that the cycle can actually operate in four different regimes, each with its specific input-output characteristics. These results are obtained using the total quasi-steady-state approximation, which is more generally valid than the typically used Michaelis-Menten approximation for enzymatic reactions. We invoke experimental data that suggest the possibility of signaling cycles operating in one of the new regimes. We then consider the cycle's dynamic behavior, which has so far been relatively neglected. We demonstrate that the intrinsic architecture of the cycles makes them act--in all four regimes--as tunable low-pass filters, filtering out high-frequency fluctuations or noise in signals and environmental cues. Moreover, the cutoff frequency can be adjusted by the cell. Numerical simulations show that our analytical results hold well even for noise of large amplitude. We suggest that noise filtering and tunability make signaling cycles versatile components of more elaborate cell-signaling pathways.

| S-EPMC2230677 | biostudies-literature

Dynamic retrospective filtering of physiological noise in BOLD fMRI: DRIFTER.

Project description:In this article we introduce the DRIFTER algorithm, which is a new model based Bayesian method for retrospective elimination of physiological noise from functional magnetic resonance imaging (fMRI) data. In the method, we first estimate the frequency trajectories of the physiological signals with the interacting multiple models (IMM) filter algorithm. The frequency trajectories can be estimated from external reference signals, or if the temporal resolution is high enough, from the fMRI data. The estimated frequency trajectories are then used in a state space model in combination of a Kalman filter (KF) and Rauch-Tung-Striebel (RTS) smoother, which separates the signal into an activation related cleaned signal, physiological noise, and white measurement noise components. Using experimental data, we show that the method outperforms the RETROICOR algorithm if the shape and amplitude of the physiological signals change over time.

| S-EPMC3303954 | biostudies-literature

Optimal noise filtering in the chemotactic response of Escherichia coli.

Project description:Information-carrying signals in the real world are often obscured by noise. A challenge for any system is to filter the signal from the corrupting noise. This task is particularly acute for the signal transduction network that mediates bacterial chemotaxis, because the signals are subtle, the noise arising from stochastic fluctuations is substantial, and the system is effectively acting as a differentiator which amplifies noise. Here, we investigated the filtering properties of this biological system. Through simulation, we first show that the cutoff frequency has a dramatic effect on the chemotactic efficiency of the cell. Then, using a mathematical model to describe the signal, noise, and system, we formulated and solved an optimal filtering problem to determine the cutoff frequency that bests separates the low-frequency signal from the high-frequency noise. There was good agreement between the theory, simulations, and published experimental data. Finally, we propose that an elegant implementation of the optimal filter in combination with a differentiator can be achieved via an integral control system. This paper furnishes a simple quantitative framework for interpreting many of the key notions about bacterial chemotaxis, and, more generally, it highlights the constraints on biological systems imposed by noise.

| S-EPMC1636674 | 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