Determination of Temporal Order among the Components of an Oscillatory System.
Ontology highlight
ABSTRACT:
SUBMITTER: Barragan S
PROVIDER: S-EPMC4495067 | biostudies-literature | 2015
REPOSITORIES: biostudies-literature
Publications
Determination of Temporal Order among the Components of an Oscillatory System.
Barragán Sandra S Rueda Cristina C Fernández Miguel A MA Peddada Shyamal D SD
PloS one 20150707 7
Oscillatory systems in biology are tightly regulated process where the individual components (e.g. genes) express in an orderly manner by virtue of their functions. The temporal order among the components of an oscillatory system may potentially be disrupted for various reasons (e.g. environmental factors). As a result some components of the system may go out of order or even cease to participate in the oscillatory process. In this article, we develop a novel framework to evaluate whether the te ...[more]
Similar Datasets
Project description:Many biological processes, such as cell cycle, circadian clock, menstrual cycles, are governed by oscillatory systems consisting of numerous components that exhibit rhythmic patterns over time. It is not always easy to identify such rhythmic components. For example, it is a challenging problem to identify circadian genes in a given tissue using time-course gene expression data. There is a great potential for misclassifying non-rhythmic as rhythmic genes and vice versa. This has been a problem of considerable interest in recent years. In this article we develop a constrained inference based methodology called Order Restricted Inference for Oscillatory Systems (ORIOS) to detect rhythmic signals. Instead of using mathematical functions (e.g. sinusoidal) to describe shape of rhythmic signals, ORIOS uses mathematical inequalities. Consequently, it is robust and not limited by the biologist's choice of the mathematical model. We studied the performance of ORIOS using simulated as well as real data obtained from mouse liver, pituitary gland and data from NIH3T3, U2OS cell lines. Our results suggest that, for a broad collection of patterns of gene expression, ORIOS has substantially higher power to detect true rhythmic genes in comparison to some popular methods, while also declaring substantially fewer non-rhythmic genes as rhythmic.A user friendly code implemented in R language can be downloaded from http://www.niehs.nih.gov/research/atniehs/labs/bb/staff/peddada/index.cfm CONTACT: peddada@niehs.nih.gov.
| S-EPMC5159537 | biostudies-literature
Project description:It is increasingly apparent that functionally significant neural activity is oscillatory in nature. Demonstrating the implications of this mode of operation for perceptual/cognitive function remains somewhat elusive. This report describes the technique of random temporal sampling for the investigation of visual oscillatory mechanisms. The technique is applied in visual recognition experiments using different stimulus classes (words, familiar objects, novel objects, and faces). Classification images reveal variations of perceptual effectiveness according to the temporal features of stimulus visibility. These classification images are also decomposed into their power and phase spectra. Stimulus classes lead to distinct outcomes and the power spectra of classification images are highly generalizable across individuals. Moreover, stimulus class can be reliably decoded from the power spectrum of individual classification images. These findings and other aspects of the results validate random temporal sampling as a promising new method to study oscillatory visual mechanisms.
| S-EPMC8556381 | biostudies-literature
Project description:INTRODUCTION:Determination of exercise oscillatory ventilation (EOV) is subjective, and the interreviewer agreement has not been reported. The purposes of this study were, among patients with heart failure (HF), as follows: 1) to determine the interreviewer agreement for EOV and 2) to describe a novel, objective, and quantifiable measure of EOV. METHODS:This was a secondary analysis of the HEART Camp: Promoting Adherence to Exercise in Patients with Heart Failure study. EOV was determined through a blinded review by six individuals on the basis of their interpretation of the EOV literature. Interreviewer agreement was assessed using Fleiss kappa (?). Final determination of EOV was based on agreement by four of the six reviewers. A new measure (ventilation dispersion index; VDI) was calculated for each test, and its ability to predict EOV was assessed with the receiver operator characteristics curve. RESULTS:Among 243 patients with HF (age, 60 ± 12 yr; 45% women), the interreviewer agreement for EOV was fair (? = 0.303) with 10-s discrete data averages and significantly better, but only moderate (? = 0.429) with 30-s rolling data averages. Prevalence rates of positive and indeterminate EOVs were 18% and 30% with the 10-s discrete averages and 14% and 13% with the 30-s rolling averages, respectively. VDI was strongly associated with EOV, with areas under the receiver operator characteristics curve of 0.852 to 0.890. CONCLUSIONS:Interreviewer agreement for EOV in patients with HF is fair to moderate, which can negatively affect risk stratification. VDI has strong predictive validity with EOV; as such, it might be a useful measure of prognosis in patients with HF.
| S-EPMC5772890 | biostudies-literature
Project description:Time has a fundamentally different character in quantum mechanics and in general relativity. In quantum theory events unfold in a fixed order while in general relativity temporal order is influenced by the distribution of matter. When matter requires a quantum description, temporal order is expected to become non-classical-a scenario beyond the scope of current theories. Here we provide a direct description of such a scenario. We consider a thought experiment with a massive body in a spatial superposition and show how it leads to entanglement of temporal orders between time-like events. This entanglement enables accomplishing a task, violation of a Bell inequality, that is impossible under local classical temporal order; it means that temporal order cannot be described by any pre-defined local variables. A classical notion of a causal structure is therefore untenable in any framework compatible with the basic principles of quantum mechanics and classical general relativity.
| S-EPMC6704104 | biostudies-literature
Project description:Episodic memory, an essential element of orderly thinking, requires the organization of serial events into narratives about the identity of cues along with their locations and temporal order (what, where, and when). The hippocampus plays a central role in the acquisition and retrieval of episodes with two of its subsystems being separately linked to what and where information. The substrates for the third element are poorly understood. Here we report that in hippocampal slices field CA3 maintains self-sustained activity for remarkable periods following a brief input and that this effect is extremely sensitive to minor network perturbations. Using behavioral tests, that do not involve training or explicit rewards, we show that partial silencing of the CA3 commissural/associational network in mice blocks acquisition of temporal order, but not the identity or location, of odors. These results suggest a solution to the question of how hippocampus adds time to episodic memories.
| S-EPMC6610080 | biostudies-literature
Project description:Incoming sensory input is condensed by our perceptual system to optimally represent and store information. In the temporal domain, this process has been described in terms of temporal windows (TWs) of integration/segregation, in which the phase of ongoing neural oscillations determines whether two stimuli are integrated into a single percept or segregated into separate events. However, TWs can vary substantially, raising the question of whether different TWs map onto unique oscillations or, rather, reflect a single, general fluctuation in cortical excitability (e.g., in the alpha band). We used multivariate decoding of electroencephalography (EEG) data to investigate perception of stimuli that either repeated in the same location (two-flash fusion) or moved in space (apparent motion). By manipulating the interstimulus interval (ISI), we created bistable stimuli that caused subjects to perceive either integration (fusion/apparent motion) or segregation (two unrelated flashes). Training a classifier searchlight on the whole channels/frequencies/times space, we found that the perceptual outcome (integration vs. segregation) could be reliably decoded from the phase of prestimulus oscillations in right parieto-occipital channels. The highest decoding accuracy for the two-flash fusion task (ISI = 40 ms) was evident in the phase of alpha oscillations (8-10 Hz), while the highest decoding accuracy for the apparent motion task (ISI = 120 ms) was evident in the phase of theta oscillations (6-7 Hz). These results reveal a precise relationship between specific TW durations and specific oscillations. Such oscillations at different frequencies may provide a hierarchical framework for the temporal organization of perception.
| S-EPMC5754799 | biostudies-other
Project description:IntroductionAlterations in narrow-band spectral power of electroencephalography (EEG) recordings are commonly reported in patients with schizophrenia (SZ). It is well established however that electrophysiological signals comprise a broadband scale-free (or fractal) component generated by mechanisms different from those producing oscillatory neural activity. Despite this known feature, it has not yet been investigated if spectral abnormalities found in SZ could be attributed to scale-free or oscillatory brain function.MethodsIn this study, we analyzed resting-state EEG recordings of 14 SZ patients and 14 healthy controls. Scale-free and oscillatory components of the power spectral density (PSD) were separated, and band-limited power (BLP) of the original (mixed) PSD, as well as its fractal and oscillatory components, was estimated in five frequency bands. The scaling property of the fractal component was characterized by its spectral exponent in two distinct frequency ranges (1-13 and 13-30 Hz).ResultsAnalysis of the mixed PSD revealed a decrease of BLP in the delta band in SZ over the central regions; however, this difference could be attributed almost exclusively to a shift of power toward higher frequencies in the fractal component. Broadband neural activity expressed a true bimodal nature in all except frontal regions. Furthermore, both low- and high-range spectral exponents exhibited a characteristic topology over the cortex in both groups.ConclusionOur results imply strong functional significance of scale-free neural activity in SZ and suggest that abnormalities in PSD may emerge from alterations of the fractal and not only the oscillatory components of neural activity.
| S-EPMC8119820 | biostudies-literature
Project description:BACKGROUND: Temporal sequence represents the main principle underlying episodic memory. The storage of temporal sequence information is thought to involve hippocampus-dependent memory systems, preserving temporal structure possibly via chaining of sequence elements in heteroassociative networks. Converging evidence indicates that sleep enhances the consolidation of recently acquired representations in the hippocampus-dependent declarative memory system. Yet, it is unknown if this consolidation process comprises strengthening of the temporal sequence structure of the representation as well, or is restricted to sequence elements independent of their temporal order. To address this issue we tested the influence of sleep on the strength of forward and backward associations in word-triplets. METHODOLOGY/PRINCIPAL FINDINGS: Subjects learned a list of 32 triplets of unrelated words, presented successively (A-B-C) in the center of a screen, and either slept normally or stayed awake in the subsequent night. After two days, retrieval was assessed for the triplets sequentially either in a forward direction (cueing with A and B and asking for B and C, respectively) or in a backward direction (cueing with C and B and asking for B and A, respectively). Memory was better for forward than backward associations (p<0.01). Sleep did not affect backward associations, but enhanced forward associations, specifically for the first (AB) transitions (p<0.01), which were generally more difficult to retrieve than the second transitions. CONCLUSIONS/SIGNIFICANCE: Our data demonstrate that consolidation during sleep strengthens the original temporal sequence structure in memory, presumably as a result of a replay of new representations during sleep in forward direction. Our finding suggests that the temporally directed replay of memory during sleep, apart from strengthening those traces, could be the key mechanism that explains how temporal order is integrated and maintained in the trace of an episodic memory.
| S-EPMC1849893 | biostudies-literature
Project description:Even though it is known that sleep benefits declarative memory consolidation, the role of sleep in the storage of temporal sequences has rarely been examined. Thus we explored the influence of sleep on temporal order in an episodic memory task followed by sleep or sleep deprivation. Thirty-four healthy subjects (17 men) aged between 19 and 28 years participated in the randomized, counterbalanced, between-subject design. Parameters of interests were NREM/REM cycles, spindle activity and spindle-related EEG power spectra. Participants of both groups (sleep group/sleep deprivation group) performed retrieval in the evening, morning and three days after the learning night. Results revealed that performance in temporal order memory significantly deteriorated over three days only in sleep deprived participants. Furthermore our data showed a positive relationship between the ratios of the (i) first NREM/REM cycle with more REM being associated with delayed temporal order recall. Most interestingly, data additionally indicated that (ii) memory enhancers in the sleep group show more fast spindle related alpha power at frontal electrode sites possibly indicating access to a yet to be consolidated memory trace. We suggest that distinct sleep mechanisms subserve different aspects of episodic memory and are jointly involved in sleep-dependent memory consolidation.
| S-EPMC3427018 | biostudies-literature
Project description:Neurophysiological field-potential signals consist of both arrhythmic and rhythmic patterns indicative of the fractal and oscillatory dynamics arising from likely distinct mechanisms. Here, we present a new method, namely the irregular-resampling auto-spectral analysis (IRASA), to separate fractal and oscillatory components in the power spectrum of neurophysiological signal according to their distinct temporal and spectral characteristics. In this method, we irregularly resampled the neural signal by a set of non-integer factors, and statistically summarized the auto-power spectra of the resampled signals to separate the fractal component from the oscillatory component in the frequency domain. We tested this method on simulated data and demonstrated that IRASA could robustly separate the fractal component from the oscillatory component. In addition, applications of IRASA to macaque electrocorticography and human magnetoencephalography data revealed a greater power-law exponent of fractal dynamics during sleep compared to wakefulness. The temporal fluctuation in the broadband power of the fractal component revealed characteristic dynamics within and across the eyes-closed, eyes-open and sleep states. These results demonstrate the efficacy and potential applications of this method in analyzing electrophysiological signatures of large-scale neural circuit activity. We expect that the proposed method or its future variations would potentially allow for more specific characterization of the differential contributions of oscillatory and fractal dynamics to distributed neural processes underlying various brain functions.
| S-EPMC4706469 | biostudies-literature