Covariation Of Signals Research Articles

COCOA: coordinate covariation analysis of epigenetic heterogeneity

A key challenge in epigenetics is to determine the biological significance of epigenetic variation among individuals. We present Coordinate Covariation Analysis (COCOA), a computational framework that uses covariation of epigenetic signals across individuals and a database of region sets to annotate epigenetic heterogeneity. COCOA is the first such tool for DNA methylation data and can also analyze any epigenetic signal with genomic coordinates. We demonstrate COCOA’s utility by analyzing DNA methylation, ATAC-seq, and multi-omic data in supervised and unsupervised analyses, showing that COCOA provides new understanding of inter-sample epigenetic variation. COCOA is available on Bioconductor (http://bioconductor.org/packages/COCOA).

Functional connectivity and the sleep-deprived brain.

Resting state functional connectivity (rsFC) evaluated by detecting temporal co-variation of BOLD signals across multiple brain regions undergoes three major changes following sleep deprivation that indicate the occurrence of sleep intrusions; a loss of integration within networks like the default mode network as well as between networks like the salience and dorsal attention systems; a loss of segregation between networks, for example, between the dorsal attention and default mode networks; and an increase in global signal. Changes in vigilance affect rsFC and these likely occur in many scans involving persons with neuropsychiatric conditions. Ensuring "healthy" or "control" participants do not fall asleep in the scanner is increasingly acknowledged as a being important for proper inference in fMRI studies. Dynamic functional connectivity analyses evaluating the relative proportion of time spent in "low" or "high" arousal states during the well-rested state can predict propensity for vigilance decline when sleep deprived.

Why Do Males Use Multiple Signals? Insights From Measuring Wild Male Behavior Over Lifespans

Why animals commonly use multiple conspicuous and presumably costly signals is poorly understood. Tests of evolutionary hypotheses comprehensively covering the signalling repertoire in wild populations are crucial to establish biological relevance, yet are relatively rare. We tested a key hypothesis for the maintenance of multiple signals in a wild population of the lizard, Psammophilus dorsalis, specifically whether multiple signals are maintained as multiple messages directed at different receivers. In addition, we also examined patterns in covariation of signals as an initial test of an alternative hypothesis, that multiple signals may be maintained as redundant signals; such traits are proposed to convey and reinforce the same component of information and are expected to be strongly correlated. Breeding male P. dorsalis display from prominent rock perches within their territories, which overlap multiple female home ranges in rocky open habitats. We repeatedly measured the display behaviour, covering the entire signalling repertoire, of individually-tagged wild males on their territories over their lifespans. We quantified patterns of covariation in multiple traits and their relationship with multiple receiver contexts, specifically competitors, mates and predators. We also examined the association between male signalling and indices of lifetime fitness. Males commonly used multiple signals, including behavioural signals and a rare dynamic colour signal. These traits were strongly correlated and seemed largely directed towards females, suggesting that they were primarily maintained as redundant signals through female choice. However, other selection pressures also appeared to be important. One colour trait seemed to be directed at competitors, providing limited support to the multiple receiver hypothesis. Several traits were reduced in the presence of predators, suggesting that they carry the cost of increased predation risk. Thus, multiple selection pressures, primarily female choice and predation risk, appear to affect male signalling. Finally, signalling traits appeared to influence a measure of lifetime reproductive success, providing rare evidence for the biological relevance of signalling traits under natural contexts.

A high-sensitive nano-modified biosensor for dynamic monitoring of glutamate and neural spike covariation from rat cortex to hippocampal sub-regions

BackgroundHippocampus is a critical part of brain tissue involved in many cognitive neural activities. They are controlled by various neurotransmitters such as glutamate (Glu), and affected by electrophysiology. New methodHerein, we fabricated a 16-site (25μm in diameter) microelectrode array (MEA) biosensor applied in dual-mode tests including Glu and neural spike measurements. MethodsAll the 16 recording sites were electrodeposited with platinum nanoparticles (PtNPs) and 8 sites were used for electrical recording. Glutamate oxidase enzyme (Gluox) and 1,3-Phenylenediamine (mPD) layer were specially modified on the other 8 sites for Glu recording. The dual-mode MEA was implanted from cortex to hippocampus of anesthetized rat to record Glu content and firing rate. ResultsThe electrical sites showed much lower impedance. The Glu sites showed much higher sensitivity(7.807 pA/μM), and ideal selectivity to the major molecules in brain. The post calibration sensitivity (3.935 pA/μM) maintained on a positive level. Different Glu content peaks including cortex (18.32μM) and hippocampal CA1 (4.39μM), CA3 (10.16μM), dentate gyrus (DG, two layers: 5.36μM and 10.34μM) have detected. The corresponded firing rate was recorded, too. Comparison with existing methodsThis modification showed much lower impedance and much higher sensitivity. We obtained more neuron activities simultaneously by dual-mode recording. The covariation of Glu and neural spike signals was discovered in the specific hippocampus sub-region. ConclusionsThe covariation between Glu and firing rate changes were synchronous, and effected by regions. The dual-mode signals were useful to find the neurology disease mechanism.

Correlation plots of the Siberian Radioheliograph

The Siberian Solar Radio Telescope [Grechnev et al., 2011] is now being upgraded. The upgrading is aimed at providing the aperture synthesis imaging in the frequency range 4–8 GHz [Lesovoi et al., 2011, 2014] instead of the single-frequency direct imaging due to the Earth rotation. The first phase of the upgrading is a 48-antenna array — Siberian Radioheliograph. One type of radioheliograph data represents correlation plots [badary.iszf.irk.ru/srhCorrPlot.php]. In evaluating the covariation of two-level signals, these plots are sums of complex correlations, obtained for different antenna pairs. Bearing in mind that correlation of signals from an antenna pair is related to a spatial frequency, we can say that each value of the plot is an integral over a spatial spectrum. Limits of the integration are defined by a task. Only high spatial frequencies are integrated to obtain dynamics of compact sources. The whole spectrum is integrated to reach maximum sensitivity. We show that the covariation of two-level values accurate to Van Vleck correction is a correlation coefficient of these values.

Корреляционные кривые Сибирского радиогелиографа

The Siberian Solar Radio Telescope [Grechnev et al., 2011] is now being upgraded. The upgrading is aimed at providing the aperture synthesis imaging in the frequency range 4–8 GHz [Lesovoi et al., 2011, 2014] instead of the single-frequency direct imaging due to the Earth rotation. The first phase of the upgrading is a 48-antenna array — Siberian Radioheliograph. One type of radioheliograph data represents correlation plots [badary.iszf.irk.ru/srhCorrPlot.php]. In evaluating the covariation of two-level signals, these plots are sums of complex correlations, obtained for different antenna pairs. Bearing in mind that correlation of signals from an antenna pair is related to a spatial frequency, we can say that each value of the plot is an integral over a spatial spectrum. Limits of the integration are defined by a task. Only high spatial frequencies are integrated to obtain dynamics of compact sources. The whole spectrum is integrated to reach maximum sensitivity. We show that the covariation of two-level values accurate to Van Vleck correction is a correlation coefficient of these values.

Decomposition of spontaneous brain activity into distinct fMRI co-activation patterns

Recent fMRI studies have shown that analysis of the human brain's spontaneous activity may provide a powerful approach to reveal its functional organization. Dedicated methods have been proposed to investigate co-variation of signals from different brain regions, with the goal of revealing neuronal networks (NNs) that may serve specialized functions. However, these analysis methods generally do not take into account a potential non-stationary (variable) interaction between brain regions, and as a result have limited effectiveness. To address this, we propose a novel analysis method that uses clustering analysis to sort and selectively average fMRI activity time frames to produce a set of co-activation patterns. Compared to the established networks extracted with conventional analysis methods, these co-activation patterns demonstrate novel network features with apparent relevance to the brain's functional organization.

Completeness of the fossil record and the validity of sampling proxies at outcrop level

Abstract: Most studies of the adequacy of the fossil record have been carried out at a global or continental scale, and they have used sampling proxies that generally do not incorporate all aspects of sampling (i.e. rock volume, accessibility, effort). Nonetheless, such studies have identified positive correlations between apparent diversity and various sampling proxies. The covariation of fossil and rock record signals has been interpreted as evidence for bias or for a common cause, such as sea level change, or as evidence that the signals are in some ways redundant with each other. Here, we compare a number of proxies representing the three main aspects of sampling, (1) sedimentary rock volume, (2) rock accessibility and (3) worker effort, with palaeodiversity in a geographically and stratigraphically constrained data set, the marine Lower Jurassic outcrop of the Dorset and East Devon Coast. We find that the proxies for rock volume and accessibility do not correlate well with the other sampling proxies, nor with apparent diversity, suggesting that the total amount of sedimentary rock preserved does not influence apparent diversity at a local scale, that is, the rock record at outcrop has been sampled efficiently. However, we do find some correlations between apparent diversity and proxies for worker effort. The fact that the proxies do not correlate significantly with each other suggests that none can be regarded as an all‐encompassing sampling proxy that covers all aspects of bias. Further, the presence of some correlations between sampling proxies and diversity most probably indicates the bonanza effect, as palaeontologists have preferentially sampled the richest rock units.

Noise correlations improve response fidelity and stimulus encoding

Computation in the nervous system often relies on the integration of signals from parallel circuits with different functional properties. Correlated noise in these inputs can, in principle, have diverse and dramatic effects on the reliability of the resulting computations 1–8. Such theoretical predictions have rarely been tested experimentally because of a scarcity of preparations that permit measurement of both covariation of a neuron’s input signals and the effect of manipulating such covariation on a cell’s output. Here we introduce a new method to measure covariation of the excitatory and inhibitory inputs a cell receives. This method revealed strong correlated noise in the inputs to two types of retinal ganglion cell. Eliminating correlated noise without changing other input properties substantially decreased the accuracy with which a cell’s spike outputs encoded light inputs. Thus covariation of excitatory and inhibitory inputs can be a critical determinant of the reliability of neural coding and computation.

Methods of detecting rotating surge and stall based on group statistical treatment of centrifugal compressor regime parameters

It is noted that one of the most promising trends in the field of detecting turbocompressor stall and revelation of the signs that characterize different forms of the development of gas dynamic instability (stall and rotating surge) is the use of statistical processing methods and signals. A procedure is presented for using statistical functions for analyzing the nonstationary nature of compression in turbocompressors and revelation of signs of stall based on calculating covariation of signals of regime parameters. Results are provided for studies based on analyzing covariation of the signals of regime parameters for centrifugal compressors of different construction that demonstrate the suitability of this parameter for detecting the phenomenon of compression gas dynamic instability. The procedure proposed is used successfully in practice in the form of special software for stall signalers used in centrifugal compressor automation systems.