An empirical comparison of information-theoretic criteria in estimating the number of independent components of fMRI data

Background

Independent Component Analysis (ICA) has been widely applied to the analysis of fMRI data. Accurate estimation of the number of independent components of fMRI data is critical to reduce over/under fitting. Although various methods based on Information Theoretic Criteria (ITC) have been used to estimate the intrinsic dimension of fMRI data, the relative performance of different ITC in the context of the ICA model hasn''t been fully investigated, especially considering the properties of fMRI data. The present study explores and evaluates the performance of various ITC for the fMRI data with varied white noise levels, colored noise levels, temporal data sizes and spatial smoothness degrees.

Methodology

Both simulated data and real fMRI data with varied Gaussian white noise levels, first-order auto-regressive (AR(1)) noise levels, temporal data sizes and spatial smoothness degrees were carried out to deeply explore and evaluate the performance of different traditional ITC.

Principal Findings

Results indicate that the performance of ITCs depends on the noise level, temporal data size and spatial smoothness of fMRI data. 1) High white noise levels may lead to underestimation of all criteria and MDL/BIC has the severest underestimation at the higher Gaussian white noise level. 2) Colored noise may result in overestimation that can be intensified by the increase of AR(1) coefficient rather than the SD of AR(1) noise and MDL/BIC shows the least overestimation. 3) Larger temporal data size will be better for estimation for the model of white noise but tends to cause severer overestimation for the model of AR(1) noise. 4) Spatial smoothing will result in overestimation in both noise models.

Conclusions

1) None of ITC is perfect for all fMRI data due to its complicated noise structure. 2) If there is only white noise in data, AIC is preferred when the noise level is high and otherwise, Laplace approximation is a better choice. 3) When colored noise exists in data, MDL/BIC outperforms the other criteria.     

Intermittent Noise Induces Physiological Stress in a Coastal Marine Fish

Anthropogenic noise in the ocean has increased substantially in recent decades, and motorized vessels produce what is likely the most common form of underwater noise pollution. Noise has the potential to induce physiological stress in marine fishes, which may have negative ecological consequences. In this study, physiological effects of increased noise (playback of boat noise recorded in the field) on a coastal marine fish (the giant kelpfish, Heterostichus rostratus) were investigated by measuring the stress responses (cortisol concentration) of fish to increased noise of various temporal dynamics and noise levels. Giant kelpfish exhibited acute stress responses when exposed to intermittent noise, but not to continuous noise or control conditions (playback of recorded natural ambient sound). These results suggest that variability in the acoustic environment may be more important than the period of noise exposure for inducing stress in a marine fish, and provide information regarding noise levels at which physiological responses occur.     

The impact of stochasticity on the behaviour of nonlinear population models: synchrony and the Moran effect

Environmental variation is ubiquitous, but its effects on nonlinear population dynamics are poorly understood. Using simple (unstructured) nonlinear models we investigate the effects of correlated noise on the dynamics of two otherwise independent populations (the Moran effect), i.e. we focus on noise rather than dispersion or trophic interaction as the cause of population synchrony. We find that below the bifurcation threshold for periodic behaviour (1) synchrony between populations is strongly dependent on the shape of the noise distribution but largely insensitive to which model is studied, (2) there is, in general, a loss of synchrony as the noise is filtered by the model, (3) for specially structured noise distributions this loss can be effectively eliminated over a restricted range of distribution parameter values even though the model might be nonlinear, (4) for unstructured models there is no evidence of correlation enhancement, a mechanism suggested by Moran, but above the bifurcation threshold enhancement is possible for weak noise through phase-locking, (5) rapid desynchronisation occurs as the chaotic regime is approached. To carry out the investigation the stochastic models are (a) reformulated in terms of their joint asymptotic probability distributions and (b) simulated to analyse temporal patterns.     

Study on the mechanism of the appearance of noise effects

This study was undertaken to investigate the dose-response relationship between the biological effect and noise exposure, and to consider the mechanism of the appearance of noise effects. Rats were exposed to noise at intensities of 60 dB (A), 80 dB (A) and 100 dB (A) for 240 min and examined for the change of activities of dopamine-beta-hydroxylase (DBH) in serum and adrenal glands. Plasma cyclic adenosine 3',5'-monophosphate (c-AMP) levels were also measured. Some rats were given 6-hydroxydopamine (6-OHDA) as a chemical sympathectomyzing agent 20 h before noise exposure in order to consider the mechanism of the appearance of noise effects. By noise exposure, serum DBH activity was significantly (P less than 0.01) increased at each intensity compared with the control group, but there were no remarkable changes in adrenal DBH activity. Plasma c-AMP level was also significantly elevated in response to the noise stress. When the rats, which had been pretreated with 6-OHDA, were exposed to noise with an intensity of 100 dB (A), the response of serum DBH activity was no longer observed. Therefore it is suggested that the effect due to noise exposure appears through the post-ganglionic sympathetic nerve fiber.     

北京市3种配置模式绿化带降噪效果的空间变化规律

为明确不同配置模式绿化带对噪声衰减效果的空间变化规律,以北京市的刺槐(Robinia pseudoacacia Linn.)纯林(代表阔叶纯林)、刺槐-小花溲疏(Deutzia parviflora Bunge)混交林(代表阔叶混交林)和侧柏〔Platycladus orientalis(Linn.)Franco〕-圆柏〔Sabina chinensis(Linn.)Ant.〕混交林(代表针叶混交林)3类绿化带为研究对象,设置不同高度、距噪声源不同水平距离和不同噪声频率3组变量,对3类绿化带的降噪值进行比较分析.结果表明:3类绿化带的降噪效果由高至低依次为针叶混交林、阔叶混交林、阔叶纯林.在不同高度和距噪声源不同水平距离处,3类绿化带对不同频率噪声有各自的降噪优势;其中,在高度0.5和1.5 m处,阔叶混交林对250~1000 Hz噪声的衰减效果总体上优于阔叶纯林,而阔叶纯林对4000 Hz的噪声衰减效果却优于阔叶混交林,并且,针叶混交林对250、500、1000和8000 Hz噪声的衰减效果总体上优于阔叶纯林;整体上看,在距噪声源水平距离超过10 m处,3类绿化带对125~1000 Hz噪声的衰减效果最优.相关性分析结果表明:3类绿化带的降噪率与噪声频率呈负相关,与距噪声源水平距离和单位面积三维绿量总体上呈正相关.其中,在高度0.5、1.5和2.5 m处,3类绿化带的降噪率与噪声频率和距噪声源水平距离总体上显著相关;而在高度0.5和1.5 m处,3类绿化带的降噪率与单位面积三维绿量总体上显著相关.从3类绿化带的降噪规律看,在距噪声源水平距离相同的位置,高度越低,绿化带的降噪值越大,其中高度2.5 m以下绿化带的降噪值均较大;在相同高度上,距噪声源水平距离10和15 m处3类绿化带的降噪值总体上较大,但在距噪声源水平距离15和20 m处针叶混交林的降噪值明显大于其他2类绿化带.根据上述研究结果,建议绿化带宽度应在10 m以上,在配置绿化带时,应选择分枝点低、枝叶密度大的树种,且在不影响树木生长的条件下尽量密植并适度配置灌木.     

Experimental Chronic Noise Is Related to Elevated Fecal Corticosteroid Metabolites in Lekking Male Greater Sage-Grouse (Centrocercus urophasianus)

There is increasing evidence that individuals in many species avoid areas exposed to chronic anthropogenic noise, but the impact of noise on those who remain in these habitats is unclear. One potential impact is chronic physiological stress, which can affect disease resistance, survival and reproductive success. Previous studies have found evidence of elevated stress-related hormones (glucocorticoids) in wildlife exposed to human activities, but the impacts of noise alone are difficult to separate from confounding factors. Here we used an experimental playback study to isolate the impacts of noise from industrial activity (natural gas drilling and road noise) on glucocorticoid levels in greater sage-grouse (Centrocercus urophasianus), a species of conservation concern. We non-invasively measured immunoreactive corticosterone metabolites from fecal samples (FCMs) of males on both noise-treated and control leks (display grounds) in two breeding seasons. We found strong support for an impact of noise playback on stress levels, with 16.7% higher mean FCM levels in samples from noise leks compared with samples from paired control leks. Taken together with results from a previous study finding declines in male lek attendance in response to noise playbacks, these results suggest that chronic noise pollution can cause greater sage-grouse to avoid otherwise suitable habitat, and can cause elevated stress levels in the birds who remain in noisy areas.     

Voltage noise influences action potential duration in cardiac myocytes

Stochastic gating of ion channels introduces noise to membrane currents in cardiac muscle cells (myocytes). Since membrane currents drive membrane potential, noise thereby influences action potential duration (APD) in myocytes. To assess the influence of noise on APD, membrane potential is in this study formulated as a stochastic process known as a diffusion process, which describes both the current-voltage relationship and voltage noise. In this framework, the response of APD voltage noise and the dependence of response on the shape of the current-voltage relationship can be characterized analytically. We find that in response to an increase in noise level, action potential in a canine ventricular myocytes is typically prolonged and that distribution of APDs becomes more skewed towards long APDs, which may lead to an increased frequency of early after-depolarization formation. This is a novel mechanism by which voltage noise may influence APD. The results are in good agreement with those obtained from more biophysically-detailed mathematical models, and increased voltage noise (due to gating noise) may partially underlie an increased incidence of early after-depolarizations in heart failure.     

Evidence of suboscine song plasticity in response to traffic noise fluctuations and temporary road closures

This study investigates how noise reduction (road closure) mitigates the effect of traffic noise on the acoustic communication of the Eastern wood pewee (Contopus virens) (EAWP), a suboscine passerine. Songs were passively recorded at sites where the traffic pattern of the nearest road was either relatively constant or reduced on a weekly basis during a 36 h road closure. Five song attributes, low frequency traffic noise amplitude (LAeq) measured within 20 s of each song, and full-spectrum background noise levels (LAeq) characteristic of each territory were measured and analysed in order to better understand how EAWP respond to variation in traffic noise levels. EAWP adjusted its spectral song attributes by increasing song tonality to improve transmission in immediate response to fluctuations in traffic noise. The results suggest that song adjustments are responses to traffic noise levels at the time of their song, instead of the average background noise level measured per territory. This study provides a better understanding of how suboscine communication is affected by traffic noise, as well as the potential mitigating effect of noise reduction for animal acoustic communication.     

Hidden hearing loss is associated with loss of ribbon synapses of cochlea inner hair cells

The present study aimed to observe the changes in the cochlea ribbon synapses after repeated exposure to moderate-to-high intensity noise. Guinea pigs received 95 dB SPL white noise exposure 4 h a day for consecutive 7 days (we regarded it a medium-term and moderate-intensity noise, or MTMI noise). Animals were divided into four groups: Control, 1DPN (1-day post noise), 1WPN (1-week post noise), and 1MPN (1-month post noise). Auditory function analysis by auditory brainstem response (ABR) and compound action potential (CAP) recordings, as well as ribbon synapse morphological analyses by immunohistochemistry (Ctbp2 and PSD95 staining) were performed 1 day, 1 week, and 1 month after noise exposure. After MTMI noise exposure, the amplitudes of ABR I and III waves were suppressed. The CAP threshold was elevated, and CAP amplitude was reduced in the 1DPN group. No apparent changes in hair cell shape, arrangement, or number were observed, but the number of ribbon synapse was reduced. The 1WPN and 1MPN groups showed that part of ABR and CAP changes recovered, as well as the synapse number. The defects in cochlea auditory function and synapse changes were observed mainly in the high-frequency region. Together, repeated exposure in MTMI noise can cause hidden hearing loss (HHL), which is partially reversible after leaving the noise environment; and MTMI noise-induced HHL is associated with inner hair cell ribbon synapses.     

Does red noise increase or decrease extinction risk? Single extreme events versus series of unfavorable conditions

Recent theoretical studies have shown contrasting effects of temporal correlation of environmental fluctuations (red noise) on the risk of population extinction. It is still debated whether and under which conditions red noise increases or decreases extinction risk compared with uncorrelated (white) noise. Here, we explain the opposing effects by introducing two features of red noise time series. On the one hand, positive autocorrelation increases the probability of series of poor environmental conditions, implying increasing extinction risk. On the other hand, for a given time period, the probability of at least one extremely bad year ("catastrophe") is reduced compared with white noise, implying decreasing extinction risk. Which of these two features determines extinction risk depends on the strength of environmental fluctuations and the sensitivity of population dynamics to these fluctuations. If extreme (catastrophic) events can occur (strong noise) or sensitivity is high (overcompensatory density dependence), then temporal correlation decreases extinction risk; otherwise, it increases it. Thus, our results provide a simple explanation for the contrasting previous findings and are a crucial step toward a general understanding of the effect of noise color on extinction risk.     

Dispersal, colored environmental noise, and spatial synchrony in population dynamics: analyzing a discrete host–parasitoid population model

Spatial synchrony is common, and its influences and causes have attracted the interest of ecologists. Spatially correlated environmental noise, dispersal, and trophic interactions have been considered as the causes of spatial synchrony. In this study, we developed a spatially structured population model, which is described by coupled-map lattices. Our recent investigation showed that trophic correlation of environmental noise was another important factor that affects spatial synchrony. As a supplement, we considered the influence of the color of the environmental noise on the spatial synchrony in this study. The noise color refers to the temporal correlation in the time series data of the noise, and is expressed as the degree of (first-order) autocorrelation for autoregressive noise. Patterns of spatial synchrony were considered for stable, periodic (quasi-periodic), and chaotic population dynamics. Numerical simulations verified that the color of the environmental noise is another mechanism that causes spatial synchrony. Generally, the effect of the color of the noise on the synchrony is dependent on the type of dynamics (stable, cyclic, chaotic) present in the population. For cyclic dynamics, simulation results clearly demonstrate that reddened noise has higher synchrony than white noise. The importance of our research is that it enriches the theory of potential causes of spatial synchrony.     

A comparison of three noise reduction procedures applied to bird vocal signals

ABSTRACT.   Recordings of avian vocal signals in natural habitats include ambient noise. Often this background noise corrupts across all frequencies and is of substantial amplitude. Reducing this ambient noise to prepare vocal signals for playback stimuli or to remove habitat-specific noise signatures prior to analyzing a signal's acoustic characteristics can be useful. We conducted experimental evaluations of three noise reduction procedures to determine their effectiveness. We embedded two bird vocalizations ("clean" signals) in four kinds of natural noise, resulting in eight noise-signal combinations. We then applied three noise reduction procedures (Noise Profile, Band Pass, and Noise Estimate) to each of the embedded signals and compared the recovered signals to the original (clean) signals. Noise Profile filtering was effective in reducing noise and returning fairly high-quality signals from even severe levels of masking noise. The other two noise reduction procedures did not perform as well. For the two most corrupting maskers, however, Noise Profile filtering also altered the signal properties by reducing signal amplitude at those frequencies containing high levels of noise. Apart from this loss of amplitude, the quantitative features of the filtered signals were similar to those of the original model sounds. We conclude that Noise Profile filtering produces good results for cases where noise is approximately constant over the signal duration and the signal intensity exceeds noise intensity over the frequencies of interest.     

Molecular mechanism of spontaneous pigment activation in retinal cones

Spontaneous current and voltage fluctuations (dark noise) in the photoreceptor cells of the retina limit the ability of the visual system to detect dim light. We recorded the dark current noise of individual salamander L cones. Previous work showed that the dark noise in these cells arises from thermal activation of the visual pigment. From the temperature dependence of the rate of occurrence of elementary noise events, we found an Arrhenius activation energy E(a) of 25 +/- 7 kcal/mol (mean +/- SD). This E(a) is similar to that reported for the thermal isomerization of 11-cis retinal in solution, suggesting that the cone pigment noise results from isomerization of the retinal chromophore. E(a) for the cone noise is similar to that previously reported for the "photon-like" noise of rods, but the preexponential factor is five orders of magnitude higher. To test the hypothesis that thermal isomerization can only occur in molecules whose Schiff base linkage is unprotonated, we changed the pH of the solution bathing the cone outer segment. This had little effect on the rate of occurrence of elementary noise events. The rate was also unchanged when the cone was exposed to Ringer solution made up from heavy water, whose solvent isotope effect should reduce the probability, that the Schiff base nitrogen is naked.     

Influence of molecular noise on the growth of single cells and bacterial populations

During the last decades experimental studies have revealed that single cells of a growing bacterial population are significantly exposed to molecular noise. Important sources for noise are low levels of metabolites and enzymes that cause significant statistical variations in the outcome of biochemical reactions. In this way molecular noise affects biological processes such as nutrient uptake, chemotactic tumbling behavior, or gene expression of genetically identical cells. These processes give rise to significant cell-to-cell variations of many directly observable quantities such as protein levels, cell sizes or individual doubling times. In this study we theoretically explore if there are evolutionary benefits of noise for a growing population of bacteria. We analyze different situations where noise is either suppressed or where it affects single cell behavior. We consider two specific examples that have been experimentally observed in wild-type Escherichia coli cells: (i) the precision of division site placement (at which molecular noise is highly suppressed) and (ii) the occurrence of noise-induced phenotypic variations in fluctuating environments. Surprisingly, our analysis reveals that in these specific situations both regulatory schemes [i.e. suppression of noise in example (i) and allowance of noise in example (ii)] do not lead to an increased growth rate of the population. Assuming that the observed regulatory schemes are indeed caused by the presence of noise our findings indicate that the evolutionary benefits of noise are more subtle than a simple growth advantage for a bacterial population in nutrient rich conditions.     

Modeling Inter-trial Variability of Saccade Trajectories: Effects of Lesions of the Oculomotor Part of the Fastigial Nucleus

This study investigates the inter-trial variability of saccade trajectories observed in five rhesus macaques (Macaca mulatta). For each time point during a saccade, the inter-trial variance of eye position and its covariance with eye end position were evaluated. Data were modeled by a superposition of three noise components due to 1) planning noise, 2) signal-dependent motor noise, and 3) signal-dependent premotor noise entering within an internal feedback loop. Both planning noise and signal-dependent motor noise (together called accumulating noise) predict a simple S-shaped variance increase during saccades, which was not sufficient to explain the data. Adding noise within an internal feedback loop enabled the model to mimic variance/covariance structure in each monkey, and to estimate the noise amplitudes and the feedback gain. Feedback noise had little effect on end point noise, which was dominated by accumulating noise. This analysis was further extended to saccades executed during inactivation of the caudal fastigial nucleus (cFN) on one side of the cerebellum. Saccades ipsiversive to an inactivated cFN showed more end point variance than did normal saccades. During cFN inactivation, eye position during saccades was statistically more strongly coupled to eye position at saccade end. The proposed model could fit the variance/covariance structure of ipsiversive and contraversive saccades. Inactivation effects on saccade noise are explained by a decrease of the feedback gain and an increase of planning and/or signal-dependent motor noise. The decrease of the fitted feedback gain is consistent with previous studies suggesting a role for the cerebellum in an internal feedback mechanism. Increased end point variance did not result from impaired feedback but from the increase of accumulating noise. The effects of cFN inactivation on saccade noise indicate that the effects of cFN inactivation cannot be explained entirely with the cFN’s direct connections to the saccade-related premotor centers in the brainstem.     

Vitamin D2 protects acute and repeated noise stress induced behavioral,biochemical, and histopathological alterations: Possible antioxidant effect

Noise is an environmental stressor which causes distress and hearing loss in individuals residing in urban areas. Psychological deficits such as anxiety, depression, impaired memory and cognitive decline are caused by noise stress. Different vitamins have been used as a potential antioxidant for neuronal protection. In this study we investigate the anxiolytic, antidepressant and memory enhancing effect of vitamin D2 (Vit D2) following noise stress. Thirty-six albino rats were randomly divided into six groups. (i) Unstressed + corn oil (ii) Unstressed + Vit D2 (iii) Acute noise stress + corn oil (iv) Acute noise stress + Vit D2 (v) Repeated noise stress + corn oil (vi) Repeated noise stress + Vit D2. 600 IU/kg body weight of Vit D2 dosage was prepared in corn oil. Corn oil is used as vehicle and all the drugs administered via oral gavage till end of the experiment (day 16). Recorded sound of generator which was amplified by speakers and had 100 dB intensity was used as noise stress. Repeated stressed animals were exposed to noise (4-hrs) daily for 14 days, while acute stressed animals were exposed to noise (4-hrs) once after 14 days. Behavioral tests (elevated plus maze, light dark box, tail suspension test and Morris water maze) of all groups were performed after15 days treatment period. After behavioral tests rats received their last dosage and decapitated after 1-hr. Brain of all animals was removed and used for biochemical (oxidative stress biomarker, antioxidant enzymes and acetylcholinesterase) and histopathological estimations. Results show that Vit D2 decreased time spent in light box and open arm of light dark activity box and elevated plus maze test respectively (used for anxiety evaluation), decreased immobility time in tail suspension test (for depression) and improved cognitive ability evaluated by Morris water maze test in acute and repeated noise stressed rats. Furthermore, increased antioxidant enzymes activity, decreased lipid peroxidation and acetylcholinesterase activity were also observed in Vit D2 treated animals following acute and repeated noise stress. Normalization in histopathological studies was also observed in Vit D2 treated following acute and repeated noise stress. It is concluded that Vit D2 protects from noise stress induced behavioral, biochemical and histopathological impairment through its antioxidant potential.     

Anthropogenic noise pollution and wildlife diseases

There is a global rise in anthropogenic noise and a growing awareness of its negative effects on wildlife, but to date the consequences for wildlife diseases have received little attention. In this paper, we discuss how anthropogenic noise can affect the occurrence and severity of infectious wildlife diseases. We argue that there is potential for noise impacts at three main stages of pathogen transmission and disease development: (i) the probability of preinfection exposure, (ii) infection upon exposure, and (iii) severity of postinfection consequences. We identify potential repercussions of noise pollution effects for wildlife populations and call for intensifying research efforts. We provide an overview of knowledge gaps and outline avenues for future studies into noise impacts on wildlife diseases.     

Chemically induced K+ conduction noise in squid axon

Internal perfusion of tetraethylammonium ions (TEA) in squid axons produces a significant high frequency noise component. Although internal TEA suppresses the potassium conductance (G _K) noise at relatively low frequencies, it induces high frequency noise which exceeds the intensity of the normal potassium and sodium noise. In addition, the induced noise is dependent on the presence of internal potassium ions (K⁺) suggesting that this source of noise arises from a modulation of the K⁺ conductance due to the blocking and unblocking of the K⁺ channel. The simplest model describing the TEA data is a two-step sequential pseudo-unimolecular reaction where TEA binds during an open conductance state. A unit channel conductance of 2 pS is estimated from the TEA data as well as noise induced by triethyldecylammonium (TEDA) ions. Thus, these data are consistent with the hypothesis that the channel is blocked whenever the quaternary ammonium ion binding site, located near or within the K⁺ channel, is occupied.     

Vocal frequency change reflects different responses to anthropogenic noise in two suboscine tyrant flycatchers

Anthropogenic noise is prevalent across the globe and can exclude birds from otherwise suitable habitat and negatively influence fitness; however, the mechanisms responsible for species' responses to noise are not always clear. One effect of noise is a reduction in effective acoustic communication through acoustic masking, yet some urban songbirds may compensate for masking by noise through altering their songs. Whether this vocal flexibility accounts for species persistence in noisy areas is unknown. Here, we investigated the influence of noise on habitat use and vocal frequency in two suboscine flycatchers using a natural experiment that isolated effects of noise from confounding stimuli common to urban habitats. With increased noise exposure, grey flycatcher (Empidonax wrightii) occupancy declined, but vocal frequency did not change. By contrast, ash-throated flycatcher (Myiarchus cinerascens) occupancy was uninfluenced by noise, but individuals in areas with greater noise amplitudes vocalized at a higher frequency, although the increase (≈200 kHz) may only marginally improve communication and may represent a secondary effect from increased vocal amplitude. Even so, the different flycatcher behavioural responses suggest that signal change may help some species persist in noisy areas and prompt important questions regarding which species will cope with an increasingly noisy world.