Dampened Oscillations Research Articles

Photoreceptor Layer Thickness Changes During Dark Adaptation Observed With Ultrahigh-Resolution Optical Coherence Tomography

PurposeTo examine outer retinal band changes after flash stimulus and subsequent dark adaptation with ultrahigh-resolution optical coherence tomography (UHR-OCT).MethodsFive dark-adapted left eyes of five normal subjects were imaged with 3-μm axial-resolution UHR-OCT during 30 minutes of dark adaptation following 96%, 54%, 23%, and 0% full-field and 54% half-field rhodopsin bleach. We identified the ellipsoid zone inner segment/outer segment (EZ[IS/OS]), cone interdigitation zone (CIZ), rod interdigitation zone (RIZ), retinal pigment epithelium (RPE), and Bruch's membrane (BM) axial positions and generated two-dimensional thickness maps of the EZ(IS/OS) to the four bands. The average thickness over an area of the thickness map was compared against that of the dark-adapted baselines. The time-dependent thickness changes (photoresponses) were statistically compared against 0% bleach. Dark adaptometry was performed with the same bleaching protocol.ResultsThe EZ(IS/OS)-CIZ photoresponse was significantly different at 96% (P < 0.0001) and 54% (P = 0.006) bleach. At all three bleaching levels, the EZ(IS/OS)-RIZ, -RPE, and -BM responses were significantly different (P < 0.0001). The EZ(IS/OS)-CIZ and EZ(IS/OS)-RIZ time courses were similar to the recovery of rod- and cone-mediated sensitivity, respectively, measured with dark adaptometry. The maximal EZ(IS/OS)-CIZ and EZ(IS/OS)-RIZ response magnitudes doubled from 54% to 96% bleach. Both EZ(IS/OS)-RPE and EZ(IS/OS)-BM responses resembled dampened oscillations that were graded in amplitude and duration with bleaching intensity. Half-field photoresponses were localized to the stimulated retina.ConclusionsWith noninvasive, near-infrared UHR-OCT, we characterized three distinct, spatially localized photoresponses in the outer retinal bands. These photoresponses have potential value as physical correlates of photoreceptor function.

Genetic algorithm learning in a New Keynesian macroeconomic setup

In order to understand heterogeneous behavior amongst agents, empirical data from Learning-to-Forecast (LtF) experiments can be used to construct learning models. This paper follows up on Assenza et al. (2013) by using a Genetic Algorithms (GA) model to replicate the results from their LtF experiment. In this GA model, individuals optimize an adaptive, a trend following and an anchor coefficient in a population of general prediction heuristics. We replicate experimental treatments in a New-Keynesian environment with increasing complexity and use Monte Carlo simulations to investigate how well the model explains the experimental data. We find that the evolutionary learning model is able to replicate the three different types of behavior, i.e. convergence to steady state, stable oscillations and dampened oscillations in the treatments using one GA model. Heterogeneous behavior can thus be explained by an adaptive, anchor and trend extrapolating component and the GA model can be used to explain heterogeneous behavior in LtF experiments with different types of complexity.

Characterisation, analysis of expression and localisation of circadian clock genes from the perspective of photoperiodism in the aphid Acyrthosiphon pisum

Aphids are typical photoperiodic insects that switch from viviparous parthenogenetic reproduction typical of long day seasons to oviparous sexual reproduction triggered by the shortening of photoperiod in autumn yielding an overwintering egg in which an embryonic diapause takes place. While the involvement of the circadian clock genes in photoperiodism in mammals is well established, there is still some controversy on their participation in insects. The availability of the genome of the pea aphid Acyrthosiphon pisum places this species as an excellent model to investigate the involvement of the circadian system in the aphid seasonal response. In the present report, we have advanced in the characterisation of the circadian clock genes and showed that these genes display extensive alternative splicing. Moreover, the expression of circadian clock genes, analysed at different moments of the day, showed a robust cycling of central clock genes period and timeless. Furthermore, the rhythmic expression of these genes was shown to be rapidly dampened under DD (continuous darkness conditions), thus supporting the model of a seasonal response based on a heavily dampened circadian oscillator. Additionally, increased expression of some of the circadian clock genes under short-day conditions suggest their involvement in the induction of the aphid seasonal response. Finally, in situ localisation of transcripts of genes period and timeless in the aphid brain revealed the site of clock neurons for the first time in aphids. Two groups of clock cells were identified: the Dorsal Neurons (DN) and the Lateral Neurons (LN), both in the protocerebrum.

Disruption to control network function correlates with altered dynamic connectivity in the wider autism spectrum.

Autism is a common developmental condition with a wide, variable range of co-occurring neuropsychiatric symptoms. Contrasting with most extant studies, we explored whole-brain functional organization at multiple levels simultaneously in a large subject group reflecting autism's clinical diversity, and present the first network-based analysis of transient brain states, or dynamic connectivity, in autism. Disruption to inter-network and inter-system connectivity, rather than within individual networks, predominated. We identified coupling disruption in the anterior-posterior default mode axis, and among specific control networks specialized for task start cues and the maintenance of domain-independent task positive status, specifically between the right fronto-parietal and cingulo-opercular networks and default mode network subsystems. These appear to propagate downstream in autism, with significantly dampened subject oscillations between brain states, and dynamic connectivity configuration differences. Our account proposes specific motifs that may provide candidates for neuroimaging biomarkers within heterogeneous clinical populations in this diverse condition.

Probing electrical tuning of hair cells with a Zap current method in the intact amphibian papilla of bullfrogs.

Most, if not all, modern vertebrate species have evolved exquisite inner ears to discriminate acoustic signals of different frequencies, through a process called frequency tuning. For non-mammalian species, at least part of frequency tuning has been attributed to intrinsic electrical properties of hair cells, i.e. electrical tuning. Since it was first discovered, the traditional method to assess electrical tuning has been to inject step current into hair cells and examine dampened membrane voltage oscillation. However, this method is not applicable for hair cells that do not oscillate. In this study, we developed a Zap current method that can be unbiasedly applied to all hair cells regardless of their oscillating behavior. Similar to a chirp sound in acoustic stimulation, a Zap current is a sinusoidal current with the frequency increased linearly with time. We first validated this new method with the traditional step current method on hair cells with dampened membrane voltage oscillation, and then applied it to all hair cells in the intact amphibian papilla of bullfrogs. We found that while hair cells with dampened membrane voltage oscillation are sharply tuned, non-oscillating hair cells are broadly tuned. In addition, we found a third type of hair cells, which oscillate continuously and are extremely sharply tuned, with multiple peaks that are reminiscent of harmonics in the mammalian cochlea. In conclusion, the new Zap current method provides an unbiased way to assess electrical tuning, and it reveals an underappreciated heterogeneity of electrical tuning in the bullfrog amphibian papilla.

Repeatable Population Dynamics among Vesicular Stomatitis Virus Lineages Evolved under High Co-infection.

Parasites and hosts can experience oscillatory cycles, where the densities of these interacting species dynamically fluctuate through time. Viruses with different replication strategies can also interact to produce cyclical dynamics. Frequent cellular co-infection can select for defective-interfering particles (DIPs): “cheater” viruses with shortened genomes that interfere with intracellular replication of full-length (ordinary) viruses. DIPs are positively selected when rare because they out-replicate ordinary viruses during co-infection, but DIPs are negatively selected when common because ordinary viruses become unavailable for intracellular exploitation via cheating. Here, we tested whether oscillatory dynamics of ordinary viruses were similar across independently evolved populations of vesicular stomatitis virus (VSV). Results showed identical cyclical dynamics across populations in the first 10 experimental passages, which transitioned to repeatable dampened oscillations by passage 20. Genomic analyses revealed parallel molecular substitutions across populations, particularly novel mutations that became dominant by passage 10. Our study showed that oscillatory dynamics and molecular evolution of interacting viruses were highly repeatable in VSV populations passaged under frequent co-infection. Furthermore, our data suggested that frequent co-infection with DIPs caused lowered performance of full-length viruses, by reducing their population densities by orders of magnitude compared to reproduction of ordinary viruses during strictly clonal infections.

Car-Following and Lane-Changing Behavior Involving Heavy Vehicles:

This paper presents empirical findings on car-following and lane-changing behavior involving heavy vehicles; trajectory data from the next generation simulation program were used in the study. It was found that when following passenger cars, heavy vehicles tended to reduce speed variations caused by traffic disturbances and thereby dampened traffic oscillations. In contrast, passenger cars following heavy vehicles tended to amplify traffic disturbances, although with lower probability and magnitude compared with the dampening effect. Moreover, heavy vehicles tended to discourage lane changes, especially behind them. This finding has convoluted implications: although reduced lane changes can improve traffic stability by preventing or reducing disturbances, large gaps can persist behind heavy vehicles and contribute to underutilization of road capacity.

Path dependent coordination of expectations in asset pricing experiments: A behavioral explanation

In the learning-to-forecast laboratory experiments in Hommes et al. (2005), three different types of aggregate asset price behavior have been observed: monotonic convergence to the stable fundamental steady state, dampened price oscillations and permanent price oscillations. We present a simple behavioral 2-type heuristics switching model explaining individual as well as aggregate behavior in the experiment. Based on relative performance, agents switch between a simple trend following and an anchor and adjustment heuristic that differ in how much weight is given to the long run average price level. The nonlinear switching model exhibits path dependence through co-existence of a locally stable fundamental steady state and a stable (quasi-)periodic orbit, created via a so-called Chenciner bifurcation. Depending on initial states, agents coordinate individual expectations either on a stable fundamental steady state path or on almost self-fulfilling persistent price fluctuations around the fundamental steady state.

Optimal weight based on energy imbalance and utility maximization

This paper investigates the optimal weight for both male and female using energy imbalance and utility maximization. Based on the difference of energy intake and expenditure, we develop a state equation that reveals the weight gain from this energy gap. We ​construct an objective function considering food consumption, eating habits and survival rate to measure utility. Through applying mathematical tools from optimal control methods and qualitative theory of differential equations, we obtain some results. For both male and female, the optimal weight is larger than the physiologically optimal weight calculated by the Body Mass Index (BMI). We also study the corresponding trajectories to steady state weight respectively. Depending on the value of a few parameters, the steady state can either be a saddle point with a monotonic trajectory or a focus with dampened oscillations.

Managing the Cayo Santiago rhesus macaque population: The role of density.

Cayo Santiago is the oldest continuously operating free-ranging rhesus monkey colony in the world. Population control of this colony has historically been carried out by periodic live capture and removal of animals. However, the effect of such a strategy on the size, growth rate, age structure, and sex ratio of the population has not been analyzed. This study reviews past removal data and uses a population projection model to simulate the effects of different removal schemes based on Cayo Santiago demographic data from 2000-2012. The model incorporates negative density-dependence in female fertility, as well as male and female survival rates, to determine the population-level effects of selective removal by age and sex. Modeling revealed that removal of sexually immature individuals has negligible effects on the population dynamics explaining why with an initial population of 1309 in 2000 and annual removals of immature monkeys a mean annual population growth rate of 12% and a final population size of ∼1,435 individuals by 2012 (∼0.009 animal/m(2) ) was observed. With no removals, the population is expected to exhibit dampened oscillations until reaching equilibrium at ∼1,690 individuals (∼0.0111 animal/m(2) ) in 2,100. In contrast, removal of adult females (≥4 yrs) would significantly reduce the population size, but would also promote an increase in population growth rate due to density feedback. A maximum annual production of 275 births is expected when 550 adult females are present in the population. Sensitivity analyses showed that removing females, in contrast to controlling their fertility through invasive treatments would contribute the most to changes in population growth rate. Given the density compensation on fertility, stabilizing the population would require removing ∼80% of the current population of adult females. This study highlights the importance of addressing the population-level density effects, as well as sensitivity analyses, to optimize management strategies.

Linking patterns and processes through ecosystem engineering: effects of shrubs on microhabitat and water status of associated plants in the high tropical Andes

Studies on alpine and semi-arid environments indicate that plants that act as ecosystem engineers improve microhabitat conditions and modify local plant abundance and diversity. However, few studies have linked these patterns with the physiological responses of associated species. We analyze the role of a dominant shrub (Hypericum laricifolium) as an ecosystem engineer in paramo ecosystems at two altitudes (3,715 and 4,300 m) in the Venezuelan Andes. Superficial soil temperatures, soil water content, and organic matter were compared under the crown and outside. We selected the species with positive and negative spatial relations with the shrub and compared their midday leaf water potentials and turgor loss points in individuals growing under shrubs and outside. Results show that H. laricifolium dampened temperature oscillations and increased soil water and organic matter contents, the effect being more pronounced at the drier, lower elevation site. While positively associated forbs showed an improvement in their water status when growing under the crown, the species with the lowest water potentials and higher water-stress tolerance were grasses with a negative spatial relation with the shrub; this was consistent at both elevations. Moreover, the effect of the shrub on the water status and abundance of the exotic herb Rumex acetosella changed from positive in the drier site to negative in the more mesic site. Our results provide mechanistic evidence for interpreting spatial association patterns between nurse plants and other species in the alpine tropics. We propose that stress-resistance strategies (tolerance vs. avoidance) and origin (native vs. exotic) influence interactions with ecosystem engineers.

Abstract LB-309: Interplay between E3 ligases modulate Per2 stability

Abstract Circadian oscillation relies on autoregulatory loops generated by sequential phases of transcription/translation, protein modification, and degradation. Interestingly, disruption of the clock gene period2 (per2) in mice is associated with a hyperplasic phenotype and loss of apoptotic response. When irradiated, per2 knockout mice show a significantly higher frequency of tumor development most likely due to loss of normal circadian control of genes concerned with the regulation of the DNA-damage response as well as partial resistance to radiation-induced apoptosis. Although evidence suggests that the per2 gene functions in tumor suppression, no mechanism of Per2 action is known. Our work show direct evidences of crosstalk mechanisms that involve Per2 and the oncogenic E3-ligase Mdm2. Whereas we know much about the role of b-TrCP in modulating the oscillatory levels of Per2 in the cell, the functional relevance of Mdm2 targeting of Per2 has just been uncovered. Bacterial two-hybrid screenings led to the identification of Mdm2 as a new PER2 binding partner, an interaction that was later validated by immunoprecipitation studies from both ectopicaly expressed and endogenous proteins. In vitro experiment show that recombinantly expressed Per2 serves as a substrate for Mdm2 and polyubiquitination takes place shortly after interaction. These results were later confirmed when Mdm2 was overexpressed and ubiquitination of Per2 was detected in immunoprecipitated samples. Interestingly, knock down of either beta-TrCP or Mdm2 dampened PER2 oscillation, although the mechanism by either E3 ligase seems to act relies in the subcellular localization of the substrate., Lastly, there is an interplay between these two ligases as we showed that downregulation of Mdm2 influences the total levels of beta-TrCP and direct interaction between these protein was confirmed by immunoprecipitation. Moreover, experiments carried out with constitutively negative active forms of each ligase show they are each other targeted for ubiquitination and that Per2 exerts a very relevant control on stability of b-TrCP by binding to Mdm2 and inhibiting its E3-ligase activity. Citation Format: jingjing liu, Carla V. Finkielstein. Interplay between E3 ligases modulate Per2 stability. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-309. doi:10.1158/1538-7445.AM2014-LB-309

Dampened hippocampal oscillations and enhanced spindle activity in an asymptomatic model of developmental cortical malformations.

Developmental cortical malformations comprise a large spectrum of histopathological brain abnormalities and syndromes. Their genetic, developmental and clinical complexity suggests they should be better understood in terms of the complementary action of independently timed perturbations (i.e., the multiple-hit hypothesis). However, understanding the underlying biological processes remains puzzling. Here we induced developmental cortical malformations in offspring, after intraventricular injection of methylazoxymethanol (MAM) in utero in mice. We combined extensive histological and electrophysiological studies to characterize the model. We found that MAM injections at E14 and E15 induced a range of cortical and hippocampal malformations resembling histological alterations of specific genetic mutations and transplacental mitotoxic agent injections. However, in contrast to most of these models, intraventricularly MAM-injected mice remained asymptomatic and showed no clear epilepsy-related phenotype as tested in long-term chronic recordings and with pharmacological manipulations. Instead, they exhibited a non-specific reduction of hippocampal-related brain oscillations (mostly in CA1); including theta, gamma and HFOs; and enhanced thalamocortical spindle activity during non-REM sleep. These data suggest that developmental cortical malformations do not necessarily correlate with epileptiform activity. We propose that the intraventricular in utero MAM approach exhibiting a range of rhythmopathies is a suitable model for multiple-hit studies of associated neurological disorders.

Entrainment of Spontaneously Hypertensive Rat Fibroblasts by Temperature Cycles

The functional state of the circadian system of spontaneously hypertensive rats (SHR) differs in several characteristics from the functional state of normotensive Wistar rats. Some of these changes might be due to the compromised ability of the central pacemaker to entrain the peripheral clocks. Daily body temperature cycles represent one of the important cues responsible for the integrity of the circadian system, because these cycles are driven by the central pacemaker and are able to entrain the peripheral clocks. This study tested the hypothesis that the aberrant peripheral clock entrainment of SHR results from a compromised peripheral clock sensitivity to the daily temperature cycle resetting. Using cultured Wistar rat and SHR fibroblasts transfected with the circadian luminescence reporter Bmal1-dLuc, we demonstrated that two consecutive square-wave temperature cycles with amplitudes of 2.5°C are necessary and sufficient to restart the dampened oscillations and entrain the circadian clocks in both Wistar rat and SHR fibroblasts. We also generated a phase response curve to temperature cycles for fibroblasts of both rat strains. Although some of the data suggested a slight resistance of SHR fibroblasts to temperature entrainment, we concluded that the overall effect it too weak to be responsible for the differences between the SHR and Wistar in vivo circadian phenotype.

Circadian rhythms in acute intermittent porphyria--a pilot study.

Acute intermittent porphyria (AIP) is an inherited disorder of haem synthesis wherein a partial deficiency of porphobilinogen (PBG) deaminase (PBGD) with other factors may give rise to biochemical and clinical manifestations of disease. The biochemical hallmarks of active AIP are relative hepatic haem deficiency and uncontrolled up-regulation of hepatic 5-aminolevulinic acid (ALA) synthase-1 (ALAS1) with over-production of ALA and PBG. The treatment of choice is intravenous haem, which restores the deficient regulatory haem pool of the liver and represses ALAS1. Recently, haem has been shown to influence circadian rhythms by controlling their negative feedback loops. We evaluated whether subjects with AIP exhibited an altered circadian profile. Over a 21-h period, we measured levels of serum cortisol, melatonin, ALA, PBG and mRNA levels (in peripheral blood mononuclear cells) of selected clock-controlled genes and genes involved in haem synthesis in 10 Caucasian (European-American) women who were either postmenopausal or had been receiving female hormone therapy, six of whom have AIP and four do not and are considered controls. Four AIP subjects with biochemical activity exhibited higher levels of PBG and lower levels and dampened oscillation of serum cortisol, and a trend for lower levels of serum melatonin, than controls or AIP subjects without biochemical activity. Levels of clock-controlled gene mRNAs showed significant increases over baseline in all subjects at 5 a.m. and 11 p.m., whereas mRNA levels of ALAS1, ALAS2 and PBGD were increased only at 11 p.m. in subjects with active AIP. This pilot study provides evidence for disturbances of circadian markers in women with active AIP that may trigger or sustain some common clinical features of AIP.

Author Reply: Coregulation is a State of a Temporal Interpersonal Emotion System

People in an emotional exchange form a temporal interpersonal emotion system (TIES), in which their emotions are interconnected over time (Butler, 2011). These systems can be in various states, defined by the pattern of emotional interconnections. We have defined coregulation as one such state involving coupled dampened oscillations between partners’ emotions that converge on a stable level. Coregulation could be distinguished from other states, such as stress buffering, by comparing statistical models that represent the theoretical distinctions between states. Optimal data for such modeling includes assessments of both partners’ emotions over time and a contrast between securely attached partners, strangers, and being alone. Research of this sort is needed to uncover the mechanisms by which emotional interdependence promotes well-being.

Modelling tides and sea-level rise: To flood or not to flood

It has been suggested in recent papers that even moderate sea-level rise (SLR) may have significant and unexpected effects on the tidal dynamics of the European Shelf. The response of the tidal amplitudes varied significantly between the studies, however. Here, it is shown that the way SLR is implemented in the tidal models used for the investigations causes significant differences between the results. When vertical walls are added at the present coastline, the changes are due to (subtly) changed properties of the propagating wave as the water depth is altered, whereas when flooding of existing land is allowed, the response is controlled by the newly introduced dissipation in the new cells. For example, the response of the Irish Sea is controlled by the flooding of estuaries, increasing the tidal amplitudes through the increased dissipation in the newly formed cells as explained by the dampened harmonic oscillator, whereas the North Sea is dominated by the flooding of the Dutch coast which shifts the areas of tidal energy dissipation from the present coastline to the new cells and thus moves the amphidromic points towards the coast. This is further supported by semi-analytical solutions to the Taylor problem. Identifying the processes which control the responses of shelf sea tides to SLR not only increase our knowledge about tidal systems, but also aids predictions of how other shelf sea systems will respond to future climate change.

Monte Carlo Study on the Water Meniscus Condensation and Capillary Force in Atomic Force Microscopy

The water meniscus condensed between a nanoscale tip and an atomically flat gold surface was examined under humid conditions using grand canonical Monte Carlo simulations. The molecular structure of the meniscus was investigated with particular focus on its width and stability. The capillary force due to the meniscus showed a dampened oscillation with increasing separation between the tip and surface because of the formation and destruction of water layers. The layering of water between the tip and the surface was different from that of the water confined between two plates. The humidity dependence of the capillary force exhibited a crossover behavior with increasing humidity, which is in agreement with the typical atomic force microscopy experiment on a hydrophilic surface.

A Mechanism for Circadian Control of Pacemaker Neuron Excitability

Although the intracellular molecular clocks that regulate circadian (~24 h) behavioral rhythms are well understood, it remains unclear how molecular clock information is transduced into rhythmic neuronal activity that in turn drives behavioral rhythms. To identify potential clock outputs, the authors generated expression profiles from a homogeneous population of purified pacemaker neurons (LN(v)s) from wild-type and clock mutant Drosophila. They identified a group of genes with enriched expression in LN(v)s and a second group of genes rhythmically expressed in LN(v)s in a clock-dependent manner. Only 10 genes fell into both groups: 4 core clock genes, including period (per) and timeless (tim), and 6 genes previously unstudied in circadian rhythms. The authors focused on one of these 6 genes, Ir, which encodes an inward rectifier K(+) channel likely to regulate resting membrane potential, whose expression peaks around dusk. Reducing Ir expression in LN(v)s increased larval light avoidance and lengthened the period of adult locomotor rhythms, consistent with increased LN(v) excitability. In contrast, increased Ir expression made many adult flies arrhythmic and dampened PER protein oscillations. The authors propose that rhythmic Ir expression contributes to daily rhythms in LN(v) neuronal activity, which in turn feed back to regulate molecular clock oscillations.

Nonlinear features in protein circuitry

The noise involved in protein circuit can result in fluctuations in protein concentrations. Then we have explored the effect of such noise on the feedback loop between p53 and its repressor Mdm2, the negative feedback dynamics and oscillatory activities are presented. Recent experimental results show that under certain conditions, the activity of the average protein level of p53 behaves with dampened oscillation in response to DNA damage, and it has non-decaying oscillatory behavior in individual cells, and we show that the dampening is induced by intrinsic noise, namely the uncertainty associated with chemical kinetics in dealing with when and in what order reactions take place in the p53 system. Furthermore, the experimental results are reproduced in this paper.