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765 results for “rhythm”
Phenology in the deep sea: Seasonal and tidal feeding rhythms in a keystone octocoral
<p>Biological rhythms are widely known in terrestrial and marine systems, where the behavior or function of organisms may be tuned to environmental variation over periods from minutes to seasons or longer. Although well characterized in coastal environments, phenology remains poorly understood in the deep sea. Here we characterized intra-annual dynamics of feeding activity for the deep-sea octocoral <em>Paragorgia</em> <em>arborea</em>. Hourly changes in polyp activity were quantified using a time-lapse camera deployed for a year on Sur Ridge (1230 m depth; Northeast Pacific). The relationship between feeding and environmental variables, including surface primary production, temperature, acoustic backscatter, current speed and direction, was evaluated. Feeding activity was highly seasonal, with a dormancy period identified between January and early April, reflecting seasonal changes in food availability as suggested by primary production and acoustic backscatter data. Moreover, feeding varied with tides, which likely affected food delivery through cyclic oscillation in current speed and direction. This study provides the first evidence of behavioral rhythms in a coral species at depth greater than 1km. Information on the feeding biology of this cosmopolitan deep-sea octocoral will contribute to a better understanding of how future environmental change may affect deep-sea coral communities and the ecosystem services they provide.</p>
Túngara frog call-timing decisions arise as internal rhythms interact with fluctuating chorus noise
<p>For chorusing males, optimally timing their calls relative to nearby rivals' calls and fluctuations in background chorus noise is crucial for reproductive success. A caller's acoustic environment will vary by chorus density and the properties of his chorus-mates' calls and will fluctuate unpredictably due to chorusing dynamics emerging among his chorus-mates. Thus, callers must continuously monitor moment-to-moment fluctuations in the acoustic scene they perceive at the chorus for advantageous times to call. In live experimental choruses, we investigated the factors influencing túngara frog call-timing responses to chorus-mates' calls on an interaction-by-interaction basis, revealing that intrinsic and extrinsic factors influenced call-timing decisions. Callers were more likely to overlap calls from smaller chorus-mates and chorus-mates at intermediate distances, as well as calls containing lower frequencies and exhibiting lower final amplitude minima. Consequently, variation among males in call properties led to variation in levels of call-interference received when calling in the same social environment. Additionally, callers were more likely to overlap chorus-mates' calls after experiencing extended periods of inhibition and were less likely to overlap synchronized chorus-mates' calls relative to single calls. In chorusing species, female choice is influenced by inter-caller dynamics, selecting for male call-timing strategies which, in turn, constitute the selective environment further refining these same strategies. Thus, understanding the specific factors driving call-timing decisions is essential for understanding how sexual selection operates in chorusing taxa.</p>
Data and Codes: Marmosets mutually compensate for differences in rhythms when coordinating vigilance
<p>Data and codes accompanying the article titled "Marmosets mutually compensate for differences in rhythms when coordinating vigilance".</p>
Crown morphology in Norway spruce (Picea abies [Karst.] L.) as adaptation to mountainous environments is associated with single nucleotide polymorphisms (SNPs) in genes regulating seasonal growth rhythm
Trees growing at high altitude or latitude have to be adapted, amongst others, to the lower temperatures, a shorter vegetation period, heavier snow load and frost desiccation. Association between molecular genetic markers and climatic variables may provide evidence for the genetic control of climatic adaptation. With increasing genomic resources, several genes with importance to climatic adaptation are identified over a wide range of tree species. Commonly, circadian clock genes are linked to the adaptation to lower temperatures and especially to a shortened vegetation period, as they are regulating metabolic and phenological processes in the day-night shift and seasonal change. Potentially adaptive "candidate" genes associated with latitudinal and elevational gradients were identified in several Picea spp. Before molecular markers became available to study climatic adaptation, phenotypic traits measured in natural populations and/or common garden studies were used to search for their association with climate variables. In Norway spruce, the crown architecture is the most noticeable trait associated with altitude and the related environment. The mountainous narrow-crowned morphotype is characterised by superior resistance to snow breakage in regions with heavy snow fall. In total, the crown shape was assessed in 765 individual trees from mountainous regions in the Thuringian Forest, the Ore Mountains (Saxony) and Harz Mountains (Lower-Saxony/Saxony-Anhalt), and they were genotyped at 44 single nucleotide polymorphisms (SNPs) in 24 adaptive trait related candidate genes. Six SNPs in three genes, APETALA 2-like 3 (AP2L3), GIGANTEA (GI), and mitochondrial transcription termination factor (mTERF) were associated with variation in crown shape. GI has previously been identified in angiosperms and gymnosperms to be associated with temperature and growth cessation. Our results showed that crown morphology in Norway spruce is associated with genetic markers which are putatively involved in the complex process of genetic adaptation to climatic conditions at high altitudes.
Figure 1 in Diversity rhythm in pontellid copepods (Pontellidae: Copepoda) from the Covelong coast pre- and post-COVID-19 lockdown, Bay of Bengal
Figure 1. Site of collection—Covelong beach, Chennai.
Circadian and circatidal rhythms of protein abundance in the California mussel (Mytilus californianus)
<p>Coastal habitats fluctuate with the 12.4 h tidal and 24 h light/dark cycle to predictably alter conditions such as air exposure, temperature, and food availability. Intertidal sessile bivalves exhibit behavioral and physiological adjustments to minimize the challenges of this environment. We investigated a high-resolution time course of the changes in protein abundance in the gill tissue of the intertidal mussel <i>Mytilus californianus</i> in a simulated tidal environment of 12:12 h light:dark cycles and a matching 6:6 h high:low tide cycle within each 12 h period. Approximately 38% of detected proteins showed significant rhythms in their abundances, with diversity in the phases of rhythmic isoforms. The circadian rhythm was dominant in protein abundance changes, particularly with oxidative metabolism. A tidal cycle elicited changes within functional groups, including in cytoskeletal proteins, chaperones, and oxidative stress proteins. In addition to protein abundance changes, we found the possibility for post-translational modifications driving rhythms, including methylation, mitochondrial peptide processing (proteolysis), and acylation. Dynamic changes in the proteome across functional categories demonstrate the importance of the tidal environment in entraining cellular processes, confirming that differential expression studies should not assume a static baseline of cellular conditions in intertidal organisms.</p>
Resource competition shapes biological rhythms and promotes temporal niche differentiation in a community simulation
<p>This is the code and dataset for the article entitled "Resource competition shapes biological rhythms and promotes temporal niche differentiation in a community simulation," in the journal Ecology and Evolution.</p> <ul> <li>Competition for resources often contributes strongly to defining an organism's ecological niche. Endogenous biological rhythms are important adaptations to the temporal dimension of niches, but how other organisms influence such temporal niches have not been much studied, and the role of competition in particular has been even less examined. We investigated how interspecific and intraspecific competition for resources shape an organism's activity rhythms.</li> <li>To do this, we simulated communities of one or two species in an agent-based model. Individuals in the simulation move according to a circadian activity rhythm and compete for limited resources. Probability of reproduction is proportional to an individual's success in obtaining resources. Offspring may have variance in rhythm parameters, which allow for the population to evolve over time.</li> <li>We demonstrate that when organisms are arrhythmic, one species will always be competitively excluded from the environment, but the existence of activity rhythms allows niche differentiation and indefinite coexistence of the two species. Two species which are initially active at the same phase will differentiate their phase angle of entrainment over time to avoid each other. When only one species is present in an environment, competition within the species strongly selects for niche expansion through arrhythmicity, but the addition of an interspecific competitor facilitates evolution of increased rhythmic amplitude when combined with additional adaptations for temporal specialization. Finally, if individuals preferentially mate with others who are active at similar times of day, then disruptive selection by intraspecific competition can split one population into two reproductively isolated groups separated in activity time.</li> <li>These simulations suggest that biological rhythms are an effective method to temporally differentiate ecological niches, and that competition is an important ecological pressure promoting the evolution of rhythms and sleep. This is the first study to use ecological modeling to examine biological rhythms.</li> </ul>
Mu-rhythm modulation associated with the observation and execution of a goal-directed action in healthy toddlers estimated using two different baseline conditions
<p>The database includes mu-rhythm ERD/ERS values elicited by the observation and execution of a goal-directed action in healthy toddlers (N=19). ERD/ERS values has been computed using to different baseline conditions: 1) observation of a black and white static image (BL1) and 2) short period of stillness (BL2).</p> <p>The first sheet of the database refers to action execution (AE) data, whereas the second sheet refers to action observation (AO) data. The database table in each sheet includes for each subject single trial ERD/ERS values (table rows) registered in 7 different scalp sites (table columns) for both BL1 and BL2.</p> <p>The database was used for the statistical analysis of the following paper: Piazza, C.; Visintin, E.; Reni, G.; Montirosso, R. The Effect of Baseline on Toddler Event-Related Mu-Rhythm Modulation. <em>Brain Sci.</em> <strong>2021</strong>, <em>11</em>, 1159. https://doi.org/10.3390/brainsci11091159 (<a href="https://www.mdpi.com/2076-3425/11/9/1159/htm">https://www.mdpi.com/2076-3425/11/9/1159/htm</a>)</p> <p>All the details about data acquisition and preprocessing are reported in the above mentioned publication.</p>
Circadian rhythm entrainment of the jewel wasp, Nasonia vitripennis, by antagonistic interactions of multiple spectral inputs
<p>Circadian light entrainment in some insects is regulated by blue-light sensitive cryptochrome (CRY) protein that is expressed in the clock neurons, but this is not the case in hymenopterans. The hymenopteran clock does contain CRY, but it appears to be light-insensitive. Therefore, we investigated the role of retinal photoreceptors in the photic entrainment of the jewel wasp <em>Nasonia</em> <em>vitripennis</em>. Application of monochromatic light stimuli at different light intensities caused phase shifts in the wasp's circadian activity from which an action spectrum with three distinct peaks was derived. Electrophysiological recordings from the compound eyes and ocelli revealed the presence of three photoreceptor classes, with peak sensitivities at 340 nm (ultraviolet), 450 nm (blue), and 530 nm (green). An additional photoreceptor class in the ocelli with sensitivity maximum at 560–580 nm (red) was found. Whereas a simple sum of photoreceptor spectral sensitivities could not explain the action spectrum of the circadian phase shifts, modelling of the action spectrum indicates antagonistic interactions between pairs of spectral photoreceptors, residing in the compound eyes and the ocelli. Our findings imply that the photic entrainment mechanism in <em>N</em>. <em>vitripennis</em> encompasses the neural pathways for measuring the absolute luminance as well as the circuits mediating colour opponency. </p>
Animal data associated with: Pattern dynamics and stochasticity of the brain rhythms
<p>Our current understanding of brain rhythms is based on quantifying their instantaneous or time-averaged characteristics. What remains unexplored, is the actual structure of the waves–their shapes and patterns over finite timescales. The data published here are used to study brain wave patterning in different physiological contexts using two independent approaches: the first is based on quantifying stochasticity relative to the underlying mean behavior, and the second assesses "orderliness'' of the waves' features. The corresponding measures capture the waves' characteristics and abnormal behaviors, such as atypical periodicity or excessive clustering, and demonstrate coupling between the patterns' dynamics and the animal's location, speed, and acceleration. Specifically, patterns of θ, γ, and ripple waves recorded in mice hippocampi and observed speed-modulated changes of the wave's cadence, an antiphase relationship between orderliness and acceleration, as well as spatial selectiveness of patterns, are derived from the data. The results offer a complementary–mesoscale–perspective on brain wave structure, dynamics, and functionality.</p>
Meta-analysis of diurnal transcriptomics in mouse liver reveals low repeatability of rhythm analyses
<p>The accumulation of public transcriptomic timeseries data enables robust meta-analyses that were not possible until recently. To assess the consistency of biological rhythms across studies, 57 public mouse liver tissue timeseries totaling 1096 RNA-seq samples were obtained and analyzed. Only the control groups of each study were included, to create comparable data. Technical factors in RNA-seq library preparation were the largest contributors to transcriptome-level differences, beyond biological or experiment-specific factors such as lighting conditions. Core clock genes were remarkably consistent in phase across all studies. Overlap of genes identified as rhythmic across studies was generally low, with no pair of studies having over 60% overlap. Distributions of phases of significant genes were remarkably inconsistent across studies, but the genes that consistently identified as rhythmic had acrophase clustering near ZT0 and ZT12. Despite the discrepancies between single-study analyses, cross-study analyses found substantial consistency. Running compareRhythms on each pair of studies identified a median of only 11% of the identified rhythmic genes as rhythmic in only one of the two studies. Data was integrated across studies in a JIVE analysis, which showed that the top two components of joint within-study variation are determined by time of day. A shape-invariant model with random effects was fit to the genes to identify the underlying shape of the rhythms, consistent across all studies, including identifying 72 genes with consistently multiple peaks.<br> <br> This dataset accumulates the quantified values from the 1096 samples along with the sample and study meta-data, and the results of JTK and BooteJTK methods run on each of the individual studies. It also includes the spline-fit curves results from the Shape Invarient Models (SIM).</p>
Data and supplementary information: Effects of lithium on locomotor activity and circadian rhythm of honey bees
<p>Data and supplementary files for publication:</p><p>Erdem, B., Arslan, O.C., Sevin, S. Gozen, A. G., Agosto-Rivera, J. L., Tugrul, G., & Alemdar, H. (2023). Effects of lithium on locomotor activity and circadian rhythm of honey bees. <i>Scientific Reports</i>, <i>13,</i> 19861. https://doi.org/10.1038/s41598-023-46777-7</p><p> </p><p>AcuteExp_Dark_ActivityData.xlsx - Total LMA counts of acute experiment in dark condition.</p><p>AcuteExp_Light_ActivityData.xlsx - Total LMA counts of acute experiment in light condition.</p><p>ChronicExp_ActivityData.xlsx - Total LMA counts of the chronic experiment.</p><p>ChronicExp_MortalityData.xlsx - Mortality data of the chronic experiment.</p><p>ChronicExp_PeriodRhytmData.xlsx - Defines rhythmic and arrhythmic individuals and the circadian periods (h) of the rhythmic individuals in chronic experiment.</p><p>LD_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the 12 h light / 12 h dark condition.</p><p>DD_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the constant dark condition.</p><p>LL_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the constant light condition.<br>In the double-plotted actograms, NR indicates "non-rhythmic" individuals.</p>
Rhythm control and cardiovascular or cerebrovascular out-comes in patients with atrial fibrillation: A study of the CODE-AF registry
<p><strong>SUPPLEMENTARY MATERIAL</strong></p> <p> </p> <p><strong><em>Rhythm control and cardiovascular or cerebrovascular outcomes in patients with atrial fibrillation: A study of the CODE-AF registry</em></strong></p> <p> </p> <p>Ho Gi Chung, MD; Junbeom Park; Jin-Kyu Park; Ki-Woon Kang; Jaemin Shim; Jin-Bae Kim; Jun Kim; Eue-Keun Choi; Hyung Wook Park; Young Soo Lee; Boyoung Joung</p> <table> <tbody> <tr> <td> <p><strong>Supplementary Table 1.</strong> Subgroup analysis of primary outcome in rate- and rhythm-control group before overlap weighting.</p> </td> </tr> </tbody> </table> <table> <tbody> <tr> <td> <p><strong>Supplementary Figure 1. </strong>Cumulative incidence of primary outcome in rhythm and rate control treatment groups before overlap weighting.</p> </td> </tr> </tbody> </table> <table> <tbody> <tr> <td> <p><strong>Supplementary Figure 2. </strong>Cumulative incidence of secondary outcomes in rhythm and rate control treatment groups before overlap weighting.</p> </td> </tr> </tbody> </table>
Effects of rhythm and accent patterns on tempo-keeping property of finger tapping
<p><span>Tempo of music performance is often accelerated irrespective of players' intention. Though the characteristics of the tempo deviation phenomenon have been investigated using a finger-tapping task, most such studies dealt with tapping with a fixed interval; few studies considered the effects of rhythm and accent, both important factors of music performance. Here, we asked how different rhythm and accent patterns affected the tempo-keeping property using a synchronization-continuation task paradigm: Participants were asked to keep tapping while reproducing the given rhythm/accent patterns designated by the target tones. Tapping tempo was significantly deviated depending on rhythm/accent patterns, but their magnitudes were only several percent in 150 seconds, much smaller than those in real music performance. We also ran experiments under the conditions that participants need to reproduce the accent patterns, but only feedback tones were modulated. These auditory modulations affected the tempo deviation, implying that not only motor process for producing the accents but also perceptual process induced by the accented auditory feedback influence the tempo maintenance of finger tapping. In sum, the present finding shows that sensorimotor processing for un-uniform finger tapping can disturb the long-term tempo-keeping process. We also discussed related topics based on the experimental findings.</span></p>
The rhythms of transient relationships: Allocating time between weekdays and weekends
<p>A fundamental question of any new relationship is, will it last? Transient relationships, recently defined by the authors, are an ideal type of social tie to explore this question: these relationships are characterized by distinguishable starting and ending temporal points, linking the question of tie longevity to relationship finite lifetime. In this study, we use mobile phone data sets from the UK and Italy to analyze the weekly allocation of time invested in maintaining transient relationships. We find that more relationships are created during weekdays, with a greater proportion of them receiving more contact during these days of the week in the long term. The smaller group of relationships that receive more phone calls during the weekend tend to remain active for more time. We uncover a sorting process by which some ties are moved from weekdays to weekends and <em>vice versa</em>, mostly in the first half of the relationship. This process also carries more information about the ultimate lifetime of a tie than the part of the week when the relationship started, which suggests an early evaluation period that leads to a decision on how to allocate time to different types of transient ties.</p>
Efficacy & Safety of Dronedarone Versus Amiodarone for the Maintenance of Sinus Rhythm in Patients With Atrial Fibrillation
ClinicalTrials.gov study NCT00489736. IPD Sharing: Not stated. Countries: 23. Publications: 2.
The Effects of Light Therapy on Circadian Rhythms, Sleep, and Mood in Postpartum Depression
ClinicalTrials.gov study NCT02769858. IPD Sharing: NO. Countries: 1. Publications: 1.
Safety and Efficacy of Vanoxerine for Conversion of Atrial Fibrillation or Flutter to Normal Sinus Rhythm
ClinicalTrials.gov study NCT01691313. IPD Sharing: Not stated. Countries: 2. Publications: 1.
Utilizing Novel Dipole Density Capabilities to Objectively Visualize the Etiology of Rhythms in Atrial Fibrillation
ClinicalTrials.gov study NCT02825992. IPD Sharing: NO. Countries: 6. Publications: 1.
Safety and Efficacy of VEC-162 on Circadian Rhythm in Healthy Adult Volunteers
ClinicalTrials.gov study NCT00490945. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.