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11,506 results for “Dynamics”
Data from: Effects of mass extinction and recovery dynamics on long-term evolutionary trends: a morphological study of Strophomenida (Brachiopoda) across the Late Ordovician mass extinction
Mass extinctions affect the history of life by decimating existing diversity and ecological structure and creating new evolutionary and ecological pathways. Both the loss of diversity during these events and the rebound in diversity following extinction had a profound effect on Phanerozoic evolutionary trends. Phylogenetic trees can be used to robustly assess the evolutionary implications of extinction and origination. We examine both extinction and origination during the Late Ordovician mass extinction. This mass extinction was the second largest in terms of taxonomic loss but did not appear to radically alter Paleozoic marine assemblages. We focus on the brachiopod order Strophomenida, whose evolutionary relationships have been recently revised, to explore the disconnect between the processes that drive taxonomic loss and those that restructure ecological communities. A possible explanation for this disconnect is if extinction and origination were random with respect to morphology. We define morphospace using principal coordinate analysis (PCO) of character data from 61 Ordovician-Devonian taxa and their 45 ancestral nodes, defined by a most parsimonius reconstruction in Mesquite. A bootstrap of the centroid of PCO values indicates that genera were randomly removed from morphospace by the Late Ordovician mass extinction, and new Silurian genera were clustered within a smaller previously unoccupied region of morphospace. Diversification remained morphologically constrained throughout the Silurian and into the Devonian. This suggests that the recovery from the Late Ordovician mass extinction resulted in a long-term shift in strophomenide evolution. More broadly, recovery intervals may hold clues to understanding the evolutionary impact of mass extinctions.
Data from: Dynamics of genomic change during evolutionary rescue in the seed beetle Callosobruchus maculatus
Rapid adaptation can be necessary to prevent extinction when populations are exposed to extremely marginal or stressful environments. Factors that affect the likelihood of evolutionary rescue from extinction have been identified, but much less is known about the evolutionary dynamics and genomic basis of successful evolutionary rescue, particularly in multicellular organisms. We conducted an evolve-and-resequence experiment to investigate the dynamics of evolutionary rescue at the genetic level in the cowpea seed beetle, Callosobruchus maculatus, when it is experimentally shifted to a stressful host plant, lentil (Lens culinaris). Low survival (~1%) at the onset of the experiment caused population decline. But adaptive evolution quickly rescued the population with survival rates climbing to 69\% by the F5 generation and 90\% by the F10 generation. Population genomic data showed that rescue likely was caused by rapid evolutionary change at multiple loci, with many alleles fixing or nearly fixing within five generations of selection on lentil. By comparing estimates of selection across five lentil-adapted C. maculatus populations (two new sublines and three long-established lines), we found that adaptation to lentil can involve a mixture of repeated and idiosyncratic evolutionary changes. Parallel evolutionary changes were particularly pronounced in sublines formed after the parent line had passed through an initial bottleneck. Overall, our results suggest that evolutionary rescue in this system can be driven by very strong selection on a modest number of loci, and these results provide empirical evidence that ecological dynamics during evolutionary rescue can cause distinct evolutionary trajectories and genomic signatures.
Data from: Nonlinear dynamics forecasting of obstructive sleep apnea onsets
Recent advances in sensor technologies and predictive analytics are fueling the growth in point-of-care (POC) therapies for obstructive sleep apnea (OSA) and other sleep disorders. The effectiveness of POC therapies can be enhanced by providing personalized and real-time prediction of OSA episode onsets. Previous attempts at OSA prediction are limited to capturing the nonlinear, nonstationary dynamics of the underlying physiological processes. This paper reports an investigation into heart rate dynamics aiming to predict in real time the onsets of OSA episode before the clinical symptoms appear. A prognosis method based on a nonparametric statistical Dirichlet-Process Mixture-Gaussian-Process (DPMG) model to estimate the transition from normal states to an anomalous (apnea) state is utilized to estimate the remaining time until the onset of an impending OSA episode. The approach was tested using three datasets including (1) 20 records from 14 OSA subjects in benchmark ECG apnea databases (Physionet.org), (2) records of 10 OSA patients from the University of Dublin OSA database and (3) records of eight subjects from previous work. Validation tests suggest that the model can be used to track the time until the onset of an OSA episode with the likelihood of correctly predicting apnea onset in 1 min to 5 mins ahead is 83.6 ± 9.3%, 80 ± 8.1%, 76.2 ± 13.3%, 66.9 ± 15.4%, and 61.1 ± 16.7%, respectively. The present prognosis approach can be integrated with wearable devices, enhancing proactive treatment of OSA and real-time wearable sensor-based of sleep disorders.
Data from: Empirical phylogenies and species abundance distributions are consistent with pre-equilibrium dynamics of neutral community models with gene flow
Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities – i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities – from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in pre-equilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under pre-equilibrium conditions.
Data from: Fine root dynamics in lodgepole pine and white spruce stands along productivity gradients in reclaimed oil sands sites
Open-pit mining activities in the oil sands region of Alberta, Canada, create disturbed lands that, by law, must be reclaimed to a land capability equivalent to that existed before the disturbance. Re-establishment of forest cover will be affected by the production and turnover rate of fine roots. However, the relationship between fine root dynamics and tree growth has not been studied in reclaimed oil sands sites. Fine root properties (root length density, mean surface area, total root biomass, and rates of root production, turnover, and decomposition) were assessed from May to October 2011 and 2012 using sequential coring and ingrowth core methods in lodgepole pine (Pinus contorta Dougl.) and white spruce (Picea glauca (Moench.) Voss) stands. The pine and spruce stands were planted on peat mineral soil mix placed over tailings sand and overburden substrates, respectively, in reclaimed oil sands sites in Alberta. We selected stands that form a productivity gradient (low, medium, and high productivities) of each tree species based on differences in tree height and diameter at breast height (DBH) increments. In lodgepole pine stands, fine root length density and fine root production, and turnover rates were in the order of high > medium > low productivity sites and were positively correlated with tree height and DBH and negatively correlated with soil salinity (P < 0.05). In white spruce stands, fine root surface area was the only parameter that increased along the productivity gradient and was negatively correlated with soil compaction. In conclusion, fine root dynamics along the stand productivity gradients were closely linked to stand productivity and were affected by limiting soil properties related to the specific substrate used for reconstructing the reclaimed soil. Understanding the impact of soil properties on fine root dynamics and overall stand productivity will help improve land reclamation outcomes.
Data from: Phylogeographic diversification and postglacial range dynamics shed light on the conservation of the kelp Saccharina japonica
Studies of postglacial range shifts could enhance our understanding of seaweed species' responses to climate change, and hence facilitate the conservation of natural resources. However, the distribution dynamics and phylogeographic diversification of the commercially and ecologically important kelp Saccharina japonica in the Northwest Pacific (NWP) are still poorly surveyed. In this study, we analyzed the evolutionary history of S. japonica using two mitochondrial markers and 24 nuclear microsatellites. A STRUCTURE analysis revealed two partially isolated lineages: lineage H, which is scattered along the coast of Japan; and lineage P, which occurs along the west coast of the Japan Sea. Ecological niche modeling projections to the Last Glacial Maximum (LGM) revealed that the southern coasts of the Japan Sea and the Pacific side of the Oshima and Honshu Peninsulas provided the most suitable habitats for S. japonica, implying that these regions served as ancient refugia during the LGM. Ancient isolation in different refugia may explain the observed divergence between lineages P and H. An approximate Bayesian computation analysis indicated that the two lineages experienced post‐LGM range expansion, and that postglacial secondary contact occurred in Sakhalin. Model projections into the year 2100 predicted that S. japonica will shift northwards and lose its genetic diversity center on the Oshima Peninsula in Hokkaido and Shimokita Peninsula in Honshu. The range shifts and evolutionary history of S. japonica improve our understanding of how climate change impacted the distribution range and diversity of this species and provide useful information for the conservation of natural resources under ongoing environmental change in the NWP.
Data from: Calcium dynamics regulating the timing of decision-making in C. elegans
Brains regulate behavioral responses with distinct timings. Here we investigate the cellular and molecular mechanisms underlying the timing of decision-making during olfactory navigation in Caenorhabditis elegans. We find that, based on subtle changes in odor concentrations, the animals appear to choose the appropriate migratory direction from multiple trials as a form of behavioral decision-making. Through optophysiological, mathematical and genetic analyses of neural activity under virtual odor gradients, we further find that odor concentration information is temporally integrated for a decision by a gradual increase in intracellular calcium concentration ([Ca2+]i), which occurs via L-type voltage-gated calcium channels in a pair of olfactory neurons. In contrast, for a reflex-like behavioral response, [Ca2+]i rapidly increases via multiple types of calcium channels in a pair of nociceptive neurons. Thus, the timing of neuronal responses is determined by cell type-dependent involvement of calcium channels, which may serve as a cellular basis for decision-making.
Data from: Colonization and extinction dynamics among the plant species at tree bases in Paris (France)
1. In cities, trees growing along streets could play an important ecological role for spontaneous plants that grow at their bases. For example, these trees could represent corridors that allow species to move in the urban matrix by potentially connecting large green spaces (e.g., parks, gardens, etc.) We considered sets of urban trees in 15 streets as metapopulations for 15 plant species. Our objective was to determine the factors influencing the dynamics of colonization and extinction of populations based on the distance of the streets from green spaces and the biological traits of each species. 2. The species in 1,324 tree bases of the Bercy district of Paris were surveyed annually from 2009 to 2015. For each species and each street, we used SPOMSIM software to identify the best-fit metapopulation model: the propagule rain model (PRM), Levins model (LM), and the PRM and LM with a fixed extinction or a rescue effect. 3. The results demonstrated that the species more often conformed to the PRM in streets near green spaces, which suggested that green spaces could act as the sources for the populations in those streets. Species with seeds with long-term persistence more often conformed to the PRM, indicating that a soil seed bank helps species invade entire streets. Finally, a higher percentage of species with a short height conformed to models with a rescue effect, which indicated that those species resisted the effects of weeding by the city technical services more often than taller species. 4. Synthesis and applications. This study showed how the biological traits of species and the geography of the district determine the dynamics of the plants in the streets, and the results may provide important information for biodiversity management in cities.
Data from: Abnormal thalamo-cortical network dynamics in migraine
Objective: To investigate the dynamic functional connectivity of thalamo-cortical networks in interictal migraine patients and whether clinical features are associated with abnormal connectivity. Methods: We investigated dynamic functional network connectivity (dFNC) of the migraine brain in 89 interictal migraine patients and 70 healthy controls. We focused on the temporal properties of thalamocortical connectivity using sliding window cross-correlation, clustering state analysis, and graph-theory methods. Relationships between clinical symptoms and abnormal dFNC were evaluated using a multivariate linear regression model. Results: Five dFNC brain states were identified to characterize and compare dynamic functional connectivity patterns. We demonstrated that migraineurs spent more time in a strongly interconnected between-network state, but they spent less time in a sparsely-connected state. Interestingly, we found that abnormal posterior thalamus (pulvinar nucleus) dFNC with the visual cortex and the precuneus were significantly correlated with headache frequency of migraine. Further topological measures revealed migraineurs had significantly lower efficiency of information transfer in both global and local dFNC. Conclusion: Our results demonstrated a transient pathological state with atypical thalamo-cortical connectivity in migraineurs and extended current findings regarding abnormal thalamo-cortical networks and dysrhythmia in migraine.
Data from: HIV dynamics linked to memory CD4+ T cell homeostasis
The dynamics of latent HIV is linked to infection and clearance of resting memory CD4+ T cells. Infection also resides within activated, non-dividing memory cells and can be impacted by antigen-driven and homeostatic proliferation despite suppressive antiretroviral therapy (ART). We investigated whether plasma viral level (pVL) and HIV DNA dynamics could be explained by HIV's impact on memory CD4+ T cell homeostasis. Median total, 2-LTR and integrated HIV DNA levels per μL of peripheral blood, for 8 primary (PHI) and 8 chronic HIV infected (CHI) individuals enrolled on a raltegravir (RAL) based regimen, exhibited greatest changes over the 1st year of ART. Dynamics slowed over the following 2 years so that total HIV DNA levels were equivalent to reported values for individuals after 10 years of ART. The mathematical model reproduced the multiphasic dynamics of pVL, and levels of total, 2-LTR and integrated HIV DNA in both PHI and CHI over 3 years of ART. Under these simulations, residual viremia originated from reactivated latently infected cells where most of these cells arose from clonal expansion within the resting phenotype. Since virion production from clonally expanded cells will not be affected by antiretroviral drugs, simulations of ART intensification had little impact on pVL. HIV DNA decay over the first year of ART followed the loss of activated memory cells (120 day half-life) while the 5.9 year half-life of total HIV DNA after this point mirrored the slower decay of resting memory cells. Simulations had difficulty reproducing the fast early HIV DNA dynamics, including 2-LTR levels peaking at week 12, and the later slow loss of total and 2-LTR HIV DNA, suggesting some ongoing infection. In summary, our modelling indicates that much of the dynamical behavior of HIV can be explained by its impact on memory CD4+ T cell homeostasis.
Data from: Expression of parasite genetic variation changes over the course of infection: implications of within-host dynamics for the evolution of virulence
How infectious disease agents interact with their host changes during the course of infection and can alter the expression of disease-related traits. Yet by measuring parasite life-history traits at one or few moments during infection, studies have overlooked the impact of variable parasite growth trajectories on disease evolution. Here we show that infection-age-specific estimates of host and parasite fitness components can reveal new insight into the evolution of parasites. We do so by characterizing the within-host dynamics over an entire infection period for five genotypes of the castrating bacterial parasite Pasteuria ramosa infecting the crustacean Daphnia magna. Our results reveal that genetic variation for parasite-induced gigantism, host castration and parasite spore loads increases with the age of infection. Driving these patterns appears to be variation in how well the parasite maintains control of host reproduction late in the infection process. We discuss the evolutionary consequences of this finding with regard to natural selection acting on different ages of infection and the mechanism underlying the maintenance of castration efficiency. Our results highlight how elucidating within-host dynamics can shed light on the selective forces that shape infection strategies and the evolution of virulence.
Data from: Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome
Plants have adapted to tolerate and survive constantly changing environmental conditions by re-programming gene expression. The dynamics of the contribution of alternative splicing (AS) to stress responses are unknown. RNA-sequencing of a time-series of Arabidopsis thaliana plants exposed to cold determines the timing of significant AS changes. This shows a massive and rapid AS response with coincident waves of transcriptional and AS activity occurring in the first few hours of temperature reduction, and further AS throughout the cold. In particular, hundreds of genes showed changes in expression due to rapidly occurring AS in response to cold ("early AS" genes); these included numerous novel cold-responsive transcription factors and splicing factors/RNA-binding proteins regulated only by AS. The speed and sensitivity to small temperature changes of AS of some of these genes suggest that fine-tuning expression via AS pathways contributes to the thermo-plasticity of expression. Four "early AS" splicing regulatory genes have been shown previously to be required for freezing tolerance and acclimation; we provide evidence of a fifth gene, U2B"-LIKE. Such factors likely drive cascades of AS of downstream genes which alongside transcription modulate transcriptome reprogramming that together govern the physiological and survival responses of plants to low temperature.
Data from: Prey diversity, prey composition, and predator population dynamics in experimental microcosms
1. Food‐web complexity‐stability relations are central to ecology, and many empirical studies show greater food‐web complexity leads to lower population stability. Here, predator population variability decreased with increasing prey diversity in aquatic microcosm experiments, an example of greater food‐web complexity leading to greater population stability. 2. Prey diversity as well as different sets of prey species within each level of prey diversity produced differences in predator population dynamics, demonstrating the importance of both prey composition and prey diversity in determining predator population stability. 3. Prey diversity can affect predator population dynamics through at least three groups of mechanisms: prey reliability, prey biomass, and prey composition mechanisms. The results suggest that greater prey reliability at higher prey diversities enhances predator stability and provide support for MacArthur (1955).
Relativistic dynamics of stars near a supermassive black hole
<p>This data was first presented in `Relativistic dynamics of stars near a supermassive black hole’ (Hamers et al. 2014, MNRAS 443, 1; http://mnras.oxfordjournals.org/content/443/1/355; doi: 10.1093/mnras/stu1126). It includes the first- and second-order diffusion coefficients (DFCs) from the S-star N-body simulations (cf. Section 5.1 from the paper) as a function of the angular-momentum variable \ell = \sqrt{1-e^2}, binned with respect to the semimajor axis (cf. Section 5.4 from the paper).</p> <p>Description of the comma-separated txt files:<br /> `a_bins.txt’ - the semimajor axis bins. Semimajor axes are given in units of mpc (milliparsec). First column: the index of the bin; second column: the lower bin value; third column: the upper bin value; fourth column: the mean value.<br /> `D12_l_index_a_bin_i.txt’ - the DFCs for the different semimajor axis bins as a function of \ell (i is the bin index). First column: the value of \ell; second column: the first-order DFC, in units of 1/Myr; third column: the second-order DFC, in units of 1/Myr.</p> <p>Adrian Hamers, 22 April 2016</p>
Three-dimensional sediment dynamics in well-mixed estuaries: importance of the internally-generated overtide, spatial settling lag and gravitational circulation
<p>model outputs</p>
Dynamic Prediction of HIV-Related Incomplete Immune Reconstitution: A Multi-Center, Large Cohort Study Using Advanced Joint Modeling
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Intra-annual dynamics of temperate glacier in the ablation season in the southeastern Tibetan Plateau
<p>Here, the data used in paper “Intra-annual dynamics of temperate glacier in the ablation season in the southeastern Tibetan Plateau” were given.</p> <p>In this database, "GlacierHeightChange_2023_0611" is the Yanong Glacier height changes that generated from six Digital Surface Models, "GlacierVelocity_2023_0644" is the Yanong Glacier surface veloicties that generated from six Digital Orthophoto Maps. The six DSMs and DOMs were derived from six UAV surveys from June to November in 2023.</p>
Statistical characterization of suspended sediment dynamics in shallow tidal environments
<p><span lang="EN-US">This study was funded by the European Union - NextGenerationEU, in the framework of the iNEST - Interconnected Nord-Est Innovation Ecosystem (iNEST ECS00000043 - CUP C43C22000340006). The views and opinions expressed are solely those of the authors and do not necessarily reflect those of the European Union, nor can the European Union be held responsible for them. The dataset was developed as part of the activities carried out by Spoke 8, Research Topic 1 (Biology of hydrosphere ecosystems), Task S8_RT1.1 (Digital Databases for Innovation in Biodiversity and Water Quality Assessment)</span></p>
Data associated with Cell Reports publication: Dura-Bernal, Griffith, et al. 2023, "Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics" (4/4)
<p>This dataset includes experimental data used to constrain and validate the model, and model simulation output data for the following Cell Reports publication: <a href="https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6">https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6</a></p><p>The source code for the associated A1 model and data analysis can be found here: <a href="https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data">https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data</a>.</p><p>All zip files should unzipped into a parent folder called /data inside the Github repository above.</p><p><strong>Important:</strong> Due to the Zenodo size limit, this dataset is split among 4 Zenodo uploads. This is upload <strong>4 out of 4</strong>. The other 3 uploads can be found at: </p><p>Upload 1/4: <a href="http://doi.org/10.5281/zenodo.10066993">http://doi.org/10.5281/zenodo.10066993</a> (https://zenodo.org/uploads/10066993)</p><p>Upload 2/4: <a href="http://doi.org/10.5281/zenodo.10069553">http://doi.org/10.5281/zenodo.10069553</a> (https://zenodo.org/uploads/10069553)</p><p>Upload 3/4: <a href="http://doi.org/10.5281/zenodo.10071726">http://doi.org/10.5281/zenodo.10071726</a> (https://zenodo.org/uploads/10071726)</p><p>For more information please contact: salvador.dura-bernal@downstate.edu </p>
EFFECT OF MINERAL FERTILISERS APPLIED TO AMARANTH PLANTS ON THE DYNAMICS OF NITROGEN IN SOIL
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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.