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15,572 results for “timescale”
Novel integrative modeling of molecules and morphology across evolutionary timescales
<p>Evolutionary models account for either population or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments, and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.</p>
Figure 2 in Reconstructing evolutionary timescales using phylogenomics
Figure 2. Phylogenomic estimates of the crown ages of major groups within mammals, birds, and insects. Black circles indicate median age estimates, whereas horizontal bars indicate the associated 95% credibility intervals. Ages for insect groups are according to Tong et al. (2015); ages of bird groups are according to Prum et al. (2015); and ages of placental mammal groups are according to dos Reis et al. (2012). The timings of four mass extinction events are also shown.
Figure 1 in Reconstructing evolutionary timescales using phylogenomics
Figure 1. An illustration of gene effects, lineage effects, and their interactions (residual effects). (a) When there are gene effects, each gene has a distinct rate of evolution, probably as a result of varying selective pressures. (b) When there are lineage effects, the evolutionary rate varies across branches of the tree. This can be caused by differences in life-history characteristics, such as generation length. (c) When there are gene-by-lineage interactions, or residual effects, rates vary across lineages in a gene-specific manner.
Reproduction package for 'Limits on long-timescale radio transients at 150 MHz using theTGSS ADR1 and LoTSS DR2 catalogues'
<p>This is a basic reproduction package for 'Limits on long-timescale radio transients at 150 MHz using theTGSS ADR1 and LoTSS DR2 catalogues' by de Ruiter et al (2021). It aims to provide the most important data products to check and reproduce the main results of the paper.</p>
Data from: Hurry Up and Wait: Managing the Inherent Mismatches in Timescales in Natural and Artificial Photosynthetic Systems
<p>Houle, Frances A.; Yano, Junko; Ager, Joel W.;<br> Hurry Up and Wait: Managing the Inherent Mismatches in Timescales in<br> Natural and Artificial Photosynthetic Systems</p> <p><strong>Files</strong><br> Supplementary data coupled reaction-transport and cascades.xlxs<br> Input parameters for Kinetiscope calculations and associated figure data</p> <p>CO2R microkinetic model-DRC.ipynb<br> CO2R microkinetic model-DRC.pdf<br> Jupyter notebook and pdf for degree of rate control in CO2 reduction<br> Packages used:<br> Python: 3.7.7<br> Numpy: 1.21.5<br> SciPy: 1.7.3<br> Matplotlib: 3.5.1</p> <p>Wang 2018 Pathway 1 only DRC.ipynb<br> Wang 2018 Pathway 1 only DRC.pdf<br> Jupyter notebook and pdf for degree of rate control photoelectrocatalytic water oxidation<br> Python: 3.7.7<br> Numpy: 1.21.5<br> SciPy: 1.7.3<br> mpmath: 1.2.1<br> Matplotlib: 3.5.1</p>
Data and software for: Temporal novelty detection and multiple timescale integration drive Drosophila orientation dynamics in temporally diverse olfactory environments
<p>To survive, insects must effectively navigate odors plumes to their source. In natural plumes, turbulent winds break up smooth odor regions into disconnected patches, so navigators encounter brief bursts of odor interrupted by bouts of clean air. The timing of these encounters plays a critical role in navigation, determining the direction, rate, and magnitude of insects' orientation and speed dynamics. Disambiguating the specific role of odor timing from other cues, such as spatial structure, is challenging due to natural correlations between plumes' temporal and spatial features. Here, we use optogenetics to isolate temporal features of odor signals, examining how the frequency and duration of odor encounters shape the navigational decisions of freely-walking <em>Drosophila</em>. We find that fly angular velocity depends on signal frequency and intermittency – fraction of time signal can be detected – but not directly on durations. Rather than switching strategies when signal statistics change, flies smoothly transition between signal regimes, by combining an odor offset response with a frequency-dependent novelty-like response. In the latter, flies are more likely to turn in response to each odor hit only when the hits are sparse. Finally, the upwind bias of individual turns relies on a filtering scheme with two distinct timescales, allowing rapid and sustained responses in a variety of signal statistics. A quantitative model incorporating these ingredients recapitulates fly orientation dynamics across a wide range of environments and shows that temporal novelty detection, when combined with odor motion detection, enhances odor plume navigation.</p>
A genomic timescale for placental mammal evolution: Datasets
<p>Datasets used in Foley N.M., Mason, V.C., Harris A.J., Bredemeyer K.R., Damas J., Lewin H.A., Eizirik E., Gatesy J., Zoonomia Consortium, Springer M.S., and W.J. Murphy (2022) A genomic timescale for placental mammal evolution. <strong><em>Science</em></strong>. x:x-x</p> <p>This repository includes</p> <p>- Alignments for whole genome analyses</p> <p>- Alignments for sliding windows analyses across chromosome 1, chromosome 21, chromosome 22 and the X chromosome</p> <p>- Sliding window alignments used to estimate divergence times</p> <p>- Preliminary topologies derived from the low recombining region on the X chromosome</p> <p>- Machine readable (.csv) versions of tables presented in the paper</p> <p>- Per chromosome fasta files referenced to the human genome exported from the HAL alignment as described in the paper.</p> <p>~~~~~~~~~~~~~~</p> <p>v1.1 added nexus topologies for datasets listed in Table S2</p>
Numerical model and natural river data for the timescale analysis of meandering channel migration
<p>This is the archive of the numerical model and river centerline data used for analyzing the timescale related to meandering channel migration, which is tied to the manuscript submitted to Journal of Geophysical Research: Earth Surface: Li, Y., and Limaye, A. B., Timescale of the morphodynamic feedback between planform geometry and lateral migration of meandering rivers.</p> <p>Running this model needs a MATLAB® software environment. The model can be launched by the wrapper scripts saved under the folder "software code/example wrappers". The wrapper script called "wrapper01a_channelOnly_runModel.m" is used to generate all model simulations in this study.</p>
Data and code for: Plants sum and subtract stimuli over different timescales
<p>This repository contains the experimental data presented in "Plants sum and subtract stimuli over different timescales" as well as the Python scripts to reproduce the figures, run simulations based on the discussed model and estimate the memory kernel for individual plant organs.</p>
Data for: Global diversity patterns are explained by diversification rates and dispersal at ancient, not shallow, timescales
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Climate change is an important predictor of extinction risk on macroevolutionary timescales
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Turnover of retroelements and satellite DNA drives centromere reorganization over short evolutionary timescales in Drosophila
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A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)
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Data for: Timescales of Autogenic Noise in River Bedform Evolution and Stratigraphy
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Timescale reverses the relationship between host density and infection risk
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Data and software for: Temporal novelty detection and multiple timescale integration drive Drosophila orientation dynamics in temporally diverse olfactory environments
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Lifetimes and timescales of tropospheric ozone: Ozone emission experiments
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Data from: Multiple timescales of streambed flux variability in two perennial mountain-front streams
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Novel integrative modeling of molecules and morphology across evolutionary timescales
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Data from: Natural tree colonisation of organo-mineral soils does not provide a net carbon capture benefit at decadal timescales
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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.