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2,308 results for “Repeatability”
Data from: Corals that survive repeated thermal stress show signs of selection and acclimatization
<p>Climate change is transforming coral reefs by increasing the frequency and intensity of marine heatwaves, often leading to coral bleaching and mortality. Coral communities have demonstrated modest increases in thermal tolerance following repeated exposure to moderate heat stress, but it is unclear whether these shifts represent acclimatization of individual colonies or mortality of thermally susceptible individuals. For corals that survive repeated bleaching events, it is important to understand how past bleaching responses impact future growth potential. Here, we track the bleaching responses of 1,832 corals in leeward Maui through multiple marine heatwaves and document patterns of coral growth and survivorship over a seven-year period. While we find limited evidence of acclimatization at population scales, we document reduced bleaching over time in specific individuals, primarily in the stress-tolerant taxa <em>Porites lobata</em>, indicative of acclimatization. For corals that survived both bleaching events, we find no relationship between bleaching response and coral growth in three of four taxa studied. This decoupling between bleaching and growth suggests that coral survivorship is a better indicator of future growth than is a coral's bleaching history. Based on these results, we recommend restoration practitioners in Hawaiʻi obtain outplants from <em>Porites</em> and <em>Montipora</em> colonies with a proven track-record of growth and survivorship, rather than devote resources toward identifying and cultivating bleaching-resistant phenotypes. Survivorship followed a latitudinal thermal stress gradient, but because this gradient was small, it is likely that local environmental factors also drove differences in coral performance between sites. Efforts to reduce human impacts at low performing sites would likely improve coral survivorship in the future.</p>
Forest gap dynamics with repeat lidar in Berchtesgaden National Park - Data and analysis scripts
<p>This repository holds data and code for the paper: Krüger, K., Senf, C., Jucker, T., Pflugmacher, D., Seidl, R. (2024). Gap expansion is the dominant driver of canopy openings in a temperate mountain forest landscape. Journal of Ecology. <span><a href="http://doi.org/10.1111/1365-2745.14320">http://doi.org/10.1111/1365-2745.14320</a> </span></p> <p><strong>NOTE:</strong> This is a static repository, but the project might evolve. See the connected GitHub repository for latest updates!</p> <p>All data to reproduce the results are available, all other layers can be generated with the code provided in this repository. The Canopy Height Models underlying the analysis and respective processing scripts for the lidar data, are available from the corresponding author upon reasonable request. Gap layers derived from the Canopy Height Models are available in this repository.</p> <p>Empty folders are set up to follow the directory structure of the scripts. </p>
Multiwavelength Constraints on the Origin of a Nearby Repeating Fast Radio Burst Source in a Globular Cluster (Public Data Release)
<p>This Zenodo dataset contains the data for radio bursts B1-B9 from FRB 20200120E, as described in A. B. Pearlman et al., <em>Nature Astronomy</em> (2024) (see: https://doi.org/10.1038/s41550-024-02386-6).</p> <p>The following data products are included:</p> <ul> <li>Channelized total intensity (Stokes I) data containing radio bursts B1-B5 from FRB 20200120E, recorded using the Effelsberg radio telescope during Pinpointing Repeating CHIME Sources with the EVN (PRECISE) VLBI observations. These data have a time resolution of 8 μs and were used in Figure 1 in A. B. Pearlman et al., <em>Nature Astronomy</em> (2024). <ul> <li>frb20200120e_b1_8us_burst_data.npy</li> <li>frb20200120e_b2_8us_burst_data.npy</li> <li>frb20200120e_b3_8us_burst_data.npy</li> <li>frb20200120e_b4_8us_burst_data.npy</li> <li>frb20200120e_b5_8us_burst_data.npy</li> </ul> </li> <li>Channelized total intensity (Stokes I) data containing radio bursts B6-B9 from FRB 20200120E, recorded using the Effelsberg radio telescope. These data have a time resolution of 64 μs and were used in Figure 1 in A. B. Pearlman et al., <em>Nature Astronomy</em> (2024). <ul> <li>frb20200120e_b6_64us_burst_data.npz</li> <li>frb20200120e_b7_64us_burst_data.npz</li> <li>frb20200120e_b8_64us_burst_data.npz</li> <li>frb20200120e_b9_64us_burst_data.npz</li> </ul> </li> <li>Frequency-summed total intensity (Stokes I) burst profiles of radio burst B4. The frequency range and time resolution of the data are listed below. These data were used in Extended Data Figure 2 (panels b, c, and d) in A. B. Pearlman et al., <em>Nature Astronomy</em> (2024).<br> <ul> <li>frb20200120e_b4_8us_1254-1510mhz_burst_profile.npz; (frequency range, time resolution) = (1254-1510 MHz, 8 μs)</li> <li>frb20200120e_b4_1us_1302-1478mhz_burst_profile.npy; (frequency range, time resolution) = (1302-1478 MHz, 1 μs)</li> <li>frb20200120e_b4_31.25ns_1398-1414mhz_burst_profile.npy; (frequency range, time resolution) = (1398-1414 MHz, 31.25 ns)</li> </ul> </li> </ul> <p>We also provide the following Python code containing functions that can be used to load and plot the radio data. The plots generated by this code are similar to those shown in Figure 1 and Extended Data Figure 2 (panels b, c, and d) in A. B. Pearlman et al., <em>Nature Astronomy</em> (2024).</p> <ul> <li>plot_frb20200120e_radio_data_pearlman+2024_nature_astronomy.py</li> </ul> <p>The X-ray data (from <em>NICER</em>, <em>XMM-Newton</em>, <em>Chandra</em>, and <em>NuSTAR</em>) used in A. B. Pearlman et al., <em>Nature Astronomy</em> (2024) are publicly available and can be accessed through NASA's High Energy Astrophysics Science Archive Research Center (HEASARC) archive.</p> <p>If the data or Python code included in this Zenodo repository are used, please include the following two citations in your work:</p> <ol> <li>Pearlman, A. B., Scholz, P., Bethapudi, S. <em>et al.</em> Multiwavelength constraints on the origin of a nearby repeating fast radio burst source in a globular cluster. <em>Nature Astronomy</em> (2024). <a href="https://doi.org/10.5281/zenodo.13359005">https://doi.org/10.1038/s41550-024-02386-6</a></li> <li>Pearlman, A. B., Scholz, P., Bethapudi, S. <em>et al.</em> Multiwavelength constraints on the origin of a nearby repeating fast radio burst source in a globular cluster (public data release). <em>Zenodo</em> (2024). <a href="https://doi.org/10.5281/zenodo.13359005">https://doi.org/10.5281/zenodo.13359005</a></li> </ol> <p>If you have questions about the contents of this Zenodo repository, please contact the lead author: Dr. Aaron B. Pearlman (<a href="mailto:aaron.b.pearlman@physics.mcgill.ca">aaron.b.pearlman@physics.mcgill.ca</a>)</p>
Predictors and predictand for "Repeatable high-resolution statistical downscaling through deep learning"
<p>Predictors and predictand for "Repeatable high-resolution statistical downscaling through deep learning". Predictors from the ERA5 reanalysis and predictand from ReKIS (https://rekis.hydro.tu-dresden.de). Data is saved in ".rda" format, to be read from R.</p>
Repeated information of benefits reduces COVID-19 vaccination hesitancy: Experimental evidence from Germany
<p>This replication package contains the raw data and code to replicate the findings reported in the paper. The data and code are licensed under a Creative Commons Attribution 4.0 International Public License. See <strong>LICENSE.txt</strong> for details.</p> <p><strong>Software requirements</strong></p> <p>All analysis were done in Stata version 16:</p> <ul> <li>Add-on packages are included in <strong>scripts/libraries/stata</strong> and do not need to be installed by user. The names, installation sources, and installation dates of these packages are available in <strong>scripts/libraries/stata/stata.trk</strong>.</li> </ul> <p><strong>Instructions</strong></p> <ol> <li>Save the folder <strong>‘replication_PLOS’</strong> to your local drive.</li> <li>Open the master script <strong>‘run.do’</strong> and change the global pointing to the working direction (line 20) to the location where you save the folder on your local drive</li> <li>Run the master script <strong>‘run.do’</strong> to replicate the analysis and generate all tables and figures reported in the paper and supplementary online materials</li> </ol> <p><strong>Datasets</strong></p> <ul> <li>Wave 1 – Survey experiment: <strong>‘wave1_survey_experiment_raw.dta’</strong></li> <li>Wave 2 – Follow-up Survey: <strong>‘wave2_follow_up_raw.dta'</strong></li> <li>Map: shape-files <strong>‘plz2stellig.shp’ ‘OSM_PLZ.shp’</strong>, area codes <em><em>‘Postleitzahlengebiete</em>-_OSM.csv’</em>_, (all links to the sources can be found in the script ‘04_figure2_germany_map.do’)</li> <li>Pretest: <strong>‘pre-test_corona_raw.dta’</strong></li> <li>For Appendix S7: <strong>‘alter_geschlecht_zensus_det.xlsx’, ‘vaccination_landkreis_raw.dta’, ‘census2020_age_gender.csv’</strong> (all links to the sources can be found in the script ‘06_AppendixS7.do’)</li> <li>For Appendix S10: ‘<strong>vaccination_landkreis_raw.dta’</strong> (all links to the sources can be found in the script ‘07_AppendixS10.do’)</li> </ul> <p><strong>Descriptions of scripts</strong></p> <p><strong>1_1_clean_wave1.do</strong><br> This script processes the raw data from wave 1, the survey experiment<br> <strong>1_2_clean_wave2.do</strong><br> This script processes the raw data from wave 2, the follow-up survey<br> <strong>1_3_merge_generate.do</strong><br> This script creates the datasets used in the main analysis and for robustness checks by merging the cleaned data from wave 1 and 2, tests the exclusion criteria and creates additional variables<br> <strong>02_analysis.do</strong><br> This script estimates regression models in Stata, creates figures and tables, saving them to <strong>results/figures and results/tables</strong><br> <strong>03_robustness_checks_no_exclusion.do</strong><br> This script runs the main analysis using the dataset without applying the exclusion criteria. Results are saved in <strong>results/tables</strong><br> <strong>04_figure2_germany_map.do</strong><br> This script creates Figure 2 in the main manuscript using publicly available data on vaccination numbers in Germany.<br> <strong>05_figureS1_dogmatism_scale.do</strong><br> This script creates Figure S1 using data from a pretest to adjust the dogmatism scale.<br> <strong>06_AppendixS7.do</strong><br> This script creates the figures and tables provided in Appendix S7 on the representativity of our sample compared to the German average using publicly available data about the age distribution in Germany.<br> <strong>07_AppendixS10.do</strong><br> This script creates the figures and tables provided in Appendix S10 on the external validity of vaccination rates in our sample using publicly available data on vaccination numbers in Germany.</p>
Individual repeatability of avian migration phenology: a systematic review and meta-analysis
<p>Changes in phenology and distribution are being widely reported for many migratory species in response to shifting environmental conditions. Understanding these changes and the situations in which they occur can be aided by understanding consistent individual differences in phenology and distribution and the situations in which consistency varies in strength or detectability.</p> <p>Studies tracking the same individuals over consecutive years are increasingly reporting migratory timings to be a repeatable trait, suggesting that flexible individual responses to environmental conditions may contribute little to population-level changes in phenology and distribution. However, how this varies across species and sexes, across the annual cycle and in relation to study (tracking method, study design) and/or ecosystem characteristics is not yet clear.</p> <p>Here, we take advantage of the growing number of publications in movement ecology to perform a phylogenetic multilevel meta-analysis of repeatability estimates for avian migratory timings to investigate these questions. Of 2,433 reviewed studies, 54 contained suitable information for meta-analysis, resulting in 177 effect sizes from 47 species.</p> <p>Individual repeatability of avian migratory timings averaged 0.414 (95% confidence interval: 0.3–0.5) across landbirds, waterbirds and seabirds, suggesting consistent individual differences in migratory timings is a common feature of migratory systems. Timing of departure from the non-breeding grounds was more repeatable than timings of arrival at or departure from breeding grounds, suggesting that conditions encountered on migratory journeys and outcome of breeding attempts can influence individual variation.</p> <p>Population-level shifts in phenology could arise through individual timings changing with environmental conditions and/or through shifts in the numbers of individuals with different timings. Our findings suggest that, in addition to identifying the conditions associated with individual variation in phenology, exploring the causes of between-individual variation will be key in predicting future rates and directions of changes in migratory timings. We, therefore, encourage researchers to report the within- and between- individual variance components underpinning the reported repeatability estimates to aid interpretation of migration behaviour. In addition, the lack of studies in the tropics means that levels of repeatability in less strongly seasonal environments are not yet clear.</p>
Genomic changes underlying repeated niche shifts in an adaptive radiation
<p>In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, i.e. the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by re-sequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets of parallel selection in the genome that are enriched for old standing genetic variation. In contrast to theoretical expectations, their genomic architecture is highly dispersed with little clustering. Candidate genes and genotype-environment correlations match the three major environmental axes predation regime, light environment and ecosystem size. In a niche space with these three dimensions, we find that the more divergent a new niche from the ancestral marine habitat, the more loci show signatures of parallel selection. Our findings suggest that the genomic architecture of parallel adaptation in adaptive radiation depends on the steepness of ecological gradients and the dimensionality of the niche space.</p>
Data from: Periodic environmental disturbance drives repeated ecomorphological diversification in an adaptive radiation of Antarctic fishes
<p><span>The ecological theory of adaptive radiation has profoundly shaped our conceptualization of the rules that govern diversification. However, while many radiations follow classic early burst patterns of diversification as they fill ecological space, the longer-term fates of these radiations depend on many factors, such as climatic stability. In systems with periodic disturbances, species-rich clades can contain nested adaptive radiations of subclades with their own distinct diversification histories, and how adaptive radiation theory applies in these cases is less clear. Here, we investigated patterns of ecological and phenotypic diversification within two iterative adaptive radiations of cryonotothenioid fishes in Antarctica's Southern Ocean: crocodile icefishes and notoperches. For both clades, we observe evidence of repeated diversification into disparate regions of trait space between closely related taxa and into overlapping regions of trait space between distantly related taxa. We additionally find little evidence that patterns of ecological divergence are correlated with evolution of morphological disparity, suggesting that these axes of divergence may not be tightly linked. Finally, we reveal evidence of repeated convergence in sympatry that suggests niche complementarity. These findings reflect the dynamic history of Antarctic marine habitats, and may guide hypotheses of diversification dynamics in environments characterized by periodic disturbance.</span></p>
Hybrid evolution repeats itself across environmental contexts in Texas sunflowers (Helianthus)
<p>To what extent is evolution repeatable? Little is known about whether the evolution of hybrids is more (or less) repeatable than non-hybrids. We used field experimental evolution in annual sunflowers (<em>Helianthus</em>) in Texas to ask the extent to which hybrid evolution is repeatable across environments compared to non-hybrid controls. We created hybrids between <em>Helianthus annuus</em> (L.) and <em>H. debilis</em> (Nutt.) and grew plots of both hybrids and non-hybrid controls through eight generations at three sites in Texas. We collected seeds from each generation and grew each generation × treatment × home site combination at two final common gardens. We estimated the strength and direction of evolution in terms of fitness and 24 traits, tested for repeated versus non-repeated evolution, and assessed overall phenotypic evolution across lineages and in relation to a locally adapted phenotype. Hybrids consistently evolved higher fitness over time while controls did not, though trait evolution varied in strength across home sites. Repeated evolution was more evident in hybrids versus non-hybrid controls, and hybrid evolution was often in the direction of the locally adapted phenotype. Our findings have implications for both the nature of repeatability in evolution and the contribution of hybridization to evolution across environmental contexts.</p>
Borg tandem repeats undergo rapid evolution and are under strong selection to create new intrinsically disordered regions in proteins
<p>This repository contains files that accompany the Schoelmerich <em>et al. </em>(2022) bioRxiv preprint.</p> <p>These files include</p> <p>- all Borg proteins used for protein family clustering (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/all_Borg_proteins.fasta">all_Borg_proteins.fasta</a>)</p> <p>- 37 additional aaTR-proteins from manually curated Borg contigs (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/37_Borg_aaTR-proteins.fasta?versionId=bfdfe7b6-e3b5-48b8-b7e6-a20304097e7d">37_Borg_aaTR-proteins.fasta</a>)</p> <p>- IQ-TREE of Borg DNA polymerases and reference sequences from doi: 10.1093/nar/gkaa760 (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/DNAPolB_iqtree.treefile?versionId=c588a98c-822d-4a2f-a92d-7dcb3b1675f0">DNAPolB_iqtree.treefile</a>)</p> <p>- Borg Sm ribonucleoprotein sequences (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/21_Borg_Sm_ribonucleoproteins.fasta">21_Borg_Sm_ribonucleoproteins.fasta</a>)</p> <p>- Borg MHC sequences (<a href="https://zenodo.org/api/files/f75689a0-d40c-44a6-b154-b74e3594fc04/14_Borg_MHC_proteins.fasta">14_Borg_MHC_proteins.fasta</a>)</p> <p>- AlphaFold2 predicted structural models of Borg Sm ribonucleoproteins and MHCs with aaTRs</p>
data for "Plant genetic effects on microbial hubs impact host fitness in repeated field trials"
<p>These are data tables required for the analysis of the paper "Plant genetic effects on microbial hubs impact host fitness in repeated field trials". <br> All scripts are available at https://forgemia.inra.fr/bbrachi/microbiota_paper.git</p> <p>The folder architecture in the zip files is the same as in the repository: https://forgemia.inra.fr/bbrachi/microbiota_paper.git</p> <p>The dataset includes: </p> <p>- OTU count tables for 16S and ITS</p> <p>- taxonomic assignation</p> <p>- plant seed-set estimates</p> <p>- plant growth data from the B38 experiment. </p> <p>- Metabolomics datasets</p>
Data for: Repeatability of the 20th Century Earthquake Cluster in Mongolia: Paleoseismology along the Tsetserleg Fault (Mongolia)
<p>This dataset is associated to the article "Repeatability of the 20<sup>th</sup> Century Earthquake Cluster in Mongolia: Paleoseismology along the Tsetserleg Fault (Mongolia)" submitted to Journal of Geophysical Research: Solid Earth.</p> <p>It includes the following:</p> <ul> <li>Dataset S1 includes the output of the horizontal offset measurements performed with the LaDiCaOz Matlab GUI.</li> <li>Dataset S2 includes the drone DEMs.</li> </ul>
Training data for 'Repeat masking with RepeatMasker' tutorial (Galaxy Training Material)
<p>Data needed for the 'Repeat masking with RepeatMasker' tutorial (Galaxy Training Material).</p> <p>The assembly was generated following the 'Genome assembly using PacBio data' tutorial</p>
Chromosomal inversions from an initial ecotypic divergence drive a gradual repeated radiation of Galápagos beetles
<p>Island faunas exhibit some of the most iconic examples where similar forms repeatedly evolve within different islands. Yet, whether these deterministic evolutionary trajectories within islands are driven by an initial, singular divergence and the subsequent exchange of individuals and adaptive genetic variation between islands remains unclear. Here, we address this issue using a gradual, repeated evolution of low-dispersive highland ecotypes from a dispersive lowland ecotype of <em>Calosoma</em> beetles along the island progression of the Galápagos. We show that repeated highland adaptation involved selection on multiple shared alleles within extensive chromosomal inversions that originated from an initial adaptation event on the oldest island. These highland inversions first spread through dispersal of highland individuals. Subsequent admixture with the widely distributed lowland ecotype resulted in polymorphic dispersive populations from which the highland populations evolved on the youngest islands. Our findings emphasize the significance of an ancient divergence in driving repeated evolution and highlight how a mixed contribution of inter-island colonization and within-island evolution can shape parallel species communities on islands.</p>
A comprehensive catalog of approxiamte short tandem repeat regions on autosomes and sex chromosomes of the human genome GRCh38
<p>To obtain a general TR catalog across the human genome, we identified genomic intervals with a stretch of approximate repetitions of a DNA motif ranging from 1-6bp on GRCh38 autosomes and sex chromosomes by using STRfinder (v1.0), and each STR region was annotated based on gencode.V38 (https://www.gencodegenes.org/human/release_38.html). To end up, we successfully found 1,656,159 TR intervals, covering 1.107653% (34.2 Mbp) of GRCh38 (https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta). </p>
Figure 2 in The bioprotective role of irradiated hibiscus against harmful effects of using repeatedly frying edible oil
Figure 2. Showing both Macroscopic images and histological study of Liver samples from all studied groups, "A" normal group, and "B" from "G2", showing completely normal liver and normal hepatic parenchyma; note the normal central vein, hepatocytes, and blood sinusoids, while in "C", frying oil group"G3" showing fibrosis and congestion in the central vein (arrow head), Swelling degeneration of some hepatocytes (arrows) with focal areas of necrotic hepatocytes. Whereas, In both "D" as well as, "E" hibiscus groups, liver is completely normal and showing healthy and normal portal area; note the normal bile duct, hepatic artery, and portal vein, (HE X400) (Score lesion: 0).
Figure 1 in The bioprotective role of irradiated hibiscus against harmful effects of using repeatedly frying edible oil
Figure 1. Showing the levels of oxygen consumption in studied groups, there are significant decreases in oxygen consumption in frying oil group "G3" compared with all groups, while there are significant increases in oxygen consumption in hibiscus groups "G4 and G5" compared with "G3".
Fig. 3 in Repeatability Analysis Of Egg Shape In A Wild Tree Sparrow (Passer Montanus) Population: A Sensitive Method For Egg Shape Description
Fig. 3. The effect of egg-photographing on the description of outline. Panel a shows ten outlines described following the photos of ten randomly chosen eggs, panel b shows ten outlines described fol-
Fig. 2 in Repeated stressors do not provoke habituation or accumulation of the stress response in the catfish Rhamdia quelen
Fig. 2. Plasma cortisol concentrations of R. quelen (Quoy & Gaimard) fingerlings exposed to sequential acute stressors. Comparison of responses to two similar stressors and a third different stressor in experiment "A" and comparison of responses to three sequential stressors of the same type in experiment "B." Data are expressed in terms of mean ± S.E.M. values. The different small letters above the histograms indicate statistical differences by ANOVA, followed by Tukey's range test. (n = 8-9).
Fig. 1 in Repeated stressors do not provoke habituation or accumulation of the stress response in the catfish Rhamdia quelen
Fig. 1. Schematic representation of the experimental design of both groups of experiments. In experiment "A," Rhamdia quelen (Quoy & Gaimard) fingerlings were sequentially exposed to the same stressors twice and to a different stress the third time. In experiment "B," R. quelen fingerlings were sequentially exposed as the same stressors 3 times.
ScienceDex guides
Understand access before you commit
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.