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4,563 results for “correlations”
Data from: Reduced skin bacterial diversity correlates with increased pathogen infection intensity in an endangered amphibian host
The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects the skin of amphibians, and has caused severe declines and extinctions of amphibians globally. In this study, we investigate the interaction between Bd and the bacterial skin microbiome of the endangered Sierra Nevada yellow-legged frog, Rana sierrae, using both culture-dependent and culture-independent methods. Samples were collected from two populations of R. sierrae that likely underwent Bd epizootics in the past, but that continue to persist with Bd in an enzootic disease state, and we address the hypothesis that such "persistent" populations are aided by mutualistic skin microbes. Our 16S rRNA metabarcoding data reveal that the skin microbiome of highly infected juvenile frogs is characterized by significantly reduced species richness and evenness, and by strikingly lower variation between individuals, compared to juveniles and adults with lower infection levels. Over 90% of DNA sequences from the skin microbiome of highly infected frogs were derived from bacteria in a single order, Burkholderiales, compared to just 54% in frogs with lower infection levels. In a culture-dependent Bd-inhibition assay, the bacterial metabolites we evaluated all inhibited the growth of Bd. Together, these results illustrate the disruptive effects of Bd infection on host skin microbial community structure and dynamics, and suggest possible avenues for the development of anti-Bd probiotic treatments.
Heterozygosity–fitness correlations reveal inbreeding depression in neonatal body size in a critically endangered rock iguana
Inbreeding depression, though challenging to identify in nature, may play an important role in regulating the dynamics of small and isolated populations. Conversely, greater expression of genetic load can enhance opportunities for natural selection. Conditional expression concentrates these opportunities for selection and may lead to failure of detection. This study investigates the possibility for age-dependent expression of inbreeding depression in a critically endangered population of rock iguanas, Cyclura nubila caymanensis. We employ heterozygote-fitness correlations to examine the contributions of individual genetic factors to body size, a fitness-related trait. Nonsignificant reductions in homozygosity (up to 7%) were detected between neonates and individuals surviving past their first year, which may reflect natural absorption of inbreeding effects by this small, fecund population. The majority of variation in neonate body size was attributed to maternal or environmental effects (i.e., clutch identity and incubation length); however, heterozygosity across 22 microsatellite loci also contributed significantly and positively to model predictions. Conversely, effects of heterozygosity on fitness were not detectable when adults were examined, suggesting that inbreeding depression in body size may be age dependent in this taxon. Overall, these findings emphasize the importance of taking holistic, cross-generational approaches to genetic monitoring of endangered populations.
Data from: Correlated divergence of female and male genitalia in replicated lineages with ongoing ecological speciation
Divergence of genital traits among lineages has the potential to serve as a reproductive isolating barrier when copulation, insemination, or fertilization are inhibited by incompatibilities between female and male genitalia. Despite widespread evidence for genital trait diversity among closely related lineages and coevolution of female and male genitalia within lineages, few studies have investigated genital evolution during the early stages of speciation. We quantified genital variation in replicated population pairs of Poecilia mexicana with ongoing ecological speciation between sulfidic (H2S-containing) and nearby non-sulfidic habitats. These analyses revealed rapid and correlated divergence of female and male genitalia across evolutionarily independent population pairs exposed to divergent selection regimes. Both sexes exhibited convergent evolution of genital traits among populations inhabiting similar habitat types. Our results demonstrate that genital evolution can occur during the early stages of speciation-with-gene-flow, potentially as a result of variation in the intensity of sexual conflict among populations. Our results suggest genitalia may contribute to early stages of divergence, and challenge the generality of previously suggested mechanisms of genital evolution in poeciliids.
Data from: Stability of spontaneous, correlated activity in mouse auditory cortex
<p>Neural systems can be modeled as complex networks in which neural elements are represented as nodes linked to one another through structural or functional connections. The resulting network can be analyzed using mathematical tools from network science and graph theory to quantify the system's topological organization and to better understand its function. Here, we used two-photon calcium imaging to record spontaneous activity from the same set of cells in mouse auditory cortex over the course of several weeks. We reconstruct functional networks in which cells are linked to one another by edges weighted according to the correlation of their fluorescence traces. We show that the networks exhibit modular structure across multiple topological scales and that these multi-scale modules unfold as part of a hierarchy. We also show that, on average, network architecture becomes increasingly dissimilar over time, with similarity decaying monotonically with the distance (in time) between sessions. Finally, we show that a small fraction of cells maintain strongly-correlated activity over multiple days, forming a stable temporal core surrounded by a fluctuating and variable periphery. Our work indicates a framework for studying spontaneous activity measured by two-photon calcium imaging using computational methods and graphical models from network science. The methods are flexible and easily extended to additional datasets, opening the possibility of studying cellular level network organization of neural systems and how that organization is modulated by stimuli or altered in models of disease.</p>
Simulating gas giant exoplanet atmospheres with Exo-FMS: Comparing semi-grey, picket fence and correlated-k radiative-transfer schemes.
<p>NetCDF dataset for paper titled: Simulating gas giant exoplanet atmospheres with Exo-FMS: Comparing semi-grey, picket fence and correlated-k radiative-transfer schemes.</p> <p> </p> <p>Contains:</p> <p>1. Heng benchmark GCM data</p> <p>2. Rauscher benchmark GCM data</p> <p>3. HD209 model using semi-grey RT</p> <p>4. HD 209 model using non-grey picket fence RT</p> <p>5. HD 209 model using corr-k RT scheme</p>
Data from: Correlated evolution between climate and suites of traits along a fast-slow continuum in the radiation of Protea
Evolutionary radiations are responsible for much of Earth's diversity, yet the causes of these radiations are often elusive. Determining the relative roles of adaptation and geographic isolation in diversification is vital to understanding the causes of any radiation, and whether a radiation may be labeled as 'adaptive' or not. Across many groups of plants, trait-climate relationships suggest that traits are an important indicator of how plants adapt to different climates. In particular, analyses of plant functional traits in global databases suggest that there is an "economics spectrum" along which combinations of functional traits covary along a fast-slow continuum. We examine evolutionary associations among traits and between trait and climate variables on a strongly supported phylogeny in the iconic plant genus Protea to identify correlated evolution of functional traits and the climatic-niches that species occupy. Results indicate that trait diversification in Protea has climate associations along two axes of variation: correlated evolution of plant size with temperature and leaf investment with rainfall. Evidence suggests that traits and climatic-niches evolve in similar ways, although some of these associations are inconsistent with global patterns on a broader phylogenetic scale. When combined with previous experimental work suggesting that trait-climate associations are adaptive in Protea, the results presented here suggest that trait diversification in this radiation is adaptive.
Data from: Functional traits and community composition: a comparison among community-weighted means, weighted correlations, and multilevel models
1. Of the several approaches that are used to analyze functional trait-environment relationships, the most popular is community-weighted mean regressions (CWMr) in which species trait values are averaged at the site level and then regressed against environmental variables. Other approaches include model-based methods and weighted correlations of different metrics of trait-environment associations, the best known of which is the fourth-corner correlation method. 2. We investigated these three general statistical approaches for trait-environment associations: CWMr, five weighted correlation metrics (Peres-Neto et al. 2017), and two multilevel models (MLM) using four different methods for computing p-values. We first compared the methods applied to a plant community dataset. To determine the validity of the statistical conclusions, we then performed a simulation study. 3. CWMr gave highly significant associations for both traits, while the other methods gave a mix of support. CWMr had inflated type I errors for some simulation scenarios, implying that the significant results for the data could be spurious. The weighted correlation methods had generally good type I error control but had low power. One of the multilevel models, that from Jamil et al. (2013), had both good type I error control and high power when an appropriate method was used to obtain p-values. In particular, if there was no correlation among species in their abundances among sites, a parametric bootstrap likelihood ratio test (LRT) gave the best power. When there was correlation among species in their abundances, a conditional parametric LRT had correct type I errors but had lower power. 4. There is no overall best method for identifying trait-environment associations. For the simple task of testing, one-by-one, associations between single environmental variables and single traits, the weighted correlations with permutation tests all had good type I error control, and their ease of implementation is an advantage. For the more complex task of multivariate analyses and model fitting, and when high statistical power is needed, we recommend MLM2 (Jamil et al. 2013); however, care must be taken to ensure against inflated type I errors. Because CWMr exhibited highly inflated type I error rates, it should always be avoided. 2. We investigated these three general statistical approaches for trait-environment associations: CWMr, five weighted correlation metrics (Peres-Neto et al. 2017), and two multilevel models (MLM) using five different methods for computing p-values. We first compared the methods applied to a plant community dataset. To determine the validity of the statistical conclusions, we then performed a simulation study. 3. CWMr gave highly significant associations for both traits, while the other methods gave a mix of support. CWMr had inflated type I errors for some simulation scenarios. The weighted correlation methods had generally good type I error control but had low power. One of the multilevel models, that from Jamil et al. (2013), had both good type I error control and high power when an appropriate method was used to obtain p-values. In particular, if there was no correlation among species in their abundances among sites, a parametric bootstrap likelihood ratio test (LRT) gave the best power. When there was correlation among species in their abundances, a conditional parametric LRT had correct type I errors but suffered from low power. 4. There is no overall best method for identifying trait-environment associations. For the simple task of testing, one-by-one, associations between single environmental variables and single traits, the weighted correlations with permutation tests all had good type I error control, and their ease of implementation is an advantage. For the more complex task of multivariate analyses and model fitting, and when high statistical power is needed, we recommend MLM2 (Jamil et al. 2013); however, care must be taken to ensure against inflated type I errors. Because CWMr exhibited highly inflated type I error rates, it should be avoided.
Data from: Artificial selection on sexual aggression: correlated traits and possible trade‐offs
<p>Forced copulation is an extreme form of sexual aggression that can affect the evolution of sex-specific anatomy, morphology and behavior. To characterize mechanistic and evolutionary aspects of forced copulation, we artificially selected male fruit flies based on their ability to succeed in the naturally prevalent behavior of forced matings with newly eclosed (teneral) females. The low and high forced copulation lineages showed rapid divergence, with the high lineages ultimately showing twice the rates of forced copulation as the low lineages. While males from the high lineages spent more time aggressively pursuing and mounting teneral females, their behavior towards non-teneral and heterospecific females was similar to that of males from the low lineages. Males from the low and high lineages also showed similar levels of male-male aggression. This suggests little or no genetic correlations between sexual aggression and non-aggressive pursuit of females, and between male aggression towards females and males. Surprisingly however, males from the high lineages had twice as high mating success than males from the low lineages when allowed to compete for consensual mating with mature females. In further experiments, we found no evidence for trade-offs associated with high forced mating rates: males from the high lineages did not have lower longevity than males from the low lineages when housed with females, and four generations of relaxed selection did not lead to convergence in forced mating rates. Our data indicate complex interactions among forced copulation success and consensual mating behaviour, which we hope to clarify in future genomic work. </p>
Data from: Correlational selection on personality and social plasticity: morphology and social context determine behavioural effects on mating success
Despite a central line of research aimed at quantifying relationships between mating success and sexually dimorphic traits (e.g., ornaments), individual variation in sexually selected traits often explains only a modest portion of the variation in mating success. Another line of research suggests that a significant portion of the variation in mating success observed in animal populations could be explained by correlational selection, where the fitness advantage of a given trait depends on other components of an individual's phenotype and/or its environment. We tested the hypothesis that interactions between multiple traits within an individual (phenotype dependence) or between an individual's phenotype and its social environment (context dependence) can select for individual differences in behaviour (i.e., personality) and social plasticity. To quantify the importance of phenotype- and context-dependent selection on mating success, we repeatedly measured the behaviour, social environment and mating success of about 300 male stream water striders, Aquarius remigis. Rather than explaining individual differences in long-term mating success, we instead quantified how the combination of a male's phenotype interacted with the immediate social context to explain variation in hour-by-hour mating decisions. We suggest that this analysis captures more of the mechanisms leading to differences in mating success. Males differed consistently in activity, aggressiveness and social plasticity. The mating advantage of these behavioural traits depended on male morphology and varied with the number of rival males in the pool, suggesting mechanisms selecting for consistent differences in behaviour and social plasticity. Accounting for phenotype and context dependence improved the amount of variation in male mating success we explained statistically by 30–274%. Our analysis of the determinants of male mating success provides important insights into the evolutionary forces that shape phenotypic variation. In particular, our results suggest that sexual selection is likely to favour individual differences in behaviour, social plasticity (i.e., individuals adjusting their behaviour), niche preference (i.e., individuals dispersing to particular social conditions) or social niche construction (i.e., individuals modifying the social environment). The true effect of sexual traits can only be understood in interaction with the individual's phenotype and environment.
Phylogenetic signal and evolutionary correlates of urban tolerance in a widespread neotropical lizard clade
<p>Urbanization is intensifying worldwide, and while some species tolerate and even exploit urban environments, many others are excluded entirely from this new habitat. Understanding the factors that underlie tolerance of urbanization is thus of rapidly growing importance. Here we examine urban tolerance across a diverse group of lizards: Caribbean members of the neotropical genus Anolis. Our analyses reveal that urban tolerance has strong phylogenetic signal, suggesting that closely related species tend to respond similarly to urban environments. We propose that this characteristic of urban tolerance in anoles may be used to forecast the possible responses of species to increasing urbanization. In addition, we identified several key ecological and morphological traits that tend to be associated with tolerance in Anolis. Specifically, species experiencing hot and dry conditions in their natural environment and those that maintain higher body temperatures tend to have greater tolerance of urban habitats. We also found that tolerance of urbanization is positively associated with toepad lamella number, and negatively associated with ventral scale density and relative hindlimb length. The identification of factors that predispose a species to be more or less urban tolerant can provide a starting point for conservation and sustainable development in our increasingly urbanized world.</p>
Data from: Comparative analysis of the shape and size of the middle ear cavity of turtles reveals no correlation with habitat ecology
<p>The middle ear of turtles differs from other reptiles in being separated into two distinct compartments. Several ideas have been proposed as to why the middle ear is compartmentalized in turtles, most suggesting a relationship with underwater hearing. Extant turtle species span fully marine to strictly terrestrial habitats, and ecomorphological hypotheses of turtle hearing predict that this should correlate with variation in the structure of the middle ear due to differences in the fluid properties of water and air. We investigate the shape and size of the air-filled middle ear cavity of 56 extant turtles using 3D data and phylogenetic comparative analysis to test for correlations between habitat preferences and the shape and size of the middle ear cavity. Only weak correlations are found between middle ear cavity size and ecology, with aquatic taxa having proportionally smaller cavity volumes. The middle ear cavity of turtles exhibits high shape diversity among species, but we found no relationship between this shape variation and ecology. Surprisingly, the estimated acoustic transformer ratio, a key functional parameter of impedance-matching ears in vertebrates, also shows no relation to habitat preferences (aquatic/terrestrial) in turtles. We suggest that middle ear cavity shape may be controlled by factors unrelated to hearing, such as the spatial demands of surrounding cranial structures. A review of the fossil record suggests that the modern turtle ear evolved during the Early to Middle Jurassic in stem turtles broadly adapted to freshwater and terrestrial settings. This, combined with our finding that evolutionary transitions between habitats caused only weak evolutionary changes in middle ear structure, suggests that tympanic hearing in turtles evolved as a compromise between subaerial and underwater hearing.</p>
Multiple Sclerosis: Cerebral Circulation Time is prolonged and not correlated with expanded disability status scale (EDSS). A study using digital subtracted angiography
<p>Dataset used to study the relationship between cerebral circulation time (CCT) and some clinical evidences, e.g. expand disability status scale (EDSS), disease duration, age at onset,... CCT was measured through the digital subtraction angiography (DSA) technique. </p> <p>Statistical Parametric Mapping software (SPM, Wellcome Department of Cognitive Neurology, Institute of Neurology, University College London; http://www.fil.ion.ucl.ac.uk/spm/) and ad-hoc scripts developed in the MATLAB scientific computing environment (http://www.mathworks.com, MathWorks, MA, USA) were applied to valuate the lesion volume and brain volume in MS patients.</p>
EEG data for "Conversation electrified: ERP correlates of speech act recognition in underspecified utterances"
<p>Please refer to the publication in Plos One for a description of the experiment and data analysis: Gisladottir RS, Chwilla DJ, Levinson SC (2015) Conversation Electrified: ERP Correlates of Speech Act Recognition in Underspecified Utterances. PLoS ONE 10(3): e0120068. doi: 10.1371/journal.pone.0120068</p>
Cortical correlates of a translating point-light walker; an event-related potentials study
<p>EEG recordings for all subjects (S1-S13) considered in the study "Cortical correlates of a translating point-light walker; an event-related potentials study". Data are in Brain Vision Analizer (BVA) format. They can be fully explored and analyzed using freely available software, like EEGLab, Brainstorm, Fieldtrip, BIOSIG or NPXLab. Trigger codes S 1, S 2, S 3 and S 4 respectively correspond to the condition 'cwalker' 'twalker' 'cscrambled' 'tscrambled' compared in the study.</p>
Digital Image Correlation Workshop at the University of Manchester, September 2016
<p>Enabling Process Technologies sponsored a Digital Image Correlation (DIC) workshop on 8 September, 2016 at the School of Mechanical, Aerospace and Civil Engineering at the University of Manchester. Alistair Tofts, Director of Sales & Marketing at Correlated Solutions attended and provided a series of presentations covering DIC theory, and the working principles of the VIC lineup of DIC software.</p> <p>Afterwards, three discrete tests were conducted with the same specimen and speckle on three different frames and setups:</p> <ul> <li>High speed: Zwick HTM-5030 test frame, Photron SA.1 high speed cameras</li> <li>Quasi-static 2D: Instron 5969 test frame, Point Grey Research machine vision camera</li> <li>Quasi-static 3D: Instron 5659 test frame, 2 Point Grey Research machine vision cameras</li> </ul> <p>The archives included in this dataset are:</p> <ul> <li>Presentations: contains the slides from the presentations given by Alistair Tofts, as well as an outline/agenda given by Matthew Roy.</li> <li>3D_fast, 2D_slow and 3D_slow: correspond to the tests/setup described above, including all calibration and test images, along with VIC metadata for replaying analyses.</li> </ul> <p>Specimen geometry is shown on slide 6 of ~/Presentation/DICWorkshopPresSept2016_MJR.pptx, and markdown readme files are included to describe the test and data.</p>
Data files related to the article "Different meditation practices share the same neuronal correlates: increased gamma brainwave amplitude compared to control in three different meditation traditions
<p>Files description:</p> <p>- EEG datasets: the EEG data preprocessed in EEGLAB format</p> <p>- chanlocs.mat: contains channel characteristics for the study / used<br> to plot topographical maps of the data</p> <p> - 60110Hz_spec_data_imw_medit_combined.mat : contains spectrum data between 60 and 110 Hz for all 4 groups of subjects in combined instructed mind-wandering and meditation condition</p> <p> - 60110Hz_spec_data_medit.mat : contains spectrum data between 60<br> and 110 Hz for all 4 groups of subjects in meditation condition</p> <p> - 711Hz_spec_data_medit: contains spectrum data between 7 and 11 Hz for each group in meditation condition</p> <p>- boxplot_gamma.csv and boxplot_alpha.csv : median spectrum in the gamma and alpha ranged used to generate figure 4 B and 6 B</p> <p>- R_code_boxplot.r : code to generate boxplot using boxplot_gamma or boxplot_alpha.csv files</p>
A Multi-Scale Correlative Investigation of Ductile Fracture: supporting data
<p>These files are the raw X-ray CT datasets captured using a Custom Bay instrument as detailed in the article: A Multi-Scale Correlative Investigation of Ductile Fracture (under review as of January 2017). </p>
Kappa matrices presented in "An EFT approach to baryon number violation: lower limits on the new physics scale and correlations between nucleon decay modes" arXiv:2312.13361
<p>In this archive we provide the kappa matrices introduced in Sec 2.4 of our paper <em>An EFT approach to baryon number violation: lower limits on the new physics scale and correlations between nucleon decay modes</em> <a href="https://arxiv.org/abs/2312.13361">2312.13361</a>, also <a href="https://link.springer.com/article/10.1007/JHEP07(2024)004">published in JHEP</a>. These are the numerical values that are presented as matrix plots in Appendix C. Here they are packaged into CSV files, whose first row is the row/column label.</p> <p>Please consult the README for further information on how to use these data.</p> <p><em>Version 3: Fixed error common to d=7 matrices.</em></p>
Data for: When Correlation Matters: On Uncertainty Propagation In The Case Of Data Disaggregation
<p>This is the data repository for our study on “When Correlation Matters: On Uncertainty Propagation In The Case Of Data Disaggregation” submitted to the Journal of Industrial Ecology (JIE).</p> <p>I contains:</p> <ul> <li>The data behind the all numeric plots</li> <li>The data needed to reproduce the case-study results in the Supplementary Information (check out V1)</li> </ul> <p> </p> <p>To reproduce our results you need to download the files from this repo, our code from Github (https://github.com/simschul/uncertainty_disaggregation) and put the data into the `./data` folder. </p> <p>The data is an intermediate output from an earlier study: https://essd.copernicus.org/articles/16/2669/2024/essd-16-2669-2024.html </p> <p>For more information how those intermediate results were created please refer to the paper and the code (https://github.com/simschul/uncertainty_GHG_accounts)</p> <p> </p> <p> </p>
Correlation challenges for North Sea offshore wind power: a Norwegian case study
<p>Dataset and results from this study: Hjelmeland, M., & Nøland, J. K. (2023). Correlation challenges for North Sea offshore wind power: a Norwegian case study. Scientific Reports 2023 13:1, 13(1), 1–17. <a href="https://doi.org/10.1038/s41598-023-45829-2">https://doi.org/10.1038/s41598-023-45829-2</a></p><p>The git hub repo with source code can be found here: <a href="https://github.com/martinhjel/wind-covariation">https://github.com/martinhjel/wind-covariation</a></p>
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.