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887 results for “relaxation”
Relaxed selection and the evolution of Chasmogamous flower of Impatiens capensis
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Data from: But the clock, tick-tock: The preeminence of relaxed clock models in total-evidence dated phylogenetics
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Habitat deterioration relaxes resource competition and sexual selection in the threespine stickleback
The operation of sexual selection depends on ecological conditions. Thus, changes in environmental conditions because of human activities can alter the strength and direction of sexual selection, with implications for evolutionary trajectories and the viability of populations. We show that aquatic algal blooms can relax the operation of sexual selection by influencing which males are available to attract females. This is by influencing the ability of males to maintain a resource needed in mate attraction. When we exposed two competing threespine stickleback males (Gasterosteus aculeatus), whose attractiveness to females was known, to either clear or algal-turbid water, nest abandonment was more common in clear water, and it was usually the unattractive male that abandoned his nest. In turbid water, on the other hand, nest abandonments were less common and when they occurred, the probability increased that the attractive male abandoned his nest, and that the unattractive male subsequently occupied it. This change in the composition of nesting males increased the mating success of unattractive males. Thus, our results reveal a new mechanism through which habitat deterioration can influence sexual selection, by altering success in the competition for a resource critical in mate attraction, a territory with a nest in this case. This could be a common mechanism, considering the prevalence of resource competition in mate choice systems. On a broader level, our results emphasise the importance of considering the impact of environmental changes on the outcome of resource competition when investigating the influence that environmental disturbances have on the operation of sexual selection and thereby on evolutionary processes and population dynamics.
The relaxed structures of PbTiO3 and F doped PbTiO3
<p>This data repository includes all the relaxed configurations of PbTiO3 and F doped PbTiO3 that were optimized using the VASP code. </p> <p>In the tetragonal P4mm phase of PTO, there are two inequivalent crystallographic sites for O, i.e. the Wyckoff 1b (1/2, 1/2, z) and 2c (1/2, 0, z) positions. Upon doping, the F ions can occupy 1b (F@1b), 2c (F@2c), or both 1b and 2c (F@1b&2c) positions. Hence, we considered all possible inequivalent doped configurations within the 1×2×5 supercell, namely 3 and 35 configurations for PTOF10 and PTOF20, respectively. For comparison, we also studied the undoped 1×2×5 PTO superlattice. Therefore, there are 39 structure files (POSCAR) in this data repository. More details can be found in the README.md file.</p>
Dataset for "Sorption, anomalous water transport and dynamic porosity in cement paste: A spatially localised 1H NMR relaxation study and a proposed mechanism"
<p>This record is the dataset for Figures 4, 5, 6, 7, 8 and 9 in the journal article "Sorption, anomalous water transport and dynamic porosity in cement paste: A spatially localised 1H NMR relaxation study and a proposed mechanism" published in Cement and Concrete Research, Volume 133, July 2020, 106045, https://doi.org/10.1016/j.cemconres.2020.106045.</p> <p>Abstract: The link between anomalous water sorption and dynamic porosity in cement pastes is explored using spatially resolved GARField1H nuclear magnetic resonance (NMR) relaxation analysis. A model is developed in which the effective capillary diffusion coefficient is dependent on the instantaneous pore size distribution. This and earlier data show changes in pore size distribution resultant from changes in saturation that do not occur instantaneously with changes in degree of saturation. Therefore, it is assumed that the pore size distribution is always relaxing exponentially towards a (saturation dependent) equilibrium. It follows that the diffusivity is sample history (i.e. time) dependent as well as saturation dependent. This is sufficient to explain anomalies in rapid capillary water sorption. The same concepts are applied to slow drying. In this case, porosity changes occur on a timescale much shorter than drying so the system is always in dynamic equilibrium and anomalies are therefore not seen.</p>
Data from: The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?
The use of nucleotide and amino acid sequences allows improved understanding of the timing of evolutionary events of life on earth. Molecular estimates of divergence times are, however, controversial and are generally much more ancient than suggested by the fossil record. The limited number of genes and species explored and pervasive variations in evolutionary rates are the most likely sources of such discrepancies. Here we compared concatenated amino acid sequences of 129 proteins from 36 eukaryotes to determine the divergence times of several major clades, including animals, fungi, plants, and various protists. Due to significant variations in their evolutionary rates, and to handle the uncertainty of the fossil record, we used a Bayesian relaxed molecular clock simultaneously calibrated by six paleontological constraints. We show that, according to 95% credibility intervals, the eukaryotic kingdoms diversified 950–1,259 million years ago (Mya), animals diverged from choanoflagellates 761–957 Mya, and the debated age of the split between protostomes and deuterostomes occurred 642–761 Mya. The divergence times appeared to be robust with respect to prior assumptions and paleontological calibrations. Interestingly, these relaxed clock time estimates are much more recent than those obtained under the assumption of a global molecular clock, yet bilaterian diversification appears to be ≈100 million years more ancient than the Cambrian boundary.
Examining the link between relaxed predation and bird colouration on islands
<p>Insular ecosystems share analogous ecological conditions, leading to patterns of convergent evolution that are collectively termed the "island syndrome". In birds, part of this syndrome is a tendency for a duller plumage, possibly as a result of relaxed sexual selection and the reduced need for species recognition. Despite this global pattern, some insular species display a more colourful plumage than their mainland relatives, but why this occurs has remained unexplained. Here, we examine the hypothesis that these cases of increased plumage colouration on islands could arise through a relaxation of predation pressure. We used comparative analyses to investigate whether average insular richness of raptors of suitable mass influences the plumage colourfulness and brightness across 110 pairs of insular endemic species and their closest mainland relatives. As predicted, we find a likely negative relationship between insular colouration and insular predation whilst controlling for mainland predation and colouration, so that species were more likely to become more colourful as the number of insular predators decreased. In contrast, plumage brightness was not influenced by predation pressure. Relaxation from predation, together with drift, might thus be a key mechanism of species phenotypic responses to insularity.</p>
Data from: Major radiations in the evolution of caviid rodents: reconciling fossils, ghost lineages, and relaxed molecular clocks
BACKGROUND: Caviidae is a diverse group of caviomorph rodents that is broadly distributed in South America and is divided into three highly divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant and diverse since the late Miocene. Caviids belongs to Cavioidea sensu stricto (Cavioidea s.s.) that also includes a diverse assemblage of extinct taxa recorded from the late Oligocene to the middle Miocene of South America ("eocardiids"). RESULTS: A phylogenetic analysis combining morphological and molecular data is presented here, evaluating the time of diversification of selected nodes based on the calibration of phylogenetic trees with fossil taxa and the use of relaxed molecular clocks. This analysis reveals three major phases of diversification in the evolutionary history of Cavioidea s.s. The first two phases involve two successive radiations of extinct lineages that occurred during the late Oligocene and the early Miocene. The third phase consists of the diversification of Caviidae. The initial split of caviids is dated as middle Miocene by the fossil record. This date falls within the 95% higher probability distribution estimated by the relaxed Bayesian molecular clock, although the mean age estimate ages are 3.5 to 7 Myr older. The initial split of caviids is followed by an obscure period of poor fossil record (refered here as the Mayoan gap) and then by the appearance of highly differentiated modern lineages of caviids, which evidentially occurred at the late Miocene as indicated by both the fossil record and molecular clock estimates. CONCLUSIONS: The integrated approach used here allowed us identifying the agreements and discrepancies of the fossil record and molecular clock estimates on the timing of the major events in cavioid evolution, revealing evolutionary patterns that would not have been possible to gather using only molecular or paleontological data alone.
Data from: Effect of Relaxation-Dependent Adhesion on Pre-Sliding Response of Cartilage
Possible links between adhesive properties and pre-sliding (static) friction response of cartilage are not fully understood in the literature. The aims of this study are to investigate the relation between adhesion and relaxation time in articular cartilage, and to investigate the effect of relaxation-dependent adhesion on pre-sliding response of cartilage. Adhesion tests were performed to evaluate the work of adhesion of cartilage at different relaxation times. Friction tests were conducted to identify the pre-sliding friction response of cartilage at relaxation times corresponding to adhesion tests. The pre-sliding friction response of cartilage was systematically linked to the work of adhesion and contact conditions by a slip-based failure model. It was found that the work of adhesion increases with relaxation time. Also, the work of adhesion is linearly correlated to the resistance to slip-based failure. In addition, as the work of adhesion increases, the critical adhered area at the moment of failure increases, and the propagation rate of the annular slip (crack) area toward its center increases. These findings offer the mechanistic explanation of the pre-sliding friction behavior and stick-slip response of soft hydrated interfaces such as articular cartilage and hydrogels. Besides, the linear correlation between adhesion and threshold to slip-based failure enables estimation of adhesive strength of such interfaces directly from pre-sliding friction response (e.g., shear wave elastography).
Data from: On the fate of seasonally plastic traits in a rainforest butterfly under relaxed selection
Many organisms display phenotypic plasticity as adaptation to seasonal environmental fluctuations. Often, such seasonal responses entails plasticity of a whole suite of morphological and life-history traits that together contribute to the adaptive phenotypes in the alternative environments. While phenotypic plasticity in general is a well-studied phenomenon, little is known about the evolutionary fate of plastic responses if natural selection on plasticity is relaxed. Here, we study whether the presumed ancestral seasonal plasticity of the rainforest butterfly Bicyclus sanaos (Fabricius, 1793) is still retained despite the fact that this species inhabits an environmentally stable habitat. Being exposed to an atypical range of temperatures in the laboratory revealed hidden reaction norms for several traits, including wing pattern. In contrast, reproductive body allocation has lost the plastic response. In the savannah butterfly, B. anynana (Butler, 1879), these traits show strong developmental plasticity as an adaptation to the contrasting environments of its seasonal habitat and they are coordinated via a common developmental hormonal system. Our results for B. sanaos indicate that such integration of plastic traits – as a result of past selection on expressing a coordinated environmental response – can be broken when the optimal reaction norms for those traits diverge in a new environment.
Data from: Diapause induction and relaxed selection on alternative developmental pathways in a butterfly
1. Seasonal phenotypic plasticity entails differential trait expression depending on the time of season. The facultative induction of winter diapause in temperate insects is a developmental switch mechanism often leading to differential expression in life history traits. However, when there is a latitudinal shift from a bivoltine to univoltine life cycle, selection for pathway-specific expression is disrupted, which may allow drift towards less optimal trait values within the non-selected pathway. 2. We use field- and experimental data from five Swedish populations of Pararge aegeria to investigate latitudinal variation in voltinism, local adaptation in the diapause switch, and footprints of selection on pathway-specific regulation of life history traits and sexual dimorphism in larval development. 3. Field data clearly illustrated how natural populations gradually shift from bivoltinism to univoltinism as latitude increases. This was supported experimentally as the decrease in direct development at higher latitudes was accompanied by increasing critical daylengths, suggesting local adaptation in the diapause switch. 4. The differential expression among developmental pathways in development time and growth rate was significantly less pronounced in univoltine populations. Univoltine populations showed no significant signs of protandry during larval development, suggesting that erosion of the direct development pathway under relaxed selection has led to the loss of its sex-specific modifications.
Hartree potentials and geometries of relaxed on-surface ice clusters in "Structure discovery in Atomic Force Microscopy imaging of ice"
<p>Hartree potentials and geometries of on-surface DFT-relaxed ice clusters used in the paper "Structure discovery in Atomic Force Microscopy imaging of ice".</p><p>The data are saved in a compressed .tar.gz archive. The unpacked archive contains the data for each ice cluster in the .xsf format. The density functional theory (DFT) calculations were done using the Vienna Ab-initio Simulation Package with the optB86b-vdW density functional.</p>
Data and GDS file for "Methods to achieve near-millisecond energy relaxation and dephasing times for a superconducting transmon qubit"
<p>Data and GDS files for "Methods to achieve near-millisecond energy relaxation and dephasing times for a superconducting transmon qubit"</p>
Data from: Relaxed risk of predation drives parallel evolution of stickleback behaviour
<p><span>The occurrence of similar phenotypes in multiple independent populations derived from common ancestral conditions (<em>viz</em>. parallel evolution) is a testimony of evolution by natural selection. Parallel evolution implies that populations share a common phenotypic response to a common selection pressure associated with habitat similarity. Examples of parallel evolution at genetic and phenotypic levels are fairly common, but the driving selective agents often remain elusive. Similarly, the role of phenotypic plasticity in facilitating early stages of parallel evolution is unclear. We investigated whether the relaxation of predation pressure associated with the colonization of freshwater ponds by nine-spined sticklebacks (<em>Pungitius pungitius</em>) likely explains the divergence in complex behaviours between marine and pond populations, and whether this divergence is parallel. Using laboratory-raised individuals exposed to different levels of perceived predation risk, we calculated vectors of phenotypic divergence for four behavioural traits between habitats and predation risk treatments. We found a significant correlation between the directions of evolutionary divergence and phenotypic plasticity, suggesting that divergence in behaviour between habitats is aligned with the response to relaxation of predation pressure. Finally, we show alignment across multiple pairs of populations, and that relaxation of predation pressure has likely driven parallel evolution of behaviour in this species.</span></p>
Short lifetime components in the relaxation of boron acceptors in silicon
<p>The data is that described in 'Short lifetime components in the relaxation of boron acceptors in silicon’, K. Saeedi et al, Physical Review B (2018).</p> <p>The data consists of the probe transmission as a function of time delay in each case. The different experiments are labelled according to the figure in which they occur in the main paper. The data are raw and have not been smoothed or otherwise processed.</p> <p>The data is in an Origin file format. Please contact the author for data in other formats.</p>
Spin relaxation data and related scripts of PaTonB-96
<p>Spin relaxation data and related scripts of PaTonB-96 used in Ollila et al. J. Phys. Chem. B <strong>DOI: </strong>10.1021/acs.jpcb.8b02250 and in Oeemig et al., NMR structure of the C-terminal domain of TonB protein from <em>Pseudomonas aeruginosa,</em> submitted<em>.</em></p> <p>The data is used in the GitHub repository https://github.com/ohsOllila/ProteinDynamics</p>
Representation of model error in convective-scale data assimilation: additive noise, relaxation methods and combinations
<p>ModelError_1_dpsdt.tar.xz for Fig. 11<br> <br> ModelError_1_innovstat.tar.xz for Fig. 4, 10 and 13<br> <br> ModelError_1_KESpectrum.tar.xz for Fig. 1<br> <br> ModelError_1_pre_veri.tar.xz for Fig. 8 and 9<br> <br> ModelError_1_precipobs_tau.tar.xz for Fig. 2<br> <br> ModelError_1_refl_veri.tar.xz for Fig. 6, 12 and 14</p> <p>For plotting, MATLAB (R2017b) and python are used</p> <p> </p>
Optimization of Gang-operated On-load Tap Changers in Multi-conductor Radial Networks: Formulation and Convex Relaxation
<p>DSS files for case studies in CIGRE conference paper</p> <p>Only the secondary of the regulator can tap between 0.9 and 1.1, this is not specified in the DSS files themselves</p>
A semi-implicit relaxed Douglas-Rachford algorithm (sDR) for Ptychography
<p>Alternating projection based methods, such as ePIE and rPIE, have been used widely in ptychography. However, they only work well if there are adequate measurements (diffraction patterns); in the case of sparse data (i.e. fewer measurements) alternating projection underperforms and might not even converge. In this paper, we propose semi-implicit relaxed Douglas-Rachford (sDR), an accelerated iterative method, to solve the classical ptychography problem. Using both simulated and experimental data, we show that sDR improves the convergence speed and the reconstruction quality relative to extended ptychographic iterative engine (ePIE) and regularized ptychographic iterative engine (rPIE). Furthermore, in certain cases when sparsity is high, sDR converges while ePIE and rPIE fail or encounter slow convergence. To facilitate others to use the algorithm, we post the Matlab source code of sDR on a public website (www.physics.ucla.edu/research/imaging/sDR) and data con zenodo. We anticipate that this algorithm can be generally applied to the ptychographic reconstruction of a wide range of samples in the physical and biological sciences.</p>
Fig. 2 in Divergence time estimation in Cichorieae (Asteraceae) using a fossil-calibrated relaxed molecular clock
Fig. 2 Chronogram of Cichorieae produced by the program BEAST based on ITS1 and ITS2 sequences (unconstrained topology; maximum clade credibility tree with mean node heights obtained by stem group node calibration). Posterior probabilities of nodes are shown
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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.