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677 results for “time of use”
Daily cross-correlation functions for "Time-lapse monitoring of seismic velocity associated with 2011 Shinmoe-dake eruption using seismic interferometry: an extended Kalman filter approach"
<p>The daily cross-correlation functions used in Nishida et al. 2020. We used three-component seismograms recorded at eight stations (six broadband sensors and two short-period sensors with a natural frequency of 1 Hz) from May 1st, 2010 to April 30th, 2018. Five stations were deployed by the Earthquake Research Institute, the University of Tokyo, and the other three were deployed by the National Research Institute for Earth Science and Disaster Prevention (NIED). The data can be found in the HDF5 file. You can also find a python code of an implementation of an extended Kalman filter/smoother for time-lapse monitoring of seismic velocity at GitHub (https://github.com/qnishida/eKlfS). The code estimates the temporal change in seismic velocities using this data set. </p>
Using naturalistic incubation temperatures to demonstrate how variation in the timing and continuity of heat wave exposure influences phenotype
<p>Most organisms are exposed to bouts of warm temperatures during development, yet we know little about how variation in the timing and continuity of heat exposure influences biological processes. If heat waves increase in frequency and duration as predicted, it is necessary to understand how these bouts could affect thermally sensitive species, including reptiles with temperature-dependent sex determination (TSD). In a multi-year study using fluctuating temperatures, we exposed <i>Trachemys scripta</i> embryos to cooler, male-producing temperatures interspersed with warmer, female-producing temperatures (heat waves) that varied in either timing during development or continuity and then analyzed resulting sex ratios. We also quantified the expression of genes involved in testis differentiation (<i>Dmrt1</i>) and ovary differentiation (<i>Cyp19A1</i>) to determine how heat wave continuity affects the expression of genes involved in sexual differentiation. Heat waves applied during the middle of development produced significantly more females compared to heat waves that occurred just 7 days before or after this window, and even short gaps in the continuity of a heat wave decreased the production of females. Continuous heat exposure resulted in increased <i>Cyp19A1 </i>expression while discontinuous heat exposure failed to increase expression in either gene over a similar time course. We report that even small differences in the timing and continuity of heat waves can result in drastically different phenotypic outcomes. This strong effect of temperature occurred despite the fact that embryos were exposed to the same number of warm days during a short period of time, which highlights the need to study temperature effects under more ecologically relevant conditions where temperatures may be elevated for only a few days at a time. In the face of a changing climate, the finding that subtle shifts in temperature exposure result in substantial effects on embryonic development becomes even more critical.</p>
Dataset for the paper: "The Gas Accessible Membrane Electrode (GAME): A Versatile Platform for Elucidating Electrocatalytic Processes Using Real Time and In Situ Hyphenated Electrochemical Techniques"
<p>The data in this spreadsheet was used to produce the figures in the paper</p> <p>Authors: Guohui Zhang, Anthony Kucernak</p> <p>Title: The Gas Accessible Membrane Electrode (GAME): A Versatile Platform for Elucidating Electrocatalytic Processes Using Real Time and In Situ Hyphenated Electrochemical Techniques </p> <p>Journal: ACS Catalysis, 2020</p> <p>DOI: 10.1021/acscatal.0c02433</p> <p>Please cite the above reference if you wish to use this data<br> DOI of data:10.5281/zenodo.3985811</p>
On the use of real-time mortality data in modelling and analysis during an epidemic outbreak - underlying data
<p>This project contains the primary data set analyzed in the paper "On the use of real-time mortality data in modelling and analysis during an epidemic outbreak ". The data was generated by downloading the <em>D<sup>T</sup></em>-series daily from the Public Health Agency of Sweden between 2020-04-02 and 2020-07-09. </p> <p>This project contains the following files:</p> <ul> <li>FHM_Covid_Download.zip. (Zip-archive of raw downloaded files with Swedish deaths data.)</li> <li>swedish_covid_deaths_data.csv. (Swedish deaths data collated from the raw data files in a .csv format.)</li> <li>swedish_covid_deaths_data.xlsx. (Swedish deaths data collated from the raw data files in a .xlsx format.)</li> </ul>
Reconstruction of magnetospheric storm-time dynamics using cylindrical basis functions and multi-mission data mining
<p>This zip file contains data used to create figures and tables, describing the results of the paper "Reconstruction of magnetospheric storm-time dynamics using cylindrical basis functions and multi-mission data mining", by N. A. Tsyganenko, V. A. Andreeva, and M. I. Sitnov.</p>
Using real-time UV-visible spectrophotometer to assess an Al-Zn-Mg-Cu alloy's dissolution in acidic solution
<p>Applicability and limitations of using online non-destructive UV-vis spectrophotometer to monitor the dissolution of an Al-Zn-Mg-Cu alloy in HCl-containing solution were studied. ICP-AES results indicate that the spectrum absorbance at 252 nm is mainly attributed to Cu-containing complexes. Surprisingly, an hours-long "induction" period was observed from UV-vis results. This is not a real indicator of induction for Al dissolution as revealed by electrochemical impedance spectrum, actually it reflects the alloy's galvanic corrosion nature that Cu species are released after Al, Zn, Mg species.</p>
Butterfly phenology in Mediterranean mountains using space-for-time substitution
<p>Inferring species' responses to climate change in the absence of long-term time series data is a challenge, but can be achieved by substituting space for time. For example, thermal elevational gradients represent suitable proxies to study phenological responses to warming. We used butterfly data from two Mediterranean mountain areas to test whether mean dates of appearance of communities and individual species show a delay with increasing altitude, and an accompanying shortening in the duration of flight periods. We found a 14-day delay in the mean date of appearance per kilometre increase in altitude for butterfly communities overall, and an average 23-day shift for 26 selected species, alongside average summer temperature lapse rates of 3°C per km. At higher elevations there was a shortening of the flight period for the community of three days/km, with an 8.8 day average decline per km for individual species. Rates of phenological delay differed significantly between the two mountain ranges, although this did not seem to result from the respective temperature lapse rates. These results suggest that climate warming could lead to advanced and lengthened flight periods for Mediterranean mountain butterfly communities. However, although multivoltine species showed the expected response of delayed and shortened flight periods at higher elevations, univoltine species showed more pronounced patterns in terms of species appearance. Hence, whilst projections of overall community responses to climate change may benefit from space-for-time substitutions, understanding species-specific responses to local features of habitat and climate may be needed to accurately predict the effects of climate change on phenology.</p>
Data from: Using adaptive traits to consider potential consequences of temporal variation in selection: male guppy colour through time and space
Temporal variation in selection is typically evaluated by estimating and comparing selection coefficients in natural populations. Meta-analyses of these coefficients have yielded important insights, but selection coefficients are limited in several respects, including low statistical power, imperfect fitness surrogates, and uncertainty regarding consequences for trait change. A complementary approach without these limitations is to examine temporal variation in adaptive traits themselves, which is mechanistically easier and more directly relevant to evolutionary consequences. We illustrate this approach by analyzing the colour patterns of male guppies, Poecilia reticulata, from each of six sites in Trinidad in each of 6 years. This system is particularly appropriate for our study because key aspects of colour variation are genetically-based and responsive to selection. However, although spatial patterns of colour variation have been extensively considered in this system, no study has yet formally assessed annual temporal variation in non-manipulated populations. Matching previous conclusions for the guppy system, we find that guppies from different sites manifest different colour patterns in association with different predation regimes. We here add the new finding that, although some temporal variation is present, spatial patterns of colour variation are generally consistent across years. These results suggest that, when considering adaptive traits, spatial variation is more important than temporal variation, although our study system might be exceptional in this regard. Additional studies examining spatiotemporal variation in adaptive traits could help to improve our understanding of the role that spatiotemporal variation in selection plays in the evolutionary process.
Data from: Bayesian estimation of species divergence times using correlated quantitative characters
Discrete morphological data have been widely used to study species evolution, but the use of quantitative (or continuous) morphological characters is less common. Here, we implement a Bayesian method to estimate species divergence times using quantitative characters. Quantitative character evolution is modelled using Brownian diffusion with character correlation and character variation within populations. Through simulations, we demonstrate that ignoring the population variation (or population "noise") and the correlation among characters leads to biased estimates of divergence times and rate, especially if the correlation and population noise are high. We apply our new method to the analysis of quantitative characters (cranium landmarks) and molecular data from carnivoran mammals. Our results show that time estimates are affected by whether the correlations and population noise are accounted for or ignored in the analysis. The estimates are also affected by the type of data analysed, with analyses of morphological characters only, molecular data only, or a combination of both; showing noticeable differences among the time estimates. Rate variation of morphological characters among the carnivoran species appears to be very high, with Bayesian model selection indicating that the independent-rates model fits the morphological data better than the autocorrelated-rates model. We suggest that using morphological continuous characters, together with molecular data, can bring a new perspective to the study of species evolution. Our new model is implemented in the MCMCtree computer program for Bayesian inference of divergence times.
Data from: Comparing diel activity patterns of wildlife across latitudes and seasons: time transformations using day length
(1) Camera trapping allows scientists to study activity patterns of animals under natural conditions. However, comparisons of activity patterns across seasons or latitudes can be biased, because activity is often attuned to sunrise and sunset, the timing of which varies with latitude and season. Existing transformation methods to solve this problem have limitations. (2) Here, we explore whether and how activity patterns can be transformed more accurately using two alternative 'double anchoring' transformations – equinoctial and average anchoring – that anchor activity time to two chosen anchor points during the study period. (3) Using simulated noisy datasets mimicking species with either crepuscular, diurnal or cathemeral activity patterns, we compared the ability of different transformation methods to extract the latent pattern and activity levels under different study conditions. We found that average anchoring best retrieved the original diel activity pattern and yielded accurate estimates of activity level. Two alternative transformation methods – single anchoring and equinoctial anchoring – performed less well. Bias in estimates from using untransformed clock times was most marked (up to 2.5-fold over-estimation) for longer studies covering 4-5 months either side of an equinox at high latitude, and focusing on crepuscular species. (4) We applied the average anchoring method to 9 months of data on Red deer (Cervus elaphus), Wild boar (Sus scrofa) and Mouflon (Ovis amon musimon) activity as captured by camera traps in National Park Hoge Veluwe, the Netherlands. Average anchoring revealed more pronounced peaks of activity after sunset than was apparent from untransformed data in red deer and wild boar, but not for mouflon, a cathemeral species. Similarly, activity level was lower when calculated using average-anchored time for red deer and wild boar, but no difference was observed for mouflon. (5) We conclude that transformation of time might not be necessary at latitudes below 20°, or in studies with a duration of less than a month (below 40° latitude). For longer study periods and/or higher latitudes, average-anchoring resolves the problem of variable day length. Code is provided. The transformation functions are incorporated in the R-package 'activity'.
Data from: Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case
Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (auto-correlated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the auto-correlated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.
Data from: Measurement of infection efficiency of a major wheat pathogen using time-resolved imaging of disease progress
Infection efficiency is a key epidemiological parameter that determines the proportion of pathogen spores able to infect and cause lesions once they have landed on a susceptible plant tissue. In this study, we present an improved method to measure infection efficiency of Zymoseptoria tritici using a replicated greenhouse experiment. Z. tritici is a fungal pathogen that infects wheat leaves and causes Septoria tritici blotch (STB), a major disease of wheat worldwide. We devised an original experimental setup, where we (i) attached living wheat leaves to metal plates allowing for time‐resolved imaging of disease progress in planta. Since lesions were continuously appearing, expanding and merging during the period of up to three weeks, daily measurements were necessary for accurate counting of lesions. We also (ii) used reference membranes to characterize the density and the spatial distribution of inoculated spores on leaf surfaces. In this way, we captured the relationship between the number of lesions and the number of viable spores deposited on the leaves and estimated the infection efficiency of about 4% from the slope of this relationship. Our study provides a proof of principle for an accurate and reliable measurement of infection efficiency of Z. tritici. The method opens opportunities for determining the genetic basis of the component of quantitative resistance that suppresses infection efficiency. This knowledge would improve breeding for quantitative resistance against STB, a control measure considered more durable than deployment of major resistance genes.
Data from: Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition
We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts of the trees we obtain agree with those on published protein ML trees. Interesting results include a preference for rodent monophyly. The detection of a few alternative signals to those on the optimal tree were obtained using the distance Hadamard transform (with results expressed as a Lento plot). One rearrangement suggested was the interchange of the position of primates and rodents on the optimal tree. The basic stability of the tree, combined with two calibration points (whale/cow and horse/rhinoceros), together with a distant secondary calibration from the mammal/bird divergence, allows inferences of the times of divergence of putative clades. Allowing for sampling variances due to finite sequence length, most major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary. Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades.
Data from: Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)
Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using 'early but risky' fossil constraints in addition to 'safe but late' constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown-group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical re-assessment of their phylogenetic position.
Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent
<p>Incomplete lineage sorting (ILS) can lead to biased divergence time estimates. To explore if and how ILS has influenced the results of a recent study of worldwide phylogeny of three-spined sticklebacks (Gasterosteus aculeatus), we estimated divergence times among major clades by applying both a concatenation approach and the multispecies coalescent (MSC) model to single-nucleotide polymorphisms. To further test the influence of different calibration strategies, we applied different calibrations to the root and to younger nodes in addition to the ones used in the original study. Both the updated calibrations and the application of the MSC model influenced divergence time estimates, sometimes significantly. The new divergence time estimates were more ancient than in the previous study for older nodes, whereas the estimates of younger nodes were not strongly affected by the re-analyses. However, given the applied MSC method employs a simple substitution model and cannot account for changes in population size, we suggest that different analytical approaches and calibration strategies should be used in order to explore uncertainty in divergence time estimates. This study provides a valuable reference timeline for the ages of worldwide three-spined stickleback populations and emphasizes the need to embrace, rather than obscure, uncertainties around divergence time estimates.</p>
Data from: Single mechanosensory neurons encode lateral displacements using precise spike timing and thresholds
During locomotion, animals rely on multiple sensory modalities to maintain stability. External cues may guide behavior, but they must be interpreted in the context of the animal's own body movements. Mechanosensory cues that can resolve dynamic internal and environmental conditions, like those from vertebrate vestibular systems or other proprioceptors, are essential for guided movement. How do afferent proprioceptor neurons transform movement into a neural code? In flies, modified hindwings known as halteres detect forces produced by body rotations, and are essential for flight. The mechanisms by which haltere neurons transform forces resulting from three-dimensional body rotations into patterns of neural spikes are unknown, however. We use intracellular electrodes to record from haltere primary afferent neurons during a range of haltere motions. We find that spike timing activity of individual neurons changes with displacement, and propose a mechanism by which single neurons can encode three-dimensional haltere movements during flight.
Data from: Synergism and antagonism of proximate mechanisms enable and constrain the response to simultaneous selection on body size and development time: an empirical test using experimental evolution
Natural selection acts on multiple traits simultaneously. How mechanisms underlying such traits enable or constrain their response to simultaneous selection is poorly understood. We show how antagonism and synergism among three traits at the developmental level enable or constrain evolutionary change in response to simultaneous selection on two focal traits at the phenotypic level. After 10 generations of 25% simultaneous directional selection on all four combinations of body size and development time in Manduca sexta (Sphingidae), the changes in the three developmental traits predict 93% of the response of development time and 100% of the response of body size. When the two focal traits were under synergistic selection, the response to simultaneous selection was enabled by juvenile hormone and ecdysteroids and constrained by growth rate. When the two focal traits were under antagonistic selection, the response to selection was due primarily to change in growth rate and constrained by the two hormonal traits. The approach used here reduces the complexity of the developmental and endocrine mechanisms to three proxy traits. This generates explicit predictions for the evolutionary response to selection that are based on biologically informed mechanisms. This approach has broad applicability to a diverse range of taxa, including algae, plants, amphibians, mammals, and insects.
Data from: Sex, size and timing: sampling design for reliable population genetics analyses using microsatellite data
1. Population genetics is used in a wide variety of fields such as ecology and biodiversity conservation. How estimated genetic characteristics of natural populations can be influenced by the sampling design has been a long-standing concern. Multiple simulation and empirical studies illustrated the influence of both sample size and polymorphism of markers. However, our review of studies on butterfly population genetics indicates no consensus on sample size for the estimation of genetic diversity or differentiation. Furthermore, other aspects of sampling design (sex ratio and timing of sampling) were not addressed and their potential impact on genetic parameter estimates rarely explored. 2. Using a large empirical dataset (with spatial and temporal replicates) collected on a butterfly species, Boloria aquilonaris, as well as simulated datasets reflecting (1) three scenarios of migration-genetic drift equilibrium and (2) one scenario of parameter stabilization after 100,000 generations, we quantified the impacts of three aspects of genetic sampling design (namely sample size, sex ratio, and timing of sampling) on the estimation of allele frequencies and its potential downstream impact on the estimation of genetic parameters. 3. With empirical data, we found that sample size and timing of sampling strongly affected the accuracy of allele frequencies and the downstream analyses, while sex ratio did not. Our results were consistent across spatial and temporal replicates. Also, with simulated data, we showed that the genetic sampling design had limited effect in systems where dispersal outweighs genetic drift, while it can have major consequences on our understanding of the genetic diversity and population differentiation in systems dominated by genetic drift (such as most study systems with conservation concerns). 4. We advocate for careful consideration of all aspects of the sampling design in population genetics studies, i.e. a sufficient number of samples, while ensuring similar sex ratio among sampling locations and collecting with timing appropriate to the question under study. This is particularly important when the study aims at species conservation.
Data from: Using molecular phylogenies in island biogeography: it's about time
Island biogeography aims at inferring the processes that govern the assembly of communities in space and time. Molecular phylogenies can tell us about the timings of island colonisations and diversification, but have rarely been used for the estimation of colonisation, speciation and extinction rates on islands. In this study we illustrate the effects of including phylogenetic information with the Galápagos avifauna. We find that by including colonisation times we obtain much more precise and accurate parameter estimates than if we rely solely on species richness and endemicity status. Inclusion of branching times improves estimates even further. As molecular phylogenies become increasingly available, we urge biogeographers to start using more of the information they contain.
Data from: Using areas of known occupancy to identify sources of variation in detection probability of raptors: taking time lowers replication effort for surveys
Species occurring at low density can be difficult to detect and if not properly accounted for, imperfect detection will lead to inaccurate estimates of occupancy. Understanding sources of variation in detection probability and how they can be managed is a key part of monitoring. We used sightings data of a low-density and elusive raptor (white-headed vulture Trigonoceps occipitalis) in areas of known occupancy (breeding territories) in a likelihood-based modelling approach to calculate detection probability and the factors affecting it. Because occupancy was known a priori to be 100%, we fixed the model occupancy parameter to 1.0 and focused on identifying sources of variation in detection probability. Using detection histories from 359 territory visits, we assessed nine covariates in 29 candidate models. The model with the highest support indicated that observer speed during a survey, combined with temporal covariates such as time of year and length of time within a territory, had the highest influence on the detection probability. Averaged detection probability was 0.207 (s.e. 0.033) and based on this the mean number of visits required to determine within 95% confidence that white-headed vultures are absent from a breeding area is 13 (95% CI: 9–20). Topographical and habitat covariates contributed little to the best models and had little effect on detection probability. We highlight that low detection probabilities of some species means that emphasizing habitat covariates could lead to spurious results in occupancy models that do not also incorporate temporal components. While variation in detection probability is complex and influenced by effects at both temporal and spatial scales, temporal covariates can and should be controlled as part of robust survey methods. Our results emphasize the importance of accounting for detection probability in occupancy studies, particularly during presence/absence studies for species such as raptors that are widespread and occur at low densities.
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.