Find research datasets worth reusing

opencc-by-4.0Jul 2024View details →

Improved version: A global dataset of spatially-dependent extreme sea levels

These files provide an improved version of the global dataset of spatially-dependent extreme sea levels (Li et al. 2023), and can be used to assess coastal flood risk considering realistic spatial dependence structure in any coastal regions around the globe. We made improvements by: <ul> <li>Estimating inter-cluster dependence by considering cluster connectivity;</li> <li>Calculating the year information for generated sythetic events.</li> </ul> More details on the new dataset can be found in Li et al. (2024) of which a preprint doi will be provided soon. If you plan to use it or have used it, feel free to contact me and please cite our 2024 paper.   References: Li, H., Haer, T., Couasnon, A., Enríquez, A. R., Muis, S., & Ward, P. J. (2023). A spatially-dependent synthetic global dataset of extreme sea level events. Weather and Climate Extremes, 41, 100596. https://doi.org/10.1016/j.wace.2023.100596 Li, H., Eilander, D., Ward, P. J., & Haer, T. (2024). Improving global-scale coastal risk estimates by considering spatial dependence. Submitted. Preprint: <a href="https://doi.org/10.22541/essoar.172641608.83190937/v1">10.22541/essoar.172641608.83190937/v1</a>.

opencc-zeroDec 2017View details →

Data from: Density-dependent disease, life history tradeoffs, and the effect of leaf pathogens on a suite of co-occurring close relatives

1. Plant pathogens reduce the performance of their hosts and therefore may contribute to ecological mechanisms of coexistence. In Chesson's framework, pathogens contribute to stabilizing mechanisms when they intensify negative intraspecific interactions, such as density-dependent disease. Additionally, pathogens contribute to equalizing mechanisms when they reduce differences in performance among species. Life history tradeoffs predict higher susceptibility to pathogens in rapidly growing species, which could equalize performance among fast- and slow-growing species in the presence of pathogens. 2. In a coastal prairie in California, we studied the impact of leaf diseases on the performance of seventeen coexisting species of Trifolium and Medicago ("clovers"). We transplanted clovers in randomized arrays into the natural prairie community in three years of common garden experiments. We quantified infection rates by isolating fungi from leaves, and we measured disease severity as percent leaf area damaged. In a fungicide experiment, we measured the impact of infection on biomass and survival. We assessed whether disease on transplants was positively related to natural abundance of that species in the surrounding community, which we monitored over 5 years. We assessed life history tradeoffs by testing whether more rapidly growing species were more susceptible to pathogens. 3. Rank abundance of clover species was stable over five years despite marked environmental fluctuations. Across hosts, fungal infection was not linearly related to density, although transplants of species that were locally absent showed lower and more variable infection. Disease severity was greater for more abundant species in only one of three years, and response to fungicide was not stronger in more abundant species. Faster-growing species experienced greater fungal infection. Consistent with predictions of the leaf economic spectrum, the impact of infection on faster-growing species was less negative than for slower-growing species. 4. Our results suggest that life history tradeoffs in plant-pathogen interactions may contribute to equalizing mechanisms among species in this guild, but that the combined effects of greater infection with greater tolerance may limit rather than promote coexistence. We also found modest evidence that density-dependent disease may contribute to stabilizing mechanisms. Lack of host specificity, rapid evolution of host use, and temporal variation in climatic conditions may all influence the role that pathogens play in coexistence of these closely related plants.

opencc-zeroDec 2019View details →

Dependence of the azure-winged magpie on nest spatial cues in offspring recognition decreases with nestling growth

Various cues have been identified as the basis for animals' discrimination between kin and non-kin. In altricial birds, these cues show temporal and spatial variations, implying that kin recognition might be condition-dependent. In this study, we hypothesize that parents might be sensitive to the changes in nest spatial position, and that their dependence on the nest spatial cue in offspring recognition decreases with offspring growth. We tested this hypothesis in a Tibetan population of the azure-winged magpie, Cyanopica cyanus, by designing a nest translocation experiment. We found that adults could return to their nest and continue caring for their offspring even if the nest had been moved to a new position. Their sensitivity to the spatial change in nest position not only varied with distance but also relied on the offspring life-history stage. Breeders were more likely to recognize their nest and offspring during the nestling period than during the incubation period, indicating that the dependence of parents on the spatial cue of the nest is higher when offspring are in the form of eggs than in the form of nestlings. Our findings suggest that azure-winged magpies mainly depend on the spatial position of the nest to recognize their nest and offspring. After nestlings establish communication with their parents, their phenotypic characteristics may replace the nests' spatial cue to play a greater role in the offspring recognition of parents.

opencc-zeroDec 2016View details →

Data from: Detrital shadows: estuarine food web connectivity depends on fluvial influence and consumer feeding mode

We measured the influence of landscape setting on estuarine food web connectivity in five macrotidal Pacific Northwest estuaries across a gradient of freshwater influence. We used stable isotopes (δ13C, δ15N, δ34S) in combination with a Bayesian mixing model to trace primary producer contributions to suspension- and deposit-feeding bivalve consumers (Mytilus trossulus and Macoma nasuta) transplanted into three estuarine vegetation zones: emergent marsh, mudflat, Japanese eelgrass (Zostera japonica), and native eelgrass (Zostera marina). Fluvial discharge and consumer feeding mode strongly influenced the strength and spatial scale of observed food web linkages, while season played a secondary role. Mussels displayed strong cross-ecosystem connectivity in all estuaries, with decreasing marine influence in the more fluvial estuaries. Mussel diets indicated homogenization of detrital sources within the water column of each estuary. In contrast, the diets of benthic deposit-feeding clams indicated stronger compartmentalization in food web connectivity, especially in the largest river delta where clam diets were trophically disconnected from marsh sources of detritus. This suggests detritus deposition is patchy across space, and less homogenous than the suspended detritus pool. In addition to fluvial setting, other estuary-specific environmental drivers, such as marsh area or particle transport speed, influenced the degree of food web linkages across space and time, often accounting for unexpected patterns in food web connectivity. Transformations of the estuarine landscape that alter river hydrology or availability of detritus sources can thus potentially disrupt natural food web connectivity at the landscape scale, especially for sedentary organisms which cannot track their food sources through space.

opencc-zeroDec 2016View details →

Data from: Stressful city sounds: glucocorticoid responses to experimental traffic noise are environmentally dependent

A major challenge in urban ecology is to identify the environmental factors responsible for phenotypic differences between urban and rural individuals. However, the intercorrelation between the factors that characterise urban environments, combined with a lack of experimental manipulations of these factors in both urban and rural areas, hinder efforts to identify which aspects of urban environments are responsible for phenotypic differences. Among the factors modified by urbanisation, anthropogenic sound, particularly traffic noise, is especially detrimental to animals. The mechanisms by which anthropogenic sound affects animals are unclear, but one potential mechanism is through changes in glucocorticoid hormone levels. We exposed adult house wrens, Troglodytes aedon, to either traffic noise or pink noise. We found that urban wrens had higher initial (pre-restraint) corticosterone than rural wrens before treatment, and that traffic noise elevated initial corticosterone of rural, but not urban, wrens. By contrast, restraint stress-induced corticosterone was not affected by noise treatment. Our results indicate that traffic noise specifically contributes to determining the glucocorticoid phenotype, and suggest that glucocorticoids are a mechanism by which anthropogenic sound causes phenotypic differences between urban and rural animals.

opencc-by-4.0May 2021View details →

Time-Dependent Probabilistic Tsunami Inundation Assessment Using Mode Decomposition to Assess Uncertainty for an Earthquake Scenario

This is the dataset of the manuscript submitted to JGR Ocean (Feb 2021).

opencc-zeroJun 2021View details →

Root responses to neighbors depend on neighbor identity and resource distribution

In a complex soil environment, competitive and environmental factors will interact with individual traits to influence a plant's root growth patterns and ability to compete for resources. Here, we examine how root growth of a focal plant, Plantago lanceolata L., responds to resource heterogeneity and to presence of two neighbor species, Centaurea jacea L.and Poa pratensis L. A full factorial experiment tested the effects of nutrient heterogeneity, neighbors, and their interaction on root responses of Plantago. Roots in shared quadrants of a pot were harvested and quantified by qPCR for plants grown alone or with a neighbor, in patchy or even soil. The effects of experimental treatments on Plantago root mass distribution were tested with two-way ANOVA. When soil resources were evenly distributed, Plantago individuals increased root allocation to soil shared with a Centaurea neighbor but not a Poa neighbor. When soil resources were patchy, Plantago responded more strongly to Poa than to Centuarea, and placed more roots in the high-resource patch. These results demonstrate that plants can respond differently to neighbors depending on species and that integrating multiple cues results in non-additive effects on root behavior.

opencc-zeroJun 2021View details →

Large seeds provide an intrinsic growth advantage that depends on leaf traits and root allocation

Seed mass and growth rate are important dimensions of plant ecological diversity, but their relationship remains unresolved. Negative relationships between relative growth rate (RGR) and seed mass are well established. However, RGR is size-dependent, so small-seeded species might achieve fast growth simply because they are initially small. Using a dataset of unprecedented size, sampling 382 grass species, we investigated seed mass and growth rate using both RGR and SGR (RGR at a specific size), accounting for diversity in phylogeny, ecology (e.g. life history, photosynthetic pathway) and environment (mean annual temperature and precipitation). RGR and SGR showed contrasting relationships with seed mass, such that large-seeded species had lower RGR but higher SGR than small-seeded species. However, the relationship between SGR and seed mass depended on leaf dry matter content (LDMC), and was only positive in high-LDMC species. When compared at a common size, the fast growth of large-seeded and low-LDMC species was associated with greater biomass allocation to roots in the hot, high-light environment used for our experiment. Photosynthetic pathway and life history contributed to variation in SGR, with C4 annuals having higher SGRs than C3 perennials regardless of seed size. Large seeds therefore afford an intrinsic growth advantage in species with resource-conserving leaf traits, and may provide a competitive edge in resource-poor environments. This work advances understanding of how seed mass and growth rate coevolve with other ecological factors.

opencc-by-4.0May 2020View details →

Supporting Dataset for "Comparing GGA, GGA+U, and Meta-GGA Functionals for Redox-Dependent Binding at Open Metal Sites in Metal−Organic Frameworks"

Supporting Dataset for "Comparing GGA, GGA+U, and Meta-GGA Functionals for Redox-Dependent Binding at Open Metal Sites in Metal−Organic Frameworks"

Heterochromatin-dependent transcription of satellite DNAs in the Drosophila melanogaster female germline

Large blocks of tandemly repeated DNAs—satellite DNAs (satDNAs)—play important roles in heterochromatin formation and chromosome segregation. We know little about how satDNAs are regulated, however their misregulation is associated with genomic instability and human diseases. We use the Drosophila melanogaster germline as a model to study the regulation of satDNA transcription and chromatin. Here we show that complex satDNAs (>100-bp repeat units) are transcribed into long noncoding RNAs and processed into piRNAs (PIWI interacting RNAs). This satDNA piRNA production depends on the Rhino-Deadlock-Cutoff complex and the transcription factor Moonshiner—a previously-described non-canonical pathway that licenses heterochromatin-dependent transcription of dual-strand piRNA clusters. We show that this pathway is important for establishing heterochromatin at satDNAs. Therefore, satDNAs are regulated by piRNAs originating from their own genomic loci. This novel mechanism of satDNA regulation provides insight into the role of piRNA pathways in heterochromatin formation and genome stability.

opencc-by-4.0Jul 2021View details →

Depth dependent spatiotemporal dynamics of overwintering pelagic Microcystis in a temperate water body

Supplementary Information for the research article 'Depth dependent spatiotemporal dynamics of overwintering pelagic Microcystis in a temperate water body'.

Robust surface-to-mass coupling and turgor-dependent cell width determine bacterial dry-mass density

During growth, cells must expand their cell volumes in coordination with biomass to control the level of cytoplasmic macromolecular crowding. Dry-mass density, the average ratio of dry mass to volume, is roughly constant between different nutrient conditions in bacteria, but it remains unknown whether cells maintain dry-mass density constant at the single-cell level and during non-steady conditions. Furthermore, the regulation of dry-mass density is fundamentally not understood in any organism. Using quantitative phase microscopy and a new image-analysis pipeline, we measured absolute single-cell mass and shape of the model organisms Escherichia coli and Caulobacter crescentus with improved precision and accuracy. We found that cells control dry-mass density indirectly, by expanding their surface, rather than volume, in direct proportion to biomass growth – according to a new surface growth law. At the same time, cell width is controlled independently. Therefore, cellular dry-mass density varies systematically with cell shape, both during the cell cycle or after nutrient shifts, while the surface-to-mass ratio remains nearly constant on the generation time scale. Transient deviations from constancy during nutrient shifts can be reconciled with turgor-pressure variations and the resulting elastic changes in surface area. Finally, we find that plastic changes of cell width after nutrient shifts are likely driven by turgor variations, demonstrating an important regulatory role of mechanical forces for width regulation. In conclusion, turgor-dependent cell width and a new, slowly varying surface-to-mass coupling constant are the independent variables that determine dry-mass density.

Data from: The effects of competition on fitness depend on the sex of both competitors

In intraspecific competition, the sex of competing individuals is likely to be important in determining the consequences of competition, both for the immediate outcome of competitive interactions, and for long-term effects of competition during development on adult fitness traits. Previous studies have explored differences between males and females in their response to intraspecific competition. However, few have tested how the sex of the competitors, or any interactions between focal and competitor sex, influence the nature and intensity of competition. We set up larval seed beetles Callosobruchus maculatus to develop either alone or in the presence of a male or female competitor, and measured a suite of traits: development time, emergence weight; male ejaculate mass, copulation duration and lifespan; and female lifetime fecundity, offspring egg-adult survival and lifespan. We found effects of competition and competitor sex on the development time and emergence weight of both males and females, and also of an interaction between focal and competitor sex: females but not males responded differently to competitor sex. There was little effect of larval competition on male and female adult fitness traits, with the exception of the effect of a female competitor on a focal female's offspring survival rate. Our results highlight the importance of directly measuring the effects of competition on fitness traits, rather than distant proxies for fitness, and suggest that competition with the sex with the greater resource requirements (here females) might have a strong effect in driving trait evolution. We also found that male-male competition during development resulted in shorter copulation times than male-female competition, a result that remained when controlling for the weight of competitors. Although it is difficult to definitively tease apart the effects of social environment and access to resources, this result suggests that something about the sex of competitors other than their size is driving this pattern.

opencc-by-4.0Jul 2021View details →

HDF files for the time-dependent inversion of the 2016 moderate earthquakes along Chaman fault

We use GAMMA software to process Sentinel-1 SLC data and generate InSAR data. After converting the data into UTM coordinates, we use LiCSBAS to perform the time-series analysis, and the resulting HDF files are imported to MATLAB to perform the time-dependent inversion. MATLAB source codes are available. Original Sentinel-1 SLC data are available from https://scihub.copernicus.eu/dhus.

opencc-zeroDec 2020View details →

Hydraulic prediction of drought-induced plant dieback and top-kill depends on leaf habit and growth form

Hydraulic failure caused by severe drought contributes to aboveground dieback and whole-plant death. The extent to which dieback or whole-plant death can be predicted by plant hydraulic traits has rarely been tested among species with different leaf habits and/or growth forms. We investigated 19 hydraulic traits in 40 woody species in a tropical savanna and their potential correlations with drought response during an extreme drought event during the El Niño–Southern Oscillation in 2015. Plant hydraulic trait variation was partitioned substantially by leaf habit but not growth form along a trade-off axis between traits that support drought tolerance versus avoidance. Semi-deciduous species and shrubs had the highest branch dieback and top-kill (complete aboveground death) among the leaf habits or growth forms. Dieback and top-kill were well explained by combining hydraulic traits with leaf habit and growth form, suggesting integrating life history traits with hydraulic traits will yield better predictions.

Biodiversity effects on grape quality depend on variety and management intensity

Interactions between plants can be beneficial, detrimental or neutral. In agricultural systems competition between crop and spontaneous vegetation is a major concern. We evaluated the relative support for three non-exclusive ecological hypotheses about interactions between crop and spontaneous plants based on competition, complementarity or facilitation. The study was conducted in Swiss vineyards with different vegetation management intensities. Thirty-three vineyards planted with two different grape varieties were studied over 3 years to determine whether low-intensity vegetation management might provide benefits for grape quality parameters. Management intensity varied with the degree of control of spontaneous inter-row vegetation. Features of spontaneous vegetation measured included total cover, total species richness and abundance of nitrogen fixing plants. Grape quality parameters of known importance to wine-making (yeast assimilable nitrogen, sugars, tartric acid, and malic acid) were determined by Fourier-transform infrared spectroscopy (FTIR). Using structural equation modeling, we evaluated hypotheses about the multivariate responses of grape quality parameters as well as the direct and indirect (plant-mediated) effects of management. Observed effects of management differed between grape varieties. Management intensity and abundance of N-fixing plants significantly influenced grape quality parameters, while total richness of spontaneous plants did not have detectable effects. Abundance of N-fixing plants was enhanced by low-intensity management resulting in increased N content in the red grape variety (Pinot noir), potentially enhancing grape quality, while measured soil N content did not explain the increase. Synthesis: Our study shows that crop quality can be enhanced by spontaneous plants, in this case by the abundance of a key functional group (N-fixers), most likely through plant-plant or plant-microbe facilitation. However, beneficial interactions may have a high specificity in terms of facilitation partners and may have contrasting effects at low taxonomic resolutions such as crop varieties. Generally increasing plant biodiversity in agricultural systems may increase competition with crops. Thus, the identification of suitable interaction partners and a careful balance between crop variety and spontaneous plant species may be necessary to utilize beneficial interactions and to reduce the trade-off between agricultural production and biodiversity to achieve a sustainable ecological benefit in agricultural systems.

Using machine learning to model nontraditional spatial dependence in occupancy data

Spatial models for occupancy data are used to estimate and map the true presence of a species, which may depend on biotic and abiotic factors as well as spatial autocorrelation. Traditionally researchers have accounted for spatial autocorrelation in occupancy data by using a correlated normally distributed site-level random effect, which might be incapable of modeling nontraditional spatial dependence such as discontinuities and abrupt transitions. Machine learning approaches have the potential to model nontraditional spatial dependence, but these approaches do not account for observer errors such as false absences. By combining the flexibility of Bayesian hierarchal modeling and machine learning approaches, we present a general framework to model occupancy data that accounts for both traditional and nontraditional spatial dependence as well as false absences. We demonstrate our framework using six synthetic occupancy data sets and two real data sets. Our results demonstrate how to model both traditional and nontraditional spatial dependence in occupancy data which enables a broader class of spatial occupancy models that can be used to improve predictive accuracy and model adequacy.

The validation of new phase-dependent gait stability measures: a modelling approach

Identification of individuals at risk of falling is important when designing fall prevention methods. Current stability measures that estimate gait stability and robustness appear limited in predicting falls in older adults. Inspired by recent findings of phase-dependent local stability changes within a gait cycle, we used compass-walker models to test several phase-dependent stability metrics for their usefulness to predict gait robustness. These metrics are closely related to the often-employed maximum finite-time Lyapunov exponent and maximum Floquet multiplier. They entail linearizing the system in a rotating hypersurface orthogonal to the period-one solution, and estimating the local divergence rate of the swing phases and the foot strikes. We correlated the metrics with the gait robustness of two compass walker models with either point or circular feet to estimate their prediction accuracy. To also test for the metrics' invariance under coordinate transform, we represented the point-feet walker in both Euler-Lagrange and Hamiltonian canonical form. Our simulations revealed that for most of the metrics, correlations differ between models and also change under coordinate transforms, severely limiting the prediction accuracy of gait robustness. The only exception that consistently correlated with gait robustness is the divergence of foot strikes. These results admit challenges of using phase-dependent stability metrics as objective measure to quantify gait robustness.

opencc-by-4.0Jul 2021View details →

Groundwater and surface water quantity and quality measurement results for groundwater dependent ecosystem in Kazu leja, Latvia in 2019 and 2020

Groundwater and surface water quantity and quality measurement results and methodology of the investigations of the groundwater dependant ecosystem in Kazu leja, Latvia in 2019 and 2020 is presented. The data comprises: <ol> <li>Methodology</li> <li>Measurement site data [2_observation_sites.csv]</li> <li>Field and laboratory measurement results [3_field_and_lab_results.csv]</li> <li>Measurement uncertainty [4_measurement_uncertainity.csv]</li> <li>Automated water level, temperature, and electrical conductivity measurements [5_level_temperature_electricConductivity_loggers.csv]</li> </ol>