Find research datasets worth reusing

opencc-by-4.0Mar 2023View details →

Data set of simulated rimed aggregates for "A riming-dependent parameterization of scattering by snowflakes using the self-similar Rayleigh-Gans approximation"

Simulated rimed aggregates generated with https://github.com/jleinonen/aggregation in setting "aggregation followed by riming". Aggregates were built from between 10 to 700 monomer crystals of columns, dendrites, needles, plates or rosettes with mean sizes of 100 or 200 micrometer. Then they were exposed to ELWP = 2.0 kg m⁻². Monomer crystals are composed of cubical elements with resolution 20 micrometer. Frozen rime droplets are also represented by 20 micrometer cubes. The data set contains folders with evolution (evol) and shape files for each monomer crystal type. For each particle one evolution and one corresponding shape file exists. The evolution (evol) file contains particle mass, rime mass, area, size, fall speed (Heymsfield&Westbrook, 2010), fall speed (Khvorostyanov&Curry, 2005) for each step during the aggregation and riming process. The corresponding shape file contains the x,y,z positions of the cubical elements that compose the particle for each step. For further documentation see readme.

opencc-zeroDec 2022View details →

Data from: Climatic water availability mainly drives context-dependency of tree functional diversity effects on soil organic carbon storage in European forests

The interplay of forest stand and environmental factors shape soil organic C (SOC) storage in forest ecosystems but little is known about their relative impacts in different soil layers. Moreover, how environmental factors modulate the impact of stand factors, particularly species mixing, on SOC storage, is largely unexplored. In this study conducted in 21 forest triplets (two-species mixed stand and respective monocultures nearby) distributed in Europe, we tested the hypothesis that stand factors (functional identity and diversity) have stronger effects on topsoil (FF+0-10 cm) C storage than environmental factors (climatic water availability, clay+silt content, oxalate-extractable Al - Alox) but that the opposite occurs in the subsoil (10-40 cm). We also tested the hypothesis that functional diversity improves SOC storage under high climatic water availability, clay+silt contents, Alox. We characterized functional identity as the proportion of broadleaved species (beech and/or oak), and functional diversity as the product of broadleaved and conifer (pine) proportions. The results show that functional identity was the main driver of topsoil C storage while climatic water availability had the largest control on subsoil C storage. Contrary to expectations, functional diversity decreased topsoil C storage under increasing climatic water availability but the opposite was observed in the subsoil. Functional diversity effects on topsoil C increased with increasing clay+silt content, while its effects on subsoil C was negative at increasing Alox content. This suggests that functional diversity effect on SOC storage along environmental gradients depends on the specific environmental factor and the soil depth under consideration.

opencc-by-4.0Mar 2023View details →

Mechanism of rotenone binding to respiratory complex I depends on ligand flexibility

Snapshots from MD simulations (with umbrella sampling and metadynamics) of respiratory complex I. Only subunits ND1, NDUFS2 and NDUFS7 (with the membrane spanning N-terminus truncated) and rotenone are shown in binding mode (see Fig. 2 of main paper):  1) ROT1:        configurations/rot1.pdb 2) pre-redox:   configurations/rot1.5.pdb 3) ROT2:        configurations/rot2.pdb Force-field and topology files in GROMACS format: 4) Bonded parameters:           parameters/rotenoids_ffBonded.itp 5) Rotenone:                    parameters/rot.itp 6) Dehydrated derivative:       parameters/dehyd_rot.itp

Data from: Beyond pollen:ovule ratios: Evolutionary consequences of pollinator dependence and pollination efficiency for pollen and ovule production in angiosperms

Premise: The relative per‐flower production of ovules and pollen varies broadly with angiosperm mating systems, with outcrossing types commonly producing more pollen grains per ovule than selfing types. The evolutionary causes of this variation are contentious, especially the relevance of pollination risk. Resolution of this debate may have been hampered by its focus on pollen:ovule (P:O) ratios rather than on the evolution of pollen and ovule numbers per se. Methods: Using published mean ovule and pollen counts, we analyzed associations with the proportion of removed pollen that reaches stigmas (pollen‐transfer efficiency) and differences between pollinator‐dependent and autogamous forms within and among species. Analyses involved Bayesian methods that simultaneously considered variation in pollen and ovule numbers and accounted for phylogenetic relatedness. We also assessed the utility of P:O ratios as mating‐system proxies and their association with female outcrossing rates. Results: Median pollen number declined consistently with pollen‐transfer efficiency among species, whereas median ovule number did not. Similarly, in both intraspecific and interspecific analyses, pollinator‐dependent plants produced more pollen than autogamous plants, whereas ovule production did not differ statistically. Distributions of P:O ratios overlapped extensively for self‐incompatible and self‐compatible species and for different mating‐system classes, and P:O ratios correlated weakly with outcrossing rate. Conclusions: Our findings demonstrate that pollinator dependence and pollination efficiency commonly influence the evolution of pollen number per flower but have more limited effects on ovule number. P:O ratios provide ambiguous, possibly misleading, information about mating systems, especially when compared among clades.

Data for: Distance and density dependence in two native Bornean dipterocarp species

The Janzen-Connell hypothesis proposes that density and distance-dependent mortality generated by specialist natural enemies prevent competitive dominance. Much literature on Janzen Connell mechanisms comes from the neotropics, and evidence of the role of distance and density-dependence is still relatively sparse. We tested the predictions of the J-C hypothesis in a South-East Asian system dominated by mast fruiting species. We hypothesized that seedling survival would decrease with distance and density, seedling growth would increase, and herbivory would decrease, according to the predictions of the Janzen-Connell hypothesis. Experiments were conducted to determine the strength of the Janzen Connell mechanism by manipulating the density and identity of tree species as a function of the distance from parent trees. Survival of conspecific seedlings was reduced near adult trees of one species, but not another. High densities of seedlings decreased the growth of conspecific seedlings of both species. In both species, herbivory rates decreased with distance in low-density areas. This study indicates that dipterocarp species experienced weak Janzen-Connell effects of distance and density dependence at the growth stage studied. Future studies in this system might focus on earlier life-history stages such as seeds and small seedlings, as well as studying mortality during mast-seeding events.

Data from: Density-dependent reproductive success among sympatric dipterocarps during a major mast fruiting event

The files hold the data for the paper entitled "Density-dependent reproductive success among sympatric dipterocarps during a major mast fruiting event", which includes (i) the weight and status of seeds collected with seed traps in a Bornean tropical forest during a mast fruiting event, and (ii) the results of a seed sowing experiment in primary and secondary forests. Study site was the Deramakot and Tangkulap Forest Reserves, Sabah, Malaysia (5°14– 30'N, 117°11–36'E).

Season-dependent impact of forage quality on stress in Alpine chamois

Chronically heightened stress levels in wildlife species may have detrimental effects on individual life history traits, for example through the increased likelihood of disease, parasitic infections, and overall reduced fitness. Understanding the drivers of stress may thus have great potential for informing wildlife conservation. Although the role of climate and individual status is well studied in stress ecology, the impact of related stressors such as dietary quality is of increasing interest to wildlife research and conservation. In this study, fecal cortisol metabolites (FCMs) in Alpine chamois Rupicapra r. rupicapra, used as bioindicators of stress, and their relationship with forage quality – measured as the percentage of fecal crude protein (CP) – were investigated. Data collection took place in 2011 and 2012 in the Gran Paradiso National Park (Western Italian Alps), on 22 individually marked adult males. The relationship between FCMs and CPs was analyzed through linear models and seperated between winter and summer months, accounting for the effect of potentially confounding exogenous and endogenous variables. After AICc-based model selection, we found that forage quality was negatively related to FCM levels in Alpine chamois during the summer months, meaning that higher quality forage was associated with the decreased expression of stress hormones. However, during the winter months, we did not find a significant relationship, potentially as a result of forage quality being ubiquitously poor. Although the mechanisms through which dietary variations impact FCM concentrations in wildlife populations are largely unknown, the occurrence of significant relationships between forage quality and stress levels supports potentially important implications for the long-term effect of climatic changes on the fitness of wildlife populations.

opencc-by-4.0Apr 2023View details →

Dataset: Long Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires

The ability to redirect electron transport to new reactions in living systems opens possibilities to store energy, generate new products, or probe physiological processes. Recent work by Huang et al. showed that 3D crystals of small tetraheme cytochromes (STC) could transport electrons over nanoscopic to mesoscopic distances by an electron hopping mechanism. Such protein-based structures with multiple localized electron carriers are promising materials for nanowires. A potential barrier to protein nanowire adoption for handling long-range electron transport is that fluctuations at room temperature may distort the nanostructure, hindering efficient electron transport. To study these fluctuations at the nano- and mesoscopic scales, we carry out classical molecular dynamics simulations for a small fragment of a STC nanowire and measure the effective distance distribution for electron tunneling. From distance distributions, we develop a graph network representation for electron transport along nanowires with varying dimensions, and through stochastic methods determine the maximum electron flow that can be driven through these STC wires. Longer nanowires were capable of carrying less electron flow than shorter nanowires with the same diameter, as long electron transfer distances that occasionally arise reduce the efficiency for electron transport. Thicker nanowires permit more alternative transport pathways, increasing electron transport beyond the increase in cross-section. Thus, this model implies that the design of protein-based nanowires that depend on electron hopping between charge carriers must consider control of the inherent protein flexibility, as more flexible protein-protein interfaces impose a limit on the required minimum diameter to carry currents commensurate with conventional electronics.

Hypermutator emergence in experimental Escherichia coli populations is stress type dependent

Genotypes exhibiting an increased mutation rate, called hypermutators, can propagate in microbial populations because they can have an advantage due to the higher supply of beneficial mutations needed for adaptation. Although this is a frequently observed phenomenon in natural and laboratory populations, little is known about the influence of parameters such as the degree of maladaptation, stress intensity and the genetic architecture for adaptation on the emergence of hypermutators. To address this knowledge gap, we measured the emergence of hypermutators over ~1000 generations in experimental Escherichia coli populations exposed to different levels of osmotic or antibiotic stress. Our stress types were chosen based on the assumption that the genetic architecture for adaptation differs between them. Indeed, we show that the size of the genetic basis for adaptation is larger for osmotic stress compared to antibiotic stress. During our experiment, we observed an increased emergence of hypermutators in populations exposed to osmotic stress but not in those exposed to antibiotic stress, indicating that hypermutator emergence rates are stress-type-dependent. These results support our hypothesis that hypermutator emergence is linked to the size of the genetic basis for adaptation. In addition, we identified other parameters that covaried with stress type (stress level and IS transposition rates) that might have contributed to an increased hypermutator provision and selection. Our results provide a first comparison of hypermutator emergence rates under varying stress conditions and point towards complex interactions of multiple stress-related factors on the evolution of mutation rates.

opencc-by-4.0May 2023View details →

The Impact of the Three-Dimensional Structure of a Subduction Zone on Time-dependent Crustal Deformation Measured by HR-GNSS

Companion data set to the paper "The Impact of the Three-Dimensional Structure of a Subduction Zone on Time-dependent Crustal Deformation Measured by HR-GNSS." The 'GNSS_Stations' folder contains the GNSS stations used for 2011 M7.9 Ibaraki, 2011 M7.4 Iwate, 2011A M7.3 Miyagi and 2003 M8.3 Tokachi 2003 earthquakes. The 'Mesh' folder contains the fault geometry mesh files for the Japan Trench, including the GMSH files. The '3D_velocity_model' folder contains the 3D velocity model for the combined West and East domains of the 3D Japan Integrated Velocity Structure Model in a rfile format and the corresponding ifile format. The 'Ruptures' folder contains the projected rupture models for each earthquake on the Japan Trench mesh and the corresponding 100 realizations of the mean rupture models generated using FakeQuakes. If you use these data, please cite the associated publication: Fadugba, O. I., Sahakian, V. J., Diego Melgar, D., Rodgers, A. & Shimony, R. (2023). The Impact of the Three-Dimensional Structure of a Subduction Zone on Time-dependent Crustal Deformation Measured by HR-GNSS.

opencc-by-4.0May 2023View details →

Dataset for "State-dependence of the equilibrium climate sensitivity in a clear-sky GCM" by Matthew Henry et al. (2023).

Dataset for "State-dependence of the equilibrium climate sensitivity in a clear-sky GCM" by Matthew Henry, Geoffrey K. Vallis, Nicholas J. Lutsko, Jacob T. Seeley, and Brett A. McKim.

The contribution of Fe(III) reduction to soil carbon mineralization in montane meadows depends on soil chemistry, not parent material or microbial community

The long-term stability of soil carbon (C) is strongly influenced by organo-mineral interactions. Iron (Fe)-oxides can both inhibit microbial decomposition by providing physicochemical protection for organic molecules and enhance rates of C mineralization by serving as a terminal electron acceptor, depending on redox conditions. Restoration of floodplain hydrology in montane meadows has been proposed as a method of sequestering C for climate change mitigation. However, dissimilatory microbial reduction of Fe(III) could lead to C losses under increased reducing conditions. In this study, we explored variations in Fe-C interactions over a range of redox conditions and in soils derived from two distinct parent materials to elucidate biochemical and microbial controls on soil C cycling in Sierra Nevada montane meadows. Differences in parent material were associated with different rates of Fe(III) reduction at increasing soil moisture levels, but not with differences in soil C mineralization. Known Fe(III)-reducing taxa were present in all samples but neither the relative abundance nor richness of Fe(III) reducers corresponded with measured rates of Fe(III) reduction. Under reducing conditions, our results suggest that Fe(III) reduction contributes to C mineralization only when Fe-bound C is present. However, Fe-bound C was not present in all of our soils and was below theoretical limits for C sorption onto Fe-oxides where it was found. Overall, our results suggest that meadow-specific soil chemistry drives Fe-C interactions and that the impact of Fe on C cycling in montane meadows may be smaller than in other ecosystems.

Condition dependence of (un)predictability in escape behavior of a grasshopper species

(Un)predictability has only recently been recognized as an important dimension of animal behavior. Currently, we neither know if (un)predictability encompasses one or multiple traits nor how (un)predictability is dependent on individual conditions. Knowledge about condition dependence, in particular, could inform us about whether predictability or unpredictability is costly in a specific context. Here, we study the condition dependence of (un)predictability in the escape behavior of the steppe grasshopper Chorthippus dorsatus. Predator–prey interactions represent a behavioral context in which we expect unpredictability to be particularly beneficial. By exposing grasshoppers to an immune challenge, we explore if individuals in poor condition become more or less predictable. We quantified three aspects of escape behavior (flight initiation distance, jump distance, and jump angle) in a standardized setup and analyzed the data using a multivariate double-hierarchical generalized linear model. The immune challenge did not affect (un)predictability in flight initiation distance and jump angle, but decreased unpredictability in jump distances, suggesting that unpredictability can be costly. Variance decomposition shows that 3–7% of the total phenotypic variance was explained by individual differences in (un)predictability. Covariation between traits was found both among averages and among unpredictabilities for one of the three trait pairs. The latter might suggest an (un)predictability syndrome, but the lack of (un)predictability correlation in the third trait suggests modularity. Our results indicated condition dependence of (un)predictability in grasshopper escape behavior in one of the traits, and illustrate the value of mean and residual variance decomposition for analyzing animal behavior.

Data from: Context-dependent thermolability of sex determination in a lacertid lizard with heteromorphic sex chromosomes

Developmental conditions can profoundly impact key life history traits of the individual. In cases where offspring sex is driven by developmental reaction norms, permanent changes to the phenotype can fundamentally alter life history trajectories. Sex determination mechanisms in reptiles are remarkable diverse including well-characterized genetic and temperature-dependent sex determination. In rarer, but increasingly more commonly documented cases, sex can also be determined by a combination of the two, with temperature overriding the genetically determined sex. Thus, sex-by-temperature interactions is a mechanism that can be contextually labile, where reaction norms of sex against developmental environment might only be observable under certain conditions. We examine the effects of incubation temperature on hatchling sex in an oviparous lizard with clearly defined heteromorphic sex chromosomes presumed to determine sex solely on a genetic basis. We also test the repeatability of our results by replicating incubation experiments across three years. We show that warmer temperatures may override chromosomal sex and cause overproduction of daughters. However, this effect was inconsistent among years, with high temperature only resulting in a daughter-significant bias in one year. Warm-incubated daughters were more efficient at converting yolk into tissue, which would allow for greater resource allocation to other fitness-related processes, such as growth. This suggests that thermolabile sex determination could be a trait under selection. More energy-efficient embryos also produced faster-growing offspring, suggesting that energy utilization patterns of the embryo were maintained into the juvenile stage, which could have important implications for the ontogenetic development and evolution of life histories.

Dietary flavanols restore hippocampal-dependent memory in older adults with lower diet quality and habitual flavanol consumption

Dietary flavanols are food constituents found in certain fruits and vegetables that have been linked to cognitive aging. Previous studies suggested that consumption of dietary flavanols might specifically be linked to the hippocampal-dependent memory component of cognitive aging and that memory benefits of a flavanol intervention might depend on habitual diet quality. Here, we tested these hypotheses in the context of a large-scale study of 3,562 older adults, who were randomly assigned to a 3-y intervention of cocoa extract (500 mg of cocoa flavanols per day) or a placebo [(COcoa Supplement and Multivitamin Outcomes Study) COSMOS-Web, NCT04582617]. Using the alternative healthy eating index in all participants and a urine-based biomarker of flavanol intake in a subset of participants [n = 1,361], we show that habitual flavanol consumption and diet quality at baseline are positively and selectively correlated with hippocampal-dependent memory. While the prespecified primary endpoint testing for an intervention-related improvement in memory in all participants after 1 y was not statistically significant, the flavanol intervention restored memory among participants in lower tertiles of habitual diet quality or habitual flavanol consumption. Increases in the flavanol biomarker over the course of the trial were associated with improving memory. Collectively, our results allow dietary flavanols to be considered in the context of a depletion–repletion paradigm and suggest that low flavanol consumption can act as a driver of the hippocampal-dependent component of cognitive aging.

The cellular response to extracellular vesicles is dependent on their cell source and dose

Extracellular vesicles (EV) have been established to play important roles in cell-cell communication and have shown promise as therapeutic agents. However, we still lack a basic understanding of how cells respond upon exposure to EVs from different cell sources at various doses. Thus, we treated fibroblasts with EVs from twelve different cell sources at doses between 20 and 200,000 per cell, analyzed their transcriptional effects, and functionally confirmed the findings in various cell types in vitro, and in vivo using single-cell RNA-sequencing. Unbiased global analysis revealed EV dose to have a more significant effect than cell source, such that high doses downregulated exocytosis and upregulated lysozomal activity. However, EV cell source-specific responses were observed at low doses, and these reflected the activities of the EV's source cells. Finally, we assessed EV-derived transcript abundance and found that immune cell-derived EVs were most associated with recipient cells. Together, this study provides important insight into the cellular response to EVs.

opencc-by-4.0May 2023View details →

Data & scripts - The effect of temperature-dependent material properties on simple thermal models of subduction zones

Data and scripts used in Van Zelst et al. (2023, Solid Earth): 'The effect of temperature-dependent material properties on simple thermal models of subduction zones'. Includes the data and figures for the benchmark of Van Keken et al. (2008) plus the results from our code xFieldstone; processing and visualisation scripts; raw and final figures; and all results for all model runs used in the publication (as listed in Table 1 in the paper).

Short-term fitness consequences of parasitism depend on host genotype and within-host parasite community

Multi-parasite communities inhabiting individual hosts are common and often consist of parasites from multiple taxa. The effects of parasite community composition and complexity on host fitness are critical for understanding how host-parasite coevolution is affected by parasite diversity. To test how naturally-occurring parasites affect host fitness of multiple host genotypes, we performed a common-garden experiment where we inoculated four genotypes of host plant Plantago lanceolata with six microbial parasite treatments: three single parasite treatments, a fungal mixture, a viral mixture, and a cross-kingdom treatment. Seed production was affected by both host genotype and parasite treatment, and their interaction jointly determined growth of the hosts. Fungal parasites had more consistent negative effects than viruses in both single mixed parasite treatments. These results demonstrate that parasite communities have the potential to affect the evolution and ecology of host populations through their effects on host growth and reproduction. Moreover, the results highlight the importance of accounting for the diversity of parasites as well as host genotypes when aiming to predict the consequences of parasites for epidemics as the effects of multi-parasitism are not necessarily additive of single parasite effects, nor uniform across all host genotypes.

opencc-by-4.0Apr 2023View details →

Raw data for: Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity

This repository contains raw data and code related to "Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity" by Goretzki et al. Included are molecular dynamics parameter files, initial structures after system equilibration, production trajectories, and final structures of simulations of: 1. coarse-grained IDRs on membrane, and force and position data for restrained c-termini. Trajectories are subsampled with one frame every 50 ns. 2. The tetrameric TRPV4 core in a POPC in atomistic resolution. Trajectories are sampled with one frame every 1 ns.  3. The isolated ARD in solution in atomistic resolution. Trajectories are subsampled with one frame every 1 ns. Contact information: Name: Stefan L. Schaefer Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany Email: stefan.schaefer@biophys.mpg.de Name: Ainara Claveras Cabezudo Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany Email: ainara.claveras@biophys.mpg.de

Density dependence of seed dispersal and fecundity profoundly alters the spread dynamics of plant populations

<ol> <li>Plant population spread has fundamental ecological and evolutionary importance. Both determinants of plant population spread, fecundity and dispersal, can be density-dependent, which should cause feedback between population densities and spread dynamics. Yet it is poorly understood how density-dependence affects key characteristics of spread: spread rate at which the location of the furthest forward individual moves, edge depth (the geographical area over which individuals contribute to spread) and population continuity (occupancy of the spreading population).</li> <li>We present a general modelling framework for analysing the effects of density-dependent fecundity and dispersal on population spread and parameterize this framework with experimental data from a common-garden experiment using five wind-dispersed plant species grown at different densities. </li> <li>Our model shows that density-dependent fecundity and dispersal strongly affect all three population spread characteristics for both exponential and lognormal dispersal kernels. Spread rate and edge depth are strongly correlated but show weaker correlations with population continuity. Positive density-dependence of fecundity increases all three spread characteristics. Increasingly positive density-dependence of dispersal increases spread rate and edge depth but generally decreases population continuity. Density-dependent fecundity and dispersal are largely additive in their effect on spread characteristics. For population continuity, the joint effects of density-dependent fecundity and dispersal are somewhat contingent on the dispersal kernel.</li> <li>The common-garden experiment and the experimentally parameterized mechanistic dispersal model revealed density-dependent fecundity and dispersal across study species. All study species exhibited negative density-dependent fecundity, but they differed qualitatively in the density-dependence of dispersal distance and probability of long-distance dispersal. The negative density-dependence of fecundity and dispersal found for three species reinforced each other in reducing spread rate and edge depth. The positively density-dependent dispersal found for two species markedly increased spread rate and edge depth. Population continuity was hardly affected by population density in all study species except Crepis sancta in which it was strongly reduced by negatively density-dependent fecundity.</li> <li> Synthesis. Density-dependent fecundity and seed dispersal profoundly alter population spread. In particular, positively density-dependent dispersal should promote the spread and genetic diversity of plant populations migrating under climate change but also complicate the control of invasive species.</li> </ol>