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560 results for “Direct effects”
Raw plot data for: Accelerating equilibrium isotope effect calculations. II. Stochastic implementation of direct estimators
<p>Data for publication: K. Karandashev, J. Vanicek, Accelerating equilibrium isotope effect calculations. II. Stochastic implementation of direct estimators, J. Chem. Phys. <strong>151</strong>, 134116 (2019) <a href="https://doi.org/10.1063/1.5124995">https://doi.org/10.1063/1.5124995</a></p> <p>This data set contains the raw numerical data for reproducing Figures 1-8 in the publication.</p>
Dataset and codes for "Direct and indirect effects of pets on the health of older adults"
<p>Dataset, codes and supplementary material for "<strong>Direct and indirect effects of pets on the health of older adults"</strong></p> <p>Life expectancy emphasizes the importance of adapting to and adopting new measures that will benefit healthy aging. A promising lead is the potential benefits of pets for older adults in their homes. This study aimed to test the influence of socio-demographic and environmental factors on the presence of dogs and cats around older adults. The direct and indirect effects of pets, using sociality and mobility factors, were tested on health variables. The social cohesion of a community and type of dwelling appeared to be related to the presence of pets. In addition, the results showed mixed effects of pets, namely a positive influence on mental health via the social network of older adults, and a negative influence in the form creation of a certain stress. In general, the effects of pets on the lives of older adults constitute an important research framework to pursue in the context of healthy aging.</p>
Data and reproducible code for Honor et al: Direct and indirect fitness effects of competition limit evolution of allelopathy in an invading plant
<p><span>Upon introduction to new continents, invading species encounter novel communities of consumers, pathogens, and competitors. Both phenotypic plasticity and rapid evolution can facilitate adaptation across these heterogenous communities, facilitating further invasion. However, the rate and extent of adaptive evolution on contemporary timescales can be constrained by phenotypic plasticity and limits imposed by genetic co-variation for traits under selection.</span></p> <p><span>We measured phenotypic plasticity and quantified genetic co-variation for growth, competition, and fitness among </span>23 naturally inbred seed families <span>of <em>Alliaria petiolata</em> (garlic mustard) </span>collected across its invasive range in eastern North America. After growing a self-pollinated generation in a uniform common garden to reduce maternal effects, we reared second-generation plants in a <span>two-year greenhouse and field experiment with naïve soil from an uninvaded habitat. W</span>e measured selection gradients and lifetime fitness when reared alone, with an intraspecific competitor, and under interspecific competition with naïve <em>Acer saccharum </em>(sugar maple) saplings.</p> <p>Total glucosinolate production was strongly correlated with the production of chlorophyll a (Chl a) (<em>R<sup>2</sup></em> = 0.45) such that first principal component (PC1) accounted for 84% of variation in these two traits. Furthermore, PC1 exhibited high plasticity across growing environments (p < 0.001) with limited broad-sense heritability (<em>H<sup>2</sup> </em>= 2.91; p = 0.08). In contrast, investment in glucosinolate production relative to Chl a (PC2) was significantly heritable (<em>H</em><sup><em>2</em> </sup>=16.91, p < 0.001) with minimal plasticity across treatments. Causal analysis revealed that plastic variation for higher Chl a + glucosinolate production (PC1) had an indirect positive effect on A. petiolata fitness via a direct, negative effect on <em>A. saccharum</em> performance. In contrast, heritable variation for higher glucosinolate investment (PC2) had a direct, positive effect on <em>A. saccharum</em> performance and an indirect negative effect on A. petiolata fitness. </p> <p>Applying causal inference, we find that evolution of allelopathy in <em>A. petiolata</em> has been constrained by (i) a lack of genetic variation, (ii) selection against glucosinolate investment under interspecific competition, and (iii) phenotypic plasticity. These factors limit adaptive evolution but maintain fitness during population growth as plants switch from interspecific to intraspecific competition during invasion.</p>
Data from: The sequential direct and indirect effects of mountain uplift, climatic niche and floral trait evolution on diversification dynamics in an Andean plant clade
<p><span>Why and how organismal lineages radiate is commonly studied through either assessing abiotic factors (biogeography, geomorphological processes, climate) or biotic factors (traits, interactions). Despite increasing awareness that both abiotic and biotic processes may have important joint effects on diversification dynamics, few attempts have been made to quantify the relative importance and timing of these factors, and their potentially interlinked direct and indirect effects, on lineage diversification.</span></p> <p><span>We here combine assessments of historical biogeography, geomorphology, climatic niche, vegetative and floral trait evolution to test whether these factors jointly, or in isolation, explain diversification dynamics of a Neotropical plant clade (Merianieae, Melastomataceae). After estimating ancestral areas and disparification over time in climate and trait space, we employ Phylogenetic Path Analyses as a synthesis tool to test eleven hypotheses on the individual direct and indirect effects of these factors on diversification rates.</span></p> <p><span>We find strongest support for interlinked effects of colonization of the uplifting Andes during the mid-Miocene and rapid abiotic climatic niche evolution in explaining a burst in diversification rate in Merianieae. Within Andean habitats, later disparification in floral trait space allowed for the exploitation of wider pollination niches (i.e., shifts from bee to vertebrate pollinators), but did not affect diversification rates. Our approach of including both vegetative and floral trait evolution, rare in assessments of plant diversification in general, highlights important pre-adaptations to mountain colonization, specifically woody habit and larger flowers. Overall, and in concert with the idea that ecological opportunity is a key element of evolutionary radiations, our results suggest that a combination of rapid niche evolution and pre-adapted traits were critical for the exploitation of newly available niche space in the Andes in the mid-Miocene. Further, our results emphasize the importance of incorporating both abiotic and biotic factors into the same analytical framework if we aim to quantify the relative and interlinked effects of these processes on diversification.</span></p>
Effect of Direct-from-blood Bacterial Testing on Antibiotic Administration and Clinical Outcomes
ClinicalTrials.gov study NCT06069206. IPD Sharing: YES. Countries: 1. Publications: 18.
Data from: Wildfire disturbance and ecological cascades: teasing apart the direct and indirect effects of fire on tick populations
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Data from: Direct and trans-generational effects of tetracyclines on the microbiome, transcriptome, and male mating behavior of the sheep blowfly Lucilia cuprina
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Data from: The sequential direct and indirect effects of mountain uplift, climatic niche and floral trait evolution on diversification dynamics in an Andean plant clade
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Quantifying direct and indirect effects of early-season herbivory on reproduction across four brassicaceous plant species
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Data and reproducible code for Honor et al: Direct and indirect fitness effects of competition limit evolution of allelopathy in an invading plant
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Direct and indirect phenotypic effects on sociability indicate potential to evolve
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Competitive interactions modify the direct effects of climate
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Diurnal cycle of the semi-direct effect from a persistent absorbing aerosol layer over marine stratocumulus in large-eddy simulations: supporting dataset
<p>Relevant data for reproducing figures and tables from Herbert et al., 2020, Atmospheric Chemistry and Physics: "Diurnal cycle of the semi-direct effect from a persistent absorbing aerosol layer over marine stratocumulus in large-eddy simulations".</p> <p>The tar file contains the relevant netcdf files that contain simulation output from the MET Office large eddy model (LEM). Each netcdf file corresponds to a single model setup and experiment - details of which can be found within the published manuscript. Information concerning the LEM, and details on how to obtain access to the code, can be found at http://appconv.metoffice.com/LEM/index.html.</p> <p>The file 'relevant_information.pdf' contains two tables. The first provides the names of each netcdf file that was used to produce each figure in the manuscript. The second provides the metadata for the netcdf variables that were used to produce the figures and tables.</p> <p>The netcdf filename provides information on the experiment setup as follows:</p> <p>run-identifier-number _ length-of-run _ AOD-of-layer _ GAP-between-cloud-and-layer _ THICKNESS-of-layer _ 'bigarray' _ special-setups-for-sensitivity-experiments</p> <p>For example, r1360_8day_transient_aod02_0dz_250th_bigarray_nodrizz is run number r1360, simulating 8 days, with the aerosol layer properties AOD=0.2, cloud-to-aerosol gap of 0m, layer thickness of 250m, in the sensitivity setup where precipitation has been switched off.</p>
Data from: Direct and indirect effect of cannibalism and intraguild predation in the two sibling Harmonia ladybird beetles
<p>In this study, we focused on the direct (i.e. predation) and indirect (i.e. potential threat from coexisting with a larger individual) effects of cannibalism and intraguild predation (IGP) during larval stages of two sibling ladybird beetles. These effects play an important role in the coexistence of the generalist–common Harmonia axyridis and specialist–rare H. yedoensis (Coleoptera: Coccinellidae). Direct predation effect of cannibalism and IGP were asymmetric in the two sibling ladybird beetles; the fourth instar larvae of H. axyridis were better intraguild predators than cannibals, while the reverse was true in the larvae of H. yedoensis. Neither cannibalism nor IGP significantly affected female body weight in either species. Larval H. axyridis surviving exposure to cannibalism or IGP had a reduced number of ovarioles as adults, whereas adult H. yedoensis ovarioles were not affected. For the indirect effects, longer developmental times in males and females and a lower total number of ovarioles in females were detected in H. axyridis. In H. yedoensis, shorter developmental time of males, lighter adult weight and fewer total ovarioles in females were observed. Olfactometer choice experiments clarified that the fourth instar larvae of H. axyridis avoided the first instar conspecific larvae, while those of H. yedoensis were attracted to the odours from H. axyridis and conspecifics. Thus, H. axyridis has an avoidance mechanism only for cannibalism but not for IGP, whereas H. yedoensis does not have any avoidance mechanism. These different behaviours in the direct and indirect effects of cannibalism and IGP observed in the laboratory may play important roles in the coexistence of generalist–common H. axyridis and specialist–rare H. yedoensis in natural conditions, compensating for the large handicap of H. yedoensis at reproductive interference from H. axyridis.</p>
Effects of soil salinity on the expression of direct and indirect defences in wild cotton (Gossypium hirsutum)
<p>Previous studies have reported effects of abiotic factors on herbivore-induced plant defences based on effects on single plant traits. However, plants commonly express multiple defences simultaneously and these traits are often correlated. Thus, a fuller understanding of abiotic-context dependency in plant defence requires measuring multiple traits and addressing their patterns of correlated expression.</p> <p>We evaluated the effects of soil salinity on the induction of direct (phenolic compounds, gossypol gland density) and indirect (volatile organic compounds, extrafloral nectar) defensive traits in wild cotton (Gossypium hirsutum). We asked whether soil salinity affects the induction of these traits, and whether it shapes trait correlations potentially underlying salinity effects on trait induction. We conducted a factorial experiment with 16 cotton genotypes where we manipulated soil salinity and defence induction by applying artificial leaf damage (25% mechanical damage and caterpillar oral secretions) and measured defence levels at different time points post-damage.</p> <p>Leaf damage induced most traits except gossypol gland density, whereas salinity did not have a mean effect (across constitutive and induced levels) on any of the measured traits. Nonetheless, salinity prevented the induction of phenolic compounds (condensed and hydrolysable tannins), and also affected trait correlations. Specifically, phenolic compounds were negatively associated with nectar production only under salinized conditions, an apparent trade-off that presumably affects the induced levels of phenolic compounds. In addition, positive correlations between phenolic compounds and gland density and root biomass observed under control conditions were lost under salinized conditions.</p> <p>By investigating the effects of soil salinity on the expression of multiple direct and indirect defensive traits and their underlying correlations, these findings build toward a better understanding of how abiotic context-dependency shapes plant allocation to and expression of multiple defensive traits.</p>
Data from: Separating differential allocation by females from direct effects of male condition in a beetle
<p>Differential allocation is the adjustment of reproductive allocation, typically by a female, in response to the quality of her male partner. A recent theoretical model suggests that differential allocation may influence trade-offs between reproductive traits within a breeding attempt. Furthermore, it is often difficult to distinguish differential allocation from direct effects of male condition. We address these gaps using a novel cross-fostering design to exclude direct effects of male condition and to test whether differential allocation affects trade-offs between and within breeding attempts. This design detects differential allocation as effects of a female's mating partner and direct effects of male condition as effects of the larvae's sire. We used the burying beetle Nicrophorus vespilloides, a species which adjusts reproductive allocation by culling some larvae after hatching. We used food-deprivation to manipulate the nutritional condition of both the female's mating partner and the larvae's sire. We find clear evidence for differential allocation as females mating with food-deprived males had fewer larvae than females mating with control males. There was a trade-off between number and size of larvae when females mated with control males, but a positive relationship when females mated with food-deprived males. Thus, differential allocation influenced relationships between reproductive traits within a breeding attempt, but not necessarily through trade-offs. Instead, we suggest that there may be cryptic heterogeneity in quality among females or their mating partners that was only exposed when females mated with a male in poor condition.</p>
Data from: Direct effects of a non-native invader erode native plant fitness in the forest understory
1. The direct role of non-native plant invaders in driving negative population- and community-level processes of native species has been recently questioned. Addressing this controversy requires determining quantitatively if invaders negatively affect native population fitness. Because the invasion of non-natives often coincides with other anthropogenic stressors, experiments that partition the putative impact of non-natives from other known stressors and assess their potential synergies are required. While many studies have examined the effects of non-natives on components of native plant performance, studies that decompose the net fitness effects of non-natives from other anthropogenic stressors on population growth rate are lacking. 2. We used six years of detailed demographic data to parameterize a size-dependent integral projection model to examine the individual and combined effects of an allelochemical-producing invader (Alliaria petiolata) and an overabundant ungulate herbivore (Odocoileus virginianus) on the population dynamics of an understory perennial (Trillium erectum). 3. We show that Alliaria consistently and negatively affects the population dynamics of Trillium. Specifically, this invader reduces native population growth rate and alters the size distribution of the population at equilibrium. Alliaria also works in concert with the known negative impacts of overabundant white-tailed deer, illustrating the additive effects of anthropogenic stressors on native plant dynamics. 4. Synthesis. Alliaria's effects on vital rates differed in magnitude and sign across the native's lifecycle, highlighting the importance of detailed demographic analyses. Globally, our study provides novel empirical support for the claim that non-native invasive species can significantly and directly reduce the fitness of native plants.
Trophic rewilding benefits a tropical community through direct and indirect network effects
Species reintroductions can be used as a conservation strategy to restore ecological interactions and the functionality of impoverished ecosystems. The ecological effects of reintroductions go beyond restoring pairwise interactions, because reintroductions can change how extant species are indirectly linked to each other in an ecological community. These indirect pathways, in turn, may shape a myriad of ecological and evolutionary processes operating in ecological systems. Here, we investigated how reintroductions may affect the direct and indirect pathways connecting species in ecological networks. We modeled the potential effects of the reintroduction of four frugivore species (channel-billed toucans, red-humped agoutis, brown howler monkeys and yellow-footed tortoises) to the local seed dispersal network in an Atlantic Forest site, the Tijuca National Park (Tijuca, Brazil). We used a seed dispersal interaction dataset together with data on species occurrences in Tijuca to build network models. Then, we calculated how network structure and the total amount of indirect effects varied across simulated networks with and without the reintroduced species. Using random reintroduction simulations, we tested if the observed network changes were expected merely from the increase in species richness. The reintroduction of the frugivore species increased network connectance, nestedness, robustness, number of pathways and total amount of indirect effects in all simulated networks. The increase in number of pathways with the addition of the four reintroduced species was greater than the sum of isolated effects for each species, as some interaction pathways contained several reintroduced species. These changes in network metrics were significantly greater than if a randomly chosen set of four species were reintroduced. Furthermore, our results indicate that multiple reintroductions in the same area, known as refaunation, may have an even greater restoration effect than single species reintroductions through increased indirect connections in the network.
Grazing changes the direction of direct effect of shrubs on nematode communities but suppresses indirect effects through microbial pathways
<p>It is well established that dominant plants shape belowground communities, which in turn influence ecosystem functioning. Similarly, herbivores affect belowground communities through physical disturbance and redistribution of organic inputs, but also through their interactions with the plants themselves. However, we know little about how grazing moderates effects of dominant plants on belowground organisms. We established a three-year removal experiment in a grazed and an ungrazed alpine meadow on the Qinghai-Tibet plateau to explore how grazing mediates the effects of the dominant shrub, <em>Dosiphora fruticosa</em>, on nematode communities. We applied structural equation modelling to assess how grazing moderates the effects of <em>D. fruticosa</em> on nematode communities both directly and indirectly via changes in soil physicochemical properties<span>, root biomass and microbial communities</span>. We found that 1) grazing changed the direction of the direct effect of shrub on nematode communities as indicated by the shift from a negative to a positive path coefficient; 2) shrub affected nematode richness mainly through microbial richness. Accordingly, nematode community composition was more closely related to microbial community composition in the ungrazed alpine meadow, while edaphic properties were stronger predictors of nematode community composition responses to shrubs in the grazed meadow; and 3) grazing suppressed the indirect effects of shrub on nematode communities via microbial communities. Our study shows that grazing plays an important role in regulating dominant plant's effects on belowground community composition and interactions in alpine meadows.</p>
Dataset for "Quantifying the effects of bed roughness on transit time distributions via direct numerical simulations of turbulent hyporheic exchange"
<p>This dataset contains the sediment models, DNS flow field data, subsurface path data, and calculated transit time distributions for both the regular- and random-interface cases used in the paper: "Quantifying the effects of bed roughness on transit time distributions via direct numerical simulations of turbulent hyporheic exchange" by Guangchen Shen, Junlin Yuan, and Mantha S. Phanikumar (Submitted to Water Resources Research). <br> Detailed introduction of each data file is as follows.</p> <p>1. DNS flow field data</p> <p>Flowfield_Reg.h5 and Flowfield_Ran.h5 contains the following fields for the regular and random cases, respectively. 'ni', 'nj', 'nk' are the numbers of grid points along x, y, and z directions. 'xc', 'yc', 'zc' are the cell center locations. 'u3d','v3d','w3d' are the three-dimensional time-averaged velocities at each grid point. 'vof' is the volume-of-fluid field used by the immersed-boundary method to prescribe the fluid-solid interface (vof=1 in fluid and 0 in solid), at each grid point. 'vof' contains the information of sediment grain distribution and bed roughness geometry. Only the subsurface data (those below the sediment crest) are shared due to dataset size limit.</p> <p>2. Particle-tracked subsurface flow paths and corresponding transit time distributions</p> <p>The mat files “xxx_pathline” store the (x,y,z) location of each point (saved as 'StrX', 'StrY, 'StrZ') along the subsurface paths, discretized by uniform steps of travel time (with time intervals of 0.1 for 'A' and 0.01 for 'MD' cases, normalized by channel height and friction velocity). The files “xxx_TT” store the array of transit times corresponding to the tracked paths, where the 1d array T is the transit time. 'A' denotes calculations based on time-mean advection only, while 'MD' denotes calculations accounting for additional molecular diffusion. 'Interface' and '3DiameterBelow' indicate that the particles were released at the interface and -3 D below the interface, respectively.</p>
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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.