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143 results for “Directed Interactions”
Data and R code from: Pollination interactions reveal direct costs and indirect benefits of plant–plant facilitation for ecosystem engineers
Ecosystem engineers substantially modify the environment via their impact on abiotic conditions and the biota, resulting in facilitation of associated species that would not otherwise grow. Yet, reciprocal effects are poorly understood as studies of plant–plant interactions usually estimate only benefits for associated species while hardly considering how another trophic level may mediate direct and indirect effects for ecosystem engineers. We run a field experiment with ecosystem engineers blooming either alone or with associated plants to decompose net effects and to test the hypothesis that pollinator-mediated interactions provide benefits which balance costs of facilitation by ecosystem engineers. We found that net costs of facilitation are accompanied by pollinator-mediated benefits. Despite ecosystem engineers producing less flowers per plant, they were visited by more and more diverse pollinators per flower when blooming with associated plants than when blooming alone. However, fruit set was unaffected by the presence of associated plants and seed production per plant was higher when ecosystem engineers bloomed alone. Our findings suggest that besides experiencing direct costs, ecosystem engineers can also benefit from facilitating other species via increasing their own visibility to pollinators. This study illuminates how the outcome of direct plant–plant interactions might be mediated by indirect interactions including third players.
Data and code for Reeb, R.A. & Kuebbing, S.E. (2024). Phenology mediates direct and indirect interactions among co-occurring invasive plant species. Ecology, e4446.
<p>Data and analysis code for:</p> <p>Reeb, R.A. & Kuebbing, S.E. (2024). Phenology mediates direct and indirect interactions among co-occurring invasive plant species. Ecology, e4446. <a href="https://doi.org/10.1002/ecy.4446">https://doi.org/10.1002/ecy.4446</a></p> <p>Repository contains R markdown analysis code, datasets, and the associated metadata file.</p>
Rhizobia-legume symbiosis mediates direct and indirect interactions between plants, herbivores and their parasitoids
<p>Data and R scripts for statistical analyses for the article:</p> <p><strong>Rhizobia-legume symbiosis mediates direct and indirect interactions between plants, herbivores and their parasitoids</strong></p> <p>By: <strong>Carlos Bustos-Segura, Adrienne L. Godschalx, Lucas Malacari, Fanny Deiss, Sergio Rasmann, Daniel J. Ballhorn, Betty Benrey</strong> </p> <p> </p> <p><strong>Abstract</strong></p> <p>Microorganisms associated with plant roots significantly impact the quality and quantity of plant defences. However, the bottom-up effects of soil microbes on the aboveground multitrophic interactions remain largely under studied. To address this gap, we investigated the chemically-mediated effects of nitrogen-fixing rhizobia on legume-herbivore-parasitoid multitrophic interactions. To address this, we initially examined the cascading effects of the rhizobia bean association on herbivore caterpillars, their parasitoids, and subsequently investigated how rhizobia influence on plant volatiles and extrafloral nectar. Our goal was to understand how these plant-mediated effects can affect parasitoids. Lima bean plants (<em>Phaseoulus lunatus</em>) inoculated with rhizobia exhibited better growth, and the number of root nodules positively correlated with defensive cyanogenic compounds. Despite increase of these chemical defences, <em>Spodoptera</em> latifascia caterpillars preferred to feed and grew faster on rhizobia-inoculated plants. Moreover, the emission of plant volatiles after leaf damage showed distinct patterns between inoculation treatments, with inoculated plants producing more sesquiterpenes and benzyl nitrile than non-inoculated plants. Despite these differences, <em>Euplectrus platyhypenae</em> parasitoid wasps were similarly attracted to rhizobia- or no rhizobia-treated plants. Yet, the oviposition and offspring development of <em>E. platyhypenae </em>was better on caterpillars fed with rhizobia-inoculated plants. We additionally show that rhizobia-inoculated common bean plants (<em>Phaseolus vulgaris</em>) produced more extrafloral nectar, with higher hydrocarbon concentration, than non-inoculated plants. Consequently, parasitoids performed better when fed with extrafloral nectar from rhizobia-inoculated plants. While the overall effects of bean-rhizobia symbiosis on caterpillars were positive, rhizobia also indirectly benefited parasitoids through the caterpillar host, and directly through the improved production of high quality extrafloral nectar. This study underscores the importance of exploring diverse facets and chemical mechanisms that influence the dynamics between herbivores and predators. This knowledge is crucial for gaining a comprehensive understanding of the ecological implications of rhizobia symbiosis on these interactions.</p>
Direct observations of wave-sea ice interactions in the Antarctic Marginal Ice Zone
<p>These are the data used in the analysis and creation of figures in S. Wahlgren, L.C. Biddle, J. Thomson and S. Swart: <em><strong>Direct observations of wave-sea ice interactions in the Antarctic Marginal Ice Zone</strong> </em>[Submitted]. Preprint: https://doi.org/10.22541/essoar.168201718.84053333/v1</p> <p>Abstract:</p> <p>Wave energy propagating into the Antarctic marginal ice zone affects the quality and extent of the sea ice, and wave propagation is therefore an important factor for understanding and predicting changes in sea ice cover. Sea ice is notoriously hard to model and in-situ observations of wave activity in the Antarctic marginal ice zone are scarce, due to the extreme conditions of the region. Here, we provide new in-situ data from two drifting Surface Wave Instrument Float with Tracking (SWIFT) buoys deployed in the Weddell Sea in the austral winter and spring in 2019. The buoy location ranges from open water to more than 200 km into the sea ice. We estimate the attenuation of swell with wave periods 8-18 s, and find an attenuation coefficient <em>α = </em>4·10<sup>-6</sup> to 7·10<sup>-5</sup> m<sup>-1</sup> in spring, and approximately five-fold larger in winter. The attenuation coefficients show a power law frequency dependence, with power coefficient 3.3 in spring and 4 in winter. The in-situ data also shows a change in wave direction, where wave direction tends to be more perpendicular to the ice edge farther into the sea ice. A possible explanation for this might be a change in the dispersion relation caused by changing sea ice composition. These observations can help shed further light on the influence of sea ice on waves propagating into the Marginal Ice Zone, aiding development of coupled wave-sea ice models.</p> <p><strong>Related code: </strong> The accompanying code can be found at <strong> </strong>https://github.com/stinawahlgren/roammiz-wave-seaice-interactions. SWIFT buoy data has been processed using https://github.com/SASlabgroup/SWIFT-codes.</p>
Data and R code from: Pollination interactions reveal direct costs and indirect benefits of plant–plant facilitation for ecosystem engineers
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Competitive interactions modify the direct effects of climate
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Optimal mechanical interactions direct multicellular network formation on elastic substrates
<p>Cells self-organize into functional, ordered structures during tissue morphogenesis, a process that is evocative of colloidal self-assembly into engineered soft materials. Understanding how intercellular mechanical interactions may drive the formation of ordered and functional multicellular structures is important in developmental biology and tissue engineering. Here, by combining an agent-based model for contractile cells on elastic substrates with endothelial cell culture experiments, we show that substrate deformation–mediated mechanical interactions between cells can cluster and align them into branched networks. Motivated by the structure and function of vasculogenic networks, we predict how measures of network connectivity like percolation probability and fractal dimension as well as local morphological features including junctions, branches, and rings depend on cell contractility and density and on substrate elastic properties including stiffness and compressibility. We predict and confirm with experiments that cell network formation is substrate stiffness dependent, being optimal at intermediate stiffness. We also show the agreement between experimental data and predicted cell cluster types by mapping a combined phase diagram in cell density substrate stiffness. Overall, we show that long-range, mechanical interactions provide an optimal and general strategy for multicellular self-organization, leading to more robust and efficient realizations of space-spanning networks than through just local intercellular interactions.</p>
Data from: Direct and higher-order interactions in plant communities under increasing weather persistence
<p>ABSTRACT: Climate change is increasing the weather persistence in the midlatitudes, prolonging both dry and wet spells compared to historic averages. These newly emerging environmental conditions destabilize plant communities, but the role of species interactions in this process is unknown. Here, we tested how direct and higher-order interactions (HOIs) between species may change in synthesized grassland communities along an experimental gradient of increasing persistence in precipitation regimes. Our results indicate that species interactions (including HOIs) are an important determinant of plant performance under increasing weather persistence. Out of the 12 most parsimonious models predicting species productivity, 75 % contained significant direct interactions and 92 % significant HOIs. Inclusion of direct interactions or HOIs respectively tripled or quadrupled the explained variance of target species biomass compared to null models only including the precipitation treatment. Drought dominated the plant responses, with longer droughts increasing direct competition but also HOI-driven facilitation. Despite these counteracting changes, drought intensified net competition. Grasses were generally more involved in competitive interactions whereas legumes had a stronger affinity for facilitative interactions. Under longer drought, species affinity for nutrient rich or wet environments resulted in more negative direct interactions or HOIs, respectively. We conclude that higher-order interactions, crucially depending on species identity, only partially stabilize community dynamics under increasing weather persistence</p>
Data from: Direct and higher-order interactions in plant communities under increasing weather persistence
<p>Climate change is increasing the weather persistence in the mid-latitudes, prolonging both dry and wet spells compared to historic averages. These newly emerging environmental conditions destabilize plant communities, but the role of species interactions in this process is unknown. Here, we tested how direct and higher-order interactions (HOIs) between species may change in synthesized grassland communities along an experimental gradient of increasing persistence in precipitation regimes. Our results indicate that species interactions (including HOIs) are an important determinant of plant performance under increasing weather persistence. Out of the 12 most parsimonious models predicting species productivity, 75 % contained significant direct interactions and 92 % significant HOIs. Inclusion of direct interactions or HOIs respectively tripled or quadrupled the explained variance of target species biomass compared to null models only including the precipitation treatment. Drought was the main driver of plant responses, with longer droughts increasing direct competition but also HOI-driven facilitation. Despite these counteracting changes, drought intensified net competition. Grasses were generally more involved in competitive interactions whereas legumes were more involved in facilitative interactions. Under longer drought, species affinity for nutrient rich or wet environments resulted in more negative direct interactions or HOIs, respectively. We conclude that higher-order interactions, crucially depending on species identity, only partially stabilize community dynamics under increasing weather persistence.</p>
AMaze: fully discrete training with three regimes (direct, scaffolding, interactive) and two algorithms (A2C, PPO)
<p>Dataset containing all training artifacts (final models, training curves, intermediate visualizations, ...) as well as the raw data used to assert generalization capabilities.</p> <p>The associated archive final_behavior.tar.gz provides a visualization of every replicate's final behavior for easier navigation.</p> <p>Distribution files contain a sampling across 1000 seeds, 5 probabilities for traps and lures, 4 sizes and 5 set sizes resulting in 486356 mazes. Descriptive graphs provide an overview of the accessible "maze space".</p> <p> </p> <p>v2: Added script to aggregate run dynamics (mean reward, errors, maze lengths...) and resulting generated dataset (csv) and plots (pdf)</p>
Supplement (interactive Excel reporting tool) to MAGIC Deliverable 5.6 'Report on Narratives behind Directives Protecting the Environment'
<p>Interactive Excel data sheets for four case studies (the Netherlands, France, Spain and European Union) illustrating the consequences of full and partial internalization of agricultural production (based on current levels of import and export) for biodiversity loss. These interactive Excel reporting tools are a supplement to: </p> <p>De Olde EM, Ripoll Bosch R, Kok A, De Boer IJM, Giampietro M and Guimaraes Pereira A (2019). Report on Narratives behind Directives Protecting the Environment (Revision). MAGIC (H2020–GA 689669) Project Deliverable 5.6. First version 30 November 2018, revision 30 June 2019. Available online: <a href="https://magic-nexus.eu/documents/d56-report-narratives-behind-directives-protecting-environment">https://magic-nexus.eu/documents/d56-report-narratives-behind-directives-protecting-environment</a> </p> <p> </p>
Coordinating directional switches in pigeon flocks: The role of nonlinear interactions
<p>MatLab Code for paper "Coordinating directional switches in pigeon flocks: The role of nonlinear interactions".</p>
Transgenerational coexistence history attenuates negative direct interactions and strengthens facilitation
<p>Data set for the study <strong>Transgenerational coexistence history attenuates negative direct interactions and strengthens facilitation</strong></p>
20230822-IKEM: Intrinsic exploration motivation (individual / social and direct / indirect curiosity, creativity and non-exploration), that influences which object and, if the agent is social, partner(s) are chosen for the interaction, is introduced.
<p>This archive contains the results of a multi-agent simulation experiment [1] carried out with Lazy lavender [2] environment.<br> <br> Experiment Label: 20230822-IKEM<br> <br> Experiment design: Agents interact by playing games with objects and adapt their ontologies to agree on decision taking. Intrinsic exploration motivation (individual / social and direct / indirect curiosity, creativity and non-exploration), that influences which object and, if the agent is social, partner(s) are chosen for the interaction, is introduced.<br> <br> Experiment setting: Agents learn decision trees (transformed into ontologies); choose the objects (and partners) to interact with; adapt by splitting their leaf nodes<br> <br> Hypotheses: 1) Agents will be able to fulfil their motivation in terms of increased exploration (exploratory motivations) and decreased exploration (non-exploratory motivation). 2) Agents with exploratory motivation will be more complete, but less accurate than the baseline and non-exploration. 3) Curious agents will be more accurate and complete, but converge slower in comparison with creativity. 4) In more complex settings (higher number of agents and properties), exploration leads to more completeness, accuracy, distance and faster convergence than the baseline. 5) Agents with non-exploratory motivation will be less accurate and complete than the baseline. 6) The indirect learning models have a higher accuracy and completeness than the direct models. 7) Agents with socially oriented intrinsic motivation will have less diverse knowledge, but agree more and converge faster than agents with individual intrinsic motivation. 8) Heterogeneously motivated agents will have a higher accuracy and completeness, but lower diversity and converge slower than homogeneously motivated agents.<br> <br> Detailed information can be found in index.html or notebook.ipynb.<br> <br> [1] <a href="\">https://sake.re/20230822-IKEM</a><br> [2] <a href="\">https://gitlab.inria.fr/moex/lazylav/</a><br> </p>
TB Treatment Support Tool Interactive Mobile App and Direct Adherence Monitoring on TB Treatment Outcomes
ClinicalTrials.gov study NCT04221789. IPD Sharing: NO. Countries: 1. Publications: 48.
Study of Truvada for HIV Pre Exposure Prophylaxis Using Daily Directly Observed Therapy to Look at Potential Interactions Between Truvada and Hormone Therapy
ClinicalTrials.gov study NCT04050371. IPD Sharing: NO. Countries: 1. Publications: 14.
Optimal mechanical interactions direct multicellular network formation on elastic substrates
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Data from: Interacting effects of sand, slugs and jute drive community composition in direct-seeded urban wildflower meadows
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Data from: Direct and higher-order interactions in plant communities under increasing weather persistence
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Data from: Magnitude and direction of stream-forest community interactions change with time scale
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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.