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108 results for “model foods”
Modeling Foundation Species in Food Webs
Foundation species are basal species that play an important role in determining community composition by physically structuring ecosystems and modulating ecosystem processes. Foundation species largely operate via non-trophic interactions, presenting a challenge to incorporating them into food-web models. Here, we used non-linear, bioenergetic predator-prey models to explore the role of foundation species and their non-trophic effects. We explored four types of models in which the foundation species reduced the metabolic rates of species in a specific trophic position. We examined the outcomes of each of these models for six metabolic rate “treatments” in which the foundation species altered the metabolic rates of associated species by one-tenth to ten times their allometric baseline metabolic rates. For each model simulation, we looked at how foundation species influenced food-web structure during community assembly and the subsequent change in food-web structure when the foundation species was removed. When a foundation species lowered the metabolic rate of only basal species the resultant webs were complex, species-rich, and robust to foundation species removals. On the other hand, when a foundation species lowered the metabolic rate of only consumer species, all species, or no species the resultant webs were species poor and the subsequent removal of the foundation species webs resulted in the further loss of species and complexity. This suggests that in nature we should look for foundation species to predominantly facilitate basal species.
Short Food Supply Chains Business and Marketing Models Categorisation
<p>The present dataset contains information about the categorisation of Business Models for Short Food Supply Chains, in the context of the <a href="http://agrobridges.eu">agroBRIDGES project</a> (Horizon 2020, GA No. 101000788). Regional information about existing and new business models for Short Food Supply Chains were collected from 12 regions and countries of focus for the project (Beacon Regions) through desk research, interviews and co-creation workshops.</p> <p>The datasets collected information provided by Beacon Region Leaders in the co-creation workshops about models applied and newly or potentially developed ones and available in the literature, to categorise them into stylized models with specific and distinguishable features and attributes, enabling a systematic approach in the development of the sustainability assessment framework. An initial ranking of local business models was provided at a regional / country level. </p> <p>Through analysis of the aggregate ranking results of business models at local level, a final list of business models for SFSCs was derived. Five different Business Model types have been addressed and developed ( i. Community Supported Agriculture - CSA, ii. Face to face trade, iii. Online Food Trade, iv. Local Food Trade, and v. Improved Logistics). The final categorization list provided valuable insights in order to represent all regional contexts and eventually offer value-added information about the main factors for developing a successful business model that can enhance market success in the long term; as well as to strengthen farmer´s strategy that eventually enhances their position within the whole value chain and improve their customer experience.</p> <p>The Value Proposition Canvas and Business Model Canvas was defined for each of the most common SFSC represented in each of the targeted regions.</p> <p><br> The dataset contains:<br> • <strong>agroBRIDGES_SFSCs-BMModels-Categorisation_2021.12.01_v1 [zip file]: </strong>The initial list of business models collected from the co-creation workshops<br> • <strong>agroBRIDGES_SFSCs-BMModels-Categorisation-Tool_2021.12.01_v1 [.xlsx file]: </strong>Internal Assessment tool for Business models regional data collection: A data collection tool was built in-house and shared to all Beacon Region Leaders in order to enable them to fill it regarding their assumptions and conclusions after the co-creation participants discussed and presented their insights from regional activities.<br> • <strong>agroBRIDGES_SFSCs-BModels-CategorisationResults_2021.12.01_v1 [.xlsx file]:</strong> SFSCs BM type results in each of the regions.<br> • <strong>agroBRIDGES_BusinessModels_Canvas_2021.12.01_v1 [zip file]: </strong>The Business Model and Value Proposition Canvas of the 5 BM categories</p>
FoodSky: A Food-oriented Large Language Model, and FoodEarth: A Foundamental Food Corpus and Instruction Dataset
<p>Food is the cornerstone of both survival and social life. With the increasing complexity of global dietary needs and preferences, there is a growing demand for food intelligence to enable tasks like recipe recommendation and diet-disease correlation discovery. To address this, we introduce the Food-oriented Large Language Model (LLM) FoodSky, which offers fine-grained perception and reasoning of food data. We constructed a food corpus, FoodEarth, from various authoritative sources to enhance FoodSky's knowledge. We also developed the Topic-based Selective State Space Model and Hierarchical Topic Retrieval Augmented Generation algorithms to improve FoodSky's ability to capture fine-grained food semantics and generate context-aware food-relevant text. Extensive experiments show that FoodSky outperforms general-purpose LLMs on the Chinese National Chef Exam and Dietetic Exam, achieving accuracies of 67.2% and 66.4%, respectively. FoodSky not only enhances culinary creativity and promotes healthier eating patterns but also establishes a new standard for domain-specific LLMs tackling real-world food-related issues.</p>
Taste responsiveness and liking of model food samples
<p>This data sheet consisted of children's taste intensity perception and liking to model food samples of grapefruit juice and vegetable broth. In addition, children's responses regarding PROP responsiveness, food familiarity, stated liking, food choice, and neophobia were also reported in this data set. </p>
Data from: A new mechanistic model for individual growth suggests upregulated maintenance costs when food is scarce in an insect
<p>In order to calibrate and evaluate a recently developed growth model, the Maintenance-Growth Model (MGM), for the case of growth under food restriction, empirical data for house crickets (<em>Acheta</em> <em>domesticus</em>) were collected and analysed. This data set contains data for individually reared crickets growing under two different regimes of controlled food limitation as well as data for food-limited cohorts of growing house crickets. The sets include temporal data for body mass and ingestion as well as age and size at maturation (imago emergence). The data for food-limited cohorts were collected prior to this study and parts of it have previously been analysed and presented in a publication on animal self-thinning. </p>
Scripts and data for: Integrating different facets of diversity into food web models: how adaptation among and within functional groups shape ecosystem functioning
<p>Adaptation of communities to environmental fluctuations can emerge from different facets of biodiversity, which may impact ecosystem functioning differently. Previous work examined how ecosystem functions can be influenced by two sources of adaptive potential: sorting (i.e., changes in community composition due to fitness differences) can occur when multiple species or groups are present (richness), and trait adaptability (i.e., trait adjustments within species or functional groups) can emerge from genetic or phenotypic diversity. However, their effect is typically studied separately, and often in the context of only one trophic level. Therefore, we used a bitrophic trait-based model varying in richness and in the presence of trait adaptability at each trophic level, to investigate how sorting and trait adaptability, at one or two trophic levels, separately or jointly shape ecosystem functions. We found that the adaptive potential emerging from any facet of diversity-induced changes in trophic interactions, in turn, affects biomass distributions within and across trophic levels, dynamical behaviour, and synchrony of biomass dynamics within a trophic level. Particularly, sorting and trait adaptability could contribute to a similar degree and at a similar time to temporal changes in ecosystem functions, but their respective contribution depended on the speed of trait adaptation, the trait range between similar functional groups, and trophic interactions. We thus suggest to consider multiple facets of diversity and their corresponding sources of adaptive potential to deepen our mechanistic understanding of ecosystem functioning, especially in a context of rapid biodiversity change.</p>
Model output data and figures' code for Fujimori & Wu et al., Land-based climate change mitigation measures can affect agricultural markets and food security
<p>Model output data and figures' code for "Fujimori & Wu et al., Land-based climate change mitigation measures can affect agricultural markets and food security" in Nature Food (DOI: 10.1038/s43016-022-00464-4)</p>
Stable Isotope Mixing Models Demonstrate the Role of an Invasive Plant in Wetland Songbirds Food Webs
<p>We used analysis of natural abundance stable isotopes of <sup>13</sup>C and <sup>15</sup>N in song sparrow blood, invertebrate food sources, <em>L. latifolium </em>seeds,<em> </em>and other marsh<em> </em>plant seeds to inform Bayesian, concentration-dependent mixing models that predicted average song sparrow diets. Data presented are the csv files and R markdown code for the isotope analysis.</p>
Code: A model of wild bee populations accounting for spatial heterogeneity and climate induced temporal variability of food resources at the landscape level
<p><span>The viability of wild bee populations and the pollination services that they provide are driven by the availability of food resources during their activity period and within the surroundings of their nesting sites. Changes in climate and land use influence the availability of these resources and are major threats to declining bee populations. Because wild bees may be vulnerable to interactions between these threats, spatially explicit models of population dynamics that capture how bee populations jointly respond to land use at a landscape scale and weather are needed. Here, we developed a spatially and temporally explicit theoretical model of wild bee populations aiming for a middle ground between the existing mapping of visitation rates using foraging equations and more refined agent-based modelling. The model is developed for <em>Bombus</em> sp. and captures within-season colony dynamics. The model describes mechanistically foraging at the colony level and temporal population dynamics for an average colony at the landscape level. Stages in population dynamics are temperature-dependent triggered with a theoretical generalized seasonal progression, which can be informed by growing degree days (GDD). The purpose of the LandscapePhenoBee model is to evaluate the impact of systematic changes and within-season variability in resources on bee population sizes and crop visitation rates. In a simulation study, we used the model to evaluate the impact of the shortage of food resources in the landscape arising from extreme drought events in different types of landscapes (ranging from different proportions of semi-natural habitats and early and late flowering crops) on bumblebee populations.</span></p>
Integration of Renewable Energy Sources into the Water-Energy-Food (WEF) Nexus – Modelling a Demand Side Management Approach and Application to a Microgrid Farm in Morocco Dataset
<p>Here you can find the official data used for the publication "Integration of Renewable Energy Sources into the Water-Energy-Food (WEF) Nexus – Modelling a Demand Side Management Approach and Application to a Microgrid Farm in Morocco"</p> <p>If you want to run the model, please update line 11 in the run.jl file, to select the dataset from the scenario you want to look at. It is also recommended to change the result path, to a directory that corresponts to the current model run in order to find the results files quicker.</p> <p> </p> <p>To create a new plot a file called newPlot.jl can be found, that already take care of most data handling, only lines 136 and 141 need to be changed, in order to read in the result files of the results you want to investigate.</p>
CROVER model output data for paper "Future Warming Decreases the Benefits of Irrigation in Global Food Production"
<p>This data is output data simulated by the CROVER crop-river coupled model for the scientific paper entitled: “Future Warming Decreases the Benefits of Irrigation in Global Food Production”. Simulations are based on 120-year simulations (1981-2100) using 20 climate projections (four Representative Concentration Pathways (RCPs) (2.6, 4.5, 6.0, and 8.5) × five General Circulation Models (GCMs) (GFDL-ESM2M, HadGEM2-ES, IPSL-CM5A-LR, MIROC-ESM-CHEM, and NorESM1-M)). The dataset includes crop yield of the modeled five crops (maize, rice, soybean, spring wheat, and winter wheat) each for irrigated and rainfed with a spatial resolution of 1.125 degree.</p> <p>The file name consists of a series of identifiers, separated by underscore, according to the following pattern.</p> <p>crover_<gcm>_<rcp>_yield_<crop>_<irrigated|rainfed>.grd</p> <p>crover_<gcm>_<rcp>_yield_<crop>_<irrigated|rainfed>.ctl</p> <p>Format: grads binary (global, 1.125 degree)</p> <p>These files were compressed as a zip file for each GCM and RCP.</p> <p> </p>
Food chain without giants: Modelling the trophic impact of bowhead whaling on little auk populations in the Atlantic Arctic
Open the record for dataset details and reuse information.
Code: A model of wild bee populations accounting for spatial heterogeneity and climate induced temporal variability of food resources at the landscape level
Open the record for dataset details and reuse information.
Data from: A new mechanistic model for individual growth suggests upregulated maintenance costs when food is scarce in an insect
Open the record for dataset details and reuse information.
Scripts and data for: Integrating different facets of diversity into food web models: how adaptation among and within functional groups shape ecosystem functioning
Open the record for dataset details and reuse information.
Eco‐evolutionary dynamics driven by fishing: from single species models to dynamic evolution within complex food webs
<p>Evidence of contemporary evolution across ecological time scales stimulated research on the eco-evolutionary dynamics of natural populations. Aquatic systems provide a good setting to study eco-evolutionary dynamics owing to a wealth of long-term monitoring data and the detected trends in fish life-history traits across intensively harvested marine and freshwater systems. In the present study, we focus on modelling approaches to simulate eco-evolutionary dynamics of fishes and their ecosystems. Firstly, we review the development of modelling from single-species to multispecies approaches. Secondly, we advance the current state-of-the-art methodology by implementing evolution of life-history traits of a top predator into the context of complex food web dynamics as described by the allometric trophic network (ATN) framework. The functioning of our newly developed eco-evolutionary ATNE framework is illustrated using a well-studied lake food web. Our simulations show how both natural selection arising from feeding interactions and size-selective fishing cause evolutionary changes in the top predator and how those feed back to its prey species and further cascade down to lower trophic levels. Finally, we discuss future directions, particularly the need to integrate genomic discoveries into eco-evolutionary projections.</p>
Data from: Ecosystem function in predator-prey food webs - confronting dynamic models with empirical data
1. Most ecosystem functions and related services involve species interactions across trophic levels, e.g. pollination and biological pest control. Despite this, our understanding of ecosystem function in multi-trophic communities is poor, and research has been limited to either manipulations in small communities or statistical descriptions in larger ones. 2. Recent advances in food web ecology may allow us to overcome the trade-off between mechanistic insight and ecological realism. Molecular tools now simplify the detection of feeding interactions, and trait-based approaches allow the application of dynamic food web models to real ecosystems. We performed the first test of an allometric food web model's ability to replicate temporally non-aggregated abundance data from the field, and to provide mechanistic insight into the function of predation. 3. We aimed to reproduce and explore the drivers of the population dynamics of the aphid herbivore Rhopalosiphum padi observed in ten Swedish barley fields. We used a dynamic food web model, taking observed interactions and abundances of predators and alternative prey as input data, allowing us to examine the role of predation in aphid population control. The inverse problem methods were used for simultaneous model fit optimization and model parameterization. 4. The model captured >70% of the variation in aphid abundance in five of ten fields, supporting the model-embodied hypothesis that body-size can be an important determinant of predation in the arthropod community. We further demonstrate how in-depth model analysis can disentangle the likely drivers of function, such as the community's abundance and trait composition. Analyzing the variability in model performance revealed knowledge gaps, such as the source of episodic aphid mortality, and general method development needs that, if addressed, would further increase model success and enable stronger inference about ecosystem function. 5. The results demonstrate that confronting dynamic food web models with abundance data from the field is a viable approach to evaluate ecological theory and to aid our understanding of function in real ecosystems. However, to realize the full potential of food web models, in ecosystem function research and beyond, trait-based parameterization must be refined and extended to include more traits than body size.
Arthropod food webs in the foreland of a retreating glacier: Gut content analysis and structural equation modeling (SEM)
<p>Below- and above-ground arthropod communities were explored at a glacier foreland area in low Arctic Southwest Greenland aiming for a better understanding of the mechanisms behind the arthropod succession driven by increasing temperatures in the context of an Arctic climate change scenario. Arthropods were sampled in 2015 and 2016 along a downslope transect where the microclimate became warmer downhill a chronosequence towards a climax vegetation. The arthropod data sets were analyzed in relation to an environmental data set. Bottom-up controlled population developments were important in the early phase of the vegetation development while top-down prevailed in the later phase of the vegetation development. The shift from bottom-up to top-down cascades between arthropod predators and their potential prey populations was mainly driven by increasing temperatures away from the glacier. Structural equation modeling (SEM) shows bottom-up and top-down controlled food chains as bottom-up control was important for spider and harvestman populations while top-down control was important for ground beetle populations. These mechanisms are closely related to the hunting strategies of the predators as bottom-up mechanisms are connected to a sit-and-wait behavior while top-down mechanisms are related to active-search behavior. The SEM analyzes were supported by DNA metabarcoding as well as by the literature. A consequence of the strong top-down cascades in the later phase of the succession is high rates of intra-guild predation (IGP) among all arthropod predators. Particularly in the guts of the linyphiid spider, <em>Collinsia holmgreni </em>Thorell 1871, trophic linkages to other linyphiid and lycosid spiders were detected. The IGP ratio of <em>C. holmgreni</em> was negatively correlated with the activity density of available ground-living prey. Probably as a consequence of the high IGP among the linyphiid spiders, cold-adapted linyphiid species like <em>C. holmgreni</em> decreased in numbers downhill and became extinct in the warmer climax vegetation, where lycosid spiders dominated. SEM shows that the declining activity densities of the soil fauna, such as collembolans and mites, due to predation, are responsible for the increase in organic matter content in the topsoil.</p>
Fine-tuning of predictive microbiology models through microlocal characterization of foods by Nuclear Magnetic Resonance (NMR)
<p>Fine-tuning of predictive microbiology models through microlocal characterization of foods by Nuclear Magnetic Resonance (NMR)</p>
Effects of enhanced productivity of resources shared by predators in a food-web module: Comparing results of a field experiment to predictions of mathematical models of intra-guild predation
<p>This dataset contains data from a field experiment described in the publication "Wise, D. H. & Farfan, M.A. (2021) Effects of enhanced productivity of resources shared by predators in a food-web module: Comparing results of a field experiment to predictions of mathematical models of intra-guild predation. Ecology and Evolution, 00: 1-11. <a href="https://doi.org/10.1002/ece3.8375">https://doi.org/10.1002/ece3.8375</a>".</p> <p>The field experiment compared the response to increased input of nutrients and energy (artificial detritus) to an empirical model of intra-guild predation (IGP) to the predictions of published, simple mathematical models of asymmetric IGP (a generalist IG Predator that feeds both on a specialist IG Prey and a Resource that it shares with the IG Prey). The empirical model was a food-web module created by pooling species abundances across many families in a community of soil micro-arthropods into three response variables: IG Predator (large predatory mites), IG Prey (small predatory mites) and a shared Resource (fungivorous mites and springtails). The pattern of change over time in densities of the three response variables (IG Predator, IG Prey and Resource) was compared to the predictions of mathematical models of IGP to determine if the feeding relationships in this community of soil micro-arthropods could be abstracted into a simple IGP module. Thus, we were testing the hypothesis that IGP is a dominant organizing principle in this community.</p> <p>Simple mathematical models predict that increased input of nutrients and energy to the shared Resource will increase the equilibrium density of Resource and IG Predator, but will decrease that of IG Prey. By the experiment's end, densities of fungivores (Resource) had increased ~1.5x (ratio of pooled fungivore densities in the High treatment to plots with no addition of detritus (None treatment); and IG Predator densities had increased ~4x. Contrary to the prediction of mathematical models, IG Prey had not decreased, but instead had increased ~1.5x. We discuss possible reasons for the failure of the empirical model to agree with IGP theory.</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.