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226 results for “growth model”
Data from: Maiasaura, a model organism for extinct vertebrate population biology: a large sample statistical assessment of growth dynamics and survivorship
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Data from: Using an integral projection model to assess the effect of temperature on the growth of gilthead seabream Sparus aurata
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R code and data for running models in "Rapid Growth of the Swainson’s Hawk Population in California since 2005"
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Data from: Are trait-growth models transferable? Predicting multi-species growth trajectories between ecosystems using plant functional traits
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Data from: Variation in growth drives the duration of parental care: a test of Ydenberg's model
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Data from: Multiple predator species alter prey behavior, population growth and a trophic cascade in a model estuarine food web
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Data from: Richards’s equation and nonlinear mixed models applied to avian growth: why use them?
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Effects of Salicaceae species litter type and moisture at 10 paired wetland by upland plots:Specialization, maintenance of diversity and ecosystem consequences of growth defense trade-offs in a model system: the hyper-diverse willow communities of Cedar Creek
Cedar Creek includes a diversity of habitats, which support an astonishing number of species (15) from a single evolutionary lineage: the willow family (Salicaceae). The physiological tolerances and abiotic mechanisms that maintain natural diversity in this hyper-diverse system are beginning to be understood; the role of biotic interactions, however, remains a major gap in understanding. We hypothesize that insect herbivory plays a critical role in niche partitioning, providing an important explanation for high willow diversity. Using a replicated series of common gardens and insect herbivore manipulations in resource rich and resource poor habitats, we are testing for evolved trade-offs between defense investment and growth rate. We expect specialized plant syndromes to emerge along the continuum from ???herbivore escape??? via fast growth in high resource environments to ???anti-herbivore protection??? via heavy investment in defense in low resource environments. Evolved growth/defense strategies that promote diversity are also likely to have ecosystem consequences due to foliar chemical influences on decomposition and the composition and diversity of the insect communities they support. The proposed research takes advantage of natural diversity, providing an important model system at Cedar Creek.
Initial Salicaceae species litter chemistry:Specialization, maintenance of diversity and ecosystem consequences of growth defense trade-offs in a model system: the hyper-diverse willow communities of Cedar Creek
Cedar Creek includes a diversity of habitats, which support an astonishing number of species (15) from a single evolutionary lineage: the willow family (Salicaceae). The physiological tolerances and abiotic mechanisms that maintain natural diversity in this hyper-diverse system are beginning to be understood; the role of biotic interactions, however, remains a major gap in understanding. We hypothesize that insect herbivory plays a critical role in niche partitioning, providing an important explanation for high willow diversity. Using a replicated series of common gardens and insect herbivore manipulations in resource rich and resource poor habitats, we are testing for evolved trade-offs between defense investment and growth rate. We expect specialized plant syndromes to emerge along the continuum from ???herbivore escape??? via fast growth in high resource environments to ???anti-herbivore protection??? via heavy investment in defense in low resource environments. Evolved growth/defense strategies that promote diversity are also likely to have ecosystem consequences due to foliar chemical influences on decomposition and the composition and diversity of the insect communities they support. The proposed research takes advantage of natural diversity, providing an important model system at Cedar Creek.
2012 growing season water table depth in common gardens:Specialization, maintenance of diversity and ecosystem consequences of growth defense trade-offs in a model system, the hyper-diverse willow communities of Cedar Creek
Cedar Creek includes a diversity of habitats, which support an astonishing number of species (15) from a single evolutionary lineage: the willow family (Salicaceae). The physiological tolerances and abiotic mechanisms that maintain natural diversity in this hyper-diverse system are beginning to be understood; the role of biotic interactions, however, remains a major gap in understanding. We hypothesize that insect herbivory plays a critical role in niche partitioning, providing an important explanation for high willow diversity. Using a replicated series of common gardens and insect herbivore manipulations in resource rich and resource poor habitats, we are testing for evolved trade-offs between defense investment and growth rate. We expect specialized plant syndromes to emerge along the continuum from ???herbivore escape??? via fast growth in high resource environments to ???anti-herbivore protection??? via heavy investment in defense in low resource environments. Evolved growth/defense strategies that promote diversity are also likely to have ecosystem consequences due to foliar chemical influences on decomposition and the composition and diversity of the insect communities they support. The proposed research takes advantage of natural diversity, providing an important model system at Cedar Creek.
Percent carbon and nitrogen in leaf tissue:Specialization, maintenance of diversity and ecosystem consequences of growth defense trade-offs in a model system, the hyper-diverse willow communities of Cedar Creek
Cedar Creek includes a diversity of habitats, which support an astonishing number of species (15) from a single evolutionary lineage: the willow family (Salicaceae). The physiological tolerances and abiotic mechanisms that maintain natural diversity in this hyper-diverse system are beginning to be understood; the role of biotic interactions, however, remains a major gap in understanding. We hypothesize that insect herbivory plays a critical role in niche partitioning, providing an important explanation for high willow diversity. Using a replicated series of common gardens and insect herbivore manipulations in resource rich and resource poor habitats, we are testing for evolved trade-offs between defense investment and growth rate. We expect specialized plant syndromes to emerge along the continuum from ???herbivore escape??? via fast growth in high resource environments to ???anti-herbivore protection??? via heavy investment in defense in low resource environments. Evolved growth/defense strategies that promote diversity are also likely to have ecosystem consequences due to foliar chemical influences on decomposition and the composition and diversity of the insect communities they support. The proposed research takes advantage of natural diversity, providing an important model system at Cedar Creek.
Data from: In silico study of the role of cell growth factors in photosynthesis using a virtual leaf tissue generator coupled to a microscale photosynthesis gas exchange model
Computational tools that allow in silico analysis of the role of cell growth and division on photosynthesis are scarce. We present a freely available tool that combines a virtual leaf tissue generator and a two-dimensional microscale model of gas transport during C3 photosynthesis. A total of 270 mesophyll geometries were generated with varying degree of growth anisotropy, growth extent and extent of schizogenous airspace formation in the palisade mesophyll. The anatomical properties of the virtual leaf tissue and microscopic cross sections of actual leaf tissue of tomato (Solanum lycopersicum L.) were statistically compared. Model equations for transport of CO2 in the liquid phase of the leaf tissue were discretized over the geometries. The virtual leaf tissue generator produced a leaf anatomy of tomato that was statistically similar to real tomato leaf tissue. The response of photosynthesis to intercellular CO2 predicted by a model that used the virtual leaf tissue geometry compared well with measured values. The results indicate that the light-saturated rate of photosynthesis was influenced by interactive effects of extent and directionality of cell growth and degree of airspace formation through the exposed surface of mesophyll per leaf area. The tool could be used further in investigations of improving photosynthesis and gas exchange in relation to cell growth and leaf anatomy.
Data and code from: Growth strategies of a model picoplankter depend on social milieu and pCO2
<p><span><span><span><span><span><span><span><span><span><span><span>Aquatic microbial primary producers exist in genetically diverse populations, but are often studied as single lineages, so that interpreting single lineage studies relies critically on understanding how microbial growth differs with social milieu. The properties of lineages grown alone often fail to predict the growth of these same lineages in the presence of conspecifics, and this discrepancy points towards an opportunity to improve our understanding of how multilineage assemblages of a species are shaped. We demonstrate that different lineages of a marine picoplankter modulate their lineage growth rate in response to the presence of non-self conspecifics, even when resource competition is effectively absent. This explains why growth rates of lineages in isolation do not reliably predict their growth rates in mixed culture, or the lineage composition of assemblages. The diversity of growth strategies observed are thus consistent with lineage-specific energy-allocation that depends on social milieu. Since lineage growth is only one of many traits determining fitness in natural assemblages, we propose that in all but the poorest quality environments where allocating maximum energy to growth is the only viable strategy, we should expect intraspecific variation in growth strategies, with more strategies possible in ameliorated environments, such as high CO<sub>2</sub> for many marine picoplankton. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Vaccination method affects immune response and bacterial growth but not protection in the Salmonella Typhimurium animal model of typhoid
Understanding immune responses elicited by vaccines, together with immune responses required for protection, is fundamental to designing effective vaccines and immunisation programs. This study examines the effects of the route of administration of a live attenuated vaccine on its interactions with, and stimulation of, the murine immune system as well as its ability to increase survival and provide protection from colonisation by a virulent challenge strain. We assess the effect of administration method using the murine model for typhoid, where animals are infected with S. Typhimurium. Mice were vaccinated either intravenously or orally with the same live attenuated S. Typhimurium strain and data were collected on vaccine strain growth, shedding and stimulation of antibodies and cytokines. Following vaccination, mice were challenged with a virulent strain of S. Typhimurium and the protection conferred by the different vaccination routes was measured in terms of challenge suppression and animal survival. The main difference in immune stimulation found in this study was the development of a secretory IgA response in orally-vaccinated mice, which was absent in IV vaccinated mice. While both strains showed similar protection in terms of challenge suppression in systemic organs (spleen and liver) as well as survival, they differed in terms of challenge suppression of virulent pathogens in gut-associated organs. This difference in gut colonisation presents important questions around the ability of vaccines to prevent shedding and transmission. These findings demonstrate that while protection conferred by two vaccines can appear to be the same, the mechanisms controlling the protection can differ and have important implications for infection dynamics within a population.
Data from: Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance
Non-parametric population genetic modeling provides a simple and flexible approach for studying demographic history and epidemic dynamics using pathogen sequence data. Existing Bayesian approaches are premised on stochastic processes with stationary increments which may provide an unrealistic prior for epidemic histories which feature extended period of exponential growth or decline. We show that non-parametric models defined in terms of the growth rate of the effective population size can provide a more realistic prior for epidemic history. We propose a non-parametric autoregressive model on the growth rate as a prior for effective population size, which corresponds to the dynamics expected under many epidemic situations. We demonstrate the use of this model within a Bayesian phylodynamic inference framework. Our method correctly reconstructs trends of epidemic growth and decline from pathogen genealogies even when genealogical data is sparse and conventional skyline estimators erroneously predict stable population size. We also propose a regression approach for relating growth rates of pathogen effective population size and time-varying variables that may impact the replicative fitness of a pathogen. The model is applied to real data from rabies virus and Staphylococcus aureus epidemics. We find a close correspondence between the estimated growth rates of a lineage of methicillin-resistant S. aureus and population-level prescription rates of beta-lactam antibiotics. The new models are implemented in an open source R package called skygrowth which is available at https://github.com/mrc-ide/skygrowth.
Data from: Ultrasonic cavitation induces necrosis and impairs growth in three-dimensional models of pancreatic ductal adenocarcinoma
Introduction: Pancreatic ductal adenocarcinoma (PDAC) is a rapidly increasing cause of mortality whose dismal prognosis is mainly due to overwhelming chemoresistance. New therapeutic approaches include physical agents such as ultrasonic cavitation, but clinical applications require further insights in the mechanisms of cytotoxicity. Three dimensional in vitro culture models such as spheroids exploit realistic spatial, biochemical and cellular heterogeneity that may bridge some of the experimental gap between conventional in vitro and in vivo experiments. Purpose: to assess the feasibility and efficiency of inertial cavitation associated or not with chemotherapy, in a spheroid model of PDAC. Methods: we used DT66066 cells ,derived from a genetically-engineered murine PDAC, isolated from KPC-transgenic mice (LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx-1- Cre). Spheroids were obtained by either a standard centrifugation-based method, or by using a magnetic nano-shuttle method allowing the formation of spheroids within 24 hours and facilitating their handling. The spheroids were exposed to ultrasonic inertial cavitation in a specially designed setup. Four conditions were studied: control, gemcitabine alone , US cavitation alone , US cavitation + gemcitabine. Five US inertial cavitation indexes, corresponding to increased US intensities, were evaluated . The effectiveness of treatment was assessed after 24 hours with the following criteria: spheroid size (growth), ratio of phase S cells (proliferation), proportion of cells in apoptosis or necrosis (cellular mortality). These parameters were assessed by quantitative immunofluorescence techniques. Results: The 3D culture model presented excellent reproducibility. Eight or nine spheroids were analyzed for each condition. Cavitation induced a significant decrease in the size of spheroids , an effect significantly correlated to an increasing cavitation index (p < 0.0001). The treatment induced cell death whose predominant mechanism was necrosis (p < 0.0001). There was a tendency to a synergistic effect of US cavitation and gemcitabine at 5μM concentration, however significant in only one of the cavitation indexes used (p = 0. 013). Conclusion: Ultrasonic inertial cavitation induced a significant reduction of tumor growth in a spheroid model of PDAC., with necrosis rather than apoptosis as a Cell dominant mechanism of cell death. More investigations are needed to understand the potential role of inertial cavitation in overcoming chemoresistance.
Data from: Modeling effects of nonbreeders on population growth estimates
Adult individuals that do not breed in a given year occur in a wide range of natural populations. However, such nonbreeders are often ignored in theoretical and empirical population studies, limiting our knowledge of how nonbreeders affect realized and estimated population dynamics and potentially impeding projection of deterministic and stochastic population growth rates. We present and analyse a general modelling framework for systems where breeders and nonbreeders differ in key demographic rates, incorporating different forms of nonbreeding, different life histories and frequency-dependent effects of nonbreeders on demographic rates of breeders. Comparisons of estimates of deterministic population growth rate, λ, and demographic variance, math formula, from models with and without distinct nonbreeder classes show that models that do not explicitly incorporate nonbreeders give upwardly biased estimates of math formula, particularly when the equilibrium ratio of nonbreeders to breeders, math formula, is high. Estimates of λ from empirical observations of breeders only are substantially inflated when individuals frequently re-enter the breeding population after periods of nonbreeding. Sensitivity analyses of diverse parameterizations of our model framework, with and without negative frequency-dependent effects of nonbreeders on breeder demographic rates, show how changes in demographic rates of breeders vs. nonbreeders differentially affect λ. In particular, λ is most sensitive to nonbreeder parameters in long-lived species, when math formula, and when individuals are unlikely to breed at several consecutive time steps. Our results demonstrate that failing to account for nonbreeders in population studies can obscure low population growth rates that should cause management concern. Quantifying the size and demography of the nonbreeding section of populations and modelling appropriate demographic structuring is therefore essential to evaluate nonbreeders' influence on deterministic and stochastic population dynamics.
Model dataset for Morrison et al. (2020) "Comparing growth rates of moist and dry convective thermals" submitted to JAS
<p>This model generated dataset includes simulation data and model files for work described in the paper "Comparing growth rates of moist and dry convective thermals" by Morrison et al., submitted to the Journal of the Atmospheric Sciences. Model data comes from the CM1 atmospheric model maintained by Dr. George Bryan at NCAR. The model data are idealized high resolution model runs. We are making this request through DASH because inclusion of these data in a public repository is now mandatory for AMS publications.</p>
Insights on SEI Growth and Properties in Na-Ion Batteries via Physically Driven Kinetic Monte Carlo Model
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Antiplaque Effect of Essential Oils With and Without Alcochol on an in Situ Model of Oral Biofilm Growth
ClinicalTrials.gov study NCT02946801. IPD Sharing: NO. Countries: 0. Publications: 1.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.