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https://www.readbyqxmd.com/read/30523383/calibration-of-parameters-in-dynamic-energy-budget-models-using-direct-search-methods
#1
J V Morais, A L Custódio, G M Marques
Dynamic Energy Budget (DEB) theory aims to capture the quantitative aspects of metabolism at the individual level, for all species. The parametrization of a DEB model is based on information obtained through the observation of natural populations and experimental research. Currently the DEB toolbox estimates these parameters using the Nelder-Mead Simplex method, a derivative-free direct-search method. However, this procedure presents some limitations regarding convergence and how to address constraints. Framed in the calibration of parameters in DEB theory, this work presents a numerical comparison between the Nelder-Mead Simplex method and the SID-PSM algorithm, a Directional Direct-Search method for which convergence can be established both for unconstrained and constrained problems...
December 7, 2018: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/30509647/combined-effects-of-thermal-conditions-and-food-availability-on-thermal-tolerance-of-the-marine-bivalve-perna-viridis
#2
Martin C F Cheng, Gianluca Sarà, Gray A Williams
Organisms can mitigate the effects of long term variation in environmental conditions through acclimation, which involves changes in various physiological responses. To elucidate the possible effects of temperature and food concentrations on acclimation capacity, physiological responses of the mussel, Perna viridis, were measured after individuals were held for six weeks under varying temperatures and food availability. Warm-acclimated mussels experiencing higher food levels had significantly greater upper thermal limits than those maintained on lower food levels...
December 2018: Journal of Thermal Biology
https://www.readbyqxmd.com/read/30467933/a-mechanistic-theory-of-personality-dependent-movement-behaviour-based-on-dynamic-energy-budgets
#3
Andrea Campos-Candela, Miquel Palmer, Salvador Balle, Alberto Álvarez, Josep Alós
Consistent between-individual differences in movement are widely recognised across taxa. In addition, foraging plasticity at the within-individual level suggests a behavioural dependency on the internal energy demand. Because behaviour co-varies with fast-slow life history (LH) strategies in an adaptive context, as theoretically predicted by the pace-of-life syndrome hypothesis, mass/energy fluxes should link behaviour and its plasticity with physiology at both between- and within-individual levels. However, a mechanistic framework driving these links in a fluctuating ecological context is lacking...
November 22, 2018: Ecology Letters
https://www.readbyqxmd.com/read/30401809/applicability-of-dynamic-energy-budget-deb-models-across-steep-environmental-gradients
#4
Cristián J Monaco, Christopher D McQuaid
Robust ecological forecasting requires accurate predictions of physiological responses to environmental drivers. Energy budget models facilitate this by mechanistically linking biology to abiotic drivers, but are usually ground-truthed under relatively stable physical conditions, omitting temporal/spatial environmental variability. Dynamic Energy Budget (DEB) theory is a powerful framework capable of linking individual fitness to environmental drivers and we tested its ability to accommodate variability by examining model predictions across the rocky shore, a steep ecotone characterized by wide fluctuations in temperature and food availability...
November 6, 2018: Scientific Reports
https://www.readbyqxmd.com/read/30294515/modelling-effects-of-time-variable-exposure-to-the-pyrethroid-beta-cyfluthrin-on-rainbow-trout-early-life-stages
#5
Elke I Zimmer, Thomas G Preuss, Steve Norman, Barbara Minten, Virginie Ducrot
Background: Available literature and regulatory studies show that the severity of effects of beta-cyfluthrin (a synthetic pyrethroid) on fish is influenced by the magnitude and duration of exposure. To investigate how the exposure pattern to beta-cyfluthrin (constant vs peak) may influence the response of the fish, we used a mechanistic effect model to predict the survival and growth of the rainbow trout over its early life stages (i.e. egg, alevin and swim-up fry). We parameterized a toxicokinetic-toxicodynamic (TKTD) module in combination with a dynamic energy budget model enabling us to describe uptake and elimination, as well as to predict the threshold concentration for survival and sublethal effects (feeding behaviour and growth)...
2018: Environmental Sciences Europe
https://www.readbyqxmd.com/read/30075055/experimental-evolution-demonstrates-evolvability-of-preferential-nutrient-allocation-to-competing-traits-in-response-to-chronic-malnutrition
#6
Roshan K Vijendravarma
Investigating the evolutionary origins of disease vulnerability is an important aspect of evolutionary medicine that strongly complements our current understanding on proximate causes of disease. Life-history trade-offs mediated through evolutionary changes in resource allocation strategies could be one possible explanation to why suboptimal traits that leave bodies vulnerable to disease exist. For example, Drosophila melanogaster populations experimentally evolved to tolerate chronic larval malnutrition succumb to intestinal infection despite eliciting a competent immune response, owing to the loss of their intestinal integrity...
November 2018: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/30034074/delivering-the-promises-of-trait-based-approaches-to-the-needs-of-demographic-approaches-and-vice-versa
#7
EDITORIAL
Roberto Salguero-Gómez, Cyrille Violle, Olivier Gimenez, Dylan Childs
Few facets of biology vary more than functional traits and life-history traits. To explore this vast variation, functional ecologists and population ecologists have developed independent approaches that identify the mechanisms behind and consequences of trait variation.Collaborative research between researchers using trait-based and demographic approaches remains scarce. We argue that this is a missed opportunity, as the strengths of both approaches could help boost the research agendas of functional ecology and population ecology...
June 2018: Functional Ecology
https://www.readbyqxmd.com/read/30030873/assessing-the-sensitivity-of-bivalve-populations-to-global-warming-using-an-individual-based-modelling-approach
#8
Yoann Thomas, Cédric Bacher
Climate change exposes benthic species populations in coastal ecosystems to a combination of different stressors (e.g., warming, acidification and eutrophication), threatening the sustainability of the ecological functions they provide. Thermal stress appears to be one of the strongest drivers impacting marine ecosystems, acting across a wide range of scales, from individual metabolic performances to geographic distribution of populations. Accounting for and integrating the response of species functional traits to thermal stress is therefore a necessary step in predicting how populations will respond to the warming expected in coming decades...
October 2018: Global Change Biology
https://www.readbyqxmd.com/read/29986322/predicting-the-effectiveness-of-oil-recovery-strategies-in-the-marine-polluted-environment
#9
A Giacoletti, S Cappello, G Mancini, M C Mangano, G Sarà
Many recent studies have focused their attention on the physiological stress experienced by marine organisms in measuring ecotoxicological responses. Here we suggest a new approach for investigating the effects of an anthropogenic pollutant on Life-History (LH) traits of marine organisms, to provide stakeholders and policy makers an effective tool to evaluate the best environmental recovery strategies and plans. A Dynamic Energy Budget (DEB), coupled with a biophysical model was used to predict the effects of a six-month oil spill on Mytilus galloprovincialis' LH traits and to test two potential recovery strategies in the central Mediterranean Sea...
October 1, 2018: Journal of Environmental Management
https://www.readbyqxmd.com/read/29931772/trait-based-predictions-and-responses-from-laboratory-mite-populations-to-harvesting-in-stochastic-environments
#10
Isabel M Smallegange, Hedwig M Ens
Predictions on population responses to perturbations are often derived from trait-based approaches like integral projection models (IPMs), but are rarely tested. IPMs are constructed from functions that describe survival, growth and reproduction in relation to the traits of individuals and their environment. Although these functions comprise biologically non-informative statistical coefficients within standard IPMs, model parameters of the recently developed dynamic energy budget IPM (DEB-IPM) are life-history traits like "length at maturation" and "maximum reproduction rate"...
July 2018: Journal of Animal Ecology
https://www.readbyqxmd.com/read/29870141/incorporating-suborganismal-processes-into-dynamic-energy-budget-models-for-ecological-risk-assessment
#11
Cheryl A Murphy, Roger M Nisbet, Philipp Antczak, Natàlia Garcia-Reyero, Andre Gergs, Konstadia Lika, Teresa Mathews, Erik B Muller, Diane Nacci, Angela Peace, Christopher H Remien, Irvin R Schultz, Louise M Stevenson, Karen H Watanabe
A working group at the National Institute for Mathematical and Biological Synthesis (NIMBioS) explored the feasibility of integrating 2 complementary approaches relevant to ecological risk assessment. Adverse outcome pathway (AOP) models provide "bottom-up" mechanisms to predict specific toxicological effects that could affect an individual's ability to grow, reproduce, and/or survive from a molecular initiating event. Dynamic energy budget (DEB) models offer a "top-down" approach that reverse engineers stressor effects on growth, reproduction, and/or survival into modular characterizations related to the acquisition and processing of energy resources...
June 5, 2018: Integrated Environmental Assessment and Management
https://www.readbyqxmd.com/read/29742099/the-amp-project-comparing-species-on-the-basis-of-dynamic-energy-budget-parameters
#12
Gonçalo M Marques, Starrlight Augustine, Konstadia Lika, Laure Pecquerie, Tiago Domingos, Sebastiaan A L M Kooijman
We developed new methods for parameter estimation-in-context and, with the help of 125 authors, built the AmP (Add-my-Pet) database of Dynamic Energy Budget (DEB) models, parameters and referenced underlying data for animals, where each species constitutes one database entry. The combination of DEB parameters covers all aspects of energetics throughout the full organism's life cycle, from the start of embryo development to death by aging. The species-specific parameter values capture biodiversity and can now, for the first time, be compared between animals species...
May 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29680449/modeling-tumor-growth-inhibition-and-toxicity-outcome-after-administration-of-anticancer-agents-in-xenograft-mice-a-dynamic-energy-budget-deb-approach
#13
N Terranova, E M Tosca, E Borella, E Pesenti, M Rocchetti, P Magni
Host features, such as cell proliferation rates, caloric intake, metabolism and energetic conditions, significantly influence tumor growth; at the same time, tumor growth may have a dramatic impact on the host conditions. For example, in clinics, at certain stages of the tumor growth, cachexia (body weight reduction) may become so relevant to be considered as responsible for around 20% of cancer deaths. Unfortunately, anticancer therapies may also contribute to the development of cachexia due to reduced food intake (anorexia), commonly observed during the treatment periods...
August 7, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29596456/modelling-southern-elephant-seals-mirounga-leonina-using-an-individual-based-model-coupled-with-a-dynamic-energy-budget
#14
Merel Goedegebuure, Jessica Melbourne-Thomas, Stuart P Corney, Clive R McMahon, Mark A Hindell
Higher trophic-level species are an integral component of any marine ecosystem. Despite their importance, methods for representing these species in end-to-end ecosystem models often have limited representation of life histories, energetics and behaviour. We built an individual-based model coupled with a dynamic energy budget for female southern elephant seals Mirounga leonina to demonstrate a method for detailed representation of marine mammals. We aimed to develop a model which could i) simulate energy use and life histories, as well as breeding traits of southern elephant seals in an emergent manner, ii) project a stable population over time, and iii) have realistic population dynamics and structure based on emergent life history features (such as age at first breeding, lifespan, fecundity and (yearling) survival)...
2018: PloS One
https://www.readbyqxmd.com/read/29550453/is-structural-sensitivity-a-problem-of-oversimplified-biological-models-insights-from-nested-dynamic-energy-budget-models
#15
Clement Aldebert, Bob W Kooi, David Nerini, Jean-Christophe Poggiale
Many current issues in ecology require predictions made by mathematical models, which are built on somewhat arbitrary choices. Their consequences are quantified by sensitivity analysis to quantify how changes in model parameters propagate into an uncertainty in model predictions. An extension called structural sensitivity analysis deals with changes in the mathematical description of complex processes like predation. Such processes are described at the population scale by a specific mathematical function taken among similar ones, a choice that can strongly drive model predictions...
July 7, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29438934/dynamic-energy-budget-models-in-ecological-risk-assessment-from-principles-to-applications
#16
REVIEW
Jan Baas, Starrlight Augustine, Gonçalo M Marques, Jean-Lou Dorne
In ecological risk assessment of chemicals, hazard identification and hazard characterisation are most often based on ecotoxicological tests and expressed as summary statistics such as No Observed Effect Concentrations or Lethal Concentration values and No Effect Concentrations. Considerable research is currently ongoing to further improve methodologies to take into account toxico kinetic aspects in toxicological assessments, extrapolations of toxic effects observed on individuals to population effects and combined effects of multiple chemicals effects...
July 1, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/28850607/a-dynamic-energy-budget-deb-model-to-describe-laternula-elliptica-king-1832-seasonal-feeding-and-metabolism
#17
Antonio Agüera, In-Young Ahn, Charlène Guillaumot, Bruno Danis
Antarctic marine organisms are adapted to an extreme environment, characterized by a very low but stable temperature and a strong seasonality in food availability arousing from variations in day length. Ocean organisms are particularly vulnerable to global climate change with some regions being impacted by temperature increase and changes in primary production. Climate change also affects the biotic components of marine ecosystems and has an impact on the distribution and seasonal physiology of Antarctic marine organisms...
2017: PloS One
https://www.readbyqxmd.com/read/28837407/a-dynamic-energy-based-model-to-analyze-sublethal-effects-of-chronic-gamma-irradiation-in-the-nematode-caenorhabditis-elegans
#18
Catherine Lecomte-Pradines, Turid Hertel-Aas, Claire Coutris, Rodolphe Gilbin, Deborah Oughton, Frédéric Alonzo
Understanding how toxic contaminants affect wildlife species at various levels of biological organization (subcellular, histological, physiological, organism, and population levels) is a major research goal in both ecotoxicology and radioecology. A mechanistic understanding of the links between different observed perturbations is necessary to predict the consequences for survival, growth, and reproduction, which are critical for population dynamics. In this context, experimental and modeling studies were conducted using the nematode Caenorhabditis elegans...
2017: Journal of Toxicology and Environmental Health. Part A
https://www.readbyqxmd.com/read/28387336/using-energy-budgets-to-combine-ecology-and-toxicology-in-a-mammalian-sentinel-species
#19
Jean-Pierre W Desforges, Christian Sonne, Rune Dietz
Process-driven modelling approaches can resolve many of the shortcomings of traditional descriptive and non-mechanistic toxicology. We developed a simple dynamic energy budget (DEB) model for the mink (Mustela vison), a sentinel species in mammalian toxicology, which coupled animal physiology, ecology and toxicology, in order to mechanistically investigate the accumulation and adverse effects of lifelong dietary exposure to persistent environmental toxicants, most notably polychlorinated biphenyls (PCBs). Our novel mammalian DEB model accurately predicted, based on energy allocations to the interconnected metabolic processes of growth, development, maintenance and reproduction, lifelong patterns in mink growth, reproductive performance and dietary accumulation of PCBs as reported in the literature...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28370293/a-framework-for-predicting-impacts-on-ecosystem-services-from-sub-organismal-responses-to-chemicals
#20
REVIEW
Valery E Forbes, Chris J Salice, Bjorn Birnir, Randy J F Bruins, Peter Calow, Virginie Ducrot, Nika Galic, Kristina Garber, Bret C Harvey, Henriette Jager, Andrew Kanarek, Robert Pastorok, Steve F Railsback, Richard Rebarber, Pernille Thorbek
Protection of ecosystem services is increasingly emphasized as a risk-assessment goal, but there are wide gaps between current ecological risk-assessment endpoints and potential effects on services provided by ecosystems. The authors present a framework that links common ecotoxicological endpoints to chemical impacts on populations and communities and the ecosystem services that they provide. This framework builds on considerable advances in mechanistic effects models designed to span multiple levels of biological organization and account for various types of biological interactions and feedbacks...
April 2017: Environmental Toxicology and Chemistry
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