Physics of metabolic organization.

[1]  M. Berberan-Santos Green’s function method and the first-order linear differential equation , 2010 .

[2]  P. Abrams,et al.  Interpreting the von Bertalanffy model of somatic growth in fishes: the cost of reproduction , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[3]  D. Houlihan Protein Turnover in Ectotherms and Its Relationships to Energetics , 1991 .

[4]  E. Kandel The Molecular Biology of Memory Storage: A Dialogue Between Genes and Synapses , 2001, Science.

[5]  Michael R Kearney,et al.  Reconciling theories for metabolic scaling. , 2014, The Journal of animal ecology.

[6]  H. Lambers,et al.  Respiratory energy requirements and rate of protein turnover in vivo determined by the use of an inhibitor of protein synthesis and a probe to assess its effect , 1994 .

[7]  Sebastiaan A.L.M. Kooijman,et al.  The “covariation method” for estimating the parameters of the standard Dynamic Energy Budget model I: Philosophy and approach , 2011 .

[8]  S. F. Hildebrand,et al.  On the Growth, Care and Behavior of Loggerhead Turtles in Captivity. , 1927, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Dominic F. Houlihan,et al.  Growth Rates and Protein Turnover in Atlantic Cod, Gadus morhua , 1988 .

[10]  S. Kooijman,et al.  Reconstructing individual food and growth histories from biogenic carbonates. , 2012 .

[11]  Tjalling Jager,et al.  A biology-based approach for mixture toxicity of multiple endpoints over the life cycle , 2009, Ecotoxicology.

[12]  Biological scaling and physics , 2002, Journal of Biosciences.

[13]  Ewald R Weibel,et al.  Scaling functions to body size: theories and facts , 2005, Journal of Experimental Biology.

[14]  Tin Klanjscek,et al.  Dynamic energy budget approach to modeling mechanisms of CdSe quantum dot toxicity , 2013, Ecotoxicology.

[15]  B. Merry,et al.  Onset of puberty and duration of fertility in rats fed a restricted diet. , 1979, Journal of reproduction and fertility.

[16]  P. Pritchard,et al.  Conservation Biology of Freshwater Turtles and Tortoises: A Compilation Project of the IUCN/SSC Tortoise and Freshwater Turtle Specialist Group , 2010 .

[17]  Frances Y. Kuo,et al.  Lifting the Curse of Dimensionality , 2005 .

[18]  D. Whiffen Thermodynamics , 1973, Nature.

[19]  G. Zug,et al.  Age and growth of loggerhead sea turtles (Caretta caretta) of coastal Georgia : An assessment of skeletochronological age-estimates , 1997 .

[20]  T. Jager,et al.  A review of DEB theory in assessing toxic effects of mixtures. , 2010, The Science of the total environment.

[21]  M. Jusup,et al.  Inferring physiological energetics of loggerhead turtle (Caretta caretta) from existing data using a general metabolic theory , 2016, bioRxiv.

[22]  Aaron A. McNevin,et al.  Indicators of Resource Use Efficiency and Environmental Performance in Fish and Crustacean Aquaculture , 2007 .

[23]  James D. Annan,et al.  Parameter estimation in an intermediate complexity earth system model using an ensemble Kalman filter , 2005 .

[24]  B. Krasnov,et al.  Time of survival under starvation in two flea species (Siphonaptera: Pulicidae) at different air temperatures and relative humidities. , 2002, Journal of vector ecology : journal of the Society for Vector Ecology.

[25]  Hal Caswell,et al.  Integrating dynamic energy budgets into matrix population models , 2006 .

[26]  A note on the von Bertalanffy growth function concerningthe allocation of surplus energy to reproduction , 2012 .

[27]  Konstadia Lika,et al.  Resource allocation to reproduction in animals , 2014, Biological reviews of the Cambridge Philosophical Society.

[28]  Gary James Jason,et al.  The Logic of Scientific Discovery , 1988 .

[29]  D. Montemurro,et al.  Survival and body composition of normal and hypothalamic obese rats in acute starvation. , 1960, The American journal of physiology.

[30]  P. Sharpe,et al.  Reaction kinetics of poikilotherm development. , 1977, Journal of theoretical biology.

[31]  Lin Wang,et al.  Coupled disease–behavior dynamics on complex networks: A review , 2015, Physics of Life Reviews.

[32]  Arild Folkvord,et al.  Growth, survival and cannibalism of cod juveniles (Gadus morhua): effects of feed type, starvation and fish size , 1991 .

[33]  M. Kearney,et al.  35 years of DEB research , 2014 .

[34]  The influence of temporal and spatial origin on size and early growth rates in captive loggerhead sea turtles Caretta caretta in the United States , 2006 .

[35]  James H. Brown,et al.  A General Model for the Origin of Allometric Scaling Laws in Biology , 1997, Science.

[36]  J. Spotila Sea Turtles: A Complete Guide to Their Biology, Behavior, and Conservation , 2004 .

[37]  Arrow Buttons Frequently asked questions , 2009 .

[38]  M. Jusup,et al.  Simple measurements reveal the feeding history, the onset of reproduction, and energy conversion efficiencies in captive bluefin tuna , 2014 .

[39]  James H. Brown,et al.  Toward a metabolic theory of ecology , 2004 .

[40]  A. Toland,et al.  Carbon , 2018, Field to Palette.

[41]  Tjalling Jager,et al.  DEBkiss or the quest for the simplest generic model of animal life history. , 2013, Journal of theoretical biology.

[42]  Craig R. White,et al.  Testing Metabolic Theories , 2012, The American Naturalist.

[43]  S. Kooijman,et al.  Sensitivity of animals to chemical compounds links to metabolic rate , 2015, Ecotoxicology.

[44]  H. Haugen,et al.  Indirect calorimetry: a practical guide for clinicians. , 2007, Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition.

[45]  R. Nisbet,et al.  Predicting Population Dynamics from the Properties of Individuals: A Cross-Level Test of Dynamic Energy Budget Theory , 2013, The American Naturalist.

[46]  G. Hays,et al.  REPRODUCTIVE INVESTMENT AND OPTIMUM CLUTCH SIZE OF LOGGERHEAD SEA TURTLES (CARETTA CARETTA) , 1991 .

[47]  Pierre Petitgas,et al.  Modeling fish growth and reproduction in the context of the Dynamic Energy Budget theory to predict environmental impact on anchovy spawning duration , 2009 .

[48]  S. J. Kline,et al.  Thermodynamics, information and life revisited, Part I: ‘To be or entropy’ , 1998 .

[49]  Michael Kearney,et al.  The potential for behavioral thermoregulation to buffer “cold-blooded” animals against climate warming , 2009, Proceedings of the National Academy of Sciences.

[50]  Nicola Bellomo,et al.  On the interplay between mathematics and biology: hallmarks toward a new systems biology. , 2015, Physics of life reviews.

[51]  J. Elser,et al.  Ecological Stoichiometry: The Biology of Elements from Molecules to the Biosphere , 2002 .

[52]  M. Witt,et al.  Home on the range: spatial ecology of loggerhead turtles in Atlantic waters of the USA , 2011 .

[53]  R. Plevin,et al.  Approximate Bayesian Computation in Evolution and Ecology , 2011 .

[54]  H. Bilton,et al.  The Effects of Starvation and Subsequent Feeding on Survival and Growth of Fulton Channel Sockeye Salmon Fry (Oncorhynchus nerka) , 1973 .

[55]  Estimating the Time Between Hatching of Sea Turtles and Their Emergence From the Nest , 2009 .

[56]  Sebastiaan A.L.M. Kooijman,et al.  Stochastic feeding of fish larvae and their metabolic handling of starvation , 2011 .

[57]  K. Mulder,et al.  Organismal stoichiometry and the adaptive advantage of variable nutrient use and production efficiency in Daphnia , 2007 .

[58]  J. Raymond [Cyclic AMP]. , 1972, La Nouvelle presse medicale.

[59]  Tânia Sousa,et al.  From empirical patterns to theory: a formal metabolic theory of life , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[60]  Donald A. Jackson,et al.  A Comparison of von Bertalanffy and Polynomial Functions in Modelling Fish Growth Data , 1992 .

[61]  N. Mitchell,et al.  Key parameters describing temperature-dependent sex determination in the southernmost population of loggerhead sea turtles , 2013 .

[62]  Graeme C. Hays,et al.  Sea turtles: A review of some key recent discoveries and remaining questions , 2008 .

[63]  Sebastiaan A.L.M. Kooijman,et al.  Comparative energetics of the 5 fish classes on the basis of dynamic energy budgets. , 2014 .

[64]  B. Stockhoff Starvation resistance of gypsy moth, Lymantria dispar (L.) (Lepidoptera: Lymantriidae): tradeoffs among growth, body size, and survival , 1991, Oecologia.

[65]  D. Kimura LIKELIHOOD METHODS FOR THE VON BERT ALANFFY GROWTH CURVE , 1980 .

[66]  Tânia Sousa,et al.  Thermodynamics of organisms in the context of dynamic energy budget theory. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[67]  A. Clarke Is there a Universal Temperature Dependence of metabolism , 2004 .

[68]  Mark Kirkpatrick,et al.  What Animal Breeding Has Taught Us about Evolution , 2010 .

[69]  H. Briegel,et al.  Aedes aegypti: size, reserves, survival, and flight potential. , 2001, Journal of vector ecology : journal of the Society for Vector Ecology.

[70]  Sebastiaan A.L.M. Kooijman,et al.  Dynamic Energy Budgets in Biological Systems: Theory and Applications in Ecotoxicology , 1993 .

[71]  S. Kooijman,et al.  From food‐dependent statistics to metabolic parameters, a practical guide to the use of dynamic energy budget theory , 2008, Biological reviews of the Cambridge Philosophical Society.

[72]  Rampal S Etienne,et al.  Testing the metabolic theory of ecology. , 2012, Ecology letters.

[73]  A. J. Hulbert,et al.  Basal Metabolic Rate: History, Composition, Regulation, and Usefulness , 2004, Physiological and Biochemical Zoology.

[74]  K. Noguchi,et al.  Costs of protein turnover and carbohydrate export in leaves of sun and shade species , 2001 .

[75]  M. Jusup,et al.  Mathematical Modeling of Bluefin Tuna Growth, Maturation, and Reproduction Based on Physiological Energetics , 2015 .

[76]  D. Hardie,et al.  AMPK: a nutrient and energy sensor that maintains energy homeostasis , 2012, Nature Reviews Molecular Cell Biology.

[77]  A. Marsh,et al.  High Macromolecular Synthesis with Low Metabolic Cost in Antarctic Sea Urchin Embryos , 2001, Science.

[78]  E. H. Battley An empirical method for estimating the entropy of formation and the absolute entropy of dried microbial biomass for use in studies on the thermodynamics of microbial growth , 1999 .

[79]  R. Nisbet,et al.  Relating suborganismal processes to ecotoxicological and population level endpoints using a bioenergetic model. , 2015, Ecological applications : a publication of the Ecological Society of America.

[80]  G. Parker The Growth of Turtles. , 1926, Proceedings of the National Academy of Sciences of the United States of America.

[81]  Denis S Loiselle,et al.  The efficiency of muscle contraction. , 2005, Progress in biophysics and molecular biology.

[82]  S. M. Van Patten,et al.  Multiple pathway signal tran sduction by the cAMP‐dependent protein kinase , 1994, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[83]  G. Barsh,et al.  Is the energy homeostasis system inherently biased toward weight gain? , 2003, Diabetes.

[84]  R. Sterner,et al.  CARBON, NITROGEN, AND PHOSPHORUS STOICHIOMETRY OF CYPRINID FISHES , 2000 .

[85]  M. Brand,et al.  Regulation analysis of energy metabolism. , 1997, The Journal of experimental biology.

[86]  Sebastiaan A.L.M. Kooijman,et al.  Waste to hurry: Dynamic energy budgets explain the need of wasting to fully exploit blooming resources. , 2013 .

[87]  Tjalling Jager,et al.  Some good reasons to ban ECx and related concepts in ecotoxicology. , 2011, Environmental science & technology.

[88]  Sebastiaan A.L.M. Kooijman,et al.  The “covariation method” for estimating the parameters of the standard Dynamic Energy Budget model II: Properties and preliminary patterns , 2011 .

[89]  S. Kooijman,et al.  Shedding Light on Fish Otolith Biomineralization Using a Bioenergetic Approach , 2011, PloS one.

[90]  Fabens Aj,et al.  Properties and fitting of the Von Bertalanffy growth curve. , 1965 .

[91]  S. Logan,et al.  The Origin and Status of the Arrhenius Equation , 1982 .

[92]  Ruben Gamboa,et al.  Solving △ = □ , 2009, ACL2 '09.

[93]  The Growth of the Loggerhead Turtle , 1929, The American Naturalist.

[94]  K. Bjorndal,et al.  Growth Rates of Immature Green Turtles, Chelonia mydas, on Feeding Grounds in the Southern Bahamas , 1988 .

[95]  A. J. Fabens,et al.  Properties and fitting of the Von Bertalanffy growth curve. , 1965, Growth.

[96]  P. Holgate,et al.  Matrix Population Models. , 1990 .

[97]  W. J. Nichols,et al.  Demographic implications of alternative foraging strategies in juvenile loggerhead turtles Caretta caretta of the North Pacific Ocean , 2011 .

[98]  Lars Garby,et al.  Bioenergetics : its thermodynamic foundations , 1995 .

[99]  Volker Grimm,et al.  Dynamic Energy Budget theory meets individual‐based modelling: a generic and accessible implementation , 2012 .

[100]  Epperly,et al.  GROWTH RATES OF LOGGERHEAD SEA TURTLES ( CARETTA CARETTA ) FROM THE WESTERN NORTH ATLANTIC , 2008 .

[101]  L. von Bertalanffy Quantitative Laws in Metabolism and Growth , 1957, The Quarterly Review of Biology.

[102]  S. Bloom,et al.  Gut hormones and the regulation of energy homeostasis , 2006, Nature.

[103]  Viktor Winschel,et al.  Solving, Estimating, and Selecting Nonlinear Dynamic Models Without the Curse of Dimensionality , 2010 .

[104]  B. Bayne,et al.  Protein turnover, physiological energetics and heterozygosity in the blue mussel, Mytilus edulis: the basis of variable age-specific growth , 1986, Proceedings of the Royal Society of London. Series B. Biological Sciences.

[105]  R. Hanlon,et al.  Effect of temperature on laboratory growth, reproduction and life span of Octopus bimaculoides , 1988 .

[106]  A. J. Tessier,et al.  Starvation in Daphnia: Energy reserves and reproductive allocation1 , 1983 .

[107]  K. Sebens The Ecology of Indeterminate Growth in Animals , 1987 .

[108]  T. Muramatsu,et al.  Energy cost of whole-body protein synthesis measured in vivo in chicks. , 1988, Comparative biochemistry and physiology. A, Comparative physiology.

[109]  Gabriele Eisenhauer,et al.  Elements Of Mathematical Ecology , 2016 .

[110]  Hal Caswell,et al.  A model for energetics and bioaccumulation in marine mammals with applications to the right whale. , 2007, Ecological applications : a publication of the Ecological Society of America.

[111]  S. Kooijman,et al.  A Full Lifecycle Bioenergetic Model for Bluefin Tuna , 2011, PloS one.

[112]  Arpit A. Almal,et al.  Lifting the Curse of Dimensionality , 2007 .

[113]  N. P. Wilkins Starvation of the herring, Clupea harengus L.: survival and some gross biochemical changes. , 1967, Comparative biochemistry and physiology.

[114]  M. Kearney,et al.  Biomechanics meets the ecological niche: the importance of temporal data resolution , 2012, Journal of Experimental Biology.

[115]  M. Becker In The Beat Of A Heart Life Energy And The Unity Of Nature , 2016 .

[116]  J. van der Meer Metabolic theories in ecology. , 2006, Trends in ecology & evolution.

[117]  Bas Kooijman,et al.  Dynamic Energy Budget Theory for Metabolic Organisation , 2005 .

[118]  Sebastiaan A.L.M. Kooijman,et al.  Metabolic acceleration in animal ontogeny: An evolutionary perspective , 2014 .

[119]  Starrlight Augustine,et al.  The bijection from data to parameter space with the standard DEB model quantifies the supply-demand spectrum. , 2014, Journal of theoretical biology.

[120]  F. J. Richards A Flexible Growth Function for Empirical Use , 1959 .

[121]  S. Asdell,et al.  The Effect of Retarded Growth Upon the Sexual Development of Rats , 1935 .

[122]  Body Depth: An Indicator of Morphological Variation among Nesting Groups of Adult Loggerhead Sea Turtles (Caretta caretta) , 1980 .

[123]  M. Vanderklift,et al.  Sources of variation in consumer-diet δ15N enrichment: a meta-analysis , 2003, Oecologia.

[124]  S. Kooijman,et al.  What the egg can tell about its hen: Embryonic development on the basis of dynamic energy budgets , 2009, Journal of mathematical biology.

[125]  Chris Carbone,et al.  Why are metabolic scaling exponents so controversial? Quantifying variance and testing hypotheses. , 2010, Ecology letters.

[126]  Peter G Schultz,et al.  Synthesis at the interface of chemistry and biology. , 2009, Journal of the American Chemical Society.

[127]  E. Ferrannini The theoretical bases of indirect calorimetry: a review. , 1988, Metabolism: clinical and experimental.

[128]  Cédric Bacher,et al.  Use of dynamic energy budget and individual based models to simulate the dynamics of cultivated oyster populations , 2006 .

[129]  R. Albert Scale-free networks in cell biology , 2005, Journal of Cell Science.

[130]  M. Gruebele,et al.  Perspective: Reaches of chemical physics in biology. , 2013, The Journal of chemical physics.

[131]  J. Blaxter,et al.  Feeding ability and survival during starvation of marine fish larvae reared in the laboratory , 1987 .

[132]  A. Dornhaus,et al.  Small worker bumble bees (Bombus impatiens) are hardier against starvation than their larger sisters , 2010, Insectes Sociaux.

[133]  C.M.G.L. Teixeira,et al.  Application of Dynamic Energy Budget theory for conservation relevant modelling of Bird life histories , 2016 .

[134]  L. von Bertalanffy,et al.  The theory of open systems in physics and biology. , 1950, Science.

[135]  T. Klanjšček Dynamic energy budgets and bioaccumulation : a model for marine mammals and marine mammal populations , 2006 .

[136]  O. Wolkenhauer,et al.  Dynamic energy budget approaches for modelling organismal ageing , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[137]  M. Jusup,et al.  Size Scaling in Western North Atlantic Loggerhead Turtles Permits Extrapolation between Regions, but Not Life Stages , 2015, PloS one.

[138]  Patricia A. Holden,et al.  Modeling Physiological Processes That Relate Toxicant Exposure and Bacterial Population Dynamics , 2012, PloS one.

[139]  J. Waterlow Protein turnover with special reference to man. , 1984, Quarterly journal of experimental physiology.

[140]  Paul S Agutter,et al.  Metabolic scaling: consensus or controversy? , 2004, Theoretical Biology and Medical Modelling.

[141]  Balázs Kégl,et al.  Intrinsic Dimension Estimation Using Packing Numbers , 2002, NIPS.

[142]  K. Bjorndal,et al.  Polymodal foraging in adult female loggerheads (Caretta caretta) , 2010 .

[143]  Bruce E. Kendall,et al.  ANALYSIS OF SIZE TRAJECTORY DATA USING AN ENERGETIC-BASED GROWTH MODEL , 2005 .

[144]  Joel E. Cohen,et al.  Mathematics Is Biology's Next Microscope, Only Better; Biology Is Mathematics' Next Physics, Only Better , 2004, PLoS biology.

[145]  Peter J. Bickel,et al.  Maximum Likelihood Estimation of Intrinsic Dimension , 2004, NIPS.

[146]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[147]  Matthew H. Godfrey,et al.  Status of nesting loggerhead turtles Caretta caretta at Bald Head Island (North Carolina, USA) after 24 years of intensive monitoring and conservation , 2005, Oryx.

[148]  T. Benton,et al.  Age and size at maturity: sex, environmental variability and developmental thresholds , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[149]  J. Beardall,et al.  Protein turnover in relation to maintenance metabolism at low photon flux in two marine microalgae , 2003 .

[150]  S. Kooijman,et al.  Dynamic energy budget theory restores coherence in biology , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[151]  Izumi V. Hinkson,et al.  The dynamic state of protein turnover: It's about time. , 2011, Trends in cell biology.

[152]  Michel Verleysen,et al.  The Curse of Dimensionality in Data Mining and Time Series Prediction , 2005, IWANN.

[153]  T. S. P. S.,et al.  GROWTH , 1924, Nature.

[154]  Elke I. Zimmer,et al.  Dynamic energy budgets in population ecotoxicology: Applications and outlook , 2014 .

[155]  L. Johnson,et al.  Dynamic energy budget theory and population ecology: lessons from Daphnia , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[156]  N. Daan,et al.  Growth of North Sea cod, Gadus morhua , 1974 .

[157]  S. Woods,et al.  Signals that regulate food intake and energy homeostasis. , 1998, Science.

[158]  R. Nisbet,et al.  Integrating dynamic energy budget (DEB) theory with traditional bioenergetic models , 2012, Journal of Experimental Biology.

[159]  M. Kleiber Body size and metabolism , 1932 .

[160]  J. V. D. Meer,et al.  An introduction to Dynamic Energy Budget (DEB) models with special emphasis on parameter estimation , 2006 .

[161]  Aida Campos,et al.  Weight–length relationships for 46 fish species of the Portuguese west coast , 2004 .

[162]  R. Bour,et al.  Turtles of the World, 2012 Update: Annotated Checklist of Taxonomy, Synonymy, Distribution, and Conservation Status , 2012 .

[163]  Sebastiaan A.L.M. Kooijman,et al.  Scenarios for acceleration in fish development and the role of metamorphosis , 2011 .

[164]  P. Fink,et al.  To be or not to be what you eat: regulation of stoichiometric homeostasis among autotrophs and heterotrophs , 2010 .

[165]  Boris Podobnik,et al.  Dynamically rich, yet parameter-sparse models for spatial epidemiology: Comment on "Coupled disease-behavior dynamics on complex networks: A review" by Z. Wang et al. , 2015, Physics of life reviews.

[166]  S. Kooijman,et al.  From molecules to ecosystems through dynamic energy budget models. , 2000 .

[167]  G. Allan,et al.  A feed is only as good as its ingredients – a review of ingredient evaluation strategies for aquaculture feeds , 2007 .

[168]  S. H. Bennett,et al.  Utilization of Posthatching Yolk in Loggerhead Sea Turtles, Caretta caretta , 1981 .

[169]  Leah R. Johnson,et al.  Bayesian inference for bioenergetic models , 2013 .

[170]  A. Microbiology Protein Turnover , 1967, Nature.

[171]  A. Lloyd,et al.  The Regulation of Cell Size , 2013, Cell.

[172]  D. Wethey,et al.  A Dynamic Energy Budget (DEB) Model for the Keystone Predator Pisaster ochraceus , 2014, PloS one.

[173]  J. Speakman,et al.  Incubation temperature and energy expenditure during development in loggerhead sea turtle embryos , 2009 .