Mathematical modelling in animal nutrition: a centenary review

A centenary review presents an opportunity to ponder over the processes of concept development and give thought to future directions. The current review aims to ascertain the ontogeny of current concepts, underline the connection between ideas and people and pay tribute to those pioneers who have contributed significantly to modelling in animal nutrition. Firstly, the paper draws a brief portrait of the use of mathematics in agriculture and animal nutrition prior to 1925. Thereafter, attention turns towards the historical development of growth modelling, feed evaluation systems and animal response models. Introduction of the factorial and compartmental approaches into animal nutrition is noted along with the particular branches of mathematics encountered in various models. Furthermore, certain concepts, especially bioenergetics or the heat doctrine, are challenged and alternatives are reviewed. The current state of knowledge of animal nutrition modelling results mostly from the discernment and unceasing efforts of our predecessors rather than serendipitous discoveries. The current review may stimulate those who wish for greater understanding and appreciation

Evaluation of models to predict the stoichiometry of volatile fatty acid profiles in rumen fluid of lactating Holstein cows

Volatile fatty acids (VFA), produced in the rumen by microbial fermentation, are the main energy source for ruminants. The VFA profile, particularly the nonglucogenic (acetate, Ac; butyrate, Bu) to glucogenic (propionate, Pr) VFA ratio (NGR), is associated with effects on methane production, milk composition, and energy balance. The aim of this study was to evaluate extant rumen VFA stoichiometry models for their ability to predict in vivo VFA molar proportions. The models were evaluated using an independent data set consisting of 101 treatments from 24 peer-reviewed publications with lactating Holstein cows. All publications contained a full diet description, rumen pH, and rumen VFA molar proportions. Stoichiometric models were evaluated based on root mean squared prediction error (RMSPE) and concordance correlation coefficient (CCC) analysis. Of all models evaluated, the 1998 Friggens model had the lowest RMSPE for Ac and Bu (7.2 and 20.2% of observed mean, respectively). The 2006 Bannink model had the lowest RMSPE and highest CCC for Pr (14.4% and 0.70, respectively). The 2008 Bannink model had comparable predictive performance for Pr to that of the 2006 Bannink model but a larger error due to overall bias (26.2% of MSPE). The 1982 Murphy model provided the poorest prediction of Bu, with the highest RMSPE and lowest CCC (24.6% and 0.15, respectively). The 1988 Argyle and Baldwin model had the highest CCC for Ac with an intermediate RMSPE (0.47 and 8.0%, respectively). The 2006 Sveinbjörnsson model had the highest RMSPE (13.9 and 34.0%, respectively) and lowest CCC (0.31 and 0.40, respectively) for Ac and Pr. The NGR predictions had the lowest RMSPE and highest CCC in the 2 models of Bannink, whereas the lowest predictive performance was in the 2006 Sveinbjörnsson model. It appears that the type of VFA produced is not a simple linear relationship between substrate inputs and pH as currently represented. The analysis demonstrates that most rumen VFA stoichiometric approaches explain a large part of the variation in VFA molar proportions among diets, in particular for Ac, whereas predictive power for Pr and Bu differ largely among approaches. The move toward feed evaluation systems based on animal response might necessitate an improved representation of rumen fermentation, focused on improving our understanding of VFA proportions in diets that vary from the mean

Deep redshift topological lensing: strategies for the T^3 candidate

The 3-torus (T^3) FLRW model better fits the nearly zero large-scale auto-correlation of the WMAP CMB sky maps than the infinite flat model. The T^3 model's WMAP parameters imply approximately equal-redshift topological lensing at z \sim 6. We investigate observational strategies for rejecting the T^3 solution or providing candidate topologically lensed galaxy pairs. T^3 holonomies are applied to (i) existing z \sim 6 observations and (ii) simulated observations, creating multiply connected catalogues. Corresponding simply connected catalogues are generated. Each catalogue is analysed using a successive filter method and collecting matched quadruples. Quadruple statistics between the multiply and simply connected catalogues are compared. The expected rejection of the hypothesis, or detection of candidate topologically lensed galaxies, is possible at a significance of 5% for a pair of T^3 axis-centred northern and southern surveys if photometric redshift accuracy is \sigma(\zphot) < 0.01 for a pair of nearly complete 100 deg^2 surveys with a total of > 500 galaxies over 4.3 < z < 6.6, or for a pair of 196 deg^2 surveys with > 400 galaxies and \sigma(\zphot) < 0.02 over 4<z<7. Dropping the maximum time interval in a pair from \Delta t =1 Gyr/h to \Delta t =0.1 Gyr/h yields a requirement of \sigma(\zphot) < 0.005 or \sigma(\zphot) < 0.01, respectively. Millions of z \sim 6 galaxies will be observed over fields of these sizes during the coming decades, implying much stronger constraints. The question is not if the hypothesis will be rejected or confirmed, it is when.Comment: 13 pages, 9 figures, 5 tables, MNRAS, accepte

The inference of gene trees with species trees

Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can co-exist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice-versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. In this article we review the various models that have been used to describe the relationship between gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a better basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree-species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution.Comment: Review article in relation to the "Mathematical and Computational Evolutionary Biology" conference, Montpellier, 201

Modelling the lactation curve of dairy cows using the differentials of growth functions

Descriptions of entire lactations were investigated using six mathematical equations. comprising the differentials of four growth functions (logistic. Gompertz, Schumacher and Morgan) and two other equations (Wood and Dijkstra). The data contained monthly milk yield records from 70 first, 70 second and 75 third parity Iranian Holstein cows. Indicators of fit were model behavior, statistical evaluation and biologically meaningful parameter estimates and lactation features. Analysis of variance with equation, parity and their interaction as factors and with cows as replicates was performed to compare goodness of fit of the equations. The interaction of equation and parity was not significant for any statistics, which showed that there vas no tendency For one equation to fit a given parity better than other equations. Although model behaviour analysis showed better performance of growth functions than the Wood and Dijkstra equations in filling the individual lactation curves, statistical evaluation revealed that there was no significant difference between file goodness of fit of the different equations. Evaluation of lactation features showed that the Dijkstra equation was able to estimate the initial milk yield and peak yield more accurately than the other equations. Overall evaluation of the different equations demonstrated the potential of the differentials of simple empirical growth functions used in file Current study as equations for fitting monthly milk records of Holstein dairy cattle

CO/H2 Abundance Ratio ~ 10^{-4} in a Protoplanetary Disk

The relative abundances of atomic and molecular species in planet-forming disks around young stars provide important constraints on photochemical disk models and provide a baseline for calculating disk masses from measurements of trace species. A knowledge of absolute abundances, those relative to molecular hydrogen (H2), are challenging because of the weak rovibrational transition ladder of H$_{2}$ and the inability to spatially resolve different emission components within the circumstellar environment. To address both of these issues, we present new contemporaneous measurements of CO and H2 absorption through the "warm molecular layer" of the protoplanetary disk around the Classical T Tauri Star RW Aurigae A. We use a newly commissioned observing mode of the Hubble Space Telescope-Cosmic Origins Spectrograph to detect warm H2 absorption in this region for the first time. An analysis of the emission and absorption spectrum of RW Aur shows components from the accretion region near the stellar photosphere, the molecular disk, and several outflow components. The warm H2 and CO absorption lines are consistent with a disk origin. We model the 1092-1117A spectrum of RW Aur to derive log10 N(H2)~=~19.90$^{+0.33}_{-0.22}$ at T$_{rot}$(H2) ~=~440~+/-~39 K. The CO $A$~--~$X$ bands observed from 1410-1520A are best fit by log10 N(CO)~=~16.1~$^{+0.3}_{-0.5}$ at T$_{rot}$(CO) ~=~200$^{+650}_{-125}$ K. Combining direct measurements of the HI, H2, and CO column densities, we find a molecular fraction in the warm disk surface of $f_{H2}$~>=~0.47 and derive a molecular abundance ratio of CO/H2~=~1.6$^{+4.7}_{-1.3}$~x~10$^{-4}$, both consistent with canonical interstellar dense cloud values.Comment: ApJ - accepted. 13 pages, 8 figure