Predicting Additive and Non-additive Genetic Effects from Trials Where Traits Are Affected by Interplot Competition

There are two key types of selection in a plant breeding program, namely selection of hybrids for potential commercial use and the selection of parents for use in future breeding. Oakey et al. (in Theoretical and Applied Genetics 113, 809-819, 2006) showed how both of these aims could be achieved using pedigree information in a mixed model analysis in order to partition genetic effects into additive and non-additive effects. Their approach was developed for field trial data subject to spatial variation. In this paper we extend the approach for data from trials subject to interplot competition. We show how the approach may be used to obtain predictions of pure stand additive and non-additive effects. We develop the methodology in the context of a single field trial using an example from an Australian sorghum breeding program.

Toward a rational-choice foundation of non-additive theories

A classical argument of de Finetti holds that Rationality implies Subjective Expected Utility (SEU). In contrast, the Knightian distinction between Risk and Ambiguity suggests that a rational decision maker would obey the SEU paradigm when the information available is in some sense good, and would depart from it when the information available is not good. Unlike de Finetti's, however, this view does not rely on a formal argument. In this paper, we study the set of all information structures that might be availabe to a decision maker, and show that they are of two types: those compatible with SEU theory and those for which SEU theory must fail. We also show that the former correspond to "good" information, while the latter correspond to information that is not good. Thus, our results provide a formalization of the distinction between Risk and Ambiguity. As a consequence of our main theorem (Theorem 2, Section 8), behavior not-conforming to SEU theory is bound to emerge in the presence of Ambiguity. We give two examples of situations of Ambiguity. One concerns the uncertainty on the class of measure zero events, the other is a variation on Ellberg's three-color urn experiment. We also briefly link our results to two other strands of literature: the study of ambiguous events and the problem of unforeseen contingencies. We conclude the paper by re-considering de Finetti's argument in light of our findings.

Laws of large numbers for non-additive probabilities

We apply the concept of exchangeable random variables to the case of non-additive robability distributions exhibiting ncertainty aversion, and in the lass generated bya convex core convex non-additive probabilities, ith a convex core). We are able to rove two versions of the law of arge numbers (de Finetti's heorems). By making use of two efinitions. of independence we rove two versions of the strong law f large numbers. It turns out that e cannot assure the convergence of he sample averages to a constant. e then modal the case there is a true" probability distribution ehind the successive realizations of the uncertain random variable. In this case convergence occurs. This result is important because it renders true the intuition that it is possible "to learn" the "true" additive distribution behind an uncertain event if one repeatedly observes it (a sufficiently large number of times). We also provide a conjecture regarding the "Iearning" (or updating) process above, and prove a partia I result for the case of Dempster-Shafer updating rule and binomial trials.

Non-additive genetic effects on weights and performance of a Brazilian Bos taurus x Bos indicus beef composite

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evidences of non-additive effects of multiple parasitoids on Diatraea saccharalis Fabr. (Lep., Crambidae) populations in sugarcane fields in Brazil

Biological control is a relatively benign method of pest control. However, considerable debate exists over whether multiple natural enemies often interact to produce additive or non-additive effects on their prey or host populations. Based on the large data set stored in the Sao Joao and Barra sugarcane mills (state of São Paulo, Brazil) regarding the programme of biological control of Diatraea saccharalis using the parasitoids Cotesia flavipes and tachinid flies, in the present study the author investigated whether the parasitoids released into sugarcane fields interfered significantly with the rate of parasitized D. saccharalis hosts. The author also observed whether there was an additive effect of releasing C. flavipes and tachinids on the rate of parasitized hosts, and looked for evidence of possible negative effects of the use of multiple parasitoid species in this biological control programme. Results showed that C. flavipes and the tachinids were concomitantly released in the Barra Mill, but not in the Sao Jao Mill. Furthermore, in the Barra Mill there was evidence that the parasitoids interacted because the percentage of parasitism did not increase after the release of either C. flavipes or tachinids. In the Sao Joao Mill, when both parasitoid species were released out of synchrony, both the percentage of parasitism by C. flavipes as well as that of the tachinids increased. When large numbers of tachinids were released in the Barra Mill, they caused a significant lower percentage of parasitism imposed by C. flavipes. The implications of the results as evidence of non-additive effects of C. flavipes plus tachinids on D. saccharalis populations are discussed.

Estimation methods of non-additive effects for characteristics of weight and scrotal circumference in crossbred beef cattle

The objective of this study was to investigate, in a population of crossbred cattle, the obtainment of the non-additive genetic effects for the characteristics weight at 205 and 390 days and scrotal circumference, and to evaluate the consideration of these effects in the prediction of breeding values of sires using different estimation methodologies. In method 1, the data were pre-adjusted for the non-additive effects obtained by least squares means method in a model that considered the direct additive, maternal and non-additive fixed genetic effects, the direct and total maternal heterozygosities, and epistasis. In method 2, the non-additive effects were considered covariates in genetic model. Genetic values for adjusted and non-adjusted data were predicted considering additive direct and maternal effects, and for weight at 205 days, also the permanent environmental effect, as random effects in the model. The breeding values of the categories of sires considered for the weight characteristic at 205 days were organized in files, in order to verify alterations in the magnitude of the predictions and ranking of animals in the two methods of correction data for the non-additives effects. The non-additive effects were not similar in magnitude and direction in the two estimation methods used, nor for the characteristics evaluated. Pearson and Spearman correlations between breeding values were higher than 0.94, and the use of different methods does not imply changes in the selection of animals.

Multi-q pattern analysis: A case study in image classification

This paper compares the effectiveness of the Tsallis entropy over the classic Boltzmann-Gibbs-Shannon entropy for general pattern recognition, and proposes a multi-q approach to improve pattern analysis using entropy. A series of experiments were carried out for the problem of classifying image patterns. Given a dataset of 40 pattern classes, the goal of our image case study is to assess how well the different entropies can be used to determine the class of a newly given image sample. Our experiments show that the Tsallis entropy using the proposed multi-q approach has great advantages over the Boltzmann-Gibbs-Shannon entropy for pattern classification, boosting image recognition rates by a factor of 3. We discuss the reasons behind this success, shedding light on the usefulness of the Tsallis entropy and the multi-q approach. (C) 2012 Elsevier B.V. All rights reserved.

Entropy of quantum states: Ambiguities

The von Neumann entropy of a generic quantum state is not unique unless the state can be uniquely decomposed as a sum of extremal or pure states. As pointed out to us by Sorkin, this happens if the GNS representation (of the algebra of observables in some quantum state) is reducible, and some representations in the decomposition occur with non-trivial degeneracy. This non-unique entropy can occur at zero temperature. We will argue elsewhere in detail that the degeneracies in the GNS representation can be interpreted as an emergent broken gauge symmetry, and play an important role in the analysis of emergent entropy due to non-Abelian anomalies. Finally, we establish the analogue of an H-theorem for this entropy by showing that its evolution is Markovian, determined by a stochastic matrix.

Complex Interactions between Dioxin-Like and Non-Dioxin-Like Compounds for in Vitro Cellular Responses: Implications for the Identification of Dioxin Exposure Biomarkers

Despite considerable advances in reducing the production of dioxin-like toxicants in recent years, contamination of the food chain still occasionally occurs resulting in huge losses to the agri-food sector and risk to human health through exposure. Dioxin-like toxicity is exhibited by a range of stable and bioaccumulative compounds including polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs), produced by certain types of combustion, and man-made coplanar polychlorinated biphenyls (PCBs), as found in electrical transformer oils. While dioxinergic compounds act by a common mode of action making exposure detection biomarker based techniques a potentially useful tool, the influence of co-contaminating toxicants on such approaches needs to be considered. To assess the impact of possible interactions, the biological responses of H4IIE cells to challenge by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in combination with PCB-52 and benzo-a-pyrene (BaP) were evaluated by a number of methods in this study. Ethoxyresorufin-O-deethylase (EROD) induction in TCDD exposed cells was suppressed by increasing concentrations of PCB-52, PCB-153, or BaP up to 10 mu M. BaP levels below 1 mu M suppressed TCDD stimulated EROD induction, but at higher concentrations, EROD induction was greater than the maximum observed when cells were treated with TCDD alone. A similar biphasic interaction of BaP with TCDD co-exposure was noted in the AlamarBlue assay and to a lesser extent with PCB-52. Surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF) profiling of peptidomic responses of cells exposed to compound combinations was compared. Cells co-exposed to TCDD in the presence of BaP or PCB-52 produced the most differentiated spectra with a substantial number of non-additive interactions observed. These findings suggest that interactions between dioxin and other toxicants create novel, additive, and non-additive effects, which may be more indicative of the types of responses seen in exposed animals than those of single exposures to the individual compounds.

Dynamical control of the mesosphere by orographic and non-orographic gravity wave drag during the extended northern winters of 2006 and 2009

A version of the Canadian Middle Atmosphere Model (CMAM) that is nudged toward reanalysis data up to 1 hPa is used to examine the impacts of parameterized orographic and non-orographic gravity wave drag (OGWD and NGWD) on the zonal-mean circulation of the mesosphere during the extended northern winters of 2006 and 2009 when there were two large stratospheric sudden warmings. The simulations are compared to Aura Microwave Limb Sounder (MLS) observations of mesospheric temperature, carbon monoxide (CO) and derived zonal winds. The control simulation, which uses both OGWD and NGWD, is shown to be in good agreement with MLS. The impacts of OGWD and NGWD are assessed using simulations in which those sources of wave drag are removed. In the absence of OGWD the mesospheric zonal winds in the months preceding the warmings are too strong, causing increased mesospheric NGWD, which drives excessive downwelling, resulting in overly large lower mesospheric values of CO prior to the warming. NGWD is found to be most important following the warmings when the underlying westerlies are too weak to allow much vertical propagation of the orographic gravity waves to the mesosphere. NGWD is primarily responsible for driving the circulation that results in the descent of CO from the thermosphere following the warmings. Zonal mean mesospheric winds and temperatures in all simulations are shown to be strongly constrained by (i.e. slaved to) the stratosphere. Finally, it is demonstrated that the responses to OGWD and NGWD are non-additive due to their dependence and influence on the background winds and temperatures.

The ex-Ante non-optimality of the Dempster-Schafer updating rule for ambiguous beliefs

The most widely used updating rule for non-additive probalities is the Dempster-Schafer rule. Schmeidles and Gilboa have developed a model of decision making under uncertainty based on non-additive probabilities, and in their paper “Updating Ambiguos Beliefs” they justify the Dempster-Schafer rule based on a maximum likelihood procedure. This note shows in the context of Schmeidler-Gilboa preferences under uncertainty, that the Dempster-Schafer rule is in general not ex-ante optimal. This contrasts with Brown’s result that Bayes’ rule is ex-ante optimal for standard Savage preferences with additive probabilities.

Integral representation with convex capacities that are squeeze of (additive) probability measures

In this paper I will investigate the conditions under which a convex capacity (or a non-additive probability which exhibts uncertainty aversion) can be represented as a squeeze of a(n) (additive) probability measure associate to an uncertainty aversion function. Then I will present two alternatives forrnulations of the Choquet integral (and I will extend these forrnulations to the Choquet expected utility) in a parametric approach that will enable me to do comparative static exercises over the uncertainty aversion function in an easy way.