Mixed model formulations for multi-environment trials

When studying genotype X environment interaction in multi-environment trials, plant breeders and geneticists often consider one of the effects, environments or genotypes, to be fixed and the other to be random. However, there are two main formulations for variance component estimation for the mixed model situation, referred to as the unconstrained-parameters (UP) and constrained-parameters (CP) formulations. These formulations give different estimates of genetic correlation and heritability as well as different tests of significance for the random effects factor. The definition of main effects and interactions and the consequences of such definitions should be clearly understood, and the selected formulation should be consistent for both fixed and random effects. A discussion of the practical outcomes of using the two formulations in the analysis of balanced data from multi-environment trials is presented. It is recommended that the CP formulation be used because of the meaning of its parameters and the corresponding variance components. When managed (fixed) environments are considered, users will have more confidence in prediction for them but will not be overconfident in prediction in the target (random) environments. Genetic gain (predicted response to selection in the target environments from the managed environments) is independent of formulation.

Comparison of identity by descent and identity by state for detecting genetic regions under selection in a sorghum pedigree breeding program

Seventy sorghum inbred lines which formed part of the Queensland Department of Primary Industries (QDPI) sorghum breeding program were screened with 104 previously mapped RFLP markers. The lines were related by pedigree and consisted of ancestral source lines, intermediate lines and recent releases from the program. We compared the effect of defining marker alleles using either identity by state (IBS) or identity by descent (IBD) on our capacity to trace markers through the pedigree and detect evidence of selection for particular alleles. Allelic identities defined using IBD were much more sensitive for detecting non-Mendelian segregation in this pedigree. Only one marker allele showed significant evidence of selection when IBS was used compared with ten regions with particular allelic identities when IBD was used. Regions under selection were compared with the location of QTLs for agronomic traits known to be under selection in the breeding program. Only two of the ten regions were associated with known QTLs that matched with knowledge of the agronomic characteristics of the ancestral lines. Some of the other regions were hypothesised to be associated with genes for particular traits based on the properties of the ancestral source lines.

Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence

Topological measures of large-scale complex networks are applied to a specific artificial regulatory network model created through a whole genome duplication and divergence mechanism. This class of networks share topological features with natural transcriptional regulatory networks. Specifically, these networks display scale-free and small-world topology and possess subgraph distributions similar to those of natural networks. Thus, the topologies inherent in natural networks may be in part due to their method of creation rather than being exclusively shaped by subsequent evolution under selection. The evolvability of the dynamics of these networks is also examined by evolving networks in simulation to obtain three simple types of output dynamics. The networks obtained from this process show a wide variety of topologies and numbers of genes indicating that it is relatively easy to evolve these classes of dynamics in this model. (c) 2006 Elsevier Ireland Ltd. All rights reserved.

Finite mixture regression model with random effects: application to neonatal hospital length of stay

A two-component mixture regression model that allows simultaneously for heterogeneity and dependency among observations is proposed. By specifying random effects explicitly in the linear predictor of the mixture probability and the mixture components, parameter estimation is achieved by maximising the corresponding best linear unbiased prediction type log-likelihood. Approximate residual maximum likelihood estimates are obtained via an EM algorithm in the manner of generalised linear mixed model (GLMM). The method can be extended to a g-component mixture regression model with the component density from the exponential family, leading to the development of the class of finite mixture GLMM. For illustration, the method is applied to analyse neonatal length of stay (LOS). It is shown that identification of pertinent factors that influence hospital LOS can provide important information for health care planning and resource allocation. (C) 2002 Elsevier Science B.V. All rights reserved.

A Score Test for Zero-Inflation in Correlated Count Data

To account for the preponderance of zero counts and simultaneous correlation of observations, a class of zero-inflated Poisson mixed regression models is applicable for accommodating the within-cluster dependence. In this paper, a score test for zero-inflation is developed for assessing correlated count data with excess zeros. The sampling distribution and the power of the test statistic are evaluated by simulation studies. The results show that the test statistic performs satisfactorily under a wide range of conditions. The test procedure is further illustrated using a data set on recurrent urinary tract infections. Copyright (c) 2005 John Wiley & Sons, Ltd.

Remotely sensed data for ecosystem analyses: Combining hierarchy and scene models

Remotely sensed data have been used extensively for environmental monitoring and modeling at a number of spatial scales; however, a limited range of satellite imaging systems often. constrained the scales of these analyses. A wider variety of data sets is now available, allowing image data to be selected to match the scale of environmental structure(s) or process(es) being examined. A framework is presented for use by environmental scientists and managers, enabling their spatial data collection needs to be linked to a suitable form of remotely sensed data. A six-step approach is used, combining image spatial analysis and scaling tools, within the context of hierarchy theory. The main steps involved are: (1) identification of information requirements for the monitoring or management problem; (2) development of ideal image dimensions (scene model), (3) exploratory analysis of existing remotely sensed data using scaling techniques, (4) selection and evaluation of suitable remotely sensed data based on the scene model, (5) selection of suitable spatial analytic techniques to meet information requirements, and (6) cost-benefit analysis. Results from a case study show that the framework provided an objective mechanism to identify relevant aspects of the monitoring problem and environmental characteristics for selecting remotely sensed data and analysis techniques.

Modelling inpatient length of stay by a hierarchical mixture regression via the EM algorithm

The modelling of inpatient length of stay (LOS) has important implications in health care studies. Finite mixture distributions are usually used to model the heterogeneous LOS distribution, due to a certain proportion of patients sustaining-a longer stay. However, the morbidity data are collected from hospitals, observations clustered within the same hospital are often correlated. The generalized linear mixed model approach is adopted to accommodate the inherent correlation via unobservable random effects. An EM algorithm is developed to obtain residual maximum quasi-likelihood estimation. The proposed hierarchical mixture regression approach enables the identification and assessment of factors influencing the long-stay proportion and the LOS for the long-stay patient subgroup. A neonatal LOS data set is used for illustration, (C) 2003 Elsevier Science Ltd. All rights reserved.

Feeding ecology of the fish ectoparasite Gnathia sp. (Crustacea: Isopoda) from the Great Barrier Reef, and its implications for fish cleaning behaviour

The feeding rate of a parasitic gnathiid isopod on fish was examined. Individual fish, Hemigymnus melapterus, were exposed to gnathiid larvae and sampled after 5, 10, 30, 60, and 240 min. I recorded whether larvae had an engorged gut, an engorged gut containing red material, or had dropped off the fish after having completed engorgement; variation among sampling times and larval stages was analyzed using generalized linear mixed model analyses. The likelihood that larvae had an engorged gut increased with time and varied with larval stage. First stage (1.45 mm) larvae. After 30 min, however, most (>93%) larvae had an engorged gut regardless of their larval stage. The likelihood of red material in the gut of third stage larvae increased over time (46% after 30 min, 70% after 60 min, and 86% after 240 min) while that of first and second stage larvae remained relatively low (

Analysis of Melanoma Onset: Assessing Familial Aggregation by Using Estimating Equations and Fitting Variance Components via Bayesian Random Effects Models

We investigate whether relative contributions of genetic and shared environmental factors are associated with an increased risk in melanoma. Data from the Queensland Familial Melanoma Project comprising 15,907 subjects arising from 1912 families were analyzed to estimate the additive genetic, common and unique environmental contributions to variation in the age at onset of melanoma. Two complementary approaches for analyzing correlated time-to-onset family data were considered: the generalized estimating equations (GEE) method in which one can estimate relationship-specific dependence simultaneously with regression coefficients that describe the average population response to changing covariates; and a subject-specific Bayesian mixed model in which heterogeneity in regression parameters is explicitly modeled and the different components of variation may be estimated directly. The proportional hazards and Weibull models were utilized, as both produce natural frameworks for estimating relative risks while adjusting for simultaneous effects of other covariates. A simple Markov Chain Monte Carlo method for covariate imputation of missing data was used and the actual implementation of the Bayesian model was based on Gibbs sampling using the free ware package BUGS. In addition, we also used a Bayesian model to investigate the relative contribution of genetic and environmental effects on the expression of naevi and freckles, which are known risk factors for melanoma.

Large-eddy simulation of heat transfer downstream of a backward-facing step

Large-eddy simulation is used to predict heat transfer in the separated and reattached flow regions downstream of a backward-facing step. Simulations were carried out at a Reynolds number of 28 000 (based on the step height and the upstream centreline velocity) with a channel expansion ratio of 1.25. The Prandtl number was 0.71. Two subgrid-scale models were tested, namely the dynamic eddy-viscosity, eddy-diffusivity model and the dynamic mixed model. Both models showed good overall agreement with available experimental data. The simulations indicated that the peak in heat-transfer coefficient occurs slightly upstream of the mean reattachment location, in agreement with experimental data. The results of these simulations have been analysed to discover the mechanisms that cause this phenomenon. The peak in heat-transfer coefficient shows a direct correlation with the peak in wall shear-stress fluctuations. It is conjectured that the peak in these fluctuations is caused by an impingement mechanism, in which large eddies, originating in the shear layer, impact the wall just upstream of the mean reattachment location. These eddies cause a 'downwash', which increases the local heat-transfer coefficient by bringing cold fluid from above the shear layer towards the wall.

Consumption habit and international stock returns

We use the consumption-based asset pricing model with habit formation to study the predictability and cross-section of returns from the international equity markets. We find that the predictability of returns from many developed countries' equity markets is explained in part by changing prices of risks associated with consumption relative to habit at the world as well as local levels. We also provide an exploratory investigation of the cross-sectional implications of the model under the complete world market integration hypothesis and find that the model performs mildly better than the traditional consumption-based model. the unconditional and conditional world CAPMs and a three-factor international asset pricing model. (C) 2004 Elsevier B.V. All rights reserved.

Modelling of entrainment in industrial flotation cells: the effect of solids suspension

Solids concentration and particle size distribution gradually change in the vertical dimension of industrial flotation cells, subject primarily to the flotation cell size and design and the cell operating conditions. As entrainment is a two-step process and involves only the suspended solids in the top pulp region near the pulp-froth interface, the solids suspension characteristics have a significant impact on the overall entrainment. In this paper, a classification function is proposed to describe the state of solids suspension in flotation cells, similar to the definition of degree of entrainment for classification in the froth phase found in the literature. A mathematical model for solids suspension is also developed, in which the classification function is expressed as an exponential function of the particle size. Experimental data collected from three different Outokumpu tank flotation cells in three different concentrators are well fitted by the proposed exponential model. Under the prevailing experimental conditions, it was found that the solids content in the top region was relatively independent of cell operating conditions such as froth height and air rate but dependent on the cell size. Moreover, the results obtained from the total solids tend to be similar to those from a particular gangue mineral and hence may be applied to all minerals in entrainment calculation. (C) 2004 Elsevier Ltd. All rights reserved.

A reassessment of genetic limits to evolutionary change

An absence of genetic variance in traits under selection is perhaps the oldest explanation for a limit to evolutionary change, but has also been the most easily dismissed. We review a range of theoretical and empirical results covering single traits to more complex multivariate systems, and show that an absence of genetic variance may be more common than is currently appreciated. From a single-trait perspective, we highlight that it is becoming clear that some trait types do not display significant levels of genetic variation, and we raise the possibility that species with restricted ranges may differ qualitatively from more widespread species in levels of genetic variance in ecologically important traits. A common misconception in many life-history studies is that a lack of genetic variance in single traits, and genetic constraints as a consequence of bivariate genetic correlations, are different causes of selection limits. We detail how interpretations of bivariate patterns are unlikely to demonstrate genetic limits to selection in many cases. We advocate a multivariate definition of genetic constraints that emphasizes the presence (or otherwise) of genetic variance in the multivariate direction of selection. For multitrait systems, recent results using longer term studies of organisms, in which more is understood concerning what traits may be under selection, have indicated that selection may exhaust genetic variance, resulting in a limit to the selection response.

Ventilatory changes following head-up tilt and standing in healthy subjects

Passive tilting increases ventilation in healthy subjects; however, controversy surrounds the proposed mechanism. This study is aimed to evaluate the possible mechanism for changes to ventilation following passive head-up tilt (HUT) and active standing by comparison of a range of ventilatory, metabolic and mechanical parameters. Ventilatory parameters (V (T), V (E), V (E)/VO2, V (E)/VCO2, f and PetCO(2)), functional residual capacity (FRC), respiratory mechanics with impulse oscillometry; oxygen consumption (VO2) and carbon dioxide production (VCO2) were measured in 20 healthy male subjects whilst supine, following HUT to 70 degrees and unsupported standing. Data were analysed using a linear mixed model. HUT to 70 degrees from supine increased minute ventilation (V (E)) (P < 0.001), tidal volume (V (T)) (P=0.001), ventilatory equivalent for O-2 (V (E)/VO2) (P=0.020) and the ventilatory equivalent for CO2 (V (E)/VCO2) (P < 0.001) with no change in f (P=0.488). HUT also increased FRC (P < 0.001) and respiratory system reactance (X5Hz) (P < 0.001) with reduced respiratory system resistance (R5Hz) (P=0.004) and end-tidal carbon dioxide (PetCO(2)) (P < 0.001) compared to supine. Standing increased V (E) (P < 0.001), V (T) (P < 0.001) and V (E)/VCO2 (P=0.020) with no change in respiratory rate (f) (P=0.065), V (E)/VO2 (P=0.543). Similar changes in FRC (P < 0.001), R5Hz (P=0.013), X5Hz (P < 0.001) and PetCO(2) (P < 0.001) compared to HUT were found. In contrast to HUT, standing increased VO2 (P=0.002) and VCO2 (P=0.048). The greater increase in V (E) in standing compared to HUT appears to be related to increased VO2 and VCO2 associated with increased muscle activity in the unsupported standing position. This has implications for exercise prescription and rehabilitation of critically ill patients who have reduced cardiovascular and respiratory reserve.

The rellationship between specific features of aphasia-friendly written material and comprehension of written material for people with aphasia: An exploratory study

Background: Written material is often inaccessible fro people with aphasia. The format of written material needs to be adapted to enable people with aphasia to read with understanding. Aims: This study aimed to further explore some issues raised in Rose, Worrall, and MacKenna (2003) concerning the effects of aphasia-friendly formats on the reading comprehension of people with aphasia. It was hypothesised that people with aphasia would comprehend significantly more paragraphs that were formatted in an aphasia-friendly manner than control paragraphs. This study also aimed to investigate if each single aspect of aphasia-friendly formatting (i.e., simplified vocabulary and syntax, large print, increased white spacem and pictures) used in isolation would result in increased comprehension compared to control paragraphs. Other aims were to compare the effect of aphasia-friendly fromatting with the effects of each single adaptation, and to investigate if the effects of aphasia-friendly formates were related to aphasia severity. Methods & Procedures: Participants with mild to moderately severe aphasia (N = 9) read a battery of 90 paragraphs and selected the best word of phrase from a choice of four to complete each paragraph. A linear mixed model (p < .05) was used to analyse the differences in reading comprehension with each paragraph fromat across three reading grade levels. Outcomes & Results: People with aphasia comprehended significantly more aphasia-friendly paragraphs than control paragraphs. They also comprehended significantly more paragraphs with each of the following single adaptations: simplified vocabulary and syntax, large ptint, and increased white spaces. Although people with aphasia tended to comprehend more paragraphs with pictures added than control paragraphs, this difference was not significant. No significant correlation between aphasia severity and the effect of aphasia-friendly formatting was found. Conclusion: This study supports the idea that aphasia-friendly formats increase the reading comprehension of people with aphasia. It suggests that adding pictures, particularly Clip Art pictures, may not significantly improve the reading the reading comprehension of people with aphasia. These findings have implications for all written communication with people with aphasia, both in the clinical setting and in the wider community. Applying these findings may enable people with aphasia to have equal access to written information and to participate in society.