Factor-Analytic Variance-Covariance Structures for Prediction Into a Target Population of Environments.

Finlay-Wilkinson regression is a popular method for modeling genotype-environment interaction in plant breeding and crop variety testing. When environment is a random factor, this model may be cast as a factor-analytic variance-covariance structure, implying a regression on random latent environmental variables. This paper reviews such models with a focus on their use in the analysis of multi-environment trials for the purpose of making predictions in a target population of environments.

The use of fixed study main effects in arm-based network meta-analysis.

Methods of network meta-analysis (NMA) can be classified as arm-based and contrast-based approaches. There are several arm-based approaches, and some of these have been criticized because they recover inter-study information and hence do not obey the principle of concurrent control. Here, we point out that recovery of inter-study information in arm-based NMA can be prevented by fitting a fixed main effect for studies.

Two-dimensional P-spline smoothing for spatial analysis of plant breeding trials.

Large agricultural field trials may display irregular spatial trends that cannot be fully captured by a purely randomization-based analysis. For this reason, paralleling the development of analysis-of-variance procedures for randomized field trials, there is a long history of spatial modeling for field trials, starting with the early work of Papadakis on nearest neighbor analysis, which can be cast in terms of first or second differences among neighboring plot values. This kind of spatial modeling is amenable to a natural extension using splines, as has been demonstrated in recent publications in the field.

Regression models for order-of-addition experiments.

The purpose of order-of-addition (OofA) experiments is to identify the best order in a sequence of m components in a system. Such experiments may be analyzed by various regression models, the most popular ones being based on pairwise ordering (PWO) factors or on component-position (CP) factors. This paper reviews these models and extensions and proposes a new class of models based on response surface (RS) regression using component position numbers as predictor variables.

Neighbor balance and evenness of distribution of treatment replications in row-column designs.

Row-column designs allow error control in field experiments by blocking in two dimensions. While this strategy can capture spatial heterogeneity aligned with blocks and account for effects due to the farming operations along rows and columns, it suffers from the occasional clustered occurrence of several replications of the same treatment. This property of classical row-column designs has hampered their more widespread use in practice.

Estimating the variance for heterogeneity in arm-based network meta-analysis.

Network meta-analysis can be implemented by using arm-based or contrast-based models. Here we focus on arm-based models and fit them using generalized linear mixed model procedures. Full maximum likelihood (ML) estimation leads to biased trial-by-treatment interaction variance estimates for heterogeneity.

Inter-block information: to recover or not to recover it?

Comparing standard errors of treatment differences using fixed or random block effects with the approximation of Kackar and Harville helps in choosing the preferable assumption for blocks in the analysis of field experiments. Blocked designs are common in plant breeding field trials. Depending on the precision of variance estimates, recovery of inter-block information via random block effects may be worthwhile.

Postprandial adiponectin and gelatinase response to a high-fat versus an isoenergetic low-fat meal in lean, healthy men.

Objective: Evidence suggests that an acute systemic inflammatory response is invoked after consumption of a high-energy meal. Postprandial regulation of adiponectin, an adipose tissue-derived, anti-inflammatory hormone, and the gelatinases, matrix metalloproteinase (MMP)-2 and MMP-9, endopeptidases implicated in a diverse range of inflammatory processes, remain inconclusive. The aim of this study was to assess the postprandial effect of a high-energy (1212 kcal) meal on plasma adiponectin, MMP-2 and MMP-9 activity, glucose, insulin, triacylglycerols, total cholesterol, high-density lipoprotein cholesterol, and the differential effects on these parameters depending on whether the test meal was high fat (HF; 46 g fat, 1210 kcal) or isoenergetic and low fat (LF; 15 g fat, 1214 kcal energy).

Multiplicative interaction in network meta-analysis.

Meta-analysis of a set of clinical trials is usually conducted using a linear predictor with additive effects representing treatments and trials. Additivity is a strong assumption. In this paper, we consider models for two or more treatments that involve multiplicative terms for interaction between treatment and trial.

Risk factors for acute respiratory infection in the Australian community.

Objectives: The objective of this study was to identify the risk factors for ARI in the Australian community.

Methods: We used a national survey of 7578 randomly selected respondents in 2008-2009 to identify the risk factors of ARI. A case was defined as a person experiencing cold or flu with one or more symptoms of: fever, chills, sore throat, runny nose, or cough in the previous four weeks.

Efficiency of augmented p-rep designs in multi-environmental trials.

The paper shows that unreplicated designs in multi-environmental trials are most efficient. If replication per environment is needed then augmented p-rep designs outperform augmented and replicated designs in triticale and maize. In plant breeding, augmented designs with unreplicated entries are frequently used for early generation testing.

Soil warming increases plant species richness but decreases germination from the alpine soil seed bank.

Global warming is occurring more rapidly above the treeline than at lower elevations and alpine areas are predicted to experience above average warming in the future. Temperature is a primary factor in stimulating seed germination and regulating changes in seed dormancy status. Thus, plant regeneration from seed will be crucial to the persistence, migration and post disturbance recruitment of alpine plants in future climates.

Associations between the sensory attributes and volatile composition of Cabernet Sauvignon wines and the volatile composition of the grapes used for their production.

The sensory properties of wine are influenced by the chemical composition of the grapes used to produce them. Identification of grape and wine chemical markers associated with the attributes perceived by the consumer of the wine will enable better prediction of the potential of a parcel of grapes to produce wine of a certain flavor. This study explores the relationships between Cabernet Sauvignon grape volatile composition and wine volatile profiles with the sensory properties of wines.

Augmented p-rep designs.

Early generation variety trials are very important in plant and tree breeding programs. Typically many entries are tested, often with very little resources available. Unreplicated trials using control plots are popular and it is common to repeat the trials at a number of locations.

Nearest neighbour adjustment and linear variance models in plant breeding trials.

This paper reviews methods for nearest neighbour analysis that adjust for local trend in one dimension. Such methods are commonly used in plant breeding and variety testing. The focus is on simple differencing methods, including first differences and the Papadakis method.

A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus.

Background: Eucalypts are the most widely planted hardwood trees in the world occupying globally more than 18 million hectares as an important source of carbon neutral renewable energy and raw material for pulp, paper and solid wood. Quantitative Trait Loci (QTLs) in Eucalyptus have been localized on pedigree-specific RAPD or AFLP maps seriously limiting the value of such QTL mapping efforts for molecular breeding. The availability of a genus-wide genetic map with transferable microsatellite markers has become a must for the effective advancement of genomic undertakings.