Statnote 28:Canonical Variate Analysis (CVA)

The pattern of correlation between two sets of variables can be tested using canonical variate analysis (CVA). CVA, like principal components analysis (PCA) and factor analysis (FA) (Statnote 27, Hilton & Armstrong, 2011b), is a multivariate analysis Essentially, as in PCA/FA, the objective is to determine whether the correlations between two sets of variables can be explained by a smaller number of ‘axes of correlation’ or ‘canonical roots’.

Canonical discriminant analysis applied to broiler chicken performance

The mechanisms involved in the control of growth in chickens are too complex to be explained only under univariate analysis because all related traits are biologically correlated. Therefore, we evaluated broiler chicken performance under a multivariate approach, using the canonical discriminant analysis. A total of 1920 chicks from eight treatments, defined as the combination of four broiler chicken strains (Arbor Acres, AgRoss 308, Cobb 500 and RX) from both sexes, were housed in 48 pens. Average feed intake, average live weight, feed conversion and carcass, breast and leg weights were obtained for days 1 to 42. Canonical discriminant analysis was implemented by SAS((R)) CANDISC procedure and differences between treatments were obtained by the F-test (P < 0.05) over the squared Mahalanobis` distances. Multivariate performance from all treatments could be easily visualised because one graph was obtained from two first canonical variables, which explained 96.49% of total variation, using a SAS((R)) CONELIP macro. A clear distinction between sexes was found, where males were better than females. Also between strains, Arbor Acres, AgRoss 308 and Cobb 500 (commercial) were better than RX (experimental), Evaluation of broiler chicken performance was facilitated by the fact that the six original traits were reduced to only two canonical variables. Average live weight and carcass weight (first canonical variable) were the most important traits to discriminate treatments. The contrast between average feed intake and average live weight plus feed conversion (second canonical variable) were used to classify them. We suggest analysing performance data sets using canonical discriminant analysis.

The use of canonical correlation analysis to assess the relationship between executive functioning and verbal memory in older adults

Executive functioning (EF), which is considered to govern complex cognition, and verbal memory (VM) are constructs assumed to be related. However, it is not known the magnitude of the association between EF and VM, and how sociodemographic and psychological factors may affect this relationship, including in normal aging. In this study, we assessed different EF and VM parameters, via a battery of neurocognitive/psychological tests, and performed a Canonical Correlation Analysis (CCA) to explore the connection between these constructs, in a sample of middle- aged and older healthy individuals without cognitive impairment (N = 563, 50+ years of age). The analysis revealed a positive and moderate association between EF and VM independently of gender, age, education, global cognitive performance level, and mood. These results confirm that EF presents a significant association with VM performance.

Canonical correspondence analysis in social science research

The use of simple and multiple correspondence analysis is well-established in socialscience research for understanding relationships between two or more categorical variables.By contrast, canonical correspondence analysis, which is a correspondence analysis with linearrestrictions on the solution, has become one of the most popular multivariate techniques inecological research. Multivariate ecological data typically consist of frequencies of observedspecies across a set of sampling locations, as well as a set of observed environmental variablesat the same locations. In this context the principal dimensions of the biological variables aresought in a space that is constrained to be related to the environmental variables. Thisrestricted form of correspondence analysis has many uses in social science research as well,as is demonstrated in this paper. We first illustrate the result that canonical correspondenceanalysis of an indicator matrix, restricted to be related an external categorical variable, reducesto a simple correspondence analysis of a set of concatenated (or stacked ) tables. Then weshow how canonical correspondence analysis can be used to focus on, or partial out, aparticular set of response categories in sample survey data. For example, the method can beused to partial out the influence of missing responses, which usually dominate the results of amultiple correspondence analysis.

Generalized canonical correlation analysis of matrices with different row and column orders

A Method is offered that makes it possible to apply generalized canonicalcorrelations analysis (CANCOR) to two or more matrices of different row and column order. The new method optimizes the generalized canonical correlationanalysis objective by considering only the observed values. This is achieved byemploying selection matrices. We present and discuss fit measures to assessthe quality of the solutions. In a simulation study we assess the performance of our new method and compare it to an existing procedure called GENCOM,proposed by Green and Carroll. We find that our new method outperforms the GENCOM algorithm both with respect to model fit and recovery of the truestructure. Moreover, as our new method does not require any type of iteration itis easier to implement and requires less computation. We illustrate the methodby means of an example concerning the relative positions of the political parties inthe Netherlands based on provincial data.

Bootstrap confidence regions for canonical variates: Application to studies of evolutionary differentiation

Theory recently developed to construct confidence regions based on the parametric bootstrap is applied to add inferential information to graphical displays of sample centroids in canonical variate analysis. Problems of morphometric differentiation among subspecies and species are addressed using numerical resampling procedures.

Canonical Correlation Analysis for Interpreting Airborne Laser Scanning Metrics along the Lorenz Curve of Tree Size Inequality

Canonical Correlation Analysis for Interpreting Airborne Laser Scanning Metrics along the Lorenz Curve of Tree Size Inequality

Morphometric discrimination of females of five species of Anopheles of the subgenus Nyssorhynchus from Southern and Northwest Colombia

The most important vectors of human Plasmodium in the neotropics belong to the subgenus Nyssorhynchus. These species are generally sympatric in terms of their geographical distributions. Some are difficult to identify based solely on examination of adult females using the available morphological keys, in these cases examination of immature stages and male genitalia is required to make correct determinations. However, in epidemiological studies it is necessary to identify the species of adult females which are found near humans, i.e. in studies of malaria transmission or evaluation of control measures. The purpose of the present study was to evaluate the discrimination of adult females of different species of Nyssorhynchus isolated mainly from Southern Colombia (department of Putumayo), using morphometric analysis. Adult females were obtained after rearing larvae collected in natural breeding places and from the progeny of females collected on humans. The morphological characteristics of the immature stages allowed the identification of four species of the subgroup Oswaldoi from Southern Colombia: Anopheles rangeli Gabaldon, Cova Garcia & Lopez, An. oswaldoi (Peryassu), An. benarrochi Gabaldon, Cova Garcia & Lopez and An. triannulatus (Neiva & Pinto). The species An. nuneztovari (Gabaldon) from the Northwest of Colombia was included for comparison. Morphometric analysis allowed differentiation of the females of all species to a confidence level approaching 90% using principal components analysis of 10 wing and leg variables, followed by canonical variate analysis of the first four principal components. We conclude that morphometrics may represent a useful taxonomic tool for this group and that its use should be further studied.

Basal ganglia-cortical structural connectivity in Huntington's disease.

Huntington's disease is an incurable neurodegenerative disease caused by inheritance of an expanded cytosine-adenine-guanine (CAG) trinucleotide repeat within the Huntingtin gene. Extensive volume loss and altered diffusion metrics in the basal ganglia, cortex and white matter are seen when patients with Huntington's disease (HD) undergo structural imaging, suggesting that changes in basal ganglia-cortical structural connectivity occur. The aims of this study were to characterise altered patterns of basal ganglia-cortical structural connectivity with high anatomical precision in premanifest and early manifest HD, and to identify associations between structural connectivity and genetic or clinical markers of HD. 3-Tesla diffusion tensor magnetic resonance images were acquired from 14 early manifest HD subjects, 17 premanifest HD subjects and 18 controls. Voxel-based analyses of probabilistic tractography were used to quantify basal ganglia-cortical structural connections. Canonical variate analysis was used to demonstrate disease-associated patterns of altered connectivity and to test for associations between connectivity and genetic and clinical markers of HD; this is the first study in which such analyses have been used. Widespread changes were seen in basal ganglia-cortical structural connectivity in early manifest HD subjects; this has relevance for development of therapies targeting the striatum. Premanifest HD subjects had a pattern of connectivity more similar to that of controls, suggesting progressive change in connections over time. Associations between structural connectivity patterns and motor and cognitive markers of disease severity were present in early manifest subjects. Our data suggest the clinical phenotype in manifest HD may be at least partly a result of altered connectivity. Hum Brain Mapp 36:1728-1740, 2015. © 2015 Wiley Periodicals, Inc.

Effects of genotype and environment on free amino acid levels in wheat grain: implications for acrylamide formation during processing

Acrylamide forms from free asparagine and reducing sugars during cooking, with asparagine concentration being the key parameter determining the formation in foods produced from wheat flour. In this study free amino acid concentrations were measured in the grain of varieties Spark and Rialto and four doubled haploid lines from a Spark x Rialto mapping population. The parental and doubled haploid lines had differing levels of total free amino acids and free asparagine in the grain, with one line consistently being lower than either parent for both of these factors. Sulfur deprivation led to huge increases in the concentrations of free asparagine and glutamine, and canonical variate analysis showed clear separation of the grain samples as a result of treatment (environment, E) and genotype (G) and provided evidence of G x E interactions. Low grain sulfur and high free asparagine concentration were closely associated with increased risk of acrylamide formation. G, E, and G x E effects were also evident in grain from six varieties of wheat grown at field locations around the United Kingdom in 2006 and 2007. The data indicate that progress in reducing the risk of acrylamide formation in processed wheat products could be made immediately through the selection and cultivation of low grain asparagme varieties and that further genetically driven improvements should be achievable. However, genotypes that are selected should also be tested under a range of environmental conditions.

Orthogonal projections and bootstrap resampling procedures in the study of infraspecific variation

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

Density and spatial pattern of the neuropathological changes in the cerebellum in the prion disease variant Creutzfeldt-Jakob disease (vCJD)

The objective of this chapter is to quantify the neuropathology of the cerebellar cortex in cases of the prion disease variant Creutzfeldt-Jakob disease (vCJD). Hence, sequential sections of the cerebellum of 15 cases of vCJD were stained with H/E, or immunolabelled with a monoclonal antibody 12F10 against prion protein (PrP) and studied using quantitative techniques and spatial pattern analysis. A significant loss of Purkinje cells was evident in all cases. Densities of the vacuolation and the protease resistant form of prion protein (PrPSc) in the form of diffuse and florid plaques were greater in the granule cell layer (GL) than the molecular layer (ML). In the ML, vacuoles and PrPSc plaques, occurred in clusters which were regularly distributed along the folia, larger clusters of vacuoles and diffuse plaques being present in the GL. There was a negative spatial correlation between the vacuoles and the surviving Purkinje cells in the ML and a positive spatial correlation between the clusters of vacuoles and the diffuse PrPSc plaques in the ML and GL in five and six cases respectively. A canonical variate analysis (CVA) suggested a negative correlation between the densities of the vacuolation in the GL and the diffuse PrPSc plaques in the ML. The data suggest: 1) all laminae of the cerebellar cortex were affected by the pathology of vCJD, the GL more severely than the ML, 2) the pathology was topographically distributed especially in the Purkinje cell layer and GL, 3) pathological spread may occur in relation to a loop of anatomical projections connecting the cerebellum, thalamus, cerebral cortex, and pons, and 4) there are differences in the pathology of the cerebellum in vCJD compared with the M/M1 subtype of sporadic CJD (sCJD).

The natural plant stress elicitor cis-jasmone causes cultivar-dependent reduction in growth of the stink bug, Euschistus heros and associated changes in flavonoid concentrations in soybean, Glycine max.

To test the hypothesis that the plant stress related elicitor cis-jasmone (cJ) provides protection in soybean pods against the seed-sucking stink bug pest, Euschistus heros, the growth of E. heros on cJ-treated pods was investigated using three soybean cultivars differing in insect susceptibility, i.e. BRS 134 (susceptible), IAC 100 (resistant) and Dowling (resistant). E. heros showed reduced weight gain when fed cJ-treated Dowling, whereas no effect on weight gain was observed when fed other treated cultivars. Using analysis of variance, a three factor (cultivar x treatment x time) interaction was observed with concentrations of the flavonoid glycosides daidzin and genistin, and their corresponding aglycones, daidzein and genistein. There were increases in genistein and genistin concentrations in cJ-treated Dowling at 144 and 120 h post treatment, respectively. Higher concentrations of malonyldaidzin and malonylgenistin in Dowling, compared to BRS 134 and IAC 100, were observed independently of time, the highest concentrations being observed in cJ-treated seeds. Levels of glycitin and malonylglycitin were higher in BRS 134 and IAC 100 compared to Dowling. Canonical variate analysis indicated daidzein (in the first two canonical variates) and genistein (in the first only) as important discriminatory variables. These results suggest that cJ treatment leads to an increase in the levels of potentially defensive isoflavonoids in immature soybean seeds, but the negative effect upon E. heros performance is cultivar-dependent.