Statnote 13: a more complex analysis of variance incorporating a 'repeated measures' factor

Experiments combining different groups or factors and which use ANOVA are a powerful method of investigation in applied microbiology. ANOVA enables not only the effect of individual factors to be estimated but also their interactions; information which cannot be obtained readily when factors are investigated separately. In addition, combining different treatments or factors in a single experiment is more efficient and often reduces the sample size required to estimate treatment effects adequately. Because of the treatment combinations used in a factorial experiment, the degrees of freedom (DF) of the error term in the ANOVA is a more important indicator of the ‘power’ of the experiment than the number of replicates. A good method is to ensure, where possible, that sufficient replication is present to achieve 15 DF for the error term of the ANOVA testing effects of particular interest. Finally, it is important to always consider the design of the experiment because this determines the appropriate ANOVA to use. Hence, it is necessary to be able to identify the different forms of ANOVA appropriate to different experimental designs and to recognise when a design is a split-plot or incorporates a repeated measure. If there is any doubt about which ANOVA to use in a specific circumstance, the researcher should seek advice from a statistician with experience of research in applied microbiology.

What counts versus what can be counted:the complex interplay of market orientation and marketing performance measurement

Market orientation (MO) and marketing performance measurement (MPM) are two of the most widespread strategic marketing concepts among practitioners. However, some have questioned the benefits of extensive investments in MO and MPM. More importantly, little is known about which combinations of MO and MPM are optimal in ensuring high business performance. To address this research gap, the authors analyze a unique data set of 628 firms with a novel method of configurational analysis: fuzzy-set qualitative comparative analysis. In line with prior research, the authors find that MO is an important determinant of business performance. However, to reap its benefits, managers need to complement it with appropriate MPM, the level and focus of which vary across firms. For example, whereas large firms and market leaders generally benefit from comprehensive MPM, small firms may benefit from measuring marketing performance only selectively or by focusing on particular dimensions of marketing performance. The study also finds that many of the highest-performing firms do not follow any of the particular best practices identified.

3D reconstruction of complex dielectric function of the glass during the femtosecond micro-fabrication

We measure complex amplitude of scattered wave in the far field, and justify theoretically and numerically solution of the inverse scattering problem. This allows single-shot reconstructing of dielectric function distribution during direct femtosecond laser micro-fabrication.

Managing uncertainty in complex stochastic models: design and emulation of a Rabies model

In this paper we present a novel method for emulating a stochastic, or random output, computer model and show its application to a complex rabies model. The method is evaluated both in terms of accuracy and computational efficiency on synthetic data and the rabies model. We address the issue of experimental design and provide empirical evidence on the effectiveness of utilizing replicate model evaluations compared to a space-filling design. We employ the Mahalanobis error measure to validate the heteroscedastic Gaussian process based emulator predictions for both the mean and (co)variance. The emulator allows efficient screening to identify important model inputs and better understanding of the complex behaviour of the rabies model.

From detection of complex motion to descriptions of moving surfaces in human vision

A preliminary study by Freeman et al (1996b) has suggested that when complex patterns of motion elicit impressions of 2-dimensionality, odd-item-out detection improves given targets can be differentiated on the basis of surface properties. Their results can be accounted for, it if is supposed that observers are permitted efficient access to 3-D surface descriptions but access to 2-D motion descriptions is restricted. To test the hypothesis, a standard search technique was employed, in which targets could be discussed on the basis of slant sign. In one experiment, slant impressions were induced through the summing of deformation and translation components. In a second theory were induced through the summing of shear and translation components. Neither showed any evidence of efficient access. A third experiment explored the possibility that access to these representations may have been hindered by a lack of grouping between the stimuli. Attempts to improve grouping failed to produce convincing evidence in support of life. An alternative explanation is that complex patterns of motion are simply not processed simultaneously. Psychophysical and physiological studies have, however, suggested that multiple mechanisms selective for complex motion do exist. Using a subthreshold summation technique I found evidence supporting the notion that complex motions are processed in parallel. Furthermore, in a spatial summation experiment, coherence thresholds were measured for displays containing different numbers of complex motion patches. Consistent with the idea that complex motion processing proceeds in parallel, increases in the number of motion patches were seen to decrease thresholds, both for expansion and rotation. Moreover, the rates of decrease were higher than those typically expected from probability summation, thus implying mechanisms are available, which can pool signals from spatially distinct complex motion flows.

3D reconstruction of complex dielectric function of the glass during the femtosecond micro-fabrication

We measure complex amplitude of scattered wave in the far field, and justify theoretically and numerically solution of the inverse scattering problem. This allows single-shot reconstructing of dielectric function distribution during direct femtosecond laser micro-fabrication.

3D reconstruction of complex dielectric function of the glass during the femtosecond micro-fabrication

We measure complex amplitude of scattered wave in the far field, and justify theoretically and numerically solution of the inverse scattering problem. This allows single-shot reconstructing of dielectric function distribution during direct femtosecond laser micro-fabrication.

Quantitative online prediction of peptide binding to the major histocompatibility complex

With its implications for vaccine discovery, the accurate prediction of T cell epitopes is one of the key aspirations of computational vaccinology. We have developed a robust multivariate statistical method, based on partial least squares, for the quantitative prediction of peptide binding to major histocompatibility complexes (MHC), the principal checkpoint on the antigen presentation pathway. As a service to the immunobiology community, we have made a Perl implementation of the method available via a World Wide Web server. We call this server MHCPred. Access to the server is freely available from the URL: http://www.jenner.ac.uk/MHCPred. We have exemplified our method with a model for peptides binding to the common human MHC molecule HLA-B*3501.

APP controls the formation of PI(3,5)P2 vesicles through its binding of the PIKfyve complex

Phosphoinositides are signalling lipids that are crucial for major signalling events as well as established regulators of membrane trafficking. Control of endosomal sorting and endosomal homeostasis requires phosphatidylinositol-3-phosphate (PI(3)P) and phosphatidylinositol-3,5-bisphosphate (PI(3,5)P2), the latter a lipid of low abundance but significant physiological relevance. PI(3,5)P2 is formed by phosphorylation of PI(3)P by the PIKfyve complex which is crucial for maintaining endosomal homeostasis. Interestingly, loss of PIKfyve function results in dramatic neurodegeneration. Despite the significance of PIKfyve, its regulation is still poorly understood. Here we show that the Amyloid Precursor Protein (APP), a central molecule in Alzheimer’s disease, associates with the PIKfyve complex (consisting of Vac14, PIKfyve and Fig4) and that the APP intracellular domain directly binds purified Vac14. We also show that the closely related APP paralogues, APLP1 and 2 associate with the PIKfyve complex. Whether APP family proteins can additionally form direct protein–protein interaction with PIKfyve or Fig4 remains to be explored. We show that APP binding to the PIKfyve complex drives formation of PI(3,5)P2 positive vesicles and that APP gene family members are required for supporting PIKfyve function. Interestingly, the PIKfyve complex is required for APP trafficking, suggesting a feedback loop in which APP, by binding to and stimulating PI(3,5)P2 vesicle formation may control its own trafficking. These data suggest that altered APP processing, as observed in Alzheimer’s disease, may disrupt PI(3,5)P2 metabolism, endosomal sorting and homeostasis with important implications for our understanding of the mechanism of neurodegeneration in Alzheimer’s disease.