A note on the use of the generalized odds ratio in meta-analysis of association studies involving bi- and tri-allelic polymorphisms

Abstract Background The generalized odds ratio (GOR) was recently suggested as a genetic model-free measure for association studies. However, its properties were not extensively investigated. We used Monte Carlo simulations to investigate type-I error rates, power and bias in both effect size and between-study variance estimates of meta-analyses using the GOR as a summary effect, and compared these results to those obtained by usual approaches of model specification. We further applied the GOR in a real meta-analysis of three genome-wide association studies in Alzheimer's disease. Findings For bi-allelic polymorphisms, the GOR performs virtually identical to a standard multiplicative model of analysis (e.g. per-allele odds ratio) for variants acting multiplicatively, but augments slightly the power to detect variants with a dominant mode of action, while reducing the probability to detect recessive variants. Although there were differences among the GOR and usual approaches in terms of bias and type-I error rates, both simulation- and real data-based results provided little indication that these differences will be substantial in practice for meta-analyses involving bi-allelic polymorphisms. However, the use of the GOR may be slightly more powerful for the synthesis of data from tri-allelic variants, particularly when susceptibility alleles are less common in the populations (≤10%). This gain in power may depend on knowledge of the direction of the effects. Conclusions For the synthesis of data from bi-allelic variants, the GOR may be regarded as a multiplicative-like model of analysis. The use of the GOR may be slightly more powerful in the tri-allelic case, particularly when susceptibility alleles are less common in the populations.

Auditory and communicative abilities in the auditory neuropathy spectrum disorder and mutation in the Otoferlin gene: clinical cases study

This study had the aim to investigate the auditory and communicative abilities of children diagnosed with Auditory Neuropathy Spectrum Disorder due to mutation in the Otoferlin gene. It is a descriptive and qualitative study in which two siblings with this diagnosis were assessed. The procedures conducted were: speech perception tests for children with profound hearing loss, and assessment of communication abilities using the Behavioral Observation Protocol. Because they were siblings, the subjects in the study shared family and communicative context. However, they developed different communication abilities, especially regarding the use of oral language. The study showed that the Auditory Neuropathy Spectrum Disorder is a heterogeneous condition in all its aspects, and it is not possible to make generalizations or assume that cases with similar clinical features will develop similar auditory and communicative abilities, even when they are siblings. It is concluded that the acquisition of communicative abilities involves subjective factors, which should be investigated based on the uniqueness of each case.

Static analysis of functionally graded cylindrical and conical shells or panels using the generalized unconstrained third order theory coupled with the stress recovery

A 2D Unconstrained Third Order Shear Deformation Theory (UTSDT) is presented for the evaluation of tangential and normal stresses in moderately thick functionally graded conical and cylindrical shells subjected to mechanical loadings. Several types of graded materials are investigated. The functionally graded material consists of ceramic and metallic constituents. A four parameter power law function is used. The UTSDT allows the presence of a finite transverse shear stress at the top and bottom surfaces of the graded shell. In addition, the initial curvature effect included in the formulation leads to the generalization of the present theory (GUTSDT). The Generalized Differential Quadrature (GDQ) method is used to discretize the derivatives in the governing equations, the external boundary conditions and the compatibility conditions. Transverse and normal stresses are also calculated by integrating the three dimensional equations of equilibrium in the thickness direction. In this way, the six components of the stress tensor at a point of the conical or cylindrical shell or panel can be given. The initial curvature effect and the role of the power law functions are shown for a wide range of functionally conical and cylindrical shells under various loading and boundary conditions. Finally, numerical examples of the available literature are worked out.

Modelling and analysis of thin-walled beams in the context of the Generalized Beam Theory

In this work, the Generalized Beam Theory (GBT) is used as the main tool to analyze the mechanics of thin-walled beams. After an introduction to the subject and a quick review of some of the most well-known approaches to describe the behaviour of thin-walled beams, a novel formulation of the GBT is presented. This formulation contains the classic shear-deformable GBT available in the literature and contributes an additional description of cross-section warping that is variable along the wall thickness besides along the wall midline. Shear deformation is introduced in such a way that the classical shear strain components of the Timoshenko beam theory are recovered exactly. According to the new kinematics proposed, a reviewed form of the cross-section analysis procedure is devised, based on a unique modal decomposition. Later, a procedure for a posteriori reconstruction of all the three-dimensional stress components in the finite element analysis of thin-walled beams using the GBT is presented. The reconstruction is simple and based on the use of three-dimensional equilibrium equations and of the RCP procedure. Finally, once the stress reconstruction procedure is presented, a study of several existing issues on the constitutive relations in the GBT is carried out. Specifically, a constitutive law based on mirroring the kinematic constraints of the GBT model into a specific stress field assumption is proposed. It is shown that this method is equally valid for isotropic and orthotropic beams and coincides with the conventional GBT approach available in the literature. Later on, an analogous procedure is presented for the case of laminated beams. Lastly, as a way to improve an inherently poor description of shear deformability in the GBT, the introduction of shear correction factors is proposed. Throughout this work, numerous examples are provided to determine the validity of all the proposed contributions to the field.

Measurement of the proton recoil spectrum in neutron beta decay with the spectrometer aSPECT : study of systematic effects

Precision measurements of observables in neutron beta decay address important open questions of particle physics and cosmology. In this thesis, a measurement of the proton recoil spectrum with the spectrometer aSPECT is described. From this spectrum the antineutrino-electron angular correlation coefficient a can be derived. In our first beam time at the FRM II in Munich, background instabilities prevented us from presenting a new value for a. In the latest beam time at the ILL in Grenoble, the background has been reduced sufficiently. As a result of the data analysis, we identified and fixed a problem in the detector electronics which caused a significant systematic error. The aim of the latest beam time was a new value for a with an error well below the present literature value of 4%. A statistical accuracy of about 1.4% was reached, but we could only set upper limits on the correction of the problem in the detector electronics, too high to determine a meaningful result. This thesis focused on the investigation of different systematic effects. With the knowledge of the systematics gained in this thesis, we are able to improve aSPECT to perform a 1% measurement of a in a further beam time.

Posterior Simulation in the Generalized Linear Model with Semiparmetric Random Effects

Generalized linear mixed models with semiparametric random effects are useful in a wide variety of Bayesian applications. When the random effects arise from a mixture of Dirichlet process (MDP) model, normal base measures and Gibbs sampling procedures based on the Pólya urn scheme are often used to simulate posterior draws. These algorithms are applicable in the conjugate case when (for a normal base measure) the likelihood is normal. In the non-conjugate case, the algorithms proposed by MacEachern and Müller (1998) and Neal (2000) are often applied to generate posterior samples. Some common problems associated with simulation algorithms for non-conjugate MDP models include convergence and mixing difficulties. This paper proposes an algorithm based on the Pólya urn scheme that extends the Gibbs sampling algorithms to non-conjugate models with normal base measures and exponential family likelihoods. The algorithm proceeds by making Laplace approximations to the likelihood function, thereby reducing the procedure to that of conjugate normal MDP models. To ensure the validity of the stationary distribution in the non-conjugate case, the proposals are accepted or rejected by a Metropolis-Hastings step. In the special case where the data are normally distributed, the algorithm is identical to the Gibbs sampler.

An efficient simulation algorithm for the generalized von Mises distribution of order two

In this article we propose an exact efficient simulation algorithm for the generalized von Mises circular distribution of order two. It is an acceptance-rejection algorithm with a piecewise linear envelope based on the local extrema and the inflexion points of the generalized von Mises density of order two. We show that these points can be obtained from the roots of polynomials and degrees four and eight, which can be easily obtained by the methods of Ferrari and Weierstrass. A comparative study with the von Neumann acceptance-rejection, with the ratio-of-uniforms and with a Markov chain Monte Carlo algorithms shows that this new method is generally the most efficient.