A Mechanistic Latent Variable Model for Estimating Drug Concentrations in the Male Genital Tract

The purpose of this study is to develop statistical methodology to facilitate indirect estimation of the concentration of antiretroviral drugs and viral loads in the prostate gland and the seminal vesicle. The differences in antiretroviral drug concentrations in these organs may lead to suboptimal concentrations in one gland compared to the other. Suboptimal levels of the antiretroviral drugs will not be able to fully suppress the virus in that gland, lead to a source of sexually transmissible virus and increase the chance of selecting for drug resistant virus. This information may be useful selecting antiretroviral drug regimen that will achieve optimal concentrations in most of male genital tract glands. Using fractionally collected semen ejaculates, Lundquist (1949) measured levels of surrogate markers in each fraction that are uniquely produced by specific male accessory glands. To determine the original glandular concentrations of the surrogate markers, Lundquist solved a simultaneous series of linear equations. This method has several limitations. In particular, it does not yield a unique solution, it does not address measurement error, and it disregards inter-subject variability in the parameters. To cope with these limitations, we developed a mechanistic latent variable model based on the physiology of the male genital tract and surrogate markers. We employ a Bayesian approach and perform a sensitivity analysis with regard to the distributional assumptions on the random effects and priors. The model and Bayesian approach is validated on experimental data where the concentration of a drug should be (biologically) differentially distributed between the two glands. In this example, the Bayesian model-based conclusions are found to be robust to model specification and this hierarchical approach leads to more scientifically valid conclusions than the original methodology. In particular, unlike existing methods, the proposed model based approach was not affected by a common form of outliers.

Structural response and dynamics of fluid-structure-control interaction in wind turbine blades

Reducing the uncertainties related to blade dynamics by the improvement of the quality of numerical simulations of the fluid structure interaction process is a key for a breakthrough in wind-turbine technology. A fundamental step in that direction is the implementation of aeroelastic models capable of capturing the complex features of innovative prototype blades, so they can be tested at realistic full-scale conditions with a reasonable computational cost. We make use of a code based on a combination of two advanced numerical models implemented in a parallel HPC supercomputer platform: First, a model of the structural response of heterogeneous composite blades, based on a variation of the dimensional reduction technique proposed by Hodges and Yu. This technique has the capacity of reducing the geometrical complexity of the blade section into a stiffness matrix for an equivalent beam. The reduced 1-D strain energy is equivalent to the actual 3-D strain energy in an asymptotic sense, allowing accurate modeling of the blade structure as a 1-D finite-element problem. This substantially reduces the computational effort required to model the structural dynamics at each time step. Second, a novel aerodynamic model based on an advanced implementation of the BEM(Blade ElementMomentum) Theory; where all velocities and forces are re-projected through orthogonal matrices into the instantaneous deformed configuration to fully include the effects of large displacements and rotation of the airfoil sections into the computation of aerodynamic forces. This allows the aerodynamic model to take into account the effects of the complex flexo-torsional deformation that can be captured by the more sophisticated structural model mentioned above. In this thesis we have successfully developed a powerful computational tool for the aeroelastic analysis of wind-turbine blades. Due to the particular features mentioned above in terms of a full representation of the combined modes of deformation of the blade as a complex structural part and their effects on the aerodynamic loads, it constitutes a substantial advancement ahead the state-of-the-art aeroelastic models currently available, like the FAST-Aerodyn suite. In this thesis, we also include the results of several experiments on the NREL-5MW blade, which is widely accepted today as a benchmark blade, together with some modifications intended to explore the capacities of the new code in terms of capturing features on blade-dynamic behavior, which are normally overlooked by the existing aeroelastic models.

Structural equation modeling of the medical outcome study: Short Form 36 (SF-36)

The factorial validity of the SF-36 was evaluated using confirmatory factor analysis (CFA) methods, structural equation modeling (SEM), and multigroup structural equation modeling (MSEM). First, the measurement and structural model of the hypothesized SF-36 was explicated. Second, the model was tested for the validity of a second-order factorial structure, upon evidence of model misfit, determined the best-fitting model, and tested the validity of the best-fitting model on a second random sample from the same population. Third, the best-fitting model was tested for invariance of the factorial structure across race, age, and educational subgroups using MSEM.^ The findings support the second-order factorial structure of the SF-36 as proposed by Ware and Sherbourne (1992). However, the results suggest that: (a) Mental Health and Physical Health covary; (b) general mental health cross-loads onto Physical Health; (c) general health perception loads onto Mental Health instead of Physical Health; (d) many of the error terms are correlated; and (e) the physical function scale is not reliable across these two samples. This hierarchical factor pattern was replicated across both samples of health care workers, suggesting that the post hoc model fitting was not data specific. Subgroup analysis suggests that the physical function scale is not reliable across the "age" or "education" subgroups and that the general mental health scale path from Mental Health is not reliable across the "white/nonwhite" or "education" subgroups.^ The importance of this study is in the use of SEM and MSEM in evaluating sample data from the use of the SF-36. These methods are uniquely suited to the analysis of latent variable structures and are widely used in other fields. The use of latent variable models for self reported outcome measures has become widespread, and should now be applied to medical outcomes research. Invariance testing is superior to mean scores or summary scores when evaluating differences between groups. From a practical, as well as, psychometric perspective, it seems imperative that construct validity research related to the SF-36 establish whether this same hierarchical structure and invariance holds for other populations.^ This project is presented as three articles to be submitted for publication. ^

Differential spatial and structural organization of the X chromosome underlies dosage compensation in C. elegans.

The adjustment of X-linked gene expression to the X chromosome copy number (dosage compensation [DC]) has been widely studied as a model of chromosome-wide gene regulation. In Caenorhabditis elegans, DC is achieved by twofold down-regulation of gene expression from both Xs in hermaphrodites. We show that in males, the single X chromosome interacts with nuclear pore proteins, while in hermaphrodites, the DC complex (DCC) impairs this interaction and alters X localization. Our results put forward a structural model of DC in which X-specific sequences locate the X chromosome in transcriptionally active domains in males, while the DCC prevents this in hermaphrodites.

Using the theory of planned behaviour to model antecedents of surgical checklist use: a cross-sectional study.

BACKGROUND Compliance with surgical checklist use remains an obstacle in the context of checklist implementation programs. The theory of planned behaviour was applied to analyse attitudes, perceived behaviour control, and norms as psychological antecedents of individuals' intentions to use the checklist. METHODS A cross-sectional survey study with staff (N = 866) of 10 Swiss hospitals was conducted in German and French. Group mean differences between individuals with and without managerial function were computed. Structural equation modelling and confirmatory factor analysis was applied to investigate the structural relation between attitudes, perceived behaviour control, norms, and intentions. RESULTS Significant mean differences in favour of individuals with managerial function emerged for norms, perceived behavioural control, and intentions, but not for attitudes. Attitudes and perceived behavioural control had a significant direct effect on intentions whereas norms had not. CONCLUSIONS Individuals with managerial function exhibit stronger perceived behavioural control, stronger norms, and stronger intentions. This could be applied in facilitating checklist implementation. The structural model of the theory of planned behaviour remains stable across groups, indicating a valid model to describe antecedents of intentions in the context of surgical checklist implementation.

Interrelationships between the structural and functional aspects of social relationships, comorbidity and health related quality of life in breast cancer survivors

It is widely acknowledged in theoretical and empirical literature that social relationships, comprising of structural measures (social networks) and functional measures (perceived social support) have an undeniable effect on health outcomes. However, the actual mechanism of this effect has yet to be clearly understood or explicated. In addition, comorbidity is found to adversely affect social relationships and health related quality of life (a valued outcome measure in cancer patients and survivors). ^ This cross sectional study uses selected baseline data (N=3088) from the Women's Healthy Eating and Living (WHEL) study. Lisrel 8.72 was used for the latent variable structural equation modeling. Due to the ordinal nature of the data, Weighted Least Squares (WLS) method of estimation using Asymptotic Distribution Free covariance matrices was chosen for this analysis. The primary exogenous predictor variables are Social Networks and Comorbidity; Perceived Social Support is the endogenous predictor variable. Three dimensions of HRQoL, physical, mental and satisfaction with current quality of life were the outcome variables. ^ This study hypothesizes and tests the mechanism and pathways between comorbidity, social relationships and HRQoL using latent variable structural equation modeling. After testing the measurement models of social networks and perceived social support, a structural model hypothesizing associations between the latent exogenous and endogenous variables was tested. The results of the study after listwise deletion (N=2131) mostly confirmed the hypothesized relationships (TLI, CFI >0.95, RMSEA = 0.05, p=0.15). Comorbidity was adversely associated with all three HRQoL outcomes. Strong ties were negatively associated with perceived social support; social network had a strong positive association with perceived social support, which served as a mediator between social networks and HRQoL. Mental health quality of life was the most adversely affected by the predictor variables. ^ This study is a preliminary look at the integration of structural and functional measures of social relationships, comorbidity and three HRQoL indicators using LVSEM. Developing stronger social networks and forming supportive relationships is beneficial for health outcomes such as HRQoL of cancer survivors. Thus, the medical community treating cancer survivors as well as the survivor's social networks need to be informed and cognizant of these possible relationships. ^

Theoretical and experimental structural studies of historical Latin-American laminated planked timber arches

This article describes a first group of theoretical and experimental works undertaken at the Polytechnic University of Madrid. One major purpose is to obtain a structural model for the assessment of historical Latin-American vertically laminated planked timber arches built by the Spanish, mainly in the XVII and XVIII centuries. Many of those constructions still stand and represent a notable historical heritage. Pedro Hurtado recently presented his Ph. D. thesis on historical and construction topics. A structural study was then undertaken. This step of the structural research focussed on static analysis, most especially the deformation in the connection system. This article describes part of this first structural research. Even though it is still at a basic level, it shows reasonable agreement with the experimental results. Further static analytical models are been now developed and implemented. The next stage will address the dynamic problem, even though improvements will be made also in the constitutive equations.

Multiobjective structural damage identification in uncertain environments

Evolutionary algorithms are suitable to solve damage identification problems in a multiobjective context. However, the performance of these methods can deteriorate quickly with increasing noise intensities originating numerous uncertainties. In this paper, a statistic structural damage detection method formulated in a multiobjective context is proposed. The statistic analysis is implemented to take into account the uncertainties existing in the structural model and measured structural modal parameters. The presented method is verified by a number of simulated damage scenarios. The effects of noise and damage levels on damage detection are investigated.

Statistical Multi-Objective Structural Damage Identification based on Dynamic Parameters

Evolutionary algorithms are suitable to solve damage identification problems in a multi-objective context. However, the performance of these methods can deteriorate quickly with increasing noise intensities originating numerous uncertainties. In this paper, a statistic structural damage detection method formulated in a multi-objective context is proposed. The statistic analysis is implemented to take into account the uncertainties existing in the structural model and measured structural modal parameters. The presented method is verified by a number of simulated damage scenarios. The effects of noise and damage levels on damage detection are investigated.

Comparison of the seismic behaviour between three building tests, all based on a two storey model house

Integral Masonry System consisting of intersecting steel trusses alo ng each of the three dimensional directions of space on walls and slabs using any masonry material, had yet been backed up by the previous adobe test for seismic areas. This paper presents the comparison this last test and the adaptation of the IMS using h ollow brick. A prototype based on a two storey model house (6mx6mx6m) has being also built in two different scales in order to maximize the load and size of the shake table: the first one half size the whole building (3mx3mx3m) and the second, a quarter of the real size (3mx3mx6m). Both tests have suffered some mild to moderate damages while supporting the higher seismic action subjected by the shake table, without even fissuring the first test and with very few damages the second one. The thickness of the hollow brick wall and the diameter of the tree - dimensional truss reinforcement were scaled to the real size test in order to ascertain its great structural behaviour in relation to the previous structural model calculations. The aim of this study is to sum marize the results of the research collaboration between the ETSAM - UPM and the PUCP in whose laboratory these tests were carried out.

Correlation of the structural and functional domains in the membrane protein Vpu from HIV-1

Vpu is an 81-residue membrane protein encoded by the HIV-1 genome. NMR experiments show that the protein folds into two distinct domains, a transmembrane hydrophobic helix and a cytoplasmic domain with two in-plane amphipathic α-helices separated by a linker region. Resonances in one-dimensional solid-state NMR spectra of uniformly 15N labeled Vpu are clearly segregated into two bands at chemical shift frequencies associated with NH bonds in a transmembrane α-helix, perpendicular to the membrane surface, and with NH bonds in the cytoplasmic helices parallel to the membrane surface. Solid-state NMR spectra of truncated Vpu2–51 (residues 2–51), which contains the transmembrane α-helix and the first amphipathic helix of the cytoplasmic domain, and of a construct Vpu28–81 (residues 28–81), which contains only the cytoplasmic domain, support this structural model of Vpu in the membrane. Full-length Vpu (residues 2–81) forms discrete ion-conducting channels of heterogeneous conductance in lipid bilayers. The most frequent conductances were 22 ± 3 pS and 12 ± 3 pS in 0.5 M KCl and 29 ± 3 pS and 12 ± 3 pS in 0.5 M NaCl. In agreement with the structural model, truncated Vpu2–51, which has the transmembrane helix, forms discrete channels in lipid bilayers, whereas the cytoplasmic domain Vpu28–81, which lacks the transmembrane helix, does not. This finding shows that the channel activity is associated with the transmembrane helical domain. The pattern of channel activity is characteristic of the self-assembly of conductive oligomers in the membrane and is compatible with the structural and functional findings.

Photoactive yellow protein: A structural prototype for the three-dimensional fold of the PAS domain superfamily

PAS domains are found in diverse proteins throughout all three kingdoms of life, where they apparently function in sensing and signal transduction. Although a wealth of useful sequence and functional information has become recently available, these data have not been integrated into a three-dimensional (3D) framework. The very early evolutionary development and diverse functions of PAS domains have made sequence analysis and modeling of this protein superfamily challenging. Limited sequence similarities between the ∼50-residue PAS repeats and one region of the bacterial blue-light photosensor photoactive yellow protein (PYP), for which ground-state and light-activated crystallographic structures have been determined to high resolution, originally were identified in sequence searches using consensus sequence probes from PAS-containing proteins. Here, we found that by changing a few residues particular to PYP function, the modified PYP sequence probe also could select PAS protein sequences. By mapping a typical ∼150-residue PAS domain sequence onto the entire crystallographic structure of PYP, we show that the PAS sequence similarities and differences are consistent with a shared 3D fold (the PAS/PYP module) with obvious potential for a ligand-binding cavity. Thus, PYP appears to prototypically exhibit all the major structural and functional features characteristic of the PAS domain superfamily: the shared PAS/PYP modular domain fold of ∼125–150 residues, a sensor function often linked to ligand or cofactor (chromophore) binding, and signal transduction capability governed by heterodimeric assembly (to the downstream partner of PYP). This 3D PAS/PYP module provides a structural model to guide experimental testing of hypotheses regarding ligand-binding, dimerization, and signal transduction.

An explanatory model of academic achievement based on aptitudes, goal orientations, self-concept and learning strategies

As a result of studies examining factors involved in the learning process, various structural models have been developed to explain the direct and indirect effects that occur between the variables in these models. The objective was to evaluate a structural model of cognitive and motivational variables predicting academic achievement, including general intelligence, academic self-concept, goal orientations, effort and learning strategies. The sample comprised of 341 Spanish students in the first year of compulsory secondary education. Different tests and questionnaires were used to evaluate each variable, and Structural Equation Modelling (SEM) was applied to contrast the relationships of the initial model. The model proposed had a satisfactory fit, and all the hypothesised relationships were significant. General intelligence was the variable most able to explain academic achievement. Also important was the direct influence of academic self-concept on achievement, goal orientations and effort, as well as the mediating ability of effort and learning strategies between academic goals and final achievement.

A carbon activation model with application to longan seed char gasification

In this paper a new structural model is presented to describe the evolution of porosity of char during the gasification process. The model assumes the char structure to be composed of bundles of parallel graphite layers, and the reactivities of each layer with the gasification agent are assumed to be different to represent the different degree of heterogeneity of each layer (i.e. each layer will react with the gasification agent at a different rate). It is this difference in the reactivity that allows micropores to be created during the course of gasification. This simple structural model enables the evolution of pore volume, pore geometrical surface area and the pore size distribution to be described with respect to the extent of char burn-off. The model is tested against the experimental data of gasification of longan seed-derived char with carbon dioxide and it is found that the agreement between the model and the data is reasonably satisfactory, especially the evolution of surface area and pore volume with burn-off.

Model reduction for nonlinear aeroelasticity using the Discrete Empirical Interpolation Method

A novel surrogate model is proposed in lieu of computational fluid dynamic (CFD) code for fast nonlinear aerodynamic modeling. First, a nonlinear function is identified on selected interpolation points defined by discrete empirical interpolation method (DEIM). The flow field is then reconstructed by a least square approximation of flow modes extracted by proper orthogonal decomposition (POD). The proposed model is applied in the prediction of limit cycle oscillation for a plunge/pitch airfoil and a delta wing with linear structural model, results are validate against a time accurate CFD-FEM code. The results show the model is able to replicate the aerodynamic forces and flow fields with sufficient accuracy while requiring a fraction of CFD cost.