Numerical assessment on the effective mechanical stimuli for matrix-associated metabolism in chondrocyte-seeded constructs

The self-regeneration capacity of articular cartilage is limited, due to its avascular and aneural nature. Loaded explants and cell cultures demonstrated that chondrocyte metabolism can be regulated via physiologic loading. However, the explicit ranges of mechanical stimuli that correspond to favourable metabolic response associated with extracellular matrix (ECM) synthesis are elusive. Unsystematic protocols lacking this knowledge produce inconsistent results. This study aims to determine the intrinsic ranges of physical stimuli that increase ECM synthesis and simultaneously inhibit nitric oxide (NO) production in chondrocyte-agarose constructs, by numerically re-evaluating the experiments performed by Tsuang et al. (2008). Twelve loading patterns were simulated with poro-elastic finite element models in ABAQUS. Pressure on solid matrix, von Mises stress, maximum principle stress and pore pressure were selected as intrinsic mechanical stimuli. Their development rates and magnitudes at the steady state of cyclic loading were calculated with MATLAB at the construct level. Concurrent increase in glycosaminoglycan and collagen was observed at 2300 Pa pressure and 40 Pa/s pressure rate. Between 0-1500 Pa and 0-40 Pa/s, NO production was consistently positive with respect to controls, whereas ECM synthesis was negative in the same range. A linear correlation was found between pressure rate and NO production (R = 0.77). Stress states identified in this study are generic and could be used to develop predictive algorithms for matrix production in agarose-chondrocyte constructs of arbitrary shape, size and agarose concentration. They could also be helpful to increase the efficacy of loading protocols for avascular tissue engineering. Copyright (c) 2010 John Wiley \& Sons, Ltd.

A Functional-Based Distribution Diagnostic for a Linear Model with Correlated Outcomes: Technical Report

Despite the widespread popularity of linear models for correlated outcomes (e.g. linear mixed modesl and time series models), distribution diagnostic methodology remains relatively underdeveloped in this context. In this paper we present an easy-to-implement approach that lends itself to graphical displays of model fit. Our approach involves multiplying the estimated marginal residual vector by the Cholesky decomposition of the inverse of the estimated marginal variance matrix. Linear functions or the resulting "rotated" residuals are used to construct an empirical cumulative distribution function (ECDF), whose stochastic limit is characterized. We describe a resampling technique that serves as a computationally efficient parametric bootstrap for generating representatives of the stochastic limit of the ECDF. Through functionals, such representatives are used to construct global tests for the hypothesis of normal margional errors. In addition, we demonstrate that the ECDF of the predicted random effects, as described by Lange and Ryan (1989), can be formulated as a special case of our approach. Thus, our method supports both omnibus and directed tests. Our method works well in a variety of circumstances, including models having independent units of sampling (clustered data) and models for which all observations are correlated (e.g., a single time series).

Cholesky Residuals for Assessing Normal Errors in a Linear Model with Correlated Outcomes: Technical Report

Despite the widespread popularity of linear models for correlated outcomes (e.g. linear mixed models and time series models), distribution diagnostic methodology remains relatively underdeveloped in this context. In this paper we present an easy-to-implement approach that lends itself to graphical displays of model fit. Our approach involves multiplying the estimated margional residual vector by the Cholesky decomposition of the inverse of the estimated margional variance matrix. The resulting "rotated" residuals are used to construct an empirical cumulative distribution function and pointwise standard errors. The theoretical framework, including conditions and asymptotic properties, involves technical details that are motivated by Lange and Ryan (1989), Pierce (1982), and Randles (1982). Our method appears to work well in a variety of circumstances, including models having independent units of sampling (clustered data) and models for which all observations are correlated (e.g., a single time series). Our methods can produce satisfactory results even for models that do not satisfy all of the technical conditions stated in our theory.

On the Behaviour of Marginal and Conditional Akaike Information Criteria in Linear Mixed Models

In linear mixed models, model selection frequently includes the selection of random effects. Two versions of the Akaike information criterion (AIC) have been used, based either on the marginal or on the conditional distribution. We show that the marginal AIC is no longer an asymptotically unbiased estimator of the Akaike information, and in fact favours smaller models without random effects. For the conditional AIC, we show that ignoring estimation uncertainty in the random effects covariance matrix, as is common practice, induces a bias that leads to the selection of any random effect not predicted to be exactly zero. We derive an analytic representation of a corrected version of the conditional AIC, which avoids the high computational cost and imprecision of available numerical approximations. An implementation in an R package is provided. All theoretical results are illustrated in simulation studies, and their impact in practice is investigated in an analysis of childhood malnutrition in Zambia.

RNAi reduces expression and intracellular retention of mutant cartilage oligomeric matrix protein.

Mutations in cartilage oligomeric matrix protein (COMP), a large extracellular glycoprotein expressed in musculoskeletal tissues, cause two skeletal dysplasias, pseudoachondroplasia and multiple epiphyseal dysplasia. These mutations lead to massive intracellular retention of COMP, chondrocyte death and loss of growth plate chondrocytes that are necessary for linear growth. In contrast, COMP null mice have only minor growth plate abnormalities, normal growth and longevity. This suggests that reducing mutant and wild-type COMP expression in chondrocytes may prevent the toxic cellular phenotype causing the skeletal dysplasias. We tested this hypothesis using RNA interference to reduce steady state levels of COMP mRNA. A panel of shRNAs directed against COMP was tested. One shRNA (3B) reduced endogenous and recombinant COMP mRNA dramatically, regardless of expression levels. The activity of the shRNA against COMP mRNA was maintained for up to 10 weeks. We also demonstrate that this treatment reduced ER stress. Moreover, we show that reducing steady state levels of COMP mRNA alleviates intracellular retention of other extracellular matrix proteins associated with the pseudoachondroplasia cellular pathology. These findings are a proof of principle and the foundation for the development of a therapeutic intervention based on reduction of COMP expression.

Matrix models for quantifying competitive intransitivity from species abundance data

In a network of competing species, a competitive intransitivity occurs when the ranking of competitive abilities does not follow a linear hierarchy (A > B > C but C > A). A variety of mathematical models suggests that intransitive networks can prevent or slow down competitive exclusion and maintain biodiversity by enhancing species coexistence. However, it has been difficult to assess empirically the relative importance of intransitive competition because a large number of pairwise species competition experiments are needed to construct a competition matrix that is used to parameterize existing models. Here we introduce a statistical framework for evaluating the contribution of intransitivity to community structure using species abundance matrices that are commonly generated from replicated sampling of species assemblages. We provide metrics and analytical methods for using abundance matrices to estimate species competition and patch transition matrices by using reverse-engineering and a colonization-competition model. These matrices provide complementary metrics to estimate the degree of intransitivity in the competition network of the sampled communities. Benchmark tests reveal that the proposed methods could successfully detect intransitive competition networks, even in the absence of direct measures of pairwise competitive strength. To illustrate the approach, we analyzed patterns of abundance and biomass of five species of necrophagous Diptera and eight species of their hymenopteran parasitoids that co-occur in beech forests in Germany. We found evidence for a strong competitive hierarchy within communities of flies and parasitoids. However, for parasitoids, there was a tendency towards increasing intransitivity in higher weight classes, which represented larger resource patches. These tests provide novel methods for empirically estimating the degree of intransitivity in competitive networks from observational datasets. They can be applied to experimental measures of pairwise species interactions, as well as to spatio-temporal samples of assemblages in homogenous environments or environmental gradients.

Bayesian generalized linear models for meta-analysis of diagnostic tests

With the recognition of the importance of evidence-based medicine, there is an emerging need for methods to systematically synthesize available data. Specifically, methods to provide accurate estimates of test characteristics for diagnostic tests are needed to help physicians make better clinical decisions. To provide more flexible approaches for meta-analysis of diagnostic tests, we developed three Bayesian generalized linear models. Two of these models, a bivariate normal and a binomial model, analyzed pairs of sensitivity and specificity values while incorporating the correlation between these two outcome variables. Noninformative independent uniform priors were used for the variance of sensitivity, specificity and correlation. We also applied an inverse Wishart prior to check the sensitivity of the results. The third model was a multinomial model where the test results were modeled as multinomial random variables. All three models can include specific imaging techniques as covariates in order to compare performance. Vague normal priors were assigned to the coefficients of the covariates. The computations were carried out using the 'Bayesian inference using Gibbs sampling' implementation of Markov chain Monte Carlo techniques. We investigated the properties of the three proposed models through extensive simulation studies. We also applied these models to a previously published meta-analysis dataset on cervical cancer as well as to an unpublished melanoma dataset. In general, our findings show that the point estimates of sensitivity and specificity were consistent among Bayesian and frequentist bivariate normal and binomial models. However, in the simulation studies, the estimates of the correlation coefficient from Bayesian bivariate models are not as good as those obtained from frequentist estimation regardless of which prior distribution was used for the covariance matrix. The Bayesian multinomial model consistently underestimated the sensitivity and specificity regardless of the sample size and correlation coefficient. In conclusion, the Bayesian bivariate binomial model provides the most flexible framework for future applications because of its following strengths: (1) it facilitates direct comparison between different tests; (2) it captures the variability in both sensitivity and specificity simultaneously as well as the intercorrelation between the two; and (3) it can be directly applied to sparse data without ad hoc correction. ^

A matrix pencil approach to the existence of compactly supported reconstruction functions in average sampling

The aim of this work is to solve a question raised for average sampling in shift-invariant spaces by using the well-known matrix pencil theory. In many common situations in sampling theory, the available data are samples of some convolution operator acting on the function itself: this leads to the problem of average sampling, also known as generalized sampling. In this paper we deal with the existence of a sampling formula involving these samples and having reconstruction functions with compact support. Thus, low computational complexity is involved and truncation errors are avoided. In practice, it is accomplished by means of a FIR filter bank. An answer is given in the light of the generalized sampling theory by using the oversampling technique: more samples than strictly necessary are used. The original problem reduces to finding a polynomial left inverse of a polynomial matrix intimately related to the sampling problem which, for a suitable choice of the sampling period, becomes a matrix pencil. This matrix pencil approach allows us to obtain a practical method for computing the compactly supported reconstruction functions for the important case where the oversampling rate is minimum. Moreover, the optimality of the obtained solution is established.

Linear instability of orthogonal compressible leading-edge boundary layer flow

Instability analysis of compressible orthogonal swept leading-edge boundary layer flow was performed in the context of BiGlobal linear theory. 1, 2 An algorithm was developed exploiting the sparsity characteristics of the matrix discretizing the PDE-based eigenvalue problem. This allowed use of the MUMPS sparse linear algebra package 3 to obtain a direct solution of the linear systems associated with the Arnoldi iteration. The developed algorithm was then applied to efficiently analyze the effect of compressibility on the stability of the swept leading-edge boundary layer and obtain neutral curves of this flow as a function of the Mach number in the range 0 ≤ Ma ≤ 1. The present numerical results fully confirmed the asymptotic theory results of Theofilis et al. 4 Up to the maximum Mach number value studied, it was found that an increase of this parameter reduces the critical Reynolds number and the range of the unstable spanwise wavenumbers.

Global Linear Instability at the Dawn of its 4th Decade: A List of Challenges (A Practical Guide on how to Contain the Euphoria and Avoid the Oversell)

Global linear instability theory is concerned with the temporal or spatial development of small-amplitude perturbations superposed upon laminar steady or time-periodic threedimensional flows, which are inhomogeneous in two (and periodic in one) or all three spatial directions.1 The theory addresses flows developing in complex geometries, in which the parallel or weakly nonparallel basic flow approximation invoked by classic linear stability theory does not hold. As such, global linear theory is called to fill the gap in research into stability and transition in flows over or through complex geometries. Historically, global linear instability has been (and still is) concerned with solution of multi-dimensional eigenvalue problems; the maturing of non-modal linear instability ideas in simple parallel flows during the last decade of last century2–4 has given rise to investigation of transient growth scenarios in an ever increasing variety of complex flows. After a brief exposition of the theory, connections are sought with established approaches for structure identification in flows, such as the proper orthogonal decomposition and topology theory in the laminar regime and the open areas for future research, mainly concerning turbulent and three-dimensional flows, are highlighted. Recent results obtained in our group are reported in both the time-stepping and the matrix-forming approaches to global linear theory. In the first context, progress has been made in implementing a Jacobian-Free Newton Krylov method into a standard finite-volume aerodynamic code, such that global linear instability results may now be obtained in compressible flows of aeronautical interest. In the second context a new stable very high-order finite difference method is implemented for the spatial discretization of the operators describing the spatial BiGlobal EVP, PSE-3D and the TriGlobal EVP; combined with sparse matrix treatment, all these problems may now be solved on standard desktop computers.

Efficient numerical methods for global linear instability. Analysis and modeling of non-orthogonal swept attachment-line boundary layer flow

The aim of this thesis is to study the mechanisms of instability that occur in swept wings when the angle of attack increases. For this, a simplified model for the a simplified model for the non-orthogonal swept leading edge boundary layer has been used as well as different numerical techniques in order to solve the linear stability problem that describes the behavior of perturbations superposed upon this base flow. Two different approaches, matrix-free and matrix forming methods, have been validated using direct numerical simulations with spectral resolution. In this way, flow instability in the non-orthogonal swept attachment-line boundary layer is addressed in a linear analysis framework via the solution of the pertinent global (Bi-Global) PDE-based eigenvalue problem. Subsequently, a simple extension of the extended G¨ortler-H¨ammerlin ODEbased polynomial model proposed by Theofilis, Fedorov, Obrist & Dallmann (2003) for orthogonal flow, which includes previous models as particular cases and recovers global instability analysis results, is presented for non-orthogonal flow. Direct numerical simulations have been used to verify the stability results and unravel the limits of validity of the basic flow model analyzed. The effect of the angle of attack, AoA, on the critical conditions of the non-orthogonal problem has been documented; an increase of the angle of attack, from AoA = 0 (orthogonal flow) up to values close to _/2 which make the assumptions under which the basic flow is derived questionable, is found to systematically destabilize the flow. The critical conditions of non-orthogonal flows at 0 _ AoA _ _/2 are shown to be recoverable from those of orthogonal flow, via a simple analytical transformation involving AoA. These results can help to understand the mechanisms of destabilization that occurs in the attachment line of wings at finite angles of attack. Studies taking into account variations of the pressure field in the basic flow or the extension to compressible flows are issues that remain open. El objetivo de esta tesis es estudiar los mecanismos de la inestabilidad que se producen en ciertos dispositivos aerodinámicos cuando se aumenta el ángulo de ataque. Para ello se ha utilizado un modelo simplificado del flujo de base, así como diferentes técnicas numéricas, con el fin de resolver el problema de estabilidad lineal asociado que describe el comportamiento de las perturbaciones. Estos métodos; sin y con formación de matriz, se han validado utilizando simulaciones numéricas directas con resolución espectral. De esta manera, la inestabilidad del flujo de capa límite laminar oblicuo entorno a la línea de estancamiento se aborda en un marco de análisis lineal por medio del método Bi-Global de resolución del problema de valores propios en derivadas parciales. Posteriormente se propone una extensión simple para el flujo no-ortogonal del modelo polinomial de ecuaciones diferenciales ordinarias, G¨ortler-H¨ammerlin extendido, propuesto por Theofilis et al. (2003) para el flujo ortogonal, que incluye los modelos previos como casos particulares y recupera los resultados del analisis global de estabilidad lineal. Se han realizado simulaciones directas con el fin de verificar los resultados del análisis de estabilidad así como para investigar los límites de validez del modelo de flujo base utilizado. En este trabajo se ha documentado el efecto del ángulo de ataque AoA en las condiciones críticas del problema no ortogonal obteniendo que el incremento del ángulo de ataque, de AoA = 0 (flujo ortogonal) hasta valores próximos a _/2, en el cual las hipótesis sobre las que se basa el flujo base dejan de ser válidas, tiende sistemáticamente a desestabilizar el flujo. Las condiciones críticas del caso no ortogonal 0 _ AoA _ _/2 pueden recuperarse a partir del caso ortogonal mediante el uso de una transformación analítica simple que implica el ángulo de ataque AoA. Estos resultados pueden ayudar a comprender los mecanismos de desestabilización que se producen en el borde de ataque de las alas de los aviones a ángulos de ataque finitos. Como tareas pendientes quedaría realizar estudios que tengan en cuenta variaciones del campo de presión en el flujo base así como la extensión de éste al caso de flujos compresibles.

SERBA: a B.I.E. program with linear elements for 2-D elastostatics analysis

The great developments that have occurred during the last few years in the finite element method and its applications has kept hidden other options for computation. The boundary integral element method now appears as a valid alternative and, in certain cases, has significant advantages. This method deals only with the boundary of the domain, while the F.E.M. analyses the whole domain. This has the following advantages: the dimensions of the problem to be studied are reduced by one, consequently simplifying the system of equations and preparation of input data. It is also possible to analyse infinite domains without discretization errors. These simplifications have the drawbacks of having to solve a full and non-symmetric matrix and some difficulties are incurred in the imposition of boundary conditions when complicated variations of the function over the boundary are assumed. In this paper a practical treatment of these problems, in particular boundary conditions imposition, has been carried out using the computer program shown below. Program SERBA solves general elastostatics problems in 2-dimensional continua using the boundary integral equation method. The boundary of the domain is discretized by line or elements over which the functions are assumed to vary linearly. Data (stresses and/or displacements) are introduced in the local co-ordinate system (element co-ordinates). Resulting stresses are obtained in local co-ordinates and displacements in a general system. The program has been written in Fortran ASCII and implemented on a 1108 Univac Computer. For 100 elements the core requirements are about 40 Kwords. Also available is a Fortran IV version (3 segments)implemented on a 21 MX Hewlett-Packard computer,using 15 Kwords.

Four Decades of Studying Global Linear Instability: Progress and Challenges

Global linear instability theory is concerned with the temporal or spatial development of small-amplitude perturbations superposed upon laminar steady or time-periodic three-dimensional flows, which are inhomogeneous in two(and periodic in one)or all three spatial directions.After a brief exposition of the theory,some recent advances are reported. First, results are presented on the implementation of a Jacobian-free Newton–Krylov time-stepping method into a standard finite-volume aerodynamic code to obtain global linear instability results in flows of industrial interest. Second, connections are sought between established and more-modern approaches for structure identification in flows, such as proper orthogonal decomposition and Koopman modes analysis (dynamic mode decomposition), and the possibility to connect solutions of the eigenvalue problem obtained by matrix formation or time-stepping with those delivered by dynamic mode decomposition, residual algorithm, and proper orthogonal decomposition analysis is highlighted in the laminar regime; turbulent and three-dimensional flows are identified as open areas for future research. Finally, a new stable very-high-order finite-difference method is implemented for the spatial discretization of the operators describing the spatial biglobal eigenvalue problem, parabolized stability equation three-dimensional analysis, and the triglobal eigenvalue problem; it is shown that, combined with sparse matrix treatment, all these problems may now be solved on standard desktop computers

Matrix-free time-stepping methods for the solution of TriGlobal instability problems

La inmensa mayoría de los flujos de relevancia ingenieril permanecen sin estudiar en el marco de la teoría de estabilidad global. Esto es debido a dos razones fundamentalmente, las dificultades asociadas con el análisis de los flujos turbulentos y los inmensos recursos computacionales requeridos para obtener la solución del problema de autovalores asociado al análisis de inestabilidad de flujos tridimensionales, también conocido como problema TriGlobal. En esta tesis se aborda el problema asociado con la tridimensionalidad. Se ha desarrollado una metodología general para obtener soluciones de problemas de análisis modal de las inestabilidades lineales globales mediante el acoplamiento de métodos de evolución temporal, desarrollados en este trabajo, con códigos de mecánica de fluidos computacional de segundo orden, utilizados de forma general en la industria. Esta metodología consiste en la resolución del problema de autovalores asociado al análisis de inestabilidad mediante métodos de proyección en subespacios de Krylov, con la particularidad de que dichos subespacios son generados por medio de la integración temporal de un vector inicial usando cualquier código de mecánica de fluidos computacional. Se han elegido tres problemas desafiantes en función de la exigencia de recursos computacionales necesarios y de la complejidad física para la demostración de la presente metodología: (i) el flujo en el interior de una cavidad tridimensional impulsada por una de sus tapas, (ii) el flujo alrededor de un cilindro equipado con aletas helicoidales a lo largo su envergadura y (iii) el flujo a través de una cavidad abierta tridimensinal en ausencia de homogeneidades espaciales. Para la validación de la tecnología se ha obtenido la solución del problema TriGlobal asociado al flujo en la cavidad tridimensional, utilizando el método de evolución temporal desarrollado acoplado con los operadores numéricos de flujo incompresible del código CFD OpenFOAM (código libre). Los resultados obtenidos coinciden plentamente con la literatura. La aplicación de esta metodología al estudio de inestabilidades globales de flujos abiertos tridimensionales ha proporcionado por primera vez, información sobre la transición tridimensional de estos flujos. Además, la metodología ha sido adaptada para resolver problemas adjuntos TriGlobales, permitiendo el control de flujo basado en modificaciones de las inestabilidades globales. Finalmente, se ha demostrado que la cantidad moderada de los recursos computacionales requeridos para la solución del problema de valor propio TriGlobal usando este método numérico, junto a su versatilidad al poder acoplarse a cualquier código aerodinámico, permite la realización de análisis de inestabilidad global y control de flujos complejos de relevancia industrial. Abstract Most flows of engineering relevance still remain unexplored in a global instability theory context for two reasons. First, because of the difficulties associated with the analysis of turbulent flows and, second, for the formidable computational resources required for the solution of the eigenvalue problem associated with the instability analysis of three-dimensional base flows, also known as TriGlobal problem. In this thesis, the problem associated with the three-dimensionality is addressed by means of the development of a general approach to the solution of large-scale global linear instability analysis by coupling a time-stepping approach with second order aerodynamic codes employed in industry. Three challenging flows in the terms of required computational resources and physical complexity have been chosen for demonstration of the present methodology; (i) the flow inside a wall-bounded three-dimensional lid-driven cavity, (ii) the flow past a cylinder fitted with helical strakes and (iii) the flow over a inhomogeneous three-dimensional open cavity. Results in excellent agreement with the literature have been obtained for the three-dimensional lid-driven cavity by using this methodology coupled with the incompressible solver of the open-source toolbox OpenFOAM®, which has served as validation. Moreover, significant physical insight of the instability of three-dimensional open flows has been gained through the application of the present time-stepping methodology to the other two cases. In addition, modifications to the present approach have been proposed in order to perform adjoint instability analysis of three-dimensional base flows and flow control; validation and TriGlobal examples are presented. Finally, it has been demonstrated that the moderate amount of computational resources required for the solution of the TriGlobal eigenvalue problem using this method enables the performance of instability analysis and control of flows of industrial relevance.