The influence of matrix integrity on stress-fiber remodeling in 3D

Matrix anisotropy is important for long term in vivo functionality. However, it is not fully understood how to guide matrix anisotropy in vitro. Experiments suggest actin-mediated cell traction contributes. Although F-actin in 2D displays a stretch-avoidance response, 3D data are lacking. We questioned how cyclic stretch influences F-actin and collagen orientation in 3D. Small-scale cell-populated fibrous tissues were statically constrained and/or cyclically stretched with or without biochemical agents. A rectangular array of silicone posts attached to flexible membranes constrained a mixture of cells, collagen I and matrigel. F-actin orientation was quantified using fiber-tracking software, fitted using a bi-model distribution function. F-actin was biaxially distributed with static constraint. Surprisingly, uniaxial cyclic stretch, only induced a strong stretch-avoidance response (alignment perpendicular to stretching) at tissue surfaces and not in the core. Surface alignment was absent when a ROCK-inhibitor was added, but also when tissues were only statically constrained. Stretch-avoidance was also observed in the tissue core upon MMP1-induced matrix perturbation. Further, a strong stretch-avoidance response was obtained for F-actin and collagen, for immediate cyclic stretching, i.e. stretching before polymerization of the collagen. Results suggest that F-actin stress-fibers avoid cyclic stretch in 3D, unless collagen contact guidance dictates otherwise. © 2012 Elsevier Ltd.

A matrix-calculation-based algorithm for numerical change propagation analysis

Engineering changes (ECs) are raised throughout the lifecycle of engineering products. A single change to one component produces knock-on effects on others necessitating additional changes. This change propagation significantly affects the development time and cost and determines the product's success. Predicting and managing such ECs is, thus, essential to companies. Some prediction tools model change propagation by algorithms, whereof a subgroup is numerical. Current numerical change propagation algorithms either do not account for the exclusion of cyclic propagation paths or are based on exhaustive searching methods. This paper presents a new matrix-calculation-based algorithm which can be applied directly to a numerical product model to analyze change propagation and support change prediction. The algorithm applies matrix multiplications on mutations of a given design structure matrix accounting for the exclusion of self-dependences and cyclic propagation paths and delivers the same results as the exhaustive search-based Trail Counting algorithm. Despite its factorial time complexity, the algorithm proves advantageous because of its straightforward matrix-based calculations which avoid exhaustive searching. Thereby, the algorithm can be implemented in established numerical programs such as Microsoft Excel which promise a wider application of the tools within and across companies along with better familiarity, usability, practicality, security, and robustness. © 1988-2012 IEEE.

An online expectation-maximisation algorithm for nonnegative matrix factorisation models

In this paper we formulate the nonnegative matrix factorisation (NMF) problem as a maximum likelihood estimation problem for hidden Markov models and propose online expectation-maximisation (EM) algorithms to estimate the NMF and the other unknown static parameters. We also propose a sequential Monte Carlo approximation of our online EM algorithm. We show the performance of the proposed method with two numerical examples. © 2012 IFAC.

Low attenuation of GHz Rayleigh-like surface acoustic waves in ZnO/GaAs systems immersed in liquid helium

Low attenuation of Sezawa modes operating at GHz frequencies in ZnO/GaAs systems immersed in liquid helium has been observed. This unexpected behaviour for Rayleigh-like surface acoustic waves (SAWs) is explained in terms of the calculated depth profiles of their acoustic Poynting vectors. This analysis allows reproduction of the experimental dispersion of the attenuation coefficient. In addition, the high attenuation of the Rayleigh mode is compensated by the strengthening provided by the ZnO layer. The introduction of the ZnO film will enable the operation of SAW-driven single-photon sources in GaAs-based systems with the best thermal stability provided by the liquid helium bath. © 2013 American Institute of Physics.

Influence of the matrix properties on the performances of Er-doped Si nanoclusters light emitting devices

We investigated the properties of light emitting devices whose active layer consists of Er-doped Si nanoclusters (nc) generated by thermal annealing of Er-doped SiOx layers prepared by magnetron cosputtering. Differently from a widely used technique such as plasma enhanced chemical vapor deposition, sputtering allows to synthesize Er-doped Si nc embedded in an almost stoichiometric oxide matrix, so as to deeply influence the electroluminescence properties of the devices. Relevant results include the need for an unexpected low Si excess for optimizing the device efficiency and, above all, the strong reduction of the influence of Auger de-excitation, which represents the main nonradiative path which limits the performances of such devices and their application in silicon nanophotonics. © 2010 American Institute of Physics.

A Hierarchical Model for Ordinal Matrix Factorization

This paper proposes a hierarchical probabilistic model for ordinal matrix factorization. Unlike previous approaches, we model the ordinal nature of the data and take a principled approach to incorporating priors for the hidden variables. Two algorithms are presented for inference, one based on Gibbs sampling and one based on variational Bayes. Importantly, these algorithms may be implemented in the factorization of very large matrices with missing entries. The model is evaluated on a collaborative filtering task, where users have rated a collection of movies and the system is asked to predict their ratings for other movies. The Netflix data set is used for evaluation, which consists of around 100 million ratings. Using root mean-squared error (RMSE) as an evaluation metric, results show that the suggested model outperforms alternative factorization techniques. Results also show how Gibbs sampling outperforms variational Bayes on this task, despite the large number of ratings and model parameters. Matlab implementations of the proposed algorithms are available from cogsys.imm.dtu.dk/ordinalmatrixfactorization.

Low-rank optimization for distance matrix completion

This paper addresses the problem of low-rank distance matrix completion. This problem amounts to recover the missing entries of a distance matrix when the dimension of the data embedding space is possibly unknown but small compared to the number of considered data points. The focus is on high-dimensional problems. We recast the considered problem into an optimization problem over the set of low-rank positive semidefinite matrices and propose two efficient algorithms for low-rank distance matrix completion. In addition, we propose a strategy to determine the dimension of the embedding space. The resulting algorithms scale to high-dimensional problems and monotonically converge to a global solution of the problem. Finally, numerical experiments illustrate the good performance of the proposed algorithms on benchmarks. © 2011 IEEE.

Optimization Algorithms on Matrix Manifolds

This book shows how to exploit the special structure of such problems to develop efficient numerical algorithms.