Sensitivity-analysis method for inverse simulation application

An important criticism of traditional methods of inverse simulation that are based on the Newton–Raphson algorithm is that they suffer from numerical problems. In this paper these problems are discussed and a new method based on sensitivity-analysis theory is developed and evaluated. The Jacobian matrix may be calculated by solving a sensitivity equation and this has advantages over the approximation methods that are usually applied when the derivatives of output variables with respect to inputs cannot be found analytically. The methodology also overcomes problems of input-output redundancy that arise in the traditional approaches to inverse simulation. The sensitivity- analysis approach makes full use of information within the time interval over which key quantities are compared, such as the difference between calculated values and the given ideal maneuver after each integration step. Applications to nonlinear HS125 aircraft and Lynx helicopter models show that, for this sensitivity-analysis method, more stable and accurate results are obtained than from use of the traditional Newton–Raphson approach

A user evaluation of hierarchical phrase browsing

Phrase browsing interfaces based on hierarchies of phrases extracted automatically from document collections offer a useful compromise between automatic full-text searching and manually-created subject indexes. The literature contains descriptions of such systems that many find compelling and persuasive. However, evaluation studies have either been anecdotal, or focused on objective measures of the quality of automatically-extracted index terms, or restricted to questions of computational efficiency and feasibility. This paper reports on an empirical, controlled user study that compares hierarchical phrase browsing with full-text searching over a range of information seeking tasks. Users found the results located via phrase browsing to be relevant and useful but preferred keyword searching for certain types of queries. Users experiences were marred by interface details, including inconsistencies between the phrase browser and the surrounding digital library interface

Feedback methods for inverse simulation of dynamic models for engineering systems applications

Inverse simulation is a form of inverse modelling in which computer simulation methods are used to find the time histories of input variables that, for a given model, match a set of required output responses. Conventional inverse simulation methods for dynamic models are computationally intensive and can present difficulties for high-speed applications. This paper includes a review of established methods of inverse simulation,giving some emphasis to iterative techniques that were first developed for aeronautical applications. It goes on to discuss the application of a different approach which is based on feedback principles. This feedback method is suitable for a wide range of linear and nonlinear dynamic models and involves two distinct stages. The first stage involves design of a feedback loop around the given simulation model and, in the second stage, that closed-loop system is used for inversion of the model. Issues of robustness within closed-loop systems used in inverse simulation are not significant as there are no plant uncertainties or external disturbances. Thus the process is simpler than that required for the development of a control system of equivalent complexity. Engineering applications of this feedback approach to inverse simulation are described through case studies that put particular emphasis on nonlinear and multi-input multi-output models

Structure and dynamics of topological defects in a glassy liquid on a negatively curved manifold

We study the low-temperature regime of an atomic liquid on the hyperbolic plane by means of molecular dynamics simulation and we compare the results to a continuum theory of defects in a negatively curved hexagonal background. In agreement with the theory and previous results on positively curved (spherical) surfaces, we find that the atomic configurations consist of isolated defect structures, dubbed "grain boundary scars", that form around an irreducible density of curvature-induced disclinations in an otherwise hexagonal background. We investigate the structure and the dynamics of these grain boundary scars

On Neural Networks as Infinite Tree-Structured Probabilistic Graphical Models

Deep neural networks (DNNs) lack the precise semantics and definitive probabilistic interpretation of probabilistic graphical models (PGMs). In this paper, we propose an innovative solution by constructing infinite tree-structured PGMs that correspond exactly to neural networks. Our research reveals that DNNs, during forward propagation, indeed perform approximations of PGM inference that are precise in this alternative PGM structure. Not only does our research complement existing studies that describe neural networks as kernel machines or infinite-sized Gaussian processes, it also elucidates a more direct approximation that DNNs make to exact inference in PGMs. Potential benefits include improved pedagogy and interpretation of DNNs, and algorithms that can merge the strengths of PGMs and DNNs

Improving Power Spectral Estimation using Multitapering: Precise asteroseismic modeling of stars, exoplanets, and beyond

Asteroseismic time-series data have imprints of stellar oscillation modes, whose detection and characterization through time-series analysis allows us to probe stellar interiors physics. Such analyses usually occur in the Fourier domain by computing the Lomb-Scargle (LS) periodogram, an estimator of the \textit{power spectrum} underlying unevenly-sampled time-series data. However, the LS periodogram suffers from the statistical problems of (1) inconsistency (or noise) and (2) bias due to high spectral leakage. In addition, it is designed to detect strictly periodic signals but is unsuitable for non-sinusoidal periodic or quasi-periodic signals. Here, we develop a multitaper spectral estimation method that tackles the inconsistency and bias problems of the LS periodogram. We combine this multitaper method with the Non-Uniform Fast Fourier Transform (\texttt{mtNUFFT}) to more precisely estimate the frequencies of asteroseismic signals that are non-sinusoidal periodic (e.g., exoplanet transits) or quasi-periodic (e.g., pressure modes). We illustrate this using a simulated and the Kepler-91 red giant light curve. Particularly, we detect the Kepler-91b exoplanet and precisely estimate its period, $6.246 \pm 0.002$ days, in the frequency domain using the multitaper F-test alone. We also integrate \texttt{mtNUFFT} into the \texttt{PBjam} package to obtain a Kepler-91 age estimate of $3.96 \pm 0.48$ Gyr. This $36$\% improvement in age precision relative to the $4.27 \pm 0.75$ Gyr APOKASC-2 (uncorrected) estimate illustrates that \texttt{mtNUFFT} has promising implications for Galactic archaeology, in addition to stellar interiors and exoplanet studies. Our frequency analysis method generally applies to time-domain astronomy and is implemented in the public Python package \texttt{tapify}, available at \url{https://github.com/aaryapatil/tapify}.Comment: 32 pages (3 pages in the Appendix), 14 figures, 2 tables, Submitted to A

The Effect of AICAR-Induced AMPK Activation on Gene Expression in Sarcopenic Muscle

The loss of muscle mass and function (sarcopenia) afflicts 11-74% of all aging adults, with prevalence increasing with age. Exercise training is clearly effective in preventing or attenuating sarcopenia. The cellular mechanisms of exercise’s protective effects are not entirely clear, but AMP-activated protein kinase (AMPK) is thought to play an important role, in part by regulating gene expression. PURPOSE: To determine the effect of chronic pharmacological AMPK activation on skeletal muscle gene expression in sarcopenic muscle. METHODS: 24-month-old C57Bl/6J mice received either one acute injection or chronic daily saline injections of the AMPK-activating drug AICAR for 31 days. 5-month-old saline-injected mice served as young controls for reference. Treadmill running capacity was measured before and after treatment. Expression of genes relating to mitochondria, muscle size regulation, and inflammation was measured by real-time polymerase chain reaction (RT-PCR). RESULTS: One hour after a single injection of AICAR, raptor phosphorylation was increased in both young and old mice, indicating AMPK activation. Phosphorylation of the mTORC1 targets 4EBP1, and S6k were both elevated in old muscle, consistent with previous reports of hyperactivated mTORC1 in aged muscle. Acute AICAR injection returned 4EBP1 and S6k phosphorylation to young levels. RNA sequencing demonstrated that chronic AICAR injections restored the expression of many genes in old muscle to the levels observed in young muscle. Among these, mitochondrial splicing suppressor 51 (Mss51) expression, which is associated with impaired mitochondrial function and muscle loss, was elevated in sarcopenic muscle but attenuated by AICAR treatment, and this was confirmed by RT-PCR analysis. CONCLUSION: AICAR treatment reverses several critical age-related changes in gene expression and mTORC1 activity. Our findings support further investigation of AMPK activation and Mss51 repression as targets for therapeutic interventions in sarcopenia

Transmission of murine scrapie to P101L transgenic mice

Rona Barron - ORCID: 0000-0003-4512-9177 https://orcid.org/0000-0003-4512-9177Item is not available in this repository.The PrP protein is central to the transmissible spongiform encephalopathies (TSEs), and the amino acid sequence of this protein in the host can influence both incubation time of disease and targeting of disease pathology. The N terminus of murine PrP has been proposed to be important in the replication of TSE agents, as mutations or deletions in that region can alter the efficiency of agent replication. To address this hypothesis and to investigate the mechanisms by which host PrP sequence controls the outcome of disease, we have assessed the influence of a single amino acid alteration in the N-terminal region of murine PrP (P101L) on the transmission of TSE agents between mice. Mice homozygous for the mutation (101LL) were inoculated with TSE strains 139A and 79A derived from mice carrying a Prnpa allele, and 79V and 301V derived from mice carrying a Prnpb allele. Incubation times in 101LL mice were extended with all four strains of agent when compared with those in the corresponding mouse genotype from which the infectivity was derived. However, the degree to which the incubation period was increased showed considerable variation between each strain of agent. Moreover, the presence of this single amino acid alteration resulted in a 70 day reduction in incubation time of the 301V strain in Prnpa mice. The effect of the 101L mutation on murine scrapie incubation time appears therefore to be strain specific.https://doi.org/10.1099/vir.0.19147-084pubpub1

Displaying desire and distinction in housing

The article discusses the significance of cultural capital for the understanding of the field of housing in contemporary Britain. It explores the relationship between housing and the position of individuals in social space mapped out by means of a multiple correspondence analysis. It considers the material aspects of housing and the changing contexts that are linked to the creation and display of desire for social position and distinction expressed in talk about home decoration as personal expression and individuals' ideas of a `dream house'. It is based on an empirical investigation of taste and lifestyle using nationally representative survey data and qualitative interviews. The article shows both that personal resources and the imagination of home are linked to levels of cultural capital, and that rich methods of investigation are required to grasp the significance of these normally invisible assets to broaden the academic understanding of the field of housing in contemporary culture