A decision-theoretic approach for segmental classification

This paper is concerned with statistical methods for the segmental classification of linear sequence data where the task is to segment and classify the data according to an underlying hidden discrete state sequence. Such analysis is commonplace in the empirical sciences including genomics, finance and speech processing. In particular, we are interested in answering the following question: given data $y$ and a statistical model $\pi(x,y)$ of the hidden states $x$, what should we report as the prediction $\hat{x}$ under the posterior distribution $\pi (x|y)$? That is, how should you make a prediction of the underlying states? We demonstrate that traditional approaches such as reporting the most probable state sequence or most probable set of marginal predictions can give undesirable classification artefacts and offer limited control over the properties of the prediction. We propose a decision theoretic approach using a novel class of Markov loss functions and report $\hat{x}$ via the principle of minimum expected loss (maximum expected utility). We demonstrate that the sequence of minimum expected loss under the Markov loss function can be enumerated exactly using dynamic programming methods and that it offers flexibility and performance improvements over existing techniques. The result is generic and applicable to any probabilistic model on a sequence, such as Hidden Markov models, change point or product partition models.Comment: Published in at http://dx.doi.org/10.1214/13-AOAS657 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Planar micromachined glass cantilevers utilising integrated Bragg Fabry-Perot cavities

Here we demonstrate a glass cantilever based on a unique micromachining and etching approach, combined with UV written Bragg gratings. We shall also discuss the increase in sensitivity by using two Bragg gratings to form Fabry-Pérot cavity. Cantilevers are in ultra sensitive force sensors used in applications such as Atomic Force Microscopy, mass sensing and acoustic transducers

Lateral groove geometry for planar UV written evanescent devices - new flexibility new devices

Conventional evanescent optical devices have made use of etched windows to allow access of an optical field to a material of interest. Such devices are a route to accurate refractive index sensors and to realising modulators, however, the geometry of etching the cladding to give the fluid access to a pre-defined core waveguide mode is limiting. In this work, we present an alternative approach in which a groove is cut using a polishing saw blade to give a vertical, high optical quality trench. Optical waveguides are then UV written to allow evanescent lateral access of the mode to a fluid placed in the trench. This seemingly subtle change in geometry provides greatly increased flexibility to tailor the interaction between the optical mode and the surrounding material, by, for example, changing the mode size and the allowing couplers or tapers to be used

New geometry for planar UV written refractive index sensors

We shall present some of our recent results from our work on UV written planar waveguide refractive index sensors. Refractive index of an analyte is measured through the perturbation of an optical mode, interrogation of the modal index is achieved via the reflected spectra from a Bragg grating defined in the same process as the channel waveguide. Here we introduce a new geometry which embraces the benefits of planar technology to realise new integrated devices. The geometry allows several different sensors to be defined on the same substrate each offering complementary information. Such information may include index as a function of penetration depth for surface binding analytes, interrogation wavelength for dispersion analysis, enhanced sensitivity in specific index ranges and temperature compensation. We shall also outline the inherent fabrication advantages and device feature benefits, including a reduction in return loss, spectral artefacts and a suggested reduction in stress induced birefringence. The silica sensing surface opposed to gold used in SPR devices opens new avenues to exploit surface binding. With a marked reduction in complexity and cost these devices may have significant impact in future sensor markets

Robust Linear Models for Cis-eQTL Analysis

Expression Quantitative Trait Loci (eQTL) analysis enables characterisation of functional genetic variation influencing expression levels of individual genes. In outbread populations, including humans, eQTLs are commonly analysed using the conventional linear model, adjusting for relevant covariates, assuming an allelic dosage model and a Gaussian error term. However, gene expression data generally have noise that induces heavy-tailed errors relative to the Gaussian distribution and often include atypical observations, or outliers. Such departures from modelling assumptions can lead to an increased rate of type II errors (false negatives), and to some extent also type I errors (false positives). Careful model checking can reduce the risk of type-I errors but often not type II errors, since it is generally too time-consuming to carefully check all models with a non-significant effect in large-scale and genome-wide studies. Here we propose the application of a robust linear model for eQTL analysis to reduce adverse effects of deviations from the assumption of Gaussian residuals. We present results from a simulation study as well as results from the analysis of real eQTL data sets. Our findings suggest that in many situations robust models have the potential to provide more reliable eQTL results compared to conventional linear models, particularly in respect to reducing type II errors due to non-Gaussian noise. Post-genomic data, such as that generated in genome-wide eQTL studies, are often noisy and frequently contain atypical observations. Robust statistical models have the potential to provide more reliable results and increased statistical power under non-Gaussian conditions. The results presented here suggest that robust models should be considered routinely alongside other commonly used methodologies for eQTL analysis.NonePublishe

Initial test results on bolometers for the Planck high frequency instrument

We summarize the fabrication, flight qualification, and dark performance of bolometers completed at the Jet Propulsion Laboratory for the High Frequency Instrument (HFI) of the joint ESA/NASA Herschel/Planck mission to be launched in 2009. The HFI is a multicolor focal plane which consists of 52 bolometers operated at 100 mK. Each bolometer is mounted to a feedhorn-filter assembly which defines one of six frequency bands centered between 100-857 GHz. Four detectors in each of five bands from 143-857 GHz are coupled to both linear polarizations and thus measure the total intensity. In addition, eight detectors in each of four bands (100, 143, 217, and 353 GHz) couple only to a single linear polarization and thus provide measurements of the Stokes parameters, Q and U, as well as the total intensity. The measured noise equivalent power (NEP) of all detectors is at or below the background limit for the telescope and time constants are a few ms, short enough to resolve point sources as the 5 to 9 arc min beams move across the sky at 1 rpm

Prenatal dexamethasone ‘programmes’ hypotension, but stress-induced hypertension in adult offspring

Low birth weight in humans is predictive of hypertension in adult life. Although the mechanisms underlying this link remain unknown, fetal overexposure to glucocorticoids has been implicated. We previously showed that prenatal dexamethasone (DEX) exposure in the rat lowers birth weight and programmes adult hypertension. The current study aimed to further investigate the nature of this hypertension and to elucidate its origins. Unlike previous studies, we assessed offspring blood pressure (BP) with radiotelemetry, which is unaffected by stress artefacts of measurement. We show that prenatal DEX during the last week of pregnancy results in offspring of low birth weight (14% reduction) that have lower basal BP in adulthood (∼4–8 mmHg lower); with the commonly expected hypertensive phenotype only being noted when these offspring are subjected to even mild disturbance or a more severe stressor (up to 30 mmHg higher than controls). Moreover, DEX-treated offspring sustain their stress-induced hypertension for longer. Promotion of systemic catecholamine release (amphetamine) induced a significantly greater rise of BP in the DEX animals (77% increase) over that observed in the vehicle controls. Additionally, we demonstrate that the isolated mesenteric vasculature of DEX-treated offspring display greater sensitivity to noradrenaline and other vasoconstrictors. We therefore conclude that altered sympathetic responses mediate the stress-induced hypertension associated with prenatal DEX programming