Degenerations and limit Frobenius structures in rigid cohomology

We introduce a "limiting Frobenius structure" attached to any degeneration of projective varieties over a finite field of characteristic p which satisfies a p-adic lifting assumption. Our limiting Frobenius structure is shown to be effectively computable in an appropriate sense for a degeneration of projective hypersurfaces. We conjecture that the limiting Frobenius structure relates to the rigid cohomology of a semistable limit of the degeneration through an analogue of the Clemens-Schmidt exact sequence. Our construction is illustrated, and conjecture supported, by a selection of explicit examples.Comment: 41 page

Thermal infrared observations of near-Earth asteroid 2002 NY40

We obtained N-band observations of the Apollo asteroid 2002 NY40 during its close Earth fly-by in August 2002 with TIMMI2 at the ESO 3.6 m telescope. The photometric measurement allowed us to derive a radiometric diameter of 0.28+/-0.03 km and an albedo of 0.34+/-0.06 through the near-Earth asteroid thermal model (NEATM) and a thermophysical model (TPM). The values are in agreement with results from radar data, visual and near-IR observations. In this first comparison between these two model approaches we found that the empirical NEATM beaming parameter $\eta$=1.0 corresponds to a thermal inertia values of about 100 $\mathrm{J m^{-2} s^{-0.5} K^{-1}}$ for a typical range of surface roughness, assuming an equator-on viewing angle. Our TPM analysis indicated that the surface of 2002 NY40 consists of rocky material with a thin or no dust regolith. The asteroid very likely has a prograde sense of rotation with a cold terminator at the time of our observations. Although both model approaches can fit the thermal spectra taken at phase angles of 22$^{\circ}$ and 59$^{\circ}$, we did not find a consistent model solution that describes all pieces of photometric and spectroscopic data. In addition to the 2002 NY40 analysis, we discuss the possibilities to distinguish between different models with only very few photometric and/or spectroscopic measurements spread over a range of phase angles.Comment: 6 pages, 4 figures, A&A accepte

Resolving the Outer Disks and Halos of Nearby Galaxies

In a hierarchical merging scenario, the outer parts of a galaxy are a fossil record of the galaxy's early history. Observations of the outer disks and halos of galaxies thus provide a tool to study individual galaxy histories and test formation theories. Locally, an impressive effort has been made to understand the halo of the Milky Way, Andromeda, and M33. However, due to the stochastic nature of halo formation, a better understanding of this process requires a large sample of galaxies with known halo properties. The GHOSTS project (PI: R. de Jong) aims to characterize the halos and outer portions of 14 nearby (D=4-14 Mpc) spiral galaxies using the Hubble Space Telescope. Detection of individual stars in the outer parts of these galaxies enables us to study both the morphological properties of the galaxies, and determine the stars' metallicity and age.Comment: Contributed talk; to appear in the proceedings of "Galaxies in the Local Volume" Sydney 8-13 July 200

Anonymising pathology data using generative adversarial networks

Anonymising medical data for use in machine learning is important to preserve patient privacy and, in many circumstances, is a requirement before data can be made available. One approach to anonymising image data is to train a generative model to produce data that is statistically similar to the input data and then use the output of the model for downstream tasks, such as image classification, instead of the original sensitive data. In digital pathology, it's not yet well understood how using generative models to anonymise histology slide data impacts the performance of downstream tasks. To begin addressing this, we present an evaluation of a histology image classifier trained using patches extracted from the Camelyon 16 dataset and compare it to a classifier trained on the same number of synthetic images generated with a Deep Convolutional Generative Adversarial Network (DCGAN), from the same data. When predicting the class of an image patch as either cancer or normal it's shown that the accuracy reduces from 0.78 for original alone to 0.59 for synthetic alone, and the recall is significantly reduced from 0.70 to 0.44 when training exclusively on the same amount of synthetic data. If retaining a similar accuracy is required for the downstream task, then either the original data must be used or an improved anonymisation strategy must be devised. We conclude that using this DCGAN to anonymise the dataset, degrades the accuracy of the classifier which implies that it has failed to capture the required variation in the original data to generalise and act as a sufficient anonymisation strategy.Publisher PDFPublisher PD

Imaging the Molecular Gas Properties of a Major Merger Driving the Evolution of a z=2.5 Submillimeter Galaxy

We report the detection of spatially extended CO 1-0 and 5-4 emission in the z=2.49 submillimeter galaxy (SMG) J123707+6214, using the Expanded Very Large Array and the Plateau de Bure Interferometer. The large molecular gas reservoir is spatially resolved into two CO(1-0) components (north-east and south-west; previously identified in CO 3-2 emission) with gas masses of 4.3 and 3.5 x 10^10 (alpha_CO/0.8) Msun. We thus find that the optically invisible north-east component slightly dominates the gas mass in this system. The total molecular gas mass derived from the CO(1-0) observations is ~2.5 times larger than estimated from CO(3-2). The two components are at approximately the same redshift, but separated by ~20 kpc in projection. The morphology is consistent with that of an early-stage merger. The total amount of molecular gas is sufficient to maintain the intense 500 Msun/yr starburst in this system for at least ~160 Myr. We derive line brightness temperature ratios of r_31=0.39+/-0.09 and 0.37+/-0.10, and r_51=0.26+/-0.07 and 0.25+/-0.08 in the two components, respectively, suggesting that the J>=3 lines are substantially subthermally excited. This also suggests comparable conditions for star formation in both components. Given the similar gas masses of both components, this is consistent with the comparable starburst strengths observed in the radio continuum emission. Our findings are consistent with other recent studies that find evidence for lower CO excitation in SMGs than in high-z quasar host galaxies with comparable gas masses. This may provide supporting evidence that both populations correspond to different evolutionary stages in the formation of massive galaxies.Comment: 6 pages, 4 figures, to appear in ApJL (accepted April 12, 2011

The velocity dispersion and mass profile of the Milky Way

We re-analyse the velocity-dispersion profile sigma(r) at radii r>10 kpc in the Galactic stellar halo, recently derived by Battaglia et al. (2005), who concluded that, for constant velocity anisotropy of the tracers, these data rule out a flat circular-speed curve for the Milky Way. However, we demonstrate that if one makes the natural assumption that the tracer density is truncated at r_t >~ 160 kpc and falls off significantly more steeply than r^-3.5 at r >~ 80 kpc, then these data are consistent with a flat circular-speed curve and a constant velocity anisotropy comparable to that observed for halo stars in the Solar neighbourhood. We also consider a more detailed mass model with an exponential stellar disc and an extended non-isothermal dark-matter halo. In this two-component model, the Milky Way's virial radius and mass are r_vir = 200 kpc and M_vir = 1.5 x 10^12 M_sun. Still assuming the tracers' velocity anisotropy to be constant (at beta=0.5) we again find good agreement with the observed sigma(r), so long as the tracer density is truncated near the virial radius. These data by themselves do not allow to differentiate between different dark-halo or total-mass models for the Milky Way, nor between different velocity-anisotropy profiles for the tracers.Comment: 5 pages, 4 figures, accepted for publication in MNRA

Generative deep learning in digital pathology workflows

Funding: Supported by the Sir James Mackenzie Institute for Early Diagnosis, University of St Andrews and Industrial Centre for Artificial Intelligence Research in Digital Diagnostics (grant number TS/S013121/1).Many modern histopathology laboratories are in the process of digitising their workflows. Once images of the tissue exist as digital data, it becomes feasible to research the augmentation or automation of clinical reporting and diagnosis. The application of modern computer vision techniques, based on Deep Learning, promise systems that can identify pathologies in slide images with a high degree of accuracy. Generative modelling is an approach to machine learning and deep learning that can be used to transform and generate data. It can be applied to a broad range of tasks within digital pathology including the removal of color and intensity artefacts, the adaption of images in one domain into those of another, and the generation of synthetic digital tissue samples. This review provides an introduction to the topic, considers these applications, and discusses some future directions for generative models within histopathology.PostprintPeer reviewe

A qualitative study of primary care professionals’ views of case finding for depression in patients with diabetes or coronary heart disease in the UK

<p>Background Routinely conducting case finding (also commonly referred to as screening) in patients with chronic illness for depression in primary care appears to have little impact. We explored the views and experiences of primary care nurses, doctors and managers to understand how the implementation of case finding/screening might impact on its effectiveness.</p> <p>Methods Two complementary qualitative focus group studies of primary care professionals including nurses, doctors and managers, in five primary care practices and five Community Health Partnerships, were conducted in Scotland.</p> <p>Results We identified several features of the way case finding/screening was implemented that may lead to systematic under-detection of depression. These included obstacles to incorporating case finding/screening into a clinical review consultation; a perception of replacing individualised care with mechanistic assessment, and a disconnection for nurses between management of physical and mental health. Far from being a standardised process that encouraged detection of depression, participants described case finding/screening as being conducted in a way which biased it towards negative responses, and for nurses, it was an uncomfortable task for which they lacked the necessary skills to provide immediate support to patients at the time of diagnosis.</p> <p>Conclusion The introduction of case finding/screening for depression into routine chronic illness management is not straightforward. Routinized case finding/screening for depression can be implemented in ways that may be counterproductive to engagement (particularly by nurses), with the mental health needs of patients living with long term conditions. If case finding/screening or engagement with mental health problems is to be promoted, primary care nurses require more training to increase their confidence in raising and dealing with mental health issues and GPs and nurses need to work collectively to develop the relational work required to promote cognitive participation in case finding/screening.</p&gt

Short chain fatty acid production from mycoprotein and mycoprotein fibre in an in vitro fermentation model

Dietary mycoprotein (marketed as QuornTM) has many health benefits, including reductions in energy intake. The majority of studies evaluating mycoprotein focus on the protein content and very few consider the fibre content. Fibre consumption is also associated with decreased energy intake, which is partly attributed to short chain fatty acids (SCFAs) from fibre fermentation by colonic bacteria. To study the SCFA-producing capability of mycoprotein, in vitro batch fermentations were conducted, and SCFA production compared with that from extracted mycoprotein fibre, oligofructose (OF), rhamnose, and laminarin. Mycoprotein and mycoprotein fibre were both fermentable, resulting in a total SCFA production of 24.9 (1.7) and 61.2 (15.7) mmol/L, respectively. OF led to a significantly higher proportion of acetate compared to all other substrates tested (92.6 (2.8)%, p < 0.01). Rhamnose generated the highest proportion of propionate (45.3 (2.0)%, p < 0.01), although mycoprotein and mycoprotein fibre yielded a higher proportion of propionate compared with OF and laminarin. Butyrate proportion was the highest with laminarin (28.0 (10.0)although mycoprotein fibre led to a significantly higher proportion than OF (p < 0.01). Mycoprotein is a valuable source of dietary protein, but its fibre content is also of interest. Further evaluation of the potential roles of the fibre content of mycoprotein is required

Second Set of Spaces

This document describes the Gloss infrastructure supporting implementation of location-aware services. The document is in two parts. The first part describes software architecture for the smart space. As described in D8, a local architecture provides a framework for constructing Gloss applications, termed assemblies, that run on individual physical nodes, whereas a global architecture defines an overlay network for linking individual assemblies. The second part outlines the hardware installation for local sensing. This describes the first phase of the installation in Strathclyde University