A history of physiological optics from 1650 to 1800

Imperial Users onl

Pragmatic Ontology Evolution: Reconciling User Requirements and Application Performance

Increasingly, organizations are adopting ontologies to describe their large catalogues of items. These ontologies need to evolve regularly in response to changes in the domain and the emergence of new requirements. An important step of this process is the selection of candidate concepts to include in the new version of the ontology. This operation needs to take into account a variety of factors and in particular reconcile user requirements and application performance. Current ontology evolution methods focus either on ranking concepts according to their relevance or on preserving compatibility with existing applications. However, they do not take in consideration the impact of the ontology evolution process on the performance of computational tasks – e.g., in this work we focus on instance tagging, similarity computation, generation of recommendations, and data clustering. In this paper, we propose the Pragmatic Ontology Evolution (POE) framework, a novel approach for selecting from a group of candidates a set of concepts able to produce a new version of a given ontology that i) is consistent with the a set of user requirements (e.g., max number of concepts in the ontology), ii) is parametrised with respect to a number of dimensions (e.g., topological considerations), and iii) effectively supports relevant computational tasks. Our approach also supports users in navigating the space of possible solutions by showing how certain choices, such as limiting the number of concepts or privileging trendy concepts rather than historical ones, would reflect on the application performance. An evaluation of POE on the real-world scenario of the evolving Springer Nature taxonomy for editorial classification yielded excellent results, demonstrating a significant improvement over alternative approaches

A Gaussian process framework for modelling instrumental systematics: application to transmission spectroscopy

Transmission spectroscopy, which consists of measuring the wavelength-dependent absorption of starlight by a planet's atmosphere during a transit, is a powerful probe of atmospheric composition. However, the expected signal is typically orders of magnitude smaller than instrumental systematics, and the results are crucially dependent on the treatment of the latter. In this paper, we propose a new method to infer transit parameters in the presence of systematic noise using Gaussian processes, a technique widely used in the machine learning community for Bayesian regression and classification problems. Our method makes use of auxiliary information about the state of the instrument, but does so in a non-parametric manner, without imposing a specific dependence of the systematics on the instrumental parameters, and naturally allows for the correlated nature of the noise. We give an example application of the method to archival NICMOS transmission spectroscopy of the hot Jupiter HD 189733, which goes some way towards reconciling the controversy surrounding this dataset in the literature. Finally, we provide an appendix giving a general introduction to Gaussian processes for regression, in order to encourage their application to a wider range of problems.Comment: 6 figures, 1 table, accepted for publication in MNRA

Implementing vertex dynamics models of cell populations in biology within a consistent computational framework

The dynamic behaviour of epithelial cell sheets plays a central role during development, growth, disease and wound healing. These processes occur as a result of cell adhesion, migration, division, differentiation and death, and involve multiple processes acting at the cellular and molecular level. Computational models offer a useful means by which to investigate and test hypotheses about these processes, and have played a key role in the study of cell–cell interactions. However, the necessarily complex nature of such models means that it is difficult to make accurate comparison between different models, since it is often impossible to distinguish between differences in behaviour that are due to the underlying model assumptions, and those due to differences in the in silico implementation of the model. In this work, an approach is described for the implementation of vertex dynamics models, a discrete approach that represents each cell by a polygon (or polyhedron) whose vertices may move in response to forces. The implementation is undertaken in a consistent manner within a single open source computational framework, Chaste, which comprises fully tested, industrial-grade software that has been developed using an agile approach. This framework allows one to easily change assumptions regarding force generation and cell rearrangement processes within these models. The versatility and generality of this framework is illustrated using a number of biological examples. In each case we provide full details of all technical aspects of our model implementations, and in some cases provide extensions to make the models more generally applicable

The Complexity of Admissibility in Omega-Regular Games

Iterated admissibility is a well-known and important concept in classical game theory, e.g. to determine rational behaviors in multi-player matrix games. As recently shown by Berwanger, this concept can be soundly extended to infinite games played on graphs with omega-regular objectives. In this paper, we study the algorithmic properties of this concept for such games. We settle the exact complexity of natural decision problems on the set of strategies that survive iterated elimination of dominated strategies. As a byproduct of our construction, we obtain automata which recognize all the possible outcomes of such strategies

Connectedness properties of the set where the iterates of an entire function are unbounded

We investigate the connectedness properties of the set I+(f) of points where the iterates of an entire function f are unbounded. In particular, we show that I+(f) is connected whenever iterates of the minimum modulus of f tend to ∞. For a general transcendental entire function f, we show that I+(f)∪ \{\infty\} is always connected and that, if I+(f) is disconnected, then it has uncountably many components, infinitely many of which are unbounded

X-ray and UV observations of V751 Cyg in an optical high state

Aims: The VY Scl system (anti-dwarf nova) V751 Cyg is examined following a claim of a super-soft spectrum in the optical low state. Methods: A serendipitous XMM-Newton X-ray observation and, 21 months later, Swift X-ray and UV observations, have provided the best such data on this source so far. These optical high-state datasets are used to study the flux and spectral variability of V751 Cyg. Results: Both the XMM-Newton and Swift data show evidence for modulation of the X-rays for the first time at the known 3.467 hr orbital period of V751 Cyg. In two Swift observations, taken ten days apart, the mean X-ray flux remained unchanged, while the UV source brightened by half a magnitude. The X-ray spectrum was not super-soft during the optical high state, but rather due to multi-temperature optically thin emission, with significant (10^{21-22} cm^-2) absorption, which was higher in the observation by Swift than that of XMM-Newton. The X-ray flux is harder at orbital minimum, suggesting that the modulation is related to absorption, perhaps linked to the azimuthally asymmetric wind absorption seen previously in H-alpha.Comment: 6 pages, 9 figures, accepted for publication in A&

A universal GRB photon energy-peak luminosity relation

The energetics and emission mechanism of GRBs are not well understood. Here we demonstrate that the instantaneous peak flux or equivalent isotropic peak luminosity, L_iso ergs s^-1, rather than the integrated fluence or equivalent isotropic energy, E_iso ergs, underpins the known high-energy correlations. Using new spectral/temporal parameters calculated for 101 bursts with redshifts from BATSE, BeppoSAX, HETE-II and Swift we describe a parameter space which characterises the apparently diverse properties of the prompt emission. We show that a source frame characteristic-photon-energy/peak luminosity ratio, K_z, can be constructed which is constant within a factor of 2 for all bursts whatever their duration, spectrum, luminosity and the instrumentation used to detect them. The new parameterization embodies the Amati relation but indicates that some correlation between E_peak and E_iso follows as a direct mathematical inference from the Band function and that a simple transformation of E_iso to L_iso yields a universal high energy correlation for GRBs. The existence of K_z indicates that the mechanism responsible for the prompt emission from all GRBs is probably predominantly thermal.Comment: Submitted to Ap

Preparation of Inner Ear Sensory Hair Bundles for High Resolution Scanning Electron Microscopy

Chemical fixation techniques for preservation of sensory hair bundles in the mammalian inner ear for scanning electron microscopy (SEM) are reviewed. Fixatives employed were glutaraldehyde, glutaraldehyde-picrate, glutaraldehyde-tannic acid, glutaraldehyde-formaldehyde, glutaraldehyde followed by postfixation with osmium tetroxide and the osmium thiocarbohydrazide (OTOTO) method. Dehydration was routinely accomplished with ascending grades of acetone followed by critical point drying with liquid CO2 or fluorocarbon sublimation. Specimens other than those prepared by the OTOTO method were metal coated with gold, gold-palladium or platinum. Material was viewed at high resolution (2-3 nm) in a transmission electron microscope (TEM) fitted with a scanning system and an LaB6 filament. A few specimens, which were either coated with platinum, carbon or uncoated, were examined in a field emission SEM. We have concluded that glutaraldehyde fixation followed by critical point drying with CO2 and coating with platinum gives the best general preservation of stereocilia and their cross-links for routine high resolution SEM, but that carbon-coated or uncoated specimens offer potentially better results free from metal coating artifacts when viewed with field emission SEM. These methods have enabled us to make novel observations upon the surface detail and cross-links of stereocilia which have helped considerably in understanding the mechanical properties of hair bundles particularly in relation to sensory transduction. We have found that stereocilial surface detail and cross-links are sensitive to fixation regimes. In particular they are degraded by exposure to osmium tetroxide; they are also highly labile since deleterious changes in their appearance can be detected as early as 15 minutes following death

The spectroscopic evolution of the symbiotic-like recurrent nova V407 Cygni during its 2010 outburst. I. The shock and its evolution

On 2010 Mar 10, V407 Cyg was discovered in outburst, eventually reaching V< 8 and detected by Fermi. Using medium and high resolution ground-based optical spectra, visual and Swift UV photometry, and Swift X-ray spectrophotometry, we describe the behavior of the high-velocity profile evolution for this nova during its first three months. The peak of the X-ray emission occurred at about day 40 with a broad maximum and decline after day 50. The main changes in the optical spectrum began at around that time. The He II 4686A line first appeared between days 7 and 14 and initially displayed a broad, symmetric profile that is characteristic of all species before day 60. Low-excitation lines remained comparatively narrow, with v(rad,max) of order 200-400 km/s. They were systematically more symmetric than lines such as [Ca V], [Fe VII], [Fe X], and He II, all of which showed a sequence of profile changes going from symmetric to a blue wing similar to that of the low ionization species but with a red wing extended to as high as 600 km/s . The Na I D doublet developed a broad component with similar velocity width to the other low-ionization species. The O VI Raman features were not detected. We interpret these variations as aspherical expansion of the ejecta within the Mira wind. The blue side is from the shock penetrating into the wind while the red wing is from the low-density periphery. The maximum radial velocities obey power laws, v(rad,max) t^{-n} with n ~ 1/3 for red wing and ~0.8 for the blue. (truncated)Comment: Accepted for publication, A&A (submitted: 9 Oct 2010; accepted: 1 Dec 2010) in press; based on data obtained with Swift, Nordic Optical Telescope, Ondrejov Observatory. Corrected typo, Fermi?LAT detection was at energies above 100 MeV (with thanks to C. C. Cheung