Integrating ontologies and argumentation for decision-making in breast cancer

This thesis describes some of the problems in providing care for patients with breast cancer. These are then used to motivate the development of an extension to an existing theory of argumentation, which I call the Ontology-based Argumentation Formalism (OAF). The work is assessed in both theoretical and empirical ways. From a clinical perspective, there is a problem with the provision of care. Numerous reports have noted the failure to provide uniformly high quality care, as well as the number of deaths caused by medical care. The medical profession has responded in various ways, but one of these has been the development of Decision Support Systems (DSS). The evidence for the effectiveness of such systems is mixed, and the technical basis of such systems remains open to debate. However, one basis that has been used is argumentation. An important aspect of clinical practice is the use of the evidence from clinical trials, but these trials are based on the results in defined groups of patients. Thus when we use the results of clinical trials to reason about treatments, there are two forms of information we are interested in - the evidence from trials and the relationships between groups of patients and treatments. The relational information can be captured in an ontology about the groups of patients and treatments, and the information from the trials captured as a set of defeasible rules. OAF is an extension of an existing argumentation system, and provides the basis for an argumentation-based Knowledge Representation system which could serve as the basis for future DSS. In OAF, the ontology provides a repository of facts, both asserted and inferred on the basis of formulae in the ontology, as well as defining the language of the defeasible rules. The defeasible rules are used in a process of defeasible reasoning, where monotonic consistent chains of reasoning are used to draw plausible conclusions. This defeasible reasoning is used to generate arguments and counter-arguments. Conflict between arguments is defined in terms of inconsistent formulae in the ontology, and by using existing proposals for ontology languages we are able to make use of existing proposals and technologies for ontological reasoning. There are three substantial areas of novel work: I develop an extension to an existing argumentation formalism, and prove some simple properties of the formalism. I also provide a novel formalism of the practical syllogism and related hypothetical reasoning, and compare my approach to two other proposals in the literature. I conclude with a substantial case study based on a breast cancer guideline, and in order to do so I describe a methodology for comparing formal and informal arguments, and use the results of this to discuss the strengths and weaknesses of OAF. In order to develop the case study, I provide a prototype implementation. The prototype uses a novel incremental algorithm to construct arguments and I give soundness, completeness and time-complexity results. The final chapter of the thesis discusses some general lessons from the development of OAF and gives ideas for future work

Exact steady state solution of the Boltzmann equation: A driven 1-D inelastic Maxwell gas

The exact nonequilibrium steady state solution of the nonlinear Boltzmann equation for a driven inelastic Maxwell model was obtained by Ben-Naim and Krapivsky [Phys. Rev. E 61, R5 (2000)] in the form of an infinite product for the Fourier transform of the distribution function $f(c)$. In this paper we have inverted the Fourier transform to express $f(c)$ in the form of an infinite series of exponentially decaying terms. The dominant high energy tail is exponential, $f(c)\simeq A_0\exp(-a|c|)$, where $a\equiv 2/\sqrt{1-\alpha^2}$ and the amplitude $A_0$ is given in terms of a converging sum. This is explicitly shown in the totally inelastic limit ($\alpha\to 0$) and in the quasi-elastic limit ($\alpha\to 1$). In the latter case, the distribution is dominated by a Maxwellian for a very wide range of velocities, but a crossover from a Maxwellian to an exponential high energy tail exists for velocities $|c-c_0|\sim 1/\sqrt{q}$ around a crossover velocity $c_0\simeq \ln q^{-1}/\sqrt{q}$, where $q\equiv (1-\alpha)/2\ll 1$. In this crossover region the distribution function is extremely small, $\ln f(c_0)\simeq q^{-1}\ln q$.Comment: 11 pages, 4 figures; a table and a few references added; to be published in PR

‘My favourite things to do’ and ‘my favourite people’: Exploring salient aspects of children’s self-concept

This study explores the potential of the ‘draw-and-write’ method for inviting children to communicate salient aspects of their self-concept. Irish primary school children aged 10–13 years drew and wrote about their favourite people and things to do (social and active self). Children drew and described many salient activities (39 in total) and people – including pets. Results suggest that widely used, adult-constructed self-esteem scales for children, while multidimensional, are limited, and that ‘draw-and-write’ is an effective multimodal method with which children can express their social and active self-concepts

Spin dynamics of a trapped spin-1 Bose Gas above the Bose-Einstein transition temperature

We study collective spin oscillations in a spin-1 Bose gas above the Bose-Einstein transition temperature. Starting from the Heisenberg equation of motion, we derive a kinetic equation describing the dynamics of a thermal gas with the spin-1 degree of freedom. Applying the moment method to the kinetic equation, we study spin-wave collective modes with dipole symmetry. The dipole modes in the spin-1 system are found to be classified into the three type of modes. The frequency and damping rate are obtained as functions of the peak density. The damping rate is characterized by three relaxation times associated with collisions.Comment: 19 pages, 5 figur

Dissipative Dynamics of a Josephson Junction In the Bose-Gases

The dissipative dynamics of a Josephson junction in the Bose-gases is considered within the framework of the model of a tunneling Hamiltonian. The effective action which describes the dynamics of the phase difference across the junction is derived using functional integration method. The dynamic equation obtained for the phase difference across the junction is analyzed for the finite temperatures in the low frequency limit involving the radiation terms. The asymmetric case of the Bose-gases with the different order parameters is calculated as well

Nanoindentation Response of 3D Printed PEGDA Hydrogels in a Hydrated Environment

Hydrogels are commonly used materials in tissue engineering and organ-on-chip devices. This study investigated the nanomechanical properties of monolithic and multilayered poly(ethylene glycol) diacrylate (PEGDA) hydrogels manufactured using bulk polymerization and layer-by-layer projection lithography processes, respectively. An increase in the number of layers (or reduction in layer thickness) from 1 to 8 and further to 60 results in a reduction in the elastic modulus from 5.53 to 1.69 and further to 0.67 MPa, respectively. It was found that a decrease in the number of layers induces a lower creep index (CIT) in three-dimensional (3D) printed PEGDA hydrogels. This reduction is attributed to mesoscale imperfections that appear as pockets of voids at the interfaces of the multilayered hydrogels attributed to localized regions of unreacted prepolymers, resulting in variations in defect density in the samples examined. An increase in the degree of cross-linking introduced by a higher dosage of ultraviolet (UV) exposure leads to a higher elastic modulus. This implies that the elastic modulus and creep behavior of hydrogels are governed and influenced by the degree of cross-linking and defect density of the layers and interfaces. These findings can guide an optimal manufacturing pathway to obtain the desirable nanomechanical properties in 3D printed PEGDA hydrogels, critical for the performance of living cells and tissues, which can be engineered through control of the fabrication parameters

Scattering of light and atoms in a Fermi-Dirac gas with BCS pairing

We theoretically study the optical properties of a Fermi-Dirac gas in the presence of a superfluid state. We calculate the leading quantum-statistical corrections to the standard column density result of the electric susceptibility. We also consider the Bragg diffraction of atoms by means of light-stimulated transitions of photons between two intersecting laser beams. Bardeen-Cooper-Schrieffer pairing between atoms in different internal levels magnifies incoherent scattering processes. The absorption linewidth of a Fermi-Dirac gas is broadened and shifted. Bardeen-Cooper-Schrieffer pairing introduces a collisional local-field shift that may dramatically dominate the Lorentz-Lorenz shift. For the case of the Bragg spectroscopy the static structure function may be significantly increased due to superfluidity in the nearforward scattering.Comment: 13 pages, 6 figures; to appear in PR

Finite temperature excitations of a trapped Bose-Fermi mixture

We present a detailed study of the low-lying collective excitations of a spherically trapped Bose-Fermi mixture at finite temperature in the collisionless regime. The excitation frequencies of the condensate are calculated self-consistently using the static Hartree-Fock-Bogoliubov theory within the Popov approximation. The frequency shifts and damping rates due to the coupled dynamics of the condensate, noncondensate, and degenerate Fermi gas are also taken into account by means of the random phase approximation and linear response theory. In our treatment, the dipole excitation remains close to the bare trapping frequency for all temperatures considered, and thus is consistent with the generalized Kohn theorem. We discuss in some detail the behavior of monopole and quadrupole excitations as a function of the Bose-Fermi coupling. At nonzero temperatures we find that, as the mixture moves towards spatial separation with increasing Bose-Fermi coupling, the damping rate of the monopole (quadrupole) excitation increases (decreases). This provides us a useful signature to identify the phase transition of spatial separation.Comment: 10 pages, 8 figures embedded; to be published in Phys. Rev.

Impacts of Climate Change on indirect human exposure to pathogens and chemicals from agriculture

Objective: Climate change is likely to affect the nature of pathogens and chemicals in the environment and their fate and transport. Future risks of pathogens and chemicals could therefore be very different from those of today. In this review, we assess the implications of climate change for changes in human exposures to pathogens and chemicals in agricultural systems in the United Kingdom and discuss the subsequent effects on health impacts. Data sources: In this review, we used expert input and considered literature on climate change ; health effects resulting from exposure to pathogens and chemicals arising from agriculture ; inputs of chemicals and pathogens to agricultural systems ; and human exposure pathways for pathogens and chemicals in agricultural systems. Data synthesis: We established the current evidence base for health effects of chemicals and pathogens in the agricultural environment ; determined the potential implications of climate change on chemical and pathogen inputs in agricultural systems ; and explored the effects of climate change on environmental transport and fate of different contaminant types. We combined these data to assess the implications of climate change in terms of indirect human exposure to pathogens and chemicals in agricultural systems. We then developed recommendations on future research and policy changes to manage any adverse increases in risks. Conclusions: Overall, climate change is likely to increase human exposures to agricultural contaminants. The magnitude of the increases will be highly dependent on the contaminant type. Risks from many pathogens and particulate and particle-associated contaminants could increase significantly. These increases in exposure can, however, be managed for the most part through targeted research and policy changes

Persistent currents in a circular array of Bose-Einstein condensates

A ring-shaped array of Bose-Einstein condensed atomic gases can display circular currents if the relative phase of neighboring condensates becomes locked to certain values. It is shown that, irrespective of the mechanism responsible for generating these states, only a restricted set of currents are stable, depending on the number of condensates, on the interaction and tunneling energies, and on the total number of particles. Different instabilities due to quasiparticle excitations are characterized and possible experimental setups for testing the stability prediction are also discussed.Comment: 7 pages, REVTex