State-space inference and learning with Gaussian processes

State-space inference and learning with Gaussian processes (GPs) is an unsolved problem. We propose a new, general methodology for inference and learning in nonlinear state-space models that are described probabilistically by non-parametric GP models. We apply the expectation maximization algorithm to iterate between inference in the latent state-space and learning the parameters of the underlying GP dynamics model. Copyright 2010 by the authors.

Bayesian inference and learning in Gaussian process state-space models with Particle MCMC

State-space models are successfully used in many areas of science, engineering and economics to model time series and dynamical systems. We present a fully Bayesian approach to inference and learning (i.e. state estimation and system identification) in nonlinear nonparametric state-space models. We place a Gaussian process prior over the state transition dynamics, resulting in a flexible model able to capture complex dynamical phenomena. To enable efficient inference, we marginalize over the transition dynamics function and, instead, infer directly the joint smoothing distribution using specially tailored Particle Markov Chain Monte Carlo samplers. Once a sample from the smoothing distribution is computed, the state transition predictive distribution can be formulated analytically. Our approach preserves the full nonparametric expressivity of the model and can make use of sparse Gaussian processes to greatly reduce computational complexity.

Single nucleon potential and effective mass with ground state correlations in hot nuclear matter

In the framework of the finite temperature Brueckner-Hartree-Fock approach including the contribution of the microscopic three-body force, the single nuclear potential and the nucleon effective mass in hot nuclear matter at various temperatures and densities have been calculated by using the hole-line expansion for mass operator, and the effects of the three-body forces and the ground state correlations on the single nucleon potential have been investigated. It is shown that both the ground state correlations and the three-body force affect considerably the density and temperature dependence of the single nucleon potential. The rearrangement correction in the single nucleon potential is repulsive and it reduces remarkably the attraction of the single nucleon potential in the low-momentum region. The rearrangement contribution due to the ground state correlations becomes smaller as the temperature rises up and becomes larger as the density increases. The effect of the three-body force on the ground state correlations is to reduce the contribution of rearrangement. At high densities, the single nucleon potential containing both the rearrangement correction and the contribution of the three-body force becomes more repulsive as the temperature increases.

SPIN AND VALENCE STATE EQUILIBRIA OF COBALT AND MAGNETIC-PROPERTIES OF LACOO3

On the basis of the spin and valence state equilibria and superexchange interaction of the various cobalt ions in LaCoO3, an approximate semiempirical formula has been proposed and used to calculate magnetic susceptibilities of LaCoO3 over a wide temperature range (100-1200 K). The results indicate that there are thermodynamic equilibria between the low spin state Co(III) (t2g6e(g)0) ion, the high spin state Co3+ (t2g4e(g)2) ion, the Co(II) (t2g6e(g)1) ion and the Co(IV) (t2g5e(g)0) ion in LaCoO3. The energy difference between the low spin state Co(III) and the high spin state Co3+ is about 0.006 eV. The content of the low spin state Co(III) ion is predominant in LaCoO3 and the content of the high spin state Co3+ ion varies with temperature, reaching a maximum at about 350 K, then decreasing gradually with increasing temperature. At low temperature the contents of the Co(II) ion and the Co(IV) ion in LaCoO3 are negligible, while above 200 K the contents of both the Co(II) ion and the Co(IV) ion increase with increasing temperature; however, the content of the Co(II) ion always is larger than that of the Co(IV) ion at any temperature. These calculated results are in good agreement with experimental results of the Mossbauer effect, magnetic susceptibility and electrical conductivity of LaCoO3.

A 3-min all-out test to determine peak oxygen uptake and the maximal steady state

Burnley, M., Doust, J., Vanhatalo, A., A 3-min all-out test to determine peak oxygen uptake and the maximal steady state, Medicine & Science in Sports & Exercise. 38(11):1995-2003, November 2006. RAE2008

Participation by place-based community organisations in local development: case studies from East Cork

The past two decades have witnessed concerted efforts by theorists and policy-makers to place civil society at the centre of social, economic and environmental development processes. To this end, policies grounded in a Third Way approach have sought to forge stronger linkages between the state and voluntary community-based organisations. Concepts such as active citizenship, social capital, partnership and sustainability have underpinned this political philosophy, which reflects a movement in development theory and political science away from notions of state-led development and unfettered neo-liberalism. In the Irish context, a series of initiatives have given expression to this new policy agenda, the foremost amongst them the publication of a White Paper in 2000. New local governance structures and development schemes have multiplied since the early 1990s, while the physical planning system has also been modified. All this has taken place against the backdrop of unprecedented economic development and social change precipitated by the ‘Celtic Tiger’.This thesis examines the interaction between community organisations, state institutions and other actors in development processes in East Cork. It focuses upon place-based community organisations, who seek to represent the interests of their particular localities. A case study approach is employed to explore the realpolitik of local development and to gauge the extent to which grassroots community organisations wield influence in determining the development of their communities. The study concludes that the transfer of decision-making power to community organisations has been more illusory than real and that, in practical terms, such groups remain marginal in the circuits of power. However, the situation of community organisations operating in different geographical locales cannot be reduced to an overarching theoretical logic. The case studies show that the modus operandi of community groups varies considerably and can be influenced by specific local geographies, events and personalities.

Crystal engineering: exploiting variation of sulfur oxidation for the control of the solid state structure of organosulfur compounds

This thesis is focused on the design and synthesis of a diverse range of novel organosulfur compounds (sulfides, sulfoxides and sulfones), with the objective of studying their solid state properties and thereby developing an understanding of how the molecular structure of the compounds impacts upon their solid state crystalline structure. In particular, robust intermolecular interactions which determine the overall structure were investigated. These synthons were then exploited in the development of a molecular switch. Chapter One provides a brief overview of crystal engineering, the key hydrogen bonding interactions utilized in this work and also a general insight into “molecular machines” reported in the literature of relevance to this work. Chapter Two outlines the design and synthetic strategies for the development of two scaffolds suitable for incorporation of terminal alkynes, organosulfur and ether functionalities, in order to investigate the robustness and predictability of the S=O•••H-C≡C- and S=O•••H-C(α) supramolecular synthons. Crystal structures and a detailed analysis of the hydrogen bond interactions observed in these compounds are included in this chapter. Also the biological activities of four novel tertiary amines are discussed. Chapter Three focuses on the design and synthesis of diphenylacetylene compounds bearing amide and sulfur functionalities, and the exploitation of the N-H•••O=S interactions to develop a “molecular switch”. The crystal structures, hydrogen bonding patterns observed, NMR variable temperature studies and computer modelling studies are discussed in detail. Chapter Four provides the overall conclusions from chapter two and chapter three and also gives an indication of how the results of this work may be developed in the future. Chapter Five contains the full experimental details and spectral characterisation of all novel compounds synthesised in this project, while details of the NCI (National Cancer Institute) biological test results are included in the appendix.

The Shawlies: A study of early neoliberal ‘gender-fication’. The Street Trading Act, 1926, modern gender-fication, and the implications for Cork’s women street traders

For centuries Cork’s Shawlies, working-class women, survived by trading on public streets. My study explores how the first Irish Free State government, and Cork’s local authority, limited the rights of poor women to earn by subsistence trading with The Street Trading Act, 1926. The government insisted this would regulate street trading. In practice it further marginalised the women economically and socially, containing them outside the privileged, commercial city centre. In Cork the legislation facilitated the gradual disappearance of the Shawlies amid entrenched social processes and relations, contingencies that allowed for the abuse of their rights in the service of amalgamated business interests. This study address the role of discourses in deepening this marginalisation. My theoretical framework is designed to demonstrate how a seemingly innocuous piece of legislation would, in practice, do this. I set out the concepts of ‘Thriving State’, ‘Prosperous State’, and state of ‘Best Intentions’ that uses gentrification to meet these goals. The existing knowledge on women in trade is then examined, highlighting the gaps in what is known about the Shawlies. Chapter 3 details the theory behind my genealogical method. The legislation, debate, and other data produced at the national level is then examined, before moving to the local data. Chapter 6 is devoted to the Shawlies, setting their stories in the larger context of the debates. An examination of studies of contemporary women street traders in poor nations follows, along with a brief history of the decline of street trading in New York city under gentrification. Points of convergence between that process and the one in Cork are identified, along with convergences between contemporary traders and the Shawlies. The conclusion sets out my methodological, theoretical and substantive discoveries, and comments on current nostalgic renderings of the Shawlies in Cork’s newly gentrified Corn Market Street.

Vibrational spectroscopy and DFT calculations of the di-amino acid peptide L-aspartyl-L-glutamic acid in the zwitterionic state

Solid state IR and Raman as well as aqueous solution state Raman spectra are reported for the linear di-amino acid peptide L-aspartyl-L-glutamic acid (L-Asp-L-Glu); the solution state Raman spectrum has also been obtained for the N,O-deuterated derivative. SCF-DFT calculations at the B3-LYP/cc-pVDZ level established that the structure and vibrational spectra of L-Asp-L-Glu can be interpreted using a model of the peptide with ten hydrogen-bonded water molecules, in conjunction with the conductor-like polarizable continuum solvation method. The DFT calculations resulted in the computation of a stable zwitterionic structure, which displays trans-amide conformation. The vibrational spectra were computed at the optimised molecular geometry, enabling normal coordinate analysis, which yielded satisfactory agreement with the experimental IR and Raman data. Computed potential energy distributions of the normal modes provided detailed vibrational assignments.

Unanticipated biological changes and global warming

Evidence of global warming is now unequivocal, and studies suggest that it has started to influence natural systems of the planet, including the oceans. However, in the marine environment, it is well-known that species and ecosystems can also be influenced by natural sources of large-scale hydro-climatological variability. The North Atlantic Oscillation (NAO) was negatively correlated with the mean abundance of one of the subarctic key species Calanus finmarchicus in the North Sea. This correlation was thought to have broken down in 1996, however, the timing has never been tested statistically. The present study revisits this unanticipated change and reveals that the correlation did not break down in 1996 as originally proposed but earlier, at the time of an abrupt ecosystem shift in the North Sea in the 1980s. Furthermore, the analyses demonstrate that the correlation between the NAO and C. finmarchicus abundance is modulated by the thermal regime of the North Sea, which in turn covaries positively with global temperature anomalies. This study thereby provides evidence that global climate change is likely to alter some empirical relationships found in the past between species abundance or the ecosystem state and large-scale natural sources of hydro-climatological variability. A theory is proposed to explain how this might happen. These unanticipated changes, also called ‘surprises’ in climatic research, are a direct consequence of the complexity of both climatic and biological systems. In this period of rapid climate change, it is therefore hazardous to integrate meteo-oceanic indices such as the NAO in models used in the management of living resources, as it has been sometimes attempted in the past.

'Foreign' Terror? London Bombings, Resistance and the Failing State

The British government's response to the London bombings sought to make the terror of that day foreign, even though it appeared largely domestic. This helped construct it as unusual, contingent, part of the uncontrollable ‘otherness’ of the ‘foreign’. However, it also drew the response into the arena of British foreign policy, where the ‘failing state’ has been the dominant conceptualisation of insecurity and terrorism, especially since September 11th. When the bombings are examined through the ‘failing state’ disturbing and important problems are uncovered. Primarily, the ‘failing state’ discourse deconstructs under the influence of the terrorism in London, revealing that Britain itself is a ‘failing state’ by its own description and producing a generalisation of state ‘failure’. It thereby reveals several possible sites for responding to and resisting the government's representation.

Control-limited perfect state transfer, quantum stochastic resonance, and many-body entangling gate in imperfect qubit registers

We propose a protocol for perfect quantum state transfer that is resilient to a broad class of realistic experimental imperfections, including noise sources that could be modeled either as independent Markovian baths or as certain forms of spatially correlated environments. We highlight interesting connections between the fidelity of state transfer and quantum stochastic resonance effects. The scheme is flexible enough to act as an effective entangling gate for the generation of genuine multipartite entanglement in a control-limited setting. Possible experimental implementations using superconducting qubits are also briefly discussed.

‘It ain’t easy being green’: Sustainable Development between Environment and Economy in Northern Ireland’

Given the relative lack of research on sustainable development in Northern Ireland, this paper focuses on the tensions between environmental governance and regulation on the one hand, and the ‘post-conflict’ imperative for Northern Ireland to compete and grow as a regional economy without continued British state subvention and subsidisation. The paper outlines how this ‘trade-off’ between ‘environment’ and ‘economy’ is essentially misplaced. It argues that this trade-off can be avoided if there is a shift in focus from an ‘environment versus the economy’ policy position to one in which the ‘triple bottom line’ (social, economic and environmental) of sustainable development becomes the over-arching policy agenda. Sustainable development, unlike either orthodox environmental or economic policy, also connects centrally with the unique ‘post-conflict transformation’ agenda of Northern Ireland. For example, promoting a human rights civic culture, tackling socioeconomic inequality and social exclusion, and building a shared future based on supporting sustainable communities and an innovative model of a ‘green(ing) economy’ goes beyond orthodox economic growth. However, it is clear from the Executive’s Programme for Government, failure to support the creation of an independent Environment Protection Agency, and above all the prioritisation of orthodox economic growth based on foreign direct investment that neither environmental protection nor sustainable development is or will be high on the political or policy agenda in Northern Ireland.

Biomarkers of fruit and vegetable intake in Human intervention studies a systematic review

Observational evidence consistently shows that consumption of a diet rich in fruit and vegetables may offer protection against diseases such as cardiovascular disease and cancer. Assessment of dietary intake is complex and prone to many sources of error. More objective biomarkers of fruit and vegetable intake are therefore of interest. The aim of this review is to examine the usefulness of the main biomarkers of fruit and vegetable intake to act as objective indicators of compliance in dietary intervention studies. A comprehensive search of the literature was conducted using six databases. Suitable papers were selected and relevant data extracted. The papers were categorized into 3 sub-groups: whole diet interventions; mixed fruit and vegetable interventions; and studies involving individual varieties of fruits or vegetables. Ninety-six studies were included in the review. Overall, the most commonly measured, and most consistently responsive, biomarkers were the carotenoids and vitamin C. Based on the results of this systematic review, it remains prudent to measure a panel of biomarkers in fruit and vegetable intervention studies. The only possible exception to this is “fruit only” intervention studies where assessment of vitamin C alone may suffice.