Soft sediment ecology of Lough Hyne Marine Reserve - spatial and temporal patterns

Distribution of soft sediment benthic fauna and the environmental factors affecting them were studied, to investigate changes across spatial and temporal scales. Investigations took place at Lough Hyne Marine Reserve using a range of methods. Data on the sedimentation rates of organic and inorganic matter were collected at monthly intervals for one year at a number of sites around the Lough, by use of vertical midwater-column sediment traps. Sedimentation of these two fractions were not coupled; inorganic matter sedimentation depended on hydrodynamic and weather factors, while the organic matter sedimentation was more complex, being dependent on biological and chemical processes in the water column. The effects of regular hypoxic episodes on benthic fauna due to a natural seasonal thermocline were studied in the deep Western Trough, using camera-equipped remotely-operated vehicle to follow transects, on a three-monthly basis over one year. In late summer, the area below the thermocline of the Western Trough was devoid of visible fauna. Decapod crustaceans were the first taxon to make use of ameliorating oxygen conditions in autumn, by darting below the thermocline depth, most likely to scavenge. This was indicated by tracks that they left on the surface of the Trough floor. Some species, most noticeably Fries’ goby Lesueurigobius friesii, migrated below the thermocline depth when conditions were normoxic and established semi-permanent burrows. Their population encompassed all size classes, indicating that this habitat was not limited to juveniles of this territorial species. Recolonisation by macrofauna and burrowing megafauna was studied during normoxic conditions, from November 2009 to May 2010. Macrofauna displayed a typical post-disturbance pattern of recolonisation with one species, the polychaete Scalibregma inflatum, occurring at high abundance levels in March 2010. In May, this population had become significantly reduced and a more diverse community was established. The abundance of burrowing infauna comprising decapods crabs and Fries’ gobies, was estimated by identifying and counting their distinctive burrow structures. While above the summer thermocline depth, burrow abundance increased in a linear fashion, below the thermocline depth a slight reduction of burrow abundance occurred in May, when oxygen conditions deteriorated again. The majority of the burrows occurring in May were made by Fries’ gobies, which are thought to encounter low oxygen concentrations in their burrows. Reduction in burrow abundance of burrowing shrimps Calocaris macandreae and Callianassa subterranea (based on descriptions of burrow structures from the literature), from March to May, might be related to their reduced activity in hypoxia, leading to loss of structural burrow maintenance. Spatial and temporal changes to macrofaunal assemblage structures were studied seasonally for one year across 5 sites in the Lough and subject to multivariate statistical analysis. Assemblage structures were significantly correlated with organic matter levels in the sediment, the amounts of organic matter settling out of the water column one month before macrofaunal sampling took place as well as current speed and temperature. This study was the first to investigate patterns and processes in the Lough soft sediment ecology across all 3 basins on a temporal and spatial scale. An investigation into the oceanographic aspects of the development, behaviour and break-down of the summer thermocline of Lough Hyne was performed in collaboration with researchers from other Irish institutions.

Synecology in soft sediment bivalves: the influence of parasites, physiological processes, and environmental stressors on health and disease

Ecosystem goods and services provided by estuarine and near coastal regions are being increasingly recognised for their immense value, as is the biodiversity in these areas and these near coastal communities have been identified as sentinels of climate change also. Population structure and reproductive biology of two bivalve molluscs, Cerastoderma edule and, Mytilus edulis were assessed at two study sites over a 16-month study period. Following an anomalously harsh winter, advancement of spawning time was observed in both species. Throughout Ireland and Europe the cockle has experienced mass surfacings in geographically distinct regions, and a concurrent study of cockles was undertaken to explore this phenomenon. Surfaced and buried cockles were collected on a monthly basis and their health compared. Age was highlighted as a source of variation between dying and healthy animals with a parasite threshold being reached possibly around age three. Local factors dominated when looking at the cause of surfacing at each site. The health of mussels was explored too on a temporal and seasonal basis in an attempt to assess what constitutes a healthy organism. In essence external drivers can tip the balance between “acceptable” levels of infection where the mussel can still function physiologically and “unacceptable” where prevalence and intensity of infection can result in physiological impairment at the individual and population level. Synecological studies of intertidal ecosystems are lacking, so all bivalves encountered during the sampling were assessed in terms of population structure, reproduction, and health. It became clear, that some parasites might specialize on one host species while others are not so specific in host choice. Furthermore the population genetics of the cockle, its parasite Meiogymnophallus minutus, and its hyperparasite Unikaryon legeri were examined too. A small nucleotide polymorphism was detected upon comparison of Ireland and Morocco.

Reasoning with sorted-pareto dominance and other qualitative and partially ordered preferences in soft constraints

In decision making problems where we need to choose a particular decision or alternative from a set of possible choices, we often have some preferences which determine if we prefer one decision over another. When these preferences give us an ordering on the decisions that is complete, then it is easy to choose the best or one of the best decisions. However it often occurs that the preferences relation is partially ordered, and we have no best decision. In this thesis, we look at what happens when we have such a partial order over a set of decisions, in particular when we have multiple orderings on a set of decisions, and we present a framework for qualitative decision making. We look at the different natural notions of optimal decision that occur in this framework, which gives us different optimality classes, and we examine the relationships between these classes. We then look in particular at a qualitative preference relation called Sorted-Pareto Dominance, which is an extension of Pareto Dominance, and we give a semantics for this relation as one that is compatible with any order-preserving mapping of an ordinal preference scale to a numerical one. We apply Sorted-Pareto dominance to a Soft Constraints setting, where we solve problems in which the soft constraints associate qualitative preferences to decisions in a decision problem. We also examine the Sorted-Pareto dominance relation in the context of our qualitative decision making framework, looking at the relevant optimality classes for the Sorted-Pareto case, which gives us classes of decisions that are necessarily optimal, and optimal for some choice of mapping of an ordinal scale to a quantitative one. We provide some empirical analysis of Sorted-Pareto constraints problems and examine the optimality classes that result.

X-ray and optical studies of soft x-ray transients in M31

Soft X-ray transients (SXTs) are a subgroup of low-mass X-ray binaries consisting of a neutron star or a black hole and a companion low-mass star. SXTs exhibit a sudden outburst by increasing the luminosity from ∼ 1033 to ∼ 1036−38ergs1. After spending a few months in outburst, SXTs switch back to quiescence. Optical study of the binary system during the quiescence state of SXTs provides an opportunity to discriminate between BH binaries and neutron star binaries. The first part ot this research is composed of result of 10 years joint project between Hubble space telescope and Chandra, to study SXTs in M31. The other part of this thesis focused on the light curve of bright SXTs in M31. Disc irradiation is thought to be capable of explaining the global behaviour of the light curves of SXTs. Depending on the strength of the central X-ray emission in irradiating the disc, the light curve may exhibit an exponential or a linear decay. The model predicts that in brighter transients a transition from exponential decline to a linear one may be detectable. In this study, having excluded super-soft sources and hard X-ray transients, a sample of bright SXTs in M31 (Lpeak > 1038ergs1) has been studied. The expected change in the shape of the decay function is only observed in two of the light curves from the six light curves in the sample. Also, a systematic correlation between the shape of the light curve and the X-ray luminosity has not been seen.

Magnetic materials and soft-switched topologies for high-current DC-DC converters

The thesis is focused on the magnetic materials comparison and selection for high-power non-isolated dc-dc converters for industrial applications or electric, hybrid and fuel cell vehicles. The application of high-frequency bi-directional soft-switched dc-dc converters is also investigated. The thesis initially outlines the motivation for an energy-efficient transportation system with minimum environmental impact and reduced dependence on exhaustible resources. This is followed by a general overview of the power system architectures for electric, hybrid and fuel cell vehicles. The vehicle power sources and general dc-dc converter topologies are discussed. The dc-dc converter components are discussed with emphasis on recent semiconductor advances. A novel bi-directional soft-switched dc-dc converter with an auxiliary cell is introduced in this thesis. The soft-switching cell allows for the MOSFET's intrinsic body diode to operate in a half-bridge without reduced efficiency. The converter's mode-by-mode operation is analysed and closed-form expressions are presented for the average current gain of the converter. The design issues are presented and circuit limitations are discussed. Magnetic materials for the main dc-dc converter inductor are compared and contrasted. Novel magnetic material comparisons are introduced, which include the material dc bias capability and thermal conductivity. An inductor design algorithm is developed and used to compare the various magnetic materials for the application. The area-product analysis is presented for the minimum inductor size and highlights the optimum magnetic materials. Finally, the high-flux magnetic materials are experimentally compared. The practical effects of frequency, dc-bias, and converters duty-cycle effect for arbitrary shapes of flux density, air gap effects on core and winding, the winding shielding effect, and thermal configuration are investigated. The thesis results have been documented at IEEE EPE conference in 2007 and 2008, IEEE APEC in 2009 and 2010, and IEEE VPPC in 2010. A 2011 journal has been approved by IEEE Transactions on Power Electronics.

The reproductive biology of the soft shell clam Mya arenaria in Ireland and the possible impacts of climate variability

Little is known about the biology of the softshell clam in Europe, despite it being identified as a potential species to culture for food in the future. Monthly samples of the softshell clam, Mya arenaria, were collected intertidally from Co. Wexford, Ireland, over a period of sixteen months. The mean weight of sampled individuals was 7 4 ± 4 . 9  g and mean length was 8 . 2 ± 0 . 2  cm. Histological examination revealed a female-to-male ratio of 1 : 1.15. In 2010, M. arenaria at this site matured over the summer months, with both sexes either ripe or spawning by August. A single spawning event was recorded in 2010, completed by November. Two unusually cold winters, followed by a warmer-than-average spring, appear to have affected M. arenaria gametogenesis in this area, potentially affecting the time of spawning, fertilisation success, and recruitment of this species. No hermaphrodites were observed in the samples collected, nor were any pathogens observed. Timing of development and spawning is compared with the coasts of eastern North America and with other European coasts.