The life history and ecology of black scabbardfish (Aphanopus carbo Lowe 1839) in the north-east Atlantic

The black scabbardfish is a deep water species that supports commercial fisheries across a large area of the NE Atlantic shelf. The life history of black scabbardfish is poorly understood and a major unresolved issue is population structure. In this study it was used a combination of methodologies to get further knowledge in the life history and population structure of A. carbo over its wide distribution range in the Northeast Atlantic. The new knowledge acquired during this study, will increase our ability to better manage this species in the NE Atlantic. It has been postulated that fish caught to the west of the British Isles are pre-adults that migrate further south (to Madeira) for spawning, implying a single panmictic population. In this study, specimens of Aphanopus carbo were sampled between September 2008 and May 2010 from two different areas: NW Scotland (French trawlers and deep water surveys) and Madeira Islands (longliners commercial landings). Geographical differences in reproductive state of scabbardfish were evident, supportive of a north-south migration theory. In the northern area, all specimens found were immature, while in Madeira all maturity stages were observed. In Madeira, spawning occurred during the fourth quarter, with peak maturity in October (males) and in November (females). The age of this species has proven difficult and has led to different and contradictory age and growth estimates. For this study, we used two reading interpretations to determine age and estimate the growth parameters. To the west of the British Isles, specimens reached a lower maximum age and had a higher growth rate than those caught off Madeira. These differences are consistent with the theory of a single population of black scabbardfish in the NE Atlantic, highly segregate, with smaller, immature and younger fish caught to the west of the British Isles and bigger and mature caught in Madeira Islands. The feeding ecology showed strong evidence that the diet of black scabbardfish is associated with the spawning migration of blue whiting, which may support a northerly feeding migration theory for black scabbardfish. The stable isotope analyses in the muscle of black scabbardfish identified that black scabbardfish feeds on species with epipelagic and benthopelagic affinities. Comparison with stable isotope analysis in Madeira samples indicated that black scabbardfish feed at a similar trophic level and has the same trophic niche width in both areas, assuming similar baseline isotope compositions. Otolith stable isotopes (oxygen - δ18O and nitrogen - δ15N) analyses were used as a tool to clarify migratory behaviour. Otolith isotope ratios can provide insight into whether adults caught around Madeira fed in an isotopically depleted northerly ecosystem (NW Scotland) during their pre-adult period and then migrate towards south to spawn. Overall, the results support a south-north migration of pre adult fish from spawning areas around Madeira and a north-south migration from the west of Scotland to the spawning areas. Given its life cycle there is an urgent need that the management process recognizes the existence of a continuous widely distributed stock of black scabbardfish between the west of the British Isles and Madeira. The results highlight large scale dispersal in this species which needs to be treated as a highly migratory species and be managed as a single population.

Functional genomics of commensal Lactobacilli

Catabolic flexibility affords a bacterium the ability to utilise different sugar sources as carbon for energy. This is important for commensal lactobacilli like Lactobacillus ruminis which can be exposed to a variety of carbohydrates in vivo. However, little is known about the fermentation capabilities, metabolic pathways, genetic diversity or potential survival mechanisms used by L. ruminis in vivo. A combination of in vitro and in silico techniques was used to identify the catabolic pathways of L. ruminis. I also compared 16 L. ruminis strains using a panel of biochemical and survival assays, genetically, whole genome sequencing and RNA sequencing. Multi locus sequence typing revealed that strains clustered according to their host sources. Transcriptome analysis by RNAseq of two motile strains under three growth conditions, including swarming, identified the up-regulation of carbohydrate-related genes under swarming conditions. This suggests that carbohydrate flexibility may have an uncharacterised role in L. ruminis swarming. Following on from the assessment of L. ruminis catabolic flexibility, the porcine diet was supplemented with galactooligosaccharides or L. ruminis ATCC 25644 plus galactooligosaccharides. Supplementation of the porcine diet with galactooligosaccharide had no effect on microbiota diversity. In contrast, the L. ruminis plus galactooligosaccharide treatment significantly reduced the microbiota diversity. Diet is a major factor that affects the diversity of the gut microbiota. In order to get a more thorough understanding of diet and gut health in animals such as racehorses and domesticated herbivores, I determined the core microbiota of animals consuming different feeds. Interestingly, the gut microbiota diversity correlated with the host phylogeny of the animal. The genome of Lactobacillus equi (2.19 Mb), isolated from a healthy Irish thoroughbred was also sequenced and annotated, and comprised 2,263 predicted genes. The large repertoire of predicted carbohydrate-related genes may offer L. equi an advantage in the complex and harsh hindgut environment. In summary, this thesis uses functional genomics to assess the effect that carbohydrates have on commensal lactobacilli and the microbiota as a whole.

Resonant power conversion topologies for inductive charging of electrical vehicle batteries

This thesis is concerned with inductive charging of electric vehicle batteries. Rectified power form the 50/60 Hz utility feeds a dc-ac converter which delivers high-frequency ac power to the electric vehicle inductive coupling inlet. The inlet configuration has been defined by the Society of Automotive Engineers in Recommended Practice J-1773. This thesis studies converter topologies related to the series resonant converter. When coupled to the vehicle inlet, the frequency-controlled series-resonant converter results in a capacitively-filtered series-parallel LCLC (SP-LCLC) resonant converter topology with zero voltage switching and many other desirable features. A novel time-domain transformation analysis, termed Modal Analysis, is developed, using a state variable transformation, to analyze and characterize this multi-resonant fourth-orderconverter. Next, Fundamental Mode Approximation (FMA) Analysis, based on a voltage-source model of the load, and its novel extension, Rectifier-Compensated FMA (RCFMA) Analysis, are developed and applied to the SP-LCLC converter. The RCFMA Analysis is a simpler and more intuitive analysis than the Modal Analysis, and provides a relatively accurate closed-form solution for the converter behavior. Phase control of the SP-LCLC converter is investigated as a control option. FMA and RCFMA Analyses are used for detailed characterization. The analyses identify areas of operation, which are also validated experimentally, where it is advantageous to phase control the converter. A novel hybrid control scheme is proposed which integrates frequency and phase control and achieves reduced operating frequency range and improved partial-load efficiency. The phase-controlled SP-LCLC converter can also be configured with a parallel load and is an excellent option for the application. The resulting topology implements soft-switching over the entire load range and has high full-load and partial-load efficiencies. RCFMA Analysis is used to analyze and characterize the new converter topology, and good correlation is shown with experimental results. Finally, a novel single-stage power-factor-corrected ac-dc converter is introduced, which uses the current-source characteristic of the SP-LCLC topology to provide power factor correction over a wide output power range from zero to full load. This converter exhibits all the advantageous characteristics of its dc-dc counterpart, with a reduced parts count and cost. Simulation and experimental results verify the operation of the new converter.

Nutrition, growth and body composition in preterm infants

The goal of neonatal nutrition in the preterm infant is to achieve postnatal growth and body composition approximating that of a normal fetus of the same postmenstrual age and to obtain a functional outcome comparable to infants born at term. However, in clinical practice such a pattern is seldom achieved, with growth failure and altered body composition being extensively reported. The BabyGrow preterm nutrition study was a longitudinal, prospective, observational study designed to investigate nutrition and growth in 59 preterm infants following the implementation of evidence-based nutrition guidelines in the neonatal unit at Cork University Maternity Hospital. Nutrient delivery was precisely measured during the entire hospital stay and intakes were compared with current international recommendations. Barriers to nutrient delivery were identified across the phases of nutritional support i.e. exclusive parenteral nutrition and transition (establishment of enteral feeds) phases of nutrition and nutritional strategies to optimise nutrient delivery were proposed according to these phases. Growth was measured from birth up to 2 months corrected age and body composition was assessed in terms of fat mass and lean body mass by air displacement plethysmography (PEA POD) at 34 weeks gestation, term corrected age and 2 months corrected age. Anthropometric and body composition data in the preterm cohort were compared with a term reference group from the Cork BASELINE Birth Cohort Study (n=1070) at similar time intervals. The clinical and nutritional determinants of growth and body composition during the neonatal period were reported for the first time. These data have international relevance, informing authoritative agencies developing evidence-based practice guidelines for neonatal nutritional support. In the future, the nutritional management of preterm infants may need to be individualised to consider gestational age, birth weight as well as preterm morbidity.

Infant milk formula manufacture: process and compositional interactions in high dry matter wet-mixes

Infant milk formula (IMF) is fortified milk with composition based on the nutrient content in human mother's milk, 0 to 6 months postpartum. Extensive medical and clinical research has led to advances in the nutritional quality of infant formula; however, relatively few studies have focused on interactions between nutrients and the manufacturing process. The objective of this research was to investigate the impact of composition and processing parameters on physical behaviour of high dry matter (DM) IMF systems with a view to designing more sustainable manufacturing processes. The study showed that commercial IMF, with similar compositions, manufactured by different processes, had markedly different physical properties in dehydrated or reconstituted state. Commercial products made with hydrolysed protein were more heat stable compared to products made with intact protein, however, emulsion quality was compromised. Heat-induced denaturation of whey proteins resulted in increased viscosity of wet-mixes, an effect that was dependant on both whey concentration and interactions with lactose and caseins. Expanding on fundamental laboratory studies, a novel high velocity steam injection process was developed whereby high DM (60%) wet-mixes with lower denaturation/viscosity compared to conventional processes could be achieved; powders produced using this process were of similar quality to those manufactured conventionally. Hydrolysed proteins were also shown to be an effective way of reducing viscosity in heat-treated high DM wet-mixes. In particular, using a whey protein concentrate whereby β-Lactoglobulin was selectively hydrolysed, i.e., α-Lactalbumin remained intact, reduced viscosity of wet-mixes during processing while still providing good emulsification. The thesis provides new insights into interactions between nutrients and/or processing which influence physical stability of IMF both in concentrated liquid and powdered form. The outcomes of the work have applications in such areas as; increasing the DM content of spray drier feeds in order to save energy, and, controlling final powder quality.

Zazen, philosophy of mind, and the practicality of realising impermanence

This dissertation involves a general overview of the meditative practice of zazen and analytic philosophy of mind while suggesting a potential bridge between them in the form of an analysis of the practicality of realising impermanence. By the end of my argument I hope to have offered up some compelling evidence in favour of the idea that analytic philosophy would benefit greatly from adopting principles which are best learned and expressed through the practice of, and scholarship around, Zen Buddhism and in particular the treatment of the concept of impermanence. I demonstrate the Western philosophical tendency to make dichotomous assumptions about the nature of mind, even when explicitly denying a dualist framework. I do so by examining the historical and philosophical precedent for dualistic thinking in the work of figures such as Plato and Descartes. I expand on this idea by examining the psychology of categorisation - i.e. creating mental categories and boundaries - and demonstrating how such categorisations feeds back into behaviour in practical ways, both positive and negative. The Zen Buddhist principle of impermanence states that all phenomena are impermanent and therefore lack essential nature; this includes intellectual concepts such as the metaphysical framework of the analytic approach to mind. Impermanence is a principle which is realised through the embodied practice of zazen. By demonstrating its application to analytic philosophy of mind I show that zazen (and mindfulness practice in general) provides an ongoing opportunity for clearing up entrenched world views, metaphysical assumptions and dogmatic thinking. This in turn may promote a more holistic and ultimately more rewarding comprehension of the role of first-person experience in understanding the world. My argument is not limited to analytic philosophy of mind but reflects broad aspects of thinking in general, and I explain its application to issues of social importance, in particular education systems.

Nutritional status of lactating mothers and their children 6-23 months of age in pre- and post-harvest seasons in two agro-ecological zones of rural Ethiopia

The objective of this study was to assess seasonal variation in nutritional status and feeding practices among lactating mothers and their children 6-23 months of age in two different agro-ecological zones of rural Ethiopia (lowland zone and midland zone). Food availability and access are strongly affected by seasonality in Ethiopia. However, there are few published data on the effects of seasonal food fluctuations on nutritional status and dietary diversity patterns of mothers and children in rural Ethiopia. A longitudinal study was conducted among 216 mothers in two agro-ecological zones of rural Ethiopia during pre and post-harvest seasons. Data were collected on many parameters including anthropometry, blood levels of haemoglobin and ferritin and zinc, urinary iodine levels, questionnaire data regarding demographic and household parameters and health issues, and infant and young child feeding practices, 24 h food recall to determine dietary diversity scores, and household use of iodized salt. Chi-square and multivariable regression models were used to identify independent predictors of nutritional status. A wide variety of results were generated including the following highlights. It was found that 95.4% of children were breastfed, of whom 59.7% were initially breastfed within one hour of birth, 22.2% received pre-lacteal feeds, and 50.9% of children received complementary feedings by 6 months of age. Iron deficiency was found in 44.4% of children and 19.8% of mothers. Low Zinc status was found in 72.2% of children and 67.3% of mothers. Of the study subjects, 52.5% of the children and 19.1% of the mothers were anaemic, and 29.6% of children and 10.5% of mothers had iron deficiency anaemia. Among the mothers with low serum iron status, 81.2% and 56.2% of their children had low serum zinc and iron, respectively. Similarly, among the low serum zinc status mothers, 75.2% and 45.3% of their children had low serum in zinc and iron, respectively. There was a strong correlation between the micronutrient status of the mothers and the children for ferritin, zinc and haemoglobin (P <0.001). There was also statistically significant difference between agro-ecological zones for micronutrient deficiencies among the mothers (p<0.001) but not for their children. The majority (97.6%) of mothers in the lowland zone were deficient in at least one micronutrient biomarker (zinc or ferritin or haemoglobin). Deficiencies in one, two, or all three biomarkers of micronutrient status were observed in 48.1%, 16.7% and 9.9% of mothers and 35.8%, 29.0%, and 23.5%, of children, respectively. Additionally, about 42.6% of mothers had low levels of urinary iodine and 35.2% of lactating mothers had goitre. Total goitre prevalence rates and urinary iodine levels of lactating mothers were not significantly different across agro-ecological zones. Adequately iodised salt was available in 36.6% of households. The prevalence of anaemia increased from post-harvest (21.8%) to pre-harvest seasons (40.9%) among lactating mothers. Increases were from 8.6% to 34.4% in midland and from 34.2% to 46.3% in lowland agro-ecological zones. Fifteen percent of mothers were anaemic during both seasons. Predictors of anaemia were high parity of mother and low dietary diversity. The proportion of stunted and underweight children increased from 39.8% and 27% in post-harvest season to 46.0% and 31.8% in pre-harvest season, respectively. However, wasting in children decreased from 11.6% to 8.5%. Major variations in stunting and underweight were noted in midland compared to lowland agroecological zones. Anthropometric measurements in mothers indicated high levels of undernutrition. The prevalence of undernutrition in mothers (BMI <18.5kg/m2) increased from 41.7 to 54.7% between post- and pre-harvest seasons. The seasonal effect was generally higher in the midland community for all forms of malnutrition. Parity, number of children under five years and regional variation were predictors of low BMI among lactating mothers. There were differences in minimum meal frequency, minimum acceptable diet and dietary diversity in children in pre-harvest and post-harvest seasons and these parameters were poor in both seasons. Dietary diversity among mothers was higher in lowland zone but was poor in both zones across the seasons. In conclusion, malnutrition and micronutrient deficiencies are very prevalent among lactating mothers and their children 6-23 months old in the study areas. There are significant seasonal variations in malnutrition and dietary diversity, in addition to significant differences between lowland and midland agro-ecological zones. These findings suggest a need to design effective preventive public health nutrition programs to address both the mothers’ and children’s needs particularly in the preharvest season.