Investigation of growth and stress tolerance characteristics of Cronobacter spp.

Cronobacter spp. are opportunistic pathogens which can be isolated from a wide variety of foods and environments. They are Gram negative, motile, non-spore forming, peritrichous rods of the Enterobacteriaceae family. This food-borne pathogen is associated with the ingestion of contaminated infant milk formula (IMF), causing necrotizing enterocolitis, sepsis and meningitis in neonatal infants. The work presented in this thesis involved the investigation and characterisation of a bank of Cronobacter strains for their ability to tolerate physiologically relevant stress conditions that are commonly encountered in the gastrointestinal tract. While all strains were able to endure the suboptimal conditions tested, noteworthy variations were observed between strains. A collection of these strains were Lux-tagged to determine if their growth could be tracked in IMF by measuring bioluminescence. The resulting strains could be easily and reproducibly monitored in real time by measuring light emission. Following this a transposon mutagenesis library was created in one of the Lux-tagged strains of Cronobacter sakazakii. This library was screened for mutants with affected growth in milk. The majority of mutants identified were associated with amino acid metabolism. The final section of this thesis identified genes involved in the tolerance of C. sakazakii to the milk derived antimicrobial peptide, Lactoferricin B (Lfcin B). This was achieved by creating a transposon mutagenesis library in C. sakazakii and screening for mutants with increased susceptibility to Lfcin B. Overall this thesis demonstrates the variation between Cronobacter strains. It also identifies genes required for growth of the bacteria in milk, as well as genes needed for antimicrobial peptide tolerance.

Characteristics of the wave energy resource at the Atlantic marine energy test site

The wave energy industry is progressing towards an advanced stage of development, with consideration being given to the selection of suitable sites for the first commercial installations. An informed, and accurate, characterisation of the wave energy resource is an essential aspect of this process. Ireland is exposed to an energetic wave climate, however many features of this resource are not well understood. This thesis assesses and characterises the wave energy resource that has been measured and modelled at the Atlantic Marine Energy Test Site, a facility for conducting sea trials of floating wave energy converters that is being developed near Belmullet, on the west coast of Ireland. This characterisation process is undertaken through the analysis of metocean datasets that have previously been unavailable for exposed Irish sites. A number of commonly made assumptions in the calculation of wave power are contested, and the uncertainties resulting from their application are demonstrated. The relationship between commonly used wave period parameters is studied, and its importance in the calculation of wave power quantified, while it is also shown that a disconnect exists between the sea states which occur most frequently at the site and those that contribute most to the incident wave energy. Additionally, observations of the extreme wave conditions that have occurred at the site and estimates of future storms that devices will need to withstand are presented. The implications of these results for the design and operation of wave energy converters are discussed. The foremost contribution of this thesis is the development of an enhanced understanding of the fundamental nature of the wave energy resource at the Atlantic Marine Energy Test Site. The results presented here also have a wider relevance, and can be considered typical of other, similarly exposed, locations on Ireland’s west coast.

Environmental and biological characteristics of lagoons on the southwest coast of Ireland

Coastal lagoons are defined as shallow coastal water bodies partially separated from the adjacent sea by a restrictive barrier. Coastal lagoons are protected under Annex I of the European Habitats Directive (92/43/EEC). Lagoons are also considered to be “transitional water bodies” and are therefore included in the “register of protected areas” under the Water Framework Directive (2000/60/EC). Consequently, EU member states are required to establish monitoring plans and to regularly report on lagoon condition and conservation status. Irish lagoons are considered relatively rare and unusual because of their North Atlantic, macrotidal location on high energy coastlines and have received little attention. This work aimed to assess the physicochemical and ecological status of three lagoons, Cuskinny, Farranamanagh and Toormore, on the southwest coast of Ireland. Baseline salinity, nutrient and biological conditions were determined in order to provide reference conditions to detect perturbations, and to inform future maintenance of ecosystem health. Accumulation of organic matter is an increasing pressure in coastal lagoon habitats worldwide, often compounding existing eutrophication problems. This research also aimed to investigate the in situ decomposition process in a lagoon habitat together with exploring the associated invertebrate assemblages. Re-classification of the lagoons, under the guidelines of the Venice system for the classifications of marine waters according to salinity, was completed by taking spatial and temporal changes in salinity regimes into consideration. Based on the results of this study, Cuskinny, Farranamanagh and Toormore lagoons are now classified as mesohaline (5 ppt – 18 ppt), oligohaline (0.5 ppt – 5 ppt) and polyhaline (18 ppt – 30 ppt), respectively. Varying vertical, longitudinal and transverse salinity patterns were observed in the three lagoons. Strong correlations between salinity and cumulative rainfall highlighted the important role of precipitation in controlling the lagoon environment. Maximum effect of precipitation on the salinity of the lagoon was observed between four and fourteen days later depending on catchment area geology, indicating the uniqueness of each lagoon system. Seasonal nutrient patterns were evident in the lagoons. Nutrient concentrations were found to be reflective of the catchment area and the magnitude of the freshwater inflow. Assessment based on the Redfield molar ratio indicated a trend towards phosphorus, rather than nitrogen, limitation in Irish lagoons. Investigation of the decomposition process in Cuskinny Lagoon revealed that greatest biomass loss occurred in the winter season. Lowest biomass loss occurred in spring, possibly due to the high density of invertebrates feeding on the thick microbial layer rather than the decomposing litter. It has been reported that the decomposition of plant biomass is highest in the preferential distribution area of the plant species; however, no similar trend was observed in this study with the most active zones of decomposition varying spatially throughout the seasons. Macroinvertebrate analysis revealed low species diversity but high abundance, indicating the dominance of a small number of species. Invertebrate assemblages within the lagoon varied significantly from communities in the adjacent freshwater or marine environments. Although carried out in coastal lagoons on the southwest coast of Ireland, it is envisaged that the overall findings of this study have relevance throughout the entire island of Ireland and possibly to many North Atlantic coastal lagoon ecosystems elsewhere.

The defining characteristics of alternative food initiatives in Ireland: a social movement battling for an alternative food future?

Alternative food initiatives (AFIs) have been described as an attempt to change and improve aspects of how the food system operates. They are focused around more traditional, local and sustainable food production and circulation. AFIs such as farmers’ markets, allotments and community gardens, share a desire to reduce the number of steps food goes through from production to plate. The role of these initiatives in the food system, and their potential to impact real change, has however been questioned. Working to better understand this issue is a central concern of this research. To do this a two tier analysis has been deployed. The first tier involves identifying the characteristics and general dynamics of AFIs. Bourdieu’s theory of practice, and the theories of field and capital, are the concepts applied. The research then uses these findings in the second tier of analysis concerned with relating AFI characteristics and dynamics back to their key traits, positive and negative, as well as arguments made about AFI’s role identified from previous research. Another part of this second tier of analysis is exploring if AFIs, the producers, consumers, organisations and groups that make up this phenomenon, can be considered a social movement. AFIs can be referred to collectively as a social movement, but are not often explored theoretically from this perspective. AFIs in Ireland provide the empirical context for this research. A series of qualitative interviews in four areas of Ireland, as well as evidence from primary and secondary sources are analysed. The research finds that AFIs can be understood as the potential beginnings of a lifestyle social movement. Leaders are of central importance to its development. It is also found that an important role of AFIs is revitalising, supporting and contributing to food culture.

Characteristics of Biodiesel Oil Atomized by a Two-Fluid Nozzle Using PDA

Drop size and velocity distribution in a spray of fuel play an important role in determining combustion efficiency. The Phase Doppler anemometer (PDA) is a well-established technique allowing simultaneous measurement of velocity and size of droplets. In this work, effect of bio-substitute component on the size and velocity of biodiesel droplets which are generated by a two-fluid nozzle are investigated comprehensively using a PDA.

STAR 3 randomized controlled trial to compare sensor-augmented insulin pump therapy with multiple daily injections in the treatment of type 1 diabetes: research design, methods, and baseline characteristics of enrolled subjects.

BACKGROUND: Sensor-augmented pump therapy (SAPT) integrates real-time continuous glucose monitoring (RT-CGM) with continuous subcutaneous insulin infusion (CSII) and offers an alternative to multiple daily injections (MDI). Previous studies provide evidence that SAPT may improve clinical outcomes among people with type 1 diabetes. Sensor-Augmented Pump Therapy for A1c Reduction (STAR) 3 is a multicenter randomized controlled trial comparing the efficacy of SAPT to that of MDI in subjects with type 1 diabetes. METHODS: Subjects were randomized to either continue with MDI or transition to SAPT for 1 year. Subjects in the MDI cohort were allowed to transition to SAPT for 6 months after completion of the study. SAPT subjects who completed the study were also allowed to continue for 6 months. The primary end point was the difference between treatment groups in change in hemoglobin A1c (HbA1c) percentage from baseline to 1 year of treatment. Secondary end points included percentage of subjects with HbA1c < or =7% and without severe hypoglycemia, as well as area under the curve of time spent in normal glycemic ranges. Tertiary end points include percentage of subjects with HbA1c < or =7%, key safety end points, user satisfaction, and responses on standardized assessments. RESULTS: A total of 495 subjects were enrolled, and the baseline characteristics similar between the SAPT and MDI groups. Study completion is anticipated in June 2010. CONCLUSIONS: Results of this randomized controlled trial should help establish whether an integrated RT-CGM and CSII system benefits patients with type 1 diabetes more than MDI.

ELGAR AND MART&: THE CELLO WORKS AND MUSICAL CHARACTERISTICS OF TWO REMARKABLE, SELF-TAUGHT, NATIONALISTIC COMPOSERS

The British Edward Elgar and Czech Bohuslav MartinB were two of the most prominent Nationalistic composers of their respective countries during the late nineteenth and early twentieth centuries. Their musical patriotism incorporates the unique paths of their lives as socially isolated and self-taught composers as expressed their outstanding Nationalistic compositions produced through the period of history encompassing the two World Wars.In the first chapter of this dissertation, a brief biography of Elgar is presented and the essential aspects of his formative years influencing him to become a self-taught musician are discussed. The second chapter demonstrates Elgar's musical characteristics through the study of a selection of his masterpieces. In the third chapter, a brief biography of Martinti is presented along with a history of his musical development, characterized by his social isolation during four different periods of his life-his residences in PoliCka, Prague, Paris, and then in the United States. The fourth chapter considers MartinB's musical characteristics as revealed through the study of a selection of his greatest works. In support of this doctoral project, I performed two recitals of cello works by Elgar and Martini3 at the University of Maryland, College Park. The first recital, accompanied by Susan Slingland and Hiroko Yamazaki, included three of Martini3's works, Sonata No. 2 for Cello and Piano (1941); Variations on a Theme of Rossini for Cello and Piano (1 942); and Sonata No. 3 for Cello and Piano (1952). The second recital, accompanied by Wonyoung Chang and Naoko Takao, presented Martini3's Sonata No. 1 for Cello and Piano (1939) and Elgar's Concerto for Cello and Orchestra Op. 85 in E minor (1 919).

Morphological characteristics of urban water bodies: mechanisms of change and implications for ecosystem function.

The size, shape, and connectivity of water bodies (lakes, ponds, and wetlands) can have important effects on ecological communities and ecosystem processes, but how these characteristics are influenced by land use and land cover change over broad spatial scales is not known. Intensive alteration of water bodies during urban development, including construction, burial, drainage, and reshaping, may select for certain morphometric characteristics and influence the types of water bodies present in cities. We used a database of over one million water bodies in 100 cities across the conterminous United States to compare the size distributions, connectivity (as intersection with surface flow lines), and shape (as measured by shoreline development factor) of water bodies in different land cover classes. Water bodies in all urban land covers were dominated by lakes and ponds, while reservoirs and wetlands comprised only a small fraction of the sample. In urban land covers, as compared to surrounding undeveloped land, water body size distributions converged on moderate sizes, shapes toward less tortuous shorelines, and the number and area of water bodies that intersected surface flow lines (i.e., streams and rivers) decreased. Potential mechanisms responsible for changing the characteristics of urban water bodies include: preferential removal, physical reshaping or addition of water bodies, and selection of locations for development. The relative contributions of each mechanism likely change as cities grow. The larger size and reduced surface connectivity of urban water bodies may affect the role of internal dynamics and sensitivity to catchment processes. More broadly, these results illustrate the complex nature of urban watersheds and highlight the need to develop a conceptual framework for urban water bodies.

Characteristics of primary care office visits to nurse practitioners, physician assistants and physicians in United States Veterans Health Administration facilities, 2005 to 2010: a retrospective cross-sectional analysis.

UNLABELLED: BACKGROUND: Primary care, an essential determinant of health system equity, efficiency, and effectiveness, is threatened by inadequate supply and distribution of the provider workforce. The Veterans Health Administration (VHA) has been a frontrunner in the use of nurse practitioners (NPs) and physician assistants (PAs). Evaluation of the roles and impact of NPs and PAs in the VHA is critical to ensuring optimal care for veterans and may inform best practices for use of PAs and NPs in other settings around the world. The purpose of this study was to characterize the use of NPs and PAs in VHA primary care and to examine whether their patients and patient care activities were, on average, less medically complex than those of physicians. METHODS: This is a retrospective cross-sectional analysis of administrative data from VHA primary care encounters between 2005 and 2010. Patient and patient encounter characteristics were compared across provider types (PA, NP, and physician). RESULTS: NPs and PAs attend about 30% of all VHA primary care encounters. NPs, PAs, and physicians fill similar roles in VHA primary care, but patients of PAs and NPs are slightly less complex than those of physicians, and PAs attend a higher proportion of visits for the purpose of determining eligibility for benefits. CONCLUSIONS: This study demonstrates that a highly successful nationwide primary care system relies on NPs and PAs to provide over one quarter of primary care visits, and that these visits are similar to those of physicians with regard to patient and encounter characteristics. These findings can inform health workforce solutions to physician shortages in the USA and around the world. Future research should compare the quality and costs associated with various combinations of providers and allocations of patient care work, and should elucidate the approaches that maximize quality and efficiency.

Phenotypic characteristics of human type II alveolar epithelial cells suitable for antigen presentation to T lymphocytes.

Type II alveolar epithelial cells (AECII) are well known for their role in the innate immune system. More recently, it was proposed that they could play a role in the antigen presentation to T lymphocytes but contradictory results have been published both concerning their surface expressed molecules and the T lymphocyte responses in mixed lymphocyte cultures. The use of either AECII cell line or fresh cells could explain the observed discrepancies. Thus, this study aimed at defining the most relevant model of accessory antigen presenting cells by carefully comparing the two models for their expression of surface molecules necessary for efficient antigen presentation.

Characteristics of the biphasic action of androgens and of the potent antiproliferative effects of the new pure antiestrogen EM-139 on cell cycle kinetic parameters in LNCaP human prostatic cancer cells

The most potent steroid in human prostatic carcinoma LNCaP cells, i.e. dihydrotestosterone (DHT), has a biphasic stimulatory effect on cell proliferation. At the maximal stimulatory concentration of 0.1 nM DHT, analysis of cell kinetic parameters shows a decrease of the G0-G1 fraction with a corresponding increase of the S and G2 + M fractions. In contrast, concentrations of 1 nM DHT or higher induce a return of cell proliferation to control levels, reflected by an increase in the G0-G1 fraction at the expense of the S and especially the G2 + M fractions. Continuous labeling for 144 h with the nucleotide analogue 5'-bromodeoxyuridine shows that the percentage of cycling LNCaP cells rises more than 90% after treatment with stimulatory concentrations of DHT, whereas in control cells as well as in cells treated with high concentrations of the androgen, this value remains below 50%. Although LNCaP cells do not contain detectable estrogen receptors, the new pure steroidal antiestrogen EM-139 not only reversed the stimulation of cell proliferation and cell kinetics induced by stimulatory doses of DHT but also inhibited basal cell proliferation.

Nanoscopic modelling of the adhesion, indentation and fracture characteristics of metallic systems via molecular dynamics simulations

Large-scale molecular dynamics simulations have been performed on canonical ensembles to model the adhesion and indentation characteristics of 3-D metallic nano-scale junctions in tip-substrate geometries, and the crack propagation in 2-D metallic lattices. It is shown that irreversible flows in nano-volumes of materials control the behaviour of the 3-D nano-contacts, and that local diffusional flow constitutes the atomistic mechanism underlying these plastic flows. These simulations show that the force of adhesion in metallic nano-contacts is reduced when adsorbate monolayers are present at the metal—metal junctions. Our results are in agreement with the conclusions of very accurate point-contact experiments carried out in this field. Our fracture simulations reveal that at low temperatures cleavage fractures can occur in both an elemental metal and an alloy. At elevated temperatures, the nucleation of dislocations is shown to cause a brittle-to-ductile transition. Limiting crack propagation velocities are computed for different strain rates and a dynamic instability is shown to control the crack movement beyond this limiting velocity, in line with the recent experimental results.

A computational study of the characteristics of aircraft post-crash fires

Full-scale furnished cabin fires have been studied experimentally for the purpose of characterising the post-crash cabin fire environment by the US Federal Aviation Administration for many years. In this paper the Computational Fluid Dynamics fire field model SMARTFIRE is used to simulate one of these fires conducted in the C-133 test facility in order to provide further validation of the computational approach and the SMARTFIRE software. The experiment involves exposing the interior cabin materials to an external fuel fire, opening only one exit at the far end of the cabin (the same side as the rupture) for ventilation, and noting the subsequent spread of the external fire to the cabin interior and the onset of flashover at approximately 210 seconds. Through this analysis, the software is shown to be in good agreement with the experimental data, producing reasonable agreement with the fire dynamics prior to flashover and producing a reasonable prediction of the flashover time i.e. 225 seconds. The paper then proceeds to utilize the model to examine the impact on flashover time of the extent of cabin furnishings and cabin ventilation provided by available exits

Analysis of the structural characteristics of an intermediate rail vehicle and their effect on vehicle crash performance

In the current paper, the authors present an analysis of the structural characteristics of an intermediate rail vehicle and their effects on crash performance of the vehicle. Theirs is a simulation based analysis involving four stages. First, the crashworthiness of the vehicle is assessed by simulating an impact of the vehicle with a rigid wall. Second, the structural characteristics of the vehicle are analysed based on the structural behaviour during this impact and then the structure is modified. Third, the modified vehicle is tested again in the same impact scenario with a rigid wall. Finally, the modified vehicle is subjected to a modelled head-on impact which mirrors the real-life impact interface between two intermediate vehicles in a train impact. The emphasis of the current study is on the structural characteristics of the intermediate vehicle and the differences compared to an impact of a leading vehicle. The study shows that, similar to a leading vehicle, bending, or jackknifing is a main form of failure in this conventionally designed intermediate vehicle. It has also been found that the location of the door openings creates a major difference in the behaviour of an intermediate vehicle. It causes instability of the vehicle in the door area and leads to high stresses at the joint of the end beam with the solebar and shear stresses at the joint of the inner pillar with the cantrail. Apart from this, the shapes of the vehicle ends and impact interfaces are also different and have an effect on the crash performance of the vehicles. The simulation results allow the identification of the structural characteristics and show the effectiveness of relevant modifications. The conclusions have general relevance for the crashworthiness of rail vehicle design

Morphological and molecular characteristics of a new species of Pasteuria parasitic on Meloidogyne ardenensis

A species of the hyper-parasitic bacterium Pasteuria was isolated from the root-knot nematode Meloidogyne ardenensis infecting the roots of ash (Fraxinus excelsior). It is morphologically different from some other Pasteuria pathogens of nematodes in that the spores lack a basal ring on the ventral side of the spore and have a unique clumping nature. Transmission electron microscopy (TEM) showed that the clumps of spores are not random aggregates but result from the disintegration of the suicide cells of the thalli. Sporulation within each vegetative mycelium was shown to be asynchronous. In addition to the novel morphological features 16S rRNA sequence analysis showed this to be a new species of Pasteuria which we have called P. hartismeri. Spores of P. hartismeri attach to juveniles of root-knot nematodes infecting a wide range of plants such as mint (Meloidogyne hapla), rye grass (unidentified Meloidogyne sp.) and potato (Meloidogyne fallax).