Synonymous co-variation across the E1/E2 gene junction of hepatitis C virus defines virion fitness

Hepatitis C virus is a positive-sense single-stranded RNA virus. The gene junction partitioning the viral glycoproteins E1 and E2 displays concurrent sequence evolution with the 3′-end of E1 highly conserved and the 5′-end of E2 highly heterogeneous. This gene junction is also believed to contain structured RNA elements, with a growing body of evidence suggesting that such structures can act as an additional level of viral replication and transcriptional control. We have previously used ultradeep pyrosequencing to analyze an amplicon library spanning the E1/E2 gene junction from a treatment naïve patient where samples were collected over 10 years of chronic HCV infection. During this timeframe maintenance of an in-frame insertion, recombination and humoral immune targeting of discrete virus sub-populations was reported. In the current study, we present evidence of epistatic evolution across the E1/E2 gene junction and observe the development of co-varying networks of codons set against a background of a complex virome with periodic shifts in population dominance. Overtime, the number of codons actively mutating decreases for all virus groupings. We identify strong synonymous co-variation between codon sites in a group of sequences harbouring a 3 bp in-frame insertion and propose that synonymous mutation acts to stabilize the RNA structural backbone.

The protection and security of vulnerable populations in complex emergencies using the Dadaab refugee camps in the north eastern province of Kenya as a case study

The past two decades has seen a dramatic upheaval in the international world order: the end of the Cold War, the 9/11 attacks and the subsequent 'War on Terror', increased Jihadist activities, the accelerated pace of globalization, climate change and the 2008 global financial crisis have contributed to fear, uncertainty, poverty, conflict, massive displacements of populations of asylum seekers and refugees globally and a proliferation of Protracted Refugee Situations (PRS), defined as situations in which refugees have been in exile 'for 5 years or more after their initial displacement, without immediate prospects for implementation of durable solutions. In the past two decades there has been a huge proliferation of these with more than 7.2 million refugees now trapped in these PRS, with a further 16 million internally displaced persons (IDPs) trapped in camps within their own countries. The Dadaab refugee complex in Kenya, which of as March 2012, holds over 463,000 refugees, is the most significant and extreme example in recent times of a PRS. It was established in 1991 following the collapse of the Somali Government of Dictator Siad Barre, and the disintegration of Somalia into the chaos that still exists today. PRS such as Dadaab raise particular issues about humanitarianism in terms of aid, protection, security, human rights and the actions (or inaction) of the various stakeholders on an international, national and local level. This thesis investigates these issues by the use of a case study methodology on Dadaab as a PRS, framed in the context of humanitarianism and in particular the issues that arise in terms of how the international community, the UN system and individual states provide assistance and protection to vulnerable populations. Although the refugee camps have been in existence (as of 2012) for over 20 years, there has never been such a detailed study of Dadaab (or any other PRS) undertaken to date and would be of interest to academics in the areas of international relations, refugee/migration studies and global Governance as well as practitioners in both humanitarian response and development

The atom pencil: serial writing in the sub-micrometre domain

The atom pencil we describe here is a versatile tool that writes arbitrary structures by atomic deposition in a serial lithographic process. This device consists of a transversely laser-cooled and collimated cesium atomic beam that passes through a 4-pole atom-flux concentrator and impinges on to micron- and sub-micron-sized apertures. The aperture translates above a fixed substrate and enables the writing of sharp features with sizes down to 280 nm. We have investigated the writing and clogging properties of an atom pencil tip fabricated from silicon oxide pyramids perforated at the tip apex with a sub-micron aperture.

Reactivity of sub 1 nm supported clusters: (TiO2)(n) clusters supported on rutile TiO2 (110)

Metal oxide clusters of sub-nm dimensions dispersed on a metal oxide support are an important class of catalytic materials for a number of key chemical reactions, showing enhanced reactivity over the corresponding bulk oxide. In this paper we present the results of a density functional theory study of small sub-nm TiO2 clusters, Ti2O4, Ti3O6 and Ti4O8 supported on the rutile (110) surface. We find that all three clusters adsorb strongly with adsorption energies ranging from -3 eV to -4.5 eV. The more stable adsorption structures show a larger number of new Ti-O bonds formed between the cluster and the surface. These new bonds increase the coordination of cluster Ti and O as well as surface oxygen, so that each has more neighbours. The electronic structure shows that the top of the valence band is made up of cluster derived states, while the conduction band is made up of Ti 3d states from the surface, resulting in a reduction of the effective band gap and spatial separation of electrons and holes after photon absorption, which shows their potential utility in photocatalysis. To examine reactivity, we study the formation of oxygen vacancies in the cluster-support system. The most stable oxygen vacancy sites on the cluster show formation energies that are significantly lower than in bulk TiO2, demonstrating the usefulness of this composite system for redox catalysis.

Characterisation of the microbiota of traditional fermented beverages and screening these and other populations for novel antimicrobial producers and gene clusters

To screen for novel ribosomally synthesised antimicrobials, in-silico genome mining was performed on all publically available fully sequenced bacterial genomes. 49 novel type 1 lantibiotic clusters were identified from a number of species, genera and phyla not usually associated with lantibiotic production, and indicates high prevalence. A crucial step towards the commercialisation of fermented beverages is the characterisation of the microbial content. To achieve this goal, we applied next-generation sequencing techniques to analyse the bacterial and yeast populations of the organic, symbiotically-fermented beverages kefir, water kefir and kombucha. A number of minor components were revealed, many of which had not previously been associated with these beverages. The dominant microorganism in each of the water kefir grains and fermentates was Zymomonas, an ethanol-producing bacterium that had not previously been detected on such a scale. These studies represent the most accurate description of these populations to date, and should aid in future starter design and in determining which species are responsible for specific attributes of the beverages. Finally, high-throughput robotics was applied to screen for the presence of antimicrobial producers associated with these beverages. This revealed a low frequency of bacteriocin production amongst the bacterial isolates, with only lactococcins A, B and LcnN of lactococcin M being identified. However, a proteinaceous antimicrobial produced by the yeast Dekkera bruxellensis, isolated from kombucha, was found to be active against Lactobacillus bulgaricus. This peptide was patially purified.

Analysis of institutional arrangements and common pool resources governance: the case of Lake Tana sub-basin, Ethiopia

Although Common Pool Resources (CPRs) make up a significant share of total income for rural households in Ethiopia and elsewhere in developing world, limited access to these resources and environmental degradation threaten local livelihoods. As a result, the issues of management, governance of CPRs and how to prevent their over-exploitation are of great importance for development policy. This study examines the current state and dynamics of CPRs and overall resource governance system of the Lake Tana sub-basin. This research employed the modified form of Institutional Analysis and Development (IAD) framework. The framework integrates the concept of Socio-Ecological Systems (SES) and Interactive Governance (IG) perspectives where social actors, institutions, the politico-economic context, discourses and ecological features across governance and government levels were considered. It has been observed that overexploitation, degradation and encroachment of CPRs have increased dramatically and this threatens the sustainability of Lake Tana ecosystem. The stakeholder analysis result reveals that there are multiple stakeholders with diverse interest in and power over CPRs. The analysis of institutional arrangements reveals that the existing formal rules and regulations governing access to and control over CPRs could not be implemented and were not effective to legally bind and govern CPR user’s behavior at the operational level. The study also shows that a top-down and non-participatory policy formulation, law and decision making process overlooks the local contexts (local knowledge and informal institutions). The outcomes of examining the participation of local resource users, as an alternative to a centralized, command-and-control, and hierarchical approach to resource management and governance, have called for a fundamental shift in CPR use, management and governance to facilitate the participation of stakeholders in decision making. Therefore, establishing a multi-level stakeholder governance system as an institutional structure and process is necessary to sustain stakeholder participation in decision-making regarding CPR use, management and governance.

An investigation of implicit measurement techniques amongst low risk and forensic samples

There are difficulties with utilising self- report and physiological measures of assessment amongst forensic populations. This study investigates implicit based measures amongst sexual offenders, nonsexual offenders and low risk samples. Implicit measurement is a term applied to measurement methods that makes it difficult to influence responses through conscious control. The test battery includes the Implicit Association Test (IAT), Rapid Serial Visual Presentation (RSVP), Viewing Time (VT) and the Structured Clinical interview for disorders. The IAT proposes that people will perform better on a task when they depend on well-practiced cognitive associations. The RSVP task requires participants to identify a single target image that is presented amongst a series of rapidly presented visual images. RSVP operates on the premise that if two target images are presented within 500milliseconds of each other, the possibility that the participant will recognize the second target is significantly reduced when the first target is of salience to the individual. This is the attentional blink phenomenon. VT is based on the principle that people will look longer at images that are of salience. Results showed that on the VT task, child sexual offenders took longer to view images of children than low risk groups. Nude over clothed images induced a greater attentional blink amongst low risk and offending samples on the RSVP task. Sexual offenders took longer than low risk groups on word pairing tasks where sexual words were paired with adult words on the IAT. The SCID highlighted differences between the offending and non offending groups on the sub scales for personality disorders. More erotic stimulus items on the VT and RSVP measures is recommended to better differentiate sexual preference between offending and non offending samples. A pictorial IAT is recommended. Findings provide the basis for further development of implicit measures within the assessment of sexual offenders.

Ecology of frontier populations of the invasive grey squirrel (Sciurus carolinensis) in Ireland

The rise in invasive species, together with habitat destruction, is associated with worldwide declines in biodiversity and ecosystem functioning. Management of invasive species, as well as amelioration of invasion impacts, provide challenges to species and ecosystem ecologists and conservation managers. Although any species can become invasive if it is transported to, establishes in and spreads in a new environment outside of its native range, rodents are a particularly frequent invader. Rodent introductions are often inadvertent but are also commonly intentional as these animals are traded and transported as pets and may escape from captivity. Tree squirrel species are attractive to humans and are able to establish populations with only a few founding individuals, making them a group well suited to performing the role of biological invaders. The eastern grey squirrel (Sciurus carolinensis) is the most commonly introduced squirrel species worldwide. This research addressed the grey squirrel invasion and frontier population biology. Novel results were generated through diverse research techniques. Public sighting surveys and hairtube surveys were used to locate the southern frontier of grey squirrel range expansion in Ireland. A 22-month intensive live trapping study of two frontier populations facilitated the collection of personality and demographic data from squirrels in increasing populations. A systematic literature search on grey squirrel demography provided context for the studied populations, among frontier and established introduced populations, as well as those in the native range. Advanced spatially explicit population modeling techniques predicted future range expansion and objectively compared the outcomes of 12 grey squirrel management strategies. The methods and results are discussed in both a basic scientific and applied invasion management context. An improved understanding of the behaviour, population dynamics, and future scenarios at the frontier of species invasions is crucial for managers worldwide and this is provided here for the grey squirrel in Ireland.

Psychosocial well-being of African migrant children in Ireland: a cultural orientation

This thesis explores the psychosocial wellbeing of sub-Saharan African migrant children in Ireland. A sociocultural ecological (Psychosocial Working Group, 2003) and resilience lens (Masten & Obradovic, 2008; Ungar, 2011) is used to analyse the experiences of African migrant children in Ireland. The research strategy employs a mixed-methods design, combining both an etic and emic perspective. Grounded theory inquiry (Strauss and Corbin, 1994) explores the experiences of African migrant children in Ireland by drawing on multi-sited observations over a period of six months in 2009, and on interviews and focus group discussions conducted with African children (aged 13-18), mothers and fathers. An emically derived ‘African Migrant Child Psychosocial Well-being’ scale was developed by drawing on data gathered through rapid ethnographic (RAE) free listing exercises carried out in Cork, Dublin and Dundalk with sixty-one participants (N=21 adults, N=28 15-18-year-olds, N=12 12-14-year-olds) and three African community key informants to elicit local understandings of psychosocial well-being. This newly developed scale was used alongside standardised measures of well-being to quantitatively measure the psychosocial adjustment of 233 African migrant children in Cork, Dublin and Dundalk aged 11-18. Findings indicate that the psychosocial wellbeing of the study population is satisfactory when benchmarked against the psychosocial health profile of Irish youth (Dooley & Fitzgerald, 2012). These findings are similar to trends reported in international literature in this field (Georgiades et al., 2006; Gonneke, Stevens, Vollebergh, 2008; Sampson et al., 2005). Study findings have implications for advancing psychosocial research methods with non-Western populations and on informing the practice of Irish professionals, mainly in the areas of teaching, psychology and community work.

The effects of copayment policies on adherence to prescription medicines in publicly insured populations

Introduction: Copayments for prescriptions are associated with decreased adherence to medicines resulting in increased health service utilisation, morbidity and mortality. In October 2010 a 50c copayment per prescription item was introduced on the General Medical Services (GMS) scheme in Ireland, the national public health insurance programme for low-income and older people. The copayment was increased to €1.50 per prescription item in January 2013. To date, the impact of these copayments on adherence to prescription medicines on the GMS scheme has not been assessed. Given that the GMS population comprises more than 40% of the Irish population, this presents an important public health problem. The aim of this thesis was to assess the impact of two prescription copayments, 50c and €1.50, on adherence to medicines.Methods: In Chapter 2 the published literature was systematically reviewed with meta-analysis to a) develop evidence on cost-sharing for prescriptions and adherence to medicines and b) develop evidence for an alternative policy option; removal of copayments. The core research question of this thesis was addressed by a large before and after longitudinal study, with comparator group, using the national pharmacy claims database. New users of essential and less-essential medicines were included in the study with sample sizes ranging from 7,007 to 136,111 individuals in different medication groups. Segmented regression was used with generalised estimating equations to allow for correlations between repeated monthly measurements of adherence. A qualitative study involving 24 individuals was conducted to assess patient attitudes towards the 50c copayment policy. The qualitative and quantitative findings were integrated in the discussion chapter of the thesis. The vast majority of the literature on this topic area is generated in North America, therefore a test of generalisability was carried out in Chapter 5 by comparing the impact of two similar copayment interventions on adherence, one in the U.S. and one in Ireland. The method used to measure adherence in Chapters 3 and 5 was validated in Chapter 6. Results: The systematic review with meta-analysis demonstrated an 11% (95% CI 1.09 to 1.14) increased odds of non-adherence when publicly insured populations were exposed to copayments. The second systematic review found moderate but variable improvements in adherence after removal/reduction of copayments in a general population. The core paper of this thesis found that both the 50c and €1.50 copayments on the GMS scheme were associated with larger reductions in adherence to less-essential medicines than essential medicines directly after the implementation of policies. An important exception to this pattern was observed; adherence to anti-depressant medications declined by a larger extent than adherence to other essential medicines after both copayments. The cross country comparison indicated that North American evidence on cost-sharing for prescriptions is not automatically generalisable to the Irish setting. Irish patients had greater immediate decreases of -5.3% (95% CI -6.9 to -3.7) and -2.8% (95% CI -4.9 to -0.7) in adherence to anti-hypertensives and anti-hyperlipidaemic medicines, respectively, directly after the policy changes, relative to their U.S. counterparts. In the long term, however, the U.S. and Irish populations had similar behaviours. The concordance study highlighted the possibility of a measurement bias occurring for the measurement of adherence to non-steroidal anti-inflammatory drugs in Chapter 3. Conclusions: This thesis has presented two reviews of international cost-sharing policies, an assessment of the generalisability of international evidence and both qualitative and quantitative examinations of cost-sharing policies for prescription medicines on the GMS scheme in Ireland. It was found that the introduction of a 50c copayment and its subsequent increase to €1.50 on the GMS scheme had a larger impact on adherence to less-essential medicines relative to essential medicines, with the exception of anti-depressant medications. This is in line with policy objectives to reduce moral hazard and is therefore demonstrative of the value of such policies. There are however some caveats. The copayment now stands at €2.50 per prescription item. The impact of this increase in copayment has yet to be assessed which is an obvious point for future research. Careful monitoring for adverse effects in socio-economically disadvantaged groups within the GMS population is also warranted. International evidence can be applied to the Irish setting to aid in future decision making in this area, but not without placing it in the local context first. Patients accepted the introduction of the 50c charge, however did voice concerns over a rising price. The challenge for policymakers is to find the ‘optimal copayment’ – whereby moral hazard is decreased, but access to essential chronic disease medicines that provide advantages at the population level is not deterred. This evidence presented in this thesis will be utilisable for future policy-making in Ireland.

Controlling alloy formation and optical properties by galvanic replacement of sub-20 nm silver nanoparticles in organic media

Galvanic replacement is a versatile synthetic strategy for the synthesis of alloy and hollow nanostructures. The structural evolution of single crystalline and multiply twinned nanoparticles <20 nm in diameter and capped with oleylamine is systematically studied. Changes in chemical composition are dependent on the size and crystallinity of the parent nanoparticle. The effects of reaction temperature and rate of precursor addition are also investigated. Galvanic replacement of single crystal spherical and truncated cubic nanoparticles follows the same mechanism to form hollow octahedral nanoparticles, a mechanism which is not observed for galvanic replacement of Ag templates in aqueous systems. Multiply twinned nanoparticles can form nanorings or solid alloys by manipulating the reaction conditions. Oleylamine-capped Ag nanoparticles are highly adaptable templates to synthesize a range of hollow and alloy nanostructures with tuneable localised surface plasmon resonance.