Experimental analysis of novel telecom source materials and devices

Incumbent telecommunication lasers emitting at 1.5 µm are fabricated on InP substrates and consist of multiple strained quantum well layers of the ternary alloy InGaAs, with barriers of InGaAsP or InGaAlAs. These lasers have been seen to exhibit very strong temperature dependence of the threshold current. This strong temperature dependence leads to a situation where external cooling equipment is required to stabilise the optical output power of these lasers. This results in a significant increase in the energy bill associated with telecommunications, as well as a large increase in equipment budgets. If the exponential growth trend of end user bandwidth demand associated with the internet continues, these inefficient lasers could see the telecommunications industry become the dominant consumer of world energy. For this reason there is strong interest in developing new, much more efficient telecommunication lasers. One avenue being investigated is the development of quantum dot lasers on InP. The confinement experienced in these low dimensional structures leads to a strong perturbation of the density of states at the band edge, and has been predicted to result in reduced temperature dependence of the threshold current in these devices. The growth of these structures is difficult due to the large lattice mismatch between InP and InAs; however, recently quantum dots elongated in one dimension, known as quantum dashes, have been demonstrated. Chapter 4 of this thesis provides an experimental analysis of one of these quantum dash lasers emitting at 1.5 µm along with a numerical investigation of threshold dynamics present in this device. Another avenue being explored to increase the efficiency of telecommunications lasers is bandstructure engineering of GaAs-based materials to emit at 1.5 µm. The cause of the strong temperature sensitivity in InP-based quantum well structures has been shown to be CHSH Auger recombination. Calculations have shown and experiments have verified that the addition of bismuth to GaAs strongly reduces the bandgap and increases the spin orbit splitting energy of the alloy GaAs1−xBix. This leads to a bandstructure condition at x = 10 % where not only is 1.5 µm emission achieved on GaAs-based material, but also the bandstructure of the material can naturally suppress the costly CHSH Auger recombination which plagues InP-based quantum-well-based material. It has been predicted that telecommunications lasers based on this material system should operate in the absence of external cooling equipment and offer electrical and optical benefits over the incumbent lasers. Chapters 5, 6, and 7 provide a first analysis of several aspects of this material system relevant to the development of high bismuth content telecommunication lasers.

Lack of effect of lowering LDL cholesterol on cancer: meta-analysis of individual data from 175,000 people in 27 randomised trials of statin therapy

Background: Statin therapy reduces the risk of occlusive vascular events, but uncertainty remains about potential effects on cancer. We sought to provide a detailed assessment of any effects on cancer of lowering LDL cholesterol (LDL-C) with a statin using individual patient records from 175,000 patients in 27 large-scale statin trials. Methods and Findings: Individual records of 134,537 participants in 22 randomised trials of statin versus control (median duration 4.8 years) and 39,612 participants in 5 trials of more intensive versus less intensive statin therapy (median duration 5.1 years) were obtained. Reducing LDL-C with a statin for about 5 years had no effect on newly diagnosed cancer or on death from such cancers in either the trials of statin versus control (cancer incidence: 3755 [1.4% per year [py]] versus 3738 [1.4% py], RR 1.00 [95% CI 0.96-1.05]; cancer mortality: 1365 [0.5% py] versus 1358 [0.5% py], RR 1.00 [95% CI 0.93-1.08]) or in the trials of more versus less statin (cancer incidence: 1466 [1.6% py] vs 1472 [1.6% py], RR 1.00 [95% CI 0.93-1.07]; cancer mortality: 447 [0.5% py] versus 481 [0.5% py], RR 0.93 [95% CI 0.82-1.06]). Moreover, there was no evidence of any effect of reducing LDL-C with statin therapy on cancer incidence or mortality at any of 23 individual categories of sites, with increasing years of treatment, for any individual statin, or in any given subgroup. In particular, among individuals with low baseline LDL-C (<2 mmol/L), there was no evidence that further LDL-C reduction (from about 1.7 to 1.3 mmol/L) increased cancer risk (381 [1.6% py] versus 408 [1.7% py]; RR 0.92 [99% CI 0.76-1.10]). Conclusions: In 27 randomised trials, a median of five years of statin therapy had no effect on the incidence of, or mortality from, any type of cancer (or the aggregate of all cancer).

Structural and agentic analysis of supply-chains: a social network analysis approach

This research adds to a body of work exploring the role of Social Network Analysis (SNA) in the study of both relational and structural characteristics of supply chain networks. Two contrasting network cases (food enterprises and digital-based enterprises) are chosen in order to elicit structural differences in business networks subject to divergences in local embeddedness and the relative materiality of the goods and services produced. Our analysis and findings draw out differences in network structure as evidenced by metrics of network centralization and cohesion, the presence of components and other sub-groupings, and the position of central actors. We relate these structural features both to the nature of the networks and to the (qualitative) experiences of the actors themselves. We find, in particular, the role of customers as co-creators of knowledge (for the Food network), the central role of infrastructure and services (for the Digital network), the importance of ICT as a source of codified knowledge inputs, along with the continuing importance of geographical proximity for the development and transfer of tacit knowledge and for incremental learning.

Molecular analysis of evolutionary relationships of Phaseolus dumosus with the gene pool of common bean

Valuable genetic variation for bean breeding programs is held within the common bean secondary gene pool which consists of Phaseolus albescens, P. coccineus, P. costaricensis, and P. dumosus. However, the use of close relatives for bean improvement is limited due to the lack of knowledge about genetic variation and genetic plasticity of many of these species. Characterisation and analysis of the genetic diversity is necessary among beans' wild relatives; in addition, conflicting phylogenies and relationships need to be understood and a hypothesis of a hybrid origin of P. dumosus needs to be tested. This thesis research was orientated to generate information about the patterns of relationships among the common bean secondary gene pool, with particular focus on the species Phaseolus dumosus. This species displays a set of characteristics of agronomic interest, not only for the direct improvement of common bean but also as a source of valuable genes for adaptation to climate change. Here I undertake the first comprehensive study of the genetic diversity of P. dumosus as ascertained from both nuclear and chloroplast genome markers. A germplasm collection of the ancestral forms of P. dumosus together with wild, landrace and cultivar representatives of all other species of the common bean secondary gene pool, were used to analyse genetic diversity, phylogenetic relationships and structure of P. dumosus. Data on molecular variation was generated from sequences of cpDNA loci accD-psaI spacer, trnT-trnL spacer, trnL intron and rps14-psaB spacer and from the nrDNA the ITS region. A whole genome DArT array was developed and used for the genotyping of P. dumosus and its closes relatives. 4208 polymorphic markers were generated in the DArT array and from those, 742 markers presented a call rate >95% and zero discordance. DArT markers revealed a moderate genetic polymorphism among P. dumosus samples (13% of polymorphic loci), while P. coccineus presented the highest level of polymorphism (88% of polymorphic loci). At the cpDNA one ancestral haplotype was detected among all samples of all species in the secondary genepool. The ITS region of P. dumosus revealed high homogeneity and polymorphism bias to P. coccineus genome. Phylogenetic reconstructions made with Maximum likelihood and Bayesian methods confirmed previously reported discrepancies among the nuclear and chloroplast genomes of P. dumosus. The outline of relationships by hybridization networks displayed a considerable number of interactions within and between species. This research provides compelling evidence that P. dumosus arose from hybridisation between P. vulgaris and P. coccineus and confirms that P. costaricensis has likely been involved in the genesis or backcrossing events (or both) in the history of P. dumosus. The classification of the specie P. persistentus was analysed based on cpDNA and ITS sequences, the results found this species to be highly related to P. vulgaris but not too similar to P. leptostachyus as previously proposed. This research demonstrates that wild types of the secondary genepool carry a significant genetic variation which makes this a valuable genetic resource for common bean improvement. The DArT array generated in this research is a valuable resource for breeding programs since it has the potential to be used in several approaches including genotyping, discovery of novel traits, mapping and marker-trait associations. Efforts should be made to search for potential populations of P. persistentus and to increase the collection of new populations of P. dumosus, P. albescens and P. costaricensis that may provide valuable traits for introgression into common bean and other Phaseolus crops.

Epidemiology of diabetes and complications among adults in the Republic of Ireland 1998-2015: a systematic review and meta-analysis

Background: Accurate estimates of the burden of diabetes are essential for future planning and evaluation of services. In Ireland, there is no diabetes register and prevalence estimates vary. The aim of this review was to systematically identify and review studies reporting the prevalence of diabetes and complications among adults in Ireland between 1998 and 2015 and to examine trends in prevalence over time. Methods: A systematic literature search was carried out using PubMed and Embase. Diabetes prevalence estimates were pooled by random-effects meta-analysis. Poisson regression was carried out using data from four nationally representative studies to calculate prevalence rates of doctor diagnosed diabetes between 1998 and 2015 and was also used to assess whether the rate of doctor diagnosed diabetes changed over time. Results: Fifteen studies (eight diabetes prevalence and seven complication prevalence) were eligible for inclusion. In adults aged 18 years and over, the national prevalence of doctor diagnosed diabetes significantly increased from 2.2 % in 1998 to 5.2 % in 2015 (p trend ≤ 0.001). The prevalence of diabetes complications ranged widely depending on study population and methodology used (6.5–25.2 % retinopathy; 3.2–32.0 % neuropathy; 2.5-5.2 % nephropathy). Conclusions: Between 1998 and 2015, there was a significant increase in the prevalence of doctor diagnosed diabetes among adults in Ireland. Trends in microvascular and macrovascular complications prevalence could not be examined due to heterogeneity between studies and the limited availability of data. Reliable baseline data are needed to monitor improvements in care over time at a national level. A comprehensive national diabetes register is urgently needed in Ireland.

Genome analysis and characterisation of the exopolysaccharide produced by Bifidobacterium longum subsp. longum 35624™

The Bifibobacterium longum subsp. longum 35624™ strain (formerly named Bifidobacterium longum subsp. infantis) is a well described probiotic with clinical efficacy in Irritable Bowel Syndrome clinical trials and induces immunoregulatory effects in mice and in humans. This paper presents (a) the genome sequence of the organism allowing the assignment to its correct subspeciation longum; (b) a comparative genome assessment with other B. longum strains and (c) the molecular structure of the 35624 exopolysaccharide (EPS624). Comparative genome analysis of the 35624 strain with other B. longum strains determined that the sub-speciation of the strain is longum and revealed the presence of a 35624-specific gene cluster, predicted to encode the biosynthetic machinery for EPS624. Following isolation and acid treatment of the EPS, its chemical structure was determined using gas and liquid chromatography for sugar constituent and linkage analysis, electrospray and matrix assisted laser desorption ionization mass spectrometry for sequencing and NMR. The EPS consists of a branched hexasaccharide repeating unit containing two galactose and two glucose moieties, galacturonic acid and the unusual sugar 6-deoxy-L-talose. These data demonstrate that the B. longum 35624 strain has specific genetic features, one of which leads to the generation of a characteristic exopolysaccharide.

Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations

The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug–resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.

Diageo's 'Stop Out of Control Drinking' campaign in Ireland: an analysis

Background: It has been argued that the alcohol industry uses corporate social responsibility activities to influence policy and undermine public health, and that every opportunity should be taken to scrutinise such activities. This study analyses a controversial Diageo-funded ‘responsible drinking’ campaign (“Stop out of Control Drinking”, or SOOCD) in Ireland. The study aims to identify how the campaign and its advisory board members frame and define (i) alcohol-related harms, and their causes, and (ii) possible solutions. Methods: Documentary analysis of SOOCD campaign material. This includes newspaper articles (n = 9), media interviews (n = 11), Facebook posts (n = 92), and Tweets (n = 340) produced by the campaign and by board members. All material was coded inductively, and a thematic analysis undertaken, with codes aggregated into sub-themes. Results: The SOOCD campaign utilises vague or self-defined concepts of ‘out of control’ and ‘moderate’ drinking, tending to present alcohol problems as behavioural rather than health issues. These are also unquantified with respect to actual drinking levels. It emphasises alcohol-related antisocial behaviour among young people, particularly young women. In discussing solutions to alcohol-related problems, it focuses on public opinion rather than on scientific evidence, and on educational approaches and information provision, misrepresenting these as effective. “Moderate drinking” is presented as a behavioural issue (“negative drinking behaviours”), rather than as a health issue. Conclusions: The ‘Stop Out of Control Drinking’ campaign frames alcohol problems and solutions in ways unfavourable to public health, and closely reflects other Diageo Corporate Social Responsibility (CSR) activity, as well as alcohol and tobacco industry strategies more generally. This framing, and in particular the framing of alcohol harms as a behavioural issue, with the implication that consumption should be guided only by self-defined limits, may not have been recognised by all board members. It suggests a need for awareness-raising efforts among the public, third sector and policymakers about alcohol industry strategies

Suicide among young people and adults in Ireland: method characteristics, toxicological analysis and substance abuse histories compared

Objective: Information on factors associated with suicide among young individuals in Ireland is limited. The aim of this study was to identify socio-demographic characteristics and circumstances of death associated with age among individuals who died by suicide. Methods: The study examined 121 consecutive suicides (2007–2012) occurring in the southern eastern part of Ireland (Cork city and county). Data were obtained from coroners, family informants, and health care professionals. A comparison was made between 15-24-year-old and 25-34-year-old individuals. Socio-demographic characteristics of the deceased, methods of suicide, history of alcohol and drug abuse, and findings from toxicological analysis of blood and urine samples taken at post mortem were included. Pearson’s χ2 tests and binary logistic regression analysis were performed. Results: Alcohol and/or drugs were detected through toxicological analysis for the majority of the total sample (79.5%), which did not differentiate between 15-24-year-old and 25-34-year-old individuals (74.1% and 86.2% respectively). Compared to 25-34-year-old individuals, 15-24-year-old individuals were more likely to engage in suicide by hanging (88.5%). Younger individuals were less likely to die by intentional drug overdose and carbon monoxide poisoning compared to older individuals. Younger individuals who died between Saturday and Monday were more likely to have had alcohol before dying. Substance abuse histories were similar in the two age groups. Conclusion: Based on this research it is recommended that strategies to reduce substance abuse be applied among 25-34-year-old individuals at risk of suicide. The wide use of hanging in young people should be taken into consideration for future means restriction strategies.