All-optical modulation converter for on-off keying to duobinary and alternate-mark inversion at 42.6 Gbps

Advanced modulation formats have become increasingly important as telecoms engineers strive for improved tolerance to both linear and nonlinear fibre-based transmission impairments. Two important modulation schemes are Duobinary (DB) and Alternate-mark inversion (AMI) [1] where transmission enhancement results from auxiliary phase modulation. As advanced modulation formats displace Return-to-zero On-Off Keying (RZ-OOK), inter-modulation converters will become increasingly important. If the modulation conversion can be performed at high bitrates with a small number of operations per bit, then all-optical techniques may offer lower energy consumption compared to optical-electronic-optical approaches. In this paper we experimentally demonstrate an all-optical system incorporating a pair of hybrid-integrated semiconductor optical amplifier (SOA)-based Mach-Zehnder interferometer (MZI) gates which translate RZ-OOK to RZ-DB or RZ-AMI at 42.6 Gbps. This scheme includes a wavelength conversion to arbitrary output wavelength and has potential for high-level photonic integration, scalability to higher bitrates, and should exhibit regenerative properties [2].

Novel all-optical on-off-keyed to alternate-mark-inversion converter

We numerically investigate a novel 40 Gbps OOK to AMI all-optical modulation format converter employing an SOA-based Mach-Zehnder interferometer.  We demonstrate operation with a 27-1 PRBS and explain the phase modulation's relationship with patterning.

Use of semiconductor optical amplifiers in signal processing applications

We describe a 42.6 Gbit/s all-optical pattern recognition system which uses semiconductor optical amplifiers (SOAs). A circuit with three SOA-based logic gates is used to identify the presence of specific port numbers in an optical packet header.

High speed nonlinear optical components for next-generation optical communications

Electronic signal processing systems currently employed at core internet routers require huge amounts of power to operate and they may be unable to continue to satisfy consumer demand for more bandwidth without an inordinate increase in cost, size and/or energy consumption. Optical signal processing techniques may be deployed in next-generation optical networks for simple tasks such as wavelength conversion, demultiplexing and format conversion at high speed (≥100Gb.s-1) to alleviate the pressure on existing core router infrastructure. To implement optical signal processing functionalities, it is necessary to exploit the nonlinear optical properties of suitable materials such as III-V semiconductor compounds, silicon, periodically-poled lithium niobate (PPLN), highly nonlinear fibre (HNLF) or chalcogenide glasses. However, nonlinear optical (NLO) components such as semiconductor optical amplifiers (SOAs), electroabsorption modulators (EAMs) and silicon nanowires are the most promising candidates as all-optical switching elements vis-à-vis ease of integration, device footprint and energy consumption. This PhD thesis presents the amplitude and phase dynamics in a range of device configurations containing SOAs, EAMs and/or silicon nanowires to support the design of all optical switching elements for deployment in next-generation optical networks. Time-resolved pump-probe spectroscopy using pulses with a pulse width of 3ps from mode-locked laser sources was utilized to accurately measure the carrier dynamics in the device(s) under test. The research work into four main topics: (a) a long SOA, (b) the concatenated SOA-EAMSOA (CSES) configuration, (c) silicon nanowires embedded in SU8 polymer and (d) a custom epitaxy design EAM with fast carrier sweepout dynamics. The principal aim was to identify the optimum operation conditions for each of these NLO device configurations to enhance their switching capability and to assess their potential for various optical signal processing functionalities. All of the NLO device configurations investigated in this thesis are compact and suitable for monolithic and/or hybrid integration.

Practical programming for static average-case analysis: the MOQA investigation

This work considers the static calculation of a program’s average-case time. The number of systems that currently tackle this research problem is quite small due to the difficulties inherent in average-case analysis. While each of these systems make a pertinent contribution, and are individually discussed in this work, only one of them forms the basis of this research. That particular system is known as MOQA. The MOQA system consists of the MOQA language and the MOQA static analysis tool. Its technique for statically determining average-case behaviour centres on maintaining strict control over both the data structure type and the labeling distribution. This research develops and evaluates the MOQA language implementation, and adds to the functions already available in this language. Furthermore, the theory that backs MOQA is generalised and the range of data structures for which the MOQA static analysis tool can determine average-case behaviour is increased. Also, some of the MOQA applications and extensions suggested in other works are logically examined here. For example, the accuracy of classifying the MOQA language as reversible is investigated, along with the feasibility of incorporating duplicate labels into the MOQA theory. Finally, the analyses that take place during the course of this research reveal some of the MOQA strengths and weaknesses. This thesis aims to be pragmatic when evaluating the current MOQA theory, the advancements set forth in the following work and the benefits of MOQA when compared to similar systems. Succinctly, this work’s significant expansion of the MOQA theory is accompanied by a realistic assessment of MOQA’s accomplishments and a serious deliberation of the opportunities available to MOQA in the future.

Identification of novel innate immune mechanisms regulating inflammation in the gastrointestinal tract

The Gastro-Intestinal (GI) tract is a unique region in the body. Our innate immune system retains a fine homeostatic balance between avoiding inappropriate inflammatory responses against the myriad commensal microbes residing in the gut while also remaining active enough to prevent invasive pathogenic attack. The intestinal epithelium represents the frontline of this interface. It has long been known to act as a physical barrier preventing the lumenal bacteria of the gastro-intestinal tract from activating an inflammatory immune response in the immune cells of the underlying mucosa. However, in recent years, an appreciation has grown surrounding the role played by the intestinal epithelium in regulating innate immune responses, both in the prevention of infection and in maintaining a homeostatic environment through modulation of innate immune signalling systems. The aim of this thesis was to identify novel innate immune mechanisms regulating inflammation in the GI tract. To achieve this aim, we chose several aspects of regulatory mechanisms utilised in this region by the innate immune system. We identified several commensal strains of bacteria expressing proteins containing signalling domains used by Pattern Recognition Receptors (PRRs) of the innate immune system. Three such bacterial proteins were studied for their potentially subversive roles in host innate immune signalling as a means of regulating homeostasis in the GI tract. We also examined differential responses to PRR activation depending on their sub-cellular localisation. This was investigated based on reports that apical Toll-Like Receptor (TLR) 9 activation resulted in abrogation of inflammatory responses mediated by other TLRs in Intestinal Epithelial Cells (IECs) such as basolateral TLR4 activation. Using the well-studied invasive intra-cellular pathogen Listeria monocytogenes as a model for infection, we also used a PRR siRNA library screening technique to identify novel PRRs used by IECs in both inhibition and activation of inflammatory responses. Many of the PRRs identified in this screen were previously believed not to be expressed in IECs. Furthermore, the same study has led to the identification of the previously uncharacterised TLR10 as a functional inflammatory receptor of IECs. Further analysis revealed a similar role in macrophages where it was shown to respond to intracellular and motile pathogens such as Gram-positive L.monocytogenes and Gram negative Salmonella typhimurium. TLR10 expression in IECs was predominantly intracellular. This is likely in order to avoid inappropriate inflammatory activation through the recognition of commensal microbial antigens on the apical cell surface of IECs. Moreover, these results have revealed a more complex network of innate immune signalling mechanisms involved in both activating and inhibiting inflammatory responses in IECs than was previously believed. This contribution to our understanding of innate immune regulation in this region has several direct and indirect benefits. The identification of several novel PRRs involved in activating and inhibiting inflammation in the GI tract may be used as novel therapeutic targets in the treatment of disease; both for inducing tolerance and reducing inflammation, or indeed, as targets for adjuvant activation in the development of oral vaccines against pathogenic attack.

Immune and stress factors in the pathophysiology of the mdx mouse model of Duchenne Muscular Dystrophy

Duchenne Muscular Dystrophy (DMD) is a fatal multi-system neuromuscular disease caused by loss of dystrophin. The loss of dystrophin from membranes of contractile muscle cells and the dysregulation of the DAPC, induces chronic inflammation due to tissue necrosis and eventual replacement with collagen which weakens muscular force and strength. Dystrophin deficiency may cause under-diagnosed features of DMD include mood disorders such as depression and anxiety and dysfunction of the gastrointestinal tract. The first study in the thesis examined mood in the dystrophin-deficient mdx mouse model of DMD and examined the effects of the tri-cyclic antidepressant, amitriptyline on behaviours. Amitriptyline had anti-depressant and anxiolytic effects in the mdx mice possibly through effects on stress factors such as corticotrophin-releasing factor (CRF). This antidepressant also reduced skeletal muscle inflammation and caused a reduction in circulating interleukin (IL)-6 levels. In the second and third studies, we specifically blocked IL-6 signalling and used Urocortin 2, CRFR2 agonist to investigate their potential as therapeutic targets in mdx mice pathophysiology. Isometric and isotonic contractile properties of the diaphragm, were compared in mdx mice treated with anti IL-6 receptor antibodies (anti IL-6R) and/or Urocortin 2. Deficits in force production, work and power detected in mdx mice were improved with treatment. In study three I investigated contractile properties in gastrointestinal smooth muscle. As compared to wild type mice, mdx mice had slower faecal transit times, shorter colons with thickened muscle layers and increased contractile activity in response to recombinant IL-6. Blocking IL-6 signalling resulted in an increase in colon length, normalised faecal output times and a reduction in IL-6-evoked contractile activity. The findings from these studies indicate that for both diaphragm and gastrointestinal function in a dystrophin-deficient model, targeting of IL-6 and CRFR2 signalling has beneficial therapeutic effects.

All-optical signal processing using semiconductor optical amplifiers for next generation optical networks

This thesis details an experimental and simulation investigation of some novel all-optical signal processing techniques for future optical communication networks. These all-optical techniques include modulation format conversion, phase discrimination and clock recovery. The methods detailed in this thesis use the nonlinearities associated with semiconductor optical amplifiers (SOA) to manipulate signals in the optical domain. Chapter 1 provides an introduction into the work detailed in this thesis, discusses the increased demand for capacity in today’s optical fibre networks and finally explains why all-optical signal processing may be of interest for future optical networks. Chapter 2 discusses the relevant background information required to fully understand the all-optical techniques demonstrated in this thesis. Chapter 3 details some pump-probe measurement techniques used to calculate the gain and phase recovery times of a long SOA. A remarkably fast gain recovery is observed and the wavelength dependent nature of this recovery is investigated. Chapter 4 discusses the experimental demonstration of an all-optical modulation conversion technique which can convert on-off- keyed data into either duobinary or alternative mark inversion. In Chapter 5 a novel phase sensitive frequency conversion scheme capable of extracting the two orthogonal components of a quadrature phase modulated signal into two separate frequencies is demonstrated. Chapter 6 investigates a novel all-optical clock recovery technique for phase modulated optical orthogonal frequency division multiplexing superchannels and finally Chapter 7 provides a brief conclusion.

“Something isn’t right here”: American exceptionalism and the creative nonfiction of the Vietnam War

In this thesis, I argue that few attempts were as effective in correcting the exceptionalist ethos of the United States than the creative nonfiction written by the veterans and journalists of the Vietnam War. Using critical works on creative nonfiction, I identify the characteristics of the genre that allowed Paul John Eakin to call it ‘a special kind of fiction.’ I summarise a brief history of creative nonfiction to demonstrate how it became a distinctly American form despite its Old World origins. I then claim that it was the genre most suited to the kind of ideological transformation that many hoped to instigate in U.S. society in the aftermath of Vietnam. Following this, the study explores how this “new” myth-making process occurred. I use Tim O’Brien’s If I Die in a Combat Zone and Philip Caputo’s A Rumor of War to illustrate how autobiography/memoir was able to demonstrate the detrimental effect that America’s exceptionalist ideology was having on its population. Utilising narrative and autobiographical theory, I contend that these accounts represented a collective voice which spoke for all Americans in the years after Vietnam. Using Neil Sheehan’s A Bright Shining Lie and C.D.B. Bryan’s Friendly Fire, I illustrate how literary journalism highlighted the hubris of the American government. I contend that while poiesis is an integral attribute of creative nonfiction, by the inclusion of extraneous bibliographic material, authors of the genre could also be seen as creating a literary context predisposing the reader towards an empirical interpretation of the events documented within. Finally, I claim that oral histories were in their essence a synthesis of “everyman” experiences very much in keeping with the American zeitgeist of the early Eighties. Focussing solely on Al Santoli’s Everything We Had, I demonstrate how such polyphonic narratives personalised the history of the Vietnam War.

Career choice in medicine

Background: Career Choice in Medicine is an important and problematic topic. Medical education has been framed as professional identity development, yet career choice has not been viewed as a matter of identity. My primary aim was to offer new insights by exploring career choice using Figured Worlds theory, a socio-cultural theory of identity. Graduate retention is a challenge for many countries, including Ireland. My secondary aim was to address a gap in the data on postgraduate trainees in Ireland and to use the Irish case to illustrate points transferable to other contexts. Methodology & Methods: This was a predominantly qualitative Mixed Methods programme of research. My qualitative studies were oriented towards social constructionism. I collated existing data from the Royal College of Physicians of Ireland (RCPI) and HSE-MET to describe trainees and their career paths. I surveyed Basic Specialist Training trainees (n=333) about their career plans. I surveyed new trainees (n=527) about their expectations of training and all RCPI trainees about their experiences of training (n=1246). I conducted semi-structured interviews with 18 medical students and doctors. A subgroup (n=6) provided longitudinal data. Figured Worlds theory and Gee’s discourse tools were used for analysis. Results: I have used the case of medical training and career choice in Ireland to explain how social, political and cultural context, and day to day experiences in the cultural world of medicine, shaped doctors’ career choices. My qualitative findings described a unifying model of career choice, consisting of priming, exposure, positioning and open-endedness, which can guide the design of interventions to shape and support career choice. Conclusion: My original contribution has been to demonstrate the fruitfulness of framing career choice in terms of identity development. This represents a turn in the conversation about career choice, which brings new starting points and moves the dialogue forward.

Textual criticism and medieval Irish studies

Many textual scholars will be aware that the title of the present thesis has been composed in a conscious revisionary relation to Tim William Machan’s influential Textual Criticism and Middle English Texts. (Tim William Machan, Textual Criticism and Middle English Texts (Charlottesville, 1994)). The primary subjects of Machan’s study are works written in English between the fourteenth and sixteenth centuries, the latter part of the period conventionally labelled Middle English. In contrast, the works with which I am primarily concerned are those written by scholars of Old and Middle Irish in the nineteenth, twentieth and twenty-first centuries. Where Machan aims to articulate the textual and cultural factors that characterise Middle English works as Middle English, the purposes of this thesis are (a) to identify the underlying ideological and epistemological perspectives which have informed much of the way in which medieval Irish documents and texts are rendered into modern editions, and (b) to begin to place the editorial theory and methodology of medieval Irish studies within the broader context of Biblical, medieval and modern textual criticism. Hence, the title is Textual Criticism and Medieval Irish Studies, rather than Textual Criticism and Medieval Irish Texts