An investigation of the heterogeneity of isolates of Mycoplasma ovipneumoniae using restriction endonuclease analysis : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University

Previous studies of Mycoplasma ovipneumoniae by Restriction Endonuclease Analysis (REA) (Mew, 1982) indicated that the species shows exceptional heterogeneity as compared to other species of pathogenic Mycoplasmas. This thesis further investigates this heterogeneity. To get confirmation of the heterogeneity of M. ovipneumoniae, sixty isolates derived from three sheep on each of twenty farms, were examined by REA. All twenty independant isolates (i.e. isolates originating from sheep on different farms) gave REA patterns that were markedly different, with at most, only 5% of bands in common. Isolates from sheep on the same farm were found to be either indistinguishable, similar (i.e. at least 95% of bands in common) or markedly different (i.e. less than 5% of bands in common). Having confirmed the heterogeneity of M. ovipneumoniae isolates from sheep on different farms further study was directed at providing an explanation for this heterogeneity. The stability of the M. ovipneumoniae genome was investigated by serial passage of a multiply cloned isolate in vitro. Three REA patterns, A, B and C (pattern A was the original pattern) were observed. These pattern changes were non-random in that they were reversible. Thus it appears that an internal rearrangement system is present in M. ovipneumoniae. No non-reversed REA pattern changes were seen. It was concluded that the pattern changes seen after serial in vitro passage were minimal, and that genomic instability could not explain the heterogeneity seen in M. ovipneumoniae. Changed REA patterns must represent DNA changes which in turn may mean changes in proteins. To attempt to detect protein changes, 3 clones which showed patterns A, B and C respectively were examined by SDS-Polyacrylamide gel electrophoresis of total cellular proteins. No differences were detected. There remains the possibility that antigenic changes occurred which might not be demonstrable by this method. A second possible explanation for the heterogeneity seen in M. ovipneumoniae is that frequent genetic interchange between initially distinct REA strains might result in the generation of many new REA types that differ markedly from both parental strains. Three approaches were taken to investigate this possibility: 1. "Classical crosses" detected by antibiotic resistance markers. 2. Mixtures of two cultures of M. ovipneumoniae with different REA patterns were mixed and propagated together. (a) Clones were selected from a mixed culture after it had been passaged for about 30 generations and examined by REA. (b) "Presumptive recombinants", i.e. clones of M. ovipneumoniae which were resistant to two antibiotics, recovered from mixtures of singly resistant clones were examined by REA. 3. M. ovipneumoniae was examined for the presence of extrachromosomal DNA which, if present, could facilitate genetic interchange. Using these three approaches, we were unable to demonstrate genetic interchange in M. ovipneumoniae so it is unlikely that genetic interchange accounts for the considerable heterogeneity seen in the species. It was concluded that the heterogeneity seen in the species is due to the presence of a large number of strains that are genetically stable with respect to REA, which have evolved over a long time period and which are independantly maintained. We estimated the minimum number of strains of M. ovipneumoniae that must exist in a population so that when 29 independent isolates are examined, all will be different. With 95% certainty, this minimum number is 150. The possibility that at least 150 M. ovipneumoniae strains could be maintained in New Zealand was discussed. By applying general epidemiological principles to M. ovipneumoniae, we concluded that many more than 150 could be independently maintained

Understanding and supporting NHS employees with long COVID return to and remain in work: key barriers and facilitators.

Long COVID (LC) is a debilitating illness with complex and dynamic symptoms, affecting all aspects of personal and work life. The process and implications of returning to work following chronic illness have been considered across various conditions; however, published literature exploring LC is sparse. Person-environment fit (PEF) theory has been used to unpick the employer-worker dynamic in the process of returning to work, providing an analytical framework that offers both an understanding of and practical means for supporting this process with a view towards a positive outcome for both parties. We apply this framework to NHS workers suffering LC, utilising PEF theory as a lens through which to provide a sociological perspective for interrogating experiences of returning to and remaining at work, while experiencing symptoms that are often fluctuating, complex and debilitating. Findings are based on a longitudinal, in-depth interview study, exploring impacts of LC on 50 NHS Scotland workers in clinical or ancillary roles. This study highlights the importance and interplay of key factors facilitating successful return to work: improvements in symptoms; specific supports and understanding; workplace flexibility; and considerations around professional role and identity. Understanding and addressing these factors is imperative, as around 10,000 NHS employees in UK are off work because of their LC, at a time of acute crisis in the NHS with understaffing and unprecedented demand. Key outcomes around how workplaces must adapt to facilitate reintegration of workers experiencing LC are discussed, and some additions to theory are proposed to allow for further application to understanding the impact of LC upon return to work

Living with long COVID: the problem of lack of legitimation.

The notion of the "sick role" (Parsons, 1951), where affected individuals are exempt from certain normative expectations and responsibilities (e.g. work) in line with societal judgements, rests heavily on the 'legitimation' of illness, principally through a formal diagnosis. Whilst extensively critiqued in later work (Frank, 2016; Vassiley, et al, 2017), and particularly in relation to chronic illness (Segall, 1976; Radley, 1994), it can be argued that critical aspects of the theory are still useful in understanding illness experiences today (Williams, 2005; Varul, 2010; Hallowell et al., 2015). Here, the sick role theory is applied to the context of long COVID, offering an understanding around the problem of the lack of legitimation of this condition amongst the medical profession. This is based on the findings of a longitudinal, qualitative study looking at the impact of long COVID on 50 NHS workers across Scotland. Presenting with a constellation of common and often debilitating symptoms, the impacts of long COVID are wide-ranging, very often necessitating suspension of normal social responsibilities, including paid work. Yet, as a relatively new condition with few visible symptoms, a lack of evidence base, and poor understanding around the condition, long COVID is generally not legitimised in the same way as other chronic conditions. Many individuals report a sense of not being 'believed', having their needs unrecognised, misdiagnosed, barriers in accessing healthcare, a lack of support at work, emotional burdens and a need for validation of their symptoms and experiences

Unforeseen emotional labour: a collaborative autoethnography exploring researcher experiences of studying long COVID in health workers during the COVID-19 pandemic.

The concept of "emotional labour" describes the regulation of feelings and expressions to fulfil a specific job role, discussed extensively in relation to commercial and caring professions, with more recent scholarship recognising the emotional role performed by qualitative researchers. During the COVID-19 pandemic, this role was likely further heightened due to changes in the socio-political context affecting both individual circumstances and research practice. Despite this, accounts of emotional labour performed by qualitative researchers during this time are lacking. This paper presents a collaborative, autoethnographic account reflecting on the emotional labour experiences of a small team of researchers working on a highly emotive and often distressing study. This longitudinal, mixed methods study: "Long COVID in Health Workers" (LoCH), investigated the lived experiences of healthcare workers from across Scotland, living with the long-term impacts of COVID-19 or Long COVID. Remote interviews were used to explore their experiences in relation to work, their personal and home lives, and coping mechanisms. Collectively, various factors served to construct and intensify our emotional labour experiences: the novelty of Long COVID; its devastating, unpredictable nature and impacts; and a web of factors pertaining to the socio-political context at the time. National lockdowns, enforced social-distancing, homeworking and inaccessibility of NHS services meant a lack of formal and informal support for participants. This heightened their willingness to share highly personal, emotional and often distressing experiences during interviews, with participants often suggesting researchers fulfilled an emotional support role - conseqentially, the usual defined research parameters became blurred. Reactively, researchers engaged in lengthy, ongoing processes in order to negotiate unintended and unforeseen levels of emotional labour, so that they could continue to collect data and remain "professional" during interviews. This was challenging to negotiate in an already difficult homeworking and lockdown climate, with researchers having their own workplace and personal challenges, concerns and responsibilities to balance, in addition to their new and unplanned emotional role. This context also dictated the use of remote methods for both data-gathering and interacting with colleagues, which impeded our ability to provide and receive support. Emotional labour needs to be recognised and acknowledged, and formal plans need to be put in place to support researchers across individual, research team and institutional levels, with critical consideration of socio-political influences at the time of study - an area which merits further consideration. This paper firstly outlines the context for the unforeseen emotional labour borne by the researchers while conducting the LoCH study during the COVID-19 pandemic, before drawing on the collected data to discuss researchers' experiences, and the strategies they employed to cope during and after interviews. Goffman's dramaturgical perspective is employed as a lens to make sense of researcher experience, and to highlight challenges with managing and maintaining professional and emotionally-neutral presentation of self during interviews. The emotional costs of such presentations are explored through emotional vignettes from the researchers. The paper also discusses implications for future research, with regards to managing difficult subject matter in challenging conditions, and mechanisms for coping, emotional management and successful project delivery. Outcomes are relevant to future studies in this subject area, and help to draw attention to and normalise discussions of researcher wellbeing and unanticipated role-pressures

Towards resilience: examining complex and hybridised coping strategies used by NHS workers experiencing long COVID illness.

NHS workers faced an increased risk of contracting COVID-19 during the pandemic and many now experience long COVID (LC). Over 10,000 NHS workers are estimated absent from work due to LC. LC represents a complex, dynamic and often serious condition, for which exist an unclear case-definition and diagnostic criteria. Common LC symptoms - such as fatigue, brain-fog and breathlessness - are debilitating, unpredictable and can significantly impact life and ability to work. Understanding factors supporting positive coping with LC are important for informing successful workplace supports. This study draws on two phases of longitudinal qualitative interviews, conducted six–months apart, with a range of NHS workers from Scotland with LC (50 interviews at first interview and 44 at follow-up). A structured, mixed inductive-deductive thematic analysis revealed that workers engaged in complex, iterative and multi-faceted strategies to approach coming to terms and coping with LC illness; intertwining processes of "illness work" and "emotional work" to generate novel conceptualisations of resilience. Strategies included: reframing LC as long-lasting but temporary; "accepting" LC recovery as "a journey", with "highs", "lows" and often frequent "setbacks"; and "letting go" of past established (pre-LC) benchmarks of health and wellness. Corbin and Strauss' notions of Illness Trajectory Theory are applied as a sociological framework, to interrogate linkages between participants' reimagining of LC illness and their journeys towards developing coping and resilience. Some meaningful outcomes for structuring workplace supports are presented, drawing on participants' narratives of "what works". Pathways are also spotlighted for advancing theory and further scholarship within this important research domain

The GP can't help me, there's no point bothering them: exploring the complex healthcare journeys of NHS workers in Scotland suffering from long COVID: a longitudinal study.

Globally, Long COVID (LC) affects around 40% of people infected with COVID-19 (Chen et al, 2022). Despite high prevalence, symptoms are variable, and no clear healthcare pathway models exist for diagnosis and treatment. The Candidacy Framework describes how individuals conceptualise their eligibility for accessing healthcare services and legitimise service engagement (Dixon-Woods et al., 2006). Anticipation of poor communication with healthcare professionals, and poor expectations of knowledge and advice, deter healthcare engagement. Conversely, positive beliefs regarding accessing clear illness information facilitate healthcare interactions. Determining factors are complicated in the context of LC, where candidacy domains such as Professional Adjudication are conflated with the high demand for NHS services and lack of knowledge surrounding diagnosis, classification and management of LC symptoms. We apply the Candidacy Framework to make sense of the often difficult and challenging healthcare journeys of NHS workers suffering from LC as they negotiate access to healthcare services. Online qualitative interviews were conducted with 50 NHS workers who reported symptoms of LC and came from a range of healthcare disciplines. Analysis identified themes of uncertainty regarding available healthcare supports, self-management and feeling abandoned. GP access was often difficult, with mixed responses surrounding LC legitimacy and diagnosis. Referrals were negotiated (i.e. cardiology consult) but often addressed single fluctuating symptoms, which impacted candidacy. Findings are used to advance three existing Candidacy Framework domains in new directions, highlighting how uncertainties surrounding LC, illness presentation, legitimacy and available recovery pathways systemically constrain health seeking behaviours in healthcare workers suffering LC in Scotland

Disrupted candidacy: a longitudinal examination of the constrained healthcare-access journeys of National Health Service workers in Scotland seeking supports for Long COVID illness.

Evidence examines how persons experiencing Long COVID (LC) struggle to secure healthcare for symptoms; however, few studies examine healthcare workers experiencing LC, nor the complex and multiple difficulties faced when seeking and receiving healthcare. This study is based upon two phases of longitudinally conducted qualitative interviews, six-months apart, with NHS (National Health Service) workers experiencing LC, from different occupational roles at NHS locales in Scotland (first interviews n=50, second interviews n=44). Multiple factors restricted healthcare-access, including worries of pressuring the NHS and concerns over LC being legitimised. When healthcare was sought, workers struggled to secure supports, referrals and treatment. Reasons included: 1) Context - the restrictive pandemic healthcare context; 2) Illness Climate - low GP knowledge surrounding LC and how this could be treated, trends for ascribing symptoms to other causes, and reluctance to diagnose LC; 3) Sense-making of LC, healthcare availability linked to occupational role-identity. To visualise and examine healthcare barriers, candidacy theory is applied, drawing inferences between healthcare context, illness climate, sense-making and identities. The study concluded that NHS workers' complex journeys represent Disrupted Candidacy: intersecting challenges across candidacy domains, restricting seeking and receive LC healthcare. Findings provide insights into why NHS workers resisted and withdrew from healthcare-seeking, and barriers faced when later attempting to secure LC supports. A pathway for future LC illness research to make use of a modified candidacy theory framework is presented. This research focusses on amplifying and learning from lived experiences; the voices of NHS workers in Scotland experiencing Long COVID. Interviews represent primary data for this study, therefore participants and their healthcare journeys are centred in this research and all aspects of production, reporting and output. Explicit discussions of stakeholder group involvement are highlighted in the methods section

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis

Protecting children in low-income and middle-income countries from COVID-19

CITATION: Ahmed, S. et al. 2020. Protecting children in low-income and middle-income countries from COVID-19. BMJ Global Health, 5:e002844. doi:10.1136/bmjgh-2020-002844.The original publication is available at https://gh.bmj.comA saving grace of the COVID-19 pandemic in high-income and upper middle-income countries has been the relative sparing of children. As the disease spreads across low-income and middle-income countries (LMICs), long-standing system vulnerabilities may tragically manifest, and we worry that children will be increasingly impacted, both directly and indirectly. Drawing on our shared child pneumonia experience globally, we highlight these potential impacts on children in LMICs and propose actions for a collective response.https://gh.bmj.com/content/5/5/e002844.abstractPublisher's versio