Study of gastrointestinal nematodes co-infecting feral Soay sheep on St Kilda

The unmanaged, feral Soay sheep population on St Kilda has survived for hundreds of years, despite enduring potentially deleterious gastrointestinal nematode co-infections. Co-infections with multiple nematode species are ubiquitous in feral and managed ruminants. Within these mixed burdens, the different species may vary in their pathogenicity, epidemiology and clinical presentation. Elucidating the diversity of different parasite species in a host, rather than studying them as a homogenous group, is a prerequisite to understanding host-parasite interactions. The primary aim of this thesis is to explore and validate non-invasive conventional and next generation molecular parasitological methods to identify and quantify mixed-species infections in feral hosts. Seasonal patterns of gastrointestinal nematode parasitism in the Soay sheep were investigated by faecal egg counts (FEC). Two FEC datasets were analysed: a large dataset, collected between 1988 and 2014, and counted by a modified McMaster method where each egg count represents 100 eggs per gram (epg); and a smaller dataset collected over one year between April 2015 and April 2016, counted by cuvette salt floatation method with a lower detection limit of 1 epg. FEC generally declined with increasing sheep age, until the animals became geriatric (8 years +). Seasonal FEC patterns in females generally followed a decline over the year starting in Spring. FEC were generally higher in males, regardless of their age category, with little seasonal variation between summer and winter once they became adults (3 years +). Monte Carlo simulations were run in order to compare the effects of different detection limits between the FEC methods detecting eggs in faeces to 100 epg and to 1 epg. The simulations suggest that the method with the detection limit of 50 – 100 epg over-estimates the true egg counts within the samples (at high counts), resulting in data that is highly negatively skewed and with an inflated mean. Despite within-year variation of egg counts, both datasets resulted in overall similar seasonal and host patterns. A shorter study with fewer replicates may benefit from a FEC method with a lower detection threshold. The eggs of most strongyle nematodes are morphologically similar, hence whilst FEC can identify general trends in parasitology, the method provides limited information about the proportions of mixed gastrointestinal nematode species burdens of the Soay sheep. The development of advanced molecular methods for the in-direct genus or species-specific diagnosis of strongyle infections in ruminants has negated many of the issues arising from traditional parasitological techniques. Chapter 3 compared two molecular methods; a semi automated multiplex-tandem PCR (AusDiagnostics™) with ITS-2 rDNA next-generation amplicon sequencing (nemabiome assay), to identify species (presence/absence), and quantify the relative proportion (%) of ovine strongyle species in naturally infected samples. This chapter provides the first, and preliminary, comparison of the sensitivity and quantitative ability of both methods. There was good agreement between both molecular tests in determining the presence/absence of species within a sample, but the correlation in their ability to quantify relative proportions of the species present was moderate (C. ovina, R2 = 0.6096) to poor (Trichostrongylus spp., R2 = 0.2334). AusDiagnostics™ characterises a priori strongyle species present, which partially suits a diagnostic tool for managed ruminant systems. The nemabiome assay proved to be the most effective method for identifying and quantifying previously unknown strongylid species, such as those associated with a feral host. The sensitivity, bias, and repeatability of the nemabiome assay was tested for the strongylid species identified in the Soay sheep of St Kilda (Chapter 4). A correction factor was calculated for each species in order to reduce potential species-specific sequencing bias. This was subsequently applied to the field data presented in Chapter 5. Chapter 5 provides an epidemiological survey of the strongyle nematode species co-infecting the Soay sheep of St Kilda. Teladorsagia circumcincta, Trichostrongylus axei, Trichostrongylus vitrinus, Chabertia ovina and Bunostomum trigonocephalum were identified by the nemabiome assay. The study highlights epidemiological trends in the Soay sheep that had not previously been identified using conventional gross and molecular parasitological methods. There were seasonal, age and sex differences in species proportions; whereby trends appeared to correspond with the dynamic life-history of the sheep. Trends included a year round prevalence of all species in lambs (males and females) to the age of one year old, high levels of T. circumcincta over summer and winter in females older than 8 years, and no clear seasonality to T. axei which persisted, at low levels, over all months in all sex/age groups sampled. However, when relative species proportions were adapted to account for average FEC, the impact of the trends seen was minimised; the adequate representation for individual nematode species relied on a high faecal egg count. This is the first study to use the nemabiome deep amplicon sequencing approach to characterise seasonal patterns in different co-infecting gastrointestinal nematodes in feral sheep. Additionally, it highlights the flexibility of the nemabiome assay as a viable non-invasive tool for parasitological surveys of wild animals. Better knowledge of the epidemiology of different co-infecting gastrointestinal nematodes in the ancient feral St Kilda Soay sheep population could help to explain the impact of grazing management and anthelmintic drug treatments in managed sheep flocks, aiding in the development of sustainable control strategies

In Pursuit of Morality: Moral Agency and Everyday Ethics of Plong Karen Buddhists in Southeastern Myanmar

This thesis explores how Buddhist Plong Karen people in Hpa-an, the capital of Karen State, Myanmar pursue morality in what is a time of momentous social, political and cultural change. As one of the rare ethnographic studies to be conducted among Plong Karen people in Myanmar in recent decades, my research problematises existing literature and assumptions about ‘the Karen’. Informed by eighteen months of participant observation in Hpa-an, I examine the multiple ways that Plong Karen Buddhists broker, cultivate, enact, traverse and bound morality. Through an analysis of local social relations and the merit-power nexus, I show that brokering morality is enmeshed in both the complexities of the Buddhist “moral universe” (Walton 2016) and other Karen ethical frameworks that define and make personhood. I examine the Buddhist concept of thila (P. sīla), moral discipline, and how the everyday cultivation of moral “technologies of the self” (Foucault 1997), engenders a form of moral agency and power for elderly Plong Karen men and women of the Hpu Takit sect. Taking the formation of gendered subjectivities during the transitional youth period as a process of “moral becoming” (Mattingly 2014), I demonstrate the ways young women employ moral agency as they test and experiment with multiple modes of everyday ethics and selfhood. The experiential tensions between the traditional habitus of morality as filial obligation and utopian aspirations for the future are then examined through the prism of youth education programmes which encourage learning as a means of individual self-actualisation. Finally, I consider how the moral ideals of Buddhist Plong Karen have contingently converged in recent years with Buddhist chauvinist ideology which excludes non-Buddhists and especially Muslims from popular notions of belonging. The thesis contributes to literature on how minority people in Myanmar see themselves beyond the ethno-nationalist narratives and movements that have defined them for decades (Sadan 2013; Thawnghmung 2012). It also advances the anthropological study of morality by arguing that ethics are best understood not according to any neutral external measure or set of binary ethical positions, but as a set of frequently contradictory and ambiguous ideals which individuals seek to cultivate and enact in the course of everyday life. Rather than searching for morality in moments of ‘moral breakdown’ or conflict, I argue that moral agency is a highly interactive process that is differentiated across people’s lifetime according to one’s circumstances, age and gender. Critiquing the notion that moral coherence is necessary for ethical selfhood, the thesis shows that contradiction and ambivalence is inherent to the pursuit of morality among Plong Karen people. While moral ideals may encapsulate diverse values, meanings and expectations, their individualised and ongoing pursuit can form the basis of a symbolically powerful collective identity

Can surveying practitioners about their practices help identify priority clinical practice guideline topics?

BACKGROUND: Clinical practice guidelines are systematically developed statements designed to assist in patient and physician clinical decision making for specific clinical circumstances. In order to establish which guideline topics are priorities, practitioners were surveyed regarding their current practice. METHODS: One hundred ninety-seven practitioners in Ontario, Canada were mailed a survey exploring their current practice or opinion regarding the prophylactic use of anticonvulsant drugs in patients with malignant glioma who had never had a seizure. The survey consisted of seven questions regarding the relevance of a guideline on the subject to the practitioner's practice, the proportion of clinical cases involving anticonvulsant use, knowledge of existing guidelines on this topic, interest in reviewing a completed practice guideline and three clinical scenarios. RESULTS: There were 122 respondents who returned the survey (62% rate of return). Eighty percent of the practitioners who responded indicated that less than 25% of their clinical cases involved the use of anticonvulsants; however, only 16% of respondents indicated that a practice guideline would be irrelevant to their practice. Eighty percent of respondents volunteered to review a draft version of a practice guideline on the use of anticonvulsants. The survey presented the practitioners with three scenarios where anticonvulsants in patients with brain tumours may be appropriate: peri-operatively in patients without seizures, postoperatively in patients currently using anticonvulsants, and thirdly in patients not currently using anticonvulsants or undergoing surgery. In contrast to the third situation, the first two situations yielded considerable variation in practitioner response. CONCLUSION: The survey established that there is some variation present in the current practice of anticonvulsant use in the patients with brain tumours. Whether there is an optimal treatment practice has yet to be determined. Practitioners do seem to feel that a guideline on anticonvulsant use in warranted, and most practitioners would be interested in being part of the guideline development process

Multi-Platform Whole-Genome Microarray Analyses Refine the Epigenetic Signature of Breast Cancer Metastasis with Gene Expression and Copy Number

BACKGROUND: We have previously identified genome-wide DNA methylation changes in a cell line model of breast cancer metastasis. These complex epigenetic changes that we observed, along with concurrent karyotype analyses, have led us to hypothesize that complex genomic alterations in cancer cells (deletions, translocations and ploidy) are superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes observed in breast cancer metastasis. METHODOLOGY/PRINCIPAL FINDINGS: We undertook simultaneous high-resolution, whole-genome analyses of MDA-MB-468GFP and MDA-MB-468GFP-LN human breast cancer cell lines (an isogenic, paired lymphatic metastasis cell line model) using Affymetrix gene expression (U133), promoter (1.0R), and SNP/CNV (SNP 6.0) microarray platforms to correlate data from gene expression, epigenetic (DNA methylation), and combination copy number variant/single nucleotide polymorphism microarrays. Using Partek Software and Ingenuity Pathway Analysis we integrated datasets from these three platforms and detected multiple hypomethylation and hypermethylation events. Many of these epigenetic alterations correlated with gene expression changes. In addition, gene dosage events correlated with the karyotypic differences observed between the cell lines and were reflected in specific promoter methylation patterns. Gene subsets were identified that correlated hyper (and hypo) methylation with the loss (or gain) of gene expression and in parallel, with gene dosage losses and gains, respectively. Individual gene targets from these subsets were also validated for their methylation, expression and copy number status, and susceptible gene pathways were identified that may indicate how selective advantage drives the processes of tumourigenesis and metastasis. CONCLUSIONS/SIGNIFICANCE: Our approach allows more precisely profiling of functionally relevant epigenetic signatures that are associated with cancer progression and metastasis

From grassroots to global: A blueprint for building a reproducibility network

Researchers, institutions, funders, and publishers are considering how to improve research culture and quality, but no single part of the research ecosystem can effect change on its own. The UK Reproducibility Network (UKRN) was established to facilitate the necessary coordination. Its experience can inform the establishment of like-minded networks around the world to drive positive change

Rights and Power: The Challenge for International Development Agencies

Rights-based approaches are increasingly part of the policy and practice of international development agencies.But how can these agencies support people’s own efforts to turn rights into reality?While som

Author Correction: A consensus-based transparency checklist.

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Attitudes, knowledge and practice behaviours of oncology health care professionals towards lesbian, gay, bisexual, transgender, queer and intersex (LGBTQI) patients and their carers : a mixed-methods study

Objective: There is growing recognition that health care professionals (HCPs) and policy makers are insufficiently equipped to provide culturally competent care to lesbian, gay, bisexual, transgender, queer and intersex (LGBTQI) cancer patients and their families. We examined HCP attitudes, knowledge, and practices regarding LGBTQI cancer care using a mixed-methods research design. Method: Surveys were completed by 357 oncology HCPs in nursing (40%), medical (24%), allied health (19%), and clinical leadership roles (11%); 48 of the surveyed HCPs were interviewed. Results: Most HCPs reported being comfortable treating LGBTQI patients, but reported low levels of confidence and knowledge and systemic barriers to LGBTQI cancer care. Most wanted more education and training, particularly on trans and gender-diverse people (TGD) and those born with intersex variations. Conclusion: Education of HCPs and health system changes are required to overcome barriers to the provision of culturally competent cancer care for LGBTQI patients. Practice implications: These findings reinforce the need for inclusion of LGBTQI content in HCP education and professional training curricula, and institutional support for LGBTQI-inclusive practice behaviours. This includes administrative and visual cues to signal safety of LGBTQI patients within cancer care, facilitating inclusive environments, and the provision of tailored patient-centred care

New metrology for radon at the environmental level

International audienc