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.

Viking Age gold and silver from Irish crannogs and other watery places

It has been observed that Viking Age gold finds in Scandinavia and Britain are frequently associated with watery environments and may represent ritual or votive depositions. There is also evidence, literary and archaeological, for the ritual deposition of some silver hoards in the Viking world. This paper considers the evidence of those Viking Age gold and silver hoards and single finds from Ireland that derive from watery locations, including crannogs and their environs. It is noted that all recorded gold hoards, with one exception, have an apparent association with water or watery places and thus conform to the patterns noted elsewhere. Most of the crannog finds, which are invariably of silver, are from the midland region, and it is noted that a high proportion of them contain ingots and hack-silver and are thus most probably economic rather than ritual in function. It is suggested that these types of hoards evidence a close economic relationship between the Hiberno-Scandinavians of Dublin and the Southern Uí Néill rulers of this area. Some of the remaining silver hoards—from bogs, rivers, lakes, small islands and shorelines—which vary in terms of their contents, with both complete ornaments and hack-silver being represented, may have been ritually deposited, but this is difficult to establish with any degree of certainty. A general discussion of ritual hoarding is presented, and it is concluded that this practice may have been more commonplace than has generally been accepted to date and that some, at least, of the ‘watery’ finds from Ireland were indeed deposited in a ritual context.

Resist-substrate interface tailoring for generating high density arrays of Ge and Bi2Se3 nanowires by electron beam lithography

The authors report a chemical process to remove the native oxide on Ge and Bi2Se3 crystals, thus facilitating high-resolution electron beam lithography (EBL) on their surfaces using a hydrogen silsesquioxane (HSQ) resist. HSQ offers the highest resolution of all the commercially available EBL resists. However, aqueous HSQ developers such as NaOH and tetramethylammonium hydroxide have thus far prevented the fabrication of high-resolution structures via the direct application of HSQ to Ge and Bi2Se3, due to the solubility of components of their respective native oxides in these strong aqueous bases. Here we provide a route to the generation of ordered, high-resolution, high-density Ge and Bi2Se3 nanostructures with potential applications in microelectronics, thermoelectric, and photonics devices.                         

On classical and other methods of discriminant analysis and estimation of log-odds

For two multinormal populations with equal covariance matrices the likelihood ratio discriminant function, an alternative allocation rule to the sample linear discriminant function when n1 ≠ n2 ,is studied analytically. With the assumption of a known covariance matrix its distribution is derived and the expectation of its actual and apparent error rates evaluated and compared with those of the sample linear discriminant function. This comparison indicates that the likelihood ratio allocation rule is robust to unequal sample sizes. The quadratic discriminant function is studied, its distribution reviewed and evaluation of its probabilities of misclassification discussed. For known covariance matrices the distribution of the sample quadratic discriminant function is derived. When the known covariance matrices are proportional exact expressions for the expectation of its actual and apparent error rates are obtained and evaluated. The effectiveness of the sample linear discriminant function for this case is also considered. Estimation of true log-odds for two multinormal populations with equal or unequal covariance matrices is studied. The estimative, Bayesian predictive and a kernel method are compared by evaluating their biases and mean square errors. Some algebraic expressions for these quantities are derived. With equal covariance matrices the predictive method is preferable. Where it derives this superiority is investigated by considering its performance for various levels of fixed true log-odds. It is also shown that the predictive method is sensitive to n1 ≠ n2. For unequal but proportional covariance matrices the unbiased estimative method is preferred. Product Normal kernel density estimates are used to give a kernel estimator of true log-odds. The effect of correlation in the variables with product kernels is considered. With equal covariance matrices the kernel and parametric estimators are compared by simulation. For moderately correlated variables and large dimension sizes the product kernel method is a good estimator of true log-odds.

Not thinking straight? A critical discourse analysis of the 2006 Irish High Court ruling in Zappone and Gilligan v. Revenue Commissioners and Attorney General

The recognition and protection of constitutional rights is a fundamental precept. In Ireland, the right to marry is provided for in the equality provisions of Article 40 of the Irish Constitution (1937). However, lesbians and gay men are denied the right to marry in Ireland. The ‘last word’ on this issue came into being in the High Court in 2006, when Katherine Zappone and Ann Louise Gilligan sought, but failed, to have their Canadian marriage recognised in Ireland. My thesis centres on this constitutional court ruling. So as to contextualise the pursuit of marriage equality in Ireland, I provide details of the Irish trajectory vis-à-vis relationship and family recognition for same-sex couples. In Chapter One, I discuss the methodological orientation of my research, which derives from a critical perspective. Chapter Two denotes my theorisation of the principle of equality and the concept of difference. In Chapter Three, I discuss the history of the institution of marriage in the West with its legislative underpinning. Marriage also has a constitutional underpinning in Ireland, which derives from Article 41 of our Constitution. In Chapter Four, I discuss ways in which marriage and family were conceptualised in Ireland, by looking at historical controversies surrounding the legalisation of contraception and divorce. Chapter Five denotes a Critical Discourse Analysis of the High Court ruling in Zappone and Gilligan. In Chapter Six, I critique text from three genres of discourse, i.e. ‘Letters to the Editor’ regarding same-sex marriage in Ireland, communication from legislators vis-à-vis the 2004 legislative impediment to same-sex marriage in Ireland, and parliamentary debates surrounding the 2010 enactment of civil partnership legislation in Ireland. I conclude my research by reflecting on my methodological and theoretical considerations with a view to answering my research questions. Author’s Update: Following the outcome of the 2015 constitutional referendum vis-à-vis Article 41, marriage equality has been realised in Ireland.

Reasoning with sorted-pareto dominance and other qualitative and partially ordered preferences in soft constraints

In decision making problems where we need to choose a particular decision or alternative from a set of possible choices, we often have some preferences which determine if we prefer one decision over another. When these preferences give us an ordering on the decisions that is complete, then it is easy to choose the best or one of the best decisions. However it often occurs that the preferences relation is partially ordered, and we have no best decision. In this thesis, we look at what happens when we have such a partial order over a set of decisions, in particular when we have multiple orderings on a set of decisions, and we present a framework for qualitative decision making. We look at the different natural notions of optimal decision that occur in this framework, which gives us different optimality classes, and we examine the relationships between these classes. We then look in particular at a qualitative preference relation called Sorted-Pareto Dominance, which is an extension of Pareto Dominance, and we give a semantics for this relation as one that is compatible with any order-preserving mapping of an ordinal preference scale to a numerical one. We apply Sorted-Pareto dominance to a Soft Constraints setting, where we solve problems in which the soft constraints associate qualitative preferences to decisions in a decision problem. We also examine the Sorted-Pareto dominance relation in the context of our qualitative decision making framework, looking at the relevant optimality classes for the Sorted-Pareto case, which gives us classes of decisions that are necessarily optimal, and optimal for some choice of mapping of an ordinal scale to a quantitative one. We provide some empirical analysis of Sorted-Pareto constraints problems and examine the optimality classes that result.

Religion, the study of religion and other products of transnational and colonial imaginings

The category of ‘religion’ as contemporary scholarship has demonstrated is a fairly recent innovation, dating back only a few hundred years in Western thought, and ‘world religions’ as we think of it and as we teach it is an even more recent category, emerging out of European colonialism. Thus the academic study of religion is both the product and, at times, the agent of colonial modes of knowledge. And yet, it is perhaps because ‘religion’ continues to be invented and reinvented through connections across cultures that investigating the work of religious ideas and practices offers such fruitful possibilities for understanding the work of culture and power. This article investigates religion and the study of religion as a mode of anti-colonial practice, seeking to understand how each have the potential to cross boundaries, build bridges and produce critical insights into assumptions and worldviews too often taken for granted.