Dlùth is Inneach: Linguistic and Institutional Foundations for Gaelic Corpus Planning

This report presents the results of a one-year research project, commissioned by Bòrd na Gàidhlig BnG) and carried out by a Soillse Research team, whose goal was to answer the following question: What corpus planning principles are appropriate for the strengthening and promotion of Scottish Gaelic, and what effective coordination would result in their implementation? This report contains the following agreed outcomes: a clear and consistent linguistic foundation for Gaelic corpus planning, according with Bòrd na Gàidhlig’s acquisition, usage and status planning initiatives, and most likely to be supported by Gaelic users. a programme of priorities to be addressed by Gaelic corpus planning. recommendations on a means of coordination that will be effective in terms of cost and management (i.e. an institutional framework

Earth-atmosphere evolution based on the new determination of Devonian atmosphere Ar isotopic composition

The isotopic composition of the noble gases, in particular Ar, in samples of ancient atmosphere trapped in rocks and minerals provides the strongest constraints on the timing and rate of Earth atmosphere formation by degassing of the Earth's interior. We have re-measured the isotopic composition of argon in the Rhynie chert from northeast Scotland using a high precision mass spectrometer in an effort to provide constraints on the composition of Devonian atmosphere. Irradiated chert samples yield 40Ar/36Ar ratios that are often below the modern atmosphere value. The data define a 40Ar/36Ar value of 289.5±0.4 at K/36Ar = 0. Similarly low 40Ar/36Ar are measured in un-irradiated chert samples. The simplest explanation for the low 40Ar/36Ar is the preservation of Devonian atmosphere-derived Ar in the chert, with the intercept value in 40Ar–39Ar–36Ar space representing an upper limit. In this case the Earth's atmosphere has accumulated only 3% (5.1±0.4×1016 mol) of the total 40Ar inventory since the Devonian. The average accumulation rate of 1.27±0.09×108 mol40Ar/yr overlaps the rate over the last 800 kyr. This implies that there has been no resolvable temporal change in the outgassing rate of the Earth since the mid-Palaeozoic despite the likely episodicity of Ar degassing from the continental crust. Incorporating the new Devonian atmosphere 40Ar/36Ar into the Earth degassing model of Pujol et al. (2013) provides the most precise constraints on atmosphere formation so far. The atmosphere formed in the first ∼100 Ma after initial accretion during a catastrophic degassing episode. A significant volume of 40Ar did not start to accumulate in the atmosphere until after 4 Ga which implies that stable K-rich continental crust did not develop until this time

An Inheritance-Based Theory of the Lexicon in Combinatory Categorial Grammar

Institute for Communicating and Collaborative SystemsThis thesis proposes an extended version of the Combinatory Categorial Grammar (CCG) formalism, with the following features: 1. grammars incorporate inheritance hierarchies of lexical types, defined over a simple, feature-based constraint language 2. CCG lexicons are, or at least can be, functions from forms to these lexical types This formalism, which I refer to as ‘inheritance-driven’ CCG (I-CCG), is conceptualised as a partially model-theoretic system, involving a distinction between category descriptions and their underlying category models, with these two notions being related by logical satisfaction. I argue that the I-CCG formalism retains all the advantages of both the core CCG framework and proposed generalisations involving such things as multiset categories, unary modalities or typed feature structures. In addition, I-CCG: 1. provides non-redundant lexicons for human languages 2. captures a range of well-known implicational word order universals in terms of an acquisition-based preference for shorter grammars This thesis proceeds as follows: Chapter 2 introduces the ‘baseline’ CCG formalism, which incorporates just the essential elements of category notation, without any of the proposed extensions. Chapter 3 reviews parts of the CCG literature dealing with linguistic competence in its most general sense, showing how the formalism predicts a number of language universals in terms of either its restricted generative capacity or the prioritisation of simpler lexicons. Chapter 4 analyses the first motivation for generalising the baseline category notation, demonstrating how certain fairly simple implicational word order universals are not formally predicted by baseline CCG, although they intuitively do involve considerations of grammatical economy. Chapter 5 examines the second motivation underlying many of the customised CCG category notations — to reduce lexical redundancy, thus allowing for the construction of lexicons which assign (each sense of) open class words and morphemes to no more than one lexical category, itself denoted by a non-composite lexical type. Chapter 6 defines the I-CCG formalism, incorporating into the notion of a CCG grammar both a type hierarchy of saturated category symbols and an inheritance hierarchy of constrained lexical types. The constraint language is a simple, feature-based, highly underspecified notation, interpreted against an underlying notion of category models — this latter point is crucial, since it allows us to abstract away from any particular inference procedure and focus on the category notation itself. I argue that the partially model-theoretic I-CCG formalism solves the lexical redundancy problem fairly definitively, thereby subsuming all the other proposed variant category notations. Chapter 7 demonstrates that the I-CCG formalism also provides the beginnings of a theory of the CCG lexicon in a stronger sense — with just a small number of substantive assumptions about types, it can be shown to formally predict many implicational word order universals in terms of an acquisition-based preference for simpler lexical inheritance hierarchies, i.e. those with fewer types and fewer constraints. Chapter 8 concludes the thesis

'Risk-free' corpus-planning for Scottish Gaelic? Collaborative development of basic grammatical norms for 21st century speakers

No abstract available

The role of regulated clinical trials in the development of bacteriophage therapeutics.

Antibiotic resistance is now recognized as a major, global threat to human health and the need for the development of novel antibacterial therapies has become urgent. Lytic bacteriophages (phages) targeting individual bacterial pathogens have therapeutic potential as an alternative or adjunct to antibiotic use. Bacteriophage therapy has been used for decades, but clinical trials in this field are rare, leaving many questions unanswered as to its effectiveness for many infectious diseases. As a consequence bacteriophage therapy is not used or accepted in most parts of the world. The increasing need for new antimicrobial therapies is driving the development of bacteriophage therapies for a number of diseases but these require the successful completion of large-scale clinical trials in accordance with US FDA or European EMA guidelines. Bacteriophages are considered as biological agents by regulatory authorities and they are managed by biological medicinal products guidelines for European trials and guidelines of the division of vaccines and related product applications in the USA. Bacteriophage therapy is typically an 'active' treatment requiring multiplication in the bacterial host and therefore the factors that govern its success are different from those of conventional antibiotics. From the pharmacokinetic and pharmacodynamic points of view, time of treatment, dosage depending on the site of infection and the composition of the bacteriophage formulation (single vs multiple strains) need careful consideration when designing clinical trials. Scientific evidence regarding inflammatory effects, potential for gene transfer and phage resistance, need to be evaluated through such trials. However purity, stability and sterility of preparations for human use can be addressed through Good Manufacturing Practises to reduce many potential safety concerns. In this review we discuss the potential for the development of bacteriophage therapy in the context of critical aspects of modern, regulated clinical trials

A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments

<p>Abstract</p> <p>Background</p> <p>Gas chromatography-mass spectrometry (GC-MS) is a robust platform for the profiling of certain classes of small molecules in biological samples. When multiple samples are profiled, including replicates of the same sample and/or different sample states, one needs to account for retention time drifts between experiments. This can be achieved either by the alignment of chromatographic profiles prior to peak detection, or by matching signal peaks after they have been extracted from chromatogram data matrices. Automated retention time correction is particularly important in non-targeted profiling studies.</p> <p>Results</p> <p>A new approach for matching signal peaks based on dynamic programming is presented. The proposed approach relies on both peak retention times and mass spectra. The alignment of more than two peak lists involves three steps: (1) all possible pairs of peak lists are aligned, and similarity of each pair of peak lists is estimated; (2) the guide tree is built based on the similarity between the peak lists; (3) peak lists are progressively aligned starting with the two most similar peak lists, following the guide tree until all peak lists are exhausted. When two or more experiments are performed on different sample states and each consisting of multiple replicates, peak lists within each set of replicate experiments are aligned first (within-state alignment), and subsequently the resulting alignments are aligned themselves (between-state alignment). When more than two sets of replicate experiments are present, the between-state alignment also employs the guide tree. We demonstrate the usefulness of this approach on GC-MS metabolic profiling experiments acquired on wild-type and mutant <it>Leishmania mexicana </it>parasites.</p> <p>Conclusion</p> <p>We propose a progressive method to match signal peaks across multiple GC-MS experiments based on dynamic programming. A sensitive peak similarity function is proposed to balance peak retention time and peak mass spectra similarities. This approach can produce the optimal alignment between an arbitrary number of peak lists, and models explicitly within-state and between-state peak alignment. The accuracy of the proposed method was close to the accuracy of manually-curated peak matching, which required tens of man-hours for the analyzed data sets. The proposed approach may offer significant advantages for processing of high-throughput metabolomics data, especially when large numbers of experimental replicates and multiple sample states are analyzed.</p

Use of Transformer-Based Models for Word-Level Transliteration of the Book of the Dean of Lismore

The Book of the Dean of Lismore (BDL) is a 16th-century Scottish Gaelic manuscript written in a non-standard orthography. In this work, we outline the problem of transliterating the text of the BDL into a standardised orthography, and perform exploratory experiments using Transformer-based models for this task. In particular, we focus on the task of word-level transliteration, and achieve a character-level BLEU score of 54.15 with our best model, a BART architecture pre-trained on the text of Scottish Gaelic Wikipedia and then fine-tuned on around 2,000 word-level parallel examples. Our initial experiments give promising results, but we highlight the shortcomings of our model, and discuss directions for future work