Statistical analysis of crystallographic data

The Cambridge structural database (CSD) is a vast resource for crystallographic information. As of 1st January 2009 there are more than 469,611 crystal structures available in the CSD. This work is centred on a program dSNAP which has been developed at the University of Glasgow. dSNAP is a program that uses statistical methods to group fragments of molecules into groups that have a similar conformation. This work is aimed at applying methods to reduce the number of variables required to describe the geometry of the fragments mined from the CSD. To this end, the geometric definition employed by dSNAP was investigated. The default definition is total geometries which are made up of all angles and all distances, including all non-bonded distances and angles. This geometric definition was investigated in a comparative manner with four other definitions. There were all angles, all distances, bonded angles and distances and bonded angles, distances and torsion angles. These comparisons show that non-bonded information is critical to the formation of groups of fragments with similar conformations. The remainder of this work was focused in reducing the number of variables required to group fragments having similar conformations into distinct groups. Initially a method was developed to calculate the area of triangles between three atoms making up the fragment. This was employed systematically as a means of reducing the total number of variables required to describe the geometry of the fragments. Multivariate statistical methods were also applied with the aim of reducing the number of variables required to describe the geometry of the fragment in a systematic manner. The methods employed were factor analysis and sparse principal components analysis. Both of these methods were used to extract important variables from the original default geometric definition, total geometries. The extracted variables were then used as input for dSNAP and were compared with the original output. Biplots were used to visualise the variables describing the fragments. Biplots are multivariate analogues to scatter plots and are used to visualise how the fragments are related to the variables describing them. Owing to the large number of variables that make up the definition factor analysis was applied to extract the important variables before the biplot was calculated. The biplots give an overview of the correlation matrix and using these plots it is possible to select variables that are influencing the formation of clusters in dSNAP

Adomnán of Iona’s Vita Sancti Columbae: a literary analysis

Written in c. 700 at the island monastery of Iona, Adomnán’s Vita Sancti Columbae (VSC) is an important source for the study of early medieval Scotland and Ireland. This thesis analyses the text as a literary work, seeking to understand more about its internal logic and the ways in which it relates to other kinds of literary texts. These include Biblical texts, other early insular, continental and late antique hagiographies, vernacular secular sagas, legal texts, scholarly literature and wisdom literature. Adomnán did not necessarily know all of these texts, and some of them post-date him, but they provide a wider interpretative context for VSC. Adomnán’s other known work, De Locis Sanctis, and texts connected to him, such as Cáin Adomnáin, will also be considered. I look for points of similarity and divergence between Vita Sancti Columbae and these other texts, which I term “adjacent literature”, looking to see how the text relates to its wider literary and intellectual context. By taking this approach, we are able to understand the text better on its own terms, making it more useful as a source for historical study. The text is studied, and set within its wider context, with respect to the following main areas: The Manuscripts of Vita Sancti Columbae: the visual construction of the text: Considering the five surviving manuscripts of the first recension of VSC, but focussing especially on the earliest (Schaffhausen Stadtbibliothek Generalia 1, of near authorial date and Ionan provenance), this chapter considers how the visual presentation of VSC relates to its production and reproduction as a literary text. Page layout, illumination, the use of the Greek alphabet and different colours of ink and manuscript context are all discussed. Structure and Narrative Sequencing in Vita Sancti Columbae: VSC is not a chronologically-structured account of Columba’s life, but rather a hagiography made up of many short narratives that demonstrate his sanctity and power in different ways. These narratives are arranged thematically, with a basic tripartite structure, with one book concerned with prophecies, one with miracles and one with visions. The narratives within the three books are often arranged into small, tightly constructed clusters of related stories. This chapter is an investigation of both the overall structure of the work and the “micro-structure” of the sequencing of narratives. Language and Vita Sancti Columbae: This chapter explores Adomnán’s style as a Hiberno-Latin writer, including discussions of such techniques as hyperbaton, alliteration and variatio. Adomnán’s use of and attitudes to Greek and Hebrew are also explored, as is his use of and attitudes to Old Irish. Sex, Women and Violence in Vita Sancti Columbae: This chapter investigates Adomnán’s presentations of sexual behaviour, the role of women as givers of advice, and the violence inflicted on the innocent. Several of the narratives about violence clearly have a strong gendered dimension, and relate in interesting ways to Cáin Adomnáin, and they are discussed in this light. Dangerous Beasts in Vita Sancti Columbae: VSC contains several encounters with dangerous beasts of various kinds, some of which are not unambiguously identifiable. These episodes are studied in turn, including discussions about identifying the beasts, and investigating the functions that they have within the text. Vita Sancti Columbae and Cult Practice: The thesis concludes with an exploration of the roles VSC might have played in the life of the Columban familia. The use of blessed objects and relics within the text is studied, with suggestions as to their relation to cult practice. The final section concerns the possibility that certain parts of VSC were intended to be used in processions, or to be read with the active participation of an audience

The Beuk o Amos

The Book of Amos is notable amongst Old Testament books for its evocative language and imagery. If we needed a fresh reminder of its power, it is ably provided here in a translation by Duncan Sneddon which displays the characteristic strength of fluent Scots speech

Speaking and Listening with the Eyes: Gaze Signaling during Dyadic Interactions

Cognitive scientists have long been interested in the role that eye gaze plays in social interactions. Previous research suggests that gaze acts as a signaling mechanism and can be used to control turn-taking behaviour. However, early research on this topic employed methods of analysis that aggregated gaze information across an entire trial (or trials), which masks any temporal dynamics that may exist in social interactions. More recently, attempts have been made to understand the temporal characteristics of social gaze but little research has been conducted in a natural setting with two interacting participants. The present study combines a temporally sensitive analysis technique with modern eye tracking technology to 1) validate the overall results from earlier aggregated analyses and 2) provide insight into the specific moment-to-moment temporal characteristics of turn-taking behaviour in a natural setting. Dyads played two social guessing games (20 Questions and Heads Up) while their eyes were tracked. Our general results are in line with past aggregated data, and using cross-correlational analysis on the specific gaze and speech signals of both participants we found that 1) speakers end their turn with direct gaze at the listener and 2) the listener in turn begins to speak with averted gaze. Convergent with theoretical models of social interaction, our data suggest that eye gaze can be used to signal both the end and the beginning of a speaking turn during a social interaction. The present study offers insight into the temporal dynamics of live dyadic interactions and also provides a new method of analysis for eye gaze data when temporal relationships are of interest

A mouse informatics platform for phenotypic and translational discovery

The International Mouse Phenotyping Consortium (IMPC) is providing the world’s first functional catalogue of a mammalian genome by characterising a knockout mouse strain for every gene. A robust and highly structured informatics platform has been developed to systematically collate, analyse and disseminate the data produced by the IMPC. As the first phase of the project, in which 5000 new knockout strains are being broadly phenotyped, nears completion, the informatics platform is extending and adapting to support the increasing volume and complexity of the data produced as well as addressing a large volume of users and emerging user groups. An intuitive interface helps researchers explore IMPC data by giving overviews and the ability to find and visualise data that support a phenotype assertion. Dedicated disease pages allow researchers to find new mouse models of human diseases, and novel viewers provide high-resolution images of embryonic and adult dysmorphologies. With each monthly release, the informatics platform will continue to evolve to support the increased data volume and to maintain its position as the primary route of access to IMPC data and as an invaluable resource for clinical and non-clinical researchers

A bioimage informatics platform for high-throughput embryo phenotyping

High-throughput phenotyping is a cornerstone of numerous functional genomics projects. In recent years, imaging screens have become increasingly important in understanding gene–phenotype relationships in studies of cells, tissues and whole organisms. Three-dimensional (3D) imaging has risen to prominence in the field of developmental biology for its ability to capture whole embryo morphology and gene expression, as exemplified by the International Mouse Phenotyping Consortium (IMPC). Large volumes of image data are being acquired by multiple institutions around the world that encompass a range of modalities, proprietary software and metadata. To facilitate robust downstream analysis, images and metadata must be standardized to account for these differences. As an open scientific enterprise, making the data readily accessible is essential so that members of biomedical and clinical research communities can study the images for themselves without the need for highly specialized software or technical expertise. In this article, we present a platform of software tools that facilitate the upload, analysis and dissemination of 3D images for the IMPC. Over 750 reconstructions from 80 embryonic lethal and subviable lines have been captured to date, all of which are openly accessible at mousephenotype.org. Although designed for the IMPC, all software is available under an open-source licence for others to use and develop further. Ongoing developments aim to increase throughput and improve the analysis and dissemination of image data. Furthermore, we aim to ensure that images are searchable so that users can locate relevant images associated with genes, phenotypes or human diseases of interest