This thesis compares how Christian thinkers John Chrysostom (349-407 CE) and Philip Melanchthon (1497-1560 CE) understood the theological concept of justification as found in Paul’s epistle to the Romans, and how their respective intellectual environments influenced their understandings of justification. Through detailed analysis of how Chrysostom and Melanchthon defined the theological concepts underlying their views of justification, it is demonstrated that, while their descriptions of justification often seem amicable, these apparent similarities are superficial. Their primary disagreement rests in their understandings of righteousness, which, for Chrysostom, was the outcome of a synergistic process wherein the faithful Christian gradually became, in actuality, more righteous by cooperating with the will and grace of God. Furthermore, Chrysostom viewed righteousness as a distinct stages in one’s struggle for salvation that followed one’s justification. Melanchthon rejected the notion that human beings themselves could become righteous, instead positing that faithful Christians are justified and simultaneously declared righteous by God based solely on their trust in the saving power of Christ’s atoning death.

Since its foundation between 1410 and 1414 the University of St Andrews has acquired what can be considered to be ‘artefacts of significance’. This somewhat nebulous phrase is used to denote items that have, for a variety of reasons, been deemed to have some special import by the University, and have been displayed or otherwise presented in a context in which this status has been made apparent. The types of artefacts in which particular meaning has been vested during the centuries under consideration include items of silver and gold (including the maces, sacramental vessels of the Collegiate Church of St Salvator, collegiate plate and relics of the Silver Arrow archery competition); church and college furnishings; artworks (particularly portraits); sculpture; and ethnographic specimens and other items described in University records as ‘curiosities’ held in the University Library from c. 1700-1838. The identification of particular artefacts as significant for certain reasons in certain periods, and their presentation and display, may to some extent reflect the University's values, preoccupations and aspirations in these periods, and, to some degree, its identity. Consciously or subconsciously, the objects can be employed or operate as signifiers of meaning, representing or reflecting matters such as the status, authority and history of the University, its breadth of learning and its interest and influence in spheres from science, art and world cultures to national affairs. This thesis provides a comprehensive examination of the growth and development of the University's holdings of 'artefacts of significance' from its foundation to the mid-19th century, and in some cases (especially portraits) beyond this date. It also offers insights into how the University viewed and presented these items and what this reveals about the University of St Andrews, its identity, which changed and developed as the living institution evolved, and the impressions that it wished to project.

This thesis examines the impact of the Reformation on the estates of ecclesiastical institutions and officials based in St Andrews. It argues that land and wealth were redistributed and power structures torn apart, as St Andrews changed from Scotland's Catholic ecclesiastical capital to a conspicuously Protestant burgh. The rapid dispersal of the pre-Reformation church's considerable ecclesiastical lands and revenues had long-term ramifications for the lives of local householders, for relations between religious and secular authorities, and for St Andrews' viability as an urban community. Yet this major redistribution of wealth has had limited attention from scholars. The first part of this study considers the role played by the Catholic Church in St Andrews before the Reformation, and the means by which it was financed, examining the funding of the city's pre-Reformation ecclesiastical foundations and officials, and arguing that (contrary to some traditional assumptions) the Catholic Church in St Andrews was on a reasonably sound financial footing until the Reformation. The second section considers the immediate disruption to St Andrews' religious lands and revenues caused by the burgh's public conversion to Protestantism, and then explores the more planned reorganisation of the 1560s. The disputes and difficulties triggered by the redistribution of ecclesiastical wealth are examined, as well as the longer term impact on St Andrews of the treatment of church revenues at the Reformation. Evidence for this study is chiefly drawn from the extensive body of manuscripts concerning St Andrews held by the National Library of Scotland, the National Records of Scotland, and the University of St Andrews Special Collections.

Urbanisation is a global issue, and rapidly gaining attention from researchers as a major cause of biodiversity loss. Gardens represent a considerable proportion of the urban landscape in the UK and have significant potential to promote urban biodiversity and reduce species loss providing they can be designed and managed appropriately. This research focused on gardens in St Andrews, Scotland, and investigated the influence of environmental variables such as age and area on arachnid and beetle biodiversity with the aim of identifying key predictors of arthropod species richness in urban environments. The key result of this research was that the age and area of individual gardens was not a strong predictor of ground active arthropod biodiversity. This suggests that more recently developed or smaller gardens can contribute to the overall urban region species richness pool as well as larger or more ancient gardens. The most important predictor of ground active arachnid and beetle species richness was the proportion of porous (or 'green') habitat surrounding each garden, and suggested that urban density and habitat connectivity at the regional scale are of key importance. In general, variables measured within gardens (e.g. the provision of microhabitats such as leaf litter, non-managed vegetation, etc.) did not exert any measurable effect on the biodiversity of arachnids or beetles. The findings of this research suggest that the regional availability of heterogeneous greenspace habitat is of high importance for promoting and maintaining urban arthropod biodiversity.

Estuarine studies worldwide have shown that sediment disturbance effects on the macrobenthos are reIated to the nature and scale of the disturbance. Decreased species densities, diversity and richness have been found where the substratum and current patterns have been altered either by direct removal or by the creation of channels . Sediment disturbance in the St. Lucia Narrows has occurred through dredging, beam trawling and episodic floods. The Narrows, a meandering tidal channel approximately 21 km long linking the st Lucia Lakes to the sea, were dredged between 1952 and 1971 to provide a greater flow of seawater to the lakes during periods of low lake levels. A canal was cut through land from the Mfolosi River to the Narrows in an attempt to ameliorate hypersaline conditions in the Lakes, but was never commissioned. Beam trawling has formed the basis of a prawn bait fishery since the 1930's. The bait boats trawl on the mudflats over the entire Narrows on a daily basis and often churn the substratum with their propellers. The objectives of this study were to determine the effects of dredging, a once-off large scale disturbance, and beam trawling, a frequent small scale disturbance, on the macrobenthos of the Narrows. Studies in 1983 and 1984 showed that the dredged channel was impoverished compared with the adjacent mudflat, and that the Link Canal was devoid of benthos. In 1988 species densities, especially of polychaetes, were found to be lower in areas open to beam trawling than in adjacent closed areas. The dredged channel during the present study was again impoverished compared with the adjacent mudflats. The three most abundant species occurring on the mudflats, the crab Tylodiplax blephariskios, the amphipod Victoriopsia chilkensis and capitellid polychaetes, were recorded at densities an order of magnitude lower in the channel than on the mudflats. The substratum in the channel was generally sandier than the mudflats, and this condition appeared to be maintained by the scouring action of tidal currents. It was calculated that the creation of the dredged channel had reduced the standing benthic biomass in the Narrows by a minimum of approximately 20%. The Link Canal was colonised by the three major mud flat species , but at densities an order of magnitude lower than the mudflats. Beam trawling of experimental sites at monthly and 6-monthly intervals on muddy and sandy substrata in the Narrows between July 1989 and July 1990 did not appear to have a negative effect on the benthos. The coverage of the bait boats was calculated to be comparable to the trawling effort in this study, and suggested that the bait fishery is not having a detrimental effect on the benthos. It was concluded that the macrobenthos in the Narrows represented a pioneering community characteristic of estuaries, either not affected by, or able to recover from small scale and episodic disturbances provided that there was no long term habitat modification. / Thesis (M.Sc.)-University of Natal, Durban, 1992.

Die Analyse von NGS Daten ist ein zentraler Aspekt der modernen genomischen Forschung. Bei der Extraktion von Daten aus den beiden am häufigsten verwendeten Quellorganismen bestehen jedoch vielfältige Problemstellungen. Im ersten Kapitel wird ein neuartiger Ansatz vorgestellt welcher einen Abstand zwischen Krebszellinienkulturen auf Grundlage ihrer kleinen genomischen Varianten bestimmt um die Kulturen zu identifizieren. Eine Voll-Exom sequenzierte Kultur wird durch paarweise Vergleiche zu Referenzdatensätzen identifiziert so ein gemessener Abstand geringer ist als dies bei nicht verwandten Kulturen zu erwarten wäre. Die Wirksamkeit der Methode wurde verifiziert, jedoch verbleiben Einschränkung da nur das Sequenzierformat des Voll-Exoms unterstützt wird. Daher wird im zweiten Kapitel eine publizierte Modifikation des Ansatzes vorgestellt welcher die Unterstützung der weitläufig genutzten Bulk RNA sowie der Panel-Sequenzierung ermöglicht. Die Ausweitung der Technologiebasis führt jedoch zu einer Verstärkung von Störeffekten welche zu Verletzungen der mathematischen Konditionen einer Abstandsmetrik führen. Daher werden die entstandenen Verletzungen durch statistische Verfahren zuerst quantifiziert und danach durch dynamische Schwellwertanpassungen erfolgreich kompensiert. Das dritte Kapitel stellt eine neuartige Daten-Aufwertungsmethode (Data-Augmentation) vor welche das Trainieren von maschinellen Lernmodellen in Abwesenheit von neoplastischen Trainingsdaten ermöglicht. Ein abstraktes Abstandsmaß wird zwischen neoplastischen Entitäten sowie Entitäten gesundem Ursprungs mittels einer transkriptomischen Dekonvolution hergestellt. Die Ausgabe der Dekonvolution erlaubt dann das effektive Vorhersagen von klinischen Eigenschaften von seltenen jedoch biologisch vielfältigen Krebsarten wobei die prädiktive Kraft des Verfahrens der des etablierten Goldstandard ebenbürtig ist. / The analysis of NGS data is a central aspect of modern Molecular Genetics and Oncology. The first scientific contribution is the development of a method which identifies Whole-exome-sequenced CCL via the quantification of a distance between their sets of small genomic variants. A distinguishing aspect of the method is that it was designed for the computer-based identification of NGS-sequenced CCL. An identification of an unknown CCL occurs when its abstract distance to a known CCL is smaller than is expected due to chance. The method performed favorably during benchmarks but only supported the Whole-exome-sequencing technology. The second contribution therefore extended the identification method by additionally supporting the Bulk mRNA-sequencing technology and Panel-sequencing format. However, the technological extension incurred predictive biases which detrimentally affected the quantification of abstract distances. Hence, statistical methods were introduced to quantify and compensate for confounding factors. The method revealed a heterogeneity-robust benchmark performance at the trade-off of a slightly reduced sensitivity compared to the Whole-exome-sequencing method. The third contribution is a method which trains Machine-Learning models for rare and diverse cancer types. Machine-Learning models are subsequently trained on these distances to predict clinically relevant characteristics. The performance of such-trained models was comparable to that of models trained on both the substituted neoplastic data and the gold-standard biomarker Ki-67. No proliferation rate-indicative features were utilized to predict clinical characteristics which is why the method can complement the proliferation rate-oriented pathological assessment of biopsies. The thesis revealed that the quantification of an abstract distance can address sources of erroneous NGS data analysis.

Immer wenn neue Anforderungen an ein System gestellt werden, müssen die Korrektheit und Konsistenz der Systemspezifikation überprüft werden, was in der Praxis in der Regel manuell erfolgt. Eine mögliche Option, um die Nachteile dieser manuellen Analyse zu überwinden, ist das sogenannte Contract-Based Design. Dieser Entwurfsansatz kann den Verifikationsprozess zur Überprüfung, ob die Anforderungen auf oberster Ebene konsistent verfeinert wurden, automatisieren. Die Verifikation kann somit iterativ durchgeführt werden, um die Korrektheit und Konsistenz des Systems angesichts jeglicher Änderung der Spezifikationen sicherzustellen. Allerdings ist es aufgrund der mangelnden Benutzerfreundlichkeit und der Schwierigkeiten bei der Interpretation von Verifizierungsergebnissen immer noch eine Herausforderung, formale Ansätze in der Industrie einzusetzen. Stellt beispielsweise der Model Checker bei der Verifikation eine Inkonsistenz fest, generiert er ein Gegenbeispiel (Counterexample) und weist gleichzeitig darauf hin, dass die gegebenen Eingabespezifikationen inkonsistent sind. Hier besteht die gewaltige Herausforderung darin, das generierte Gegenbeispiel zu verstehen, das oft sehr lang, kryptisch und komplex ist. Darüber hinaus liegt es in der Verantwortung der Ingenieurin bzw. des Ingenieurs, die inkonsistente Spezifikation in einer potenziell großen Menge von Spezifikationen zu identifizieren. Diese Arbeit schlägt einen Ansatz zur Erklärung von Gegenbeispielen (Counterexample Explanation Approach) vor, der die Verwendung von formalen Methoden vereinfacht und fördert, indem benutzerfreundliche Erklärungen der Verifikationsergebnisse der Ingenieurin bzw. dem Ingenieur präsentiert werden. Der Ansatz zur Erklärung von Gegenbeispielen wird mittels zweier Methoden evaluiert: (1) Evaluation anhand verschiedener Anwendungsbeispiele und (2) eine Benutzerstudie in Form eines One-Group Pretest-Posttest Experiments. / Whenever new requirements are introduced for a system, the correctness and consistency of the system specification must be verified, which is often done manually in industrial settings. One viable option to traverse disadvantages of this manual analysis is to employ the contract-based design, which can automate the verification process to determine whether the refinements of top-level requirements are consistent. Thus, verification can be performed iteratively to ensure the system’s correctness and consistency in the face of any change in specifications. Having said that, it is still challenging to deploy formal approaches in industries due to their lack of usability and their difficulties in interpreting verification results. For instance, if the model checker identifies inconsistency during the verification, it generates a counterexample while also indicating that the given input specifications are inconsistent. Here, the formidable challenge is to comprehend the generated counterexample, which is often lengthy, cryptic, and complex. Furthermore, it is the engineer’s responsibility to identify the inconsistent specification among a potentially huge set of specifications. This PhD thesis proposes a counterexample explanation approach for formal methods that simplifies and encourages their use by presenting user-friendly explanations of the verification results. The proposed counterexample explanation approach identifies and explains relevant information from the verification result in what seems like a natural language statement. The counterexample explanation approach extracts relevant information by identifying inconsistent specifications from among the set of specifications, as well as erroneous states and variables from the counterexample. The counterexample explanation approach is evaluated using two methods: (1) evaluation with different application examples, and (2) a user-study known as one-group pretest and posttest experiment.

In model-driven development (MDD), domain-specific modeling languages (DSMLs) act as a communication vehicle for aligning the requirements of domain experts with the needs of software engineers. With the rise of the UML as a de facto standard, UML/MOF-based DSMLs are now widely used for MDD. This paper documents design decisions collected from 90 UML/MOF-based DSML projects. These recurring design decisions were gained, on the one hand, by performing a systematic literature review (SLR) on the development of UML/MOF-based DSMLs. Via the SLR, we retrieved 80 related DSML projects for review. On the other hand, we collected decisions from developing ten DSML projects by ourselves. The design decisions are presented in the form of reusable decision records, with each decision record corresponding to a decision point in DSML development processes. Furthermore, we also report on frequently observed (combinations of) decision options as well as on associations between options which may occur within a single decision point or between two decision points. This collection of decision-record documents targets decision makers in DSML development (e.g., DSML engineers, software architects, domain experts). (authors' abstract) / Series: Technical Reports / Institute for Information Systems and New Media

In model-driven development (MDD), domain-specific modeling languages (DSMLs) act as a communication vehicle for aligning the requirements of domain experts with the needs of software engineers. With the rise of the UML as a de facto standard, UML/MOF-based DSMLs are now widely used for MDD. This paper documents design decisions collected from 90 UML/MOF-based DSML projects. These recurring design decisions were gained, on the one hand, by performing a systematic literature review (SLR) on the development of UML/MOF-based DSMLs. Via the SLR, we retrieved 80 related DSML projects for review. On the other hand, we collected decisions from developing ten DSML projects by ourselves. The design decisions are presented in the form of reusable decision records, with each decision record corresponding to a decision point in DSML development processes. Furthermore, we also report on frequently observed (combinations of) decision options as well as on associations between options which may occur within a single decision point or between two decision points. This collection of decision-record documents targets decision makers in DSML development (e.g., DSML engineers, software architects, domain experts). / Series: Technical Reports / Institute for Information Systems and New Media

According to tradition, but not definitely corroborated by either historical or archaeological sources, the Maltese islands received their seed of faith in A.D. 60 by the Apostle Paul, when he was on his way to Rome, as recorded in the Acts of the Apostles. The aim of this study is to examine the background of the cult of St Paul in Malta; to investigate the efforts of Mgr G. De Piro and Fr G. Preca in safeguarding the Roman Catholic faith and the cult of St Paul; specifically their contributions when Malta became a British colony and was placed under a Protestant administration; and whether or not their contributions are still valid today. To achieve this, we will carry an exegetical research of the Acts of the Apostles chapters 27, 28:1-10, historiography, modern literary studies. The best primary sources to investigate these two personalities are the archives of the Missionary Society of St Paul (MSSP), and of the Society of Christian Doctrine (SDC). These archives provide the core of the authentic findings of the enormous wealth of religious literature these priests were able to produce, as well as the testimonies of both Founders. Their spiritual and theological writings include books, pamphlets, articles, sermons, letters and other religious materials. When the British settled in Malta (1800-1964), the Maltese were very religious and completely loyal to the Roman Catholic Church, but their religiosity had no sound theological basis. Hence, the majority of the Maltese could have been easily influenced by Protestant proselytism and Freemasonry. Both Mgr De Piro and Fr Preca foresaw the need of a sound catechetical teaching, so that the Roman Catholic faith would be better understood and appreciated. They could read the signs of the times. Mgr De Piro and Fr Preca provided catechetical information and spiritual literature in Maltese, which were almost non-existent at the time; and groups of lay persons were well trained and educated in religious matters. To understand better how the contributions of Mgr De Piro and Fr Preca were so vital to safeguard the Roman Catholic faith and the cult of St Paul, it was imperative to study the history of the local church during the nineteenth and twentieth centuries, the socio-political situation, and the Church-State problems. This study shows the indefatigable work and sacrificial life led by both Founders and how the Roman Catholic faith was not only saved during the British administration but also became much stronger. In the course of this study, we will investigate how the faith of the Maltese and the cult of St Paul helped to save them from calamities, misery and in time of war; and if the contributions given by Mgr De Piro and Fr Preca are still valid today where the roots of Christianity and Christian tradition are being threatened once again. / PhD (Church and Dogma History), North-West University, Potchefstroom Campus, 2014