Optical Analysis of Hg2+ Ions by Oligonucleotide–Gold-Nanoparticle Hybrids and DNA-Based Machines

Zwei verschiedene optische Methoden für die Analyse von Hg2+-Ionen, die auf der Bildung von Thymin-Hg2+-Komplexen beruhen, werden vorgestellt. Bei diesen Methoden werden die Hg2+-Ionen mithilfe aggregierter Goldnanopartikel und einer auf der DNA-Chemie basierenden Maschine (siehe Schema) analysiert.

Residual Vibration Reduction in Computer Controlled Machines

Control of machines that exhibit flexibility becomes important when designers attempt to push the state of the art with faster, lighter machines. Three steps are necessary for the control of a flexible planet. First, a good model of the plant must exist. Second, a good controller must be designed. Third, inputs to the controller must be constructed using knowledge of the system dynamic response. There is a great deal of literature pertaining to modeling and control but little dealing with the shaping of system inputs. Chapter 2 examines two input shaping techniques based on frequency domain analysis. The first involves the use of the first deriviate of a gaussian exponential as a driving function template. The second, acasual filtering, involves removal of energy from the driving functions at the resonant frequencies of the system. Chapter 3 presents a linear programming technique for generating vibration-reducing driving functions for systems. Chapter 4 extends the results of the previous chapter by developing a direct solution to the new class of driving functions. A detailed analysis of the new technique is presented from five different perspectives and several extensions are presented. Chapter 5 verifies the theories of the previous two chapters with hardware experiments. Because the new technique resembles common signal filtering, chapter 6 compares the new approach to eleven standard filters. The new technique will be shown to result in less residual vibrations, have better robustness to system parameter uncertainty, and require less computation than other currently used shaping techniques.

Syntax-Based Analytic Reading of Musical Scores

As part of a larger research project in musical structure, a program has been written which "reads" scores encoded in an input language isomorphic to music notation. The program is believed to be the first of its kind. From a small number of parsing rules the program derives complex configurations, each of which is associated with a set of reference points in a numerical representation of a time-continuum. The logical structure of the program is such that all and only the defined classes of events are represented in the output. Because the basis of the program is syntactic (in the sense that parsing operations are performed on formal structures in the input string), many extensions and refinements can be made without excessive difficulty. The program can be applied to any music which can be represented in the input language. At present, however, it constitutes the first stage in the development of a set of analytic tools for the study of so-called atonal music, the revolutionary and little understood music which has exerted a decisive influence upon contemporary practice of the art. The program and the approach to automatic data-structuring may be of interest to linguists and scholars in other fields concerned with basic studies of complex structures produced by human beings.

Reading the rhetoric of nationhood in two Reformation pamphlets by Richard Morison and Nicholas Bodrugan

Mottram, S. (2005). Reading the rhetoric of nationhood in two Reformation pamphlets by Richard Morison and Nicholas Bodrugan. Renaissance Studies. 19(4), pp.523-540. RAE2008

Reading Scripture in Conflicts

sermon text; MS Word document

A Christian Reading of History

This recording is part of the Marsh Chapel Audio Collection.

Reading Between the Lines: The Potential of Popular Young Adult Fiction in Adolescent Spiritual Formation

Popular culture is a powerful, shaping force in the lives of teenagers between the ages of fourteen through eighteen in the United States today. This dissertation argues the importance of popular fiction for adolescent spiritual formation and it investigates that importance by exploring the significance of narrative for theology and moral formation. The dissertation employs mythic and archetypal criticism as a tool for informing the selection and critique of narratives for use in adolescent spiritual development and it also incorporates insights gained from developmental psychology to lay the groundwork for the development of a curriculum that uses young adult fiction in a program of spiritual formation for teenagers in a local church setting. The dissertation defends the power of narrative in Christian theology and concludes that narrative shapes the imagination in ways that alter perception and are important for the faith life of teenagers in particular. I go on to argue that not all narratives are created equal. In using literary myth criticism in concert with theology, I use the two disciplines’ different aims and methods to fully flesh out the potential of theologies intrinsic to works meant for a largely secular audience. The dissertation compares various works of young adult fiction (M.T. Anderson’s Feed and Terry Pratchett’s Nation in dialogue with a theology of creation; Marcus Zusak’s I am the Messenger and Jerry Spinelli’s Stargirl in dialogue with salvation and saviors; and the four novels of Stephanie Meyer’s Twilight saga in dialogue with a theology of hope (eschatology). The dissertation explores how each theme surfaces (even if only implicitly) from both literary and theological standpoints. The dissertation concludes with a sample four-week lesson plan that demonstrates one way the theological and literary critique can be formed into a practical curriculum for use in an adolescent spiritual development setting. Ultimately, this dissertation provides a framework for how practitioners of young adult formation can select, analyze, and develop materials for their teenagers using new works of popular young adult fiction. The dissertation comes to the conclusion that popular fiction contains a wealth of material that can challenge and shape young readers’ own emerging theology.

Visualising ribosome profiling and using it for reading frame detection and exploration of eukaryotic translation initiation

Ribosome profiling (ribo-seq) is a recently developed technique that provides genomewide information on protein synthesis (GWIPS) in vivo. The high resolution of ribo-seq is one of the exciting properties of this technique. In Chapter 2, I present a computational method that utilises the sub-codon precision and triplet periodicity of ribosome profiling data to detect transitions in the translated reading frame. Application of this method to ribosome profiling data generated for human HeLa cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame. Since the initial publication of the ribosome profiling technique in 2009, there has been a proliferation of studies that have used the technique to explore various questions with respect to translation. A review of the many uses and adaptations of the technique is provided in Chapter 1. Indeed, owing to the increasing popularity of the technique and the growing number of published ribosome profiling datasets, we have developed GWIPS-viz (http://gwips.ucc.ie), a ribo-seq dedicated genome browser. Details on the development of the browser and its usage are provided in Chapter 3. One of the surprising findings of ribosome profiling of initiating ribosomes carried out in 3 independent studies, was the widespread use of non-AUG codons as translation initiation start sites in mammals. Although initiation at non-AUG codons in mammals has been documented for some time, the extent of non-AUG initiation reported by these ribo-seq studies was unexpected. In Chapter 4, I present an approach for estimating the strength of initiating codons based on the leaky scanning model of translation initiation. Application of this approach to ribo-seq data illustrates that initiation at non-AUG codons is inefficient compared to initiation at AUG codons. In addition, our approach provides a probability of initiation score for each start site that allows its strength of initiation to be evaluated.

The political philosophy of Miki Kiyoshi: A close reading of the philosophical foundations of cooperative communitarianism

The thesis is a historical and philological study of the mature political theory of Miki Kiyoshi (1897-1945) focused on Philosophical Foundations of Cooperative Communitarianism (1939), a full translation of which is included. As the name suggests, it was a methodological and normative communitarianism, which critically built on liberalism, Marxism and Confucianism to realise a regional political community. Some of Miki’s Western readers have wrongly considered him a fascist ideologue, while he has been considered a humanist Marxist in Japan. A closer reading cannot support either view. The thesis argues that the Anglophone study of Japanese philosophy is a degenerating research programme ripe for revolution in the sense of returning full circle to an original point. That means returning to the texts, reading them contextually and philologically, in principle as early modern European political theory is read by intellectual historians, such as the representatives of Cambridge School history of political thought. The resulting reading builds critically on the Japanese scholarship and relates it to contemporary Western and postcolonial political theory and the East Asian tradition, particularly neo-Confucianism. The thesis argues for a Cambridge School perspective radicalised by the critical addendum of geo-cultural context, supplemented by Geertzian intercultural hermeneutics and a Saidian ‘return to philology’. As against those who have seen radical reorientations in Miki’s political thought, the thesis finds gradual progression and continuity between his neo-Kantian, existentialist, Marxian anthropology, Hegelian and finally communitarian phases. The theoretical underpinnings are his philosophical anthropology, a structurationist social theory of praxis, and a critique of liberalism, Marxism, nationalism and idealism emphasising concrete as opposed to abstract theory and the need to build on existing cultural traditions to modernise rather than westernise East Asia. This post-Western fusion was imagined to be the beginning of a true and pluralistic universalism.

Reading Lydgate's Troy Book: patronage, politics, and history in Lancastrian England

This thesis, Reading Lydgate's Troy Book: Patronage, Politics and History in Lancastrian England, discusses the relationship between John Lydgate as a court poet to his patron Henry V. I contend that the Troy Book is explored as a vehicle to propagate the idea that the House of Lancaster is the legitimate successor to King Richard II in order to smooth over the usurpation of 1399. Paul Strohm's England's Empty Throne was a key influence to the approach of this thesis' topic. I examine that although Chaucer had a definitive impact on Lydgate's writing, Lydgate is able to manipulate this influence for his own ambitions. In order to enhance his own fame, Lydgate works to promote Chaucer's canon so that as Chaucer's successor, he will inherit more prestige. The Trojan war is seen in context with the Hundred Years War, and can be applied contextually to political events. Lydgate presents characters that are vulnerable to human failings, and their assorted, complicated relationships. Lydgate modernises the Troy Book to reflect and enhance his Lancastrian society, and the thesis gives a contextual view of Lydgate's writing of the Troy Book. Lydgate writes for a more varied target audience than his thirteenth-century source, Guido delle Colonne, and there is a deliberation on the female characters of the Troy Book which promulgates the theory that Lydgate takes a proactive and empathetic interest in women's roles in society. Furthermore Lydgate has never really been accepted as a humanist, and I look at Lydgate's work from a different angle; he is a self-germinating humanist. Lydgate revives antiquity to educate his fifteenth-century audience, and his ambition is to create a memorial for his patron in the vernacular, and enhance his own fame as a poet separate from Chaucer's shadow.

Within the carnal: re-reading Merleau-Ponty through the language of drawing

In order to present visual art as a paradigm for philosophy, Merleau-Ponty investigated the creative processes of artists whose work corresponded closely with his philosophical ideas. His essays on art are widely valued for emphasising process over product, and for challenging the primacy of the written word in all spheres of human expression. While it is clear that he initially favoured painting, Merleau-Ponty began to develop a much deeper understanding of the complexities of how art is made in his late work in parallel with his advancement of a new ontology. Although his ontology remains unfinished and only exists as working notes and a manuscript entitled The Visible and Invisible, Merleau-Ponty had begun to appreciate the fundamental role drawing plays in the making of art and the creation of a language of expression that is as vital as the written or spoken word. Through an examination of Merleau-Ponty’s unfinished manuscript and working notes my thesis will investigate his working methods and use of materials and also explore how he processed his ideas by using my own art practice as the basis of my research. This research will take the form of an inquiry into how the unfinished and incomplete nature of text and artworks, while they are still ‘works in progress’, can often reveal the more human and carnal components of creative processes. Applying my experience as a practitioner and a teacher in an art school, I focus on the significance of drawing practice for Merleau-Ponty’s later work, in order to rebalance an overemphasis on painting in the literature. Understanding the differences between these two art forms, and how they are taught, can offer an alternative engagement with Merleau-Ponty’s later work and his struggle to find a language to express his developing new ontology. In addition, by re-reading his work through the language of drawing, I believe we gain new insights which reaffirm Merleau-Ponty's relevance to contemporary art making and aesthetics.

Production and recognition bias of stylistic sentences using a story reading task.

Four experiments examined participants' ability to produce surface characteristics of sentences using an on-line story reading task. Participants read a series of stories in which either all, or the majority of sentences were written in the same "style," or surface form. Twice per story, participants were asked to fill in a blank consistent with the story. For sentences that contained three stylistic regularities, participants imitated either all three characteristics (Experiment 2) or two of the three characteristics (Experiment 1), depending on the proportion of in-style sentences. Participants demonstrated a recognition bias for the read style in an unannounced recognition task. When participants read stories in which the two styles were the dative/double object alternation, participants demonstrated a syntactic priming effect in the cloze task, but no consistent recognition bias in a later recognition test (Experiments 3 and 4).

Scheduling for parallel dedicated machines with a single server

This paper examines scheduling problems in which the setup phase of each operation needs to be attended by a single server, common for all jobs and different from the processing machines. The objective in each situation is to minimize the makespan. For the processing system consisting of two parallel dedicated machines we prove that the problem of finding an optimal schedule is NP-hard in the strong sense even if all setup times are equal or if all processing times are equal. For the case of m parallel dedicated machines, a simple greedy algorithm is shown to create a schedule with the makespan that is at most twice the optimum value. For the two machine case, an improved heuristic guarantees a tight worst-case ratio of 3/2. We also describe several polynomially solvable cases of the later problem. The two-machine flow shop and the open shop problems with a single server are also shown to be NP-hard in the strong sense. However, we reduce the two-machine flow shop no-wait problem with a single server to the Gilmore-Gomory traveling salesman problem and solve it in polynomial time. (c) 2000 John Wiley & Sons, Inc.

[Book review] Peter Reimann and Hans Spada (eds), Learning in Humans and Machines: Towards an Interdisciplinary Learning Science

Review of: Peter Reimann and Hans Spada (eds), Learning in Humans and Machines: Towards an Interdisciplinary Learning Science, Pergamon. (1995). ISBN: 978-0080425696

Scheduling parallel dedicated machines under a single non-shared resource

The scheduling problem of minimizing the makespan for m parallel dedicated machines under single resource constraints is considered. For different variants of the problem the complexity status is established. Heuristic algorithms employing the so-called group technology approach are presented and their worst-case behavior is examined. Finally, a polynomial time approximation scheme is presented for the problem with fixed number of machines.