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Repeated Stories is an exploratory project in textile design where the aim is to explore the design of storytelling patterns addressed to children. More precisely, the work examines how patterns can be designed as a tool to encourage curiosity and creativity among children. The work is practice-based, building on concrete experiments with a workshop character, where combinations of textile material, colour, printing techniques and scale are explored. The primary motive for this work is to take advantage of textile design expertise in a social context, to find new areas for competence in making repeats and patterns, and how a social value can be added to patterns. The result is an installation of three hanging textiles, meant for a public space, such as waiting room in a hospital. The work proposes an alternative approach to surface patterns by adding storytelling and give the patterns both a communicative and decorative function.

Little research has been undertaken into the rapidly expanding genre of rephotography, where many developments have taken place in response to advancing technology. This thesis is practice-based and incorporates long-term fieldwork in Scotland. The primary rephotographic projects undertaken by practitioners in North America are reviewed and their innovative presentation of material to interpret changes to space and place through time, are assessed and analysed. This study considers the application of some of these practices in a Scottish context. The research sets out to collate and explore repetition through the construction of visual narratives and to better understand the representation of change in people and places over time. The narratives unintentionally formed when places are photographed and rephotographed by multiple practitioners are considered along with the establishment and consequences of iconicity. In a Scottish context, the research identifies three major sources of photographs: the closely aligned nineteenth century tourism-generated catalogues of George Washington Wilson and Valentines of Dundee and the Catalogue of the Countryside of Scotland created by Robert Moyes Adam. The overall picture that emerges from the research is one of opportunity with increasing democratic application, improved accuracy and greater ability to present and share results. Rephotography is known to be a powerful tool for the discernment and measurement of visible change and suggests avenues that might inform the interpretation and utility of repeated images. This research provides an overview from which limitations can be assessed or innovative application devised. While comparative monitoring may remain a primary application, projects – some sentimental and reflective - that explore personal experience, memory and loss can be explored with rephotography.

Background: Repeat renal biopsies in patients with lupus nephritis (LN) are usually done to guide treatment or to establish disease chronicity. Their value is not clear from available literature. There is also no available data in Africa to guide clinicians. Methods: This was a retrospective study of patients undergoing a repeat renal biopsy between January 2003 and December 2014 from a single centre in Cape Town, South Africa. Relevant demographic, clinical and histological records of patients with repeat renal biopsies were documented. Comparison of data from 1st and 2nd renal biopsy was performed. Results: 44 patients had at least 2 biopsies done during the study period. Most patients were females (81.8%). The mean biopsy interval was 2.8± 1.8 (range 0.38 – 9.4) years. Proteinuria was the main indication for the repeat biopsy (36.1%). The glomerular filtration rate and proteinuria worsened between the two biopsies (p=0.001 and 0.019) respectively suggesting disease progression. Most patients (65.4%) with a non-proliferative class of LN at first biopsy progressed into a proliferative class whereas patients with initial proliferative LN at first biopsy (77.8%) remained as proliferative at repeat biopsy. Treatment was changed in 85% of patients at second biopsy. Conclusion: Repeat renal biopsies in patients with LN presents a useful means of assessing disease progression and provides guidance regarding modification of treatment. More studies are however required to evaluate the value of repeat biopsies and perhaps the need for protocol renal biopsies in patients with LN.

This thesis explores the Natchez Trace Parkway using the method of repeat photography to determine whether or not the design intent of the Trace has changed since its beginning. Based upon fifteen matched pairs of photographs, which are evaluated based on a content analysis matrix, the original design intent, recent design guidelines, and planned land use maps, the degree of change that has occurred along the Trace is measured. Time has wrought inevitable change along the Trace. The changes that have occurred indicate a further effort to preserve the original design intent of the Trace rather than a shifting of the design intent. No change in design intent is evident in the matched pairs of photographs.

<p> Learning processes have been demonstrated to play an integral role in drug tolerance. More recently, researchers have found that associative mechanisms also play an important role in the adaptation to cold exposure (Riccio, MacArdy & Kissinger, 1991). The present study investigated the effect of contextual stimuli on temperature response to repeated heat stress. Rats receiving repeated heat exposures (56°C, 10 min, 6 trials) demonstrated adaptation to the heat as measured by a decrease in hyperthermia. The tolerance to the heat stress was not disrupted by changing the contextual cues associated with the heat. These findings demonstrate tolerance to repeated heat stress but do not provide evidence of associative learning in this adaptation. Future experiments should assess the question of thermoregulation and associative processes using highly discriminant conditioning environments.</p> / Thesis / Master of Science (MSc)

The requirement for identical inverted terminal repeats (ITRs) for viral viability and the role of internal viral sequences in the specification of the sequences of the termini were investigated. The viral strains used in this study were a variant Ad2 strain Ad2 (mac) and the wild type Ad5 strain which was very similar to the former one in sequence except at the extreme end of the terminal repeat. A hybrid virus (sub54), obtained by recombination between Ad2 (mac) and Ad5, derived the left 41-51% of its genome from Ad2 (mac) and the right 59-49% from Ad5. The identity of the termini was determined by Southern blotting analysis using 32p end labeled oligocleoxynucleotides. Analysis of the sub54 isolate indicated that both Ad2 (mac) and Ad5 ITRs were present. Plaque purification of sub54 demonstrated that viruses with non identical terminal sequences were viable and allowed their characterization. This analysis also indicated that Ad5 ITRs are converted to Ad2 (mac) ITRs possibly as a result of repair of the ends to yield viruses with identical termini. A model involving replication and emphasizing the importance of panhandle formation as a replicative intermediate is proposed. These results also indicated a possible role of the internal sequences of adenovirus in the selection and maintenance of serotype specific ITRs. The preference for Ad2 (mac) termini observed during repair of the ends of sub54 may be related to the origin of the genes coding for the adenoviral polymerase and/or the terminal protein both of which were derived from Ad2 (mac). Further investigation would be required to determine whether these replicative proteins are actually involved in ITR conversion. Transformation of Escherichia coli with a DNA preparation from sub54 infected rat embryo cells resulted in the isolation of the plasmid pFG154. This plasmid contained the entire adenovirus genome with an Ad2 (mac) ITR at the "left" terminus covalently linked to an Ad5 ITR at the "right". Analysis of the viral progeny generated upon transfection of mammalian cells with pFG154 indicated that the Ad2 (mac) ITRs were very efficiently converted to Ad5 termini. These results, although apparently contradictory to those initially obtained from the plaque purification of sub54, may be explained by an ITR repair model which is specific for infectious circles. / Thesis / Master of Science (MS)

The inherent design freedom of protein engineering and recombinant protein production enables specific tailoring of protein structure, function, and properties. Two areas of research where protein engineering has allowed for many advances in biomedical materials include the design of novel protein scaffolds for molecular recognition, as well as the use of recombinant proteins for production of next generation biomaterials. The main focus of my dissertation was to develop new biomedical materials using protein engineering. Chapters three and four discuss the engineering of repeat proteins as bio-recognition modules for biomedical sensing and imaging. Chapter three provides an overview of the most recent advances in engineering of repeat proteins in the aforementioned field. Chapter four discusses my contribution to this field. We have designed a de novo repeat protein scaffold based on the consensus sequence of the leucine rich repeat (LRR) domain of the NOD family of cytoplasmic innate immune system receptors. Innate immunity receptors have been described as pattern recognition receptors in that they recognize "global features" of a family of pathogens versus one specific antigen. In mammals, two main protein families of such receptors are: extracellular Toll-like receptors (TLRs) and cytoplasmic Nucletide-binding domain- and Leucine-rich Repeat-containing proteins (NLRs). NLRs are defined by their tripartite domain architecture that contains a C-terminal LRR (Leucine Rich Repeat) domain, the nucleotide-binding oligomerization (NACHT) domain, and the N-terminal effector domain. It is proposed that pathogen sensing in NLRs occurs through ligand binding by the LRR domain. Thus, we hypothesized that LRRs would be suitable for the design of alternative binding scaffolds for use in molecular recognition. The NOD protein family plays a very important role in innate immunity, and consequently serves as a promising scaffold for design of novel recognition motifs. However, engineering of de novo proteins based on the NOD family LRR domain has proven challenging due to problems arising from protein solubility and stability. Consensus sequence design is a protein design tool used to create novel proteins that capture sequence-structure relationships and interactions present in nature in order to create a stable protein scaffold. We implement a consensus sequence design approach to develop proteins based on the LRR domain of NLRs. Using a multiple sequence alignment we analyzed all individual LRRs found in mammalian NLRs. This design resulted in a consensus sequence protein containing two internal repeats and separate N- and C- capping repeats named CLRR2. Using biophysical characterization methods of size exclusion chromatography, circular dichroism, and fluorescence, CLRR2 was found to be a stable, monomeric, and cysteine free scaffold. Additionally, CLRR2, without any affinity maturation, displayed micromolar binding affinity for muramyl dipeptide (MDP), a bacterial cell wall fragment. To our knowledge, this is the first report of direct interaction of a NOD LRR with a physiologically relevant ligand. Furthermore, CLRR2 demonstrated selective recognition to the biologically active stereoisomer of MDP. Results of this study indicate that LRRs are indeed a useful scaffold for development of specific and selective proteins for molecular recognition, creating much potential for future engineering of alternative protein scaffolds for biomedical applications. My second research interest focused on the development of proteins for novel biomaterials. In the past two decades, keratin biomaterials have shown impressive results as scaffolds for tissue engineering, wound healing, and nerve regeneration. In addition to its intrinsic biocompatibility, keratin interacts with specific cell receptors eliciting beneficial biochemical cues, as well as participates in important regulatory functions such as cell migration and proliferation and protein signalling. The aforementioned properties along with keratins' inherent capacity for self-assembly poise it as a promising scaffold for regenerative medicine and tissue engineering applications. However, due to the extraction process used to obtain natural keratin proteins from natural sources, protein damage and formation of by-products that alter network self-assembly and bioactivity often occur as a result of the extensive processing conditions required. Furthermore, natural keratins require exogenous chemistry in order to modify their properties, which greatly limits sequence tunability. Recombinant keratin proteins have the potential to overcome the limitations associated with the use of natural keratins while also maintaining their desired structural and chemical characteristics. Thus, we have used recombinant DNA technology for the production of human hair keratins, keratin 31 (K31) and keratin 81 (K81). The production of recombinant human hair keratins resulted in isolated proteins of the correct sequence and molecular weight determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis and mass spectrometry. Proteins with no unwanted sequence truncations, deletions, or mutations indicate recombinant DNA technology can be used to reliably generate full length keratin proteins. This allows for consistent starting materials with no observable impurities or undesired by-products, which combats a major challenge associated with natural keratins. Additionally, recombinant keratins must maintain the intrinsic propensity for self-assembly found in natural keratins. To test the propensity for self-assembly, we implemented size exclusion chromatography (SEC), dynamic light scattering (DLS), and transmission electron microscopy (TEM) to characterize K31, K81, and an equimolar mixture of K31 and K81. The results of the recombinant protein characterization reveal novel homo-polymerization of K31 and K81, not previously reported, and formation of characteristic keratin fibers for the K31 and K81 mixture. Therefore, recombinant K31 and K81 retain the intrinsic biological activity (i.e. self-assembly) of natural keratin proteins. We have also conducted a comparative study of recombinant and extracted heteropolymer K31/K81. Through solution characterization and TEM analysis it was found that use of the recombinant heteropolymer allows for increased purity of starting material while also maintaining self-assembly properties necessary for functional use in biomaterials design. However, under the processing condition implemented, extracted keratins demonstrated increased efficiency of assembly. Through each study we conclude that recombinant keratin proteins provide a promising solution to overcome the challenges associated with natural protein materials and present an exceptional design platform for generation of new biomaterials for regenerative medicine and tissue engineering. / Ph. D. / Protein engineering and synthetic protein production enables the creation of new proteins that can perform specific tasks. Many advances in biomedical materials and medical diagnostic tools stem from the use of synthetic proteins. The main focus of my dissertation was to develop new biomedical materials using protein engineering. In chapters three and four of the dissertation development of synthetic proteins for medical diagnostics is discussed. We have designed artificial protein sensors based on natural innate immunity proteins, which function in the body as the source for recognition of foreign pathogens, such as bacteria and viruses. Our goal was to create synthetic proteins with similar characteristics to the innate immunity receptors for the purpose of sensing bacteria and viruses in the form of a biosensors or medical diagnostic. Through our work we have developed an artificial protein scaffold that can selectively interact with a relevant biological target. This research provides the ground work for future development of proteins that can sense a wide variety of important pathogens and subsequently be manufactured into diagnostic devices. Our research involving protein design for biomaterials is the focus of chapters five and six of the dissertation. Keratin is a ubiquitous protein found in the human body. It functions as a structural protein and helps create the complex network that makes up skin, hair, and epidermal appendages. We have created synthetic keratin proteins in an effort to fabricate biomaterials that can be used for regenerative medicine and tissue engineering applications. Our strategy allows for development of proteins that can be designed to have characteristics not afforded to naturally occurring keratin proteins, and thus presents the opportunity to make materials with unique properties and characteristics that may make them more successful in our intended applications of tissue engineering. From our work we have shown that synthetic production of these proteins is possible and that the synthetically produced proteins retain the essential structural and functional properties associated with natural keratin proteins. Thus, this work highlights the potential for use of synthetic proteins for production of biomaterials with new and important features that cannot be obtained through use of natural proteins.

The aim of this study was to provide deeper insights in passerine phylogenetic relationships using new molecular markers. The monophyly of the largest avian order Passeriformes (~59% of all living birds) and the division into its suborders suboscines and oscines are well established. Phylogenetic relationships within the group have been extremely puzzling, as most of the evolutionary lineages originated through rapid radiation. Numerous studies have hypothesised conflicting passerine phylogenies and have repeatedly stimulated further research with new markers. In the present study, I used three different approaches to contribute to the ongoing phylogenetic debate in Passeriformes. I investigated the recently introduced gene ZENK for its phylogenetic utility for passerine systematics in combination and comparison to three already established nuclear markers. My phylogenetic analyses of a comprehensive data set yielded highly resolved, consistent and strongly supported trees. I was able to show the high utility of ZENK for elucidating phylogenetic relationships within Passeriformes. For the second and third approach, I used chicken repeat 1 (CR1) retrotransposons as phylogenetic markers. I presented two specific CR1 insertions as apomorphic characters, whose presence/absence pattern significantly contributed to the resolution of a particular phylogenetic uncertainty, namely the position of the rockfowl species Picathartes spp. in the passerine tree. Based on my results, I suggest a closer relationship of these birds to crows, ravens, jays, and allies. For the third approach, I showed that CR1 sequences contain phylogenetic signal and investigated their applicability in more detail. In this context, I screened for CR1 elements in different passerine birds, used sequences of several loci to construct phylogenetic trees, and evaluated their reliability. I was able to corroborate existing hypotheses and provide strong evidence for some new hypotheses, e.g. I suggest a revision of the taxa Corvidae and Corvinae as vireos are closer related to crows, ravens, and allies. The subdivision of the Passerida into three superfamilies, Sylvioidea, Passeroidea, and Muscicapoidea was strongly supported. I found evidence for a split within Sylvioidea into two clades, one consisting of tits and the other comprising warblers, bulbuls, laughingthrushes, whitethroats, and allies. Whereas Passeridae appear to be paraphyletic, monophyly of weavers and estrild finches as a separate clade was strongly supported. The sister taxon relationships of dippers and the thrushes/flycatcher/chat assemblage was corroborated and I suggest a closer relationship of waxwings and kinglets to wrens, tree-creepers, and nuthatches. / Das Ziel dieser Arbeit war es, mittels neuer molekularer Marker zusätzliche Informationen über die phylogenetischen Verwandtschaftsverhältnisse der Sperlingsvögel (Passeriformes) zu erhalten. Die Monophylie der Passeriformes, der größten Vogelgruppe (~59% aller lebenden Arten), sowie ihrer Unterteilung in Suboscines und Oscines sind gut belegt. Die phylogenetischen Verwandtschaftsverhältnisse innerhalb dieser Gruppen sind jedoch seit jeher sehr schwer zu entschlüsseln, da sich die meisten Linien durch eine schnelle Radiation entwickelten. Zahlreiche Studien haben verschiedene Hypothesen zur Phylogenie der Sperlingsvögel aufgestellt und damit die Suche nach neuen Markern initiiert. In meiner Untersuchung habe ich drei verschiedene Ansätze benutzt, um zur Klärung der Phylogenie beizutragen. Ich untersuchte das kürzlich als Marker eingeführte ZENK-Gen im Hinblick auf seinen Nutzen in der Systematik der Sperlingsvögel in Kombination und im Vergleich zu drei bereits etablierten nukleären Markern. Meine phylogenetischen Analysen eines umfassenden Datensatzes ergaben hoch aufgelöste, konsistente und stark unterstütze Stammbäume, so dass ich den hohen Nutzwert des ZENK-Gens für die Klärung phylogenetischer Verwandtschaftsverhältnisse der Passeriformes zeigen konnte. Für den zweiten und dritten Ansatz habe ich Chicken Repeat 1 (CR1) Retrotransposons als phylogenetische Marker benutzt. Anhand zweier spezifischer CR1 Insertionen als apomorphe Merkmale und deren Insertionsmuster in verschiedenen Sperlingsvögeln konnte ich die phylogenetische Position der afrikanischen Felshüpfer, Picathartes spp., klären. Aufgrund meiner Ergebnisse schließe ich auf eine engere Verwandtschaft der Felshüpfer zu den Rabenvögeln. Durch meinen dritten Ansatz konnte ich nachweisen, dass CR1-Sequenzen phylogenetische Informationen enthalten, und untersuchte detailliert deren Anwendung als Marker. Dafür habe ich in verschiedenen Sperlingsvögeln nach CR1 Elementen gesucht und mit einigen dieser Sequenzen Stammbäume berechnet, um die Verlässlichkeit der Marker zu überprüfen. Durch meine Untersuchungen konnte ich existierende Hypothesen stützen und zusätzlich starke Hinweise auf neue Hypothesen finden. Beispielsweise schlage ich eine Revision der Taxa Corvidae und Corvinae vor, da Vireos eng mit den Rabenvögeln verwandt sind. Die Unterteilung der Passerida in die drei Unterfamilien Sylvioidea, Passeroidea und Muscicapoidea konnte deutlich bestätigt werden. Ich habe Hinweise auf eine Trennung der Sylvioidea in zwei taxonomische Gruppen erhalten, einer bestehend aus Meisen und Verwandten und der andere aus Grasmücken, Bülbüls, Häherlingen, Brillenvögeln und Verwandten. Während die Passeridae paraphyletisch sind, wurde die Monophylie der Weber und Astrilden als ein eigenes Taxon unterstützt. Das Schwestergruppenverhältnis zwischen Wasseramseln und dem Drossel/Fliegenschnäpper/Schmätzer-Taxon wurde ebenfalls bestätigt. Außerdem habe ich Hinweise auf eine nähere Verwandtschaft zwischen Seidenschwänzen und Goldhähnchen zu Zaunkönigen, Baumläufern und Kleibern gefunden.

This analysis explores the formation of stable hot spots and the overall shifts of repeat and near repeat residential burglary over time. Data were obtained from a small college town police department. There were 1,513 repeat residential burglaries between January 2003 and December 2009 that occurred at a total of 356 addresses. Based upon past research it is thought that repeat residential burglaries will cluster in time and space creating stable hot spots and that the centrographic measures of the burglaries will remain relatively constant from year to year. The results found support for the formation of stable hot spots but found that the area in which the repeat residential burglaries were occurring increased over time.