Remembering Richard

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Developmental dynamics of transcription and genome architecture

Abstract Regulation of gene expression is necessary for the control of complex developmental processes. The genome has to shape in specific conformations to fit inside the nucleus and to tether specific regulatory elements to their target genes. Although the linear composition of many genomes is largely known, their three dimensional (3D) organization and dynamics are largely unknown. Hence, in order to unravel gene regulation, it is necessary to understand the chromatin structure and organization. Furthermore, developmental procedures are controlled by complex combinatorial transcription factor (TF) networks. Hence, unveiling those networks will provide a better insight towards understanding those developmental procedures. The work described in this thesis aims to study the genome conformation/interactome and their effect on gene regulation and to unveil the role of transcription factor proteins (TFs) in complex developmental processes

Contextualizing the Archives

Article

Tides of Cooperation: The Ebb and Flow of Regional Cooperation in Latin America

Regional organizations have developed into important global actors as they negotiate inter-regional trade agreements, regulate economic policies, and develop international security communities. States have much to gain from such regional cooperation efforts particularly in emerging regions such as Latin America. Such gains can include increased trade and economic relations, enhanced security, attracting external investment, and increasing bargaining power at the international level. With such gains to be had, one might expect states in these regions to regularly cooperate in order to achieve their common interests. However, this is clearly not always the case. Latin America has struggled for decades with an ebb and flow of regional cooperation schemes. Why do we see variation in levels of regional cooperation in Latin America? More specifically, given the potential gains from regional cooperation, why do we see periods of defection within these organizations? Historical cases within the Latin America suggest that regional cooperation suffers under conditions of unequal gains. Asymmetrical distribution of economic gains from cooperation efforts hinder further integration and increase the chance a state will defect from the group\u27s arrangements. This study uses a mixed methods approach to explore the impact of economic asymmetry on regional cooperation in Latin America. Beginning with a large-N statistical analysis utilizing a cross-nested model to capture variance within and between organizations, it finds evidence that asymmetric distribution of investment and trade hinders political indicators of cooperation. Additional in-depth case analysis of the Andean Community and Mercosur further highlight these trends through showing country-specific data and diplomatic statements during periods of major defection within the groups. Based on these findings, this study demonstrates the importance of the distribution of gains expected from regional cooperation efforts as it concludes that increasing economic asymmetry within a region leads to lower overall cooperation among an organization\u27s member-states

Archiving Culture: American Folklore Archives in Theory and Practice

Thesis (Ph.D.) - Indiana University, Folklore and Ethnomusicology, 2010American folklorists have long preserved their research materials in repositories dedicated to this purpose. The motivations for saving these items and the methods of doing so have changed over time, but the practice of preserving research materials has persisted as a central aspect of folkloristics into the present--one that distinguishes it from other ethnographic disciplines such as anthropology. Although these collections go by many names--including folk archives, folklife archives, and ethnographic archives--for the sake of this dissertation I label these collections categorically as folklore archives. Issues related to intellectual property rights and intangible cultural heritage, while important to consider, are beyond the scope of this project. Despite the ubiquity of folklore archives in the discipline, they are an understudied aspect of historical and contemporary practice in folkloristics. This dissertation examines the role of folklore archives in the field, the nature of these collections, and the growing influence on them from theories and practices originating in the fields of library science and archival management. Folklore archives were at one time a distinct product of the discipline of folkloristics, reflecting disciplinary practice and responding to disciplinary need. As theoretical and methodological approaches within the field changed, the utility of these old archival forms diminished dramatically. Rather than abandoning the creation of archives all together, folklorists began to modify archival practice to suit changing needs. Of particular significance is the impact of the requirements of public folklore work on folklore archives, including the reuse and repurposing of archival materials in publications, exhibitions and public events, as well as an increased emphasis on collaborative engagement with communities of origin. Folklore archives in the present are increasingly shaped by the theories and methods of professionally trained archivists. Folklore archives are developing into a hybrid form that draws on both the legacy of archiving in folkloristics and aspects of the well-developed body of theory that informs the work of professional archivists outside of folklore

Cardiovascular Disease and Chronic Inflammation in End Stage Kidney Disease

Background: Chronic Kidney Disease (CKD) is one of the most severe diseases worldwide. In patients affected by CKD, a progressive destruction of the nephrons is observed not only in structuralbut also in functional level. Atherosclerosis is a progressive disease of large and medium-sized arteries. It is characterized by the deposition of lipids and fibrous elements and is a common complication of the uremic syndrome because of the coexistence of a wide range of risk factors. High blood pressure, anaemia, insulin resistance, inflammation, high oxidative stress are some of the most common factors that cause cardiovascular disease and atherogenesis in patients suffering from End Stage Kidney Disease (ESRD). At the same time, the inflammatory process constitutes a common element in the apparition and development of CKD. A wide range of possible causes can justify the development of inflammation under uremic conditions. Such causes are oxidative stress, oxidation, coexistentpathological conditions as well as factors that are due to renal clearance techniques. Patients in ESRD and coronary disease usually show increased acute phase products. Pre-inflammatory cytokines, such as IL-6 and TNF-a, and acute phase reactants, such as CRP and fibrinogen, are closely related. The treatment of chronic inflammation in CKD is of high importance for the development ofthe disease as well as for the treatment of cardiovascular morbidity.Conclusions: The treatment factors focus on the use of renin-angiotensic system inhibitors, acetylsalicylic acid, statins and anti-oxidant treatment in order to prevent the action of inflammatorycytokines that have the ability to activate the mechanisms of inflammation

Partial loading of XMI models

XML Metadata Interchange (XMI) is an OMG-standardised model exchange format, which is natively supported by the Eclipse Modeling Framework (EMF) and the majority of the modelling and model management languages and tools. Whilst XMI is widely supported, the XMI parser provided by EMF is inefficient in some cases where models are readonly (such as input models for model query, model-to-model transformation, etc) as it always requires loading the entire model into memory. In this paper we present a novel algorithm, and a prototype implementation (SmartSAX), which is capable of partially loading models persisted in XMI. SmartSAX oérs improved performance, in terms of loading time and memory footprint, over the default EMF XMI parser. We describe the algorithm in detail, and present benchmarking results that demonstrate the substantial improvements of the prototype implementation over the XMI parser provided by EMF

Προγραμματισμός μεθόδου συναρτήσεων ακτινικής βάσης (RBF) για τη μετατόπιση υπολογιστικών πλεγμάτων σε κάρτες γραφικών

Εθνικό Μετσόβιο Πολυτεχνείο--Μεταπτυχιακή Εργασία. Διεπιστημονικό-Διατμηματικό Πρόγραμμα Μεταπτυχιακών Σπουδών (Δ.Π.Μ.Σ.) “Υπολογιστική Μηχανική