VictorJuiz/thesis huggingface dataset:
Circadian Hallmarks of the Aging Epigenome
Keywords: Aging
Circadian Rhythmicity
Complex Disease
DNA Methylation
Epigenetics

Circadian rhythmicity governs a remarkable array of fundamental biological functions in eukaryotes which is mediated by cyclical metabolomic, transcriptomic, and proteomic activities. Histone modifications and other epigenetic factors are also involved in the circadian machinery; however, despite significant efforts detection of circadian DNA (cytosine) modification has remained elusive. In this study, we aimed to document and explore the features of circadian oscillations of cytosine modifications. We discovered that a substantial number of cytosines show a circadian pattern in their modification status in mouse liver and lung, as well as human neutrophils. Furthermore, we found that circadian oscillations of cytosine modification are linked to circadian transcription. Our findings also indicate that circadian oscillations explain a portion of the epigenetic variation which traditionally has been called random or stochastic. There are numerous clinical and molecular studies showing strong associations between declining circadian rhythmicity and aging, but the molecular underpinnings of this association are not clear. Since epigenetic alterations accompany aging, we aimed to investigate the relationship between daily cytosine modification oscillations and the aging epigenome. We discovered that cytosines which exhibited circadian epigenetic oscillations significantly overlapped with the cytosines exhibiting age-related modification changes. Furthermore, the amplitude of these oscillations strongly correlated with the degree of age-dependent changes. Finally, the day or night timing of circadian peaks were accurate predictors of whether a specific cytosine will lose or gain modification in the aging tissue. Epigenetic changes, circadian dysregulation, and age have all been implicated in a number of complex diseases. Consequently, our third aim was to examine the contributions of DNA modification oscillations to the epigenetic changes identified in epigenome-wide association studies of complex disease. We tested leukemia, Alzheimerâ s disease, and schizophrenia, and in all cases, we found a significant overlap between cytosines exhibiting daily oscillations and those identified in disease studies. We therefore propose that circadian epigenetic oscillations may contribute not only to aging but also to disease. Based on our findings, further studies are warranted for a more complete understanding of how evolutionary advantageous processes like circadian rhythmicity can also mediate an organismâ s demise.
India On the Line: Globalized labour in postmillennial Indo-Anglian literature
Keywords: Chetan Bhagat
globalization
India
outsourcing
postcolonial
pulp

In this dissertation I look at the eruption of new subjectivities in postmillennial Indo-Anglian literature in an era of globalization and neoliberalism, and, concurrently, the seeming disappearance of old myths and identities – at how, for example, the telephone of the call centre, in joining one person to another, is shown to create fissures in identity, family, and what is described as “traditional” Indian culture. I also examine the ways in which technology, particularly in the form of machines like the tape recorder, industrial factory equipment, and the Internet, is depicted as mapping the formation of cyborg subjectivities in an era of rapidly changing and ever-broadening and improving modes of communication. These technologies seem at once to bring us closer together and further apart, fostering a greater sense of global solidarity and “connectivity” in previously isolated communities, in John Tomlinson’s terms (1999, 30), but also setting out battle lines for revolutionary new Indian movements: between the international rich and poor, and more frequently the US and India. In the “pulp fiction” books addressed in this dissertation, written by such authors as Chetan Bhagat, Neelesh Misra, and Brinda S. Narayan, globalization is depicted as oppressing and poisoning Indians but also freeing them from the chains of Western capitalism and even providing routes for nationalist innovation, creativity, and solidarity. Meanwhile, the more “highbrow” cosmopolitan texts, written by Aravind Adiga, Bharati Mukherjee, Indra Sinha, and Altaf Tyrewala, tend to evince a greater suspicion of nationalism and the utopian promises of neoliberalism. Each dissertation chapter addresses a different type of depressed and alienated protagonist – from the call-centre worker to the entrepreneur, to the cyborg-sahiborg and the exorcist-hacker – whose various triumphs of upward mobility and community-building are often, ultimately, oddly unconvincing and unmoving. Indian neoliberalism leads to a sense of anomie among these characters; even when they find community or professional and economic success, it never seems to be entirely or effectively dispelled. The unhappiness of these globalized literary avatars serves as warning – in some cases, probably involuntary – of the dark side of the glamour and glitz of globalized labour in India.
A Bumpy Landing: Airports and the Making of Jet Age Canada
Keywords: Airports - Canada
Air Travel
Infrastructure
Mobility
Postwar Canada

This dissertation examines changes at and around Canadaâ s major airports in the early jet age. It traces how airports in major Canadian cities evolved into mass transport hubs between the 1950s and 1980s and also materialized as complex technical systems that connected aviation to wider contemporary issues. During this period these airports assumed a dual role, operating in the background to help move people and planes and emerging at key times to occupy public consciousness. Historical changes there can thus help explain how airports grew increasingly visible as fixed, but active, modern infrastructure that both facilitated jet age mobility and were deeply embedded in the postwar order. This dissertation links the transformation of major airports to the rise of mass air travel, postwar change, and federal stewardship. Aviationâ s rapid growth and technological advances beginning in the 1950s invariably transformed how these airports looked, worked, and were experienced by different groups of people. Various central developments in postwar Canada beyond aviation also migrated to these airports and made them more visible as public infrastructure that were both imagined in the national sphere and part of globalization. Moreover, airports were federally operated until the early 1990s and thus a state infrastructure project. The federal government and its partners used a combination of anticipatory and reactive strategies to manage airports that emphasized national interests, but also cared about cities and capital. This approach blended multiple scales and dynamics and constantly shifted as conditions changed, generating problems and tensions along the way that shaped the particular trajectory of airport development between the 1950s and 1980s. Taken together, this dissertation strengthens and advances historical knowledge about airports and aviation in Canada. It also contributes to the history of technology and mobility and its relationship to social and cultural change. Lastly, it contributes to the political, social, and cultural history of postwar Canada by bringing air travel into the narrative. In so doing, it shows how airports helped to make jet age Canada, a process that encompassed the local, national, and global arena and stretched well into the late twentieth century.
Teaching the Tradition: Twelfth-Century Scholastic Commentaries on Paul's Letter to the Romans
Keywords: exegesis
Glossa
Pauline epistles
Peter Lombard
Stephen Langton
theology

This thesis provides the first study of the relationship between three of the most important commentaries on Paul’s Letter to the Romans produced in the cathedral schools of northern France during the twelfth century, a period usually defined as “early scholasticism.” Studies of this period normally focus on the theological works of the teachers in these schools, leaving to one side their biblical exegesis. This thesis argues for the central importance of biblical exposition to the study of theology in early scholasticism by emphasizing two related aspects of these commentaries: first, that they are the result of classroom teaching rather than written treatises, and second, that the primary goal of this teaching was the handing on of a tradition of reflection on the Bible. The first chapter studies the so-called Glossa ‘ordinaria’ on Romans. The Glossa was the most important exposition of Romans in the twelfth century, existing in hundreds of manuscripts and forming the basis for teaching. The first chapter traces the sources and methodology of the Glossa, arguing that it is better understood as a classroom text than as a reference work. The second chapter turns to the Glossa’s most influential user, Peter Lombard (d. 1160), whose Magna glosatura on Romans also exists in hundreds of manuscripts. Chapter two analyzes Lombard’s use of the Glossa and how he uses it as the gateway to his own teaching of Romans. The third chapter studies the Postille in Apostolum of Stephen Langton (c.1150-1228), tracing Langton’s use of Lombard’s Magna in his own teaching of Romans and arguing for the unity of Langton’s biblical lectures and his theological works. This study therefore establishes a trajectory of teaching the tradition of reflection on the Pauline Epistles, from the Glossa, through Lombard’s Magna, to Langton’s Postille.
Probing cosmic inflation with the Spider experiment
Keywords: Balloon-borne
Cosmic Microwave Background
Cosmology
Inflation
Instrumentation
Polarization

Spider is a balloon-borne cosmic microwave polarimeter designed to operate for up to two weeks on a Long Duration Balloon platform. From above 99.5% of the atmosphere, Spider flew over Antarctica for 16 days observing the sky with over two thousand detectors housed inside a 1300 L liquid helium cryostat, distributed amongst 6 telescopes that span two frequency channels: 95 GHz and 150 GHz. By focusing its observing time over a 10% patch of the sky at high galactic latitude, Spider targets the degree-scale BB spectrum in search of the pattern that would have been imprinted by gravitational waves propagating in the early universe, a key prediction of inflation. In order to probe the physics of the very early universe the experiment needs to operate in the harsh environment of the upper atmosphere for multiple days. This work discusses at length the detailed thermal modeling and analysis leading up to the 2015 flight which ensured the correct thermal operation of every component while at 36 km of altitude. The flight is followed by a data analysis that will ultimately produce a constraint on the amplitude of the primordial gravitational wave background from bandpowers of the BB spectrum of the CMB. In order to measure the CMB itself, contamination to the BB spectrum by polarized galactic foreground emission needs to be quantified. To improve its ability to characterize polarized foregrounds, Spider will have a second flight in 2018-2019 which will add a 285 GHz frequency channel. In this work, we explore a component separation technique involving Planck HFI data. A power spectrum estimator used to produce bandpower estimates from maps is also discussed.
Exit the King: Sovereignty and Subjectivity in the English Baroque
Keywords: Baroque
Donne
Milton
Political Theology
Renaissance
Shakespeare

This dissertation argues for a conception of the English 17th century as participating in a common aesthetic of dissonance – an aesthetic which it calls the “Baroque.” More than just a term for the ornate or profuse, its revival of the Baroque designation (and its contentious application to English literature) is a means of describing the period’s fascination with staging artistic figurations in which radically contradictory religious, social, and political paradigms cannot possibly be made to cohere yet must nevertheless coexist. Through readings of Marlowe’s Faustus, Shakespeare’s Tempest, Donne’s Holy Sonnets, and Milton’s Paradise Lost, it traces the period’s apprehension of, and neurotic fixation upon, the incompatibility of these proliferating new epistemologies: Lucretian atomism, the geo-political vistas of the “New World,” the schisms of Reformation, the Copernican revolution, the waning of Church power, and the rise of the Absolutist state. These destabilizing elements are worked asymmetrically into these texts’ designs and suspended in unreconciled dynamic tension, each work culminating in a moment when a figure – Faustus, Prospero, Donne’s speaker, even the Miltonic God – considers the inconsistent logics in which they are now enclosed and imagines a self-annihilation that would afford an escape from an unstable and collapsing system. The Baroque has not been a popular name for English poetry. 20th century scholarship deemed it inapt for British literature, invoking it only for the overt, fussy Catholicism of Crashaw or Southwell or to taxonomize heavily brocaded stylistic moments in Marvell or Cowley. My analysis instead uses the concept of the Baroque to diagram this period’s unresolved secularizing pressures, not just in its margins but in texts at the heart of the traditional canon. These disparate works amount to a systemic, self-coherent cultural revolution: a networked era of artistic production that is congruent (but not identical) with the continent’s own counter-reformational renovations, that is distinct from the Renaissance that precedes it, and that anticipates its neo-classical and transatlantic successors. Anatomizing this Baroque therefore troubles a long-standing neo-liberalist narrative of a self-evidently progressive democratic secular age and names the 17th century’s own apprehension of this new era’s tensions at its source.
Fateful Decisions: The Polish Policemen and the Jewish Population of Occupied Poland, 1939-1945
Keywords: Collaboration
Complicity
Holocaust
Polish (Blue) Police
Second World War

This dissertation analyzes the activities of the Polish police during the Second World War with particular attention paid to their triangulated relationship with the German authorities and Jewish population. To properly situate their activities, the interwar period is also covered, as it forms the historical antecedent of their creation. The position of the dissertation is that the participation of the Polish police enabled the Germans to be more successful in their implementation of the Holocaust in Poland. Alongside this contention, evidence supporting the attempts of some Polish policemen to help and assist the Jewish population is also presented. This complex and multilayered portrait is articulated while maintaining that there is sufficient evidence to challenge conventional historical views that have downplayed the Polish policeâ s involvement in the murder of Polish Jews. The evidence presented throughout the dissertation is distinct from previous research into the activities of the Polish police as the policemenâ s actions against the Jewish population have not been subject to thorough research. In comparison with the only available book on the Polish police, which minimizes their role in implementing the Holocaust in Poland, this dissertation draws extensively on archival sources that were not previously accessed such as post-war trial records and eyewitness written and oral testimony. This dissertation is organized chronologically and its structure reflects the stages of the Polish policeâ s involvement in the persecution of Polish Jews. The tasks of the Polish policemen depended on the current German policies against the Jews in the General Government. Gradually, they expended from guarding ghettos and preventing the movement of people and products in and out of ghettos to securing the perimeters of ghettos during liquidation actions and searching for those who attempted to avoid transports to killing centres. The Polish policemen, often in cooperation with the rural population, played a significant role in the last phase of the Holocaust. It was at this stage that they discovered and killed many Jews in hiding. In those cases, the policemen were autonomous as a significant number of the killings were carried out without the orders or knowledge of their German superiors.
Identifying the Functions and Regulatory Mechanisms of Shikimate Dehydrogenase Homologs in Bacteria
Keywords: bacteria
LTTR
metabolism
quinate
shikimate
transcription

The shikimate pathway is required for synthesis of the aromatic amino acids as well as other aromatic compounds in bacteria. The prototypical member of the shikimate dehydrogenase (SDH) enzyme family, AroE, catalyzes the fifth step in this pathway; the reduction of dehydroshikimate to shikimate. In addition to AroE, four other SDH family members have been identified: YdiB, Ael1, RifI, and SdhL. However, the metabolic functions of Ael1, RifI, and SdhL are poorly characterized, and few studies focus on the regulation of SDH enzymes. This thesis investigates the biological functions of the SDH family of enzymes, and explores the systems that govern their expression in bacteria. We use Pseudomonas putida to investigate the functions of the SDH family of enzymes, as it has one representative homolog of each family member. The differences in expression profiles observed among these SDH homologs in P. putida, along with existing kinetic data, suggest that each homolog performs a distinct biological role related to the shikimate pathway. Additionally, we identified multiple novel metabolic disturbances due to SDH disruptions in P. putida that allow us to propose putative roles for the SDH enzymes in bacterial metabolism. The quinate utilization operons in Listeria monocytogenes encode two SDH proteins among other enzymes that act in the quinate/shikimate utilization metabolic pathway. These operons are activated by a LysR Type Transcriptional Regulator (LTTR), called QuiR1, in response to shikimate. The structure of the QuiR1 effector binding domain with shikimate bound reveals overall LTTR structural conservation as well as the architecture of the shikimate binding site. This work sheds light on the mechanism of transcriptional regulation of the genes encoding enzymes involved in metabolism of the plant derived compound quinate, as well as shikimate, in L. monocytogenes. This intricate regulation may allow for an optimized metabolic response to changing environmental conditions.
Characterization of novel GH115 Îą-glucuronidases for enzymatic tailoring of xylans
Keywords: alpha-glucuronidase
biomaterials
LC-MS/MS
synergism
xylan

Xylans represent abundant renewable resources for developing applications ranging from prebiotics to plastic-replacing packaging materials. Accessory hemicellulases can be used to tailor the side-group chemistry of xylans to thereby control properties such as nutrient value, rheology, solubility, adsorption behavior, as well as barrier characteristics of xylan-based films and coatings. Glucopyranosyluronic acid (GlcA) and (methyl)-glucopyranosyluronic acid (MeGlcA) are common substituents of the major forms of xylan in hardwood and coniferous softwoods as well as many cereal grains. α-Glucuronidases from glycoside hydrolase family GH115 have the potential to tailor high-molecular-weight xylans, because they are the only known enzymes that can target GlcA/MeGlcA from both internally and terminally substituted regions of xylans. Two family GH115 enzymes (SdeAgu115A from the marine bacterium Saccharophagus degradans 2-40T and AxyAgu115A from alkaliphilic bacterium Amphilbacillus xylanus) were selected for characterization. Both enzymes demonstrated activity towards glucuronoxylans and oligomers thereof with preference towards internally substituted residues. The first five-domain crystal structure of a GH115 enzyme was also reported, which comprised an additional insertion C+ domain likely to participate in substrate binding. Consistent with the natural habitats of the source organisms, AxyAgu115A demonstrated better performance in alkaline condition compared to other reported GH115 α-glucuronidases, whereas salt activation was only observed for SdeAgu115A. Unlike SdeAgu115A, AxyAgu115A displayed similar activity towards beechwood glucuronoxylan and the more highly branched spruce arabinoglucuronoxylan. The ability of AxyAgu115A to accommodate comparatively complex xylans was consistent with conclusions that could be drawn through docking analysis. Synergistic action between SdeAu115A and AxyAgu115A, and two α-arabinofuranosidases from families GH51 (E-AFASE) and GH62 (SthAbf62A) towards spruce arabinoglucuronoxylan was identified, suggesting that MeGlcA and Araf could sterically hinder α-arabinofuranosidase and/or α-glucuronidase activity. Finally, AxyAgu115A was applied herein to recover xylan-derived oligosaccharides extracted from mixed hardwood chips through liquid hot water extraction. As part of this study, an LC-MS/MS method was developed to facilitate label-free characterization of diverse xylooligosaccharides.
Offshoring International Law? Australia and the Right to Seek Asylum
Keywords: Border control
Global Governance
International Law
Migration
Refugees

For many years now, liberal democracies have pursued controversial asylum and border control practices to prevent and deter potential asylum seekers from accessing their in-country asylum systems. Australia is arguably the most extreme and visible proponent of this broader trend in its response to boatpeople arrivals. How can we explain Australia’s shift from implementing and supporting an onshore asylum and border control system (1950s to late 1990s) to one in which those practices are carried out offshore (2001 to present)? Understandably, most observers evaluate this development using arguments about domestic politics and self-interest to explain Australia’s shift in practices. Others maintain that these states actually acknowledge international law, but only because of its instrumental and strategic value. Finding prevailing accounts incomplete and unsatisfying, my dissertation takes a different approach. I use a longitudinal assessment of the relationship between the legal norm governing the right to seek asylum and Australia’s response to boatpeople over time. I argue that the legal norm both shaped and was shaped by Australia’s response to boatpeople. By straddling the divide between domestic and international levels of analysis and treating legal norms as dynamic, I find that Australia’s response to boatpeople can be more accurately explained using a constructivist theory of legal norms.