VictorJuiz/thesis huggingface dataset:
The Role of Dietary N-6 Polyunsaturated Fatty Acids on Lipid Mediators and Inflammation in the Mouse Brain
Keywords: brain
gene expressions
lipid
mouse
n-6 polyunsaturated fatty acids
neuroinflammation

N-6 polyunsaturated fatty acids (PUFA) such as arachidonic acid (ARA, 20:4) and n-3 PUFA as docosahexaenoic acid (DHA, 22:6) are precursors to bioactive lipid mediators, which have important roles in many brain functions including inflammation. Previous studies have shown that dietary n-6 PUFA deprivation in pups can change brain ARA and DHA levels. However, the effects of n-6 PUFA deprivation on brain lipid metabolism during maternal stage has yet to be studied. Moreover, n-6 PUFA have been linked to the pathogenesis of many neurological disorders through many mechanisms, including conversion to ARA-derived lipid mediators (pro-inflammatory mediators) in the brain. Though diets low in n-6 PUFA are known to reduce levels of ARA and ARA-derived lipid mediators, no one has yet investigated the effects of lowering dietary n-6 PUFA on modulating brain inflammation and resolution in neuroinflammation. The first objective of this thesis was to examine how lowering dietary n-6 PUFA, from gestation, would change levels of hippocampal n-6 and n-3 PUFA and their lipid mediators in comparison to the offspring period. We found that maternal exposure to an n-6 PUFA deprived diet does not exacerbate the reduction in ARA and ARA-derived lipid mediators within hippocampal phospholipids (PL) relative to offspring exposure, which suggests that offspring exposure is a main regulating factor of these PUFA and their derivatives. Therefore, we used the offspring stage as the feeding period for the subsequent neuroinflammation study. Neuroinflammation was induced using intracerebroventricular injection of lipopolysaccharide (LPS) and the hippocampus was examined at several time points. Following LPS, different pro-inflammatory gene expression was associated with enrichment in gene expression categories associated with inflammation. However, these pro-inflammatory markers were not reduced by lowering dietary n-6 PUFA and importantly did not impair the resolution of neuroinflammation. In conclusion, we found that exposure of the offspring to an n-6 PUFA deprived diet was sufficient to lower the concentrations of ARA and other n-6 PUFA in hippocampal total PL. In a neuroinflammation model, the expression in gene ontology categories associated with inflammation was significantly increased and then resolved in response to LPS administration, however, irrespective of an n-6 PUFA diet.
TamilThanmai: A Historical Ethnography Of Public Political Lives in Tamilnadu (1950-1970)
Keywords: Caste
Dravidian
Feminist
Public Politics
Social Movement
Tamil

This dissertation is a historical ethnography of Sulur, a town in Coimbatore district of Tamilnadu, India. Through in-depth interviews and archives, both personal and public, of textual and visual sources, I have evolved an analytical framework from which to understand everyday public political lives. Using a spatial analysis, this dissertation has documented the lives of men in Sulur who were engaged in public politics. I have contextualized these life stories in a range of socio-economic and political histories of Tamilnadu during that time. The period between the 1950-70 is when the political parties that were to influence the landscape of electoral power and political discourse in the second half of the 20th C were forming their base in Tamilnadu. This period, before the consolidation of state power and political discourses, is an ideal time from which to understand the history of such political formations from the perspective of the everyday lives of its ordinary members, all of whom are men. Based on this narrative I have identified and explored elements of what I term TamilThanmai. TamilThanmai, I propose is a historically grounded analytical framework which simultaneously describes the essence of public political lives that provided a way of being and sense of self for all those who lived it. This dissertation is a history of and through TamilThanmai. In the dissertation themes of public political life has been explored through three main chapters. These include a focus on Dalit public political lives; the affective ties that hold together the non-Brahmin, non-Dalit men engaged in such lives; and the embodiment of such a politics through physical training culture. This three-pronged exploration is grounded in a critical spatial framework. Through this exploration of TamilThanmai I propose a theoretical framework from which to understand the persistence of caste-based thinking and masculinization of public political lives in Tamilnadu.
Feeding in the Blood-gorging Bug Rhodnius prolixus: The Role of Sulfakinin Signaling
Keywords: Chagas Disease
Feeding
Molecular
Receptor Assay
Satiety
Sulfakinin

Sulfakinins (SKs) are neuropeptides that have been shown to function as feeding satiety factors in insects. We confirmed the presence of two SKs (Rhopr-SK-1 and Rhopr-SK-2) in Rhodnius prolixus. Reverse transcriptase quantitative PCR (RT-qPCR) demonstrated that the Rhopr-SK transcript is mainly expressed in the central nervous system (CNS) in unfed fifth-instar R. prolixus. Fluorescent in situ hybridization (FISH) showed transcript expression only in neurons in the brain. Immunohistochemical staining of SK-like peptides was observed in the same neurons in the brain and in processes extending throughout the CNS, as well as over the posterior midgut and anterior hindgut. Rhopr-SK-1 induced contractions of the hindgut in a dose-dependent manner, but had no effect on heartbeat frequency. Injection of Rhopr-SK-1 significantly decreased the overall size of the blood meal consumed, suggesting SK’s role as a satiety factor in R. prolixus. Two seven-transmembrane Rhopr-SK G protein-coupled receptors (GPCRs), Rhopr-SKR-1 and Rhopr-SKR-2, were cloned and characterized. RT-qPCR of the two Rhopr-SKR transcripts revealed that the target tissues for Rhopr-SK-1 and Rhopr-SK-2 are located in the CNS, heart, gut, salivary glands, Malpighian tubules, fat body, as well as, male and female reproductive systems. Rhopr-SK-1 inhibits contractions of the oviduct and ejaculatory duct in adult R. prolixus, whilst having no effect on contractions of the bursa. A functional receptor assay that utilized Human Embryonic Kidney (HEK)-293 cells stably expressing a modified cyclic nucleotide-gated (CNG) channel (HEK293/CNG) characterized the two Rhopr-SK receptors. Modified HEK293/CNG assays showed that the PLC/IP3 pathway, and not the cAMP pathway, is solely initiated upon the activation of either Rhopr-SK receptor. Nonsulfated Rhopr-SK-1 was not able to activate either Rhopr-SK receptor. Both Rhopr-SKRs were exclusively activated via Rhopr-SK-1 and Rhopr-SK-2. The importance of the SK signaling pathway in the modulation of feeding was demonstrated by the knockdown of the transcripts for Rhopr-SKs and Rhopr-SKRs, which led to an increase in the overall intake of blood during feeding.
Al-'Asabiyya in Context: Choice and Historical Continuity in Al-Muqaddima of Ibn Khaldūn
Keywords: Al-'Aṣabiyya
Al-Muqaddima
Economic policies and Injustice
Historical and Political Continuity
Ibn Khaldūn
Linguistic-Contextual Method of Interpretation

The purpose of this dissertation is to understand the meaning of the term Al-'Aṣabiyya in Al-Muqaddima of Ibn Khaldūn in context. In Al-Muqaddima, he constructs a method for the scientific study of history, the subject matter of which is human association. Human association is necessary for human beings, but by its nature, it requires political authority and economic organization. By order of existence, political authority is acquired only by al-‘aṣabiyya. Therefore, al-‘aṣabiyya is an “essential condition” in the world, and it can be perceived by the senses and the intellect. It is a power that “secures” political victory, and as such, it becomes the source that enables protection and the preservation of human life, the development of urban culture through the management of economic cooperation, and social harmony. In this study, I use a linguistic-contextual method to show that the form of al-'aṣabiyya that secures political authority is not natural, irrational, or aggressive. Rather, it is the fruit of the labour of unity and agreement between individuals and groups (‘aṣabiyyāt). It is a power that individuals manufacture intentionally either by way of descent, alliance, or allegiance to gain political authority. They are ahl al-‘aṣabiyya who achieve their goal “in the ordinary way,” that is, by overcoming others by their power of unity, and praiseworthy qualities. This study also shows that there is no organic connection between al-‘aṣabiyya and the form or quality of rulership. In fact, Ibn Khaldūn’s rejection of hereditary rule, condemnation of tyranny, and argument against the necessity of prophecy show that rational politics suffices for the management of human association. His statement on the science of physics, the use of the term “matter” in an economic sense to mean money, and the connection between injustice and economic policies show that the decline of the polity is not natural but a matter of choice between moderation and excessiveness. The detailed exposition of these various elements shows that the pattern of history in Al-Muqaddima is not cyclical. Instead, history is a narrative about cultural transmission, political and historical continuity, the expansion of one power, and the contraction of another.
Dying as a Process – A Temporal Look at the Ordered Events that Occur at an Organellar Level in Saccharomyces cerevisiae
Keywords: cell death
confocal fluorescence microscopy
high-content screening
high-throughput microscopy
terminal phenotype
yeast

Cell death is a dynamic, complex process. In this thesis, I describe the development of an automated imaging pipeline for detecting the changes in subcellular morphology that cells undergo through time as they are dying, known as a terminal phenotype. I captured terminal phenotypes over a 24-hour time course, for 352 temperature sensitive mutants of essential genes each expressing a panel of diagnostic GFP markers, representing 21 major subcellular compartments and structures. The pipeline used an unsupervised One-Class support vector machine outlier detection method to calculate single-cell penetrance, the percentage of cells for a given mutant population that look different from wild-type. Penetrance was calculated for each mutant and consisted of 9 timepoints for 21 GFP markers, for a total of 189 measured variables per terminal phenotype profile. A logistic function was fitted to the time-course data to extract the time at which half of the maximum penetrance occurred, which served as a marker for first-occurrence of a phenotypic change for a given GFP marker. Clustering of half-max times revealed grouping of terminal phenotypes according to biological process, and ordering of half-max times for each functional class revealed 9 divergent terminal phenotype trajectories that differ in compartments affected, and timing.
Reconstructing the Evolution of Xylose Fermentation in Scheffersomyces Stipitis
Keywords: biotechnology
evolution
flux balance analysis
metabolism
xylose
yeast

Lignocellulose is a renewable feedstock that can be fermented to biofuels and biochemicals, but its use is limited by several techno-economic challenges, including xylose fermentation. Scheffersomyces stipitis has been identified as an efficient xylose fermenter, but does not ferment well in industrial conditions. The scientific community has been engineering Saccharomyces cerevisiae, the preferred yeast for industrial biotechnology, to ferment xylose to ethanol with the xylose reductase (XR)-xylitol dehydrogenase (XDH) genes from Sch. stipitis for 30 years; however, recombinant Sac. cerevisiae's titres, rates, and yields for ethanol from xylose lags Sch. stipitis. This performance gap may be due to aspects of Sac. cerevisiae's metabolism that hinders xylose fermentation, aspects of Sch. stipitis' metabolism that enables xylose fermentation, or a combination of both. The focus of this thesis is to improve our understanding of budding yeast metabolism beyond Sac. cerevisiae, and ultimately reverse engineer how Sch. stipitis' metabolism has evolved to ferment xylose to ethanol efficiently with improved genome annotations and metabolic modelling. To obtain higher-quality genome annotations, ortholog groups in 33 yeasts and fungi spanning 600 million years in Dikarya were predicted using OrthoMCL. Over 500 enzyme families were curated with phylogenetic reconstruction to resolve inconsistencies. These ortholog assignments are more accurate than existing ortholog databases, and span diverse yeasts. Next, the gains and losses of metabolic genes were reviewed to identify important and reoccurring events in the evolution of metabolism in budding yeasts. Duplications were found to play an important role in the evolution of metabolism, including changes in enzyme cofactor preference and localization. The curated pan-genome and functional annotations were used to reconstruct genome-scale metabolic networks of the 33 species; the reconstructions have more genomic and metabolic coverage than those made with previous methods. Finally, the Sch. stipitis metabolic network was used to simulate xylose fermentation. NADH kinase and NADP phosphatase (NADPase), an orphan enzyme in eukaryotes, were found to be critical to xylose fermentation in these metabolic flux simulations. Pho3.2p was the sole NADPase candidate showing expression during xylose fermentation; its activity was confirmed in vitro. Xylose fermentation evolved in the Scheffersomyces-Spathaspora clade following genes duplications for XR and an acid phosphatase. This thesis provides a foundation for unravelling how metabolism has evolved in the yeast pan-genome.
Microtruss Design for Strength and Energy Absorption
Keywords: Carburizing
Electroplating
Energy Absorption
Microtruss
Optimization
Strength

The question of information flow within an inverse design problem is tackled with focus on thermodynamically irreversible phenomena, i.e. strength and energy absorption. Microtruss materials are used as a platform for the study as their individual building units, i.e. struts, possess uniform geometry, known properties, and can be tuned to achieve a desired level of performance; a much simpler task than attempting to design bulk microstructure. Elements of compositing are utilized to alter the performance of the microtrusses, namely nanocrystalline nickel electroplating and carburizing. In terms of strength, both compositing approaches produced microtrusses with superior performance. Additionally, the strength property was optimized using classical optimization approaches since the strength is determined by the onset of the first failure mechanism to be activated; a task that can be completed using conventional analytical models, such as the Shanley-Engesser buckling equation. The problem becomes more complicated for energy absorption since the onset and progression of the deformation and damage need to be readily describable analytically, which is not possible due to the distortion and deformation of the collapsing struts, i.e. geometrical and material non-linearities need to be considered. A primarily experimental approach is therefore followed to first identify the active failure mechanisms and their influence on the energy absorption property. The carburized microtrusses were modified with post-carburizing heat treatments such as tempering and decarburizing to enhance their post-buckling behavior and energy absorption capability. The nickel-coated microtrusses were plated using various plating conditions to control the hardness, thickness, composition, and adhesion of the coatings. With the proper plating parameters, nickel-phosphorous coatings introduced pre-buckling damage that nearly eliminated the post-peak softening in conventionally buckled microtrusses and resulted in an enhanced energy absorption response placing these hybrid microtrusses ahead with the top commonly reported energy absorbers in literature, such as foams and honeycombs.
School choice in deindustrialized cities: A mixed method comparison of charter and public schools on safety and parental involvement in Detroit, Michigan
Keywords: Charter schools
Detroit
Parental involvement
School choice
School safety

Charter schools have rapidly expanded in deindustrialized American cities over the past twenty-five years where they have been touted as a solution to pressing school safety problems, low parent participation, and educational underperformance. Yet, research on charter schools has focused on student achievement, largely overlooking school safety and parental involvement. This thesis compares charter and public schools on perceived school safety and parental involvement in Detroit, Michigan in three studies in the sandwich format. With its large charter school sector, Detroit is a highly relevant setting, embodying the social and economic challenges of deindustrialized cities that have undergone charter school reforms. In the first study, charter schools exhibited statistically higher perceived school safety, net of controls for neighborhood, school, and demographic characteristics. However, this relationship was largely diminished after accounting for parent-related characteristics. In the second study, non-profit managed charter schools elicited statistically higher parental involvement than for-profit managed charter and public schools while public schools reported greater parent decision-making, net of controls. The third study examined the mechanisms underlying the statistical results by conducting site observations (n = 40), interviews with parents (n = 20) and teachers (n = 20), and numerous informal interviews with different groups of stakeholders. Findings indicated that although charter school strategies were partly attributable to school performance, distinguishing attributes of school choosers conferred a self-selection advantage to charter schools. Overall, charter schools in deindustrialized cities appear to offer a modest improvement on perceived school safety and parental involvement, but they are not accessed by the most disadvantaged students. Extending access to information and transportation may enable greater access, but policy remedies beyond school choice may be needed to address challenges in neighborhood public schools where extraordinarily disadvantaged students are likely to remain enrolled. Additionally, relationship-building and a parent presence in school may be strategies for improving perceived school safety. This thesis furthers existing scholarship by demonstrating the following: the importance of safety to school choice processes in deindustrialized cities; distinguishing features of school choosers among demographically similar families; and differences in safety and parental involvement strategies by school type.
Umanesimo volgare nellâ Italia del Cinquecento: la vita e le opere di Lattanzio Benucci (1521-1598)
Keywords: Humanism
Italian Studies
Poetry
Renaissance

In the sixteenth century the Republic of Siena played an important role in the development of the Renaissance. The contribution Sienese writers made to Italian literature and history is still to be written, but it is impressive to see how many men, and women were part of it. One such case is represented by the scholar and writer Lattanzio Benucci, born near Siena in 1521. A cultured member of the nobility, Benucci studied at the local university and then served his city as ambassador to Florence, where he entered the salon of the poet and courtesan Tullia d’Aragona. Subsequently, Benucci moved to Rome where he was a courtier first of Cardinal Antonio Trivulzio and then of Cardinal Alfonso Carafa. In 1565 Benucci returned to Siena. Duke Cosimo de’ Medici employed him in Florence, where he died in 1598. The details of his biography are analyzed in the first chapter of this thesis. Over the centuries, some of Benucci’s literary works were lost. What has survived, however, is very revealing of his learning and letters: at least three poetry collections (see the second chapter), together with some others transcribed after his death (analyzed in the third chapter), a Dialogo de la lontananza (“Dialogue on Distance”), and a commentary (Osservazioni) on Dante’s Divine Comedy (both examined in the fourth chapter). All these works are still unpublished: in the second volume of this thesis, most of them have been transcribed in five appendices with philological apparatuses. This dissertation aims not only to increase our knowledge of a productive and well-connected intellectual of the sixteenth century, but also at offering a much more nuanced understanding of the complexity of late Renaissance Humanism. In so doing, it helps to shift the traditional focus away from much-examined Florence, Rome, and Venice, in order to place it on another crucially important city, Siena, and thereby widen our views on Renaissance Italy.
Pharmacological Manipulation of Long-term Potentiation and Cortical Inhibition from the Dorsolateral Prefrontal Cortex, a Model to Understand Cognitive Deficits of Schizophrenia
Keywords: brain stimulation
lon-term potentiation
neuroimaging
schizophrenia

Several studies have assessed the pharmacological modulation of cortical inhibition (CI) and long-term potentiation (LTP) using transcranial magnetic stimulation (TMS) from the motor cortex and recorded these effects through surface electromyography (EMG). However, recording CI and LTP from the dorsolateral prefrontal cortex (DLPFC), a cortical region that is more closely associated with the pathophysiology of severe psychiatric disorders including schizophrenia were previously not done. Objectives: This study, therefore, was designed to investigate whether CI, indexed by long interval cortical inhibition (LICI), and LTP measured using paired associative stimulation (PAS) could be modulated and measured from the DLPFC in healthy participants through the use of TMS combined with electroencephalography ( EEG ) using a placebo-controlled, randomized double-blinded crossover study design. Methods: 12 healthy participants were given a single oral dose of baclofen, a GABAB agonist, dextromethorphan, a NMDA antagonist, L-DOPA, a dopamine precursor, rivastigmine, an acetylcholine esterase inhibitor for each arm of the study. Results: LICI was enhanced and suppressed by increasing GABAergic tone and cholinergic tone, respectively. LTP was increased by enhancing cholinergic tone and dopaminergic tone and abolished when NMDA receptors were blocked. Conclusion: These results are important and have the potential for therapeutic application in manipulating neural plasticity and CI in the DLPFC to treat a variety of conditions, including depression, Parkinson's disease, and schizophrenia.