VictorJuiz/thesis huggingface dataset:
Microfluidic Frameworks to Elucidate Mass Transfer Dynamics in Sheared Dispersions

Innovations in the area of microfluidics have enabled researchers to develop microfluidic techniques, as an alternative to macroscale methods, to measure scale invariant quantities pertinent to mass transfer operations. The ability to control variables precisely and accurately, and the possibility of employing analytical approaches owing to simpler fluid flow equations makes microfluidics an attractive platform for such measurements. This thesis establishes microfluidic protocols and theoretical frameworks to measure thermodynamics and kinetic parameters pertinent to mass transfer dynamics in three classes of sheared dispersions: gas-in-liquid dispersions, emulsions and rigid particle suspensions. The first platform is designed to measure gas solubility and diffusivity in a liquid by observing the shrinkage of a train of relatively long bubbles flowing through a microchannel. This data is analyzed by using a mathematical model that considers the local concentration gradients and the flow profiles, without resorting to the computationally expensive, full numerical simulations of the fluid flow and concentration distribution equations. The developed microfluidic platform can be applied to diverse gas-liquid reaction systems to determine the equilibrium and kinetic parameters conveniently and rapidly. The second platform is an automated feedback-control based hydrodynamic trap, that has enabled control and observation of a Hele-Shaw oil droplet for long residence times (minutes to hours). It has allowed us to measure oil solubility in an aqueous medium by analyzing the temporal radii using an appropriate mass transfer theory. This platform can also be used to monitor solvent extraction dynamics in the synthesis of polymer microparticles. The final platform is designed to measure mixing lengths of a tracer in moderately concentrated suspension flows (>30% volume fraction of rigid, spherical particles). For such suspensions, mixing is understood to result from a complex interplay between three mechanisms: (a) molecular diffusion, (b) shear-induced self-diffusion, and (c) second normal stress difference induced secondary convection. A comprehensive numerical study and a thorough scaling analysis is carried out to outline this interplay. Using confocal microscopy and a fluorescently-labeled dye in the medium, we present the first experimental study that observes the dynamic process of mixing in suspensions due to secondary currents. Our experiments also reveal a fourth mechanism of mixing - hydrodynamic instabilities arising from nonlinear effects at high volume fractions. The quantification and modeling of the fundamental mechanisms of mass transfer will serve as the basis for the prediction of solute mixing rates in sheared suspensions at larger scales.

Keywords: Emulsions
Mass transfer
Microfluidics
Mixing
Multiphase flows
Suspensions
Advisor: Ramchandran, Arun
Approaches to Anti-sedentary Behaviour in Chronic Obstructive Pulmonary Disease

Background: Decreasing sedentary behaviour has emerged as a distinct health target in individuals with chronic obstructive pulmonary disease (COPD), but effective approaches to reducing it are unclear. Objective: To explore the perspectives of people with COPD and healthcare professionals on reducing sedentary behaviour in people with COPD, to develop and test a sedentary behaviour reduction intervention for people with COPD, and to examine the feasibility of an alternate exercise modality (dance) to decrease sedentary behaviour for people with COPD. Methods: Two qualitative research studies, informed by the Theoretical Domains Framework, were conducted with 14 people with COPD (Study 1) and 16 healthcare professionals (Study 2). The feasibility of the “Get Up for Your Health” behaviour change reduction intervention, which was informed by the findings from Study 1, was tested in Study 3 using a single group, pre- and post-intervention design, among those with COPD enrolled on a PR program. Study 4 was a single group, pre-and post- study, which involved examining the feasibility of dance as an alternate exercise modality in individuals with COPD. Results: Study 1 revealed a lack of knowledge on the concept of sedentary behaviour among study participants. It identified behavioural determinants that could be targeted for a reduction in sedentary behaviour among people with COPD. Study 2 found that healthcare professionals need more education on sedentary behaviour with information about the determinants of behaviour relating to healthcare professionals targeting a reduction in sedentary behaviour in people with COPD. In study 3, the “Get Up for Your Health” intervention, emerged as being feasible, with an enrolment rate of 75%, a completion rate of 90%, adherence to wearing the activity monitor of 84% and participant satisfaction of 90%. The impact of the intervention on sitting time was unclear. In study 4, a dance program was safe and feasible, with an enrolment rate of 49%, a mean attendance rate of 78%, an absence of adverse events and a high participant satisfaction Conclusion: The current thesis provides important information for future sedentary behaviour research to support people with COPD.

Keywords: Behaviour Change
COPD
Health Promotion
Pulmonary Rehabilitation
Advisor: Brooks, Dina
Effects of Altered 7q11.23 Copy Number on Neural Stem Cell Physiology and Cortical Organization during Embryonic Development

Williams-Beuren syndrome (WBS) and 7q11.23 duplication syndrome (Dup7) are two rare neurodevelopmental disorders caused by deletion and duplication respectively, of 25 genes on chromosome 7q11.23. Individuals with WBS or Dup7 present with an array of cognitive and behavioural phenotypes, including anxiety, autism, speech and language delay, and intellectual disability, but the biological basis for these neuropsychiatric symptoms remain unknown. Structural and functional abnormalities of the cortex have been identified in both WBS and Dup7, suggesting that cortical development is perturbed in these disorders. The effects of altered copy number variation (CNV) of two candidate genes, GTF2I and GTF2IRD1, on neural stem cell growth and fate determination was investigated using primary neuronal precursor cultures derived from mouse models with CNV of these genes. Altered Gtf2i and/or Gtf2ird1 expression disturbed neural stem cell physiology in early corticogenesis leading to abnormal cortical cytoarchitecture in late gestation embryos, in a gene dose dependent manner. Genome wide expression analysis of embryonic cortices of mouse models of Gtf2i and Gtf2ird1 CNV identified changes in transcriptome profiles underlying dysregulated corticogenesis. These data will help us understand how the developing brain is perturbed in people with WBS and Dup7 and may give insight into the pathological causes and possibly help identify therapeutic interventions to treat their cognitive symptoms.

Keywords: autism
copy number variation
neural stem cell
neurodevelopmental disorders
Williams Beuren syndrome
Advisor: Osborne, Lucy
Assessing the Effect of Tree Nut and Peanut Consumption on Adiposity: Is a Calorie a Calorie?

Nuts have been shown to have diabetes and cardiovascular related health benefits, yet there remains concern that nuts may contribute to weight gain due to their high energy density. To address this concern, the research carried out in this thesis includes a systematic review and meta-analysis (SRMA) of prospective cohorts and randomized controlled trials (RCTs) to investigate the role of nuts on measures of adiposity, and an exploratory analysis of a randomized crossover trial to assess the bioaccessibility of energy and macronutrients of almonds. The SRMA identified 7 prospective cohort studies and 86 RCTs involving 569,910 and 12,092 participants, respectively. Nut consumption was inversely associated with the primary outcome overweight/obesity, as well secondary outcomes (body weight, risk of ≥5 kg weight gain, waist circumference) in prospective cohort studies. Similarly, there was no adverse effect of nuts on the primary outcome of body weight or any of the secondary outcomes (BMI, body fat, waist circumference, waist-to-hip ratio or visceral adipose tissue) in RCTs. The 3-phase randomized crossover trial including 22 participants with hyperlipidemia indicated fat from almonds was only 78.5±3.1% bioaccessible with an average overall energy loss of 21.2±3.1% (40.6 kcal/d). When considering the diet as a whole, there was significantly less bioaccessibility of energy and fat with almond consumption, but not carbohydrate or protein, compared to the control. Inclusion of ~73 g of almonds each day decreased the energy bioaccessibility of the diet by approximately 2%. Thus, the energy content of almonds may not be as bioaccessible as predicted by Atwater factors. Current evidence demonstrates that nuts are not associated with increased overweight/obesity incidence or weight gain, possibly due to the reduced bioaccessibility of energy and fat content of nuts. The research conducted in this thesis suggest nuts may be recommended without the concern that they contribute to weight gain.

Keywords: Adiposity
Bioaccessibility
Fatty acids
Meta-Analysis
Nuts
Randomized Controlled Trial
Advisor: Sievenpiper, John L
Bazinet, Richard P
Safety and Accuracy of a Novel MR Imaging Based Method for Optimizing Deep Brain Stimulation Settings.

Deep brain stimulation (DBS) is most commonly used in Parkinson’s disease (PD) to modulate dysregulated motor circuits. This surgical treatment can produce striking clinical benefits when stimulation is properly programmed. DBS programming, the process of individually titrating the dose of electrical stimulation delivered to achieve maximal clinical benefits, remains largely a trial-and-error process predicated on clinical observations. This process imposes significant time and financial stress upon patients and healthcare systems. Hence, there is a need for a physiological marker that can rapidly and accurately predict clinical response to DBS parameters. We hypothesized that functional magnetic resonance imaging (fMRI) could serve as an objective predictor of treatment efficacy in PD DBS patients. This led to a four-step process: (1) determine the safety of 3 Tesla (T) MRI using a phantom model; (2) highlight the importance of using native optimal DBS programming settings; (3) determine the safety, and feasibility of 3T MRI in a large cohort of patients receiving DBS; and, (4) define a typical fMRI pattern resulting from clinically optimal stimulation in PD patients. Our results showed that optimal functional neuroimaging data (i.e., 3T MRI and body-transmit coil) could be acquired safely and effectively in patients with DBS. Then, we demonstrated that ethic approvals enabling the use of optimal native settings should be obtained since converting optimal native settings (i.e., non-bipolar) to equivalent bipolar settings — to meet MRI safety guidelines — does not yield equivalent fMRI maps. Finally, we defined a characteristic pattern of brain responses associated with clinically optimal stimulation. By contrasting the fMRI patterns obtained during optimal and non-optimal stimulations, we built a machine learning model classifying whether a given stimulation setting could be considered optimal based on its fMRI pattern of brain changes. Our results show that fMRI can rapidly define the optimal DBS stimulation in PD patients. Obtaining DBS-induced fMRI brain signatures associated with optimal clinical benefits, will not only allow us to obtain a better understanding of the mechanism of action of DBS, but could also facilitate individualized medicine for our patients and may represent a small step towards the possibility of autonomous, closed-loop DBS programming.

Keywords: deep brain stimulation
functional magnetic resonance imaging
magnetic resonance imaging
neuroimaging
neurosurgery
safety
Advisor: Lozano, Andres M.
IDENTIFICARE IL DISAGIO: crisi esistenziale, affettività e binarismo di genere nel cinema italiano LGBTQ del XXI secolo

This work aims to investigate the cinematographic representation of the relationship between the individual and his or her gender identity in LGBTQ Italian films by Donatella Maiorca (Viola di mare, 2009), Ferzan Özpetek (Hamam/Il bagno turco, 1997; Saturno contro, 2007), Nicolo Donato (Brotherhood/Fratellanza, 2009), Ivan Cotroneo (Un bacio, 2016), Sebastiano Riso (Più buio di mezzanotte, 2014), Maria Sole Tognazzi (Io e lei, 2015), Fabio Mollo (Il padre d’Italia, 2017), Cristina Comencini (Il più bel giorno della mia vita, 2002), Francesco Henderson Pepe (Amaro amore, 2013), Stefano Calvagna (Un nuovo giorno, 2016) and Margherita Ferri (Zen sul ghiaccio sottile, 2018). The analysis is carried out through a social and psychological perspective that underscores how this relationship is influenced by emotions that pervade the protagonists. In particular, the existential crisis within contemporary LGBTQ Italian cinema is examined, including the discrepancy between sexual identity and gender identity. This study aims to portray ways in which the conflict between sex and gender inside the subjects in question can be a source of a profound existential crisis as a motive for rejection and/or discrimination by society. Through a study of the characters’ affectivity, the emotional turmoil experienced by LGBTQ subjects becomes evident through the emphasizing of the influence such states of being have on their behavior, while modalities of inclusion/exclusion within their respective societies are also brought to light. In its conclusions, this work establishes that our emotions control, even though unconsciously and peculiarly, our behaviours, and ultimately determine who we are. Such behaviors characterize us as social actors in revealing the significance of non-verbal communication, which is an undeniable source of truth on a subliminal level. Through a critical context, this work enriches the pre-existing debate on masculinity by proposing a new interpretive perspective that considers the ways in which emotions interact with our free will, thereby becoming an indisputable indicator of our hidden inclinations. The study of such factors is instrumental in demonstrating how sexual or gender identity influence the characters in question, who, in turn, through their emotions display a sense of existential crisis tied to their non-binary and/or dysphoric condition.

Advisor: Lettieri, Michael
Public Art, Private Land: Settler Colonialism and Environment in New Deal Murals on the Great Plains

“Public Art, Private Land: Settler Colonialism and Environment in New Deal Murals on the Great Plains” analyzes government-sponsored public art produced in the context of the Dust Bowl. While the national print media was dominated by images of environmental and economic disaster, the Treasury Department’s Section of Fine Arts (1934-1943) placed murals in post offices across the country to provide an uneasy population with a reassuring vision of America. This dissertation focuses on the Great Plains, a region defined by environmental disaster narratives and the celebratory recent histories of white settlement. While the land appeared to be rejecting settlers through drought and dust storms, muralists offered scenes of reassuring history and agricultural bounty. However, the Dust Bowl was but one symptom of the ongoing disaster of settler colonialism. Through four thematic chapters, I ask how these artworks functioned to shore up settler faith in the land during a period of environmental crisis. In Chapter One, I examine land claim murals, works that emphasized settler arrivals and European histories on the Plains. Chapter Two considers extinction narratives that were employed against Native peoples and bison as a means of further solidifying settler land claims. However, these murals are considered alongside cultural production from Native artists that refutes settler claims and asserts survivance against colonization. Chapter Three examines agricultural murals, arguing that while some depictions of bounty ignored the surrounding Dust Bowl, others directly engaged with symbols of disaster. Finally, Chapter Four posits that symbols of oil extraction became hopeful signs of modernity and wealth for communities characterized by the Dust Bowl. In each chapter, I situate murals in a wider visual landscape that includes the visual culture of preceding festivals, photographs and print media of the 1930s, and more recent examples of community public art. My analysis draws from the rich archive of the Section of Fine Arts and from the fields of ecocritical art history, environmental and labor history, and settler colonial studies to argue that post office murals on the Plains worked to both reflect and to shape a community’s land ethic.

Keywords: Dust Bowl
Great Plains
Murals
Public Art
Settler Colonialism
Advisor: Cheetham, Mark A
Owning Implicit Attitudes

In this thesis I defend the view that we are attributability-responsible for at least some of our “implicit” attitudes, because they are propositional attitudes. Implicit attitudes are attitudes that can be measured by indirect tests, those tests where subjects are not informed what the test is measuring. It is often claimed that indirect tests are measuring uncontrolled or unconscious attitudes, and researchers draw a contrast with “explicit” attitudes, that are thought to be controlled or conscious attitudes. Unsurprisingly, the claims about control and consciousness seemingly map on to debates about responsibility for attitudes. It is often thought that to be responsible for an attitude, it must be a conscious attitude or a controlled attitude. A natural conclusion is that we are never responsible for our implicit attitudes. In this thesis I distinguish different senses of “control” and “conscious” from each other, and I show that implicit attitudes are not best understood as attitudes that we lack the ability to become aware of, nor as attitudes that we lack the ability to control. These abilities (to know or control one’s own attitudes) may be important for responsibility as accountability, but I argue that these abilities are not important for responsibility as attributability. I argue that we are attributability-responsible for an attitude when that attitude is a part of our self. Since implicit and explicit attitudes may dissociate, this commits me to a “mosaic” conception of the self, where our “selves” are often dissociated and contradictory, and not necessarily rationally consistent.

Keywords: belief
conscious awareness
implicit attitudes
rationality
responsibility
the self
Advisor: Misak, Cheryl
Nagel, Jennifer
Nerves on the Loose: Gendering Nervousness in Ottoman and Early Republican Turkish Novels

This dissertation analyzes the literary representations of nervousness and its cognates, such as neurasthenia, hysteria, and nervous sensibility, which were coded as feminine in the novels of several canonical Ottoman-Turkish authors in the period between 1880 and 1940. It explores the complexity and many idiosyncrasies surrounding the idea of female nervousness together with its relevance to cultural and political discourse within the late Ottoman Empire and early Republican Turkey. Although its relevance has eluded scholars, the notion of female nervousness, as represented both in fiction and nonfiction, deserves its place as a noteworthy category within Ottoman and Turkish narratives of disease. Two chapters of this dissertation examine the array of hysteric and neurasthenic female characters in Ottoman-Turkish literature and demonstrate that these disorders were malleable and varied in definition, drawing from changing socio-cultural and medical contexts. The other two chapters focus on different manifestations of female nervousness. Inspired by the frequent references to the concepts of nerves, the nervous system, and female nervousness in print media from the turn of the century, this dissertation ultimately demonstrates four things. First, the ways in which the authors narrativize female nervousness in their novels reveal prevailing gender and class norms of the era. A closer analysis of the novels supported by secondary sources called for widening the analysis beyond gender and class to include race, ethnicity and socio-economic expectations of the period. Second, female nervousness is rarely treated as a mere medical condition or diagnosis; authors often capitalize on nervousness, or any related diagnostic label, to promote their own views of concepts such as civilization (medeniyet) or emotional etiquette (hiss-i terbiye). Third, female nervousness is mobilized to cast a light on the conditions of modernity, and to express anxieties around it. Lastly, with the collapse of the Ottoman Empire and the rise of Turkey as a nation state, female nervousness takes on metaphorical meanings in the service of nation-building and the construction of a national identity. Together, these four arguments demonstrate that the exploration of female nervousness cannot be contained within a single, definitive narrative.

Keywords: hysteria
nervousness
neurasthenia
Ottoman
tuberculosis
Turkish
Advisor: Nyquist, Mary
Control of Ribosomal DNA Loci by Nucleolar RNA Polymerase II and Its Intergenic R-loops

Proteins are universally manufactured by ribosomes, which are assembled within phase-separated nuclear compartments called nucleoli. In the heart of nucleoli, ribosomal RNA (rRNA) molecules are transcribed from ribosomal DNA (rDNA) loci, thus initiating the process of ribosome biogenesis. Traditionally, RNA polymerase I (Pol I) is believed to be the sole polymerase responsible for this fundamental process. The rDNA repeats also contain nested intergenic spacer (IGS) elements that are naturally enriched in co-transcriptionally generated triplex nucleic acid structures termed R-loops. At budding yeast IGSs, RNA polymerase II (Pol II) generates R-loops, and can drive genome instability and ageing. Whether nucleolar Pol II exists in higher organisms, modulates life-sustaining ribosome biogenesis in any species, or is relevant to human aging and age-related disease is unknown. Here, we uncover nucleolar Pol II and identify its co-transcriptional R-loops as deleterious and beneficial protagonists in genome instability and ribosome biogenesis, respectively. First, via dual interrogation of yeast and human cell systems, we identify neurodegeneration-linked ATXN2 as a conserved suppressor of genome-destabilizing rDNA/nucleolar R-loops, while uncovering Mg2+ as a biochemical signal of R-loop-combating and lifespan-prolonging calorie restriction (CR) [1]. Second, we uncover a nucleolar Pol II-dependent mechanism that operates across human IGSs to maintain nucleolar organization and drive rRNA expression, reveal disease-associated disruption of nucleoli by non-coding RNAs, and establish locus-targeted R-loop modulation via a novel RNaseH1-EGFP-dCas9 system (denoted ‘red laser’). Our results challenge the current schema of labour division between different RNA polymerases and have implications for our understanding of disease entities linked to R-loop and nucleolar dysfunction.

Advisor: Mekhail, Karim