VictorJuiz/thesis huggingface dataset:
Towards an Understanding of Dissolved Organic Matter Molecular Composition and Reactivity in the Environment
Keywords: Dissolved organic matter
Photochemistry
NMR
FT-ICR-MS
GCxGC-TOFMS

Dissolved organic matter (DOM), one of the most complex naturally occurring mixtures, plays a central role in the biogeochemistry and the photochemistry of natural waters. A complete understanding of the environmental role of DOM will come only from the elucidation of the relationship between its structure and function. This thesis presents new work on the separation, characterization, and reactivity of DOM in rainwater, freshwater, and seawater. A new separation technique based on counterbalance capillary electrophoresis was developed for the separation of Suwannee River NOM. A comparative study of the organic content of rainwater was accomplished using nuclear magnetic resonance (NMR) with spectral database matching ,Fourier transform ion cyclotron mass spectrometry (FT-ICR-MS), and comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC-TOFMS). Three complementary, non-overlapping datasets identified of over 400 compounds. Analysis of the FT-ICR-MS data using van Krevelen diagrams and the carbon oxidation state showed variation in the elemental composition and molecular size. Over 50% of the compounds identified in this study were known components of secondary organic aerosol (SOA) and volatile organic carbon (VOCs). Dissolved organic matter (DOM) plays a central role in the photochemistry of natural waters through the production of reactive oxygen species and the triplet excited state of DOM (3DOM*). These reactive species are central to the reactivity, transport, and fate of both natural and anthropogenic chemicals in the environment. Laser flash photolysis (LFP) was used to demonstrate that particulate organic matter (POM) generates a triplet excited state species (3POM*). LFP of seawater from the Pacific Ocean and the Bermuda Atlantic Time Series Station detected similar excited state species from surface to 4535m. Metal speciation has been implicated in the photochemistry of natural waters. Copper immobilized metal affinity chromatography (IMAC) of seawater and freshwater isolated a low and a high affinity fraction that generated excited state transients. Excitation-emission matrix spectroscopy showed that while the seawater fractions were autochthonous, freshwater fractions enriched in chromophoric DOM (CDOM), were allochthonous. The discovery of these different classes of compounds in freshwater and seawater has important implications both for the mineralization of DOM and the removal of xenobiotics in the aquatic environment.
Supporting the Use of Causally Related Functions in Biomimetic Design
Keywords: Biomimetic design
Design cognition
Design methodology
Conceptual design

Biomimetic design uses biological analogies to produce innovative engineering solutions. However, designers face challenges in identifying useful biological analogies and correctly applying the analogies identified to design solutions. To overcome these challenges, this thesis proposes the use of causally related functions in biomimetic design. Causally related functions describe how a desired function is enabled by another function. To support the use of causally related functions, a set of tools was developed. First, the causal relation template and mapping techniques (one-to-one mapping instructions and problem-independent scenario mapping) were devised to assist designers to identify and apply causally related functions from descriptions of biological phenomena. In pen-and-paper experiments with senior undergraduate engineering students, the causal relation template, if used correctly, facilitated the development of design concepts that were analogous to biological phenomena provided as sources of analogy. In addition, the mapping techniques reduced the percentage of participants who made non-analogous associations from biological phenomena to develop design concepts. Another tool developed was the causal relation retrieval method. The method uses syntactic information in natural language sentences to explicitly identify causally related functions. A modified verbal protocol study with graduate engineering students revealed that the retrieval method increased the likelihood of locating biological phenomena relevant to given design problems compared to a single verb-keyword search method. Also, the search matches located with the retrieval method were more likely to facilitate functional association to develop design concepts. These results demonstrate that the knowledge structure of causally related functions can support both the identification of relevant biological phenomena in natural language text and use of analogical reasoning between the biological phenomena and design solutions. The causal relation template and mapping strategies developed contribute to the field of biomimetic design as training methods for designers; and the causal relation retrieval method could serve a technique to bridge the gap between the natural language approach and the modeling approach to biomimetic design.
Matrix Mechanical and Biochemical Regulation of Multipotent Stromal Cell Osteogenesis
Keywords: mesenchymal stromal cell
substrate stiffness
osteogenesis

Biochemical and mechanical properties of the extracellular matrix (ECM) are known to independently influence cell function. Given the complexity of cellular responses, I hypothesized that the integration of multiple matrix factors as opposed to their individual contribution is key to understanding and controlling cell function. The objective of this thesis was to systematically investigate matrix biochemical and mechanical regulation of multipotent stromal cell (MSC) osteogenesis. First, I demonstrated that substrate stiffness-dependent MSC spreading, proliferation and osteogenic response were differentially regulated by matrix protein type (collagen I vs. fibronectin) and concentration. Second, I developed and characterized a matrix microarray platform that enabled the efficient screening of multiple matrix-derived cues (substrate stiffness, ECM type and density). I implemented the matrix microarray platform together with parametric regression models to elucidate novel matrix interactions in directing mouse MSC osteogenic and adipogenic differentiation. Third, I extended the screening study to examine matrix-dependent human MSC osteogenesis. Non-parametric regression models were used to provide a nuanced description of the multi-factorial matrix regulation in MSC osteogenesis. The response surfaces revealed a biphasic relationship between osteogenesis and substrate stiffness, with the exact location and magnitude of the optimum contingent on matrix composition. Guided by the screening results and perturbation to key cytoskeletal regulators, I identified a novel pathway involving Cdc42 in matrix mechanical and biochemical regulation of MSC osteogenesis. Surprisingly, Cdc42 mediated stiffness-dependent MSC osteogenesis independent of ROCK, suggestive of a contractility-independent mechanism in matrix rigidity signal transduction. In summary, the integration of cell-based arrays and statistical modeling has enabled the systematic investigation of complex cell-matrix interactions. This generalizable approach is readily adaptable to other cellular contexts, complementing hypothesis-driven strategies to facilitate non-intuitive mechanistic discovery. Moreover, the improved understanding of matrix-dependent MSC function also has practical relevance to the development of biomaterials for tissue engineering applications.
Not "Just Staying": How Health and Development Programming is Reshaping the Past, Present and Future for Rural Youth in Malawi
Keywords: Health and Development Programming
HIV/AIDS
Malawi
Africa
Youth
Anticipation
Human Rights
Gender

Drawing on ethnographic and visual anthropological data, this dissertation explores the anticipated and unanticipated effects of youth-targeted health and development programmes in rural Malawi. Contemporary development programmes are anticipatory in nature: they are focused on managing health, behaviour, education and social relations today in ways that are believed to open opportunities for some distant and better future. Working with rural youth who “just stay,” an idiom youth use to describe their “failure” to make progress towards desired futures, I show how discourses and ideals espoused in anticipatory programmes including human rights, education, gender and love are slippery concepts. As they percolate through this particular social, political, historical and demographic context and into the imaginaries of young people, these discourses often become something new and unexpected. In particular I show how: i) a discursive elision occurs between the rights discourse and other markers of modernity and youth take up their “right” to wear modern clothing and drink commercial alcohol, ii) selfish behaviours including alcoholism and womanising surface in boys’ self-constructions as innate tendencies rather than part of a socially produced and constantly shifting construction of masculinity, iii) audit cultures, critical to the operation of anticipatory programmes, reduce gender equality to something “countable,” which, in turn, alters programme activities, leads to performances by participants and filters into youth subjectivities, and iv) discourses on modern and “healthy” loves, free from HIV/AIDS, lead to re-arrangements in romantic relations and friendships that provide new and positive opportunities for women not always available in customary marriages. By privileging the future over the present and the past, programmes overlook numerous structural barriers to improving the lives of the youth who “just stay.” I argue that the unanticipated effects of these programmes constitute and give rise to several invisible forms of violence. On the other hand, however, some effects are generative of new and positive subjectivities and relationships that are egregiously overlooked by programmes. This ignorance prevents programmes from building upon positive effects to generate desired change and sometimes even undermines their own stated goals.
The Fabrication of Direct Oxidation Solid Oxide Fuel Cell Anodes Using Atmospheric Plasma Spraying
Keywords: Solid Oxide Fuel Cell
Anode
Direct Oxidation
Plasma Spray
Copper
Ceria

Solid oxide fuel cells (SOFCs) that operate directly on hydrocarbon fuels eliminate the requirement for costly and complex external reforming systems. Atmospheric plasma spraying (APS) is an established manufacturing method that offers the potential to fabricate direct oxidation SOFC anodes in a single step, instead of the multiple steps currently required. Manufacturing by APS also allows the use of metal supports, which improve thermal shock resistance, allow rapid cell heat-up, and reduce total cost. In this study, direct oxidation SOFC anodes based on Cu and samaria-doped ceria (SDC) in combination with Co and/or Ni were investigated for their stability and performance in H2 and CH4 when plasma sprayed on ferritic stainless steel supports. Several different APS techniques were investigated. Two of these techniques were hybrid methods involving a combination of dry powder plasma spray and suspension plasma spray (SPS) processes. These techniques were proposed to help balance the degree of melting of the lower melting temperature oxides of the metals Cu, Co, and Ni with that of the higher melting temperature SDC. The use of a single suspension containing all of the anode component feedstocks was also investigated. Multi-component aqueous suspensions of CuO, Co3O4, and NiO were developed with or without the addition of carbon black and SDC. It was found that the use of a hybrid plasma spray technique can help to improve deposition efficiency (D.E.) and enhance partial melting of the low melting temperature feedstocks. However, plasma spraying all of the components in a single suspension can lead to more homogeneous mixing and greater resistance to metal coarsening at SOFC operating temperatures. In electrochemical tests of plasma-sprayed metal-supported cells containing these anodes, peak power densities as high as 0.6 W/cm2 were achieved at 750 deg C in humidified H2. In CH4, power density was limited by the activity of the anodes. Stability in CH4 was poor because of oxidation of the metal support and enhanced coking behaviour resulting from interactions between Fe in the support and Co and Ni in the anodes. When separated from the supports, the anodes demonstrated very low coking rates in thermogravimetric analysis experiments in CH4.
Multipartite Entangled States: Transformations, Entanglement Monotones, and Applications
Keywords: Multipartite entanglement
W-type state
Random distillation

Entanglement is one of the fundamental features of quantum information science. Though bipartite entanglement has been analyzed thoroughly in theory and shown to be an important resource in quantum computation and communication protocols, the theory of entanglement shared between more than two parties, which is called multipartite entanglement, is still not complete. Specifically, the classification of multipartite entanglement and the transformation property between different multipartite states by local operators and classical communications (LOCC) are two fundamental questions in the theory of multipartite entanglement. In this thesis, we present results related to the LOCC transformation between multipartite entangled states. Firstly, we investigate the bounds on the LOCC transformation probability between multipartite states, especially the GHZ class states. By analyzing the involvement of 3-tangle and other entanglement measures under weak two-outcome measurement, we derive explicit upper and lower bound on the transformation probability between GHZ class states. After that, we also analyze the transformation between N-party W type states, which is a special class of multipartite entangled states that has an explicit unique expression and a set of analytical entanglement monotones. We present a necessary and sufficient condition for a known upper bound of transformation probability between two N-party W type states to be achieved. We also further investigate a novel entanglement transformation protocol, the random distillation, which transforms multipartite entanglement into bipartite entanglement ii shared by a non-deterministic pair of parties. We find upper bounds for the random distillation protocol for general N-party W type states and find the condition for the upper bounds to be achieved. What is surprising is that the upper bounds correspond to entanglement monotones that can be increased by Separable Operators (SEP), which gives the first set of analytical entanglement monotones that can be increased by SEP. Finally, we investigate the idea of a new class of multipartite entangled states, the Absolutely Maximal Entangled (AME) states, which is characterized by the fact that any bipartition of the states would give a maximal entangled state between the two sets. The relationship between AME states and Quantum secret sharing (QSS) protocols is exhibited and the application of AME states in novel quantum communication protocols is also explored.
Three Essays in Urban Economics
Keywords: urban density
transportation

This thesis studies the benefits and costs of urban living. Chapter 1 is a theoretical and empirical analysis of the benefits of urban density for consumers, while Chapter 2 proposes a model of how cities enhance the incentives for knowledge diffusion. Chapter 3 investigates the costs of congestion and the determinants of car travel speed across US cities. In Chapter 1, I study the consumption value of urban density by combining Google’s local business data with microgeographic travel data. I show that increased density enables consumers to both realize welfare gains from variety and save time through shorter trips. I estimate the gains from density in the restaurant industry, identifying willingness to pay for access to a slightly preferred location from the extra travel costs incurred to reach it. The results reveal large but very localized gains from density. Increasing the density of destinations generates little reduction in trip times, so most of these gains from density are gains from variety, not savings on travel time. In Chapter 2, I propose a new micro-foundation for knowledge spillovers. I model a city in which uncompensated knowledge transfers to entrepreneurs are bids by experts in auctions for jobs. The model derives from the key ideas about how knowledge differs from other inputs of production, namely that knowledge must be possessed for its value to be assessed, and that knowledge is freely reproducible. Agglomeration economies result from growth in the number of meetings between experts and entrepreneurs, and from heightened competition for jobs among experts. In Chapter 3, written jointly with Gilles Duranton and Matt Turner, we investigate the determinants of driving speed in large US cities. We first estimate city level supply functions for travel in an econometric framework where both the supply and demand for travel are explicit. These estimations allow us to calculate a city level index of driving speed. Our investigation of the determinants of speed provides the foundations for a welfare analysis. This analysis suggests large gains in speed if slow cities can emulate fast cities, and sizable deadweight losses from congestion.
Investigating the Roles of Follicular Dendritic Cells and Activation-induced Deaminase in Germinal Centers
Keywords: Germinal Center
B cell

During a T-dependent immune response, activated B cells enter structures called germinal centers (GC) in the follicles of secondary lymphoid organs. GC B cells proliferate and undergo diversification of their Ig through somatic hypermutation and class-switch recombination. These Ig diversifications require the activity of the enzyme activation-induced deaminase (AID). Clonal selection within GCs selects GC B cells with the highest affinities for antigen to mature into plasma cells and memory B cells. GCs are underpinned by stromal cells called follicular dendritic cells (FDC). FDC functions include secretion of B cell chemokines and the retention of Ag complexes that allow GC B cells to test the affinity of their Ig. FDCs require constitutive signaling through lymphotoxin beta receptor (LTβR) from lymphotoxin alpha-beta (LTαβ) on the surface of B cells to maintain their functions. In these studies, I investigated the properties of GCs using two primary experimental models. First, I employed genetic and pharmacological ablation of LTβR signaling to investigate the expression of AID and the function of GCs in the absence of FDCs. I determined that FDCs are not required for GC formation or the expression of AID in lymph nodes, but that FDCs are crucial for affinity maturation. Second, I examined the competition between AID-/- and WT B cells in the GCs of mixed BM chimeras to investigate the role of affinity maturation during clonal selection. I found that AID increases GC B cell apoptosis, likely by inducing DNA damage, and that this is important in regulating GC size. I also found that AID-/- B cells accumulate at the centrocyte stage of the GC reaction and that this is due to a partial block in plasma cell maturation.
The Relationship between Dominance and Vocal Communication in the Male Ring-tailed Lemur (Lemur catta)
Keywords: vocalization rate
sexual selection
dominance
lemur

Sex-specific calls are used in male-male agonistic encounters and male-female courtship in many animal species. The ring-tailed lemur (Lemur catta) is a gregarious Malagasy strepsirhine with twenty-two distinct vocalizations for adults, including two male-specific vocalizations and an additional vocalization with male-specific functions: the howl, the squeal, and the purr. Proposed intra-sexual agonistic functions for these three vocalizations have never been empirically tested. This study&rsquo;s purpose was to investigate the functions of howling, squealing, and purring in the ring-tailed lemur, and to assess the relationships between the rates of these vocalizations and male dominance. From March to July 2010, I collected 600 hours of total data and 480 hours of focal data on male ring-tailed lemurs aged three and older at Beza Mahafaly Special Reserve, Madagascar. I observed each male continuously for 30 minutes at a time and noted behaviours including all vocalizations and all agonism using one&ndash;zero sampling at 2.5-min intervals. I calculated male dominance rank and vocalization rates from these data. My results indicated that male dominance rank is correlated with male purring rate and with squealing rate, but not with howling rate. Male purring rate increased during intra-sexual agonism and was associated with aggression in agonistic encounters. Squealing rate increased during male-male agonism and indicated both aggression and submission in male-male encounters. Howling rate increased during inter-group encounters and a greater number of males participated in multi-male howling choruses when non-group members were present. Purring and squealing are agonistic vocalizations and used in male-male agonism in the ring-tailed lemur, while howling is used in inter-group encounters.