VictorJuiz/thesis huggingface dataset:
The Challenge of Guinean Independence, 1958-1971
Keywords: Guinea
International relations
Africa
United States

Since the end of French colonial rule in Guinea, “independence” has held a central place in its political culture. Implying both dignity and self-determination for the sovereign people which possesses it, independence is a concept that has meaning only in relation to other nation-states and cultures. Yet the political elite that dominated Guinea’s First Republic constructed a new national culture around this concept. The Challenge of Guinean Independence, 1958-1971 examines Guinea’s assertion of its right to independence and the response of powerful Western players, especially the United States and France, as Guinea challenged their assumptions about the nature of African sovereignty. Considering the history of the international relations of a single African state that enjoyed limited international power and prestige challenges conventions in the historiography of both Africa and international relations. It illuminates and contextualizes expectations concerning the meaning of modernity, African sovereignty as a matter of international law, and the end of formal colonial rule coinciding with the tensions and competitions of the Cold War. The study demonstrates that the international context played a crucial role, both in conditioning the timing and form of decolonization and in shaping the international community’s adaptation of colonial patterns of economic and political interaction to the new reality of African nation-states. Focusing on the invention, development and reception of one country’s insistence on independence in turn illuminates significant issues and events: the end of French colonial rule; limitations on the sovereignty of non-European postcolonial states; the advent of neocolonialism and the failure of the nominally anti-colonial United States to oppose it; the ideological appeal of African unity as a means of safeguarding sovereignty and the compromises that its institutional form entailed; foreign aid and the notion that development for modernization could be stimulated from outside; and the implications of unlimited internal autonomy for a state’s people. Guinea’s independence ultimately challenged developing norms of Western economic and political interaction with new African states by complicating assumptions about the universality of Western notions of economic development, justice and morality.
The Effect of Insulin and Insulin Resistance on Glucagon-like Peptide-1 Secretion from the Intestinal L Cell
Keywords: insulin
diabetes
insulin resistance
glucagon-like peptide-1
actin cytoskeleton
intestine

Glucagon-like peptide-1 (GLP-1) is secreted from the enteroendocrine L cell following nutrient ingestion. Although GLP-1 regulates several aspects of nutrient homeostasis, one important function is to enhance glucose-dependent insulin secretion. In type 2 diabetes, post-prandial GLP-1 secretion is impaired. Insulin resistance, which is required for the pathogenesis of type 2 diabetes, is also associated with impaired GLP-1 secretion. I, therefore, hypothesized that insulin modulates GLP-1 secretion from the intestinal L cell and, furthermore, insulin resistance directly impairs the function of the endocrine L cell. In well-characterized L cell models, I established that insulin stimulates GLP-1 secretion through the MEK1/2-ERK1/2 pathway, and induction of insulin resistance in vitro attenuated insulin- and heterologous secretagogue-induced GLP-1 release. Furthermore, glucose-stimulated GLP-1 secretion was decreased in hyperinsulinemic-insulin resistant MKR mice, demonstrating that insulin resistance is associated with impaired L cell function. I next examined the role of the actin cytoskeleton in insulin-stimulated GLP-1 secretion. Insulin treatment transiently induced actin depolymerization, and depolymerization of the actin cytoskeleton potentiated insulin-stimulated GLP-1 release from the L cell, demonstrating that the cytoskeleton functions as a permissive barrier. Central to insulin’s effects on actin dynamics is the Rho GTPase, Cdc42, as siRNA-mediated knockdown and over-expression of a dominant-negative mutant, prevented insulin-stimulated actin remodeling and GLP-1 release. Insulin also promoted activation of PAK1, the downstream kinase of Cdc42, and over-expression of a kinase-dead PAK1 mutant attenuated insulin-stimulated GLP-1 release. In cells that expressed dominant-negative Cdc42 or kinase-dead PAK1, activation of ERK1/2 following insulin treatment was attenuated, demonstrating that the Cdc42-PAK1 axis regulates the activity of the canonical ERK1/2 pathway. In summary, this thesis demonstrates, for the first time, that insulin is a GLP-1 secretagogue, and this effect of insulin is mediated through the canonical ERK1/2 pathway and the Cdc42-PAK1 axis. Insulin resistance in the L cell impairs the responsiveness of the L cell to heterologous secretagogues. Collectively, these findings suggest that an alternative approach to treat type 2 diabetes and/or insulin resistance may be to directly improve the function of the L cell, thereby enhancing endogenous GLP-1 release.
Mechanisms of Cell Nucleation, Growth, and Coarsening in Plastic Foaming: Theory, Simulation, and Experiment
Keywords: Plastic Foaming
Cell Nucleation
Cell Growth
Cell Coarsening
Computer Simulation
Foaming Mechanisms
Cellular Structure

This thesis highlights a comprehensive research for the cell nucleation, growth and coarsening mechanisms during plastic foaming processes. Enforced environmental regulations have forced the plastic foam industry to adopt alternative blowing agents (e.g., carbon dioxide, nitrogen, argon and helium). Nevertheless, the low solubilities and high diffusivities of these viable alternatives have made the production of foamed plastics to be non-trivial. Since the controls of the cell nucleation, growth and coarsening phenomena, and ultimately the cellular morphology, involve delicate thermodynamic, kinetic, and rheological mechanisms, the production of plastics foams with customized cell morphology have been challenging. In light of this, the aforementioned phenomena were investigated through a series of theoretical studies, computer simulations, and experimental investigations. Firstly, the effects of processing conditions on the cell nucleation phenomena were studied through the in-situ visualization of various batch foaming experiments. Most importantly, these investigations have led to the identification of a new heterogeneous nucleation mechanism to explain the inorganic fillers-enhanced nucleation dynamics. Secondly, a simulation scheme to precisely simulate the bubble growth behaviors, a modified heterogeneous nucleation theory to estimate the cell nucleation rate, and an integrated model to simultaneously simulate cell nucleation and growth processes were developed. Consequently, through the simulations of the cell nucleation, growth, and coarsening dynamics, this research has advanced the understanding of the underlying sciences that govern these different physical phenomena during plastic foaming. Furthermore, the impacts of various commonly adopted approximations or assumptions were studied. The end results have provided useful guidelines to conduct computer simulation on plastic foaming processes. Finally, an experimental research on foaming with blowing agent blends served as a case example to demonstrate how the elucidation of the mechanisms of various foaming phenomena would aid in the development of novel processing strategies to enhance the control of cellular structures in plastic foams.
Viral Mineralization and Geochemical Interactions
Keywords: microbial geochemistry
viral ecology
bacteriophage
biomineralization
extreme environments
geomicrobiology

Viruses are ubiquitous biological entities whose importance and role in aquatic habits is beginning to take form. However, several habitats have undergone limited to no examination with viral-geochemical parameters minimally examined and viral-mineral relationships in the natural environment and the role of mineralization on viral-host dynamic completely lacking. To further develop knowledge on the presence and abundances of viruses, how viruses impact aquatic systems, and how viral-host interactions can be impacted under mineralizing conditions, viruses were examined under a variety of habitats and experimental conditions. Water samples were collected from the deep subsurface (up to 450 m underground) and acid mine drainage (AMD) systems in order to determine the presence, abundance, and viral-geochemical relationships within the systems. Samples were also collected from a variety of freshwater habitats, which have undergone limited examination, to determine viral-geochemical and viral-mineral relationships. Lastly, bacteriophage-host dynamics were examined under authigenic mineral precipitation to determine how mineralization impacts this relationship. Results reveal that not only are viruses present in the deep subsurface and AMD systems, but they are abundant (up to 107 virus-like particles/mL) and morphogically diverse. Viruses are also the strongest predictor of prokaryotic abundance in southern Ontario freshwater systems where potential nutrients are rich. Geochemical variables, such as pH and Eh, were shown to have negative impacts of viral abundance indicting that AMD environments are detrimental for free viruses (i.e. not particle associated). Direct evidence of viral-mineral interactions was found using transmission electron microscopy as viral particles were shown attached to iron-bearing mineral phases (determined through elemental analysis). In addition, evidence of viral participation in mineralization events was found in both AMD and freshwater environments where inverse correlations were noted between viral abundance and jarosite saturation indices (r = -0.71 and r = -0.33, respectively), and goethite saturation indices were also noted to be the strongest predictor of VLP abundance in freshwater habitats explaining 78% of the variability in the data. Lastly, iron precipitation and/or metal ion binding to bacterial surfaces greatly reduced phage replication (~98%) revealing bacterial mineralization has a protective benefit strongly hindering viral replication.
Sequential Agroforestry systems for Improving Fuelwood Ssupply and Crop Yield in Semi-arid Tanzania
Keywords: Acacia
Improved fallows
Litter quality
Manure
Nutrient use efficiency
Soil fertility
Sustainability
Vector analysis

Promotion of agroforestry practices in sub-Sahara Africa may help sustain subsistent food and wood production by integrating trees and crops on farmlands to replenish soil fertility and improve crop yield. Using rotational woodlot and pigeonpea intercropping systems in semi-arid Tanzania as case studies, my research screened suitable tree species to increase fuelwood supply and examined mechanisms for reducing tree-crop competition. By adopting nutrient use efficiency (the ratio of biomass yield to nutrient uptake) as a criterion, I found that selecting tree species of low wood nutrient concentrations would minimize nutrient exports by 42 – 60 %, thus reducing soil nutrient depletion while concurrently sustaining local fuelwood supply harvested from rotational woodlots. Currently smallholder farmers cannot afford to replenish soil fertility because of high fertilizer costs. However, 5-year tree fallowing raised soil N and P levels for maize culture as high as those from recommended fertilizer applications. Post-fallow maize yield was also increased significantly over natural fallow practices. Apparently there is a trade-off between yields of maize and fuelwood under rotational woodlot culture providing farmers the choice to proportion tree and crop composition based on priority demands. An alternative practice of intercropping pigeonpea with maize may also rapidly replenish soil fertility as well as enhance maize yield when competitive interactions between trees and crops are controlled. Vector analysis revealed that such interactions suppressed biomass yields of maize and pigeonpea by 30 % and 60 %, respectively, due to limited soil nutrients and/or moisture. Optimizing yields of both crops would require prescribed fertilizer addition when intercropped, but dose rates can be lowered by half under the improved fallow system due to alleviating interspecific competition. My findings form the basis of a plea for greater use of rotational woodlot and pigeonpea intercropping systems in semi-arid areas. I conclude that smallholder farm management of rotational agroforestry systems can be significantly improved by refining tree selection criteria and mitigating nutrient competition between trees and crops to maintain food and fuelwood production.
Mechanistic Investigation of Penicillamine-induced Autoimmunity: Covalent Binding of Penicillamine to Macrophages, Involvement of Th17 cells, and Its Relation to Idiosyncratic Drug-induced Liver Injury
Keywords: idiosyncratic
macrophages
aldehyde
penicillamine
liver injury
Th17

The mechanisms of idiosyncratic drug reactions (IDRs) are unknown; however, most appear to be immune-mediated. Their idiosyncratic nature and the paucity of animal models make mechanistic studies very difficult. One of the few animal models is penicillamine-induced autoimmunity in Brown Norway rats. The major focus of this thesis was the use of this model to study the interaction between penicillamine and macrophages, the involvement of Th17 cells, and extension of this model to idiosyncratic drug-induced liver injury. One of the costimulatory signals leading to T cell activation appears to be reversible Schiff-base formation between an amine on T cells and an aldehyde on macrophages. We hypothesized that penicillamine binds to these aldehydes leading to macrophage activation and autoimmunity. By using biotinylated aldehyde-reactive agents such as ARP, we demonstrated the existence of aldehydes on the surface of macrophages. We synthesized biotinylated-penicillamine and it also binds to macrophages. Several proteins to which ARP binds were identified providing clues to the signal transduction pathways leading to macrophage activation. Biological consequences of this binding were investigated with a microarray study. ARP binding was also observed in the macrophage cell line, RAW264.7, and incubation with penicillamine stimulated the production of TNF-α, IL-6, and IL-23. Hydralazine and isoniazid, which are known to cause a lupus-like syndrome in humans and irreversibly bind to aldehyde groups, were also found to activate RAW264.7 cells. Th17 cells are prominent in autoimmune syndromes and Th17-associated cytokines such as IL-17 were elevated in the penicillamine-treated animals that developed autoimmunity. We have hypothesized that some drug-induced liver injury has an autoimmune component. A pilot study quantified serum concentrations of 26 cytokines/chemokines in patients with various forms of acute liver failure (ALF): idiosyncratic drug-induced ALF, acetaminophen-induced ALF, and viral hepatitis. IL-17 was elevated in 60% of patients with idiosyncratic drug-induced ALF, which supports an autoimmune component in these patients; however, it was also elevated in many cases of acetaminophen-induced ALF, presumably released by the innate immune system. These studies provide important insights into the mechanism of penicillamine-, hydralazine-, and isoniazid-induced autoimmunity and also provide clues to other IDRs that may have an autoimmune component.
Astrometry.net: Automatic Recognition and Calibration of Astronomical Images
Keywords: Astrometry
Computer vision
Astronomy

We present Astrometry.net, a system for automatically recognizing and astrometrically calibrating astronomical images, using the information in the image pixels alone. The system is based on the geometric hashing approach in computer vision: We use the geometric relationships between low-level features (stars and galaxies), which are relatively indistinctive, to create geometric features that are distinctive enough that we can recognize images that cover less than one-millionth of the area of the sky. The geometric features are used to generate rapidly hypotheses about the location---the pointing, scale, and rotation---of an image on the sky. Each hypothesis is then evaluated in a Bayesian decision theory framework in order to ensure that most correct hypotheses are accepted while false hypotheses are almost never accepted. The feature-matching process is accelerated by using a new fast and space-efficient kd-tree implementation. The Astrometry.net system is available via a web interface, and the software is released under an open-source license. It is being used by hundreds of individual astronomers and several large-scale projects, so we have at least partially achieved our goal of helping ``to organize, annotate and make searchable all the world's astronomical information.''
Plasticity and Gene by Environment Interactions in Complex Phenotypes of Adult Drosophila melanogaster
Keywords: behaviour genetics
systems biology

Behaviour genetics deals with complex phenotypes which respond flexibly to environments animals experience. Change of phenotype in response to environment is phenotypic plasticity. A central question is how genes influence plasticity. I study plasticity and gene by environment interactions (GEI) relating to behaviours, metabolic, and genomic phenotypes of adults of the fruit fly Drosophila melanogaster. Chapters 1-3 study cuticular hydrocarbon (CH) levels of male flies. Chapter 1 shows male CH levels respond to time of day and light. Methods are developed to reduce high variability of CH. I show variation in CH parallels activity of two classes of CH synthesis hormones. Analysis of rate of variation gives estimates of turnover rates of CH and the metabolic cost of signaling. Chapter 2 studies mixed groups of genetically different flies, “hosts” and “visitors”. GEI of CH are found with both abiotic factors and with social mix. Social mix results in GEI as strong as abiotic factors. Indirect Genetic Effects (IGE) theory is used to show frequency-dependent IGE interactions. Chapter 3 shows that males in mixed social environments reduce expression of clock and CH synthesis genes, resulting in different signals. Females mate more often with males in a mixed group than with single-genotype males. Plasticity in male gene expression in response to social environment leads to different signals, mating levels, and potentially different fitness. Chapter 4 deals with behaviour, metabolite, and genomic phenotypes in flies differing in foraging gene alleles, as the food environment is changed. Strong GEI is found, structured by food type, chemical class of metabolite, and gene metabolic roles. A concept called “relative nutrient sensitivity” suggests an interaction between foraging and the insulin signaling pathway. I demonstrate epistasis between for and insulin with quantitative genetic methods and bioinformatics. These results lead to the conclusion that GEI are common in many fly phenotypes in response to well studied environments such as food and less studied ones such as social group. Some implications of this for maintenance of genetic variance are discussed.
Interacting Disturbances in the Boreal Forest and the Importance of Spatial Legacies at Multiple Scales
Keywords: landscape ecology
wavelet analysis
forest disturbance
spruce budworm

Forest disturbances and the spatial patterns they create affect ecosystem processes through their influence on forest vegetation from individual trees to landscapes. In the boreal and mixed-wood forests of eastern Canada the main agents of disturbance are logging, fire, and defoliation by the spruce budworm (SBW, Choristoneura fumiferana). These disturbances are similar in that they remove forest biomass and influence forest succession but also distinct in that logging creates patterns that are different than those created by natural disturbances. All disturbances are indirectly linked to each other through their mutual effects on forest spatial structure and succession. Through such feedbacks, spatial disturbance legacies can facilitate or constrain further disturbances, including forest management. Surprisingly, the long term spatial consequences of interactions among multiple natural and anthropogenic disturbances remain largely unexplored. This thesis investigates how, and at what spatial scale, legacies in forest composition and age structure influence natural disturbance dynamics, and how natural disturbances constrain forest management. I address four specific questions: (i) For how long do spatial legacies of different forest management strategies persist on the landscape? (ii) How do interactions among logging, fire, SBW, and succession affect timber availability and long term forest patterns in age and composition? (iii) How do these patterns differ from those created by each disturbance individually? And, (iv) How can management be used to reduce the extent and severity of fires and SBW defoliation through the manipulation of forest structure? The key scientific innovations of this thesis are: (i) Characterization of the duration and influence of spatial legacies on forest disturbances and sustainability; (ii) Development of a dynamic spatial forest simulation model that includes distinct successional rules that respond to different types of disturbance and shifts in disturbance regimes; and, (iii) Development and application of a wavelet-based significance testing framework to identify key scales of expression in forest spatial patterns. These innovations provide a scientific basis for landscape level forest management strategies designed to reduce the long term impacts of defoliating insects and to meet multiple objectives.
Phagosome Maturation: Aging with pH, Lysosome-associated membrane proteins, and Cholesterol; while staying young with Burkholderia cenocepacia
Keywords: phagocytosis
phagosome maturation
lysosome
cholesterol
acidification

Phagocytosis is an innate immune response that is paramount in the clearance of pathogenic particles. Recognition of target particles by phagocytic receptors expressed on phagocytes induces modifications in the underlying actin cytoskeleton to form pseudopods that encircle and internalize the target particle into a membrane bound organelle called the phagosome. The nascent phagosome undergoes a maturation sequence that is characterized by substantial remodeling of the membrane and its luminal contents through interactions with components of the endocytic pathway, culminating in an acidic and hydrolytic organelle capable of digesting and elminating pathogens. Phagosome maturation is a complicated pathway that involves many protein and lipid signaling molecules. Several factors that influence phagosome maturation particularly the participation of pH, lysosome-associated membrane proteins-1 and –2, cholesterol, in addition to the survival and escape mechanisms used by, Burkholderica cenocepacia were explored. All three tenets are essential for phagosome maturation, although each factor has different mechanistic consequences. Acidification alters Rab5 activation, while ablation of LAMPs and accumulation of cholesterol interferes with various aspects of Rab 7 turnover in phagosomes and/or endosome membranes. Moreover, Burkholderia cenocepacia, an intracellular pathogen, inactivates Rab7 on phagosome membranes from within the vacuole lumen. Herein, mechanisms that govern phagosome maturation are explored and several molecules are added to the long list of essential players in this complicated pathway.