VictorJuiz/thesis huggingface dataset:
A Study of the Composition of Carryover Particles in Kraft Recovery Boilers

Carryover particles are partially/completely burned black liquor particles entrained in the flue gas in kraft recovery boilers. Understanding how carryover particles form and deposit on heat transfer tube surfaces is critically important in the design and operation of a recovery boiler. The tendency for a carryover particle to deposit on a tube surface depends on the particle temperature and composition at the moment of impact. This study was the first to examine systematically how carryover particle composition changes with the black liquor chemistry and burning conditions. The effect of black liquor composition and particle size, gas composition (O2 and SO2 concentrations) and temperature on the composition of carryover particles were studied using an Entrained Flow Reactor (EFR). Field studies were conducted on three operating boilers, where an air-cooled probe was used to collect carryover samples at the superheater entrance. The results show that the chloride (Cl) and potassium (K) contents in carryover particles were linearly proportional to their contents in black liquor. Cl and K were depleted during black liquor combustion due mainly to the vaporization of NaCl and KCl. The depletion of Cl is about three times greater than that of K. The significant depletion of Cl implies that carryover particles contain much less Cl, and hence, are less sticky than previously expected from black liquor composition. A dynamic model was also developed to predict the composition of carryover particles as a function of black liquor composition and burning conditions. Based on the data obtained experimentally in this study, the kinetic equations for the oxidation of sulphide available in the literature were modified and incorporated into the model to improve its sulphide and sulphate predictions. The model predicts the main components of carryover particles formed in both the EFR and three operating recovery boilers reasonably well, except for the K content, which is slightly over-predicted at high O2 concentrations (or high particle temperatures). Based on the predicted composition, it is possible to determine the thermal properties of carryover and to assess its fouling propensity in the boiler. The information helps boiler manufacturers and operators to identify locations in the boiler where massive carryover deposition may occur and to devise appropriate control strategies to minimize fouling and to improve boiler thermal efficiency.

Keywords: Carryover
Composition
Black Liquor
Recovery Boiler
Advisor: Kuhn, David
Tran, Honghi
Integration of Micro and Nanotechnologies for Multiplexed High-Throughput Infectious Disease Detection

This thesis presents the development and optimization of a high-throughput fluorescence microbead based approach for multiplexed, large scale medical diagnostics of biological fluids. Specifically, different sizes of semiconductor nanocrystals, called quantum dots, are infused into polystyrene microspheres, yielding a set of spectrally unique optical barcodes. The surface of these barcodes are then used for sandwich assays with target molecules and fluorophore-conjugated detection antibodies, changing the optical spectra of beads that have associated with (or captured) biomolecular targets. These assayed microbeads are analyzed at a single bead level in a high-throughput manner using an electrokinetic microfluidic system and laser induced fluorescence. Optical signals collected by solid state photodetectors are then processed using novel signal processing algorithms. This document will discuss developments made in each area of the platform as well as optimization of the platform for improved future performance.

Keywords: Nanotechnology
Infectious Disease Diagnostics
Microfluidics
Multiplexed Detection
Advisor: Chan, Warren C. W.
Design and Characterization of Novel Nanomaterials for Cancer Imaging and Therapy

The emergence of bionanotechnology has allowed the design of novel technological tools for a variety of biomedical applications. Despite the incompatibility of native semiconductor quantum dots with biological environment, this class of nanocrystals was among the first nanomaterials to demonstrate their use in biological labeling and imaging applications. In this thesis, new surface modification chemistry and synthetic strategies were developed to produce high quality biocompatible and bioconjugatable near-infrared emitting quantum dots for deep tissue in vivo imaging and detection applications. By carefully selecting a specific mixture of semiconductor elements to obtain a desired bandgap energy and optimizing the procedure for surface coating, successful synthesis of high quality, watersoluble, near-infrared emitting quantum dots were demonstrated. These developments allows for the use of quantum dots as alternative contrast agents for sophisticated biological imaging applications that are currently unachievable using conventional uorophores. In addition, using metallic nanoparticles, it was found that cells possess the ability to differentiate nanoparticles of various sizes upon their binding with specific membrane receptors. These receptors undergo rapid cellular internalization which altered their trafficking dynamics and down-stream signaling processes. The amplitude of such alteration was highly dependent on the size of the nanoparticle with most efficient internalization occurring at 40 nm - 50 nm size range. These observations raise important questions regarding the mechanisms governing similar processes and cell behaviours documented during viral infections. Whether such biological phenomenon are evolutionarily conserved as natural defense mechanisms to counter foreign invasion, or whether many of the known viruses are naturally selected to breach the primary defense of cells - the plasma membrane, remains to be elucidated. In summary, nanotechnology offers great promises for biological research and medicine. This thesis demonstrates the use of semiconductor and metallic nanostructures for imaging, detecting and administrating therapeutics in cancerous cells, tissues and animal models. Although the results presented in this thesis are preliminary, and the technologies demonstrated are still years away from practical use, these studies nevertheless, pave the way for future experimental researches within the field of nanomedicine, and provide insights into the understanding of the most fundamental yet highly complex processes in cell biology.

Keywords: Biomedical Engineering
Bionanotechnology
Advisor: Chan, Warren C. W.
High throughput Detection of Molecular Targets in Cancer Using Nanoparticles: Application in Diagnostics

In light of cancer as a multi-parameter disease, technological advancements are being developed to obtain automated and high throughput assessment of molecular targets in diagnostics, with the aim to reduce subjective analytical assessment of tumours and/or to integrate molecular data obtained from different tests on given tumour samples. Towards this goal, a multi-disciplinary approach is presented in this dissertation using nanotechnology. First, by combining quantum dot (QD) nanocrystals, tissue microarray, optical spectroscopy, and algorithm design, an automated and high throughput quantitative approach in the assessment of biomarker surrogates in neoplastic tissue is introduced. The validation study was performed using epidermal growth factor (EGFR) in 8 formalin-fixed paraffin-embedded (FFPE) xenografts of lung adenocarcinoma (r2=0.9) (chapter 2). Furthermore, in chapter 3 a novel design of QD-based fluorescent probes, nanobeads, was presented by encapsulation of QDs in polystyrene in an emulsion polymerization reaction. Nanobeads exhibited resistance to fluorescent quenchers such as solutions of extreme pH and colorimetric dyes of hematoxylin & eosin (H&E) and Giemsa, key standard dyes used in cancer diagnostic. Comparative studies with organic dye, phycoerythrin (PE), and QDs demonstrated significant (P<0.001) fluorescent quenching in H&E and Giemsa using Kruskal Wallis test. The design allowed a simultaneous consolidation of fluorescent immunoassaying, using nanobeads, and morphologic and parametric visualization of cellular features, using colorimetric stains, in a given biopsy. Sten-volmer analysis demonstrated a reduction of fluorescence resonance energy transfer among nanobead610nm and nanobead560nm. The application of the QD-based methods bears potential significance in cancer diagnosis and in tumor management, especially human core biopsies of limited quantity. In chapter 4, cellular endocytosis of gold particles was shown to be size dependence, with gold particles of 50 nm demonstrating the highest uptake. The cellular response subsequent to gold uptake was assessed using 10k cDNA microarrays. Significant analysis of microarray (SAM) showed the gene expression of treated and non-treated particles to be 99.65% similar. The remaining 35 genes however, demonstrated down regulation of apoptosis, cell proliferation and cell adhesion responses in treated cells. While promising, future research and development are required to adopt nanoparticles in diagnostics.

Advisor: Chan, Warren C. W.
Constitutive versus Regulated Traffic of GLUT4

Glucose transporter GLUT4 allows glucose uptake into muscle and adipose cells. Insulin promotes recruitment and plasma membrane insertion of GLUT4 vesicles that can recycle constitutively. Obesity and type 2 diabetes mellitus are associated with defects in insulin-induced GLUT4 recruitment. Knowledge of alternative modes and steps of GLUT4 traffic in L6-GLUT4myc muscle cells may reveal possible targets for therapeutic intervention in insulin-resistant patients. Hypertonicity and Platelet Derived Growth Factor also increase surface GLUT4 levels but it was unknown if they tap on the same intracellular GLUT4 depots as insulin. We explored whether GLUT4 vesicles recycle using different compartments and mechanisms for the surface gain elicited by each stimulus. We hypothesized that all vesicle fusion steps require NSF but depend on individual v-SNAREs. Specifically, we tested effects of ATPase-deficient NSF or VAMP7 siRNA transfections, and endosomal ablation on GLUT4 traffic. We show that VAMP7 was required for basal and hypertonic recycling, while VAMP2 is exclusively used in response to insulin. As insulin action bifurcates downstream of phosphatidylinositol 3-kinase, we also hypothesized that the Rac-to-actin and Akt-to-AS160 branches regulate distinct GLUT4 traffic steps. For this we determined GLUT4myc localization in rounded myoblasts relative to a surface marker. Interfering with Rac, actin dynamics or actin-binding α-actinin4 maintained GLUT4 in a perinuclear region even under insulin-stimulation. Interfering with AS160 allowed significant GLUT4 accumulation beneath the membrane, but not fusion. We propose that actin dynamics and α-actinin4 are required for cortical GLUT4 tethering mechanisms, and AS160 contributes to GLUT4 docking/fusion. We confirmed that VAMP2 facilitates GLUT4 fusion, as tetanus toxin-based cleavage did not inhibit peripheral GLUT4 recruitment. Finally, AS160 targets Rab8A and Rab14 in muscle respectively affected GLUT4 availability for membrane fusion, and basal GLUT4 retention. This work will lead to future testing of strategies to selectively enhance vesicle availability, tethering, or surface fusion, for bypassing insulin resistance.

Keywords: Type 2 Diabetes Mellitus
GLUT4 Glucose Transporter Traffic in Muscle
Advisor: Klip, Amira
Translational Regulation in the Early Drosophila Embryo

Translational regulation is an important mechanism for regulating gene expression. Regulation of specific transcripts is often mediated by elements present in the 3′ untranslated region (UTR) of the mRNA. In the Drosophila embryo, translational repression of nanos mRNA is mediated by Smaug protein bound to specific sequences present in the 3′ UTR of the mRNA. Here I show that Smaug recruits Cup protein to the mRNA and that Cup in turn binds to the translation initiation factor eIF4E that is present at the 5′. The interaction between Cup and eIF4E prevents formation of a productive translation initiation complex on the mRNA. Therefore, Smaug-dependent translational repression functions at the initiation step via the indirect interaction of Smaug with eIF4E, which is mediated by Cup. In the second example of translational regulation presented here, I show that an element present in the 3′ untranslated region of the Hsp83 mRNA mediates translational enhancement in the Drosophila embryo. I have identified three proteins, Hrp48, DDP1 and PABP that interact with this element and have demonstrated that Hrp48 and DDP1 function in translational enhancement.

Keywords: Drosophila
Translational regulation
RNA
Advisor: Smibert, Craig
Regulation of GLUT4 Intrinsic Activity and Internalization in L6 Muscle Cells

GLUT4 is the principal insulin-responsive glucose transporter in skeletal muscle. Insulin stimulation leads to exocytosis of intracellular GLUT4-containing vesicles to the cell surface, thereby increasing glucose uptake. Muscle contraction also elevates cell surface GLUT4 by a less understood mechanism. Once at the cell surface, GLUT4 may be subject to additional regulation, such as by modulation of its internalization rate or its intrinsic activity. The objective of this thesis was to identify the mechanism of GLUT4 internalization in muscle cells and to determine whether it is regulated by insulin treatment or by the signals elicited by muscle contraction. Skeletal muscle cells in culture stably expressing myc-tagged GLUT4 were used. We found that GLUT4 internalizes simultaneously through a clathrin-dependent and a clathrin- and caveolae-independent and cholesterol- and dynamin-dependent pathway. Insulin did not regulate GLUT4 internalization. In contrast, mitochondrial uncoupling, which may mimic the heightened energy demand that occurs during muscle contraction, retarded GLUT4 internalization by inhibiting the clathrin-independent route. Activation of both AMP-dependent kinase (AMPK) and protein kinase C (PKC) was necessary and sufficient for this response. We further hypothesized that the intrinsic activity of GLUT4 may be regulated under some conditions, based on a discrepancy between the amount of cell surface transporters and the rate of glucose uptake. In particular, inhibitors of p38 mitogen-activated protein kinase (p38MAPK) lowered insulin-dependent glucose uptake without reducing the number of GLUT4 units at the surface. We found that p38MAPK is activated by insulin through TAB1-dependent autophosphorylation, yet p38MAPK was dispensable for insulin-stimulated glucose uptake. Mechanisms other than p38MAPK must be involved in the regulation of GLUT4 intrinsic activity. In conclusion, in addition to its exocytosis, the activity and endocytosis of GLUT4 are regulated by stimuli that increase the rate of glucose uptake into muscle.

Keywords: insulin
GLUT4
muscle contraction
glucose
muscle
diabetes
membrane traffic
endocytosis
Advisor: Klip, Amira
A Bioarchaeological Study of Mid-Holocene Communities in the Eastern Cape, South Africa: the Interface between Foraging and Pastoralism

The late Holocene marks a period of significant population movement and subsistence change throughout much of sub-Saharan Africa. Around 3500 BP it appears that foraging populations in southernmost South Africa began to experience stress related to an increasing population and changing climatic conditions. Approximately 1500 years later a new form of subsistence - sheep herding – emerged in areas previously occupied solely by foragers, but was not exclusively adopted. The mechanisms surrounding the introduction of this new subsistence strategy – an indigenous adoption via diffusion or a foreign migration - remain unresolved. This study takes a biological approach to this significant question in southern African prehistory by exploring a collection of Later Stone Age skeletal remains that predate and postdate the appearance of pastoralism in order to determine if any significant changes in skeletal morphology indicative of population discontinuity can be identified at 2000 BP. A collection of seventy-three Later Stone Age adult skeletons (31 M, 42 F) with newly generated radiocarbon dates ranging from 8000 BP to 300 BP (uncalibrated) from the Eastern Cape Province of South Africa forms the basis of this study. Questions surrounding population continuity or discontinuity associated with the advent of sheep herding are investigated by examining metric variables collected from the cranium, post cranial skeleton and dentition, in conjunction with cranial discrete traits. Some changes in skeletal morphology are observed, but the timing, pattern and magnitude of these changes are not consistent with a foreign migration. A reduction in overall skeletal size in the absence of changes in shape corresponds with the period of forager intensification. Body size rebounds at around 2000 BP when evidence for a new form subsistence, sheep herding, is first observed in this region, suggesting that some foragers may have adopted sheep and the herding way of life as a stress relieving mechanism, while others maintained the foraging lifestyle. The timing of the observed changes in skeletal size, the absence of shape changes and the homogeneity in cranial discrete trait frequencies through time argues against the idea that sheep herding was introduced to the Cape region by outsiders. Rather, the findings of the current study suggest sheep herding was an indigenous development among existing foragers.

Keywords: bioarchaeology
South Africa
Later Stone Age
foraging
pastoralism
Advisor: Pfeiffer, Susan
Understanding Community: A Comparison of Three Late Neolithic Pottery Assemblages from Wadi Ziqlab, Jordan

This study presents the results of an analysis of three Late Neolithic pottery assemblages from Wadi Ziqlab, northern Jordan. These sites were occupied during the 6th millennium BC (calibrated) and are therefore contemporary with sites in other parts of the southern Levant that are attributed to the Wadi Rabah culture. The assemblages are analyzed from a stylistic perspective, broadly defined, which includes an examination of technological style in addition to a more traditional examination of vessel form and surface treatment. Different stages in the pottery production sequence are investigated using a range of analytical techniques, including thin-section petrography and xeroradiography. While there are some similarities between the assemblages, there are also some noticeable differences. The results of the pottery analysis are used to explore the nature of community in the context of the Late Neolithic. A critique of more traditional archaeological approaches to prehistoric communities leads to a re-conceptualization of community that combines interactional and ideational perspectives. Similarities in pottery among the sites, especially technological similarities, suggest that pottery producers may have comprised a dispersed community of practice. At the same time, pottery may have also been a symbolic marker of community boundaries. Differences in pottery among the sites, including surface treatment, may reflect the flexibility of these boundaries as different parts of the dispersed community negotiated their place in it. The presence of variation among contemporary pottery assemblages in a localized area suggests that social organization during the 6th millennium may have been more complex than is normally assumed for the Late Neolithic in the southern Levant. A dispersed community, with its members spread throughout the wadi, would require a sufficiently complex and flexible system of relationships to maintain it. Failing to acknowledge this has contributed to the difficulties archaeologists have encountered when trying to understand the culture-history of the 6th millennium BC in and east of the Jordan Valley.

Keywords: archaeology
Late Neolithic
Near East
pottery
community
technology
Wadi Ziqlab
Jordan
Advisor: Banning, E. B.
Spatially Explicit Modeling of Hydrologically Controlled Carbon Cycles in a Boreal Ecosystem

Current estimates of terrestrial carbon (C) fluxes overlook explicit hydrological controls. In this research project, a spatially explicit hydro-ecological model, BEPS-TerrainLab V2.0 was further developed to improve our understanding of the non-linearities associated with various hydro-ecological processes. A modeling study was conducted in a humid boreal ecosystem in north central Quebec, Canada. The sizes and nature of various ecosystem-C-pools were comprehensively reconstructed under a climate change and disturbance scenario prior to simulation in order to ensure realistic biogeochemical modeling. Further, several ecosystem processes were simulated and validated using field measurements for two years. A sensitivity analysis was also performed. After gaining confidence in the model’s ability to simulate various hydrologically controlled ecophysiological and biogeochemical processes and having understood that topographically driven sub-surface baseflow is the main process determining the soil moisture regime in humid boreal ecosystem, its influence on ecophysiological and biogeochemical processes were investigated. Three modeling scenarios were designed that represent strategies that are currently used in ecological models to represent hydrological controls. These scenarios were: 1) Explicit, where realistic lateral water routing was considered 2) Implicit, where calculations were based on a bucket-modeling approach 3) NoFlow, where the lateral sub-surface flow was turned off in the model. In general, the Implicit scenario overestimated GPP, ET and NEP, as opposed to the Explicit scenario. The NoFlow scenario underestimated GPP and ET but overestimated NEP. The key processes controlling the differences were due to the combined effects of variations in plant physiology, photosynthesis, heterotrophic respiration, autotrophic respiration and nitrogen mineralization; all of which occurred simultaneously in different directions, at different rates, affecting the spatio-temporal distribution of terrestrial C-sources or sinks (NEP). From these results it was clear that lateral water flow does play a significant role in the net terrestrial C distribution and it was discovered that non-explicit forms of hydrological representations underestimate the sizes of terrestrial C-sources rather than C-sinks. The scientific implication of this work demonstrates that regional or global scale terrestrial C estimates could have significant errors if proper hydrological constraints are not considered for modeling ecological processes due to large topographic variations of the Earth’s surface.

Keywords: hydrology
ecology
soil science
carbon cycle
eco-hydrology
modelling
Advisor: Chen, Jing Ming