VictorJuiz/thesis huggingface dataset:
Ptolemy’s Planetary Theory: An English Translation of Book One, Part A of the Planetary Hypotheses with Introduction and Commentary

This study comprises a translation and commentary of Book I of the Planetary Hypotheses by the second century A.D. Greco-Roman astronomer, Claudius Ptolemy. It closely examines the Planetary Hypotheses on its own and in relation to Ptolemy’s other writings. Where necessary I rely on astronomical, philosophical, and technological works by other writers in order to better situate Ptolemy’s ideas into the context of Greco-Roman science. The dissertation is organized into three sections. Section I consists of an extended introduction to the Planetary Hypotheses. I offer a synopsis of the Planetary Hypotheses and a history of the text in Sections I.1 and I.2. Section I.3 consists of a brief introduction to notation and sexagesimal numbers while Section I.4 analyzes the aim and function of Ptolemy’s planetary models. Section II is a translation of the existing Greek text of the Planetary Hypotheses, namely Book I Part A, and a précis of Book I, Part B. The translation is made from J.L. Heiberg’s edited Greek text and the précis relies on the English translation by Bernard Goldstein, the French translation by Regis Morelon, and the Arabic Manuscripts found in the British Library (Arabic-A) and the Library at the University of Leiden (Arabic-B). The footnotes include variant readings from the different Greek and Arabic Manuscripts. A list of all existing manuscripts of the Planetary Hypotheses can be found in Section I.2 Section III is a commentary of the entirety of Book I (Parts A and B). This section is arranged so that it loosely follows the order of topics found in the Planetary Hypotheses. Section III.1 examines the Planetary Hypotheses in terms of instrument-making. Section III.2 discusses the geometric models that Ptolemy presents along with a discussion of the changes that he makes. I give an overview of the period relations and mean motions presented in the Planetary Hypotheses in Section III.3 and III.4 and the new frame of reference in Section III.5. Section III.6 briefly examines Book II of the Planetary Hypotheses and Section III.7 addresses the relationship of Book I and Book II and contextualizes this work in the history of Greco-Roman science. Finally, Section III.8 examines the role the Planetary Hypotheses played in developments within Medieval Islamic astronomy. While I focus on the changes that Ptolemy made to the models in the Planetary Hypotheses from his theories in the Canobic Inscription, Handy Tables, and the Almagest, this work aims to explore the motivations behind these changes. Additionally, I contextualize the Planetary Hypotheses within Greco-Roman and Islamic astronomy and technology. What emerges from this dissertation is a consideration of Ptolemy’s ideas about the practice of science and an analysis of how he modeled astronomical observations.

Keywords: History of Science
Ptolemy
Ancient Science
Advisor: Jones, Alexander
Human Lung Progenitor Populations in End-stage Lung Disease and Transplantation.

Bone marrow-derived progenitor cell populations have been implicated in tissue regeneration and also in human disease pathology. This thesis investigated the hypothesis that Clara Cell Secretory Protein positive (CCSP+) epithelial-like progenitor cells and circulating fibrocyte numbers are altered in human lung disease and injury, and aimed to determine the predictive value of these cell profiles. It was found that cystic fibrosis patients have an increased number of CCSP+ cells in their bone marrow and peripheral blood, while patients with bronchiolitis obliterans syndrome (BOS) have a decreased number. In addition, BOS and pulmonary fibrosis patients have increased circulating fibrocytes. In response to ischemia reperfusion injury, an increase in CCSP+ cells in the peripheral blood was found at 24 hrs following lung transplant. Lastly, in patients studied greater than 1-year from transplant, those diagnosed with BOS had a higher number of fibrocytes and a loss of CCSP+ peripheral blood cells when compared to patients with stable lung function, with increased fibrocytes being associated with time post-transplant. In these patients, the ratio of fibrocytes-to-CCSP+ cells was predictive of lung function. Multiplex protein arrays were used to investigate corresponding patient plasma, aiming to elucidate key mediators of progenitor cell recruitment. While differences in various cytokines were found between end-stage diseases, a specific relationship between Stem Cell Growth Factor- and CCSP+ cells was identified and between Monocyte Chemotactic Protein-1 and fibrocytes. Conversely, response of CCSP+ cells following transplant appears to be mediated by known mobilizing factors SDF-1 and GM-CSF. Interestingly, in patients followed long-term after transplant, MCP-1 was associated with the number of CCSP+ cells, while SDF-1 correlated with fibrocyte numbers. These observations suggest common pathways acting on both populations that may be altered by the microenvironment, and may further suggest a common origin. This work contributes important information regarding changes in lung progenitor cells and their association with human disease and tissue repair, which could ultimately support future directions that directly advance therapy and improve patient care.

Keywords: lung transplant
progenitor cell
Advisor: Waddell, Thomas K.
Sessile Water Droplets: Equilibrium and Evaporation

The ζ-adsorption isotherm was used along with Gibbsian thermodynamics to determine an expression for the surface tension of solid-vapour interface. This expression was examined at low pressures to predict the surface tension of solids in the absence of adsorption, γS0. The method indicated the same value of γS0 for a solid using different vapour adsorption isotherms. A method based on the system stability was developed to predict the contact angle. The findings indicated that the contact angle is a thermodynamic property which depends on the state of the system. Furthermore, the dependence of contact angle on the curvature of three-phase contact line was described by the adsorption at the solid-liquid interface without the introduction of line tension. The energy transport mechanisms during steady-state evaporation of water-sessile droplets were studied. By suppressing the buoyancy-driven convection, the active modes of energy transport were thermal conduction and thermocapillary convection. The experiments on Cu, Au (111) and PDMS showed that the dominant mode of energy transport varies along the liquid-vapor interface. Near the droplet apex, thermal conduction provides enough energy for the evaporation. However, close to three-phase contact line where most of the evaporation occurs, thermocapillary convection is by far the dominant mode of energy transport. In the evaporation experiments on PDMS, the measured directions of thermocapillary convection were opposite of the predicted ones by other studies, since the energy carried by thermocapillary convection was neglected in the previous studies. The study was followed by examination of temperature boundary condition and energy transport at the solid-liquid interface. It was concluded that there is an adsorbed layer at the solid-liquid interface with different thermal properties compared to those of bulk liquid phase. This layer causes a resistance (Kapitsa resistance) and consequently a temperature discontinuity at the adsorbed layer-bulk liquid interface. Due to the high resistance at this interface, only a small portion of energy conducted by solid substrate enters directly to the bulk liquid phase. The remainder was transported through the adsorbed layer to the three-phase contact line. This energy was then distributed along the liquid-vapour interface by thermocapillary convection to be consumed by the evaporation process.

Keywords: Water Sessile Droplet
Evaporation
Advisor: Ward, Charles A.
Generation and Characterization of Induced Neural Progenitor Cell Lines

Large-scale expansion of lineage-committed stem cells can provide an excellent ex vivo model for studying complex molecular pathways governing cell fate choices. Also, such cells could be useful for implementing cell therapeutic approaches for treatment of specific disorders involving extensive cellular damage within that lineage. Using growth factors, pluri- and multipotent stem cells have been successfully isolated and cultured from pre- and peri-implantation stage embryos, including trophectoderm, primitive ectoderm, epiblast and primitive endoderm. However, ex vivo expansion of lineage restricted cells from later embryonic lineages and adult tissues have been a challenge. N-myc is a well-characterized member of myc gene family that is known to be essential for the proliferation of numerous progenitor cell types during normal embryonic development of diverse organs including lungs, liver, heart, kidneys and brain. Considering this important role of N-myc, we hypothesized that its regulated activation in these progenitors might allow their expansion in culture. To test this hypothesis, we generated a novel doxycycline-inducible transgenic mouse line that expresses N-myc uniformly across all tissues. Using cortical precursors derived from mid-gestation embryos of these mice, we show that upon doxycycline induced N-myc expression, we can achieve at least a million-fold expansion of multipotent neural precursors within a short span of time in culture. When doxycycline is withdrawn, N-myc expression is turned off and the cells differentiate into neurons and glia. An extensive characterization of the expanded cells revealed that the cells retained their differentiation potential, genomic stability and commitment specific to their origin. The tetracycline-inducible N-myc expressing mouse line might also serve as a source for establishing other than neural lineage committed progenitor cell lines where N-myc has a known role in regulating cell proliferation and differentiation decisions.

Keywords: Neural Progenitor Cells
Doxycycline Inducibile Expression
N-MYC
Regenerative Medicine
Advisor: Nagy, Andras
Biomarkers of Severe Malaria: Complement Activation and Dysregulated Angiogenesis in Placental Malaria and Cerebral Malaria

Biomarkers measured in the blood can provide information about disease pathophysiology, diagnosis and prognosis. Pronounced proinflammatory responses are characteristic of severe malaria, and excessive activation of the immune system is central to the pathophysiology of both cerebral malaria and placental malaria. Severe malaria is characterized by cytoadherence of parasitized erythrocytes to the microvasculature; impaired tissue perfusion; dysregulated inflammatory responses; and activation of the complement system, mononuclear cells, and endothelium. Despite the availability of effective antimalarial drugs, the mortality rate in severe malaria remains unacceptably high. To glean further insight into malaria pathophysiology, we investigated host biomarkers of immune activation in the blood of subjects with different manifestations of severe disease. C5 has been identified as being necessary and sufficient for the development of experimental cerebral malaria. We hypothesized that C5a (a terminal component of the complement cascade with potent inflammatory properties) may mediate its action by inducing and exacerbating inflammatory processes in severe malaria, leading to endothelial activation and dysregulated angiogenesis. I tested this hypothesis in vitro, and found that C5a interacted with malaria toxin PfGPI to drive deleterious inflammatory and anti-angiogenic responses. As C5a and anti-angiogenic factor sFlt-1 have been implicated in models of pathologic pregnancies, we asked whether increased levels of C5a in subjects with placental malaria were associated with altered angiogenesis and poor birth outcomes. Our results suggest that C5a impairs angiogenic remodelling in placental malaria leading to vascular insufficiency and fetal growth restriction. Further, altered profiles of inflammatory and angiogenic biomarkers in the periphery may identify occult placental malaria infections. We extended these observations to cerebral malaria where similar pathogenic pathways contribute to disease pathophysiology. In adults and children with cerebral malaria, altered profiles of angiogenic proteins were associated with disease severity and mortality and represent putative diagnostic and prognostic biomarkers in severe malaria.

Keywords: Malaria
Biomarker
Pregnancy
Complement
Angiogenesis
Advisor: Kain, Kevin C.
The Role of Concepts in Perception

The claim of my dissertation is that some basic concepts are required for perception. Non-basic concepts, we acquire, and I give an account as to how that process changes our perception. Suppose you are looking at the Mona Lisa. It might seem that you can perceive a lot more shades of color and a lot more shapes than for which you possess precise concepts. I argue against this. For every color or shape in appearance you have the ability to categorize it as that color or shape. It’s just that this is done by your sensory system prior to appearance. I argue that empirical studies show this. Blindsighted patients, for instance, are blind in part of their visual field. But they can use color and shape information received through the blind portion. I take this, along with other studies, to show that once you perceive a color or shape, it has already been categorized. I then argue that we perceive only low-level properties like colors and shapes. For in-stance, we don’t perceive high-level kind properties like being a table or being a wren. I do think that wrens or tables might look different to you after you become disposed to recognize them. Some take this to show that being a wren or being a table can be represented in your perception. I argue that this inference does not follow. If you are not disposed to recognize wrens, but we track the attention of someone who is, and we get you to attend to wrens in that same way, your visual phenomenology might be exactly the same as theirs. But there is no reason to think that it represents a wren. After all, you lack a recognitional disposition for wrens. I take this and other arguments to show that we perceive only low-level properties like colors and shapes.

Keywords: Perception, Concepts, Epistemology, Kant, Color, Shape, Justification, Crossmodal Experience, Vision
Advisor: Matthen, Mohan
Bacterial Adhesin Proteins Associated with Microbial Flocs and EPS in the Activated Sludge

Microbial flocculation is important in wastewater treatment process for an efficient separation of the solid and liquid phases and the removal of organics. Bacterial adhesins may contribute to the formation of microbial flocs since they have been previously found to play a significant role in the formation of biofilms. The overall objective of this work was to analyze bacterial protein adhesins present in the extracellular polymeric substances (EPS), mainly those associated with pili, fimbriae, flagella, and curli, and to determine their role in microbial floc structure and function. Identification of these EPS adhesins may explain their role in biofouling and enhance our understanding regarding the manipulation of bioflocculation. With the exception of flagellin protein FliC, which was distributed towards the outer region of the floc, all the adhesins appeared to be concentrated within the core region of the floc. Antibody staining coupled with confocal microscopy indicated that adhesin proteins associated with flagella (FliC), pili (PilA), fimbriae (FimH), and curli (CsgA, CsgB) represent a significant fraction (10-27%) within microbial flocs. Western blot analyses demonstrated that with the exception of FliC, all the studied adhesins were detected in the EPS matrix. Furthermore, mass spectrometry indicated the presence of pili in the EPS matrix. Under Phosphorus (P)-limited conditions, with the exception of fliC, all the studied genes (fimH, pilO, psiF) exhibited a change in response to P reduction, with fimH gene at the highest expression and an earliest response (1 d). During the nutritional downshift analyses, fimH and pilO genes were expressed within the first six hours of the reaction at significantly greater levels than during P-limited conditions. Taken together, these studies suggest that adhesins associated with pili, fimbriae, and curli play an important role in initial floc formation, and that adhesins associated with flagella either recruit planktonic bacteria to a growing floc or are involved in the interfacial relationships at the floc surface. This information may assist researchers and engineers in broadening the understanding of bioflocculation in conventional biologically based wastewater treatment systems and in advanced technologies, such as hybrid and membrane bioreactors. In addition, this knowledge will be useful in creating molecular tools to aid in the design and monitoring of bioflocculation.

Keywords: adhesin proteins
flocs
Advisor: Liss, Steven N.
A Comparison of Two Methods of Adjusted Attributable Fraction Estimation as Applied to the Four Major Smoking Related Causes of Death, in Canada, in 2005

The main objective of the thesis was to compare two methods of calculating adjusted attributable fractions and deaths as applied to smoking exposure and four health outcomes, lung cancer, ischaemic heart disease, chronic obstructive pulmonary disease, and cerebrovascular disease, for Canadians 30 years or older in the year 2005. An additional objective was to calculate variance estimates for the evaluation of precision. Such estimates have not been published for Canada to date. Attributable fractions were calculated using the fully adjusted method and the partial adjustment method. This method requires confounder strata specific (stratified) estimates of relative risk, along with accompanying estimates of variance. These estimates have not previously been published, and were derived from the Cancer Prevention Study II cohort. Estimates of the prevalence of smoking in Canada were obtained from the Canadian Community Health Survey 2005. Variance estimates were calculated using a Monte Carlo simulation. The fully adjusted method produced smaller attributable fractions in each of the eight disease-sex-specific categories than the partially adjusted method. This suggests an upwards bias when using the partial adjustment method in the attributable fraction for the relationship between cigarette smoking and cause-specific mortality in Canadian men and women. Summed across both sexes and the four smoking related causes of death, the number of deaths attributable to smoking was estimated to be 25,684 using the fully adjusted method and 28,466 using the partial adjustment method, an upward bias of over ten percent, or 2,782 deaths. It is desirable, theoretically, to use methods which can fully adjust for the effect of confounding and effect modification. Given the large datasets required and access to original data, using these methods may not be feasible for some who would wish to do so.

Keywords: attributable fraction
adjustment
attributable death
confounder
modifier
covariate
Advisor: Rehm, Jürgen
Mathematical Theory of van der Waals forces

The van der Waals forces, which are forces between neutral atoms and molecules, play an important role in physics (e.g. in phase transitions), chemistry (e.g. in chemical reactions) and biology (e.g. in determining properties of DNA). These forces are of quantum nature and it is long being conjectured and experimentally verified that they have universal behaviour at large separations: they are attractive and decay as the inverse sixth power of the pairwise distance between the atoms or molecules. In this thesis we prove the van der Waals law under the technical condition that ionization energies (energies of removing electrons) of atoms are larger than electron affinities (energies released when adding electrons). This condition is well justified experimentally as can be seen from the table, \newline \begin{tabular}{|c|c|c|c|} \hline Atomic number & Element & Ionization energy (kcal/mol)& Electron affinity (kcal/mol) \\ \hline 1 & H & 313.5 & 17.3 \\ \hline 6 & C & 259.6 & 29 \\ \hline 8 & O & 314.0 & 34 \\ \hline 9 & F & 401.8 & 79.5 \\ \hline 16 & S & 238.9 & 47 \\ \hline 17 & Cl & 300.0 & 83.4 \\ \hline \end{tabular} \newline where we give ionization energies and electron affinities for a small sample of atoms, and is obvious from heuristic considerations (the attraction of an electron to a positive ion is much stronger than to a neutral atom), however it is not proved so far rigorously. We verify this condition for systems of hydrogen atoms. With an informal definition of the cohesive energy $W(y),\ y=(y_1,...,y_M)$ between $M$ atoms as the difference between the lowest (ground state) energy, $E(y)$, of the system of the atoms with their nuclei fixed at the positions $y_1,...,y_M$ and the sum, $\sum_{j=1}^M E_j$, of lowest (ground state) energies of the non-interacting atoms, we show that for $|y_i-y_j|,\ i,j \in \{1,...,M\}, i \neq j,$ large enough, $$W(y)=-\sum_{i<j}^{1,M} \frac{\sigma_{ij}}{|y_i-y_j|^6}+O(\sum_{i<j}^{1,M} \frac{1}{|y_i-y_j|^7})$$ where $\sigma_{ij}$ are in principle computable positive constants depending on the nature of the atoms $i$ and $j$.

Keywords: van der Waals forces
Advisor: Sigal, Israel Michael
Exploring the Nature and Extent of Leadership Distribution in Elementary Schools

This study explored forms of distributed leadership in schools and the relationship between these forms and various personal and organizational factors. Though all empirical constructs used in this study were carefully grounded in the existing literature on the topic, the organization and empirical investigation of these constructs in a systemic manner is a distinct contribution of the study. The research was conducted in one large Ontario district that had been promoting distribute leadership for years. The evidence consisted of the surveys of 92 principals, 52 vice-principals, and 2190 teachers from the district’s elementary schools. Various statistical analyses, including descriptive, correlation, regression, and multi-level modeling analyses, were used to analyze the gathered data. In the study schools, administrators and teachers perceived leadership for high-priority school initiatives being mostly distributed in an egalitarian and coordinated manner. They also associated this coordinated way of distribution with wider distribution of leadership. At the same time, teachers often experienced leadership being distributed by principals in an authoritative manner as well. This finding indicates that principal delegation remains a dominant form of leadership and should be studied alongside more egalitarian distributed forms. This research brings to light the differences in principals’, vice-principals’, teacher-leaders’, and classroom teachers’ experiences with distributed leadership. It is recommended for researchers to take into account these differences in their studies of school leadership. District and school leaders should also consider staff’s varied leadership experiences while developing distributed leadership forms in schools. The study also suggests that school conditions have more effect on the way leadership gets distributed in schools than personal beliefs and experiences of principals, vice-principals, and teachers do. This implies that in order to develop extensive and coordinated distributed leadership forms, which are believed to be more productive, school administrators should devote considerable effort to encourage teachers’ engagement in leadership activities, build cultures of trust and collaboration, develop structures supporting shared decision making, ensure staff’s commitment to shared goals and provide incentives and relevant resources.

Keywords: distributed leadership
leadership
elementary school
collaboration
quantitative
multi-level modeling
HLM
school leadership
educational leadership
teacher leadership
Advisor: Leithwood, Kenneth