VictorJuiz/thesis huggingface dataset:
Excited state and energy transfer dynamics in natural and artificial light harvesting systems

Inspiration from nature is a dominant force in generating creative solutions to important problems on our planet. There is no area more relevant to seeking guidance from nature than the area of harvesting sunlight for our energy needs on this planet. After 3.5 billion years of evolution, photosynthetic organisms have mastered this task and their study is relevant to not only solving world issues, but to advancing fundamental biophysical knowledge about the properties of living machines. What makes photosynthesis especially desirable to study for these outcomes is the remarkable quantum efficiency of energy transfer events that initiate the process and this thesis studies both natural (phycobiliproteins) and artificial (model dimer) light-harvesting systems in order to advance our understanding of light-harvesting events. Two topics are the main features of this work: coherences (excitonic/vibrational) and the biological environment (characterization/influence) that make up the four projects pursued. In the first project, we find that excited state dynamics in the model dimer system exhibit ultrafast relaxation from the upper to lower exciton state on the

Keywords: Crowding
Energy Transfer
Exciton Dynamics
Light Harvesting
Photosynthesis
Solvation Dynamics
Advisor: Scholes, Gregory D
Quantifying Positive and Negative Selection in Natural Populations

The strength and direction of natural selection are key parameters that are predicted to influence the maintenance of genetic variation, genome structure, and the long-term evolutionary fate of populations. New technologies now allow us to estimate these quantities across the entire genomes of organisms, and to examine the variation in selection across the genome and across species. In chapter two we review the state of knowledge about selection on plant genomes and discusses the key factors that may drive differences across species in the strength and direction of selection. In my third chapter I infer the strength and extent of positive and negative selection across the genome of an outcrossing plant, with emphasis on comparing selective differences between coding and noncoding DNA. I find evidence that both positive and negative selection are widespread in protein coding regions, but primarily restricted to a subset of highly conserved sites in noncoding DNA. In my chapter four I investigate the extent to which a shift to asexuality within a single diploid plant species affects the accumulation of deleterious alleles across the genome. I find evidence for a significant increase in the numbers of deleterious mutations in the asexual haplotypes, consistent with a reduced efficacy of selection in asexual populations due to selective interference. My final chapter focuses on the effects of a strong demographic event on the efficacy of selection in a pathogenic fungus. The patterns show evidence for a severe loss of neutral diversity and a weakening of purifying selection following this colonization bottleneck. My results reveal an important contrast in the nature of selective constraint in plant genomes relative to animal taxa, provide genomic evidence for the advantage of sexual reproduction, and show how rapid shifts in the efficacy of selection can arise in non-equilibrium populations.

Keywords: population genetics
selection
Advisor: Wright, Stephen I
UNDERSTANDING THE WORK OF FEMALE TEACHERS IN LOW FEE PRIVATE SCHOOLS IN PUNJAB, PAKISTAN

While Low Fee Private Schools (LFPSs) and Public Private Partnership (PPPs) initiatives have been widely promoted in various contexts including Pakistan, they have seldom been viewed through the lens of the teacher’s life and work. To understand the work of female teachers in LFPSs, I apply a conceptual framework that demonstrates the interconnectedness of teachers’ career and working conditions, gender and teacher labour markets in looking at the work of teachers. Specifically I ask, how female teachers perceive and experience their careers, working conditions and gendered labour in LFPSs with regards to the occupational labour market for teachers in Punjab, Pakistan. My qualitative study is based on interviews and focus group discussions with teachers and principals in LFPSs located in Punjab. In addition, NGO fieldworkers and civil society members who work on education were also interviewed to gain a better understanding of the context. Findings from my study point to how haphazard recruitment, lack of career paths and the diminishing social image and status of teachers negatively affect the work and motivation of female teachers in LFPSs in Punjab. A crucial argument that emerges from my study is that while teachers in LFPS themselves are willing to learn and improve their performance, they do not have enough opportunities for in-service training in challenging areas such as multi-grade teaching, subject specialisation, changing syllabus and dealing with students who have very poor learning levels. While for young, single and female teachers a major reason for leaving employment in LFPSs was their inability to work after getting married, many teachers argued that a low salary and tough working conditions, often caused women to move to other jobs. The study affirms the observation that female teachers in LFPS are paid lower wages and are increasingly being hired in private schools due to their gender. Women in LFPSs face much different working conditions, management attitudes and salary as compared to male teachers. Findings show that women’s work in LFPSs teaching in Pakistan takes place in a social, economic and political environment that constrains women’s labour force participation.

Keywords: career
female teachers
low fee private schools
teachers work
Advisor: Bascia, Nina
Latitudinal Gradients in Herbivory and Plant Defence Across the Onagraceae

Herbivory is predicted to increase at lower latitudes, leading to the evolution of increased plant defence towards the tropics. These ideas are known as the Latitudinal Herbivory-Defence Hypothesis (LHDH). While initial empirical tests supported this hypothesis, it has been challenged by new studies leading to controversy. I tested LHDH at the micro- and macroevolutionary scale, through a series of well-replicated studies. At the microevolutionary scale I surveyed common evening primrose (Oenothera biennis), which has a well characterized herbivory community, and diverse and abundant ellagitannins. First, I sampled herbivory across 79 populations of O. biennis in Eastern North America. Latitudinal gradients in herbivory varied depending on herbivore guild and degree of specialization. In particular damage by specialist seed predators was greater at higher latitudes. To explain these patterns, I then studied genetically based latitudinal clines in plant defences across 137 populations of O. biennis by growing them in a common garden. Populations from lower latitudes showed greater resistance to all herbivores. Increased chemical defences best predicted this resistance. A subsequent growth chamber experiment then examined latitudinal gradients in constitutive versus induced defences. Genotypes from lower latitudes were less damaged by a generalist caterpillar, although there was no pattern by a specialist weevil. Total phenolics were greater at lower latitudes when measuring constitutive defences, but were greater at higher latitudes in induced plants. These results suggest there might be increased herbivory at higher latitudes because of relatively low constitutive defences, but that induced defences may be used to prevent additional damage. At the macroevolutionary scale, gradients in chemical defences were assessed across 80 species of Onagraceae. Latitude did not predict defence patterns. Instead colder climates, temperature variability, and hemisphere of origin were associated with greater levels of defence. These results challenge the validity of LHDH at the macroevolutionary scale. The utility of LHDH varies across different scales. This generates the need for more robust theory that can incorporate these scales into predictions. I advance new lines of inquiry that should be explored, by analyzing the assumptions used in LHDH through a critical review. I also recommend increased rigor and consistency in chemical and herbivory metrics. I apply some of these recommendations throughout my work, including confirming the effect of phenolics and ellagitannins on herbivore performance.

Keywords: ellagitannins
herbivory
latitude
LHDH
Oenothera biennis
plant defence
Advisor: Johnson, Marc TJ
Postcolonial Theory Reconsidered: Discourses of Race, Gender, and Imperialism in the German-Japanese Realm

This study explores the intersections of race and gender as they manifest in film and print media across a century of transnational flows between Germany and Japan. I argue that German-Japanese relations in the twentieth century invite novel re-readings of existing postcolonial theories, resulting in a productive re-evaluation of inherited terms such as ‘hybridity’ and ‘race’. Each chapter of my dissertation is devoted to a particular strand of the cultural fabric woven between Germany and Japan and its consequences for the broader relationship between East Asia and Europe. Chapter two focuses on the German-language magazine East Asia (Ost-Asien) published by the Japanese Tamai Kisak from 1898-1910 in Berlin, on Kitasato Takeshi’s German-language drama Fumio (1900), and on the silent film Bushido (1926). These works negotiate Japan’s complex situation as simultaneously belonging to an Asian and a European cultural realm in often contradictory ways. Chapter three pursues an in-depth analysis of the German-Japanese relationship between 1932 and 1945 via such diverse cultural artifacts as the results of a German-Japanese essay contest held in 1944, German newsreels, and German-Japanese filmic co-productions. My research demonstrates how the cultural co-productions between Nazi Germany and Imperial Japan downplayed questions of race and gender in an attempt to forge a shared identity as Soldatenvölker (soldier people). In my fourth and final chapter, I analyze the contemporary work of one Japanese filmmaker and two Japanese authors who migrated from Japan to Germany after the Second World War: Marie Miyayama, Yoko Tawada and Hisako Matsubara. I will demonstrate how tourism, commodity culture, as well as notions of transculturalism and an increasing convergence of ‘East’ and ‘West’ are paramount for shaping the German-Japanese discourse in the late 20th and early 21st century.

Keywords: gender
Germany
imperialism
Japan
postcolonial
race
Advisor: Fenner, Angelica
Genetic and Developmental Contributions to Reproductive Isolation in Caenorhabditis Nematodes

The process of speciation is central to the origins of biodiversity. Therefore, understanding how and why species form and persist represents one of the major goals of evolutionary biology. Speciation involves the evolution of reproductive isolation, which prevents gene flow between diverging lineages. Complete reproductive isolation typically results from the accumulation of multiple reproductive barriers. A particularly important reproductive barrier, when hybrid offspring are intrinsically sterile or inviable, follows repeated genetic patterns in many taxa. This consistency suggests fundamental rules to how speciation proceeds. I analyzed these patterns using two pairs of species in the Caenorhabditis genus, from the nematode phylum that has largely been neglected in the study of speciation. First, I examined how inviability manifests over hybrid development and found that, in contrast to predictions, nearly all inviability that occurs takes places during embryogenesis, even in closely related species that produce fertile adult offspring. This result indicates that the embryonic stage of development is particularly sensitive to disruption in this genus. I explored whether the inviability can be traced to the first cell division in hybrids, and found that the first cell division is often disrupted in hybrids between distantly-related species, but not in those between closely related species. I also compared the genetic complexity of hybrid inviability and hybrid sterility, and found that hybrid male sterility is best explained by a simple two-locus incompatibility while hybrid inviability is genetically complex, in contrast to other taxa. I demonstrated that reproductive barriers that act after mating but before zygote formation contribute to reproductive isolation by depressing progeny production in hybrid crosses. Finally, I tested the role that temperature, an environmental factor, might exert on intrinsic reproductive isolation, to show that hybrid males are particularly sensitive to environmental perturbations. Overall, my research reinforces the generality of common â rulesâ of speciation across diverse taxa, and yet I also identified distinctive phenomena to Caenorhabditis, highlighting the importance of extending speciation research into new study organisms.

Keywords: Caenorhabditis
Evolution
Reproductive isolation
Speciation
Advisor: Cutter, Asher D
China's Outward-Oriented Higher Education Internationalization: A Multidimensional Analysis and an Empirical Inquiry into the Views of International Students

This study investigates China’s present situation of shifting from a mainly inward-oriented higher education internationalization to a more balanced approach, and the existing gaps between China’s goals of using outward-oriented higher education internationalization to enhance its international influence and status in the world knowledge system, also the challenges it faces in the response to this approach. According to a new typology proposed by the author, “outward-oriented higher education internationalization” refers to the process of exporting/introducing domestic knowledge, culture, higher education models and norms, and educational philosophies to the world through higher education internationalization primarily for the sake of enhancing worldwide influence. This study examines the three major dimensions of China’s outward-oriented HE internationalization: 1) Cultural diplomacy based on Sino-foreign higher education collaboration (i.e. the Confucius Institute program), 2) international development aid for higher education in developing countries, and 3) international student recruitment at the higher education level. The theoretical framework of this study is developed based on several interrelated neo-Marxist theories and concepts including dependency theory, the center-periphery model, and world-system theory, as well as the notions of soft power, public diplomacy, and knowledge diplomacy. China’s outward-oriented higher education internationalization can be understood as a reciprocally beneficial instrument used by the Chinese government for enhancing its international status, as it attempts to move from the periphery to the center of the world knowledge system. Using the problem approach in comparative education developed by Brian Holmes, a post-positivist methodology is developed. One part of it constitutes an exploratory survey of international graduate students in English instruction programs in education-related majors in three Chinese universities to explore their attitudes towards China’s related strategies, as well as policy formulation and implementation. This unique population is selected due to their “triple identity” as 1) foreigners in China and thus outsider observers; 2) international students in Chinese universities and thus policy recipients; and 3) graduate students in education-related majors and thus insiders of this research field. Through both quantitative and qualitative data analysis, this study tests and modifies hypothetical policy solutions developed on the basis of a comprehensive review of relevant literature that makes possible an intellectualization of China’s present challenges and opportunities.

Keywords: center-periphery
Confucius Institute
development aid
higher education
internationalization
international student
Advisor: Hayhoe, Ruth
Functional characterization of N6- threonylcarbamoyladenosine biosynthesis by the universally conserved Sua5/YrdC and Kae1/Qri7/YgjD protein families

N6-threonylcarbamoyladenosine (t6A) is a universally conserved tRNA modification found on nearly all tRNA molecules that recognize ANN codons on messenger RNAs. The presence of t6A in the anticodon stem loop of tRNAs ensures proper codon recognition and high fidelity during protein translation. Cells deficient in t6A-modified tRNAs exhibit defects in starting AUG codon recognition and also an increase rate of frameshift errors during translation elongation. Although the function of t6A is critical for protein translation and cellular physiology, it was only recent that the Sua5/YrdC and the Kae1/Qri7/YgjD protein families were discovered to catalyze the formation of t6A. Archaea and eukaryotic Kae1 operate as part of the KEOPS complex with Bud32, Cgi121, Pcc1 and Gon7 proteins. Eukaryotic mitochondrial Qri7 operates in isolation. Bacterial YgjD operates as part of the YgjD-YeaZ-YjeE ternary complex. How the Sua5/YrdC family, the Kae1/Qri7/YgjD family and the additional subunits in the KEOPS and YgjD-YeaZYjeE complexes contribute to t6A biosynthesis were open questions at the beginning of my thesis work. Towards understanding the mechanisms of t6A biosynthesis, I reconstituted and characterized a minimal in vitro t6A biosynthesis reaction using Sua5 and Qri7 proteins. I established that the Sua5/YrdC and Kae1/Qri7/YgjD protein families are the core catalytic enzymes required for t6A biosynthesis and that the additional protein factors in the KEOPS and YgjD-YeaZ-YjeE complexes must serve augmenting regulatory roles. Qri7, the most primitive member of the Kae1/Qri7/YgjD family, by virtue of its ability to function on its own, operates independent of additional regulating protein factors. I then characterized the functions of the KEOPS accessory subunit Pcc1 and demonstrated that Pcc1-mediated KEOPS dimerization is not important for t6A biosynthesis by archaea KEOPS in vitro but is important for yeast KEOPS function in vivo. Lastly, I discovered and proved that human C14ORF142 is the human ortholog of yeast Gon7. This analysis showed that C14ORF142 disrupts KEOPS dimerization and potentiates the t6A biosynthesis activity of KEOPS in vitro.

Advisor: Sicheri, Frank
Investigating the Mechanisms by which Serotonin Influences Incentive Motivation

Many lines of evidence suggest that the monoamine neurotransmitter serotonin (5-hydroxytryptamine; 5-HT) plays an important role in modulating incentive motivation â the process by which stimuli with motivational value elicit appetitive behaviour. However, the mechanisms by which 5-HT exerts its effects on incentive motivation are unclear. In this thesis, I systematically investigated how complementary manipulations that enhance 5-HT function alter multiple measures of incentive motivation in mice. In Chapter 3, I examined the effects of acute, pharmacological increases in 5-HT activity and environmental conditions experienced during rearing on two measures of incentive motivation: responding for a conditioned reinforcer (CRf) and an unconditioned sensory reinforcer (USRf). These studies found that the selective 5-HT reuptake inhibitor citalopram consistently reduced responding for a CRf and USRf irrespective of rearing condition. In Chapter 4, I further showed that constitutive genetic deletion of the 5-HT transporter (SERT-KO) and acute citalopram treatment reduced operant responding for a primary reinforcer, a CRf, and a USRf. Additionally, the 5-HT2C receptor antagonist SB 242084 prevented some of the inhibitory effects of SERT-KO and citalopram on incentive motivation. Thus, the results of Chapter 4 provide comprehensive evidence that increasing 5-HT activity inhibits incentive motivation, and that this is mediated in part by 5-HT2C receptor signalling. In Chapter 5, I further explored how the 5-HT2C receptor modulates incentive motivation and linked the behavioural effects of 5-HT2C receptor signalling to an inhibitory interaction with the mesolimbic dopamine (DA) system. In Chapter 6, I used an optogenetic approach to delineate a 5-HT pathway that mediates the inhibitory influence of 5-HT on incentive motivation, with a focus on dorsal raphe nucleus (DRN) projections to the ventral tegmental area (VTA) of the mesolimbic DA system. These studies found that optogenetic stimulation of both DRN 5-HT neurons and their inputs to the VTA reduced responding for the primary reinforcer saccharin. Based on the results of this thesis, I propose the following mechanism by which 5-HT can influence incentive motivation: DRN 5-HT input to the VTA stimulates inhibitory interneurons by action at 5-HT2C receptors leading to a suppression of mesolimbic DA output and, consequently, incentive motivation.

Keywords: Behavioural Neuroscience
Dopamine
Mice
Motivation
Optogenetics
Serotonin
Advisor: Fletcher, Paul J
Circular Probabilistic Based Color Processing: Applications in Digital Pathology Image Analysis

Cancer is the leading cause of death in Canada. As the only definitive diagnosis for cancer, pathology confronts more challenges with the severe social issue of aging population. Past decade has witnessed the advent of whole-slide imaging, which fosters the research of digital pathology image understanding and automatic cancer diagnosis to address challenges in pathology. Color plays a vital role in digital pathology image analysis due to the use of chemical staining in pathology examination. However, unclear color mixing due to histological substances' co-localization and color variation among pathology images introduced by the inconsistency in pathology image preparation make reliable color-based quantitative pathology image analysis challenging. To overcome these problems, this research investigates the unique imaging model of pathology images, and introduces pathology image centered color processing algorithms based on two novel color signal treatments in the cylindrical color domain: circular probabilistic color-based pixel clustering and saturation-weighted color statistics. In the first treatment, aware of the directional nature of hue, the study innovates to model a hue distribution of an image using a circular mixture distribution, and provides a complete hue-based pixel clustering solution through maximum likelihood estimation. The second method aims to address the singularity of the HSV space in color processing. Motivated by the close relationship between saturation and hue in color perception, saturation-weighted statistics is generalized to mitigate effects of achromatic pixels on color analysis. The proposed two color treatments benefit the understanding of color content in an image. Based on the proposed color treatments, image-dependent color estimation, blind stain decomposition for color unmixing, and a complete color normalization scheme are proposed in this dissertation. The color estimation pipeline computes the representative color of histological substances in a pathology image, building an adaptive mapping between image color and tissue content. Toward accurate stain decomposition, taking color cues obtained from the novel color treatments and the problem's physical constraint into consideration, the introduced method obtains an optimal stain separation with minimal decomposition residue in an iterative manner. In the pathology image centered color normalization scheme, by implicitly distinguishing causes of color variation, illuminant normalization and stain spectral normalization are cascaded. Extensive experimentation suggests that the introduced solutions are superior to prior arts in terms of robustness to achromatic noise, effectiveness, and capability for histological information preservation.

Keywords: color normalization
color processing
digital pathology image analysis
stain decomposition
von Mises mixture model
Advisor: Plataniotis, Konstantinos N