VictorJuiz/thesis huggingface dataset:
Characterizing the genetic basis, fitness effects, and predictability of adaptive evolution [electronic resource]
Keywords: Biology.

The idea that species can change in response to their fitness effects was famously proposed by Charles Darwin more than a century ago and merged with our burgeoning understanding of genetics as the "modern synthesis" in the early 20th century. The relationship between genotype and fitness has been studied extensively in the decades since, with the goal of not only understanding evolutionary history, but to predict future evolution. Evolutionary prediction is critical for solving problems of biomedical interest such as drug resistance evolution in pests and pathogens or the evolution of cancers. Major questions in the field include understanding the distribution of selective effects of new mutations, the number and types of loci that are targets of adaptive mutations, and the dependency of the fitness effect of a mutation on its genetic background or the environment. In the first chapter of this thesis, I present a theoretical treatment of the predictability of evolution, by studying predictability via historical reconstruction as well as more traditional methods looking at the similarity of independently evolving populations starting from the same initial condition. I relax the assumption made in this prior work that adaptation always proceed through the successive fixation of adaptive mutations, and characterize the changes in evolutionary predictability that result. I find that the two approaches to studying predictability are not identical, and can even be anti-correlated. Remarkably, I find that stable polymorphisms can make the historical reconstruction method unreliable even with perfect sampling, which would never occur under the successive fixation assumption. In order to predict evolution in biological systems, we need a comprehensive genome-wide survey of all possible adaptive mutations in a system and their fitness effects, not just the ones that occurred during a single bout of evolution. In the next chapter, I present a novel and highly extensible approach to overcome the current technical limitations in conducting such a survey in experimentally evolving yeast populations based on recently developed the DNA barcoding technology. In the final chapter, I use the methods developed in the second chapter to study how the genotype-fitness map changes under different growth conditions by remeasuring the fitness of the same clones under many alternative conditions. These conditions were chosen to specifically vary different parts of the yeast growth cycle, such as the exponential growth phase or stationary phase, giving us additional insight into the physiological basis of adaptation in this system. In sum, the work presented in this thesis studies the predictability of evolution using theoretical models and develops the experimental tools necessary to empirically study evolutionary predictability by comprehensively characterizing the genotype-fitness map in experimentally evolving yeast.
"Characterizing the Overexpression of YY1 in differentiating cardiac progenitor cells in vitro and in vivo"
Keywords:  Department of Biology
Biology
Cardiac development
YY1
cardiomyocyte
stem cell
cardiac progenitor cell
Thesis

Understanding the mechanisms of cardiac cell lineage commitment is important for improving the understanding of cardiogenesis and the pathophysiological basis of congenital heart disease. Cardiogenesis is regulated by complex interactions between many transcription factors; however, not much is understood about the specific transcription factors that govern cardiac progenitor cell differentiation into cardiomyocytes. One ubiquitous transcription factor, YY1, has been shown to activate and repress genes in other developing tissues, but has not been studied in the differentiation of cardiomyocytes. We have found that YY1 is vastly down-regulated just prior to cardiomyocyte differentiation and think that this down-regulation may play an important part in the differentiation of cardiac progenitor cells into cardiomyocytes. To understand the role of this down-regulation, we created and differentiated mouse embryonic stem cell (mESC) lines that overexpress YY1 during the time that YY1 would normally be down-regulated in the developing embryo. Cells that overexpressed YY1 increased the expression of both cardiac transcription factors and cardiac sarcomeric proteins. We therefore believe that YY1 plays an important role in the process cardiac lineage commitment and these experiments give some insight into one of the many facets that control the differentiation of cardiac progenitor cells into cardiomyocyte.
Charge transport and open-circuit voltage in semicrystalline polymer solar cells [electronic resource]
Keywords: Applied Physics.

Semiconducting polymers have the potential to be used in electronic devices ranging from solar cells to biosensors. These materials offer advantages over traditional inorganic devices that include decreased materials cost, cheaper and low-temperature processing, and the enabling of fully flexible devices on plastic or for incorporation into textiles. However, the performance of organic photovoltaics in particular has not yet reached comparable levels to that of silicon, due to the disordered nature of the polymers and complex interfacial processes within the active layer. In this thesis, I will discuss several sources of inefficient performance in a polymer-fullerene heterojunction film. First, after the absorption of light creates an electron-hole pair, the charges form a charge transfer state at the interface between the polymer and fullerene which fundamentally limits the possible open-circuit voltage (Voc). I experimentally probe the Voc losses in these solar cells and show that populating higher energy interfacial states is not the cause of increases in Voc, but rather that local aggregation or delocalization effects shift the low-energy interfacial state. Extraction of charges via the polymer phase is also the source of significant losses in current as well as in voltage. In particular, the mobility of the polymer phase is often the limiting carrier mobility of the device, and optimizing this mobility holds many applications in organic electronics beyond solar cells. In the latter part of the thesis I focus therefore on understanding the source of traps in pristine semicrystalline polymer films. I develop a model that relates the physical properties and parameters of the semicrystalline material to the charge transport and analyze the effects on transport pathways. Finally, this model is applied to understanding a number of experimentally observed features of charge transport, including the effects of molecular weight and applied electric field.
Chemodetection and response to host signals facilitate helicobacter pylori colonization of the gastric epithelium [electronic resource]
Keywords: Microbiology and Immunology.

Helicobacter pylori is a Gram-negative bacterium that has co-evolved with humans since the beginning of human history. It is one of the most successful human-associated microbes infecting more than half of the world's population. Chronic infection with H. pylori can lead to several disease outcomes ranging from asymptomatic colonization in the majority of those infected to gastric and peptic ulcers in about ten percent of those infected and gastric cancer in about one percent of those infected. Gastric cancer remains the third leading cause of cancer-related deaths in the world, which continues to motivate ongoing research to uncover novel strategies to control H. pylori infection. The human stomach is one of the most challenging environments for microorganisms due to its contents of hydrochloric acid, digestive enzymes, and antimicrobial compounds. Unlike most microbes that enter the stomach, H. pylori is able to colonize and persist in this harsh environment. It does so by sensing environmental signals that allow it to avoid the microbicidal acid in the stomach and navigate to the gastric epithelium where it is protected. This thesis elucidates the host signals that direct H. pylori to the gastric epithelium and the molecular mechanisms of how H. pylori senses and responds to gradients of these host signals. Chapter 1 highlights what is known of H. pylori's life in the stomach and the strategies that enable H. pylori to establish colonization in the stomach. In Chapter 2, I describe how H. pylori chemotax towards host metabolites emanating from the gastric epithelium. In Chapter 3, I describe H. pylori's detection and response to another important signal in the stomach -- hydrochloric acid. Chapter 2 and 3 describe two prominent chemical gradients in the stomach that help drive H. pylori to the gastric epithelium. However, there are many more gradients that haven't been thoroughly investigated. In Chapter 4, I discuss other chemicals gradients that H. pylori may be responding to in the stomach. I also summarize and consider the implications of chemotaxis to host signals in enabling H. pylori to establish colonization and persist in the stomach.
Chinese heirs to Muhammad [electronic resource] : writing islamic history in early modern China
Keywords: Religious Studies.

This project tells the story of history as imagined by Hui Muslims in late nineteenth and early twentieth century China. I argue that this was an especially productive period for historical thought, bookended by the establishment of a robust Sino-Islamic knowledge base by Liu Zhi on one end and Republican China on the other end. Histories from this period unify a vast temporal and spatial expanse: from genesis to antiquity to the modern era, from Arabia to Central Asia to China. Hui historians string together places and times into a coherent, continuous narrative for the community. I examine surviving woodblock prints and manuscripts including a compendium of Islamic knowledge by Lan Xu, a biographical collection of Hui who served the Chinese state by Li Huanyi, and the genealogy of a sayyid family in Yunnan by Ma Yunhua. In reading these works together, I argue that they engage with an overlapping group of key events, figures, and landmarks in the Sino-Islamic past. This past begins in Arabia and ends in China. Each of these locations, however, is limited in time. Arabia holds authority over antiquity while China becomes a greater concern as history approaches the modern era. The early chapters of this project treat the intellectual realm of Hui religious thought. I stress the extent to which ideas about the placement of Muhammad and other elevated beings in the cosmos reflect the sociohistorical conditions of the thinkers. The later chapters address how Hui history is written in response to recent events and societal concerns, attesting to the political power and religious architecture behind these creations. The case of nineteenth century Hui offers a unique perspective on the study of Islam and the study China. However, the type of political, intellectual, and social efforts exerted by these authors to claim a tradition is indicative of all history writing. The accounts written here remake China into an Islamic space, and into a safe place for Muslims. In these histories, that Islam moved to China where Muslims flourished for centuries is but a natural progression. This study calls for a careful treatment of historical narratives for their highly generative power and for the dense intellectual and religious realms upon which they are built.
Chromogenic behaviors and mechanisms of chromatophore control in squid [electronic resource]
Keywords: Biology.

Cephalopod chromatophores are small organs that provide the means for much of the elaborate color changing behaviors frequently observed in squid, octopus, and cuttlefish. The vast majority of what is currently known about the anatomy, physiology, and use of chromatophores in squid derives from studies conducted on species of squid from the primarily shallow water dwelling family Loliginidae. This thesis examines the natural chromogenic behaviors and the anatomy and physiology of the chromatophore layer in the ommastrephid squid, Dosidicus gigas, and compares the findings to the chromatophores of the loliginid squid Doryteuthis opalescens. Video of free-swimming Dosidicus from the animal-borne video package Crittercam revealed two novel dynamic displays that differ greatly from the primarily static displays previously documented in loliginid squids. The "flashing" display in Dosidicus is characterized by a rapid oscillation of body coloration from red to white, and is likely a form of intraspecific communication. "Flickering" on the other hand consists of oscillating waves of chromatophore activity that propagate across the skin and is likely a form of dynamic camouflage. These differences in chromatophore use compared to loliginid squids are reflected in the anatomy and physiology of the chromatophore layer in Dosidicus. As in loliginid squids, L-glutamate (L-Glu) and serotonin (5-HT) are both endogenous neurotransmitters to the chromatophore system with excitatory and inhibitory effects respectively. However, the chromatophores of Dosidicus are much more sparsely innervated compared to what has been documented in loliginid squids. Furthermore, spontaneous waves of chromatophore activity are frequently observed in excised skin samples of recently dead Dosidicus. Similar waves can only be elicited in D. opalescens after 5-7 days of chronic denervation of the chromatophore layer, a process that results in almost total degradation of both glutamatergic and serotonergic axons in the chromatophore layer in D. opalescens. In both species, spontaneous wave were resistant to the inhibitory effects of the potent neurotoxin tetrodotoxin (TTX) at concentrations that abolished electrically stimulated chromatophore activity, indicating a separate control mechanism. The waves were sensitive to the inhibitory effects of 5-HT. These results indicate one role of 5-HT in the chromatophore system of both the ommastrephid squid Dosidicus and in loliginid squids may be to regulate spontaneous waves of chromatophore activity without interfering with the excitatory innervation of the chromatophores to different degrees depending on chromatophore use in each species.
Climate Policy and Income Inequality: Distributional Implications of Cap and Trade System Design Choices in Ontario
Keywords:  Department of Economics
Climate change
carbon pricing
Canada
Stanford Department of Economics
Thesis

Climate change poses a challenge to Canadian policy-makers: how can Canada reduce its greenhouse gas emissions in a way that is cost effective but also equitable? In this paper, I explore the distributional impacts across income groups of cap and trade in Ontario, modeling the impacts of changes in commodity prices, changes in labour and capital returns, and program revenue use. In particular, I examine three different permit allocation methods and revenue recycling schemes: (1) 100% free allocation, (2) 100% auctioning of permits paired with a per capita fixed rebate, and (3) 25% free allocation, 75% auctioning with revenues used for public spending on transit, building retrofits, and clean technology subsidies. I find that the policy-induced commodity price increases put a greater burden on poorer households relative to their income. The decrease in returns to labour is progressive across quintiles, but likely not enough to counteract the regressive spending side impact. Overall, program revenue use maybe the deciding factor in whether Ontario’s cap and trade system is equitable across income groups.
Closing the maize yield gap in the North China Plain [electronic resource]
Keywords: Earth System Science.

The gap between yield potential and average farmers' yield measures the capacity for yield improvement with current technology. The North China Plain (NCP) is a major maize producing region of China, and improving maize yield of NCP is essential to food security of the country. Some previous studies have found a substantial maize yield gap in this region (~100% of average yields), whereas others have reported much smaller gaps. In this thesis, multi-year satellite images were used to quantify field-scale maize yield variation in Quzhou County of NCP, and this variation was then analyzed to determine the role of soil type and persistent management factors in explaining yield gaps. The method was then applied to 76 counties in NCP. The aggregated average yield was 8.66 t/ha across county years, and the aggregated yield gap was 0.76t/ha. The weighted average of yield persistence was 25.9% of the average yield gap, or 2.3% of average yield. The results showed tremendous spatial heterogeneity in yield persistence level across NCP, and further analysis within individual counties is required to better prioritize means to shrink the yield gap. In order to further understand the underlying causes to this yield gap, we conducted a case study in Quzhou County, which is typical of NCP such that the average plot size is less than 0.2 ha. First, we identified fields that were either persistently higher or lower yielding according to remote sensing yield estimates, and then conducted detailed field surveys. We found irrigation facility to be a major constraint to yield both in terms of irrigation water quality and farmers' access to wells. In addition, farmers' method of choosing cultivar, which likely relates to their overall knowledge level, significantly explained yield variation. These results inspired possible future research topics in assessing the efficacy of farmer extension programs and the effect of farm size on productivity.
Coded computational illumination and detection for three-dimensional fluorescence microscopy [electronic resource]
Keywords: Electrical Engineering.

In vivo calcium imaging enables the optical monitoring of neural activity at the level of individual neurons in real time, necessitating the development of high speed, three-dimensional (3D) fluorescence microscopy techniques with at least single-neuron spatial resolution. Because a typical widefield microscope intrinsically produces only two-dimensional images, various illumination and detection coding strategies have been implemented to address the challenge of 3D fluorescence microscopy, utilizing either precisely structured and temporally scanned illumination patterns, such as in two-photon laser scanning microscopy or coding of the emission, as in light field microscopy, respectively. However, many single-focal illumination coding strategies have limited acquisition speeds, while detection-coding-only strategies requiring computational reconstruction of the 3D volume are limited by optical aberrations of the tissue. We present a 3D calcium imaging approach utilizing both multifocal scanned two-photon laser excitation for illumination coding and detection coding with the light field microscopy approach suitable for in vivo mammalian calcium imaging. A holographic 3D multifocal illumination pattern is targeted only towards pre-localized neurons avoiding the unnecessary illumination of other regions. The resulting fluorescence emission is coded and detected on an image sensor and deconvolution is used to recover the neural activity at each site. We present the design and optimization of such an imaging strategy, and validate the approach with experimental measurements. Finally, we demonstrate the application of this approach to in vivo mouse calcium imaging. The design and implementation of another technique, frame-projected independent fiber photometry, enabling the optical recording and control of neural activity in freely moving mammals with region-level spatial resolution, is presented in a dedicated chapter as well, including simultaneous recording from multiple brain regions in a mouse during social behavior, two-color activity recording, and optical optogenetic stimulation eliciting dynamics matching naturally observed patterns.
Coherent feedback control and nonlinear optics in cavity QED systems [electronic resource]
Keywords: Applied Physics.

In order to capitalize on their promise of high-bandwidth, ultra-low power operation, future nanophotonic devices will have to contend with quantum and coherent effects inherent to the small-volume, few-photon limit. The theoretical development of general, systematic frameworks for describing quantum feedback networks enables us to leverage established optical technologies, from single and multi-atom cavity quantum electrodynamics to ultrafast multimode optics, as an essential test bed for establishing direct contact between coherent-feedback control theory and first generation nanophotonic circuits. For interesting regimes for photonic logic, we want to work where switching energies become on the order of attojoules. Within atomic cavity QED systems, this regime occurs where the number of atoms within the typical cavity is on the order of 1-10. In this regime, each atom is a quantum emitter and must be treated with a full quantum model. As the atom number is increased, a mean field theory can be applied and the dynamics can be modeled using the optical Bloch equations. Full quantum modelling of systems with the atom number $> 10$ are not tractable computationally and a simpler semi-classical model does not fully capture the dynamics correctly. Thus we must investigate an intermediate regime where it may not be necessary to keep track of all quantum degrees of freedom and treat them semi-classically. I will present experimental data showing the effects of coherent feedback on a test cavity QED system alongside switching dynamics and other non-linear behavior in a few atom regime. Studying experimental data to help formulate new models will greatly help in the push towards practical optical non-linear systems for ultra low power photonic logic.
Coherent LQG control, free-carrier oscillations, optical ising machines and pulsed OPO dynamics [electronic resource]
Keywords: Physics.

Broadly speaking, this thesis is about nonlinear optics, quantum mechanics, and computing. More specifically, it covers four topics: Coherent LQG Control, Free-Carrier Oscillations, Optical Ising Machines and Pulsed OPO Dynamics. Tying them all together is a theory of open quantum systems called the SLH model, which I introduce in Chapters 1-2. The SLH model is a general framework for open quantum systems that interact through bosonic fields, and is the basis for the quantum circuit theory developed in the text. Coherent LQG control is discussed in Chapters 3-4, where I demonstrate that coherent feedback outperforms measurement-based feedback for certain linear quadratic-Gaussian (LQG) problems, and explain the discrepancy by the former's simultaneous utilization of both light quadratures. Semiclassical truncated-Wigner techniques for quantum-optical networks are discussed in Chapter 5, leading to a thorough discussion of quantum noise in systems with free-carrier nonlinearities (Chapter 6), comparison to the Kerr nonlinearity, and potential applications for analog computing based on limit cycles and amplification (Chapters 7-8). Ising machines based on optical parametric oscillators (OPOs) are discussed in Chapters 9-10, the former focusing on large 1D and 2D networks of OPOs, and the latter on the dynamics of a single OPO in the ultrafast, synchronously-pumped regime. Optical properties and design considerations for silicon photonic waveguides are are treated in Chapter 11.