VictorJuiz/thesis huggingface dataset:
Dynamics of Mode-Switching in Neural Networks: How nonlinear systems generate behaviour via a thermodynamic process
Keywords:  Department of Physics
Computational neuroscience
Theoretical neuroscience
Nonlinear dynamical systems
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Thesis

Animals engage in specific motivated actions, such as feeding and drinking, to maintain homeostasis. However, the neural correlates of motivational states--and the mechanisms through which animals transduce internal need into action--remain largely unknown. In this thesis, we study motivational drives by examining what happens when they come into conflict. We begin by developing a simple behavioural task to interrogate the balance of homeostatic needs in mice. While the mouse performs this task, we record activity from a large population of neurons distributed across its brain. We characterize the dynamics of these neurons using dimensionality reduction techniques, with the goal of distilling our dataset into its most informative components. To understand the mechanism underlying behavioural mode-switching, we train a recurrent neural network to capture the salient features of its biological counterpart. We then reverse-engineer this computational model by linearizing in the vicinity of its stable states, demonstrating the existence of two basins of attraction--corresponding, physically, to food-seeking and water-seeking behaviour--joined by a smooth line of intermediate semi-stable states. Finally, we discuss how the system's motion along this continuous manifold can give rise to two robust and distinct actions: cue-driven eating and drinking. In order to do so, we recast our discussion of homeostatic need selection as a thermodynamic process, illustrating this analogy with an out-of-equilibrium Ising model that reproduces the relevant behaviour of our biological system.
The E. coli whole-cell modeling project : growth rate control and environmental responses
Keywords: Bioengineering.

Whole-cell modeling is an approach to building fine-grained computational models that accounts for every molecule and the known mechanisms and interactions of gene products in a cell. The E. coli Whole-Cell Modeling Project applies this approach to the model organism E. coli by integrating data and mechanistic understanding of E. coli generated by many labs and has the potential to lead to rapid biological discovery while providing a means of assessing the body of work representing our collective understanding of E. coli physiology. Creating a model of this scale can provide deep biological insights into complex regulatory networks and growth control, identify inconsistencies between datasets used to construct the model, demonstrate emergent behavior to suggest novel behavior arising from complex interactions, and make biological predictions that have been experimentally validated. Growth and environmental responses are essential for living organisms like bacteria to survive and adapt to constantly changing environments and the model can also be used to better understand these processes. With the inclusion of regulation and kinetics rates, the E. coli model exhibits a mechanistic growth rate that is dependent on the environment and internal simulation state and no longer confined to environmental growth conditions used to parameterize the model. Importantly, the model also demonstrates more appropriate responses to environmental limitations and shifts and provides a means to assess the factors that control growth rate in the context of the entire cell. This sets a critical foundation for expanding the model to new environmental conditions and allows for additional predictive capabilities
Early relationship development : a prospective longitudinal study on new online dating relationships
Keywords: Communication.

The beginning of a relationship's trajectory, after two partners first meet but before they become an official couple, is a period of uncertain, potentially turbulent, and often exciting growth. All relationships -- successful or not -- go through these early stages and the decisions made during this period could be life-changing. What does this early period of relationship development look like and how do we know whether a new potential relationship will succeed or fail? The present dissertation longitudinally and prospectively followed 82 single online daters across 12 weeks to study real-world early relationship development as it occurs. I tested and found support for the positive association between sociosexuality and the number of potential partners a person is romantically interested in at a given period of time. I then explored a subsample of the data, focusing on new potential relationships (i.e., relationships in which participants met the potential partner within 72 hours of first reporting on them), using descriptive analyses, survival analyses, and growth modeling. I found that there is great variation in relationship trajectories during this early period -- with each trajectory differing in their intercepts, slopes, and shapes -- and this variation made it difficult to capture a systematic effect of time on romantic interest in the growth models. From the survival analyses, I found that most new potential relationships do not last beyond a week, and of the ones that do last, most become romantic after about three weeks of dating. These findings provide insight into early relationship development and future directions for the fields of close relationships and communication
Early Warning Signal Detection for Ross River Virus in Queensland, Australia
Keywords:  Department of Biology
Ross River Virus
infectious disease
temperature
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Thesis

Over the past few decades, there have been resurgences in vector-borne diseases that may have been driven by factors such as climate change, drug resistance, and urbanization. To predict these changes, forecasting methods and simulation models have been developed, but they are difficult to apply to vector-borne diseases due to limited case data available and the complex dynamics of arthropod vectors. Having the ability to predict imminent outbreaks before cases increase is imperative to mitigate the consequences of early exponential growth. One promising approach applies the theory of critical slowing down, which predicts that as a system approaches a critical transition (for example, from disease elimination to resurgence), its ability to return to stability following minor disturbances diminishes. This phenomenon results in particular patterns in disease incidence that are detectable as characteristic changes in summary statistics prior to the critical transition. Additionally, temperature strongly influences mosquito traits and life cycles, which in turn affect disease transmission. Detection of thermal thresholds, temperature moving from an inhibitory range to a suitable range for transmission, can allow us to take timely preventative actions prior to a potential outbreak. We tested for early warning signals of critical slowing down of Ross River virus in Queensland, Australia, by calculating nine summary statistics across a rolling window. The summary statistics were then compared to the temperature suitability for transmission (defined as relative R0(T) from a previous model) to determine whether the system crossed a thermal threshold. Five of the 15 HHS regions exhibited critical slowing down, primarily in variance, skewness, kurtosis, autocorrelation, and index of dispersion. Gold Coast exhibited the strongest evidence for critical slowing down occurring when temperatures crossed a threshold between 18.2-18.3 degrees Celsius. This shows that early warning signal detection can aid in predicting disease outbreaks and determining possible influential variables such as temperature.
Earthquakes and the structuring of Greco-Roman society : the longue durée of human-geological environment relationships in Helike, Greece
Keywords: Classics.

Earthquakes have been linked with societal collapse in various places throughout the past, most notably in the eastern Mediterranean with the end of the Late Bronze Age (c. 1200 BCE) and the division and decline of the Roman Empire from the fourth to sixth centuries CE. Archaeological evidence of widespread destruction, complemented by an inflation of historical earthquake records for late Roman contexts, points to periods of higher seismicity coinciding with political and economic weakening and socio-cultural downturn. However, since ancient times, people living with persistent earthquake hazards have demonstrated forms of resilience. Just as Amartya Sen (1983) and Peter Garnsey (1989) revealed famines and food shortages as social, not natural, problems, I show how earthquakes traditionally perceived as 'natural' disasters are not 'natural' but social and a critical factor in political ecological relationships. My dissertation exposes the persistent factor of earthquake hazards in Greco-Roman society. I analyze Greco-Roman accounts of earthquakes together with targeted architectural and geological remains from six occupational phases of settlements spanning the third millennium BCE to fifth century CE in Helike, Greece. Applications of resilience theory from archaeology focus on effects of earthquakes in not only destruction but also invention and innovation in society. The results reveal a political ecology of human-earthquake relationships in the Greco-Roman world. The case of Helike demonstrates how earthquake factors persistently shaped and were shaped by political, economic, and cultural developments. The use of novel methodological approaches and techniques from geoarchaeology and soil micromorphology to new types of data proves catastrophe narratives to be false or too simplistic and reveals a political ecology of human-earthquake relationships. I contribute the earthquake and geological environmental context of Greco-Roman societal development and change, transforming scholarly attitudes toward earthquakes, disaster, and the environment in societal development and change
Ecological and evolutionary mechanisms for emerging infectious diseases : case studies in humans and mammalian wildlife
Keywords: Biology.

SARS. Ebola. Zika. COVID-19. The majority of all new infectious diseases discovered in the last decades are transmitted from animals to humans. More and more diseases have "spilled over" from wildlife to humans and escalated into pandemics, largely due to anthropogenic activities and global change, including climate change and land use change. Emerging diseases in wildlife can spill over from one species to another, decimating many vulnerable species. However, because human and wildlife systems are so complex, we still lack a clear understanding of the mechanisms driving disease emergence. My dissertation fills some critical gaps in our understanding of the ecological and evolutionary drivers of infectious diseases within and across species. In Chapter 1, I showed how temperature, rainfall and susceptible population size (ecological drivers) affect the (re)emerging mosquito-borne disease dengue. I used a data-driven approach for inferring causal relationships in nonlinear systems and demonstrated that suitable climate can only promote epidemics when the susceptible population is sufficiently large. In Chapter 2, I uncovered ecological and evolutionary drivers of pathogen sharing between different species using datasets of organisms and their pathogens, and their ecological and phylogenetic similarities, to understand how pathogens have adapted to multiple organisms. Here, I quantified the relative importance between ecological and evolutionary factors for predicting pathogen sharing by taxonomic level. Finally, Chapter 3 highlights a wildlife disease case study using genomic analyses of canine distemper virus (CDV) sampled from different carnivores in Alaska and Yellowstone to understand how viruses evolve in wildlife and what disease dynamics they cause. All these findings will help facilitate more effective preventative disease management strategies to improve human and animal health. In sum, my dissertation will help bridge the knowledge gap between ecological and evolutionary drivers of infectious diseases to better understand spillover and subsequent outbreaks. My research will help lay the foundation for future interdisciplinary studies in disease ecology and molecular evolution and will improve the effectiveness of both public health strategies and wildlife conservation
Economic Inequality and Local Political Trust in Modern China: Exploring the Role of Social Values
Keywords:  Stanford Global Studies
Economic inequality
Political trust
Social values
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Thesis

Economic inequality can lead to various sociopolitical consequences and declining political support is one of them. Previous empirical studies have reported the negative effects of economic inequality on political trust in societies with different economic and political systems. This study aims to examine the relationship between economic inequality and local political trust in Mainland China using the 2018 CFPS data, with special attention paid to the role of social values, including the belief in upward social mobility and the belief in the relationship between inequality and economic growth. Particularly, it focuses on the effects of both objective and subjective economic inequality.
Using multilevel ordinal logistic regression models, this study finds that 1) Both objective and subjective economic inequality is significantly negatively associated with local political trust. Respondents who have perceived the severity of economic inequality in the current society or live in areas with a large income gap between rich and poor families are more likely to consider local cadres as distrustful. 2) Two social values are both significantly negatively associated with perceived economic inequality. Individuals who have much confidence in opportunities for upward social mobility based on personal merits or agree with the statement that the income gap should be enlarged for economic growth are less likely to perceive economic inequality as highly severe. Moreover, the effect of the belief in social mobility is larger than the belief in economic growth. 3) Social values moderate the negative effect of economic inequality on local political trust. This study makes contributions to the literature by providing new understandings of mechanisms of economic inequality’s influence on political trust as well as the relationship between inequality and regime legitimacy in China.
EdConnect, empowering support teams to share knowledge and collaborate
Keywords: Special Education; Individualized Education Plan
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Thesis

The world of special education is complex. Families and general education teachers struggle to understand the characteristics of a student’s specific disability as well as how to implement the recommended supports that can positively impact the student’s learning. Stakeholders on the support team for students such as the special education teacher and intervention specialists are experts in implementing effective support for students with special needs. But other stakeholders such as general education teachers or families may lack knowledge needed to ensure the student is receiving consistent support in and outside of the classroom.
To address this knowledge gap and better ensure that students are getting adequate services, we are creating a centralized digital platform for a community of learners (the support team) engaged in collective knowledge exchange. Research from the learning sciences undergirds each core feature of our platform, EdConnect.Through these selected features, teachers can leverage the expertise of the specialists and families on the support team to customize and implement student supports, while engaging within a community of learners focused around the issue of best supporting learners with special needs. Preliminary user studies indicate that users perceive the application to be helpful and value the affordances of the platform in various contexts.
Education, Collective Memory and Transitional Justice in postcolonial Britain
Keywords: British Empire
Education
Collective memory
Transitional justice
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Thesis

What role do textbooks and educational materials have in institutionalizing officially-sanctioned narratives of the past? How can history education be used to inculcate national identity and inform collective historical memory? My research seeks to answer these questions with regard to the case of modern Britain, specifically how the British education system has shaped the collective historical memory of the British Empire since 1900. Through textual analysis of history textbooks from 1900-1960 and an original survey connecting educational experience with opinions about the empire, I seek to critically analyze the dominant narratives of the empire within educational materials from the twentieth century to the present and analyze their impact on collective memory. My empirical research finds that the national history curriculum has institutionalized a glorified view of the past while omitting key historical episodes that do not fit the narrative of imperialism as a “civilizing mission.” The thesis concludes by examining how education reform can be leveraged to promote truth, reconciliation, and justice at the systemic level in Britain and other postcolonial societies.
EDUCATIONAL DISPOSSESSION AND RE-ENVISIONING EQUITABLE FUTURES: HOW MARGINALIZED STUDENTS INTERNALIZE, RESIST, OR DEFY EXPECTATIONS OF A FLIPPED CLASSROOM IN GENERAL CHEMISTRY
Keywords: Equity in STEM
Education, Higher
Active learning
Flipped classrooms
Chemistry education
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Thesis

Research demonstrates that STEM education before college often excludes members of marginalized communities, including female , ethnic- and racial-minoritized, first-generation college, and low socioeconomic status students. The same pattern continues in college, where introductory STEM courses act as gateways into careers in STEM and medicine. As reforms in introductory STEM classes focus on academic outcomes, they miss key insights about students’ experiences, particularly students’ psychological character. Using grounded theory and narrative inquiry, this research will center the voices of marginalized students. Evaluating fifty-seven interviews with students of various backgrounds, this paper argues that the implementation of the flipped classroom in the introductory chemistry series prevents the success of students with medium to low incoming preparation in chemistry. Inaccessible pedagogical practices such as speed learning, assessing primarily problem solving on exams, and a lack of transparency create academic and psychological vulnerabilities in students that lead to long-term lowered confidence and belonging. As the series acts as a gateway for marginalized students, their life trajectories are most affected by their experience, either positive or negative, in the series. By closing doors of opportunity for students, we fail to uphold equity and uplift student agency. Therefore, issues of equity and access must be addressed at the pedagogical level to create a more inclusive pipeline into STEM and medicine at Stanford and beyond.
Effects of numerical centrosome aberrations on cell division and mitotic spindles
Keywords: Biology.

Most cycling animal cells contain one or two centrosomes depending on cell cycle stage. However, alternative centrosome states are crucial to who we are: We all come from an mother cell lacking centrosomes, the acentrosomal human oocyte, which, after fertilization, developed into a conceptus that invaded the maternal endometrium using trophoblast giant cells containing more than two centrosomes. However, while numerical centrosome aberrations occur as physiological phenomena, they can also occur pathologically, such as in tumorigenesis and microcephaly. Centrosomes are non-membrane-bound organelles that are in the cytosol of most cycling animal cells and are major microtubule organizing centers during mitosis. During mitosis, one centrosome consisting of two centrioles and surrounding pericentriolar material (PCM) is present at each side of the mitotic spindle apparatus, which separates chromosomes into two future daughter cells. In late G2 and early mitosis, centrosomes undergo a PCM expansion that increases the capacity to nucleate and organize microtubules. The two centrosomes then become separated, defining the spindle poles. However, cells can build bipolar spindles and divide into two without centrosomes or with extra centrosomes. Nevertheless, numerical centrosomes aberrations, whether greater or less than two during mitosis, influence the progression and, in some cases, outcome of cell division. In absence of centrosomes mitotic duration becomes elongated and PCM proteins localize to the spindle poles. In presence of supernumerary centrosomes, multiples spindle poles can form and either become clustered into two poles, resulting in bipolar division, or remain as multiple poles, resulting in multipolar division. After a brief introduction to centrosomes and numerical centrosome aberrations in Chapter 1, I present an experimental analysis of cell division in mammalian cells without centrosomes (Chapters 2-3) or with supernumerary centrosomes (Chapter 4). In Chapter 2, I investigate the cause of the mitotic elongation in acentrosomal cells and specifically assess whether the spindle assembly checkpoint, which halts mitotic progression until chromosomes are correctly attached to the mitotic spindle, is responsible for this elongation. Furthermore, I assess whether the temporal delay is necessary for completion of cell division in acentrosomal cells. In Chapter 3, I investigate the spatiotemporal arrangement of normally centrosome-localized proteins, with focus on the PCM proteins γ-tubulin and Cep192, during mitosis in absence of centrosomes. In Chapter 4, I investigate how cells with supernumerary centrosomes return to homeostatic centrosome numbers on a population level. In Chapter 5, I present general conclusions as well as ideas for future investigation of numerical centrosome aberrations in mammalian cells
The efficacy of beauty : aesthetics and action in the thought of Xenophon of Athens
Keywords: Classics.

This dissertation examines the role of aesthetics, art and visual culture in the thought of Xenophon of Athens (c. 430-354 BCE). Although his diverse writings offer many insights into the visual culture of 4th century Greece, no study has yet attempted to explain them as pertaining to a consistent thinker. I argue Xenophon's engagement with art is both coherent and original. His thought about art and beauty was grounded in a conception of their functionality and practical applicability: the experience and value of beauty and art, in other words, are to be explained and considered in relation to human needs and human action. Unlike what the modern concept to aesthetics often implies, Xenophon's approach to art treats it not as a domain separated to itself but as a practice that is organically interwoven with the life of action. I develop my argument in four chapters. In chapter 1, I examine the theoretical principles discussed by Xenophon's Socrates in the Memorabilia, which show that in contrast to contemporary intellectuals, he saw value in the realm of the visual and argued that the phenomenon of beauty should not be abstracted but rather seen in relation to human needs. In chapters 2-4, I demonstrate how this conception of the visual is represented in his other works: in his representation of leisure in the Symposium (chapter 2), of practical domestic life in the Oeconomicus (chapter 3), and in his political thought in the Agesilaus, Cyropaedia and Hipparchicus (chapter 4). I argue that throughout these distinct fields, for Xenophon art and beauty are fundamental forces in human life that inform domestic economy and provide avenues for understanding and practicing politics