VictorJuiz/thesis huggingface dataset:
Nucleic acid-based fluorescent probes [electronic resource]

This thesis describes the development of novel nucleic acid-based fluorescent probes. Chapters 2 and 3 describe the rational design of fluorogenic probes that measure the activity of specific DNA-targeting enzymes. These probes rely on fluorophores that are quenched in the initial probe state, and demonstrate a 40- to 250-fold increase in fluorescence following reaction of the probe with its target enzyme. The probes function both in vitro with recombinant enzyme and in more biologically relevant samples such as bacterial cell culture and cell lysate. One of the probes was applied in a high-throughput screen for enzyme inhibitors, and was used to identify a potential inhibitor. These probes are expected to be useful for screening the effects of polymorphisms, mutations, post-translational modifications, and competitive inhibitors of enzyme activity. Chapter 4 describes a method to identify the sequence of unnatural nucleic acids on single beads. Combinatorial one-bead-one-compound libraries are commonly used to identify library members with a desired property. Identification of the library member on a selected bead is essential to this approach. A method for determining the sequence of nucleic acids (including unnatural nucleic acids, which cannot be identified by traditional polymerase-based methods) was demonstrated on natural DNA and on oligodeoxyfluorosides (ODFs). This method has the potential to improve the way our lab discovers ODFs by decreasing library synthesis time and by decreasing bead identification time. In addition to using this method to sequence beads from our one-bead-one-compound combinatorial ODF libraries, we anticipate that this method can be expanded to sequence anything synthesized in a step-wise fashion where the mass difference between each intermediate can give the identity of the intermediates (e.g. backbone or sugar modifications such as LNA, PNA, DNA, RNA; or non-canonical nucleotides). Chapter 5 describes work towards selecting an RNA molecule that binds a fluorophore and catalyzes the release of a fluorescent quencher to covalently attach the fluorophore to itself. Such a tool will allow us to monitor the fluorescently tagged RNA spatiotemporally in live cells.

Keywords: Biophysics.
Advisor: Kool Eric T. primary advisor. Thesis advisor
Smolke Christina D. advisor. Thesis advisor
Wandless Thomas advisor. Thesis advisor
Numeric invariants from multidimensional persistence [electronic resource]

Throughout the past decade, there have been many developments and innovations in topological data analysis and persistent homology. The theory of persistent homology is a powerful tool which assigns to any filtered space a persistence module, which is typically interpreted as a module over a ring of polynomials. Although persistent homology serves as a powerful method of analysis for filtered spaces, persistence modules can exhibit a large degree of complexity, especially if the dimension of the filtration is greater than one. Because of the high complexity of persistence modules, they cannot be used directly in the study of concrete data. Instead, one must utilize the structure of persistence modules in order to derive easily understood invariants which provide useful information about the underlying data. This thesis examines the algebraic geometric structure of the space of multidimensional persistence modules and uses the information gleaned to construct numeric invariants. Moreover, these numeric invariants are geometrically meaningful -- if we had calculated these numeric invariants from a filtered space constructed from a (finite) data set, we expect these numeric invariants to encode information about the size, shape, and prominence of the topological features of the data set.

Keywords: Mathematics.
Advisor: Carlsson Gunnar
Cohen Ralph
Vakil Ravi advisor. Thesis advisor
Numerical investigations of scarmjet unstart [electronic resource]

Supersonic combusting ramjets (scramjets) have been envisioned as an economic means for long-range hypersonic delivery system and access to outer space. If strong disturbances such as those due to combustion occur in the engine, a failure mode called unstart could result. When unstart occurs, the mass flow rate through the engine inlet cannot be maintained, leading to loss-of-thrust and engine stall. Because the probability of unstart grows with increasing heat release from combustion, the danger of unstart is an important factor limiting the performance of scramjets. The present studies perform calculations of scramjet unstart in both cold and hot airflows based on Reynolds-averaged Navier-Stokes (RANS) turbulence closures. The flow solver is first validated against a Mach 5 experiment without combustion, aiming at establishing confidence in the unstart-prediction capability of the solver. Modifications to the solver are then proposed to improve its convergence rate to steady-state solutions and to provide tools for the analysis of unstart dynamics. Finally, the solution curve of a Mach 8 scramjet is calculated in a wide range of heat-release rates in conjunction with studies of the bifurcation structure of scramjet systems. We will also discuss linearized system dynamics that provide insight into a metric to forewarn unstart and unstart-mitigation mechanisms.

Keywords: Mechanical Engineering.
Advisor: Moin Parviz primary advisor. Thesis advisor
Alonso Juan José
Lele Sanjiva K. (Sanjiva Keshava)
A nutritional perspective on the Lepidopteran gut microbial community [electronic resource]

The overarching goal of this dissertation is to better understand how host nutrition mediates the relationship between the gut microbiota and their host, using adult butterflies as a novel and uniquely informative study system. In Chapter 2 (previously published as Ravenscraft and Boggs (2016) in Oecologia), I lay the nutritional foundations of the research by studying the relationship between the primary foods of butterflies and butterfly nutrient limitation. I show that flower nectar has much lower concentrations of sodium and amino acids than fruit juice. Consistent with the predictions of nutritional theory, nectivorous butterflies have a stronger preference for sodium, but contrary to expectations, frugivores respond more strongly to amino acids than nectivores. In Chapter 3, I investigate how the community composition and functional potential of the butterfly gut flora vary among host species and between host feeding guilds. I find that host species identity explains more variation in gut community composition than host diet. However, host diet still affects the functional potential of the gut flora: gut communities of frugivores exhibit higher levels of amino acid catabolism and lower levels of sugar catabolism than the gut communities of nectivores. In Chapter 4 I ask how gut bacteria are related to butterfly performance and fitness. I find that abundance of the bacterium Commensalibacter intestini is positively correlated with host lifespan, and maternal abundances of a Caulobacter species and a Streptococcus species are associated with faster larval development and increased adult food consumption, respectively, in the F1 offspring. All of these associations are maintained when maternal food is limited, thus there is no evidence that quantitative dietary restriction influences the outcomes of the host-gut flora relationship. In sum, this research develops adult butterflies as a study system for gut flora and thereby advances our understanding of nutritional interactions between a host and its gut microbial community.

Keywords: Biology.
Advisor: Boggs Carol L.
Peay Kabir
Dirzo Rodolfo advisor. Thesis advisor
Fukami Tadashi
Objective assessment of manual dexterity for surgeons [electronic resource]

I present the design and implementation of a manual dexterity assessment system that can measure hand movement data using Inertial Measurement Unit (IMU) sensors. These wireless sensors consist of a 3-axis accelerometer, a 3-axis gyroscope, and a 3-axis magnetometer; and record at the rate of 30 data samples per second. The Purdue Pegboard test and the O'Connor Tweezer Dexterity test are timed manual dexterity assessment tests with accomplishment measured by a single outcome metric -- speed. However, accuracy is often more important than speed in surgical tasks. I have modified both of these standardized tests to incorporate an assessment of accuracy. For the integrated system, I show the results of two validation studies: (1) Construct validity and (2) Concurrent validity. I also propose a new method to interpret hand movement data for objective assessment of manual dexterity, called EDGE (ElectroDextroGramExam). The EDGE model derives analogies from the gait analysis and the ECG (ElectroCardioGram). By dividing each cycle of a repetitive task into discrete phases, we can better understand the differences between the motion characteristics of a novice versus an expert surgeon. This would help in providing a meaningful feedback to the learners for improving their manual skills.

Keywords: Electrical Engineering.
Advisor: Srivastava Sakti primary advisor. Thesis advisor
Nishimura Dwight George advisor. Thesis advisor
Shenoy Krishna V. (Krishna Vaughn) advisor. Thesis advisor
Observation of supermode-density-wave-polariton condensation in a multimode cavity QED-BEC system [electronic resource]

Investigations of many-body physics in an AMO context often employ a static optical lattice to create a periodic potential. Such systems, while capable of exploring, e.g., the Hubbard model, lack the fully emergent crystalline order found in solid state systems whose stiffness is not imposed externally, but arises dynamically. In this thesis we describe a new multimode cavity — 87Rb Bose-Einstein Condensate (BEC) apparatus aimed at introducing a new method of generating fully emergent and compliant optical lattices to the ultracold atom toolbox and providing new avenues to explore quantum liquid crystalline order. We describe the design and construction of the apparatus which combines a 87Rb BEC and an adjustable-length high-finesse optical cavity that can be tuned from single to multimode configuration. We will present calibration of the machine in both single and multimode configurations, as well as the first observation of a supermode- density-wave-polariton condensate, where the BEC develops density-wave order in the linear combination of cavity modes that optimizes the superradiant self-organization transition induced by transverse pumping.

Keywords: Applied Physics.
Advisor: Lev Benjamin L. primary advisor. Thesis advisor
Hollberg Leo (Leo William)
Kivelson Steven advisor. Thesis advisor
Of polyketides and fatty acids [electronic resource] : in vitro reconstitution and analysis of metabolic pathways

As a tool, in vitro reconstitution of metabolic pathways has a strong record of illuminating biological processes. The pathways for biosynthesis of secondary metabolite polyketides and primary metabolite fatty acids involve very similar catalytic steps and related protein machinery. Each strategy has a growing intermediate chain elongated stepwise with acetate-based building blocks. Here, two main systems were reconstituted in vitro: an unusual assembly line polyketide synthase from human pathogenicity-associated Nocardia bacteria, and the fatty acid synthase of cyanobacterium Synechococcus sp. PCC 7002, a potentially industrially relevant strain for alkane production. While polyketides have been a rich source of antibiotics and other useful molecules, the majority currently in use were discovered decades ago by searching cultured microorganisms or soil samples for produced molecules and screening for a specific function, such as antibacterial activity. Though fruitful in the past, a newer approach is to use sequenced genomes. Here the discovery method using in vitro reconstitution began the decoding process for a so-called "orphan" (natural product unknown) gene cluster. Interestingly, the cluster was found in nine related potentially pathogenic species isolated from nocardiosis-diseased patients. Proteins of the system were heterologously expressed and purified from E. coli. Adding cofactors and substrates and using a stable isotope 13C-labeling strategy, heptaketide and octaketide products were identified from in vitro reactions and characterized by 2D NMR. Looking at another system, kinetic analysis was performed on the in vitro reconstituted fatty acid synthase (FAS) of Synechococcus sp. PCC 7002. Cyanobacteria are desirable hosts for biodiesel production, because they are photosynthetic, relatively fast growing, and can secrete products. The overall FAS rate was exclusively limited by the FabH ketosynthase, which initiates product synthesis. This finding sharply contrasts with the related E. coli FAS, which is predominantly limited by its dehydratase (FabZ) and enoyl reductase (FabI) activities, showing that the FAS regulatory behavior is a property of controlling enzyme(s). In all cases, the goal was to learn something by taking Nature's complex biosynthetic machinery outside of a cell and placing it into a test tube, allowing near complete control over what components are added in a reaction.

Keywords: Chemical Engineering.
Advisor: Khosla Chaitan
Sattely Elizabeth advisor. Thesis advisor
Smolke Christina D. advisor. Thesis advisor
On a Journey of Struggle, Strength, and Human Flourishing: Understanding the Lived Experiences of Mental Health (Holistic Well-being) Among Undergraduate Students of Color at Stanford University

This study examines the lived experiences of mental health (holistic well-being) among a purposefully selected sample of undergraduate students of color at Stanford University. As previous research has focused primarily on the quantitative measurement of student mental health, specifically among Caucasian, female undergraduate samples, and with a tendency towards focusing on illness rather than health, little is known about how mental health is experienced among a diverse undergraduate population. The current study utilizes a phenomenological, inductive qualitative research design to investigate what factors affect student holistic well-being. Data were collected through the use of grounded, semi-structured in-person interviews and a final sample population of 22 undergraduates, all of whom self-identified as a person of color, were analyzed. Thematic analysis revealed the emergence of three main categorical themes that affect student mental health: independent, interdependent, and sociocultural factors. Within these categories, there arose independent (e.g., self-care practices) and interdependent (social support) perceived enhancers to student mental health and independent (e.g., being overwhelmed), interdependent (e.g., disconnection), and sociocultural (e.g., societal pressures) perceived detractors to undergraduate holistic well-being. Findings from this research have important implications for expanding awareness and education of student mental health, taking prevention, strengths-based approaches into consideration.

Keywords:  Graduate School of Education
mental health
undergraduate students of color
stress
human connection
vulnerability
holistic well-being
qualitative research
positive psychology
higher education
“single story"
Thesis
Advisor: Padilla Amado
Willinsky John
Wolf Jennifer
On the applicability of mathematics in physics [electronic resource] : a critical review of Wigner's puzzle

This dissertation takes up on the question of why mathematics is effective in the natural sciences, especially in physics. The answer proposed is that modern physics is the result of a historical idealization, began by Galilee and developed fully by Newton, which makes its mathematization possible. Physicists of the modern era came up with a set of idealized assumptions, invariance principles in our jargon, that allowed them to abstract from many conditions that could in principle effect the result of an experiment, and if so would make the formulation of the laws of nature impossible (or far too complicated to be of any use). Among these invariance principles, there is the assumption that time is uniform and space homogenous. Thus the regularity that the experimenter detects among events at the time t and location x of the experiment holds elsewhere, in fact universally, under the same initial conditions. Such idealizations make for the mathematical and precise formulation of laws of physics. This precision has proved to be extremely useful in the study of nature, which itself is a very complicated and at times unpredictable totality. Chapter 2 (first main chapter) examines the physicist Eugene Wigner's remarkable paper on "The Unreasonable Effectiveness of Mathematics in the Natural Sciences", offers an original and contextual reading of the paper, and explains the role of invariance principles in modern physics. Chapter 3 examines two common readings of the "Unreasonable Effectiveness", by the philosopher Mark Steiner and the mathematician Richard Hamming, and responds to their criticisms based on the reading proposed in chapter 2. Chapter 4 examines the case of quantization as one of the most difficult cases of the "Unreasonable Effectiveness", and proposes a solution on the basis of the early developments of quantum mechanics and the route to the canonical commutation relations. Chapter 5 examines the development of complex numbers from their first appearance in the 16th century to their use in the fundamental equations of quantum mechanics, and explains their effectiveness based on their calculational power demonstrated in a series of mathematical theorems. It is my hope that this dissertation sheds light on the much debated question of the applicability of mathematics through a historical understanding of the relationship between mathematics and physics. The uncriticized philosophical idealization surrounded the applicability problem so far, I hope, finds a historical grounding through the study of the kind conducted in this dissertation.

Keywords: Philosophy.
Advisor: Ryckman Thomas primary advisor. Thesis advisor
Donaldson Tom (Philosopher) advisor. Thesis advisor
Friedman Michael advisor. Thesis advisor
Lawlor Krista advisor. Thesis advisor
On the free-boundary mean curvature flow [electronic resource]

We investigate the free-boundary mean curvature flow. This is an evolution of surfaces by "steepest descent for area,'' while preserving the Neumann-type condition that all the surfaces meet some fixed barrier orthogonally. For example, a bubble in a sink. We first prove the Huisken-Sinestrari convexity estimates for free-boundary mean curvature flow, which classifies "type-II'' singularities. We then develop the notion of weak free-boundary mean curvature flow, extending Brakke's original definition, and proving a local regularity theorem. We also prove a geometric eigenvalue gap estimate, extending results of Ashbaugh-Benguria and Benguria-Linde.

Keywords: Mathematics.
Advisor: Brendle Simon
White Brian T.
Simon L. (Leon)
On the Highly Dubious Intrinsic Moral Value of Human Suffering: Retribution and the Fourth Great Ape

The question that must be answered – and the question that to which two different answers are given – is this: are human actions influenced by factors outside of the actor’s control in a way that mitigates moral culpability? In other words, can the physical, psychological, and social circumstances surrounding a human action render that human morally inculpable? In summary, there are two incompatible belief frameworks contained within United State criminal justice legislation. Diminished responsibility relies on mind-body supervenience, in which the mind is necessarily affected by the physical circumstances of the brain— such as psychology, biology, and sociology. Ordinary criminal punishment, however, relies on a view of the mind-body connection that does not allow for moral culpability to be mitigated by physical circumstances – mind-body independence. Both of these views
cannot be incorporated into a single coherent framework. Empirical evidence indicates that external factors significantly affect human behavior. Given this, we should view all criminals as being subject to a diminished moral responsibility. In current law, those with diminished responsibility are not punished retributively. Thus we should eliminate retribution as a justification for all cases of criminal punishment.

Keywords: Nicholas Hansen
Stanford University
Honors Theses
STS
Program in Science Technology and Society
Human Suffering
Thesis
Advisor: Skokowski Paul
On the psychology of privilege [electronic resource] : merit and maintenance motives in the concealment of advantages

Invisibility makes privilege powerful. Hard to notice and easy to deny, privilege perpetuates intergroup inequality by giving unearned advantages to certain groups. However, recent social movements (Occupy, Black Lives Matter protests) threaten this invisibility. I argue that a useful way to understand the psychology of privilege is through the lens of two critical motives: the merit motive and the maintenance motive. Together, these motives lead people to mobilize their advantages during competition in order to secure desired outcomes, but to conceal these advantages under the cloak of merit by construing their own actions differently. In Chapter 1, I suggest the privileged manage threats to their sense of merit by creating a false dichotomy between group and personal privilege: they accept group privilege exists, but deny personally benefiting. When exposed to evidence of privilege, the upper class and Whites claim more personal hardships (Experiments 1-3). Consistent with a merit motivation account, self-affirmation reverses this effect (Experiment 3). Importantly, self-affirmed participants acknowledge greater personal privilege, and as a result support inequality-reducing policies. In Chapter 2, I demonstrate these claims are motivated specifically be merit concerns: The privileged claim hardship (and effort) so they can continue attributing outcomes to their own merit. When they have or are provided alternatives to merit, however, they no longer claim hardships (Experiments 4-5). Further, when they first affirm evidence of personal merit (as compared to team accomplishments), they no longer claim hardship (Experiment 6). Finally, the privileged also claim personal effort in response to evidence of privilege, so long as that privilege is ingroup relevant (Experiment 7) and they have not previously been able to claim hardships as an alternate defense (Experiment 8). In Chapter 3, I explore the limits of the merit motive and how it interacts with a maintenance motive. That is, the privileged want to protect their sense of personal merit, but also want to protect the resources this privilege provides; how do they navigate the two? I find that the privileged construe their advantages strategically in ways that allow them to claim personal effort while maintaining the benefits. They deny that unearned advantage is advantageous (Experiments 9a-e) or is unearned (Experiments 10-11). Exploring the psychology of privilege enriches understanding of intergroup inequality, generating new avenues for interventions.

Keywords: Business.
Advisor: Lowery Brian
Miller Dale T. advisor. Thesis advisor
Tiedens Larissa Z.