VictorJuiz/thesis huggingface dataset:
Examining the Effect of a Redox-Active Metallo-porphyrin on Staphylococcus Biofilms

Background: Staphylococcus aureus is a leading pathogen and cause of orthopedic implant infections. S. aureus infections are often resistant to numerous antibiotic treatments and frequently grow in biofilm structures. Biofilms occur when microorganisms adhere to surfaces and grow in networks that are phenotypically different from planktonic counterparts. These differences make biofilms resistant to traditional antibiotic treatment. Biofilms actively modulate their redox environments suggesting the utility of a potent small molecule redox-active compound in treating biofilm infections.
Methods: S. aureus (ATCC 29213) biofilms were established and were then treated with either a potent redox-active metalloporphyrin MnTE-2-PyP (chemical name: manganese (II) meso-tetrakis-(N-methylpyridinium-2-yl) porphyrin) or phosphate-buffered saline (PBS). The matrix was quantified with crystal violet and confocal microscopy. An animal model was conducted using an S. aureus infected intramedually fixed femur fracture. This murine model ran over a two week time course and mice were treated with either no treatment, MnTE-2-PyP, antibiotic, or a combined therapy of antibiotic and MnTE-2- PyP. Femurs were collected at the experimental endpoint and were analyzed for CFUs.
Results: MnTE-2-PyP was found to significantly reduce the extracellular matrix in the in vitro studies. In the murine fracture model, combined MnTE-2-PyP -antibiotic treatment resulted in lower CFU/g bacteria counts in harvested femurs as compared with the other treatment groups.
Conclusions: Changes in redox environment seem to have significant effects on biofilm structure and robustness. Utilization of a redox-active metalloporphyrin in conjunction with antibiotics may be an effective therapeutic possibility in treating biofilm infections.

Keywords:  Department of Biology
Biology
Biofilm
Infection
Antioxidant
Free Radical
Thesis
Advisor: Cyert Martha
Heller H. Craig
Examining the Implementation of Culturally Responsive Schooling in Karuk Ancestral Territory

Exploring teacher approaches to culturally responsive schooling (CRS) among schools serving Indigenous youth is critical, given low achievement rates and the sociohistorical context of Indian education in the United States. The purpose of the study was to explore this aspect of curricular implementation in the context of the Karuk Tribe’s pilot program of curriculum, Nanu’ávaha. Interviews examined teachers' perceptions of the ways in which they feel that the different elements of Nanu'ávaha and their associated training have prepared them to implement culturally responsive curriculum and schooling methods. Data and thematic analysis supported the use of formal training methods to prepare teachers for curricular programs and the sociopolitical context of Native communities and classrooms. Results also supported a need for increased support from tribal programs to increase CRS implementation. Conclusions include an affirmation of the need for CRS in classrooms serving Native youth and a responsibility on part of educators to display commitment in that process. Limitations, directions for future research, and implications for future Karuk tribal education programs are discussed.

Keywords: Karuk Tribe
Culturally responsive schooling
Native American
Karuk Tribe
teacher
Thesis
Advisor: Lotan Rachel
Willinsky John
Exclusion in the era of multicultural recognition [electronic resource] : cultural heritage, Afro-descendants, and the politics of diversity in Colombia and Brazil

Colombian and Brazilian bureaucrats readily agree that recognizing their nation's cultural heritage and ethno-racial diversity is inherently good. My dissertation questions this premise and examines the unexpected and often-harmful consequences that, in practice, heritage declarations have on minorities. Based on multi-sited ethnographic research in Colombia, Brazil, and UNESCO headquarters in France, this dissertation examines how polices that recognize Afro-descendant groups can also increase their economic and political marginalization. This dissertation focuses on two formerly enslaved Afro-descendant communities, San Basilio de Palenque in Colombia, inscribed on UNESCO's "Representative List of the Intangible Cultural Heritage of Humanity, " and Quilombo dos Palmares in Brazil, declared as a National Heritage Site. Using ethnographic methods including participant observation, semi-structured interviews, and archival analysis, my research traces a series of unintended outcomes wrought by cultural heritage policies on the ground and critically considers the structural limitations that characterize these kinds of initiatives. Regardless of their positive aims, I argue that the very policies intended to proffer empowerment to some, actually exacerbate inequality for others. The ethnographic evidence I collected between 2009 and 2013 shows that while heritage recognition brings visibility to the cultural practices of Afro-descendants, it also masks the deep-seated struggles of minorities and cements categorical boundaries between different ethnic groups. This dissertation highlights the paradox of heritage recognition policies, which tend to be understood as part of a broader agenda to promote ethno-racial diversity. Though these policies strive to expand Afro-descendants' social, political, and symbolic membership as citizens of multicultural nations, they end up also entrenching exclusion, buttressing elitism, and reinforcing inequality within and between communities of African descent. My ethnographically based insights are helpful for examining the real-time effects of multicultural policies on the ground, as well as informing a largely theoretical debate on how to value cultural difference. Ultimately, my dissertation contributes to develop new theory and methods for evaluating the impacts of heritage declarations on ethno-racial minorities. By elucidating the limits of cultural heritage recognition to provide reparation for Afro-descendants, my research is of crucial importance for wider debates regarding politics of diversity in the Global South.

Keywords: Anthropology.
Advisor: Meskell Lynn primary advisor. Thesis advisor
Hodder Ian advisor. Thesis advisor
Voss Barbara L.
Exemplary teachers of culturally and linguistically diverse students [electronic resource] : what are the knowledge and skills that undergird their classroom practices?

This study identifies and characterizes the knowledge and skills exhibited by three exemplary teachers of culturally and linguistically diverse students in bilingual elementary classrooms. Numerous studies have demonstrated low levels of educational achievement for culturally and linguistically diverse student such as Latino English Learners yet research has also shown that teachers can be a powerful factor in students' learning and achievement. Teachers often cite lack of skills and preparation needed to effectively teach this population of students effectively. This study identifies and describes the classroom practices of three first grade teachers that promoted academic achievement and acquisition of English. This study also explores how it is that these teachers believe they learned to be successful teachers as well as details their efforts to advocate for Latino ELs.

Keywords: Education.
Advisor: Darling-Hammond Linda
Lotan Rachel A. advisor. Thesis advisor
Valdés Guadalupe advisor. Thesis advisor
Experimental and numerical tools to investigate ringing in IC engines [electronic resource]

According to the International Energy Agency, mitigating greenhouse gas emissions to limit global temperature increase to 2 degrees Celsius will require efficient, combustion-based systems for light-duty transportation to take the place of conventional spark-ignited gasoline engines in the next 25 years. One of the barriers to high-efficiency combustion strategies such as homogeneous charge compression ignition (HCCI) is a phenomenon known as ringing, the formation of damaging pressure waves in the engine during the combustion process. Previous experimental results indicate that disruption of ringing is possible, to achieve high efficiency and high power density. Two tools to obtain spatially-resolved information during the ringing combustion process are the primary contributions described in this dissertation. A quasi-1D reacting compressible flow model captures the essential physics of the ringing phenomenon, to target experimental investigation and to interpret experimental results. To obtain spatially-resolved experimental data, an optically accessible engine capable of 250 bar peak pressure and Schlieren imaging was designed, manufactured, and demonstrated.

Keywords: Mechanical Engineering.
Advisor: Edwards C. F. (Christopher Francis) primary advisor. Thesis advisor
Lele Sanjiva K. (Sanjiva Keshava)
Mitchell Reginald advisor. Thesis advisor
Exploring Dark Matter Bound During the Formation of the Solar System

We estimate the expected population density of Dark Matter bound to the solar system in a number of different limits in order to better inform direct detection searches. At Earth, we expect the population captured during the formation of the sun to be reduced by a factor of more than $10^{-4}$ from the initial background population, making it negligibly small. However, in the adiabatic limit we expect an enhancement of $10^{11}$ on the population of Dark Matter initially bound to the gas cloud which will collapse to form the sun, which could be a relevant population. The result is reproduced by treating the Dark Matter as a classical field. We expect distortions in this population during the lifetime of the Solar System due to Jupiter to be insignificant.

Keywords: Wiser, Timothy
Wagoner, Robert
Dark Matter
Axion
Solar System
Thesis
Exploring How the Human Brain Learns to Recognize New Visual Symbols

The process of associating meaning with a visual symbol, such as a number or a letter, is established through learning that involves interactions of specific regions of the brain. In this study a visual learning task was created through which subjects learned to first categorize previously unknown symbols as letters or numbers (categorical learning) and then associate each symbol with a specific letter or number (translation learning). The protocol was tested in three consecutive stages: 1) behavioral analysis in a healthy control group (n=21), 2) behavioral analysis in an epileptic nonsurgical group (n=5), 3) and a combined behavioral and electrophysiological study in an epileptic surgical group implanted with intracranial recording electrodes (n=3). Efficacy of the protocol was proven with behavioral data collected among the three groups that tested response time to stimuli, accuracy of response, and confidence interval. Groups all had similar upward learning trends towards 80% accuracy in categorical learning phase before moving to the translation learning phase. This study validated that the protocol could be completed within a one-hour time frame. Intracranial electrophysiological recordings were also used to capture the spatial and temporal dynamics of brain activity during the testing protocol. As indicated by the power of high-gamma activity recorded from individual electrodes over the posterior superior temporal region, there was a medial to lateral build-up of neural activity over the course of the testing phases of the protocol. Our findings validated the feasibility of a novel experimental paradigm for studying the human brain during learning of new symbols. Future empirical knowledge obtained with this paradigm will provide valuable mechanistic information about the interactions among different brain regions when human subjects learn new visual symbols.

Keywords:  Department of Biology
Neurobiology
electrophysiology
behavior
epilepsy
learning
visual symbols
Thesis
Advisor: Parvizi Josef
Heller H. Craig
Chen Xioake
Exploring shared structure among vehicle trajectories [electronic resource]

Trajectory data, which record the evolution of objects in space and time, are everywhere. Examples are GPS trajectories recording the moving traces of a group of people, video sequences of moving cars, etc. Such trajectory collections contain rich and diverse information about their surrounding environment, as well as the collective behavior of their human agents. A common characteristic of trajectory data collected from mobile platforms is data uncertainty. The uncertainty comes from sensor noise, low sampling rate due to power, storage, or data transmission constraints. However, large amounts of trajectories traversing the same spatial-temporal space imply that the trajectories share a lot of common structures. A good understanding of this shared structure can benefit many applications, including route planning, autonomous driving, and ride sharing. In this work, we explore shared structure among trajectory collections and show their usefulness in various applications. We begin with the physical shared structure, i.e., the road network, and show that trajectory collections, such as GPS trajectories, or driving video sequences, have great value in creating and maintaining up-to-date, information-rich maps of the underlying road network. We then explore shared mobility patterns among trajectories from a unique and knowledgeable group of people, specifically taxi drivers. We describe common mobility patterns in such groups using pathlets, which represent popular sub-trajectories shared by many trajectories. We present an unsupervised pathlet learning framework that extracts a compact pathlet dictionary from a collection of GPS traces and demonstrate various applications.

Keywords: Electrical Engineering.
Advisor: Guibas Leonidas J. primary advisor. Thesis advisor
Girod Bernd advisor. Thesis advisor
Ye Yinyu advisor. Thesis advisor
Exploring the Process of Critical Reflection in Photovoice with Youth in the Cape Flats

Critical consciousness is theorized to be an “antidote” to structural oppression for marginalized youth. Though founded on principles of critical pedagogy, Photovoice has largely been used as a needs assessment tool founded in community-based participatory research. There has only been limited study of the potential for Photovoice to be used as a tool to develop critical consciousness, particularly among youth. This study explores how youth in a Photovoice program participate in the process of critical reflection, which has been identified as one of the core and most understudied components of critical consciousness. Working in the Coloured Cape Flats context in Cape Town, South Africa, this phenomenological case study recruited 7 participants, ages 13 - 17, to participate in a 10-week Photovoice program that asked them to identify strengths and opportunities for improvement in their communities, participate in dialogue, and present their photos at a photo exhibition for community members and policy makers. Methods from visual sociology were used to analyze the primary source of data, 35 photos presented by participants and their matched captions, along with field notes, recordings of classroom discussions, interviews, and other photos that helped contextualize these photos. This analysis showed that participants display levels of critical consciousness matching the stages as Paulo Freire described – magic, naïve, and critical. This analysis also found that intentionality and forethought before and during photo-taking, using the imagination during photo interpretation and captioning, and group dialogue that facilitated collective introspection and helped push participants towards the critical level of consciousness. These results are aimed to be a guide for educators and community researchers who want to engage youth in critical pedagogy and emancipatory practice through Photovoice, and hope to inform previous frameworks created to conceptualize critical reflection.

Keywords:  Graduate School of Education
Graduate School of Education
Stanford University
Photovoice
Cape Town
Cape Flats
Critical Pedagogy
Critical Consciousness
Critical Reflection
Visual Research
Participatory Research
Youth
Urban Youth
Thesis
Advisor: Alim H. Samy
Willinsky John
Naim Kamran
Extending single-molecule microscopy using optical processing techniques [electronic resource]

In recent years, single-molecule fluorescence microscopy has revolutionized the field of biological imaging. Using single-molecule localization techniques combined with control of the emitting concentration and time-sequential imaging, it is now possible to image structures with resolution an order of magnitude smaller than the classical diffraction limit, thus achieving 'super-resolution'. Such advances have established the fluorescence microscope as a powerful non-invasive imaging technology, and have been recognized with the 2014 Nobel Prize in Chemistry. This thesis aims to further extend the limits of super-resolution and single-molecule microscopy. Fluorescent molecules are versatile probes that provide a wealth of information about their nanoscale environment. However, the majority of super-resolution applications measure only the two-dimensional positions of single molecules during a typical experiment. By constructing multimodal imaging systems that sense additional physical parameters on a molecule-by-molecule basis, additional biological insight may be gleaned. Over the course of my PhD, I have developed a suite of experimental methods and computational algorithms for encoding a molecule's three-dimensional position, its orientation, and its rotational dynamics into the image that its fluorescence forms on a camera sensor. In this thesis, these techniques are combined with super-resolution microscopy, and have been demonstrated to be useful tools for cellular imaging, and for the characterization of stretched DNA strands.

Advisor: Moerner W. E. (William Esco)
Bryant Zev David advisor. Thesis advisor
Dror Ron
Extrinsic stabilizers of proteins: their roles in acclimatizing to fluctuating temperatures in the rocky intertidal environment

Organisms living in rocky intertidal habitats endure extremely variable conditions. Body temperatures of sessile invertebrates can vary by over 25°C in concert with the tidal cycle. Proteins are temperature-sensitive, and many denature at the highest temperatures intertidal species encounter. This study sought to elucidate whether and how the adjustment of organic cellular solutes known as “osmolytes” helps protect proteins in the California ribbed mussel Mytilus californianus against heat-denaturation. I approached these questions by directly measuring the extrinsic stability, i.e. stability afforded by co-solutes, of M. californianus malate dehydrogenase, and by measuring osmolyte concentrations after heat stress in the laboratory and in the field.
Though malate dehydrogenase was much more stable in cytosol than in buffer as expected, prior heat stress did not strongly alter its stability in the cell (p=0.14). Changes in the osmolyte composition of gill tissue were observed after twenty-three days of heat stress in the intertidal zone, but not after one eight-hour heating-cooling cycle in the laboratory. Thus, induction of a putative osmolyte response requires multiple thermal stress episodes. Cellular concentrations of alanine, taurine, and glycine varied significantly (p<0.05) with mean daily maximum body temperature measured over twenty-three days in the field. Taurine, by far the most abundant osmolyte and a strong protein stabilizer, showed a significant increase with acclimatization to higher temperatures, consistent with an increase in extrinsic stabilization under heat stress. A weak trend (p=0.14) in the concentration of the stabilizer glycine betaine also supports a model in which osmolyte synthesis pathways are regulated in a way that protects proteins. I discuss the plausible role of osmolytes in mussels’ acclimatization to repetitive heat stress, and suggest further experiments to isolate and quantify this function.

Keywords:  Department of Biology
Biology
intertidal
heat stress
acclimatization
Mytilus californianus
proteins
osmolytes
extrinsic stability
Thesis
Advisor: Somero George N.
Heller H. Craig
Factor analysis for high dimensional data [electronic resource]

Factor analysis is a powerful dimension reduction tool with explicit statistical model and assumptions. It assumes that the data matrix can be decomposed as linear combinations of latent factors plus independent noise which has heteroscedastic variances for each variable. This dissertation provides two approaches estimating the factor analysis model for high-dimensional data and an application of factor analysis to confounder adjustment in high-throughput genetics experiments. One approach, BCV-ESA, uses an early stopping iterative algorithm to estimate the model and a bi-cross-validation technique to select the number of factors to retain. The other approach, POT-S, starts with a joint convex optimization using perspective transformation and nuclear penalty and estimates the tuning parameter by a Wold-style cross-validation. Both methods are superior to previous methods in the accuracy of estimating the weak factors and the noise variances. For the confounder adjustment application, the mathematical properties of a two-step algorithm estimating the individual effects of the primary variable after confounding factors adjustment has been carefully studied. It is shown that under regularity conditions, the estimators of the individual effects can asymptotically achieve an oracle efficiency and eliminate bias or correlations in the p-values of individual effects.

Keywords: Statistics.
Advisor: Owen Art B. primary advisor. Thesis advisor
Walther Guenther advisor. Thesis advisor
Wong Wing Hung advisor. Thesis advisor
Fast Krylov subspace methods for geostatistical inverse problems [electronic resource]

Inverse problems are part of a mathematical framework used to estimate parameters that characterize a physical system but are difficult to measure directly. An example application is hydraulic tomography which is a method of imaging the subsurface. Water is pumped at designated pumping wells and the measured pressure response is recorded at corresponding observation wells. These noisy measurements of pressure are then used to obtain tomographic reconstructions of important hydrogeological parameters such as hydraulic conductivity and storage. Inverse problems of this type are particularly challenging both mathematically as they are ill-posed, and computationally as they generally require repeated solutions of large-scale partial differential equations. In this dissertation, we discuss in detail a method of imaging based on oscillatory pumping tests. We discuss methods to extract the signal from the noise and examine the duration of the transient. For this class of inverse problems, solving shifted systems of linear equations is a major computational bottleneck. In the dissertation, we describe an iterative algorithm for solving shifted linear systems. Krylov subspace methods are particularly appealing because of their shift-invariant property. By exploiting this property, only a single Krylov basis is computed and the solution for multiple shifts can be obtained at a cost that is nearly equal to the cost of solving a single system. We then show how the time dependent inverse problems can be accelerated using these Krylov subspace solvers using a Laplace-transform approach.

Advisor: Kitanidis P. K. (Peter K.) primary advisor. Thesis advisor
Poulson Jack Lesly advisor. Thesis advisor
Saunders Michael A. advisor. Thesis advisor