VictorJuiz/thesis huggingface dataset:
More than Medical Records: Uncovering how Childhood Cancer Survivors learn about and interact with their Cancer Histories
Keywords:  department of Science
Childhood cancer survivor
cancer
survivor
cancer histories
cancer narratives
Science Technology and Society
Stanford University
Thesis

From 1971 to 2010 the combined 5-year childhood cancer survival rate has increased from 40 percent to 82 percent (Cancer Research UK, 2015). With more children surviving cancer, more adults will live with the long-term effects of cancer treatments. 70 percent of childhood cancer survivors (CCS) are at risk of physical, psychological, and social late effects of treatment and 66 percent reported living with at least one chronic health condition 30 years post diagnosis (Hewitt, Weiner, & Simone, 2003). Amplifying the likelihood of poor health outcomes, CCS with limited access to their health histories have greater risk for poor health outcomes (Hóven, Lannering, Gustaffson, & Bownman, 2018). To limit some of this risk for poor health outcomes and to properly manage their healthcare, CCS need access to their health histories. Despite the importance for survivors to understand their health histories, research neglects to explore how CCS learn about and interact with their cancer histories as young adults. To fill this gap in the literature I interviewed 9 CCS between the ages of 18 and 29 that were treated for cancer at 10 years of age or younger. With these interviews I conducted a content analysis to identify common themes. I present how CCS learned about and continue to learn about their cancer histories. CCS reported using the following resources to learn about their cancer histories: parents, healthcare professionals knowledgeable of their cancer histories, scientific literature, summer camps for CCS, and survivor clinics. Although participants each reported using some of these resources, many of them still have questions about their cancer histories and relevant long-term effects. CCS interact with their cancer histories through feelings of uncertainty, fearing long-term side effects, feeling fortunate for good health, and feeling guilty for their limited knowledge of their cancer histories. The research reveals needed improvements in health education programs for CCS.
Movement representation in human motor cortex and applications to brain-computer interface control
Keywords: Mechanical Engineering.

Intracortical brain-computer interfaces (iBCIs) have largely built upon work investigating the neural representation of overt reaching movements in nonhuman primates (NHPs). However, in people with paralysis, iBCIs leverage neural features related to attempted movement of paralyzed limbs, which may differ substantially from that of overt movement of unparalyzed limbs. To understand how paralysis affects movement representation in the motor cortex, we first compared direction- and distance-related neural tuning of a human participant's attempted arm movements and overt head movements to that of NHP overt arm movements. The participant's neural activity during overt head movement was most similar to NHP overt arm movement with strongest tuning to distance. To further clarify how attempted movement-related neural activity translates into iBCI control, the participant controlled a cursor using a series of different attempted movement strategies. We found that neural activity changes during iBCI control, becoming more similar across different strategies. Applying these gained insights, we designed and demonstrated a discrete neural decoding system which leveraged the neural representation of both overt and attempted movements to enable classification of up to 32 discrete movements across the body. The attempt to move a paralyzed limb also differs from overt movement of an unparalyzed limb in that haptic feedback normally accompanying the movement is lost or diminished. To better understand how haptic stimulation affects motor cortical neurons and iBCI control, we integrated a haptic feedback device into our iBCI system, which provided skin-shear haptic stimulation at the back of the participant's neck. We found motor cortical units that exhibited sensory responses to the stimuli, some of which were significantly tuned to the stimuli and well modeled by cosine-shaped functions. We also demonstrated online iBCI cursor control with continuous skin-shear feedback driven by decoded command signals. Cursor control performance increased slightly but significantly when the participant was given haptic feedback as compared to the visual feedback condition. This work deepens our understanding of how paralysis affects movement representation, delivers a novel discrete neural decoding system leveraging the movement representation of both paralyzed and unparalyzed limbs, provides insight into how motor cortical units respond to haptic stimulation, and shows how this stimulation affects iBCI control performance. These results can help guide and inform the design of future neural prostheses.
Multi-dimensional imaging of immune response
Keywords: Bioengineering.

Improvements in our understanding of the immune system have led to radical paradigm shifts in medicine including the advent of vaccines and cancer immunotherapy. New "high-dimensional" techniques promise to guide the next generation of immune based therapies, yet thus far, have failed to fully predict patient response or elucidate therapeutic mechanism of action. For this, a "multi-dimensional" approach is needed, as immunity occurs across space, time, and scale (e.g. cells to organ systems). To realize this goal, an immuno-imaging toolbox capable of multi-dimensional interrogation of immune response was built. This dissertation describes engineering principles learned and biological insights gained from developing imaging probes capable of non-invasively monitoring whole body immune response across space and time. This dissertation discusses how to select and validate appropriate imaging biomarkers of immune response, and provides several examples of applications for immuno-imaging in monitoring cancer immunotherapies. Some of the approaches and imaging probes developed in this work are currently being clinically translated for applications from selecting the right cancer patients for immune checkpoint inhibitors, to diagnosing and preventing immune-mediated organ transplant rejection. The state-of-art immuno-imaging toolbox described herein provides a previously unprecedented "multi-dimensional" view of the immune system in action and has the potential to guide future patient care.
Multi-Disciplinary Argument for Recognition of Term: Immigration Detention-Industrial Complex and A Case for its Abolition
Keywords: immigration detention-industrial complex
prison-industrial complex
abolition
prison abolition
immigration
race
black
brown
Stanford University
Center for Latin American Studies
Thesis

A case for the abolition of immigration detention centers in the United States using the framework of prison abolition studies. This paper presents an argument using evidence from legal, historical, psychological, and cultural perspectives across various mediums to acknowledge the institutionalization of an immigration detention-industrial complex modeled and proliferated along the better recognized prison-industrial complex. Research across academic disciplines reveal a disproportionate imprisonment of black and brown people in relation to population---residue of buried histories of racial violence that procreated structures to sustain and proliferate a punitive society post formal recognition of slavery. A critical understanding of the role race plays in law enforcement can inform development of new resources and institutions in tune with local communities’ specific needs to protect communities most persecuted by law enforcement efforts. An intercommunity accountability system phases out the need to cage adults and children to death.
Multifidelity Framework for Uncertainty Quantification with Multiple Quantities of Interest
Keywords: reservoir simulation
multilevel
multifidelity
uncertainty quantification
representative models
Thesis

A systematic framework, involving ﬂow simulation and model selection at many ﬁdelity (resolution) levels, is introduced to accurately quantify the impact of geological uncertainty on multiple output quantities of interest (QoIs). The methodology considers large numbers of realizations (O(1000) in the cases presented), though very few (O(10)) simulations are performed at the highest resolutions. We proceed from coarser to ﬁner resolution levels, and at each stage simulation results are used to select a subset of realizations to simulate at the next (higher) ﬁdelity level. Models are constructed at all resolution levels through upscaling of the underlying ﬁne-scale realizations. A global transmissibility upscaling procedure is applied for this purpose. Approximate cumulative distribution functions (CDFs) are constructed for all QoIs considered. The QoI values themselves are always computed at the ﬁnest scale, but corresponding percentile values are determined using results at a rank-preserving (coarser) ﬁdelity level. Detailed results are presented for oil-water ﬂow in two channelized system examples. Simulations at seven diﬀerent ﬁdelity levels are used, and eight QoIs are evaluated. Results for the examples considered demonstrate accurate reconstruction of ﬁne-scale CDFs for all QoIs, with a speedup factor of about 18 relative to performing all simulations on the ﬁne scale.
Multifunctional energy storage composites with built-in health monitoring capabilities
Keywords: Aeronautics and Astronautics.

Vehicle electrification provides a means to transition away from fossil fuels. However, the widespread adoption of electric vehicles requires sustainable solutions to their short driving range, slow charging, high purchase cost, and safety concerns. Traditional research efforts have focused on developing new battery materials with higher energy densities which are inherently more mechanically fragile, undergo large volume expansion, and are difficult to monitor. These batteries in turn require proportionally larger weight overhead in the form of protection, restraining devices, and a contingency reserve capacity at the vehicle level. Thus, to maximize the performance of existing and new battery chemistries, it is desirable to i) make batteries more mechanically robust while maintaining minimal volume expansion and ii) accurately measure physical changes inside the battery and monitor battery health using built-in sensors. The first part of this work proposed and investigated a novel structurally-integrated Li-ion battery, called multifunctional energy storage composites (MESCs). MESCs encapsulate lithium-ion battery materials inside high-strength carbon-fiber composites using interlocking polymer rivets to mechanically stabilize the electrode layer stack. These rivets enable load transfer between battery layers, allowing them to contribute to load carrying capabilities. First-generation MESCs showed comparable electrochemical performance to standard lithium-ion cells, while also demonstrating significantly higher mechanical stiffness and the ability to restrain intercalation-induced expansion of electrodes. MESCs were also capable of maintaining their structural integrity and energy-storage capabilities under realistic repeated loading. The second part of this thesis developed and evaluated an acousto-ultrasonic system that measures battery state of charge and, in particular, its state of health using a built-in, low-profile piezoelectric transducer system. A diagnostic method was proposed that relates changes in the guided wave signals to the charge, discharge, and aging processes, via electrochemically-induced changes in mechanical properties. A matching-pursuit-based feature extraction scheme was developed to allow an efficient, in-operando decomposition of signals into a set of predictors correlated with battery states. A particle filter framework was established which provides state estimation and remaining life prognostics to allow ultrasonic features to be used as measurements. It was shown on several types of off-the-shelf batteries and MESCs that the ultrasonic technique significantly improved the prediction performance and contained uncertainties.
Multi-functional protective coatings for plastics using open-air spray plasma deposition
Keywords: Materials Science and Engineering.

Transparent plastics are increasingly important to emerging technologies such as light-weight transportation, flexible electronics, and display technologies. However, due to the low surface hardness, plastics can be easily scratched and degraded which significantly reduce their optical qualities and lifetimes. In this dissertation, I will focus on the development of durable functional protective coatings for plastics and new understandings of their mechanical properties including adhesion, stiffness, and moisture-assisted cracking behavior. I will demonstrate two scalable processing strategies for synthesizing these coatings, namely, spray deposition of sol-gel precursors and open-air plasma deposition. Firstly, I will focus on the processing of an organosilicate-based bilayer coating with unprecedented combination of adhesion and stiffness using open-air spray and plasma depositions. The bilayer coating exhibited a > 90% transparency in the visible wavelengths, 8-fold the adhesion energy and 4-fold the Young's modulus of commercial sol-gel polysiloxane coatings. The coating deposition rate, elastic modulus, hardness and adhesion to poly methyl methacrylate (PMMA) substrates will be discussed and correlated to the molecular structures and chemical compositions of the coatings. Secondly, I will demonstrate the molecular design strategies for engineering coating's deformation rate sensitivity and fracture resistance in a moist environment. With increasing non-hydrolysable organic network connectivity, the mechanical behavior of the coatings can vary from almost perfectly elastic to increasingly viscoelastic in a controlled fashion. The related fracture resistance was also found to be significantly improved. New insights into the fundamental molecular-scale relaxation and cracking mechanisms of the coatings will also be highlighted. Finally, I will describe a novel and versatile dual-source deposition method involving ultrasonic spraying and open-air plasma deposition for making durable multifunctional nanocomposite coatings. Previous work for making nanocomposites focused on incorporating nanoparticles by either in-situ growth in the matrix or by dispersing into the matrix precursor before deposition. However, in this new method, the nanoparticles and coating matrix are independently deposited which eliminate the potential difficulties associated with preparing high mass fraction composites with well-dispersed nanoparticles. The capability of incorporating several different functional nanoparticles into durable coating matrix with good nanoparticle dispersity, uniformity and strong matrix-nanoparticle interfacial interactions will be highlighted. The effect of nanoparticle concentration, size, and film thicknesses on coatings surface morphology, optical properties and mechanical properties will also be discussed.
Multimodal imaging of immune cell therapies against cancer
Keywords: Bioengineering.

Immunotherapies focus on reprogramming a patient's immune system to better recognize and target tumor cells. In particular, T-cells can be engineered ex vivo to either target a specific tumor antigen (via a chimeric antigen receptor) or a diverse tumor antigen repertoire (via a dendritic cell vaccine). As novel adoptive T-cell strategies progress through preclinical development and clinical trials, the ability to accurately monitor therapeutic response becomes of even greater need. Molecular imaging allows for real-time insight of the local and systemic patient response to immunotherapies, providing more dynamic information than anatomic tumor volume alone. Here I will discuss molecular imaging strategies for the in vivo monitoring and visualization of immunotherapies and their impact to elucidate the therapeutic efficacy of clinically-relevant adoptive T-cell therapies. First, I will discuss the PET reporter gene imaging and drug-induced ablation of chimeric antigen receptor (CAR) T-cells in solid tumors through the HSV1-sr39tk gene. This dual-function system can provide insight into systemic CAR T-cell migration and proliferation during clinical trials while serving as a suicide switch to limit potential toxicities. Secondly, I will present the first longitudinal fluorescence-based intravital microscopy imaging of CAR T-cells within an orthotopic glioblastoma preclinical model to illustrate the necessity of radiation therapy for complete therapeutic response. This preclinical imaging technique can help us understand immune cell dynamics within the tumor microenvironment with a high-level of spatial and temporal resolution. Third, I will utilize intravital imaging to understand the potential for dendritic cell vaccines in the treatment of glioblastoma. These strategies highlight the potential of molecular imaging both to lend insight on fundamental adoptive T-cell biology and to translate these therapies into the clinic.
A multimodal understanding of allergic disease
Keywords: Bioengineering.

Allergic diseases such as allergic rhinitis, food allergies, and allergic asthma are characterized by an inappropriate immune response towards otherwise harmless environmental substances. Food allergies are a particularly extreme form of allergic disease as exposure to minute amounts of an allergen can lead to the rapid onset of potentially fatal anaphylaxis. In this thesis I address outstanding questions related to food allergies and their practical consequences using multiple modalities. First, I discuss the use of targeted mass spectrometry to answer a recurring question that plagues allergic consumers: is a food with precautionary allergen labeling, such as "may contain, " safe to consume? Second, I discuss the use of single-cell RNA sequencing to isolate and characterize rare B cells in a manner that informs our mechanistic understanding of allergic memory while also providing insight into individual IgE antibodies that directly mediate allergic reactivity.
Multiple testing with structure and exploration
Keywords: Statistics.

The last couple decades have seen the proliferation of high-throughput biological assays as well as the use of electronic medical records for research purposes. For example, the UK Biobank data set contains both genotype and electronic medical record data for half a million individuals. Such data give scientists an unprecedented ability to probe large numbers of scientific hypotheses simultaneously. The statistical field of multiple testing addresses the question of how to sort through all these potential associations without making too many false discoveries. However, modern data sets create new multiple testing challenges for which existing tools are insufficient. In this thesis, we explore some such challenges in the context of two themes: structure and exploration. While many traditional multiple testing methods implicitly treat their hypotheses exchangeably, structure is ubiquitous in hypotheses of interest for biomedical applications. These structures should be accounted for by multiple testing procedures for better power and interpretability. Additionally, most traditional testing procedures formally prohibit exploration of the data, as this would invalidate their inferential guarantees. On the other hand, the analysis of scientific data often involves at least some exploration, which leads to the need for procedures that can provide inferential guarantees while accommodating exploration. In this dissertation, we elaborate on these new challenges, review some existing work to address them, and present new proposals towards this end.
Multipoint optimal control with applications to space flight
Keywords: Aeronautics and Astronautics.

Pontryagin's Maximum Principle is generalized to multipoint optimal control with a proof given that is based entirely on the original principle. Accommodations are made for interdependency of constraints and parametric representation of the dynamics and cost function. The approach naturally applies to impulsive as well as continuous control. Periodic optimal control is an important consequence. Cost sensitivity of the performance index is also proven and demonstrated to be useful in understanding and solving optimal control problems. Three applications from space flight are solved to demonstrate the theory: optimal attitude scheduling of an imaging satellite, optimization of impulsive orbital transfer, and finding periodic orbits near the Earth-Moon Lagrange points.
A multi-scale examination of protein surface layer assembly and function in bacteria and archaea
Keywords: Structural Biology.

Surface layers (S-layers) are nanoporous shells of crystalline protein surrounding a great diversity of bacteria and nearly all known archaea. As the outermost component of the cell envelope, S-layers are one of the most abundant biopolymers on earth and are implicated in functions ranging from providing the structural integrity of the cell to mediating host-pathogen interactions. In this thesis, I report a multi-scale analysis of S-layers from the model bacterium Caulobacter crescentus and a more recently cultivated thaumarchaeote, Nitrosoarchaeum limnia. By first biophysically characterizing the S-layer protein (SLP) from C. crescentus, RsaA, I discovered that environmental calcium mediates multiple physical states of the S-layer. I leveraged this knowledge to reconstitute and specifically image S-layer assembly in living cells. Super-resolution fluorescence microscopy and single-molecule tracking demonstrated that remarkably fast and efficient continuous 2D protein crystallization governs S-layer self-assembly. I further examined the rapid 2D crystallization of RsaA using a combination of time-resolved small angle x-ray scattering (SAXS) and electron cryo-microscopy (Cryo-EM). These observations revealed that a multi-step crystallization pathway involving a short-lived crystalline intermediate is responsible for rapid self-assembly of RsaA. Robust S-layer lattice formation has implications for essential cell functions such as energy production, which in the ammonia-oxidizing archaeaon N. limnia likely occurs within the pseudo-periplasmic space between the cell's only lipid membrane and the extracellular S-layer. Electrodiffusion simulations of the N. limnia cell envelope suggest that the S-layer facilitates diffusion of its main energy source, ammonium ions, through the nanopores of the S-layer by creating a charged protein surface. As such, we propose ion transport as an evolutionary basis for conservation of charged amino acids among archaeal SLPs. Taken together, these findings inform the development of antibiotics mediating S-layer biology and provide insight into possible avenues to design biologically inspired self-assembling macromolecular nanomaterials.