VictorJuiz/thesis huggingface dataset:
Antecedents and Outcomes Associated with Hospital Participation in a Clinically Integrated Network

Health care delivery and payment reform have intended to redesign care in a manner that is higher quality, better coordinated, and more efficient. As part of this shift, delivery systems are increasingly organizing in new ways, often moving toward greater organizational integration. One model that has emerged is the Clinically Integrated Network, or CIN, a set of independent provider organizations such as hospitals and physician groups that collaborate to provide high-value care. This dissertation examines antecedents and outcomes associated with hospital participation in a CIN./nThe first study uses national survey data to identify the organizational characteristics and other foundational collaboration arrangements associated with hospital participation in a CIN. The second study evaluates CIN processes, using a survey of hospital activities to ask whether CIN-affiliated hospitals offer more integrated care delivery than hospitals not affiliated with CINs. The third study uses inpatient hospitalization data to evaluate care coordination outcomes associated with hospital participation in a CIN by testing for an association between CINs and potentially preventable inpatient utilization. Taken together, these studies provide the first national empirical evidence describing CIN activities, and the findings can help inform decisions of CIN leadership and regulatory authorities.

Advisor: Rodriguez, Hector P.
Catching up to fungal plant pathogens: A characterization of extrachromosomal circular DNAs and gene presence absence variation in Magnaporthe oryzae

Fungal plant pathogens have major impacts on agriculture and global food security and are likely to have an even greater impact in the future. The current tools that we have available to combat them are insufficient, in part because these fungi can quickly adapt to these tools. Understanding fungal plant pathogen evolution is therefore essential to curbing the threat these pathogens pose. In Chapter 1, I describe the motivations for my dissertation work and the state of the field of fungal plant pathogen evolution. I also introduce the model organism I used in my research, Magnaporthe oryzae, which causes the blast disease. Chapter 2 describes my characterization of the extrachromosomal circular DNAs (eccDNAs) of M. oryzae. EccDNAs are a diverse class of molecules that can contribute to phenotypic and genotypic plasticity in eukaryotes, and I hypothesized that these may be involved in fungal plant pathogen evolution. I show that M. oryzae has a more diverse set of eccDNAs than other organisms and that these are enriched in LTR retrotransposons. I also show that many genes are found on eccDNAs in M. oryzae, and that effectors are enriched on eccDNAs. Finally, I show that eccDNAs are associated with gene presence-absence variation (PAV). Next, in Chapter 3, I discuss in greater detail the results presented in Chapter 2, as well as their implications and potential future directions. I also further discuss evidence in Chapter 2 that led me to believe that eccDNAs do not play a major role in fungal plant pathogen evolution and led me to focus directly on gene PAV in M. oryzae in the remainder of my dissertation. Subsequently, in Chapter 4, I describe my characterization of these events in M. oryzae. I find that genes experiencing PAV between lineages of M. oryzae are enriched in disease-causing and non-self-recognition genes. I describe how gene PAV events in the rice and wheat pathotypes show clear differences in their count and genomic location. Through comparing PAV genes to conserved genes, I show that these had distinct distances to TEs, distances to other genes, lengths, GC content, expression, and epigenetic marks. I also describe how a machine learning model can be trained to take advantage of these features to predict genes prone to PAV in the M. oryzae genome. Finally, in Chapter 5, I further discuss the implications of the results I describe in this dissertation, as well as future directions for implementing machine learning models and general knowledge of fungal plant pathogen evolution to help guide rational disease resistance engineering in crops.

Advisor: Krasileva, Ksenia V
An Exploration of Whiteness in Social Work

This study explores whiteness in social work, starting from the root of whiteness as a social problem; namely, how we understand the phenomenon of whiteness in the first place—an issue that remains contested, notwithstanding oversimplifying claims to the contrary and tendencies both within and beyond social work to rush to ostensibly multi-cultural or anti-racist projects despite never having established foundational understanding of the central definitional issue to begin with. Specifically, this study raises the question of how whiteness manifests in contemporary social work according to social workers who do not identify as white./nResearch and scholarship on the topic of whiteness are grounded overwhelmingly in the perspectives of white people and institutions. The present study sees this as a problem and seeks to ascertain the long misconceived, always evolving, immediately relevant phenomenon of whiteness from a vantage point outside of whiteness by relying upon the interpretations of people who do not identify as white. To that end, this study interviews a national sample (n=30) of U.S. social work master’s students, doctoral students, and faculty who do not identify as white in order to collect data capable of clarifying how to understand whiteness in social work in the present moment. Participants report their experiences with and perceptions of whiteness in social work curricula, in their own work, and in their institutions. The results of these interviews, therefore, incorporate viewpoints from previously overlooked and excluded populations; voices without which whiteness cannot be fully apprehended./nThrough individual, semi-structured, in-depth, qualitative, interviews, participants’ reports cohere inductively around three categories of experience: the “what” of whiteness (i.e., description), the “why” of whiteness (i.e., interpretation), and the “how” of whiteness (i.e., explanation). Taken together, and scaffolded by existing sociological and psychoanalytic theories, these categories render a typology by which to better understand whiteness in social work today. In response to this newly articulated framework, participants outline implications for a social work profession at a historical crossroads, including needs for curricular reform, increased practical emphasis, and collective politicization. These broad changes, participants assert, are imperative in order for social work to meet the contemporary challenge of the social problem of whiteness.

Advisor: Sacks, Tina
When Dementia Caregiving Ends: The Role of Caregivers’ Emotional Connection to the Patient in Current and Former Caregivers’ Health

Caring for a person with dementia (PWD) can be associated with considerable declines in health and well-being during active caregiving, although less is known about how former caregivers fare after caregiving has ended (i.e., after the death of the PWD). There is striking variability in the extent to which caregivers experience declines in health, so it is important to identify factors related to their vulnerability and resilience in order to reveal potential intervention targets. Studies have linked the quality of the PWD-caregiver relationship to caregivers’ health, but little is known about the specific interpersonal emotional mechanisms that contribute to long-term caregiver health. The present study addresses these gaps by evaluating caregivers’ emotional connection to the PWD in two independent samples and examining associations with caregivers’ depression, anxiety, and physical health—concurrently (in current caregivers) and longitudinally (in former caregivers, after caregiving has ended). In Study 1 (N = 82), caregivers and PWDs engaged in a conflict conversation in the laboratory, after which caregivers viewed video recordings of the conversation and provided second-by-second ratings of their own affective valence and the PWD’s affective valence during the conversation using a rating dial. Caregivers’ emotional connection to the PWD was operationalized by summing the number of seconds in which they reported experiencing positive or negative affect simultaneously with the PWD (i.e., co-experienced positive or negative affect). In Study 2 (N = 335), caregivers were asked to describe a recent time they felt connected to the PWD, and their responses were recorded verbatim. Caregivers’ emotional connection to the PWD was operationalized by summing the number of positive and negative words from the transcripts using text analysis software (i.e., positive and negative emotional connection language). Results revealed that greater co-experienced negative affect between caregivers and PWDs (Study 1) and caregivers’ lower positive emotional connection language (Study 2) were associated with higher levels of caregiver depression. In addition, caregivers’ positive emotional connection language predicted longitudinal decreases in caregiver depression after caregiving had ended (Study 2), which was robust when accounting for relevant covariates (e.g., caregiver demographics, PWD dementia severity). These findings identify caregivers’ greater negative and lower positive emotional connection to the PWD as potential risk factors for caregivers’ mental health problems. Future research should explore whether interventions that enhance social connection between caregivers and PWDs are effective in reducing depression and increasing quality of life.

Advisor: Levenson, Robert W
Fluids for Soft Gripper Design: Robots in Real-World Environments

For forceful and dexterous manipulation, robots must be able to physically interact with the environment. In the real-world, the environment is dynamic and unstructured. For example, fragile objects and adversarial contact conditions, e.g. a slippery fluid film, may be present. Embodied intelligence and active control strategies are two approaches that tackle these challenges. Soft robots and grippers exemplify embodied intelligence, as the inherent behavior of soft materials allows passive compliance and distributed loading. A sense of touch, also known as tactile sensing, provides feedback for active controllers to provide additional adaptability and articulation. Human hands seamlessly integrate both compliance and tactile sensing, with underactuated joints and soft compliant skin covered with nerve endings. While case studies demonstrate soft robots or tactile sensors in the field, few systems have both./nMy dissertation explores the design of embodied dexterity and tactile sensing in robots through fluids. Fluids – liquids, gasses – are ubiquitous. Many soft robots use fluids for actuation, e.g. pneumatic or hydraulic. Fluids for robotic sensing and contact design are less prevalent. In this dissertation, I first present how we can employ airflow for tactile sensing. This design uses pneumatic acoustic resonance to sensitize soft, skin-like surfaces and grippers. I then show how we can mitigate the slippery effects of lubrication for frictional grasping by adding soft, patterned finger pads to existing grippers.

Advisor: Stuart, Hannah
Blasting off at the speed of light: Exploring relativistic quantum chemistry for core spectroscopy and heavy elements

Quantum mechanics is one of the most predictive theories that we have at our disposal to explain natural phenomena with atomistic detail. Yet, applying it to complex system, such as chemical reactions, is an extremely demanding task. Approximations justified by physical principles are necessary to reduce the computational cost of these simulations. This dissertation analyzes two classes of problems in molecular quantum mechanics, highlighting the main ingredients necessary to qualitatively and quantitatively describe them. First, we look at how the choice of orbitals influences the description of strong-field ionization processes in simple systems, drawing an analogy to the well-known symmetry dilemma within quantum chemistry. We show that, through a simple model and a mean-field treatment, allowing the wavefunction to simply separate pairs of electrons is not enough to understand the ionization process, requiring additional flexibility to allow for spin rotations./nThe second class of problems discussed in this dissertation concerns the description of excited states that arise when promoting one of the electrons in an inner-shell of a system. X-ray spectroscopy is a vibrant field that has been explored in great detail over recent years due to advances in light sources. From a theory perspective, these core-excited states also pose some challenges to existing quantum chemical methods, especially due to lack of relaxation effects after creating a hole in one of the core orbitals. We discuss different approaches to model X-ray emission and absorption, as well as the role of scalar relativistic effects in accurately modeling the core-excitation energies and the spectra of heavy elements. In doing so, we have devised both state-specific and linear-response methods to model core-excited states, expanding the toolbox available to quantum chemists to interpret new experiments in the X-ray range of the electromagnetic spectrum.

Advisor: Head-Gordon, Martin
Interplay between structural dynamics and optoelectronic properties in lead halide perovskites

Lead halide perovskites are the subject of great interest owing to the unique photophysical properties of perovskites where elucidating the nature of those properties highly relies on the understanding the photophysics of semiconducting materials. Upon photoexcitation, excited electrons and holes are generated, where bound electron-hole pair is called an exciton, what decides the optoelectronic properties depends on how charges carriers are relaxed back to their ground state. Given that the charges carriers can be coupled to lattice vibrations, called phonons, while relaxing, taking a closer look at how the structural fluctuations produced by the lattice affects the behavior of charge carriers is crucial to elucidate the microscopic origin of the properties of semiconducting materials. However, including the dynamical effects of phonons is in general difficult. Although the study on how phonons affect the properties of free charges has a long history, there still remains active open area for studying how excitonic properties are altered by the interaction with phonons. Especially for perovskites, the complex structure and anharmonic nature makes theoretical study even more challenging./nHerein, in this thesis, we explore the properties of lead halide perovskites in various dimensions by using an atomistic molecular dynamics simulations, allowing us to capture all orders of anharmonicity. For the system of layered perovskites with bulky organic molecules, it is showed that how the anharmonicity of organic molecules affects the vibrational relaxation dynamics following photoexcitation. And for a system of single chain perovskite nanowire, we are able to analyze the structural dynamics. In terms of studying excitonic properties in bulk perovskites, with this explicit anharmonic perovskite lattice, we describe quantum particles with path integral framework and we have developed a Gaussian field theory to describe the effective interactions between electrons and holes as mediated by the perovskite lattice using path integral molecular dynamics, illustrating the method of use to study exceptional excitonic properties of perovskites. Lastly, we end this by briefly introducing the application of this framework for studying the multiparticle excitations in perovskite nanocrystals.

Advisor: Limmer, David T
Multimodal Long-Term Video Understanding

The internet hosts an immense reservoir of videos, witnessing a constant influx of thousands ofuploads to platforms like YouTube every second. These videos represent a valuable repository of multimodal information, providing an invaluable resource for understanding audio-visual-text relationships. Moreover, understanding the content in long videos (think 2 hours), is an open problem. This thesis investigates the intricate interplay between diverse modalities—audio, visual, and textual—in videos and harnesses their potential for comprehending semantic nuances within long videos. My research explores diverse strategies for combining information from these modalities, leading to significant advancements in video summarization and instructional video analysis. The first part introduces an approach to synthesizing long video textures from short clips by rearranging segments coherently, while also considering audio conditioning. The second part discusses a novel technique for generating concise visual summaries of lengthy videos guided by natural language cues. Additionally, we focus specifically on summarizing instructional videos, capitalizing on audio-visual alignments and task structures to produce informative summaries./nTo further enrich the comprehension of instructional videos, the thesis introduces a cutting-edgeapproach that facilitates the learning and verification of procedural steps within instructional content, empowering the model to grasp long and complex video sequences and ensure procedural accuracy. Lastly, the potential of large language models is explored for answering questions about images through code generation. Through comprehensive experiments, the research demonstrates the efficacy of the proposed methodologies, envisioning promising future prospects in the field of semantics in long videos by integrating audio, visual, and textual relationships.

Advisor: Darrell, Trevor
Study of Halide Perovskites at the Level of Ionic Octahedron

Metal halide perovskites, a class of semiconducting materials with remarkable optoelectronic properties, have attracted considerable attention in recent years. This dissertation delves into innovative design and synthesis approaches, as well as structural transformations and applications of halide perovskites, with a focus on the fundamental properties of the metal halide ion octahedron [MX6]n– (M = metal cation, X = halide anion) as the primary building block and functional unit. By examining the assembly, connection, and interaction of these octahedra, this research aims to establish a solid foundation for the future development and application of halide perovskites.Chapter 1 provides a comprehensive overview of halide perovskites, covering their fundamentals, structural chemistry, stimulus response, and applications, with particular emphasis on the metal halide octahedron as the key building block and functional unit. In Chapter 2, we propose a new design principle for halide perovskite structures based on ionic octahedron networks (IONs) and report the first experimental synthesis of a novel halide perovskite, Cs8Au3.5In1.5Cl23, which adopts an ABO3-type ION. Chapter 3 examines the stimulus-responsive behavior of metal halide perovskites, using Cs3Bi2Br9 as a model compound. By employing in situ characterization techniques, we identify two distinct distortion classes of [BiBr6]3– octahedra and analyze the changes in exciton emissions in relation to the octahedral distortion. In Chapter 4, we utilize our understanding of [MX6]n– octahedra to establish the electronic band structure and photoexcitation model of molecule-like halide perovskite Cs2TeBr6. We demonstrate that different LED wavelengths can generate holes in various valence bands and differentially activate benzyl alcohol molecules. Lastly, Chapter 5 summarizes the research findings and provides insights into future directions for halide perovskite studies, emphasizing the significance of understanding the metal halide ion octahedron.

Advisor: Yang, Peidong
Atomistic Simulations of Dislocation Core Reconfiguration in FCC Metals and Alloys

Dislocations are line defects present in crystalline materials that govern the plastic deformationof metals and metallic alloys. These defects are described by continuum approaches in the far field, but the center of a dislocation core requires atomistic detail. The computational efficiency of continuum approaches allows for the use of mesoscale models probing length and time scales beyond those available in atomistic simulations. However, many of the assumptions involved which sacrifice finer details associated with dislocation core reconfiguration have been left unchecked. This dissertation presents the methodology and results of atomistic simulations applied to three main dislocation processes relevant for mesoscale modeling of FCC metals and alloys. The first is the process of dislocation climb, where dislocations migrate through the absorption/emission of point defects. Mesoscale models typically assume a dislocation to be an ideal cylindrical sink. This assumption is only valid when there is a sufficient density of jogs along the dislocation line, and through the combination of atomistic calculations of jog free energies and analytical theory, it is shown that obtaining such a sufficient density of jogs requires high homologous temperatures and/or a high supersaturation of defects. The second application is on the process of dislocation cross-slip in the presence of short-range ordering (SRO). Mesoscale models typically do not include the effect of solutes on cross-slip, and if they do, assume them to be distributed in a random fashion instead of having SRO. Through the atomistic calculation of many dislocation cross-slip energy barriers with and without the presence of SRO, it is shown that the effect of SRO on planar defect energies can significantly increase the cross-slip energy barrier, potentially reducing cross-slip rates by orders of magnitude and altering work-hardening processes during deformation. The third and final application is on the process of core restructuring of Lomer/Lomer-Cottrell dislocations as a function of stress and alloy composition. Mesoscale models assume that these dislocations, which are central to the work-hardening of FCC metals and alloys, evolve under stress through only one mechanism. It is shown through atomistic simulations that a variety of evolution mechanisms, including twin nucleation, can occur through the core restructuring of these dislocations depending on the local stress and alloy composition.

Advisor: Asta, Mark