This data was used to compare the performance of a urine point-of-care assay and interviewer-administered timeline follow-back to the gold-standard for measuring recent and longer-term adherence of pre-exposure prophylaxis (PrEP) in dried blood spots (DBS). This data was used to produce the research findings presented in the peer-reviewed journal cited...
Data for manuscript submission to PLoS ONE entitled:
Prior Uncertainty Impedes Discrete Locomotor Adaptation
Authors:
Jiang, Aojun
Grover, Francis M.
Bucklin, Mary
Deol, Jasjit
Shafer, Anna
Gordon, Keith E.
Human skin oils are significant scavengers of atmospheric oxidants in occupied indoor environments. Many techniques used to study gas-phase transformations of surface films indoors have been limited to off-line bulk analysis, although more surface-selective methodologies are emerging. Here, we present a multi-prong analytical approach to characterizing skin oil ozonolysis. Skin...
The Operating System (OS) kernel is a key component of modern computing infrastructure, yet it is prone to numerous vulnerabilities, many of which cause memory corruptions that can be exploited by attackers to perform malicious activities. While various techniques have been introduced to secure the Linux kernel, it still constantly...
In the first two decades of the twenty-first century, we have witnessed a surge of public interest in and discussion around racial reckoning. Universities in the United States and across the globe are grappling with their historical associations with transatlantic and chattel slavery. This dissertation takes up the question of...
Metal-organic frameworks (MOFs) are porous, crystalline materials synthesized by combining metal nodes and organic linkers through self-assembly. The diverse range of building blocks available allows for extensive tunability of MOFs, enabling the optimization of these materials for various applications, such as gas storage, separations, and catalysis. This study aimed to...
Glioblastoma (GBM) is the most common aggressive primary malignant brain tumorin adults with a median age of onset of 65 years of age. Although advanced age is often associated with worse GBM patient survival, the predominant source(s) of maladaptive aging
effects remains to be established. Here we studied intra-tumoral and...
Metal–Organic Frameworks (MOFs) is a class of material comprising organic linkers and inorganic, metal-ion-containing nodes, with diverse functionalities and wide-range of applications. Because of their porous nature and functional nodes and linkers, they are competent candidates for gas storage, separation, catalysis, and so on. Most MOFs, however, are intrinsically insulating,...
In recent years, we have seen the embryo of Industry 4.0 which has been promoting manufacturing processes towards the future with better efficiency, higher accuracy and better reliability. However, manufacturing precision has been restricted by the precision of metrology and material characterization. In other words, one can only manufacture parts...
Stairs and curbs often present as an exhausting environmental barrier for individuals with bilateral cerebral palsy (CP) due to their lower limb motor impairments. Indeed, performance in stair-climbing in this population has a higher correlation with disruption of mobility than walking. Community members affected by CP consider impaired mobility a...
Anthropologists engaging with biopolitical theory have commonly assumed that biomedicine is a tool for enacting state-based policies to manage population health. Recent insights in medical anthropology have troubled this assumption, calling into question the role of physicians as “handmaidens” of state-based health policy. I use my position as a physician-anthropologist...
The role of providing care for a loved one with Alzheimer’s disease can expose friends and family caregivers to significant stress over an extended period of time, resulting in a host of negative outcomes like increased depression and anxiety, and diminished quality of life. However, previous studies have found that...
This thesis document is comprised of three research projects. The first investigates the active vibrational modes involved in twisted intramolecular charge transfer in a Julolidine-BODIPY dyad using two-dimensional electronic spectroscopy along with DFT calculations. We identified two types of vibrations, compression and torsional motion, as playing an important role in...
Renewable energy technology, more so than ever before, is critical to the survival of humanity. For decades, concentrated efforts into designing and developing such novel devices resulted in the innovation of solar-driven photovoltaics that were competitive with nonrenewable alternatives. This thesis explores the dynamic behavior of alternative material candidates that...
The work presented in this thesis is to describe the fabrication of the nano-composites of carbonaceous materials (e.g. graphene oxide) and metal oxides (e.g. Titanium dioxide TiO2) for two specific applications in the field of public health protection: 1.) removal of micropollutants (MPs) in the aqueous environment; 2.) antimicrobial coating.The...
The need for complex and sophisticated materials continues to grow as society becomes more advanced. For many chemists, the design of these materials begins by looking towards model molecular systems for the identification of desirable properties and functions. As such, restricting oneself to C, H, N, O, and the other...
Each neuron in the primary motor cortex (M1) is like a musician in an orchestra, contributing to a larger harmony under the constraint of a “neural manifold”—a geometric score describing the correlated signals produced by the neural musicians that drive movement. Despite the widespread recognition of the importance of M1...
Interpenetrating polymer networks (IPNs) are multicomponent materials that enhance the compatibility of otherwise immiscible polymers by trapping the microstructure in a non-equilibrium state. By combining polymers with vastly different moduli, IPNs effectively disperse rigid polymers within a soft matrix, resulting in a reinforced elastomer. This approach significantly increases the modulus...
Large scale adoption of sustainable technologies for energy productionand storage can be greatly facilitated by scientific advances impacting efficiency, cost and availability. The study of materials is instrumental in both upgrading the performance of existing technologies and enabling the development of new ones, and ab-initio methods and machine learning represent...
Chronic stress is a significant risk factor for the development of numerous psychiatric disorders, including major depressive disorder (MDD). Individuals with MDD exhibit impairments in reward processing and decreased motivation to engage in previously-rewarding activities. Importantly, there is a large sex disparity in MDD diagnosis, such that it affects nearly...
The rise in children’s media use (Rideout & Robb, 2020) and the prioritization of STEM learning (Fayer et al., 2017) has led to the development of new STEM-related apps, TV shows, and other media for young children. One topic in this area gaining popularity is computational thinking (CT). Researchers refer...
A proliferation of new media platforms have upended the traditional roles that journalists have played in society, placing their work into content streams that are populated by creators who mimic the surface features of their work but not their methods. As a result, journalists’ practices and news media that they...
In this dissertation, we aim to develop a theoretical understanding of foundation models and reinforcement learning. We delve into a comprehensive analysis of specific aspects within these domains. The focal points of our study are as follows: • Generative Adversarial Imitation Learning (GAIL) with Neural Networks: GAIL is poised to...
Rivers and streams play a critical role in connecting major global carbon pools – land, oceans, and atmosphere. The longitudinal flow in rivers and streams allows for the integration and transport of fluvial particulate organic carbon (POC) from various sources and its continual transformation. A continuum-oriented perspective suggests longitudinal variations...
Kaposi’ sarcoma-associated herpesvirus (KSHV) causes primary effusion lymphoma (PEL). PEL cell lines require expression of the cellular FLICE inhibitory protein (cFLIP) for survival, although KSHV encodes a viral homolog of this protein (vFLIP). Cellular and viral FLIP proteins have several functions, including, most importantly, the inhibition of pro-apoptotic caspase 8...
The relationship between the structure and function of proteins is a fundamental problem in biology with implications for the future of biotechnology and global health. For example, changes to the structure of a coronavirus spike protein led to a global pandemic where our best defenses were vaccines that could only...
Scholarly inquiry has yielded a wealth of evidence in support of narrative-based strategies for persuasion, and yet support for this approach is less consistent in relation to contentious or controversial issues. To better understand why this might be the case, the first part of this dissertation reports a theoretically-guided content...
Prisoner reentry has become an increasingly popular topic of research in the past few decades due to the phenomenon of mass return as a result of the era of mass incarceration. While research has been done on the experiences of the returning population before mass incarceration, few contemporary researchers have...
Ankle sprains are the most common musculoskeletal injury. After an ankle sprain, about 40% of individuals develop Chronic Ankle Instability (CAI), resulting in recurrent sprains, the ankle giving way, or feelings of instability. Most sprains occur due to excess inversion of the ankle. Frontal-plane ankle stiffness quantifies the ankle’s ability...
“National Acts: Performance, Commemoration, and the Construction of American Public Memory” explores how sites of public commemoration created during and after the American Civil War crafted conceptions of American public memory and identities through performative processes. This dissertation looks at three commemorative efforts: the Freedmen’s Memorial Monument to Abraham Lincoln,...
Dental enamel is a complex bio-composite with compositional and structural features across a wide range of length scales. Defects in these features can compromise enamel’s ability to protect the tooth, resulting in adverse health outcomes. Acquired defects like tooth decay are familiar to most people and are the subject of...
Many processes in nature and human-made settings rely on the unique properties of charged metal oxide:aqueous interfaces. Despite their ubiquity, these buried interfaces are challenging to study, since any analytical technique aiming to overcome the relatively small number density of interfacial versus bulk species must be highly sensitive and surface-selective....
Caves are accessible windows into the shallow subsurface, serving as transitional ecosystems between the photosynthesis-dependent surface and the deeper subsurface. Without a source of solar energy to ultimately power carbon (C) fixation (photolithoautotrophy), cave ecosystems are either reliant on surface-derived nutrients, recovering reducing power from the microbial oxidation of redox-sensitive...
Global dementia diagnoses are steeply increasing. While advances in neuroimaging, neuropathology, and genetics research have improved our understanding of neurodegenerative diseases causing dementia, precise antemortem diagnosis, as well as sensitive and specific biomarkers that can facilitate a differential diagnosis and aid in participant recruitment in clinical trials, remains elusive. The...
This dissertation explores critiques of mass education alongside the rise of the research university as they appear in the early writings of Friedrich Nietzsche and Walter Benjamin. More specifically, it traces the development of a theory of (un)learning that inserts distance into the pedagogical relation to produce a discretized educational...
Cancer is a complex and heterogeneous disease characterized by aberrant gene regulation. Gene regulation is fundamentally orchestrated by the 3D genome organization which involves chromatin looping, compartmentalization, and the formation of topologically associating domains (TADs). Structural variations (SVs), such as genomic rearrangements, deletions, inversions, and duplications, are commonly observed in...
This dissertation explores how dominant U.S. constructions of race, class, and gender are embedded into and inscribed onto artificially intelligent virtual assistants and the labors they perform. I examine virtual assistants like Amazon’s Alexa, Apple’s Siri, and Microsoft’s Cortana, interrogating their complex relationship to humanness, the tasks they are programmed...
This thesis explores how beyond-the-Standard-Model physics interactions could lead to the detection of neutrino decay with lifetimes that are orders of magnitude smaller than a second. I mainly focused on right-handed neutrino fields, new heavy states, and non-zero daughter neutrino masses, assuming the neutrinos are Dirac fermions. An extensive description...
Clustering is a fundamental task in unsupervised learning, which aims to partition the data set into several clusters. It is widely used for data mining, image segmentation, and natural language processing. One of the most popular clustering methods is centroid-based clustering, including k-medians and k-means clustering. k-medians and k-means clustering...
This dissertation focuses on the study of the superionic state in multicomponent systems, where the smaller component exhibits delocalization and mobility while still maintaining system compactness through component attractions. Superionic behavior is widely observed in various systems and plays a crucial role in ceramic superionic conductors, which offer high ion...
One of the greatest challenges in heterogeneous catalysis is the rational design and development of new catalytic systems, due to synthetic limitations in the design of solid catalysts and inhomogeneity of chemical sites at solid surfaces. This obfuscates understanding of catalyst behavior and slows improvements of processes. One approach to...
Clean water supplies are required for industry and general life. However, water shortages dueto pollution and human activity are increasingly common, and new, more efficient, materials need
to be made to increase clean water supplies. To do this, fundamental information on the interaction
of water with ions at the atomic...
The functions of lubricants in moving interfaces are extensive; lubricants minimize friction, transfer heat, clean the rubbing surfaces, extract debris, and diminish wear. Rather than using separate lubricants for each of the functions, it is more desirable to make one lubricant serve multiple purposes, or a muti-functional lubricant. The goals...
Morality has been viewed as a core aspect of the self and even a basic psychological need. Strategies for regulating threats to moral self-views may therefore be distinct from regulating threats to other self-aspects. Consistent with research on the regulation of basic psychological needs, I hypothesized that threats to the...
The continuing increase in atmospheric CO2 to concentrations exceeding 400 ppm has attracted considerable attention from both scientists and policymakers. Industrial fossil fuel consumption generates a significant amount of CO2 emissions, and in particular, energy-intensive molecular separations that require thermal processes, such as distillation, drying, or evaporation, are responsible for...
Performing complex reasoning has been a long-standing challenge in artificial intelligence (AI).This thesis describes a class of AI systems designed to reason, extract knowledge, and answer
questions on various domains such as process understanding, elementary science, and math word
problems. Our approach differs from traditional logical reasoning systems since we...
Lignin is the largest store of renewable aromatic carbon. Due to its refractory nature, however, its chemical potential is not fully realized, rather, most lignin is treated as a waste, burned for low-value energy. Here, we propose a biorefinery where the treatment of wastewater by a microbial electrolysis cell (MEC)...
In shared workspaces users have real-time access to others’ actions, allowing greater access to potentially informative cues. However, there has been little exploration about what impact the ability to view each other’s work in real time has on group members’ perception of both each other and their understanding of the...
The COVID-19 pandemic disrupted the status quo of the telemobility landscape in the United States, forcing millions of Americans into lock down, significantly changing the way we work, travel, and spend our time and money for an extended period of time. After several months of adaptation, adoption, learning, and unlearning,...
Assistive robots have the potential to support motor recovery after an injury as well as to alleviate the burden of physical tasks for both impaired and able-bodied individuals. Over the last few decades assistive robots have become increasingly more capable. Many can now provide task-specific assistance and can be safe...
Directional freeze-casting is a porous materials fabrication technique that is used to create materials with complex, three-dimensional pore structures. Particle suspensions are solidified under a thermal gradient, promoting anisotropic growth of dendrites and incorporation of particles within interdendritic space. A fully-solidified directional freeze-cast structure is composed of dendrites that are...
This thesis investigates Hugo von Hofmannsthal’s undermining of soteriological poetics in his comedy Der Schwierige (“The Difficult Man”), with a focus on the complex interplay between meta-language (e.g., stage directions) and dramatic dialogue, normative and contingent speech (i.e., ‘ironic speech’). By challenging what I term the “soteriological agenda” of comedy...
This dissertation proves several results for first passage percolation on graphs of polynomial growth.The class of limit shapes for first passage percolation with stationary weights on Cayley
graphs of virtually nilpotent groups is characterized.
Then strict monotonicity theorems for independent first passage percolation on graphs of
polynomial growth and quasi-trees...
Herein, we present an overview of our studies of the morphology, dynamics, and formation of heterogeneous soft matter systems via the emerging technique of liquid phase transmission electron microscopy (LPTEM). This particular subset of materials, more commonly referred to as emulsions, is tremendously commercially and biologically relevant, encompassing applications in...
Conversation is an important part of human life. Given globalization and the numerous languages around the world, it is increasingly likely that we will be communicating with others speaking in their second language (L2) rather than their first language (L1). In these situations, communication may require more effort. However, people...
Transnational adoption from Asia to the U.S. was institutionalized in the 1950s, when the Korean War left an estimated 100,000 Korean children orphaned or displaced. At the time, the practice was situated as a form of emergency rescue, an act of win-win humanitarianism in which average Americans could take part...
Transcription plays a pivotal role in the transfer of genetic information within living organisms. It serves as the initial step in gene expression, allowing cells to convert the instructions encoded in their DNA into functional molecules. Eukaryotic transcription initiation is a complex and dynamic process that requires joint efforts from...
Gastrointestinal (GI) colonization by Klebsiella pneumoniae is a risk factor for subsequent infection as well as transmission to other patients. Additionally, colonization is achieved by many strain types that exhibit high diversity in genetic content. However, how K. pneumoniae achieves colonization and whether the genetic factors it uses differ by...
Mission-critical systems are those imperative systems whose failures can result in catastrophic consequences. Traditional techniques, such as manual investigation and testing, cannot ensure the absence of errors and security vulnerabilities within these systems. This dissertation leverages formal methods to comprehensively examine several mission-critical systems and their essential components. For each...
The advent of advanced computing and AI has led to social technologies becoming agentic teammates in human-autonomy teams. Interpersonal trust, vital for team functioning, is crucial in determining these teams' success or failure. Trust, while essential, can be easily broken and requires maintenance and repair. This dissertation addresses two questions:...
Breast cancer patients have reported nonspecific neurologic symptoms such as fatigue, depression, and cognitive concerns while undergoing adjuvant therapy. Few neuroimaging studies have examined hormone therapy, an adjuvant therapy, and more research is needed to determine possible neurologic and cognitive effects. Previous estrogen research has found alterations in gray matter...
This dissertation uses the case of Colombia to examine the causes and reproductive mechanisms of civil wars that last more than fifty years, which I call perpetual civil wars. It draws on network analysis of violent events and political claims, content analysis of official archival documents and historical records of...
Swallowing impairment or dysphagia has many possible causes with severe sequelae. One major mediator of the relationship between causes and sequelae is the physiologic impairment of the swallowing mechanism. Assessing the physiology of swallowing impairment is of great importance so that treatment can target physiology to mitigate sequelae. The assessment...
The political history of late twentieth-century Southern Africa was dominated by violent liberation struggles against settler-colonial domination in Angola, Mozambique, Namibia, South Africa, and Zimbabwe. All five countries experienced prolonged settler colonialism, followed by conflicts in which revolutionary national liberation movements (NLMs) sought to both end settler-colonial domination and build...
Recent experiments in participatory democracy, such as Iceland’s 2013 Constitutional Reform process to Chicago’s annual participatory budgeting process, have empowered members of the public to directly make policy decisions. These new participatory democratic institutions depend on citizens having capacity to organize new institutions and the capacity to participate in them....
Derivative-free optimization (DFO) has received growing attention due to important problems arising in practice. Various research communities, ranging from machine learning to engineering design, have adopted distinct DFO methods. In this thesis, we present extensive studies as a meaningful step towards a comprehensive understanding of DFO methods. We study the...
In this work, I try to understand how the movements, attitudes, styles, and positions of the body in representational artworks can be understood as gestures—that is, as moments that interrupt the unfolding of narrative time and produce an interval. The interval is not merely a space that opens up between...
This dissertation theorizes the relation between blackface minstrelsy and contemporary Black performance. The project analyzes the use of nineteenth-century blackface minstrel conventions in Black theatrical performances during later eras where its usage seems counter-intuitive: during the Black freedom struggles of the 1960s; within Black feminist and queer performance of the...
In recent years, the understanding and identification of quantum materials supporting non-trivial band topology has progressed rapidly. This progress has been motivated in part by the potential application of topological quantum materials in quantum computers, sensors, and other next-generation devices. Despite this progress, the computation of bulk topological invariants in...
This dissertation focuses on quantifying protein folding stability determinants and presenting initial experiments that can guide the development of a novel assay that identifies cell-penetrating miniproteins. First, despite over a century of scholarship on protein folding stability, applying this knowledge to design proteins computationally remains limited. Usually, protein designers generate...
This project explores how the variation in language experiences and attitudes that Mexican American Spanish heritage speaker bilinguals in the United States have affects their speech perception in both their languages. Heritage language bilinguals speak as a first language a minority language that they have cultural ties to (e.g., Spanish...
This dissertation investigates how scope relations are constructed and evaluated during real-time human sentence processing. Theoretical approaches to processing scope relations exist in a multi-dimensional space where trade-offs are made around how quickly scope relations can be computed, how many mistakes are made in computing scope relations, and how many...
The field of distributed optimization algorithms is wide and growing, and new techniques for categorizing and analyzing existing algorithms are continually being developed. In this Thesis, we leverage control theoretic analysis and block diagram interpretations for existing algorithms to synthesize entirely new families of algorithms. These new algorithm families have...
Transitioning energy systems from a reliance on fossil fuels to low carbon energy sources is an essential solution for climate change mitigation. However, the industrial sector, which is directly responsible for more than a quarter of global carbon dioxide (CO2) emissions, continues to use fossil fuels for energy and feedstocks....
Necessity is the mother of innovation. In the wake of the pandemic, with no flow of samples and limited fabrication techniques available, necessity demanded a new material platform and adaptable methods to make complex oxide samples worth measuring. The material platform was KTaO3 , the younger successor to the mainstay...
This manuscript describes and contextualizes the research I performed as a PhD student in Northwestern University. The first three chapters, on Markov chains, stochastic thermodynamics, and large deviation theory, describe three interrelated topics that serve as the background for subsequent research detailed in the next three chapters, on understanding the...
This dissertation aims to develop innovative analytical methods that integrate engineering, marketing, and social science disciplines to incorporate heterogeneous consumer preferences into product design using network-based customer preference modeling. Both companies and designers frequently face difficulties in understanding and addressing customer preferences, which can result in product failure and loss...
Machine learning and deep learning have been proven successful across various scientific fields, such as computer vision, natural language processing, and recommendation systems. As models become more complex, with more parameters and intricate architectures, they can achieve higher prediction accuracy when trained on larger datasets. However, despite the great prediction...
The action of the automorphisms of a formal group on its deformation space is crucial to understanding periodic families in the homotopy groups of spheres and the unsolved Hecke orbit conjecture for unitary Shimura varieties. This action is called the Lubin-Tate action. We first show sufficient conditions for geometrically modelling...
Despite the increasing interest in biogenic secondary organic aerosols (SOAs), their role in the climate system remains the greatest source of uncertainty in global models. Cloud formation, critical for the net cooling effect provided by cloud cover, is dependent on the abundance of SOA particles and their ability to activate...
Although elevated stress and dietary change have each been associated with metabolic health decline for resettled populations in the Global North, considerably less attention is paid to the links between these two biosocial pathways. Addressing these linkages can elucidate interrelated diet and stress mechanisms that affect population health disparities over...
Submodularity is a well-known concept in integer programming and combinatorial optimization. Submodular set functions capture the diminishing returns phenomenon, which has wide-ranging applications in various domains. Typically, a submodular set function models the utility of homogenous items selected from a single ground set. Selecting an item or not is naturally...
Controlled delivery of foreign cargo into cells is a critical step in many biological studies and in cell engineering and analysis workflows. Recent advances in micro and nanotechnology, specifically in microfluidics and microfabrication have added significantly to the precision, accuracy, resolution and throughput of cell manipulation and analysis pipelines. These...
Metalloenzymes catalyze remarkable reactions in Nature using transition metal ions. Common earth-abundant metals like copper, iron, zinc, and magnesium catalyze reactions that are the basis of life. These metal sites lend their chemistries to facilitate these reactions, making studying the structure and properties important in understanding the enzymes' abilities and...
For many years silicon tethers have been used to increase yields and control the stereochemical and regiochemical outcomes of coupling reactions. Silicon tethers may be incorporated into a wide range of reaction types including alkene metathesis, cycloadditions, and glycosylations. This thesis focuses on the development of the use of silicon...
Drying oils have been used as a binding medium for oil paints since the 15th century. These oil paints transition from a liquid-like paste to a solid-like film as a result of crosslinks forming between the oil molecules. These reactions have been extensively studied chemically, but other material properties are...
Pollution-intensive industrial manufacturing processes threaten the health of ecosystems and societies through toxic waste streams and energy intensive processes that lead to greenhouse gas emissions. Biological systems present more sustainable routes to many useful industrial chemicals by using enzymes at low temperatures, but the time and effort required to optimized...
This dissertation focuses on quantifying protein folding stability determinants and presenting initial experiments that can guide the development of a novel assay that identifies cell-penetrating miniproteins. First, despite over a century of scholarship on protein folding stability, applying this knowledge to design proteins computationally remains limited. Usually, protein designers generate...
Temperature affects all biological processes, from the rate of cellular growth and metabolism to the stability of proteins that make up the machinery of life itself. Thus, all organisms must have the capacity to detect and respond to external temperature. Thermosensation endows animals with the ability to sense and respond...
This dissertation presents novel advancements in the field of continuous nonlinear optimization, focusing on the development of efficient second-order methods for second-order conic programs (SOCPs) and continuous nonlinear two-stage optimization problems. The primary focus is on the theory and computations of Sequential Quadratic Programming (SQP) methods, which are widely used...
Recent progress in semiconductor synthesis and photophysics has revealed a host of new materials with exciting properties for applications in optoelectronic devices such as sensors, photovoltaics, solid state lighting, and more. One of the most significant recent additions to the field is the class of hybrid and inorganic materials that...
Bacterial infections (BI) are a frequent, expensive, and life-threatening condition for critically ill patients. For patients with serious BI, minimizing the time between admission to the
intensive care unit (ICU) and administration of appropriate antibiotic therapy is crucial to
improve prognosis. However, the current gold-standard for identifying the appropriate
antimicrobials...
Herein, we present an overview of our studies of the morphology, dynamics, and formation of heterogeneous soft matter systems via the emerging technique of liquid phase transmission electron microscopy (LPTEM). This particular subset of materials, more commonly referred to as emulsions, is tremendously commercially and biologically relevant, encompassing applications in...