VictorJuiz/thesis huggingface dataset:
Modeling virtual environments 3D assets from visual inputs

Modeling the physical world is crucial for many applications that significantly impact society, includ- ing robotics, autonomous vehicles, virtual and augmented reality (AR/VR). Research works com- monly leverage 3D virtual environments as a proxy for real environments to perform experiments. By using virtual environments, experiments like robotic simulations, navigation, and interactions can be performed safely and at a lower cost compared to real-world environments. 3D geometric and material assets are the building blocks of virtual environments. However the process of creating 3D assets from scratch is mostly manual, time-consuming, and requires significant expertise. This challenge motivates the development of automated methods for 3D assets generation. We introduce a Computer Vision framework for generating 3D assets from visual inputs that include images and 3D point clouds from real scenes. Visual inputs from a scene are parsed into individual objects, structures, and materials which can be processed into 3D assets. This framework involves four key tasks: 3D semantic segmentation, shape completion, shape modeling, and material prediction. We introduce representations, algorithms, machine learning models, and datasets to address the chal- lenges associated with each of these tasks. We introduces new models for 3D semantic segmentation and shape completion. It also introduces a graph representation and search algorithm that facilitates generating multiple variations of a given shape. Last, it contributes a large scale dataset of procedu- ral materials along with a neural network model that generates procedural materials from images. The results of this thesis is a set of methods addressing the aforementioned tasks and supporting the creation of realistic virtual environments at scale

Keywords: Engineering.
Electrical Engineering.
Advisor: Savarese Silvio
Bambos Nicholas
Pauly John (John M.)
Modulation of regulatory T cell function by tissue extracellular matrix

Regulatory T lymphocytes are an essential component of the immune system -- in their absence, autoimmunity develops. Maintenance of regulatory T cells is thought to rely predominately on the transcription factor Foxp3, IL-2 signaling and T cell receptor stimulation. While these three factors are essential for regulatory T cell function, interactions with the tissues may also play a critical role in their function and persistence. To carry out their nonredundant role in immune suppression, these T cells must navigate the extracellular matrix -- the cellular environment composed of proteins, proteoglycans, and glycosaminoglycans. Our current understanding of regulatory T cells does not fully account for how the matrix interacts with and contributes to regulatory T cell function. To better understand this relationship, we examined two extracellular matrix glycopolymers, hyaluronan and heparan sulfate, and their respective receptors, CD44 and heparanase. We investigated the role of these polymers and receptors in regulatory T cell stability, function, and persistence. Hyaluronan is a glycosaminoglycan composed of repeating disaccharides subunits, N-acetyl glucosamine, and D-glucuronic acid. Hyaluronan is abundant in tissues, with elevated expression during inflammation. CD44 is an alternatively spliced glycoprotein that serves as the cognate receptor for hyaluronan and is ubiquitously expressed on hematopoietic cells. Herein we examined the function of hyaluronan CD44 interactions on primary mouse and human CD4+ regulatory T cells. Engagement of CD44 with hyaluronan or overexpressing CD44, improves regulatory T cell activation and increases regulatory T cell suppression. Heparan sulfate is another glycosaminoglycan abundant within the matrix but differs from hyaluronan in that heparan sulfate is covalently linked to a protein backbone. Heparan sulfate itself is known to bind many diverse protein ligands and modulate ligand-receptor signaling. Heparanase is an enzyme that binds and cleaves heparan sulfate polymers. The cytokine interleukin 2 exhibits heparan sulfate binding, yet little is known about its contribution to regulatory T lymphocyte biology. We discovered the role for heparan sulfate interleukin 2 complexes and heparanase in modulating regulatory T lymphocyte function. Specifically, we found that heparan sulfate interleukin 2 complexes exert increased signaling agonism compared to interleukin 2 alone. Additionally, heparanase is required for optimal regulatory T lymphocyte function and survival; without it, mice undergoing experimental autoimmune encephalomyelitis exhibit worse disease. This thesis provides evidence that the ECM components hyaluronan, heparan sulfate, and their respective receptors contribute to regulatory T cell homeostasis. Future work in understanding autoimmunity and associated therapeutics needs to consider the role of the extracellular matrix in regulatory T cell fate.

Keywords: Medicine.
Microbiology and Immunology
Advisor: Bollyky Paul
Jagannathan Prasanna
Maltzman Jonathan
Meyer Everett
Molecular checkpoints in myeloid and B cell responses

After physical barriers, the innate immune response is the first line of defense against pathogens. The adaptive immune confers long-lasting pathogen-specific immune memory poised to be rapidly recruited upon secondary infection. Innate responses rest on the ability of immune cells to recognize pathogens associated molecular patterns (PAMPs) via pattern recognition receptors (PRRs) thus triggering activation of an inflammatory response that together with adaptive immunity aids pathogen clearance. PRRs are also expressed by adaptive immune cells. PRR signaling in adaptive immune cells can promote their activation and skew maturation. Although the role of PRRs in sensing PAMPs is well established, it is becoming increasingly clear that the immune system can also by activated by certain endogenous ("self") molecules. Immune cell activation also often includes substantial metabolic reprogramming. In this thesis we investigate the role of two pathways necessary for optimal immune responses: self-dsRNA/ADAR1 and sterol/SREBP. Cytosolic double stranded RNA (dsRNA) is recognized as a viral PAMP. However, dsRNA can also be generated as a byproduct of the transcription of repetitive genomic elements. Under normal homeostatic conditions, the enzyme adenosine deaminase acting on RNA-1 (ADAR1), modifies self-dsRNA to prevent sensing by PRRs. Despite evidence that ADAR1 is a central negative regulator of self-dsRNA sensing, our understanding of the contribution of the self-dsRNA/ADAR1 axis to the initiation, propagation, and durability of the immune response is limited. Here, we demonstrate a role for ADAR1 in CD11c+ myeloid antigen presenting cells (APCs) and germinal center (GC) B cells. We show that ADAR1 loss in APCs skews the composition of the myeloid cellular compartment and imprints a functional antiviral transcriptional signature in the lungs. Meanwhile, ADAR1 loss in GC B cells leads to a failure to generate successful humoral and memory B cell responses to immunization. These results reveal a fundamental role for ADAR1 in regulating the innate and adaptive immune response. Sterol regulatory element binding proteins (SREBPs) are transcription factors that promote the expression of genes involved in cholesterol uptake. The SREBP cleavage activating protein (SCAP) mediates SREBP activation. Our previous work identified an association between the magnitude of the antibody response in humans and targets of SREBP. To understand whether this effect was mediated by APCs or was B cell intrinsic, we generated mouse models of conditional SCPAP deletion in both CD11c+ myeloid APCs and B cell. We demonstrated that SREBP signaling in B cells (but not APCs) was essential for effective B cell response. SCAP deficiency led to cell cycle progression and maturation defects. Taken together, our findings provide new mechanistic insights about the regulation of immune responses by the RNA-editing enzyme ADAR1 and by SREBP/SCAP mediated cholesterol biosynthesis.

Keywords: Medicine.
Microbiology and Immunology.
Advisor: Li Jin (Billy)
Pulendran B. (Bali)
Engleman Edgar G.
Kirkegaard Karla
Mellins Elizabeth
Molecular identification of neural circuits controlling vocalization and cardiopulmonary physiology

The nucleus ambiguus is a small column of several hundred neurons in the brainstem that is essential for critical functions including speech and neural control of the heart and lungs, but the cell types that control these distinct functions have not been molecularly identified. Here I describe my work dissecting this region using retrograde labeling, single-cell RNA sequencing, single-molecule fluorescent in situ hybridization, and functional experiments in mice. These experiments revealed the first molecularly defined neurons that control vocalization and cardiopulmonary physiology. One of the identified cell types consists of ~160 neurons adjacent to the nucleus ambiguus that express a specific neuropeptide and are necessary and sufficient for producing sound and controlling sound volume. Activating these neurons finely coordinates laryngeal and expiratory muscles, revealing the neural mechanism for sound production and volume control. I then identified two additional molecularly distinct cell types, one that selectively controls the heart and maintains blood pressure homeostasis (~35 neurons), and another that coordinates heart and lung function during an ancient physiological reflex (~15 neurons). Taken together, this work revealed intermingled but specialized neural circuits for three critical physiological and social functions: cardiovascular control, cardiopulmonary control, and vocalization, laying a foundation for precisely modulating these circuits in health and disease

Keywords: Engineering.
Bioengineering.
Advisor: Krasnow Mark
Kingsley David M. (David Mark)
Lee Jin Hyung
Molecular Layer Deposition of Hybrid Organic-Inorganic Resists for Electron-Beam and Extreme Ultraviolet (EUV) Lithography

The development of new resist materials is vital to fabrication techniques for next- generation microelectronics. Hybrid organic-inorganic materials are a promising class of resists because they have higher etch resistance, are more impervious to pattern collapse, and are more absorbing of extreme ultraviolet (EUV) radiation than organic resists. However, there is limited understanding about how they behave under irradiation. In this work, we study the molecular layer deposition of Hf- and Al-based hybrid thin film resists, known as “hafnicone,” “oxygen- rich alucone,” and “standard alucone.” These resists were grown at 100ºC using the metal precursor tetrakis(dimethylamido)hafnium(IV) or trimethylaluminum as well as the organic precursor ethylene glycol. Electron-beam lithography, scanning electron microscopy and profilometry are used to investigate the resist performance of hafnicone, oxygen-rich alucone, and standard alucone. Like hafnicone, oxygen-rich alucone behaves as a negative tone resist that can resolve 50-nm line widths, though the line patterns of oxygen-rich alucone are more sharply defined than those of hafnicone. Whereas hafnicone displays a sensitivity of 400 μC/cm2 using 3 M HCl as the developer, the sensitivity of oxygen-rich alucone—4800 μC/cm2 using 0.125 M HCl—is not as good. Compared to oxygen-rich alucone, standard alucone offers superior (sub-25 nm) resolution at the expense of lower sensitivity (>13,000 μC/cm2 using 0.01 M HCl). In addition to determining the resist properties of the three films, we characterize hafnicone via x- ray photoelectron spectroscopy (XPS) and infrared spectroscopy (IR) to investigate its patterning mechanism, which is described in the context of classical nucleation theory. This study of hafnicone and alucone hybrid MLD demonstrates the ability for the bottom-up vapor deposition of inorganic resists to be used in advanced e-beam and EUV lithographic techniques.

Keywords: photoresists, molecular layer deposition, thin films, electron-beam lithography
Text
Thesis
Advisor: Bent Stacey
Clemens Bruce
The molecular mechanism for ionic stress sensing and adaptation in mammalian cells

Homeostatic control of intracellular ionic strength is essential for protein, organelle and genome function, yet mechanisms that sense and enable adaptation to ionic stress remain poorly understood in animals. We find that the transcription factor NFAT5 directly senses solution ionic strength using a C-terminal intrinsically disordered region. Both in intact cells and in a purified system, NFAT5 forms dynamic, reversible biomolecular condensates in response to increasing ionic strength. This self-associative property, conserved from insects to mammals, allows NFAT5 to accumulate in the nucleus and activate genes that restore cellular ion content. Mutations that reduce condensation or those that promote aggregation both reduce NFAT5 activity, highlighting the importance of optimally tuned associative interactions. Remarkably, human NFAT5 alone is sufficient to reconstitute a mammalian transcriptional response to ionic or hypertonic stress in yeast. Thus NFAT5 is both the sensor and effector of a cell-autonomous ionic stress response pathway in animal cells.

Keywords: Medicine.
Biochemistry.
Advisor: Rohatgi Rajat
Brandman Onn
Harbury Pehr
Krasnow Mark
MoneyMouth: A Machine Learning Analysis of Altruistic Crowdfunding Success on GlobalGiving.org

NGOs often face knowledge barriers regarding how to write effective fundraising requests on crowdfunding platforms. This issue motivates the use of mixed computational methods to identify the linguistic features associated with successful campaigns and predict whether a campaign will succeed. The research incorporates Linguistic Inquiry and Word Count (LIWC), Pearson correlation coefficients (PCC), logistic regression (LR), Bidirectional Encoder Representations from Transformers (BERT), and Local Interpretable Model-Agnostic Explanations (LIME) with the goal of unifying computer and social science. The PCCs calculated on GlobalGiving.org projects suggest that community-based thinking, storytelling, and readability are characteristics of campaigns that reach their target fundraising amount. The LR model’s most heavily-weighted linguistic features corroborate those results. The fine-tuned BERT model performed slightly better than the logistic regression at predicting a crowdfunding campaign’s success.

Keywords: Machine learning
Deep learning (Machine learning)
Altruism
Social service
Statistics
Social sciences > Statistical methods > Computer programs
Communication
Crowd funding
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Thesis
Advisor: Hancock Jeffrey
Wu Jiajun
The more complete female athlete : physical health, mental health, and how we talk about it

After decades of work to identify and remove barriers to sports participation, female athletes are now participating in recreational and competitive sports at record numbers. However, female athletes are still underrepresented in sports research, leaving dangerous gaps in knowledge that we need to fill to encourage the development of more complete female athletes with better performance, healthier bodies, and improved mental health. Epidemiology provides a helpful framework for confronting these knowledge gaps and preventing them from undercutting the next generation of female athletes. It's urgent that female athletes are not treated as "smaller" male athletes, or worse—ignored altogether. By studying female athletes and addressing the unique physiological and sociological challenges they face, then translating the research into practical guidance and education, we have an opportunity to support generations of athletes to come. Every female athlete should have the tools to find their personal definition of "strong, " understanding how that individual and evolving strength will bring out their best in sports and in life. In this dissertation, I address pressing problems facing female athletes to evaluate new strategies for improving health and well-being by applying epidemiological principles and studies on research translation. The chapters in this dissertation intersect to cover six themes: (1) mental health; (2) bone health; (3) energy availability; (4) menstrual cycle; (5) performance; and (6) research translation (Figure 1-1). Chapter 1 introduces the scope of the field and how the themes intersect. In Chapters 2 and 3, we evaluate the effect of a nutrition education intervention on bone stress injury rates among female distance runners at two NCAA Division I institutions across a seven-year prospective study. In Chapter 4, we examine how a five-part video education series compares to online educational pamphlets for improving high school female runners' knowledge and for capturing their interest. In Chapter 5, we assess the risk of the Female Athlete Triad in ultramarathoners and complete exploratory analyses examining hormonal biomarkers and bone mineral density. And finally, in Chapter 6, we examine how early COVID-19 restrictions impacted the mental health and training of endurance athletes, which provides a broader context for how mental and physical health can be impacted by external factors, and how we can support athletes who are navigating prolonged breaks from competition. Recognizing and uplifting female athletes requires understanding their unique mental and physical health contexts, addressing the specific challenges they face, and empowering them to find their strong, in sports and in life

Keywords: Medicine.
Advisor: Fredericson Michael
Sainani Kristin
Nelson Lorene M.
Morphological Analysis of Axo-Axonic Cell Variability

Several neurological disorders are characterized by a pathological overexcitation of neurons. However, little is known about the precise mechanisms that underlie inhibition, or the repression of overactivity, which could potentially restore function lost due to overexcitation. One promising area of research is axo-axonic cells in the hippocampus, a class of cells that has been implicated as one of the most important inhibitory circuit elements due to their innervation of axon initial segments of pyramidal cells. As axon initial segments are the site of action potential generation, and pyramidal cells are the primary excitatory unit in the brain, axo-axonic cells and their direct connection to pyramidal cells may play a uniquely important inhibitory role. Previous research has shown variability in activity patterns of axo-axonic cells, suggesting further subtypes within this group, which this study aimed to further investigate. The research discussed in this thesis involved confocal imaging of immunostained axo-axonic cells in mouse hippocampal subsections, followed by recording these cells' location within the hippocampus, bouton connectivity, laminar distribution, and protein expression, attempting to identify trends in variability. We found significant variability, but no evidence of distinct subtypes. This information can be used to contribute to a growing body of work on the role of these cells within healthy neuron networks, and potentially contribute to future research into applications of harnessing axo-axonic cells' natural inhibitory ability in diseases involving overexcitation.

Keywords:  Department of Biology
axo-axonic cells
Interneurons
Epilepsy
Hippocampus (Brain)
Inhibition
parvalbumin
Text
Thesis
Advisor: Dudok Barna
Soltesz Ivan
Chen Xiaoke
Morphological, mechanical and electrochemical investigations into the solid electrolyte interphase

Despite their importance to an array of technologies, many processes in lithium-ion batteries are incompletely understood, especially those involving air sensitive interfaces such as the solid electrolyte interphase (SEI). Motivated by a desire enable next generation lithium-ion battery chemistries, this thesis attempts to shed light on the SEI in its native environment by a combination of in-situ and operando techniques including atomic force microscopy (AFM), selected because its ability to take nanoscale measurements of the SEI in its native liquid environment. To further capture insights into the SEI's formation and evolution, electrochemical impedance spectroscopy (EIS) is leveraged since its quantitative and nondestructive capabilities are highly synergistic with AFM operando techniques. First this thesis explores the process by which the SEI self-passivates, combining data from AFM thickness measurements and electrochemical capacity to demonstrate to demonstrate that models assuming a single SEI phase cannot simultaneously describe capacity and thickness of the initially grown SEI. Second the nanomechanical capabilities of the AFM are leveraged to study SEI grown on lithium metal, a promising next-generation anode material. While the Young's modulus has of SEI has been previously reported, lack of replicates and poor reproducibility of experiments makes interpreting the relationship between mechanics and performance difficult. Further non-elastic mechanical properties are rarely reported, despite their key role in many types of solid electrolyte and protective coating. Combining a more complex indentation protocol with the use of replicates and careful statistics, this work demonstrates that although the elastic properties are uncorrelated to cell performance, the inelastic properties are and that SEI creep under load is correlated with poor cycling efficiency of lithium metal in the associated electrolyte. The final scientific question tackled by this work is how the impedance of the SEI varies during formation, both as a function of potential and time. The SEI resistance is shown to grow linearly with SEI capacity once past the very initial formation. Further, the low frequency portion of the EIS spectra, which is not frequently studied, is discussed and shown to relate both to blocking processes at the copper-SEI interface as well as electrolyte reactivity that gives rise to the formation of new SEI.

Keywords: Engineering.
Materials Science and Engineering.
Advisor: Chueh William
Cui Yi
Gu Wendy (Professor of mechanical engineering)