VictorJuiz/thesis huggingface dataset:
Ubiquitin-Dependent Control of Myogenic Development: Mechanistic Insights into Getting Huge, and Staying Huge

Metazoan development is dependent on the robust spatiotemporal execution of stem cell cell-fate determination programs. Although changes in transcriptional and translational landscapes have been well characterized throughout many differentiation paradigms, their regulatory mechanisms remain poorly understood. Ubiquitin has recently been found to be a key modulator of developmental programs. Ubiquitylation of target proteins occurs through a cascade of enzymatic reactions beginning with a ubiquitin activating enzyme (E1) which transfer the ubiquitin moiety to a ubiquitin conjugating enzyme (E2). The reaction is finalized by the transfer of ubiquitin to its target protein by a ubiquitin ligase (E3). Post-translational modification of proteins can lead to several different outcomes, depending on the context of the modification, known as the ubiquitin code. The precise spatiotemporal execution of ubiquitylation is critical for organismal development and homeostasis. Due to the modular and reversible nature of ubiquitylation, it is an ideal moiety in the control of a plethora of cellular processes./nCell-cell fusion is a frequent and essential event during development, whose dysregulation causes diseases ranging from infertility to muscle weakness. Critical to this process, cells repeatedly need to remodel their plasma membrane through orchestrated formation and disassembly of cortical actin filaments. In Chapter 2, I describe the identification of a ubiquitin-dependent toggle switch that establishes reversible actin bundling during mammalian cell fusion. My work identified KCTD10 as a modulator of the EPS8-IRSp53 complex, which stabilizes cortical actin bundles at sites of cell contact to push fusing cells towards each other. This work highlights how cytoskeletal rearrangements during development are precisely controlled, raising the possibility of modulating the efficiency of cell fusion for therapeutic benefit./nOrganismal development must rely on the timely and robust execution of quality control responses. However, how these responses modulate metazoan development is poorly understood. Showcasing the versatility of ubiquitin signaling, Chapters 3 and 4 provide insight into the role of ubiquitin in controlling stress and quality control responses. Chapter 3 describes the reductive stress response, in which FEM1B senses and reacts to persistent depletion of reactive oxygen species. Loss of ROS is detrimental for development, as it inhibits myogenesis. Concomitant to this stress response is the identification of multimerization quality control, regulated by BTBD9. MQC surveys multimeric BTB complex composition, ensuring that multimeric complexes contain the correct stoichiometries and compositions. MQC is critical for development, as loss of MQC als prevents myogenesis. These two chapters showcase the integration of ubiquitin signaling, stress/quality control pathways, and development. These writings provide a more holistic understanding into the robust regulatory underpinnings of organismal formation

Advisor: Rape, Michael
Metabolic and Mechanical Maturation of hiPSC-Derived Heart-on-a-Chip platform for COVID-19 Therapeutics Cardiac Liability Screens

With highly regulated safety requirements, the average cost of drug development is $2.5B, which has increased by more than 9-fold since 1979. Preclinical studies include both in vitro and in vivo studies in non-human models to determine the efﬁcacy and toxicity of the compound before any administration to people. However, no commonly used platforms accurately predict drug effects on patients, since they do not mimic human physiology. The fourth reason for drug withdrawal from the market in the last 70 years were unexpected side effects on the cardiovascular system, such as toxicity or dysfunction of the heart, associated with life-threatening conditions. Accordingly, the FDA has mandated that all drugs must be screened for the potential to alter ventricular repolarization prior to human studies. There is an urgent need to develop tools to diminish time and costs of the drug development pipeline while getting safer and more efﬁcient cardiotoxicity screening. A big advance for 2D in vitro assays for cardiotoxicity screens was the discovery of human induced pluripotent stem cells (hiPSC) from which cardiomyocytes with patients genetics could be derived. However, one challenge remains : hiPSC-derived cardiomyocytes (CM) show immature metabolic and mechanical properties, questioning their prognostic capabilities. In this thesis, we demonstrated that the combination of 3D culture of hiPSC-CM in microphysiological systems (heart-on-a-chip) with fatty-acid based media, synergized to promote maturation of hiPSC-CM metabolism and electrophysiology. To further improve the maturation of the tissues we screened through different confinement chamber designs and selected for parameters that enhance mechanical, morphological and contractility outcomes of tissues. As the COVID-19 pandemic hit, we saw the opportunity for our matured cardiac system to rapidly predict cardiotoxicity associated with potential therapeutics (hydroxychloroquine combination with azithromycin) in a mock clinical trial experimental design as well as in an acute dose escalation study. The high content system can help clinicians rapidly evaluate safety properties of potential therapeutics in crisis times to hopefully accelerate access of patients to treatment.

Advisor: Healy, Kevin E
The Genomic Basis of Desert Adaptation in Rodents

Understanding the genomic architecture of complex adaptive traits in natural populations has long been a central goal in evolutionary biology. Of particular interest is the extent of the “genetic toolbox,” that is: how many evolutionarily viable solutions are there to a common evolutionary problem? To get at this question, I looked at convergent adaptation to desert environments across the order Rodentia. In mammals, the problem of living in an extremely arid environment with limited access to free water has been solved in a variety of different ways. For granivorous desert rodents, many have developed ultra-efficient osmoregulatory systems, including highly modified kidneys, to handle the problem of salt and water homeostasis. Here, I examined the genomic basis of adaptation across multiple evolutionary timescales./nIn chapter one, I studied the recent invasion of a North American desert by the house mouse, Mus musculus. I compared this desert population with a non-desert population and examined organismal phenotypes and gene expression profiles in the lab for experimentally dehydrated mice and for control mice. I discovered significant differences in the response to water stress in these two populations. Mice derived from a desert population showed a less extreme response to water stress, suggesting they may have adapted to live in deserts. Non-desert mice showed shifts towards desert-like gene expression after water stress, consistent with adaptive plasticity. Further, I identified candidate genes underlying desert adaptation in this population./nIn chapter two, I leveraged three phylogenetically distinct species pairs, one a desert specialist and the other a mesic representative, from three families of rodents over ~70 million years of divergence and found convergent patterns of evolution using sequences of expressed genes (RNA-seq data). First, I looked for convergent shifts in gene expression associated with desert living in each species pair and identified genes displaying this pattern. Next I used multiple methods to test for aspects of convergence at the DNA sequence level and found that few genes showed both convergence in DNA expression and convergence in protein structure. I found that a greater proportion of genes tested show convergent patterns in gene expression suggesting that changes in the regulation of genes may have a greater impact than changes in protein structure during adaptation to desert environments./nIn chapter three, I sequenced and assembled de novo the genome of the rock pocket mouse, Chaetodipus intermedius (Heteromyidae) using MaSuRCA. This species, found in the Sonoran and Chihuahuan deserts of North America, is a desert specialist and a model for understanding the genetics of coat color variation in wild populations. This genome is a resource to be used to further understand the genomics of adaptation in this unique lineage.

Advisor: Nachman, Michael W.
Round-Optimal Secure Multiparty Computation from Minimal Assumptions

Secure Multiparty Computation (MPC) allows a set of parties, each having its own private data, to compute a function of their joint data such that the parties only learn the output of this function and everything else about their data is hidden. MPC is a fundamental cryptographic abstraction that captures many other natural cryptographic primitives as special cases. It also has a wide range of practical applications such as conducting secure electronic auctions, delegating sensitive computation to untrusted cloud service providers, secure computation on genomic data and training machine learning models on private data./nA long-standing open problem in this area is to construct MPC protocols that have {\it optimal} (two-round) round complexity under the {\it weakest} possible cryptographic hardness assumptions./nWe {\it completely resolve} this problem by showing lower bounds and matching upper bounds on the hardness assumptions required for constructing round-optimal MPC. Specifically, we obtain the following results./n\begin{itemize}/n\item \textbf{Black-Box Separation.} We show that there exists no construction of two-round semi-honest MPC protocol for general functions that makes black-box use of a two-round oblivious transfer. As a corollary, a similar separation holds when starting with any 2-party functionality other than oblivious transfer./n\item \textbf{Non-Black-Box Construction.} We show that the above negative result can be bypassed by making non-black-box use of a two-round oblivious transfer. Specifically, starting from a semi-honest (resp. malicious) secure two-round oblivious transfer protocol, we construct a two-round MPC protocol against semi-honest (resp. malicious) adversaries./n\end{itemize}/nSince any two-round MPC protocol for general functionalities implies a two-round oblivious transfer as a special case, the above two results show that non-black-box use of oblivious transfer is {\it necessary and sufficient} to construct round-optimal MPC protocols.

Advisor: Garg, Sanjam
Physics-based Learning for Large-scale Computational Imaging

In computational imaging systems (e.g. tomographic systems, computational optics, magnetic resonance imaging) the acquisition of data and reconstruction of images are co-designed to retrieve information which is not traditionally accessible. The performance of such systems is characterized by how information is encoded to (forward process) and decoded from (inverse problem) the measurements. Recently, critical aspects of these systems, such as their signal prior, have been optimized using deep neural networks formed from unrolling the iterations of a physics-based image reconstruction./nIn this dissertation, I will detail my work, physics-based learned design, to optimize the performance of the entire computational imaging system by jointly learning aspects of its experimental design and computational reconstruction. As an application, I introduce how the LED-array microscope performs super-resolved quantitative phase imaging and demonstrate how physics-based learning can optimize a reduced set of measurements without sacrificing performance to enable the imaging of live fast moving biology./nIn this dissertation’s latter half, I will discuss how to overcome some of the computational challenges encountered in applying physics-based learning concepts to large-scale computational imaging systems. I will describe my work, memory-efficient learning, that makes physics-based learning for large-scale systems feasible on commercially-available graphics processing units. I demonstrate this method on two large-scale real-world systems: 3D multi-channel compressed sensing MRI and super-resolution optical microscopy.

Advisor: Waller, Laura
Lustig, Michael
To Fix the Image in Memory: Adaptive Analog Coding in Emerging Memory Systems

Motivated by (i) nature’s ability to perform reliable, efficient computation with stochastic components, (ii) the end of Moore’s Law (and other associated scaling laws) for our current computational paradigm, and (iii) the exponentially increasing amount of data (especially of the image variety) generated over the last decade, we examine herein the ability of analog valued emerging memory devices to directly store analog valued data. Specifically, we start by recasting the problem of data storage as a communication problem, and then use tools from the field of analog communications and show, using Phase Change Memory (PCM) as a prototypical multi-level storage technology, that analog-valued emerging memory devices can achieve higher capacities when paired with analog codes. Further, we show that storing analog signals directly through joint coding can achieve low distortion with reduced coding complexity. We then scale the problem up to store natural images on a simulated array of PCM devices. Here, we construct an autoencoder framework, with encoder and decoder implemented as neural networks with parameters that are trained end-to-end to minimize distortion for a fixed number of devices. We show that the autoencoder achieves a rate-distortion performance above that achieved by a separate JPEG source coding and binary channel coding scheme. Next, we demonstrate, this time by experiment, an image storage and compression task by directly storing analog image data onto an analog-valued ResistiveRAM (RRAM) array. A joint source-channel coding algorithm is developed with a neural network to encode and retrieve natural images. This adaptive joint source-channel coding method is resilient to RRAM array non-idealities such as cycle-to-cycle and device-to-device variations, time-dependent variability, and non-functional storage cells, while achieving a reasonable reconstruction performance of ~20 dB using only 0.1 devices/pixel for the analog mage. Finally, in an attempt to explicitly tackle device-device variation and drift, we use data from a commercial fabrication facility at TSMC and demonstrate preliminary results showing the ability to create an effective drift model capable of inferring values stored at previous times.

Advisor: DeWeese, Michael R
Olshausen, Bruno
Studies on the Bursting Kinetics of even-skipped Transcription

Enhancers drive the transcription of genes in defined spatio-temporal patterns of gene expression that orchestrate the development of animal body plans. The spatial aspects of enhancer function and gene expression pattern formation have been elucidated with elegant experiments in Drosophila melanogaster and other organisms. However, our knowledge regarding the temporal dynamics of pattern formation is still incomplete./nIn this work, I coupled the MS2 reporter system, which enables real-time, single-locus analysis of transcription, with the regulatory sequences of the gene even-skipped (eve), a fine model of enhancer function active in seven antero-posterior stripes that ring the fruit fly embryo before gastrulation./nOur results show highly dynamic expression patterns that emerge from stochastic bursts of transcription in single loci. We found that the dynamic expression of eve stripes stems from shared transcriptional kinetics. Nuclei at the center of all stripes increase their frequency of transcriptional bursting. Nuclei in the inter-stripe boundaries remain quiescent and do not show any detectable bursting. All the while stripes shift anteriorly, propelled by expression flow. The bursting kinetics in the ectopic patterns of eve expression that result from lifting the repression of eve enhancers are similar to the kinetics in the endogenous stripes. These observations show that the various eve enhancers generate similar bursting kinetics regardless of the myriad of distinct inputs that shape their activity./nThis dissertation consists of four chapters. Chapter 1 describes the construction of our MS2-based eve reporter and the generation of the transgenic fruit flies carrying it. Chapter 2 goes through our imaging methods and their optimization. It ends with an account of our data analysis to turn movies of transcription in embryonic development into meaningful and quantifiable data. Chapter 3 summarizes our findings regarding the conserved kinetics of even-skipped transcriptional bursting. Finally, Chapter 4 explores the activity of eve enhancers in body regions where they are not normally active.

Advisor: Eisen, Michael B
Garcia, Hernan G
Innovations on Small-Scale Mechanical Testing to Characterize the Structure-Property Relationships of SiC/SiC Composite Interfaces

Silicon carbide / silicon carbide (SiC/SiC) composites have emerged as a leading candidate for accident tolerant fuel cladding in light water reactors (LWR)s. Their high temperature strength and oxidation kinetics offer marked improvement for enduring severe loss of coolant accidents, thereby providing additional coping time for proper response. A key factor for qualification and implementation of these composites is the ability to model and predict their behavior over ranges of temperature, irradiation, and cyclic fatigue. To do so requires a fundamental understanding of the constituent property evolution and interplay at the fiber/matrix interphase./nThis dissertation asserts that small-scale mechanical testing provides the resolution and versatility required to capture structure-property relationships of the interphase, at its engineered length scale. This was explored by developing four novel experiments to probe the interphase properties that control composite toughness. First, high-resolution SEM DIC quantified the microscale elasticity across the pyrolytic carbon (PyC) bond layer, finding a gradient in Young’s Modulus and Poisson’s ratio that is directly linked to the PyC graphitic texture. Second, application of a self-aligning microtensile test enabled reliable extraction of the tensile strength and weakest link characteristics of the SiC/PyC/SiC interphase. Third, micropillar compression was used to evaluate 11 composite interphase conditions, defining a phenomenological equation for ultimate shear strength as a function of fiber roughness, PyC thickness, and residual compressive stress normal to the fiber surface. The effects of irradiation and fabrication-induced defects were also quantified. And fourth, a novel fiber fretting technique was developed for direct extraction of the cyclic degradation at the fiber/matrix interphase. Testing across four conditions revealed friction dependence on adhesive and abrasive mechanisms up to 1000 cycles. Post hoc characterization of the tribo-surface revealed a crystalline to amorphous transition of the PyC structure./nThe relatively accessible lab equipment and straightforward test configurations lend themselves to application in high temperature and oxidative environments, offering a robust toolkit for composite characterization and integrated design feedback on irradiated and next generation composite concepts. It is hoped that this research will open new doors to advanced optimization and modelling opportunities in the field of ceramic composites.

Advisor: Hosemann, Peter
Hopping Control and Estimation for a High-performance Monopedal Robot, Salto-1P

Jumping is an exciting locomotion mode that can enable small ground-based robots to maneuver around large obstacles and gaps. A high-power jumping robot can rapidly traverse obstacles, but the resulting fast and forceful stance phases are challenging for control and estimation. This dissertation presents control and estimation for precise hopping, operation using only onboard sensors, and precise leaps and balanced landings. These algorithms place an emphasis on simple models of motion to gain insights about jumping dynamics and to derive simple programs that can run on a small robot's computationally-limited onboard processor./nControl and estimation algorithms are experimentally demonstrated with Salto-1P, a small 0.1 kg robot with a 0.15 m leg exhibiting a 1.83 m/s vertical jumping agility, the highest of any untethered electrically actuated robot when introduced. First, with precise foot placement, Salto-1P climbs and descends obstacles higher than its bodylength without missing a step or crashing. Second, onboard estimation of attitude and jumping velocity enable Salto-1P to operate without offboard sensing or processing and run fully autonomously or accept human guidance to hop outdoors. Finally, using high-performance balance control, Salto-1P demonstrates precisely targeted leaps and balanced landings to jump to and stand on narrow targets.

Advisor: Fearing, Ronald
Tagging Small Molecule Natural Products with Functional Chemical Probes To Enable New Techniques in the Discovery and Development of Pharmaceuticals

Humans have exploited small molecule natural products have exploited throughout history. Recently, advances in chemistry and biology have led to an explosion in drug development, revolutionizing the treatment of infectious diseases, cancer, and other ailments. However, current techniques have already been exploited nearly to their limits. The work described in this dissertation aims to expand the pharmacological potential of small molecule natural products by developing a range of techniques that exploit functional chemical tags that are chemically bonded to the small molecules. These tags enable natural products to be studied in new ways using techniques such as Raman microscopy, computational analysis of LCMS data, and optical lock-in detection of FRET. By fundamentally altering small molecule natural products, we have raised the possibility to discover and study drug-like molecules that would be inaccessible using traditional techniques.

Advisor: Zhang, Wenjun
Supernovae as Dark Matter Signals

The empirical study of ultraheavy dark matter (DM) requires astrophysical probes. We present here a detailed study of DM-induced type Ia supernovae as one such probe. Dark matter may heat a small region in a white dwarf (WD) sufficient to trigger runaway fusion and ignite a supernova. We consider DM candidates that heat through the production of high-energy standard model (SM) particles, and show that such particles efficiently thermalize the WD medium and ignite supernovae. Based on the existence of long-lived WDs and the observed supernovae rate, we put new constraints on ultra-heavy DM candidates with masses above 10^{16} GeV that produce SM particles through annihilation, decay, and DM-SM scattering in the stellar medium. As a concrete example, this rules out supersymmetric Q-ball DM in parameter space complementary to terrestrial bounds. We further consider the possibility of DM capture by WDs, leading to the formation and self-gravitational collapse of a DM core within the star. This process allows two additional mechanisms for DM-induced particle heating, which we study here. For asymmetric DM, such a core may form a black hole that ignites a supernovae via Hawking radiation. For DM with a sufficiently small but nonzero annihilation cross section the core may cause ignition via a burst of annihilation during gravitational collapse. These processes are sensitive to much less massive candidates, down to 10^7 GeV, than are the mechanisms involving a single DM particle. It is also intriguing that these DM-induced ignition scenarios provide an alternative mechanism of triggering supernovae from sub-Chandrasekhar mass progenitors.

Advisor: Rajendran, Surjeet
Hall, Lawrence J