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Now showing 1 - 10 of 6692
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    Chordate-specific gene regulatory network of neuron development in Ciona.
    (Georgia Institute of Technology, 2023-12-12) Kim, Kwantae
    In this research, I investigated the complex gene regulatory networks underlying neurogenesis, taking advantage of the unique neurons of the Ciona model system. I revealed that Fgf signaling is crucial for the neurogenesis of Bipolar Tail Neurons (BTNs) by controlling the expression of Neurogenin, the fate-determining transcription factor in these neurons. Then I also characterized multiple effector genes functioning in the development of BTNs. Additionally, I determined the vital role of the Pax3/7 transcription factor in the neural plate border to induce the neural tube closure. Finally, I demonstrated how the Pax3/7 also orchestrates an intricate gene regulatory network upstream of multiple transcription factors and functional effectors during the neurogenesis of Descending Decussating Neurons (ddNs). I found that the majority of this network’s regulatory branches are shared with other neurons in Ciona or even other organisms including vertebrates. Moreover, I revealed the role of key putative effector genes during the neurogenesis of ddNs. These findings will provide profound insights into developmental mechanisms in the central nervous system of chordates.
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    Improving Foundation Models
    (Georgia Institute of Technology, 2023-12-10) Komatsuzaki, Aran
    Foundation models are the family of models (e.g. GPT-4, CLIP) that are trained on a massive dataset and perform various down-streaming tasks, usually with either zero- or few-shot learning, optionally after fine-tuning. This dissertation presents a wide range of important measures we have made to make foundation models more efficient, performant and versatile. In particular, we focus on three points of improvement: architecture, dataset and training. We first present our findings on how to optimally scale language models, which leads to significant performance improvement. We then present GPT-J, one of the earliest open-source large language models. We then show that the performance of ViT and T5, both Transformer-based foundation models, can be greatly improved for a given compute budget using Sparse Upcycling, which is to resume training a sparsely gated model made out of pretrained dense models. We also briefly discuss LAION datasets, massive open-source datasets with around one billion pairs of text and image that are used to train various state-of-the-art multimodal models, and ARB benchmark, a highly challenging benchmark to measure the state-of-the-art LLMs such as GPT-4. On the theoretical side, we prove that feedforward layers of a transformer cannot be compressed without information loss, which may explain the power of sparsely gated models such as mixture-of-experts.
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    Optically Modulated Fluorescence-Informed Photoacoustic Imaging
    (Georgia Institute of Technology, 2023-12-10) Islam, Md Shariful
    Advanced imaging technology is crucial for detecting early anomalies in deep tissue. While current medical imaging techniques show great potential, there is still a persistent need for improvements in sensitivity, resolution, penetration depth, and cost-effectiveness. Photoacoustic imaging combines optical excitation with acoustic detection to enhance tissue penetration depth and functional imaging capabilities. However, despite these advantages, photoacoustic imaging still suffers from poor signal-to-noise ratio and interference from endogenous chromophores in the background. Dual-laser background suppression techniques have the potential to enhance imaging sensitivity, especially in high-background noise situations. Synchronously amplified fluorescence image recovery (SAFIRe) reduces background interference in fluorescence imaging by manipulating ground-state and intermediate-state populations of contrast agents through pump and probe excitations. The main focus of this thesis is to combine the benefits of SAFIRe with photoacoustic imaging using the same pump-probe technique. Photoacoustic imaging provides signals from deep tissue, and SAFIRe removes the background from that signal. To achieve this objective, optically modulatable contrast agents and their nanoparticles, such as Rose Bengal (RB) and Eosin Y (EY), were used to produce synchronously amplified photoacoustic image recovery (SAPhIRe) signals from tissue-mimicking phantoms and dead rat muscles. This thesis explores the possible uses of SAPhIRe in temporal unmixing, a technique that allows for the separate detection of multiple contrast agents with the same absorption window simultaneously by using their unique triplet-state lifetimes. The study demonstrated the unmixing of RB and EY signals using both fluorescence and photoacoustic techniques. This was achieved by adjusting the pump-probe delay to distinguish their distinct triplet-state lifetimes. The fitting coefficients of triplet-state lifetimes were used to reconstruct images within tissue-mimicking phantoms. Prior to photoacoustic imaging, fluorescence was used for modulation screening. In addition, this work investigates the photophysical properties of three near-infrared (NIR) thiacarbocyanine dyes. Various optical modulation techniques, such as single and dual laser modulation, were conducted to explore their modulation depth, optical properties, and dark-state lifetimes. The results revealed that 3,3'-Diethylthiatricarbocyanine iodide (DTTCI) and 3,3'-Diethylthiacarbocyanine (DTCI) iodide have long dark states and are optically modulatable. Among the two, DTTCI appears to be an ideal candidate for SAPhIRe as it absorbs around 760 nm.
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    Synthesis and analysis of low-valent NHC supported nickel complexes
    (Georgia Institute of Technology, 2023-12-10) Dodd, Neil Alexander
    This thesis focuses on the synthesis of N-heterocyclice carbene (NHC) supported nickel complexes and their reactivity in bond-breaking and bond forming reactions. The body of this work discusses isolation of (NHC)Nickel(I) alkoxides and their subsequent chemical transformations into different (NHC)Nickel complexes. First, we demonstrate that (IDipp)Ni(I) hexamethyldisilazide (IDipp = 1,3-bis(2,6- diisopropylphenyl)-imidazole-2-ylidene) cleanly deprotonates neopentyl and methyl alcohols to form the corresponding (IDipp)Ni(I) alkoxides. Both alkoxides form dimeric solid-state structures. Abstraction of one alkoxide fragment forms the corresponding alkoxy-bridged dinickel cation species with an inner sphere bridging triflate. Abstraction of both neopentoxide fragments result in formation of (IDipp)Ni(OTf)(Et2O), a synthetic equivalent of (IDipp)Ni(I)+. Next, we show that the reaction of [(IDipp)Ni)]2(μ-ONp)(μ-OTf) with pentamethyldisiloxane results in isolation of {[(IDipp)Ni]2(μ-H)}[OTf]. Deprotonation of this hydride complex results in formation of [(IDipp)Ni]2, further supporting the interpretation of {[(IDipp)Ni]2(μ-H)}+ as proton bridging two (IDipp)Ni(0) fragments. The reactivity of {[(IDipp)Ni]2(μ-H)}[OTf] with alkyl nitriles was further studied by 1H NMR. [(IDipp)Ni(CN)2]4, a product of the reaction between {[(IDipp)Ni]2(μ-H)}+ with alkyl nitriles, can be synthesized by the reaction of [(IDipp)Ni(Cl)]2(μ-Cl)2 with trimethylsilyl cyanide. Subsequently, we show that the mixed valent complex, {[(IDipp)Ni]2}+ [OTf]− can be synthesized by combining synthetic equivalents of (IDipp)Ni(0) and (IDipp)Ni(I)+. Computational studies of this complex classify it as Robin-Day Class II. Cyclic voltammetry shows that the [Ni2]2+/+ and [Ni2]+/0 couples are reversible. The reactions of {[(IDipp)Ni]2}+ [OTf]− with CO and NO form mononuclear products and the reaction of {[(IDipp)Ni]2}+ [OTf]− with aryl bromide leads to predominant C-arylation of IDipp. Lastly, we show our pursuit of the first reported (NHC)Ni(I) fluoride. The reaction of [(IDipp)Ni)]2(μ-ONp)(μ-OTf) with benzoyl fluoride resulted in isolation of crystals of {[(IDipp)Ni]2(μ-F)(μ-C7H8)}[OTf] suitable for study by X-ray diffraction. Despite varying synthetic attempts, bulk isolation of {[(IDipp)Ni]2(μ-F)(μ-C7H8)}[OTf] was ultimately unsuccessful. Next, we show that {[(IDipp)Ni]2(μ-PPh2)}[OTf] can be isolated from the reaction of [(IDipp)Ni)]2(μ-OMe)(μ-OTf) with (trimethylsilyl)diphenylphosphine. We also show that (IDipp)Ni(C6H6) reacts with acyl fluorides to form the corresponding [(IDipp)Ni(R)(μ-F)]2 complexes. Lastly, we show that sodium naphthalenide can reduce [(IDipp)Ni(μ-Cl)]2 to form a synthetic equivalent of (IDipp)Ni(0).
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    Uncertainties in Projections of Tropical Precipitation and Atmospheric Circulation and Their Remote Impacts
    (Georgia Institute of Technology, 2023-12-10) Lu, Kezhou
    My doctoral work focuses on understanding anthropogenic responses of precipitation and atmospheric circulation by employing both statistical methods and climate models of varying levels of complexity. My research has two main goals: (1) to understand the forced response of tropical air-sea interactions across different time scales and their subtropical impact, and (2) to investigate the reasons underlying the uncertainties in climate models when simulating tropical and extra-tropical climate. My dissertation research comprises four individual projects. For my first project, I have explored the mechanism of how the Walker circulation (WC) responds to CO2 forcing across different time scales. The WC, a significant tropical atmospheric circulation spanning both horizontally and vertically, plays a crucial role in the tropical climate and is closely related to phenomena such as the Madden–Julian Oscillation and El Nino-Southern Oscillation. The prevailing consensus suggests that the long-term weakening of the WC is primarily driven by the sea surface temperature (SST) warming caused by increased greenhouse gases, while the fast response of the WC appears largely independent of changes in SST. However, my findings indicate that the air-sea interactions play a substantial role. By analyzing data output from Coupled Model Intercomparison Project Phase 5 (CMIP5) under abrupt4xCO2 scenarios, models with a stronger air-sea coupling in the equatorial Pacific are discovered to simulate an initial strengthening of the WC following the external forcing, which contrasts with the long-term response. Conversely, models characterized by weaker air-sea coupling simulate a monotonically weakening of the WC. My results suggest that the inter-model discrepancy in the WC changes is associated with then uncertainty in the fast component. My second project focuses on understanding the summer North Pacific subtropical high (NPSH). As part of the planetary wave system, the NPSH integrates both tropical and extra-tropical impacts on the monsoons and typhoons over East Asia and hydroclimate over California. Given its considerable socioeconomic significance, reliable future projections of the NPSH are crucial for preparing adaptation plans. However, state-of-the-art climate models exhibit diverging responses of the NPSH to anthropogenic CO2 forcing. This project has revealed that model variability in the future projection of the summer NPSH originates from both inter-model SST-driven and non-inter-model SST-driven uncertainties in the tropical precipitation. Specifically, I investigate the connection between the tropical precipitation and the NPSH by modifying the diabatic heating in both a baroclinic stationary wave model and a comprehensive climate model, i.e. the Community Atmospheric Model version 5 (CAM5). Drawing upon the knowledge acquired from the previous two chapters, my third project has explored how the tropical air-sea interaction and the summer NPSH are influenced by anthropogenic forcing, as well as their interplay. I have discovered that the inter-model spread in projecting the fast changes of the WC directly contributes to the inter-model spread in tropical SST responses. By analyzing CMIP5 and CMIP6 data under abrupt4xCO2 scenario, models with a stronger tropical equatorial Pacific air-sea coupling simulate a strengthening of the WC and a La Nina-like central Pacific cooling. And this La Nina-like SST anomaly induces anomalous tropical precipitation and further modulates the NPSH via the Matsuno-Gill wave response. During the collaboration with my advisor on the fourth project, we have found considerable inter-basin variations in the future projection of the tropical Hydrological sensitivity (HS) regardless of how SST warms. I have further demonstrated the remote impact of the inter-basin discrepancy in HS on land precipitation and surface temperature by understanding the corresponding tropical-extra-tropical teleconnections. Specifically, I have analyzed the atmospheric circulation response induced by tropical precipitation with and without inter-basin discrepancy in HS by conducting diabatic heating adjustment experiments in CAM5.
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    Seed-Mediate Synthesis of Gold Nanocrystals: The Effects of Lattice Mismatch on Growth Patterns
    (Georgia Institute of Technology, 2023-12-08) Pawlik, Veronica Dana
    Nanomaterials have long fascinated both the casual observer and scientific mind alike. The utility of Au nanocrystals in particular has inspired applications ranging from plasmonics to catalysis. Over time, the ability to finely tune both shape and size has greatly improved their merits for these applications. To further expand and enhance the properties of Au nanocrystals, bimetallic compositions were introduced. Of the various atomic arrangements possible for bimetallic nanocrystals, the core-shell structure is most commonly utilized. This morphology is typically synthesized through a seed-mediated process. Growing one metal on another can introduce challenges. In this dissertation, I explore the effects that increasing lattice mismatch has on the seed-mediated growth of noble-metal nanocrystals. First, the case of no lattice mismatch was investigated during the growth of Au on Au spherical seeds to generate AuRD fully enclosed by {110} facets. The lack of lattice mismatch led to layer-by-layer growth. The kinetics of the synthesis could easily be tuned to favor either deposition or diffusion to achieve concave RD, trisoctahedra, or octahedra. These AuRD were then utilized in another seed-mediated growth to improve the thermal stability of the AuRD. Specifically, 1 ML of Pt was added and this ultrathin layer of Pt was able to improve the thermal stability of the high energy {110} facets from degrading at 100 °C to persisting at 450 °C. Computational studies revealed that the thermal stability of the Au-supported Pt skin was even greater than that expected for pure Pt. This effect was attributed to the strain induced by the formation of a 3.8% lattice-mismatched Pt overlayer on Au. Finally, single-crystal Rh@Au truncated octahedra were synthesized at a lattice mismatch of 7.2%. The large mismatch led to an island growth mode, which, could be tuned through the use of gentle kinetic knobs. The addition of NaOH indirectly increased the reduction rate to help modulate the number of Au islands formed on the Rh seeds. Conversely, the addition of KBr slowed down the reduction, allowing the Au adatoms to diffuse across the Rh seed. This work provides insight into the effects of lattice mismatch on the growth mode of nanocrystals, moving one step closer to the rational synthesis of novel nanomaterials with desired characteristics.
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    Abstract and Physical Effects of Curvature on Dynamics of Extended Body Systems
    (Georgia Institute of Technology, 2023-12-07) Day, Brian
    The presence of intrinsic curvature of an ambient space influences the dynamics of point particles moving through it as typically considered in applications of differential geometry in physical contexts, such as general relativity. We aim to utilize the mathematics of differential geometry to instead consider the collective curvature effects on extended body systems in some generic curved space. To this end we develop a mathematical framework which serves as the foundation of a general dynamics solver numerical toolkit in which users can simulate the dynamics of discrete extended body systems in generic curved spaces. Through analyzing the dynamics of such extended body systems we recognized a relationship between deformation of the body during its dynamics as a result of the ambient curvature. This led us to expand our mathematical model of extended bodies to include deformable bodies. We find that such deformable bodies can generate collective motion via deforming their body even in a ambient space lacking curvature. This is due to the presence of an abstract notion of curvature defined on the configuration space of the system via considering the system as being described by a mathematical object known as a fiber bundle. This revelation allows us to discuss the dynamics of such deformable control systems using the ideas of geometric mechanics. In particular, we consider recasting our system in a geometric mechanics framework to address the question of determining optimal controls of how to deform the system so as to minimize some cost function. This is based on considering the optimization problem as a variational problem whose solutions correspond to optimal controls of the system. We develop this variational approach into a numerical toolkit acting as the foundation of a more general purpose optimization toolkit for deformable control systems described by fibers bundles.
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    Interlaboratory Comparison of a Complex Targeted Assay: Improving Consistency and Reliability in Metabolomics Analyses
    (Georgia Institute of Technology, 2023-12-07) Phillips, Emily R.
    Ideal isotope-labeled internal standards for analysis via targeted metabolomics approaches are presented for negative and positive ion modes for both hydrophilic interaction liquid chromatography (HILIC) and reverse phase liquid chromatography (RPLC) chromatography coupled to mass spectrometry. These best performing analytes (BPA) were deduced after experimentation from a collaborative research project involving six top metabolomics research laboratories in the country. These results are detailed in this work, supported by observed behaviors of included chemical classes and chromatographic behaviors, and align with the group hypothesis and expectations
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    Evolution in real time: insights from micro- to macroscopic multicellular organisms
    (Georgia Institute of Technology, 2023-12-06) Pineau, Rozenn
    Multicellularity has evolved independently at least 50 times and fundamentally transformed life on Earth, yet basic questions remain about how this transition initially occurs and shapes ecological dynamics. Understanding this transition and its underlying mechanisms is essential to better understand the evolution of life on Earth. The first part of this work examines the emergence of a common yet understudied multicellular organism morphology, cuboidal packing. Spherical fission yeast (Schizosaccharomyces pombe) mutants were experimentally evolved via daily settling selection favoring larger size. Within 20 days, multicellular clusters evolved cuboidal cellular packing, a topology found across the tree of life. These clusters displayed traits of multicellular individuals: reproduction via cluster fracture, heritability in size, and response to group selection. Our genetic analysis reveals mutations in the ACE2 gene underlying this transition to multicellularity. This is an example of a deep convergent evolution, as this gene has also been implicated in the transition to multicellularity in Saccharomyces cerevisiae, a yeast species that diverged from S. pombe 300 millions of years ago. Next, we explore the ecological implications of the transition to multicellularity and show how the formation of groups itself is an opportunity for niche expansion and divergence. Using long-term experimental evolution of snowflake yeast (S. cerevisiae), we show that the fundamental trade-off between growth and survival facilitated the evolution of two distinct coexisting phenotypes: one Small phenotype specialized in growth, and one Large phenotype specialized in survival. Coexistence is maintained by negative frequency dependent selection, and sequencing reveals that the dominant lineages present after 715 daily transfers have coexisted throughout the duration of the experiment. This work demonstrates how a simple and yet fundamental trade-off between growth and survival can immediately drive adaptive diversification and maintain increased ecological diversity. Overall, this work provides experimental and theoretical insights into eco-evolutionary niche construction and long-term population dynamics following multicellularity's origins. Finally, the last part of this dissertation sheds light on mutation dynamics in complex and ancient multicellular organisms. We explore the evolutionary history of an ancient and still-living clonal forest, the Pando aspen clone. Harnessing the genetic signal generated by the accumulation of somatic mutations in the different tissues of the Pando clone, we detect spatial genetic structure, and estimate Pando's minimum age around 2,000 years. Together, this thesis uses experimental evolution in unicellular microbes and natural experiments in clonal macrobes, contributing fundamental knowledge to our understanding of multicellular evolution, from the initial emergence of multicellular groups to the formation of complex, ancient organisms.
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    Directability Through AI Customization: The Effect of Choice on Trust and Acceptance in Highly Automated Vehicles
    (Georgia Institute of Technology, 2023-12-05) Scott-Sharoni, Sidney Tammie
    People feel apprehensive about using or relying on highly automated vehicles (American Automotive Association, 2019). One method of assuaging fears involves providing explanations for the system’s behaviors using a Human-Machine Interface (HMI). However, understanding the amount of information for optimal human-automation interaction can prove difficult due to differences in individuals’ preferences, experiences, and needs. An underexplored method that may account for these discrepancies involves providing users with choices or customization. The Coactive Design Approach suggests that including directability, or the power to influence a system’s actions, may improve how users interact with systems (Johnson et al., 2014). The following study investigated how customization affordances and modified vehicle aspect of a Level 4 automated vehicle affected trust and acceptance. One hundred twenty participants experienced one highly automated simulator drive, during which they engaged in a visually demanding game. A MANOVA assessed the interaction of and main effects of customization availability and modified vehicle aspect on trust and acceptance. While participants who customized had higher average trust and acceptance in the automated vehicle than participants who did not customize, only the main effect of vehicle aspect significantly impacted the multivariate dimension of trust and acceptance in the automated vehicle. That is, modifications to the vehicle impacted users regardless of whether they chose the modification. The game score and subjective trust did significantly correlate to a small, positive extent, indicating that higher trust in a system may improve non-driving related task performance. Future research should continue to investigate the role of choice in the interaction between individuals and highly automated systems to understand the psychological impacts of directability.