VictorJuiz/thesis huggingface dataset:
Dissecting Novel Grapevine-Mealybug-Virus Interactions

The biological mechanisms underlying vector transmission of grapevine leafroll-associated virus 3 (GLRaV-3) remain poorly understood due to limitations of a technically challenging host- pathogen system in Vitis vinifera. GLRaV-3 was able to infect the model organism Nicotiana benthamiana by insect-vector mediated transmission using the vine mealybug, Planococcus ficus. Working with GLRaV-3 infected N. benthamiana revealed distinct advantages in comparison with its natural host Vitis vinifera, yielding both higher viral protein and virion concentrations in western blot and transmission electron microscopy (TEM) observations, respectively. Immunogold labelling of thin sections through N. benthamiana petioles revealed filamentous particles in the phloem cells of GLRaV-3 positive plants. Comparison of assembled whole genomes from GLRaV-3 infected V. vinifera vs. N. benthamiana revealed identical sequences. High throughput sequencing was used to compare host response to GLRaV-3 infection between V. vinifera and N. benthamiana. General families of differentially expressed genes (DEGs) common in both hosts followed similar expression changes with six upregulated, seven downregulated, and two stably expressed genes in common. Overall, both hosts have many DEGs unique to each host as well as responses in common to GLRaV-3 infection. The vine mealybug, Planococcus ficus, fed through a membrane feeding system on GLRaV-3 viral purifications from both V. vinifera and N. benthamiana, and transmitted the virus to test plants./nAn immunofluorescence approach was used to localize virions to two retention sites in P. ficus mouthparts. Assays testing molecules capable of blocking virus transmission demonstrated that GLRaV-3 transmission by P. ficus can be disrupted. Our results indicate that our membrane feeding system and transmission blocking assays are a valid approach and can be used to screen other candidate blocking molecules. GLRaV-3 continues to impact grape-growing regions worldwide and the lack of knowledge surrounding virus-vector interactions remains limiting to the field. Elucidating the transmission biology of this important virus contributes to the eventual goal of blocking of transmission in insect vectors and the development of improved control strategies in vineyards.

Advisor: Almeida, Rodrigo P.P.
The Affordances of Item Response Theory: The Case of a Complex Learning Progression about Evolution

The National Research Council (NRC) has published multiple reports in recent years that describe potential improvements to elementary science instruction, and call for higher standards for the development of related assessments. To meet this charge, the Development of the Conceptual Underpinnings of Evolution (CUE) project was funded by the National Science Foundation and produced the data analyzed with item response theory in this dissertation./nThe CUE project team designed curricula for introducing concepts of micro-evolution to second- and third-grade students to engage young learners in reasoning about complex scientific phenomena. The team studied student capacities for understanding concepts in micro-evolution, while investigating the interplay of cognitive development, learning, and instruction. The team also developed one-on-one interview assessments, based on a learning progression that describes children’s pathways to more sophisticated types of reasoning about micro-evolution. The design of this progression was a novel attempt to model early learning in this context, informed by cognitive development theory, classroom experiences, and assessment activities in an iterative process. Throughout this work, the CUE team examined the complexity of children’s conceptualization of the concepts under study, especially with respect to the differentiation and order of conceptual levels within the learning progression and their multidimensional nature./nThis dissertation examines the affordances of Item Response Theory (IRT) in investigating and validating the hypothetical learning progression and representing the range of student thinking, while enabling the quantitative assessment of learning gains. The empirical findings address practical questions about item function, multidimensionality, open-ended items, and pre-post effects, and ultimately support the use of this complex learning progression to model student thinking. This dissertation presents an uncommon case where IRT is applied to interview data, and complementary outcome measures were chosen to best represent the complex phenomenon under study. This work provides a model for strengthening validity arguments by examining assumptions about how items, responses, and coding schemes relate to the theoretical construct, and how the scores they yield inform what we know about student reasoning and learning gains.

Advisor: Wilson, Mark
Interfacing chemistry and biology for new approaches to site-selective peptide modification and mycobacteria-specific fluorogenic probes

Selective labeling of biological matter enables not only basic research but also improved diagnostic platforms and therapeutics. Bioorthogonal chemistry provides a set of tools for researchers to study biomolecules of interest by inserting selectively reactive chemical partners into living systems. In the case of proteins, genetic manipulation can allow the introduction of uniquely reactive peptide sequences for small-molecule or enzymatic labeling. For molecules that cannot be genetically manipulated, metabolic probes provide an attractive alternative; by exploiting gaps in substrate specificity, a biomolecule can be modified with a bioorthogonal functional group without the need to extensively engineer the living system. In some cases, these biomolecules are organism- or cell type-specific, allowing them to be used as diagnostics for cancer or bacterial infection./nIn Chapter 1 of this dissertation, I provide an overview of commonly used methods for selective protein modification as well as for selective labeling of the bacterial cell wall. In Chapter 2, I describe the computation-guided rational design of a cysteine- and lysine-containing 11-residue peptide sequence that reacts with 2-cyanobenzothiazole (CBT) derivatives. Our data show that the cysteine residue reversibly reacts with the nitrile group on the CBT moiety to form an intermediate thioimidate, which undergoes irreversible SN transfer to the lysine residue, yielding an amidine-linked product. The concepts outlined herein lay a foundation for future development of peptide tags in the context of site-selective modification of lysine residues within engineered microenvironments. In Chapter 3, I outline our ongoing efforts to optimize this motif for protein labeling. In Chapter 4, I describe the synthesis and characterization of several mycobacteria-selective environment-sensitive fluorogenic probes as well as their potential applications in studies of host-pathogen interactions and diagnostics.

Advisor: Bertozzi, Carolyn R
Wemmer, David E
Development and Applications of Highly Multiplexed Super-Resolution Microscopy

Single-molecule localization based super-resolution imaging methods have seen considerable/ndevelopment since their inception over a decade ago. Such advances have enabled countless/nbiological discoveries and have positioned the field of single-molecule localization microscopy/n(SMLM) at the forefront of biological research. This dissertation describes the expansion of/nconventional SMLM methodologies to facilitate multicolor, true-color, and correlative imaging,/nand details specific applications for each of these developments. First, we utilize a split-emission/noptical setup to enable facile multicolor super-resolution imaging of 3 or more fluorophores./nThen, we develop a novel technique in which a dispersive prism is used to obtain the entire/nfluorescence spectra of millions of single molecules. Finally, we apply nonrigid image/nregistration techniques to enable the correlative imaging of live and fixed Drosophila larvae. We/nthen describe the application of advanced multicolor imaging methods to the study of/nfundamental biological processes. These include the discovery of a novel organization of/nmembrane ion channels in sperm cells, the identification of proteins responsible for force/ngeneration in mitotic spindles, and the characterization of new structure-function relationships in/nvesicular transport pathways such as COPII protein trafficking and autophagy.

Advisor: Xu, Ke
Design, Modeling and Control of the Integrated Stacked Resonant Switched Capacitor DC-DC Converter

Mobile, wearable, and internet of things (IOT) electronic systems are typically powered by a single cell Lithium-Ion (Li-ion) battery. Increasing demand for battery life and the constraint of the overall platform size impose an emerging desire for an efficient and com- pact power conversion stage that can directly deliver power from the battery, which ranges from 3.2V to 4.2V, to the supplies of application/communication processors in the range of 1V. The conventional buck converter, dimensioned for the 3.2-4.2 V input range, requires switches that are not typically available in standard sub-micron CMOS technology. Efficient implementation of the conventional buck converter has required a rather bulky off-chip inductor. The switched capacitor (SC) converter, though promising for a fully integrated solution, is inefficient at voltage regulation and is limited in capacitor energy utilization. In addition, with the SC converter, to cover the input range of a Li-ion battery to the processor supply voltage, topology reconfiguration has to be adopted. This additional functionality requires some additional design and implementation complexity./nGiven the limitations of either pure inductive or pure capacitive converter topologies, various hybridized power conversion architectures have been proposed recently. The hybrid approaches leverage minimum magnetic components to mitigate the intrinsic charge sharing loss in the standard SC operation while still maintaining a better switch utilization inherent in some SC topologies. This thesis introduces a hybrid dc-dc converter topology named stacked resonant switched capacitor (Stack-ResSC) that eliminates charge sharing losses with a small inductor. Consequently, capacitor energy utilization is improved and lossless voltage regulation is enabled. Since the necessary inductance is small, the magnetic component can still be tightly integrated within the package with a PCB trace or a bondwire. The proposed topology can also adapt to any N-to-1 conversion ratio, which extends the topology for wider applications. Harmonic averaging is used in this thesis to develop the large and small signal model of the converter. A tight load line regulation can be effected with the designed controller according to the developed small signal model./nIn addition to the Stack-ResSC, this thesis also introduces the stacked dual active bridge (Stack-DAB) as a derivative of the Stack-ResSC. An integrated circuit example is demonstrated with a nominal 3:1 conversion ratio. It supports a 3.2V-4.2V input voltage with a continuous output regulation of 0.8V-1.5V. The circuit delivers 83.4% efficiency at a power density of 0.46 W/mm2. The converter also shows superior transient response compared to state-of-art integrated implementation. This work demonstrates the advantage of the pro- posed hybrid approach in terms of tight integration and voltage regulation. The scope of the resonant switched capacitor based DC-DC converter is thus further extended.

Advisor: Sanders, Seth R
“Singing by Course” and the Politics of Worship in the Church of England, c1560–1640

“Singing by course” was both a product of and a rhetorical tool within the religious discourses of post-Reformation England. Attached to a variety of ostensibly distinct practices, from choirs singing alternatim to congregations praying responsively, it was used to advance a variety of partisan agendas regarding performance and sound within the services of the English Church./nThis dissertation examines discourses of public worship that were conducted around and through “singing by course,” treating it as a linguistic and conceptual node within broader networks of contemporary religious debate. I thus attend less to the history of the vocal practices to which “by course” and similar descriptions were applied than to the polemical dynamics of these applications. Discussions of these terms and practices slipped both horizontally, to other matters of ritual practice, and vertically, to larger topics or frameworks such as the nature of the Christian Church, the production of piety, and the roles of sound and performance in corporate prayer. Through consideration of these issues, “singing by course” emerges as a rhetorical, political, and theological construction, one that circulated according to changing historical conditions and to the interests of various ecclesiastical constituencies.

Advisor: Moroney, Davitt
Flammability of Combustible Solids in Spacecraft Environments

The flammability of combustible materials inside a spacecraft environment is of importance for fire safety applications because the conditions in this type of environments can greatly differ from those on earth, and a fire could have catastrophic consequences. Moreover, experimental testing in space can be difficult and expensive, and ground-based microgravity facilities such as drop towers or parabolic flights are limited to a few second duration. Additionally, future space missions may require spacecraft cabin environments different than those currently used in the International Space Station, 21% O2 by volume and 101.3 kPa, moving to reduced cabin pressure and increased oxygen concentration. These new conditions may result in an increased fire risk of the materials used due to the higher flame temperatures and the reduction in the convective losses from the heated solid surfaces. In particular, the influence of low pressure on material flammability and flame spread behavior is emphasized here because of the similarities existing in between the flow field produced in reduced pressure environments and microgravity./nChapter 1 presents an introduction to material flammability and flammability testing, focusing particularly on flame spread over solid fuels and previous related research. Chapter 2 presents a description of the experimental setups used for the normal gravity and the microgravity tests presented as part of this work. Chapter 3 is an experimental study covering flammability boundaries for flame spread of fire resistant fabrics exposed to different environmental conditions. In Chapter 4 and 5, an experimental study is presented along with a phenomenological analysis to simulate the burning behavior of thin and thick solids in microgravity conditions by using reduced pressure environments. Then, in Chapter 6 a similar approach is presented to study the flame spread behavior under the effect of external radiant heating, making comparisons with low pressure and microgravity environments.

Advisor: Fernandez-Pello, Carlos
On-Surface Synthesis and Local Electronic Structure Characterization of Low-Dimensional Nano-Materials

Understanding of the electronic properties of new materials is of central importance for science and technology. In particular, low-dimensional nano-materials exhibit exotic properties that are determined by quantum mechanics. Rapid development of reticular chemistry has enabled the syntheses of a variety of low-dimensional condensed matter systems that are formed by linking up molecular building blocks. This dissertation focuses on the on-surface synthesis of such materials and consequent characterization of their local electronic structure with scanning tunneling microscopy (STM)./nThe structure － property relationship of two low-dimensional nano-materials will be described: quasi-one-dimensional (1D) graphene nanoribbons (GNRs) and two-dimensional (2D) covalent organic frameworks (COFs). In the case of GNRs, we first show that two compatible molecular precursors with different sizes lead to GNR heterojunctions with atomically precise interfaces. In order to test predictions for how doped GNRs should behave, we synthesized B-doped GNRs with different doping concentrations on Au(111). Characterization of their electronic properties revealed a symmetry-dependent hybridization between the dopant states and the underlying Au substrate. We also describe our efforts to synthesize N=11 armchair GNRs through sp3-to-sp2 conversion of carbon atoms. In the case of 2D COFs, we first show that formation of imine linkages within COF366-OMe causes a downshift in the frontier orbital energy of porphyrin cores due to the electron-withdrawing characteristics of imine bonds. We then demonstrate the ability to achieve a 2D lattice of type II heterojunctions through judicious choice of molecular precursors that result in an asymmetrical bonding scheme within a 2D COF./nOur studies show that on-surface synthesis can lead to the realization of target nanostructures that are unreachable via solution-based methods, as demonstrated by intra-molecular reactions that lead to new “nano-graphene” species.

Advisor: Crommie, Michael F
Mechanisms and treatment of blood-brain barrier dysfunction and related pathology during aging

Aging involves a decline in neural function that contributes to cognitive impairment and disease. However, the causes of the transition from a “young-and-healthy” to “aged-and-dysfunctional” brain are not well understood. The following studies all address the mechanisms by which the blood-brain barrier (BBB) declines during aging, and how genetic and pharmacological inhibition of inflammatory signaling ameliorates aging-related neuropathology. Chapter 2 describes how the blood-brain barrier (BBB) deteriorates during aging, starting as early as middle age and continuing to the end of the lifespan. This vascular damage activates inflammatory transforming growth factor β (TGFβ) signaling in astrocytes. Using gain-of-function and loss-of-function manipulations in mice, we show that astrocytic TGFβ signaling is necessary and sufficient to cause neural dysfunction and pathological outcomes, including aberrant electrocorticographic activity, vulnerability to seizures, and cognitive impairment. Furthermore, inhibition of TGFβ signaling reverses these symptomatic hallmarks of aging. Chapter 3 delves deeper into the mechanism by which molecular correlates of neurosynaptic transmission become dysregulated during aging, focusing specifically on how TGFβ signaling contributes to aging-related cognitive decline via selective remodeling of glutamatergic and GABAergic receptor subunits. Chapter 4 investigates the core mechanism of decline of the transcriptional machinery that governs BBB permeability during aging, and also explores the potential of a novel pharmacological approach aimed at restoring the structural and functional integrity of the BBB. Together, these studies reveal the neurovascular unit as one of the earliest triggers of neurological aging, indicating that the aging brain may retain considerable latent capacity which can be revitalized by therapeutic inhibition against TGFβ signaling.

Advisor: Kaufer, Daniela
Representations for Visually Guided Actions

In recent times, computer vision has made great leaps towards 2D understanding of sparse visual snapshots of the world. This is insufficient for robots that need to exist and act in the 3D world around them based on a continuous stream of multi-modal inputs. In this work, we present efforts towards bridging this gap between computer vision and robotics. We show how thinking about computer vision and robotics together brings out limitations of current computer vision tasks and techniques, and motivates joint study of perception and action. We present some initial efforts towards this and investigate a) how we can move from 2D understanding of images to 3D understanding of the underlying scene, b) how recent advances in representation learning for images can be extended to obtain representations for varied sensing modalities useful in robotics, and c) how thinking about vision and action together can lead to more effective solutions for the classical problem of visual navigation.

Advisor: Malik, Jitendra
The Art of the Archive: Uses of the Past in the German Essay Film

This dissertation tracks the changing conception of the archive in film and media art. It examines filmmakers who reflect upon the historicity of cinema in their work and use the archive as a model for creating their essay films, video essays and installations. The four filmmakers whose work is under examination—Alexander Kluge, Hartmut Bitomsky, Harun Farocki and Hito Steyerl—have each played an instrumental role in the development of the film industry in postwar and contemporary Germany. Considered in a constellation with one another, they cover an important period of German—and global—media history, in which the forms of moving images and their mode of exhibition have diversified. New archival sources and media technology expanded the possibilities for these filmmakers to explore the contents of the German cinematographic archive and to integrate moving images from previous sources into their works. Taking their cue from Walter Benjamin’s concept of history and his practices of citation, these filmmakers use montage to put films from the past into constellation with present-day film and media. Their montages unearth aspects of earlier films that were not visible in their original context and they reveal the shifting configurations between past and present in film history, illustrating the need for a non-linear film historiography./nIn these works, film history and the cinematographic archive become a site of potentiality that offers alternative paths for film in the art gallery and museum, and on the Internet. Their works collectively demonstrate how essayistic practices have expanded from the essay film of auteur cinema to the video and digital essay of media artists featured in art installations and on the Internet. The evolution of these essayistic practices testifies to the essay’s continued ability to function as a form that runs against the grain of commercial production. If, as some theorists argue, the bureaucratic documentation of the archive is now the primary force through which biopolitics renders life deathlike, then the archival practices exhibited by these filmmakers not only illustrate how the past might gain a functional, creative use for the present, but they also provide an example for ways in which the archive might be employed against existing forms of control. Their works illustrate the need for increased access to the archive and a democratization of who has the authority to investigate its contents and document its histories today.

Advisor: Kaes, Anton