VictorJuiz/thesis huggingface dataset:
Biomolecular Plasmonics: Fundamentals and Applications

Decades of extensive research into metallic nanostructures have deepened our understanding of plasmonic phenomena. In turn, plasmonics have been utilized in various applications in a broad range of research fields. Plasmonic-aided biomolecular detection is highlighted due to its ability to obtain biomolecular fingerprint information in a non-invasive, in-situ, and single molecule resolution manner. However, its applicability to various fields still faces practical limitations such as reliable plasmonic structure fabrication, signal instability (or blinking), and signal variation amongst different plasmonic structures for the same molecule. In this respect, this thesis discusses the fundamentals of plasmonic phenomena and molecular interaction with excited plasmonic structures./nHere we demonstrate the designs of plasmonic structures: eagle-beak nanoantenna, gold nanoflake on photonic crystal, and gold viruses. The first two are for large-area uniform substrates that enable single-molecule sensitivity. The last one is a mobile nanoparticle that continuously interacts with a cellular system with multiple functions including molecular imaging, targeting, and drug delivery. We also suggest preconcentration-based non-blinking single-molecule detection. Electric and temperature fields were considered in moving molecules towards excited nanostructures. By using an eagle-beak nanoantenna, we demonstrate single-molecule, non-blinking surface-enhance Raman scattering. Furthermore, variation of molecular scattering from a curved Poynting vector and depolarized scattering from nonparallel electron motion to incident light are discussed as a new molecular detection scheme. Lastly, we provide a design concept that utilizes temperature and a thermal gradient to activate carrier molecules on nanoparticles, in particular for extrinsic gene delivery. By varying the thermal profile around plasmonic structures, diverse gene activation schemes are available for biological experiments./nWhen the electric and thermal fields around excited plasmonic structures are considered in terms of gradients and vectors, we can enhance detection capabilities while conferring multiple functionalities to structures. We believe this series of new approaches to plasmonic-aided molecular detection can elevate molecular imaging potential in real fields, and further expand to other types of applications such as plasmonic energy harvest, optical communication and biomedical applications.

Advisor: Lee, Luke P.
Lin, Liwei
Differentiated Instruction: Understanding the personal factors and organizational conditions that facilitate differentiated instruction in elementary mathematics classrooms

Differentiated instruction is a widely held practice used by teachers to provide diverse learners with complex learning opportunities in the area of mathematics. Research on differentiated instruction shows a multitude of factors that support high quality instruction in mixed-ability elementary classrooms. These factors include small-class size, extra time and resources that allow for a highly individualized approach to instruction, teacher commitment, and subject-matter competency in mathematics. The literature also points to the role of leadership in providing a greater investment in teachers' professional development to improve teacher practice. This in-depth case study is an attempt to understand what resources and supports are needed to build teachers' capacity to effectively implement differentiated instruction to meet the challenges of teaching diverse learners found in classrooms today. For this study, I developed a conceptual framework to map the territory for understanding what personal factors and organizational conditions facilitate high quality implementation of differentiated instruction. Drawing from the literature, I identified specific personal factors and organizational conditions to study. I incorporated these criteria when I observed and interviewed the nine participants selected for this study. During the course of the study, I investigated across two different school environments, a high wealth and a low wealth district, and the dimensions that shaped the practices identified as high quality implementation of differentiated instruction. Overall, this framework allowed me to examine the differences in teacher practice that are not currently found in the literature. The findings of the study indicate several personal dimensions that distinguish a high implementer from a low and average implementer of differentiated instruction in mathematics. The dimensions are: a willingness to forge ahead and overcome obstacles; willingness to grow professionally and improve practice; strong competency, capability, and confidence teaching the subject matter; and ability to implement complex instruction in a variety of situations. All these coupled with prior teaching at the same grade level and strong classroom management skills increased the level of implementation quality. But even the high implementers made it clear that organizational conditions specifically, the pressure of daily work demands, put severe constraints on their ability to differentiate instruction in their classrooms. No amount of skill and determination or ample organizational resources could overcome these constraints.

Advisor: Mintrop, Heinrich
Newton, Xiaoxia
Determining the Role of the Mycobacterium tuberculosis Serine/Threonine Protein Kinase, PknH, in Cell Signaling

The survival of the pathogenic bacterium, Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, depends on its ability to sense and respond to a hostile and constantly changing environment within the host. Cell-wall components--such as peptidoglycan, arabinogalactan, mycolic acids and lipoarabinomannan--perform critical structural and biological functions that allow Mtb to survive and persist inside of human cells. Despite the critical roles of the cell wall in the pathogenicity of Mtb, surprisingly little is known about how this complex structure is built and remodeled in response to environmental cues. Recent evidence, however, implicates membrane-bound serine/threonine protein kinases (STPKs) in the coordinating cell-wall synthesis with growth and division. These eukaryotic-like STPKs play critical roles in Mtb signal transduction by sensing extracellular stimuli and catalyzing the reversible phosphorylation of cytoplasmic target proteins./nTo further understand the mechanisms that regulate STPKs and cell wall architecture in Mtb, I biochemically and structurally characterized the extracellular sensor domain of one STPK receptor kinase, PknH. Initial analysis of recombinantly produced PknH sensor domain by size-exclusion chromatography and small-angle x-ray scattering indicated the protein was soluble but completely unfolded. On-column oxidative refolding produced a properly folded protein that crystallized as a monomer with a novel protein fold made up of six alpha helices, seven beta strands, and two disulfide bonds. The PknH sensor domain has a large conserved cleft with a mixed polar and hydrophobic surface. These results indicated PknH binds a small molecule ligand which may affect its quarternary structure and/or its localization./nIn order to determine what ligand binds to the PknH sensor domain, I conducted native gel binding assays using purified Mtb arabinogalactan, lipoarabinomannan, and lipomannan. These assays indicated that in vitro, the PknH sensor domain does not bind to any of these purified cell wall components. Affinity chromatography with His6-tagged PknH incubated with Mtb H37Rv cell lysate followed by intact mass, LC-MS, and ESI-MS analysis indicated that PknH does not bind glycolipids such as phosphoinositol or Ac1PIM2. Although the ligand for PknH was not identified, these studies set the stage for future researchers to identify the ligand and discover the function of PknH.

Advisor: Alber, Tom
Mood-Congruency versus Mood-Incongruency in Aesthetic Preferences: The Role of Interpersonal Relationships

Whereas negative feelings sometimes increase preference for mood-incongruent aesthetic experiences (e.g., cheerful music, comedy), they also sometimes increase preference for mood-congruent ones (e.g., sorrowful music, drama). In this paper, we address the causes of this apparent discrepancy. We hypothesize that (1) mood-congruent aesthetic experiences offer a sense of bonding and emotional sharing, akin to interacting with an empathetic friend and thus (2) they are preferred when individuals are deprived of a sense of bonding from dissolving interpersonal relationships. Consistent with our hypotheses, three experiments show that negative feelings from broken interpersonal bonds increase preferences for mood-congruent aesthetic experiences, whereas negative feelings from non-interpersonal problems increase mood-incongruent preferences. Our results also help account for the inconsistencies in the literature.

Advisor: Andrade, Eduardo B
La comunita' mutilata: Embodiment, Corporality, and the Reconstruction of the Italian Body Politic in the Works of F.T. Marinetti and Gabriele D'Annunzio

"La comunità mutilata: Embodiment, Corporality, and the Reconstruction of the Italian Body Politic in the works of F.T. Marinetti and Gabriele D'Annunzio", is a study in how discourses of technological modernism, nationality, and woundedness operate on the longstanding metaphor of the body politic. It focuses on the writings of two of Italy's most controversial, and influential, figures during and after the First World War. I show how mutilated and prosthetic bodies become powerful political metaphors for both Marinetti and D'Annunzio, which upend and transform the notion of the body politic in posthuman, postliberal and antidemocratic ways. This study is grounded in literary analysis, but draws from political philosophy, art history and rhetoric to examine Marinetti's futurist manifestos, novels, and poetry (1909-1921), and D'Annunzio's political speeches relating to the occupation of the city of Fiume (1919-1920)./nIn Chapter 1, I analyze Marinetti's manifestos produced between 1909 and 1918 in order to demonstrate how Marinetti inaugurates the post-humanist discourse of cybernetics. In Chapter 2, I provide a reading of two of Marinetti's prose works, L'alcova d'acciaio (1921), and Come si seducono le donne (1917), in order to demonstrate the connection between the representation of prosthesis and the attempt to construct an anti-democratic mode of political subjectivity in Italy. In Chapters 3 and 4, I analyze the speeches and writings of Gabriele D'Annunzio during his occupation of the eastern Adriatic city of Fiume (now Rijeka) as they pertain to the promotion of the concept of Italian irredentism as a means of overcoming the "mutilated victory" of World War One, and the construction of a postliberal form of italianità./nThis study takes as its guiding premise the notion that metaphors of corporality act upon the experiences of individual and collective embodiment, and that they provide forms in which the body politic is recognized. I illustrate how the language of nationalism converges with the desire to enhance, extend, and expand the limits of the self to produce a model of Italian national identity that is grounded upon an embrace of the traumatic possibilities of war and technological modernization in the works of these two figures. In doing so, I aim to demonstrate how both F.T. Marinetti's and Gabriele D'Annunzio's texts reflect a transitional moment for the discourse of Italian national identity between the Liberal nation and the Fascist state.

Advisor: Spackman, Barbara G
Spatial Attention Improves Retinotopic Mapping

The visual world is represented in the brain in numerous retinotopic maps that extend along the cortical surface. Directing spatial attention to a given location in the visual scene enhances perception of that location, and strengthens the neural response to visual stimulation at the attended location. However, the effects of attention on neural responses differ across visual cortical regions./nThis thesis is concerned with the study of the variety of effects of visual spatial attention on cortical responses. In the following chapters, we describe results from three major research projects. In the first project, we discovered that spatial attention improves response reliability (a signal-to-noise measure) in every cortical region we measured. The magnitude of these effects were greatest in regions with weak retinotopic signals, suggesting the importance of attention for discovering new areas of cortex with topographic organization. In the second project, we demonstrate that the attention-induced enhancement of response reliability results not only from a strengthening of the cortical response, but also a suppression of slow fluctuations in brain activity that are unrelated to the visual input. Moreover, the suppression of these slow fluctuations predicted performance on a visual detection task, whereas the enhancement of response magnitude did not. Finally, in the third project, we demonstrate attention's effect on response magnitude differs as a function of eccentricity; in early visual areas attention enhanced response strength the most for representations of central vision, whereas in dorsal regions attention enhanced response strength most for representations of peripheral vision. Moreover, we discovered that attention expanded the extent of visual space that generated a significant cortical response, and that this effect also differed across eccentricities and visual regions.

Advisor: Silver, Michael
A Rasch Item Response Modeling Approach to Validation: Evidence Based on Test Content and Internal Structure of the Life Effectiveness Questionnaire

This study applies the Standards for Educational and Psychological Testing to appraise validity evidence for the interpretation of test scores that are used in experiential education, adventure education, and out-of-school time programs. Specifically, Rasch item response modeling is applied as a primary tool to examine validity evidence for the Life Effectiveness Questionnaire (LEQ). Hypotheses and assumptions about test content and test structure are evaluated using technically calibrated responses to items as empirical evidence. This evidence, produced in the form of Wright maps, allows for a combined focus on the qualitative, substantive meaning of the test scores, as well as their technical, statistical properties./nThe partial credit model fit better than the rating scale model for the composite unidimensional and multidimensional models (p>0.05) of the LEQ, and for seven of the eight consecutive unidimensional models of LEQ subscales (p>0.05). DIF analyses found no meaningful statistical evidence of construct-irrelevant variance by gender, age, or voluntary status. Analyses of person to item distributions found a mismatch between the intended meaning of item content and empirical item difficulties, so that the test developers' initial hypothesis about item content was not supported. Evidence from Wright maps indicates no order or sequencing of LEQ test content, and also that items oversample from one easy level of the Life Effectiveness continuum. These findings suggest that item content does not adequately represent the Life Effectiveness construct./nEvidence from Wright maps indicates that respondents did not interpret and differentiate between response categories equivalently within items or across subdomains, so that assumptions of interval, Likert scaling that are the basis of the averaged scores for the LEQ are not supported. Wright maps provided evidence of good respondent-to-item threshold distribution for the composite LEQ. However, item thresholds are skewed to the lower levels of life effectiveness, so that standard errors are higher for respondents with higher ability estimates. Despite reasonable reliability coefficients, sizable standard errors and large confidence intervals associated with the LEQ subscales, in particular, as well as for high ability respondents in the composite LEQ, caution against over-confidence in using student ability estimates to make claims about change.

Advisor: Wilson, Mark R
Conditional Sampling Distributions for Coalescent Models Incorporating Recombination

With the volume of available genomic data increasing at an exponential rate, we have unprecedented ability to address key questions in molecular evolution, historical demography, and epidemiology. Central to such investigations is population genetic inference, which seeks to quantify the genetic relationship of two or more individuals provided a stochastic model of evolution. A natural and widely-used model of evolution is Kingman's coalescent (Kingman, 1982), which explicitly describes the genealogical relationship of the individuals, with various extensions to account for complex biological phenomena. Statistical inference under the coalescent, however, remains a challenging computational problem. Modern population genetic methods must therefore realize a balance between computational efficiency and fidelity to the underlying model. A promising class of such methods employ the conditional sampling distribution (CSD)./nThe CSD describes the probability of sampling an individual with a particular genomic sequence, provided that a collection of individuals from the population, and their corresponding sequences, has already been observed. Critically, the true CSD is generally inaccessible, and it is therefore necessary to use an approximate CSD in its place; such an approximate CSD is ideally both accurate and computationally efficient. In this thesis, we undertake a theoretical and algorithmic investigation of the CSD for coalescent models incorporating mutation, homologous (crossover) recombination, and population structure with migration./nMotivated by the work of De Iorio and Griffiths (2004), we propose a general technique for algebraically deriving an approximate CSD directly from the underlying population genetic model. The resulting CSD admits an intuitive coalescent-like genealogical interpretation, explicitly describing the genealogical relationship of the conditionally sampled individual to the previously sampled individuals. We make use of the genealogical interpretation to introduce additional approximations, culminating in the sequentially Markov CSD (SMCSD), which models the conditional genealogical relationship site-by-site across the genomic sequence. Critically, the SMCSD can be cast as a hidden Markov model (HMM), for which efficient algorithms exist; by further specializing the general HMM methods to the SMCSD, we obtain optimized algorithms with substantial practical benefit. Finally, we empirically validate both the accuracy and computational efficiency of our proposed CSDs, and demonstrate their utility in several applied contexts.

Advisor: Song, Yun S
Plum Blossom Warm Gentle Wind Shimmering Stillness (for Bass Trombone and Ensemble)

Plum Blossom Warm Gentle Wind Shimmering Stillness is a composition for solo bass trombone and accompanying ensemble. It is in six movements and is approximately 12 minutes long. The piece is dedicated to my grandfathers Benjamin A. Levis, and Harbert S. Gregory, who have passed away in recent years. I initially began work on concepts for the composition while studying with Professor John Thow, and then with Professor Jorge Liderman, but put it away after their untimely passing. Movement four is dedicated to both of them. The composition was written for my good friend and unparalleled bass trombonist, Marc Bolin./nThe title reflects my interest in haiku, and the possibility of containing in a brief statement, a moment of total clarity and harmony. While reflecting on Professor Thow's passing, sitting on my front porch, watching the blooming plum tree in front of my house shake and stir ever so gently when the wind would pick up, I experienced one of these moments of deep quietude. Even as the title is not a haiku in its traditional form, it contains a moment for me where something brief and subtle can have a sudden impact and lasting resonance. Even though the composition is inspired by this moment, it is not an impressionistic, sonic image of the natural world. Rather, it is a metaphor for the complex relationships that make up our human experience, the impact those relationships have on us, and the lasting effects and reverberations they create./nThe work employs a myriad of extended techniques, engendering layers of timbral commonality. This allows the ensemble to fuse into blended "meta-instruments" and magnify the sonic landscape of the bass trombone. The composition is influenced by my interest in the sometimes antagonistic aims of post-spectral harmony and orchestration, self-similarity modeling of the new complexity school, and large-scale architecture in improvisation./nThe instrumentation for Plum Blossom Warm Gentle Wind Shimmering Stillness is bass trombone, four percussionists, piano, two violins, viola, violoncello, and contrabass.

Advisor: Cox, Cindy
The Theology of Hathor of Dendera: Aural and Visual Scribal Techniques in the Per-wer Sanctuary

The Ptolemaic temples are some of the best-preserved examples of Egyptian religious architecture; they represent the culmination of a long line of development, reflected in an increase in the number and polyvalency of hieroglyphic signs and iconographic elements in the wall reliefs. This development widened the scribal playing field for creating expressions that function on multiple aural, visual, and thematic levels./nThere have been few scholarly studies of these plays on words, signs, and iconography; despite the intrinsic relationship of texts, reliefs, and architecture in Egyptian monuments, there have been no comprehensive studies of these techniques within a unified architectural space. I was therefore motivated to study these scribal methods within the most important cult chamber of the Temple of Hathor at Dendera: the Per-wer Sanctuary. Building upon the work of Gutbub, Guglielmi, and Derchain, I extended their approaches to the material in several ways: examining these techniques on both micro- and macro-levels, from their smallest details to their broadest thematic connections; foregrounding individual techniques to determine the words and phrases singled out for emphasis; synthesizing their use in the interconnections formed between scenes and texts within the three-dimensional space of the cult chamber./nI found that these scribal techniques support the three main themes of the Per-wer: Hathor as Creator and solar goddess; the Myth of the Distant Goddess; the King as Intermediary between the human and divine worlds. The myth creates the context for the King's interaction with the goddess, allowing his ritual actions to restore cosmic balance and activate the creative process. By communicating across boundaries, the scenes link complementary pairs, creating a network of interrelationships that mirrors the perfection of the divine Creation./nThe results of my study suggest that this three-pronged approach could profitably extend to those of other cult chambers at Dendera, and to other Graeco-Roman temples, whose reliefs also contain plays on words, signs, and iconography. By studying these complex techniques of the ancient scribes, we can thereby come closer to understanding how they envisioned the universe and the place of humankind within it.

Advisor: Dieleman, Jacco
Redmount, Carol A.