VictorJuiz/thesis huggingface dataset:
Social Identity Over the Lifecourse at Historic Middenbeemster: A Biocultural Approach

Clinical and osteological studies have provided evidence that patterns in human skeletal morphological variations can be correlated with general patterns of activity. A whole-body life-course approach, which combines a variety of activity pattern analyses, provides the strongest support for activity related morphological variations and their development during life. By understanding the patterns of types of activities and their associated strain levels, applying biological characteristics of individuals in a life-course perspective, it becomes possible to frame biological and cultural data within a social narrative. This study examines social identity over the life course in the historic dairy farming community of Middenbeemster, NL, through the examination of skeletal markers of bone growth and maintenance and activity-related stress. It was hypothesized that the high demand for Dutch dairy products during the occupation of Middenbeemster would be reflected in the manifestation and intensity of skeletal markers of activity, suggesting sex and age-related patterns of activity and workload. A total of 87 adults (M=46, F=41) were chosen to be analyzed for the following variables: non-pathological osteoarthritis of all appendicular joints, 8 non-genetic non-metric traits, and 27 entheseal insertions (per side) chosen to represent a variety of major muscle groups/movements. Additionally, humeral and femoral diaphyseal cross-sectional geometry was examined in 108 adults (M=57, F= 51) and 22 subadults. Musculoskeletal development analyses provide strong support for a sex-based division of labor with several changes in activity patterns over the life-course for both sexes. Men from Middenbeemster exhibited changes in types of activities that most likely reflect an age-associated change in duties of daily farm life from an apprentice-like position involving milking the herd to more strenuous and variable activities. Women from Middenbeemster also exhibited age-associated changes in types of activities. Overall, the patterns of the results suggest that younger women were involved not only in the caretaking of the home, but were also important contributors in the dairy production process. A review of historical literature provides support for the inferred sex and age-based divisions of labor, however, the conclusions reached in this dissertation suggest a far more active role for women in the economic success of the dairy farms than was historically recorded.

Advisor: Agarwal, Sabrina C
The Cold War Comic: Power and Laughter in Taiwan and South Korea 1948-1979

The affective landscape of the global Cold War is commonly associated with fear and paranoia about ubiquitous enemies who had to be purged to preserve life worth living. My dissertation argues instead that the Cold War was one of the most comic times in recent history; not in spite of, but because of the apocalyptic stakes of the global stand-off. In East Asia, where authoritarian governments carried out the ideological war through tight media policy and censorship, comic culture became a vital form of mass communication out of necessity. Comic culture’s circuitous nature allowed transgressive public affects to gather in plain sight, fostering new rituals of collective understanding that bypassed state control./nThis dissertation demonstrates the regional resonance of the Cold War comic aesthetic through a comparative methodology, revealing cultural convergences among two US-allied East Asian countries that were also former Japanese colonies, Taiwan and South Korea. The similar contours of their comic cultures arise from these historical factors, as well as their common participation in global anti-Communism and their rapid industrialization under developmental policies. Nevertheless, the comic cultural field became a particularly important space of vernacularization for Taiwan and South Korea as they encountered the norms of new global cultures under Pax Americana, and it was there that the differences between them were articulated and amplified./nI identify three intertwined comic aesthetics that side-stepped the state’s totalizing machine of anti-Communist, developmental ideology, creating a counterpublic in the process of coming into being. Caricature, genre game, and nonsense were the three intermedial aesthetics that forged new forms of communication by cleaving to the margins of expression. If caricature suggests the method of minimalism, of communicating with the least amount of visual information possible, genre games offer the method of maximalism, of engaging heterogenous genres all at once. Nonsense, in turn, suggests the liberating possibility that reckoning with the impossibility of communication in the Cold War era is itself the most honest act of communication. Together, these aesthetics playfully invert the power structures of the era by making the trivial aim of collective laughter a primary and immediate affective objective.

Advisor: Jones, Andrew F
Differential methods for phase imaging in optical lithography

Differential methods are shown to reveal inherent phase in light, corresponding to either the structure of the scattering object, or to aberrations in the imaging medium. Intensity measurements of scattered electromagnetic fields are related to the phase structure of the underlying coherent wavefronts. For an ideal imaging system, intensity differentials with varying focus encode the phase and hence optical density distribution of a scattering object. This is used to characterize diffraction due to thick absorber topography in deep UV lithography (193nm wavelength) using a focus stack from a mask imaging tool. The imaging methods thus developed enable feature-specific process window calibration during lithography, while supplementing mask design capabilities from experimental data./nSwitching from strongly absorbing , patterned lithography masks to weakly scattering phase diffusers allows probing the imaging system as well, much like audio system characterization using wide spectrum noise. This enables in-situ characterization of optical-system transfer functions using the speckle generated from the rough diffuser. Under a linear approximation between the diffuser phase and speckle intensity, system aberrations are shown to be encoded in the power spectrum of the speckle. This proves to be an effective way of probing the imaging system in extreme UV lithography (13.5nm wavelength), where mask roughness naturally creates weak speckle in the image intensity. A new theoretical formulation demonstrates that the phase of the pupil can be completely recovered in a band-limited imaging system by computing image intensity differentials created by tilting the illumination angle on the EUV mask. Experiments on a synchrotron EUV imaging tool validate the method, showing real time recovery of imaging system aberrations, simply from differentials of speckle images from a blank mask.

Advisor: Waller, Laura A
One Shell, Two Shell, Red Shell, Blue Shell: Numerical Modeling to Characterize the Circumstellar Environments of Type I Supernovae

Though fundamental to our understanding of stellar, galactic, and cosmic evolution, the stellar explosions known as supernovae (SNe) remain mysterious. We know that mass loss and mass transfer are central processes in the evolution of a star to the supernova event, particularly for thermonuclear Type Ia supernovae (SNe Ia), which are in a close binary system. The circumstellar environment (CSE) contains a record of the mass lost from the progenitor system in the centuries prior to explosion and is therefore a key diagnostic of SN progenitors. Unfortunately, tools for studying the CSE are specialized to stellar winds rather than the more complicated and violent mass-loss processes hypothesized for SN Ia progenitors./nThis thesis presents models for constraining the properties of a CSE detached from the stellar surface. In such cases, the circumstellar material (CSM) may not be observed until interaction occurs and dominates the SN light weeks or even months after maximum light. I suggest we call SNe with delayed interaction SNe X;n (i.e. SNe Ia;n, SNe Ib;n). I per- formed numerical hydrodynamic simulations and radiation transport calculations to study the evolution of shocks in these systems. I distilled these results into simple equations that translate radio luminosity into a physical description of the CSE. I applied my straightfor- ward procedure to derive upper limits on the CSM for three SNe Ia: SN 2011fe, SN 2014J, and SN 2015cp. I modeled interaction to late times for the SN Ia;n PTF11kx; this led to my participation in the program that discovered interaction in SN 2015cp. Finally, I ex- panded my simulations to study the Type Ib;n SN 2014C, the first optically-confirmed SN X;n with a radio detection. My SN 2014C models represent the first time an SN X;n has been simultaneous modeled in the x-ray and radio wavelengths.

Advisor: Kasen, Daniel N
Nugent, Peter E
Investigations of the Optoelectronic and Structural Properties of Semiconductor Nanocrystals Under Perturbative Environments

Semiconducting nanocrystals have shown great use in a variety of light emitting and absorb- ing applications, such as solar cells, light emitting diodes, displays, and even stress sensors. These materials exhibit size-tunable physical properties, such as phase transition pressures and band gaps. Although a lot of work has gone into understanding the structure-property relationships in these materials, a fundamental understanding of how these materials in- teract under various perturbations is necessary to understand the material’s applicability in applications. This dissertation outlines the characterization of various nanocrystals and nanocrystal composites under two different perturbations: self-absorption of luminesced light and elevated pressure./nChapter 1 outlines the general properties of semiconducting nanocrystals and gives a background on previously studied perturbations. Optoelectronic and structural studies of cadmium chalcogenide nanocrystals are highlighted and the complex phase transitions ob- served in CsPbBr3 are discussed in detail./nIn Chapter 2 we investigate how the reabsorption of photoluminesced light, an effect known as the inner filter effect (IFE), can affect the nanocomposite’s properties under illu- mination. The IFE has been well studied in solutions, but has garnered less attention in regards to solid-state nanocomposites. We demonstrate that the IFE can result in a large spectral red-shift of over a third of the linewidth of the photoluminescence of the nanocom- posites over a distance of 100 μm. We then utilize this red-shift to develop a displacement sensor with sub-micrometer resolution that has high-temporal and spatial resolution./nWe investigate the effects of pressure on NCs in Chapters 3-4. Chapter 3 outlines the use of a diamond anvil cell for generating gigapascal pressures. This technique is then utilized to understand how CsPbBr3 nanocrystals respond to pressure in Chapter 4. The crystal structure of CsPbBr3 is composed of corner sharing lead bromide octahedra with Cs+ sitting in the cavities. By investigate the optical shifts and structural changes in the material with applied pressure, we find that the material transitions to a high-pressure phase around 1.4 GPa. A crystal structure of this high pressure phase has not been previously reported and we find that it has P21/m symmetry. We further find that CsPbBr3 exhibits a size-dependent compressibility where we find that nanocrystals are at least 40% more compressible than the bulk material./nWe finally present an outlook for future studies in Chapter 5. We present ideas for determining additional fundamental properties of the CsPbBr3 high-pressure phase transition and investigating the effect of the inorganic-inorganic interface in nanocrystal core/shell heterostructures on crystallographic phase stability.

Advisor: Alivisatos, A. Paul
A Monte Carlo Method for Identifying Imaging Systematics in Galaxy Surveys

The Dark Energy Spectroscopic Instrument (DESI) will soon start to obtain optical spectra for tens of millions of galaxies and quasars, constructing a 3-dimensional map spanning the nearby universe to 10 billion light-years. DESI aims to use the fossil imprint of sound waves from the first 380,000 years of the universe, which is still detectable as a pattern of temperature variations in the cosmic microwave background radiation (CMB), to measure how the universe has evolved since then the Baryon Acoustic Oscillations (BAO) technique. The early CMB temperature differences map early variations in density (the sound waves) that subsequently evolved into the clustering of galaxies and intergalactic gas (the baryons), as well as dark matter at recurrent intervals throughout space. These regularly spaced clusterings are consistent over time, very much like a ruler to measure the universe, with the CMB at one end. This allows one to measure the effect of dark energy on the expansion of the universe./nThis thesis presents my work as a member of the DESI Imaging Team, for which I received DESI Builder status. We transform images of the night sky into a catalog of positions properties of automatically detected and measured astrophysical sources. This catalog will contain billions of astrophysical sources, but just a subset (tens of millions) of sources will be selected for spectroscopic observation with DESI. I was involved in all stages of the Legacy Surveys, from carrying out observations to building the large–scale-structure catalogs./nA major challenge for they Legacy Surveys is understanding the inevitable biases and systematics in their galaxy samples. The key product of my thesis is a Monte Carlo method, called Obiwan, that adds simulated sources to random locations in astronomical images and then performs source detection and measurement, characterizing the complex selection inherent in large-scale-structure catalogs. The process is repeated until the injected source density is high enough to satisfy one’s science objectives. For instance, the DESI target density for emission line galaxies (ELGs) is 2400 deg2, so simulated ELGs should be injected at more than 10 times this density.

Advisor: Nugent, Peter E
Trophic niche differentiation within the adaptive radiation of Hawaiian Tetragnatha spiders

The Hawaiian Tetragnatha spiders are a remarkable and well-documented example of adaptive radiation. With ca. 50 species exhibiting a diverse range of morphologies and ecological affinities, all having evolved within the last few million years, this system has a great deal to offer for studies of evolutionary ecology. Furthermore, due to Hawaii’s age-structured arrangement of islands, it is possible to infer past processes in this lineage’s evolutionary history by using a space-for-time substitution. Although the ecological affinities of some Hawaiian Tetragnatha, notably the members of the Spiny Leg (actively hunting) clade, have been well documented, much is still unknown about the ecological niches of web-builders, and about the precise nature of ecological interactions that occur among both Spiny Leg and web-building species. Importantly, little is yet known about the dietary compositions of different Hawaiian Tetragnatha species. Diet is likely to play a critical role in the ecology of these spiders, all of which are obligate predators and therefore potentially compete for prey; and because the need to hunt prey can exert significant selective pressure, trophic ecology may also have played a part in driving the evolutionary diversification of this lineage./nThe work presented here examines the trophic niche ecology of Hawaiian Tetragnatha in a geographic and evolutionary context. Working at multiple geographic scales – within a single forest site, among sites on an island, and across sites on three different islands – I characterize the trophic niches of several Tetragnatha species and probe the extent to which these niches overlap. I use multiple types of data to describe trophic niche, including web architecture (i.e., hunting behavior), stable isotope signatures of N and C in the spiders’ tissues, and molecular identification of gut contents. Additionally, I present a phylogenetic hypothesis for the entire adaptive radiation, which lays the foundation necessary for analyzing ecological dynamics in the context of the spiders’ evolutionary history. My work adds critical information to our knowledge of the natural history, evolutionary history and ecology of Hawaiian Tetragnatha, and builds on our understanding of the ecological and evolutionary dynamics of adaptive radiation.

Advisor: Gillespie, Rosemary G
A Tail of Two Signaling Pathways; How Xenopus Patterns its Posterior

The development of multicellular organisms relies on extracellular signaling pathways regulating the patterning and specification of tissues, with the same pathway often being deployed to serve many different functions. The development of Xenopus laevis has served as a classic model for identifying context specific transcriptional targets of signaling pathways and the regulatory loci responsible for their precise expression. The focus of this dissertation was to understand the regulation of the Wnt/ -catenin transcriptional target genes such that the correct patterns of expression are formed during gastrulation. During gastrulation Wnt, along with FGF, function to form the anterior to posterior axis of the embryo by inducing expression of target genes necessary for posterior identity. Target genes of the Wnt signaling pathway during gastrulation are not the same as those induced at early and later times and in addition, form different patterns. I begin in Chapter I by summarizing the early inductive events during Xenopus development that form the proper tissues for Wnt to act on as well as provide an overview of our current understanding of gene regulation and methods used to discover gene regulatory networks. In Chapter II, I explain the methods used in my dissertation. Then in Chapter III, I identify direct transcriptional targets of the Wnt signaling pathway. I found that this set of target genes are expressed around the blastopore during gastrulation, contain -catenin bound regions within 50kb of the gene, and are reduced in expression as a result of Wnt signaling knockdown. Next, in Chapter IV, I focus on two transcription factors, Sox2 and Zic1/2/3, to explore whether they are co-regulating a subset of Wnt target genes to provide context dependent activation. Lastly, in Chapter V, I aim to understand if FGF directly posteriorizes the embryos by activating either all or a subset of Wnt target genes identified in Chapter III. I found that FGF directly regulates all Wnt target genes during gastrulation. In addition, I found -catenin preferentially binds at the promoter of a subset of genes and that negative regulation in the absence of Wnt signaling may be responsible for the expression patterns of this subset of genes. Together, these results reveal the complex mechanisms of gene regulation that are necessary to insure the precise expression of Wnt and FGF target genes such that they form the anterior to posterior axis.

Advisor: Harland, Richard
Using bioconjugation reactions for protein detection, intracellular delivery, and the study of protein conformation

The synthetic modification of proteins has significantly contributed in the fields of chemical biology and material science. Choosing an appropriate chemical strategy that involves the controlled coupling of biomolecules in aqueous solution and in a well-defined manner is key. This work describes the use of suitable bioconjugation reactions for a variety of applications. Firstly, oxidative coupling of o-aminophenols and anilines was used for the detection of nitrotyrosine-containing proteins. In this work, we demonstrated that the chemoselectivity of the tandem nitro reduction/oxidative coupling sequence was sufficiently high to label nitrated proteins among thousands of others in complex mixtures. Second, we constructed protein-polymer conjugates using 2-pyridinecarboxaldehyde reaction for intracellular protein delivery. The polymers were endowed with 2-pyridinecarboxaldehyde (2PCA) groups, which modify proteins selectively at their N-terminal positions through imidazolidinone formation. The polymer-modified proteins were delivered into the cytosolic compartment of various cancer cells and the function of the proteins was retained during the process. Importantly, mechanistic studies have revealed that the internalization pathways of the constructs are likely to occur through a membrane fusion mechanism, thus at least partially circumventing the protein inactivation that occurs through endocytosis. Finally, we adapted 2PCA and oxidative coupling reactions to create a Förster resonance energy transfer construct of an intrinsically disordered protein (IDP) to monitor protein folding. A library of IDP with different lengths and densities of polyethylene glycol (PEG) through lysine modifications was constructed. We demonstrated that the size and density of the PEG chains had little to no effect on the conformation of IDPs.

Advisor: Francis, Matthew B
Photoluminescence Blinking, Stimulated Emission, and Charge Carrier Dynamics in Single Semiconductor Nanostructures

Semiconductor nanostructures are a class of materials that have many attractive properties for optoelectronic applications and incorporation into solid-state devices. Compared to bulk semiconductors, they offer discrete, tunable electronic energy levels and an enhancement of many charge carrier interactions. Improving our understanding of the charge dynamics in these materials and how their behavior fundamentally differs from bulk solids will be crucial for ongoing and future development of semiconductor nanostructure devices. In this dissertation, the use of single particle spectroscopy to probe charge carrier dynamics in semiconductor nanostructures is described./nThe first introductory chapter provides an overview of some elementary background knowledge regarding the unique electronic structure of confined semiconductors and how this results in their distinct carrier dynamics. The advantages of single particle experiments are discussed as well as the detection methods available to obtain a sufficiently high signal-to-noise ratio, focusing primarily on the photoluminescence (PL) detection of a single optically excited particle. Finally, PL blinking in single semiconductor nanocrystals (NCs) is introduced and the leading theories proposed to account for the phenomenon are summarized. The second chapter details an experimental setup optimized for studying the PL emission from single particles, including an ultrafast, tunable laser system as the excitation source, a confocal microscope to obtain a small focal volume for single particle excitation, and the detection and acquisition components, namely sensitive photodiodes and time-correlated single photon counting techniques./nThe subsequent three chapters present results from a range of semiconductor nano-materials. The third and fourth chapters focus on PL blinking in semiconductor NCs, beginning with the use of PL blinking results in thick-shell CdSe/CdS chalcogenide NCs to compare the effectiveness of two distinct analysis methods for probing multi-level emission. Extending to lead halide CsPbBr3 perovskite NCs, PL blinking is investigated to understand how charge trapping in these newly available compositions compares to traditional chalcogenide NCs. The next chapter provides three condensed summaries of PL studies in semiconductor nanowires (NWs). Time-resolved PL experiments of colloidal CsPbX3 (X = Cl, Br, I) NWs and InP NWs are detailed, and a spectroscopic study of stimulated emission in isolated CsPbBr3 NWs is described. Finally, the last chapter offers concluding remarks of the dissertation as well as a glimpse into the possible future directions of the laboratory.

Advisor: Leone, Stephen R