VictorJuiz/thesis huggingface dataset:
The origins of marine biodiversity: Speciation and diversification in Caribbean corals (family Faviidae) and Indo-Pacific parrotfishes (genus Scarus).

Species-rich coral reef systems present a paradox to evolutionary biologists. Many reef invertebrates and fish have enormous dispersal potential via a planktonic larval stage, presumably leading to widespread patterns of genetic panmixia at large spatial scales. In the context of such high connectivity, how can we begin to get diversification? In this dissertation, I examine this question in two different systems, Caribbean corals and Indo-Pacific parrotfishes, and in two dimensions - time and space. The timing and tempo of species diversification can tell us how geological and environmental change is correlated to species formation. At the same time, the spatial distribution of genetic variation can reveal how contemporary processes may have contributed to population splitting and eventually speciation./nIn Chapter 1, I examine the history of reef systems in the Caribbean basin by looking at macroevolutionary patterns in faviid coral. Combining a newly compiled fossil stratigraphy with a time-calibrated molecular phylogeny of extant Caribbean Faviidae, I show that these Caribbean corals are not related to their Mediterranean confamilials, and that all living species appear to have originated during a period of rapid environmental change in Mio-Pliocene. In Chapter 2, I examine cryptic speciation and the patterns of diversity in the parrotfish, Scarus ghobban. Though this species was thought to have a pan-Indo-Pacific distribution, a new mitochondrial phylogeny shows deep divergence between Indian and Pacific Ocean clades. Furthermore, these clades form a species complex with a Panamanian endemic species, Scarus compressus, and a newly described Western Australian endemic species. Finally, in Chapter 3, I use population genetics methods to take a deeper look at the history of these fishes in the Pacific and assess the spatiotemporal structuring of diversity. My results suggest those Pleistocene sea level fluctuations, peripheral isolation, and hybridization all played significant roles in creating and maintaining diversity in this complex./nBy assessing taxonomic and population dynamics in the framework of historic environmental processes, I begin to answer fundamental questions about evolution in both Caribbean and Indo-Pacific tropical marine systems. The linking of patterns of diversity over multiple time scales can provide clues about processes that are important to ecology of marine taxa both in the past and in the present. Further, understanding the distribution of basic evolutionary units (e.g. species or ESUs) identifies fundamental units for conservation. With coral reef ecosystems currently highly threatened by anthropogenic change, this knowledge will be essential in future conservation efforts.

Advisor: Roderick, George K
Impossible Diplomacies: Japanese American Literature from 1884 to 1938

This dissertation examines writings by and about Japanese men---students, gentlemen, vagrants, and servants---who lived and worked in the United States prior to 1938. The goal of this dissertation is to outline what "Japanese American literature" might look like if its basis was not a subject position but a series of diplomatic relations./nThe central argument of this dissertation is that during a time when the "Japanese American" was an "impossible subject" from the vantage of the laws of the United States, Japanese men who lived and worked in the United States staged---through literature---an "impossible diplomacy." The writers I consider in this dissertation---Sadakichi Hartmann (1867-1944), Arishima Takeo (1878-1923), Nagahara Shoson (1901--??), and Kato Saburo (??--??)---were not official cultural brokers, but subjects estranged both from their country of origin (Japan), and the nation where they lived and worked (the United States). As aliens ineligible to citizenship in the United States as a "republic" of letters, these writers turned to literature as a means to mediate their estrangement from both Japan and the United States./nThe four chapters trace a historical arc through key shifts in the diplomatic and legal paradigms which governed the status of Japanese residents in the Untied States: the Treaty of Amity and Commerce (1858), the Gentlemen's Agreement of 1907-1908, the Asian Exclusion Act of 1924, and the Neutrality Act of 1935. In Chapter One, I read Sadakichi Hartmann's Conversations with Walt Whitman (1895) in concert with Whitman's Calamus sequence, tracing how the logic of ``engrafting" in the texts parallels structures of equality and inequality in the Treaty of Amity and Commerce. In Chapter Two, I read Arishima Takeo's Labyrinth(1918) arguing that the novel describes an economy of tears shared by men which reveals underlying contradictions of the Gentlemen's Agreement of 1907-1908. In Chapter Three, I recover Lament in the Night (1925), a novel written by Nagahara Shoson (1901--), a young immigrant who entered the United States ten years after the institution of the Gentlemen's Agreement. I construct an ``epistemology of the pocket" to address the intimacies and exposures of the Japanese American urban vagrant. In Chapter Four, I read a short story by Kato Saburo (??-??) titled, ``Mr. Yama and the China Incident" (1938). I argue that the story stages a form of ``vernacular diplomacy" which counters, through script and gesture, the discourse of ``national people's diplomacy" formed during the Second Sino-Japanese War. In turn, Kato's introduction of a third party---a speaking Chinese subject---opens the field of impossible diplomacy from the bilateral scheme of the Japanese American to the multilateral question of Asian American literature.

Advisor: Lye, Colleen
Digital Fluorescence Microscopy for Tuberculosis Diagnosis

This thesis describes the conceptualization, design, creation, and testing of a portable digital LED fluorescence microscope for use in diagnosing M. tuberculosis in low-resource settings. Over a century after its introduction, sputum microscopy remains an essential technique for tuberculosis diagnosis even in wealthy countries: sputum from a patient is smeared on a slide, stained for visibility, and examined for the presence of microscopic tuberculosis bacteria, requiring both a high resolution microscope and substantial technician skill in interpreting what is observed. Our device is ≤ 3kg and 18 x 18 x 8 cm; battery-powered, charging off 12V solar or auto power; and controlled via USB 2.0 by a low-cost laptop. It is capable of digital fluorescence imaging in direct sunlight of Auramine O-stained sputum smears over a 0.64 x 0.49 mm field of view with a nominal resolution of 0.76 µm resolution and image display at ≳ 2500X magnification. Diagnostic sensitivity is 63% and specificity 85% when used by individuals with ~ 10 hours of training in reading sputum smears. Images are uploaded automatically via the local mobile phone network to district hospitals for quality assurance and record-keeping. We have also developed a diagnostic image-processing algorithm with accuracy equivalent to our human readers when applied to images taken with the device; in the future we will integrate diagnostic image processing at the time of imaging in order to reduce technician training requirements, increase repeatability, and potentially increase sensitivity and specificity. The system is currently deployed in Hanoi, Vietnam as part of an effort to extend tuberculosis diagnosis to peripheral levels of the healthcare system.

Advisor: Fletcher, Daniel A
Saykally, Richard J
Numerical Models of Galaxy Evolution: Black Hole Feedback and Disk Heating

This thesis explores two topics in contemporary galaxy evolution using numerical models and N-body simulation: feedback in active galactic nuclei and the heating of stellar disks./nTwo numerical models of feedback from active galactic nuclei are developed and applied to the case of a major merger between two disk galaxies. Accretion into central black holes is modeled via a subgrid prescription based on angular momentum transport on unresolved scales. Feedback from black holes is modeled in two ways, both of which deposit a momentum &tau L / c into the surroundings, where L is the luminosity of radiation produced by the galactic nucleus. In the first model, the momentum is divided equally among the nearby gas particles to model processes like the absorption of ultraviolet light by dust grains. The second model deposits the same amount of momentum into the surroundings, but it does so by launching a wind with a fixed speed, which only has a direct effect on a small fraction of the gas in the black hole's vicinity. Both models successfully regulate the growth of the black hole, reproducing, for example, the MBH-&sigma relationship, albeit for large amounts of momentum deposition (large &tau). This regulation is largely independent of the fueling model employed, and thus is `demand limited' black hole growth, rather than a `supply limited' mode. However, only the model that implements an active galactic nucleus wind explicitly has an effect on large scales, quenching star formation in the host galaxy, and driving a massive galaxy-scale outflow./nIn a separate set of calculations, a method for including a stellar disk in cosmological zoom-in simulation is presented and applied to a set of realistic dark matter halos taken from the Aquarius suite of simulations. The halos are adiabatically adjusted from z = 1.3 to z = 1.0 by a rigid disk potential, at which point the rigid potential is replaced with a live stellar disk of particles. The halos respond to the disks, in every orientation simulated, by contracting in their central regions and by becoming oblate instead of prolate. The resulting disks, with few exceptions, form large bars which contain a fair fraction of the mass of the disk. These bars buckle and dominate the dynamics of the disk, increasing not only the scale height of the disk, but also the vertical velocity dispersion. During the simulations, the disks tumble coherently with their host halo, but can leave the outermost edges of the disk behind, creating streams that are far out of the plane of the disk. Some first steps are taken to relate the evolution of the disk to the substructure in the halo, but the situation is complicated by the massive bar.

Advisor: Ma, Chung-Pei
Quataert, Eliot
Contributions to Descriptive Inner Model Theory

Descriptive inner model theory is the study of connections between descriptive set theory and inner model theory. Such connections form the basis of the core model induction, which we use to prove relative consistency results relating strong forms of the Axiom of Determinacy with the existence of a strong ideal on having a certain property related to homogeneity. The main innovation is a unified approach to the "gap in scales" step of the core model induction.

Advisor: Steel, John R
Novel Analytical Methods for Examining Biomolecular Complexes Using Electrospray Ionization Mass Spectrometry

Several analytical strategies and investigations are presented in this dissertation to improve the quantification, sensitivity, and structural information that can be obtained for gaseous biomolecular ions in electrospray ionization (ESI) mass spectrometry (MS) experiments. Internal or external standards are commonly employed to quantify molecules in complex mixtures because molecular ion abundances cannot be directly related to the concentration of the molecules in solution. A new standard-free quantitation method is used to obtain the relative concentrations of components in a mixture using the abundances of large, nonspecific clusters formed by ESI. Large non-covalent clusters overcome differences in ionization efficiencies between molecules, and are representative of the solution-phase mixture. The sensitivity in MS experiments can be significantly lowered by the presence of high concentrations of salts in the ESI solution because nonspecific ion adduction to biomolecules distributes ion signal into different forms with various numbers of adducts. Studies here demonstrate the extent of both sodium ion and acid molecule adduction to proteins are inversely related, and both depend significantly on the proton affinity of the anion in the ESI solution. Several solution-phase additives that contain anions with low proton affinity values are shown to effectively desalt protein ions generated by ESI, which should result in improved detection limits, more accurate mass measurements, and improved tandem MS sensitivity. Additionally, a solution-phase additive (HClO4) is discovered that can be used to count the number of basic sites accurately in peptides and proteins based on the number of HClO4 adducts to low charge states. High charge states of peptides and proteins can be readily formed by ESI of aqueous solutions that contain trivalent metal ions, and fragmentation of these trivalent metal ion-peptide or protein complexes by electron capture dissociation can be used to increase the structural information obtained from these experiments. Metal ion-biomolecule interactions are ubiquitous in nature where they play a role in many biological processes. Here, nonspecific metal ion adduction to protein cation and anions is shown to result in more compact conformations compared to the bare protein ion, likely a result of salt-bridge interactions between the metal ion and the biomolecule.

Advisor: Williams, Evan R
Mechanisms of Ubiquitin-Driven Cell Cycle Control

Posttranslational modification of proteins with ubiquitin, ubiquitylation, is essential in all eukaryotes. Ubiquitylation is accomplished by an enzymatic cascade: E1 activates ubiquitin and transfers it to E2, which works with E3 to transfer ubiquitin to substrate residues, usually lysines. Once attachment of the first ubiquitins to substrate, chain initiation, has occurred, E2 and E3 modify one of the seven lysine residues in ubiquitin itself, resulting in formation of polymeric ubiquitin chains, chain elongation. Ubiquitylation is involved in nearly every cellular process, and is central to cell cycle control. Ubiquitin-dependent protein degradation is especially important during mitosis, as cells must turn over many proteins within a short time-window. The anaphase-promoting complex (APC/C) is an essential E3 that targets cell cycle regulators for degradation during mitosis. The APC/C must degrade many substrates within a short period of time, and likely acts under saturation. Furthermore, APC/C substrates are required at different times during mitosis. Therefore, the APC/C cannot degrade all substrate at once, but rather must order substrate degradation so that substrate proteins can accomplish their functions. The balance between efficiency and regulated degradation is the APC/C's major challenge as it orchestrates mitotic exit./nIn this dissertation I address how human APC/C targets its many substrates for degradation. First, I report our finding that APC/C functions by decorating its substrates with Lys11-linked ubiquitin chains. Lys11-linked chains target substrates to the 26S proteasome and are essential for cell division in human cells, Drosophila cells, and Xenopus tropicalis embryos. The human APC/C uses a dedicated E2, Ube2C/UbcH10, to perform chain initiation while a second E2, Ube2S, elongates these first modifications using exclusively Lys11 on ubiquitin. Ube2C and Ube2S likely function simultaneously, thus allowing APC/C to overcome its massive substrate workload. Efficient chain initiation by Ube2C is made possible by conserved initiation motifs in substrates. Initiation motifs do not regulate substrate binding to APC/C, but instead control the efficiency with which Ube2C and APC/C attach the first ubiquitin moieties to substrates. I will show that chain initiation by Ube2C is the rate-limiting, regulated step during Lys11-linked chain formation by the APC/C. Once Ube2C has initiated chains on APC/C substrates, Ube2S takes over, rapidly elongating Lys11-linked ubiquitin chains that target substrates to the 26S proteasome. Finally, I address how use of two E2 enzymes performing different functions allows APC/C to overcome its major challenge: rapid yet regulated turnover of essential cell cycle regulators. The separation of ubiquitin chain formation by the APC/C into initiation and elongation steps, with initiation being rate-limiting and tightly regulated, draws parallels between ubiquitylation and other processive reactions such as transcription and translation.

Advisor: Rape, Michael
Essays on Macroeconomics and International Finance

In Chapter 1, I develop a New Keynesian model with inventories and convex costs of labor adjustment. For each of the three empirically observed responses to monetary policy shocks: (1) the slow adjustment of inventories compared to changes in sales; (2) the delayed and gradual response of inflation; and (3) the transitory movement in the aggregate price level in the same direction as the interest rate, also known as the "price puzzle," my model has important implications. First, adjustment costs counteract the financing-cost effect of interest rate changes on inventory holdings, but are still inadequate for the calibrated model to generate countercyclical inventory-to-sales ratios. I find that this financing-cost effect needs to be reduced by 80 percent for the model to predict inventory behavior correctly. Second, firm-specific adjustment costs in production increase the degree of real rigidity for price adjustment, so the response of inflation in the presence of high aggregate marginal costs is still slow-moving and persistent. Finally, the motive of cost smoothing for holding inventories implies that marginal costs should move in the opposite direction as the interest rate, which casts doubt on the use of the cost channel to explain the "price puzzle."/nIn Chapter 2, I propose a theory of the information channel between home consumption bias and home equity bias. Consumption-revealed information is acquired spontaneously in an investor's daily life and thus is naturally immobile. For this reason, consumption experience more concentrated in home-produced goods endows domestic residents with information advantage in home equities. This channel also helps to explain many empirical facts such as the 90\% correlation between import shares and foreign equity shares./nIn Chapter 3, I use individual portfolio data from a China's brokerage firm to test the predictions of Chapter 2. I find that the fraction of local stocks in the brokerage portfolio is 143 percent higher than the fraction of local stocks in the market portfolio. One third of this portfolio locality is explained by business exposure of listed firms, measured by their sales per capita in the brokerage city. The result shows that a rise in sales per capita by $2.75 leads to a 32 percent increase in the portfolio share relative to the mean. To examine whether business exposure helps investors to gain information other than familiarity, several indicators of business exposure in nonlocal areas are included in a regression. The result suggests that if a nonlocal firm's business is concentrated in other areas, local investors tend to shy away from its stock. However, some coefficients are not statistically significant, so we still cannot reach the conclusion that a firm's sales business has significant amount of information content on stock returns.

Advisor: Gourinchas, Pierre-Olivier
Long range dependent models in information theory

Long range dependence refers to stochastic processes for which correlations persist/nat much longer time scales as compared to traditional models. For such processes the/ncentral limit theorem does not in general hold, and the smoothing effect of the law of/nlarge numbers takes more time to settle in. Such phenomena have been observed in/nmany different fields including financial time series, DNA sequences, network traffic/nand variable bit-rate video. The bursty nature and persistent correlation structure of/nlong range dependent processes make them tough to control and predict in practice,/nand tough to analyze in theory. In this thesis we look at the origins of long range/ndependence through the use of Markov models./nWe first introduce a model of long range dependence using countable state Markov/nchains. A positive recurrent, aperiodic Markov chain is said to be long range dependent/n(LRD) when the indicator function of a particular state is LRD. This happens/nif and only if the return time distribution for that state has infinite variance./nWe investigate the question of whether other instantaneous functions of the Markov/nchain also inherit this property. We provide conditions under which the function/nhas the same degree of long range dependence as the chain itself. We illustrate/nour results through three examples in diverse fields: queuing networks, source/ncompression, and finance. We then prove information-theoretic pointwise lossless source/ncoding theorems for a class of sources constructed from this model. We are able/nto show that the code length process at the output of an encoder inherits the long/nrange dependent nature of the source irrespective of the coding algorithm chosen./nWe extend our results to lossy source coding under suitable conditions, demonstrating/nquite generally the information-theoretic relevance of long range dependence.

Advisor: Anantharam, Venkat
Oscillatory integrals and extremal problems in harmonic analysis

Oscillatory integrals appear naturally in a variety of problems related to harmonic analysis, and have been a part of the subject since its creation. One is generally interested in quantifying how certain degeneracies of the phase affect the behavior of the integral. Numerous generalizations of the so-called stationary phase method have been the focus of past and current research, and the study of multilinear oscillatory forms with rough amplitudes falls into this category./nIn the first part of this thesis, in a joint work with Michael Christ, we examine a certain class of trilinear integral operators which incorporate oscillatory factors e^iP , where P is a real-valued polynomial, and prove smallness of such integrals in the presence of rapid oscillations./nOscillatory integrals provide a link between geometric properties of manifolds and harmonic analysis related to them, as illustrated by a multitude of restriction theorems for the Fourier transform which have been the object of careful investigation since the late 1960's./nIn the second part of this thesis, we establish the existence of extremizers for a Fourier restriction inequality on planar convex arcs whose curvature satisfies a natural assumption. More generally, we prove that any extremizing sequence of nonnegative functions has a subsequence which converges to an extremizer. By studying the three-fold convolution of arclength measure on the curve with itself we additionally show that, if the geometric assumption on the curvature fails in a strong sense, then extremizing sequences concentrate at a point on the curve and extremizers do not exist.

Advisor: Christ, Michael