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Applying structure-from-motion photogrammetry to high-resolution terrain modeling of Barva Volcano’s southeastern parasitic cones
No full textSituated within the Cordillera Central massif, Barva Volcano casts its shadow over the population, industrial, and agricultural centers of Costa Rica’s Central Valley. Unlike its more recently active volcanic neighbors, Barva has received limited attention regarding its shape and eruptive history. This issue is compounded by the extent of dense vegetation covering Barva’s slopes, which hinders ground-based surveying efforts. Consequently, remote sensing techniques are essential for studying Barva’s morphology effectively. This project improves our understanding of Barva through the development of high-resolution decimeter-accurate elevation data from six suspected parasitic cones located on its southeastern flank. These features are in proximity to populated areas and were hypothesized by a prior study to be related to Barva’s summit cones through a volcano-tectonic feature. Aerial imagery was captured using drones at each of these parasitic cones, supplemented by surface GNSS measurements calibrated by PostProcessed Kinematics (PPK) for accurate georeferencing. The resulting data were processed into digital surface models (DSMs) and orthomosaics of each parasitic cone using the Structure-from-Motion program Agisoft Metashape. Two methods were tested for further processing of these DSMs into approximate bare Earth digital terrain models (DTMs): Agisoft Metashape’s built-in ground point filtering method and the Random Forest classification algorithm. The Agisoft Metashape workflow demonstrates effectiveness in constructing approximate DTMs for the partially canopied cones, while both methods struggle to effectively produce approximate DTMs for the densely canopied cones. These digital elevation models provide significant morphological context to supplement future geochemical and LiDAR-based studies of these cones for comprehensive hazard assessments.M.S.Includes bibliographical reference
Search for new resonances decaying to pairs of merged diphotons with the CMS detector at √S = 13 TEV
No full textA search is presented for an extended Higgs sector with a massive resonance (X) decayingto a pair of spin-0 bosons (φ) that themselves decay to pairs of photons (γ). The search is
based on CERN LHC proton-proton collision data at √s = 13 TeV, collected with the CMS
detector, corresponding to an integrated luminosity of 138 fb−1. The analysis considers
masses mX between 0.3 and 3 TeV, and values of mφ for which the ratio mφ /mX is between
0.5 and 2.5%. In this range, the two photons from each φ boson are expected to spatially
overlap significantly in the detector. Two neural networks are created, based on computer
vision techniques, to first classify events containing such merged diphotons and then to
reconstruct the mass of the diphoton object. The mass spectra are analyzed for the presence
of new resonances and are found to be consistent with standard model expectations. Model-
specific limits are set at 95% confidence level on the production cross section for X → φφ →
(γγ)(γγ) as a function of the resonance masses, where the X → φφ and φ → γγ branching
fractions are assumed to be 100%. Observed (expected) limits range from 0.03–1.06 fb (0.03–
0.79 fb) for the masses considered, representing the most sensitive search in this channel.Ph.D.Includes bibliographical reference
On the mechanics of retinal detachment due to low-velocity, blunt-force trauma
No full textRetinal detachment is an ocular condition where the neurosensory retina separates from its blood supply risking atrophy and subsequent vision loss. This dissertation presents a mechanics based mathematical model of the transient response of the eye and associated retinal detachment. The model is used to study the time-dependent response of the ocular system and the associated retinal detachment spurred by low velocity blunt force impact at the anterior of the eye. Specifically, mechanics-based models for the cornea, the anterior ciliary body, the vitreous, the retina, and the aggregated RPE-choroid-sclera are developed. Short-time duration impact loading that is transmitted to the corneoscleral limbus as well as to the posterior vitreous via impression of the anterior oculus are both developed. Detachments emanating from the peripapillary region of the optic nerve head as well as from the ora serrata are formulated with results presented for the case of peripapillary detachment. The problem is formulated as a propagating boundary value problem in the calculus of variations where the location of the detachment front is allowed to vary as well as the displacement measures. This yields self-consistent governing equations and boundary conditions for each of the sub-structures within the intact and detached subregions. In addition, the variation of the interior boundaries themselves leads to a transversality condition which yields the locations of the propagating detachment front. Modal analysis via spectral expansion and displacement transformation is employed for exact solution to the governing equations subject to time-dependent boundary conditions. Modal displacements are found for the vitreous in terms of the spherical Bessel functions and Legendre polynomials and for the sclera and retina in terms of the associated Legendre functions. Modal participation loci for each structure are presented in response to their associated loadings. Analyses of the intact ocular system indicate that the maximum membrane stress, bending moment, and transverse shear stress in the intact structure occurs near the peripapillary region. Detachment is found to be precipitous when the energy release rate within the ocular structure surpasses the bond energy of the neurosensory retina’s adhesion to its retinal pigmented epithelium. For all but the smallest specimen bond energies, retinal detachments undergoing precipitation (spurred by sufficient energy release) are attenuated after achieving a new stably detached size. For small specimen bond energies, retinal detachment progresses catastrophically past the macula rendering the translatory function of the light to neuronal impulse, usually provided by the intact retina, severely diminished.Ph.D.Includes bibliographical reference
Essay on inference for low-rank models in econometrics
No full textMy dissertation consists of three chapters. Chapter 1 and Chapter 2 propose asymptotically normal estimators for low-rank models. Chapter 1 demonstrates that iterative least squares based on singular vectors, following nuclear norm penalization, achieves asymptotic normality. Interestingly, even without sample splitting, this procedure can eliminate the penalization bias. Chapter 2 adopts pre-specified weighting matrices, known as diversified projections, in the debiasing procedure of the nuclear norm penalized estimator in lieu of singular vector projections. This approach is shown to be robust to rank misspecification. Chapter 3 presents an empirical study using the two aforementioned estimation methods. The goal is to test the existence of pork-barrel politics in the history of the United States presidential elections. Chapter 1 explores the inferential theory of the (debiased) nuclear norm penalized estimator for the approximately low-rank matrix when observation is incomplete. This estimator is then applied to the heterogeneous treatment effect model. While the nuclear norm penalization itself suffers from shrinkage bias, the iterative least squares based on the singular vectors of the penalized estimator can successfully removes the bias and achieve asymptotic normality. Unlike other existing debiasing schemes, this debiasing method does not resort to sample splitting, making the estimation steps simpler and avoiding several drawbacks of sample splitting.
Chapter 2 introduces an alternative debiasing procedure for the nuclear norm penalized estimator, which does not require the knowledge of the true rank. The procedure consists of two main components: bias corrections and low-rank projections. Importantly, the low-rank spaces for projection are estimated through pre-specified weighting matrices, called diversified projections. The rank of these matrices does not need to be equal to the true rank. As a result, this procedure offers a promising alternative to existing debiasing methods, particularly in applications where rank estimation can be unreliable.
Chapter 3 applies the two estimation methods to test the existence of pork-barrel politics in the United States since the 1950s. We collect historical data on federal grant allocation to states and president elections, resulting in the two incomplete panel data: one for the federal grant allotted to states when they supported the incumbent presidents (the treatment sample), and another when they did not (the control sample). Our approaches are employed to estimate the underlying low-rank matrices. The first estimator is applied after several rank estimators, which select rank 2. The second estimator is also used with various choices of overestimated rank and diversified weights.Ph.D.Includes bibliographical reference
Semi-supervised classification and regression analysis
No full textIn this dissertation, we study semi-supervised learning (SSL) where unlabeled data may be utilized together with labeled data to potentially improve classification and regression analysis. To this end, we conduct the following two projects. In the first project, we study a binary classification SSL problem where the conditional mean model is assumed to be correct. Specifically, we consider a semi-supervised setting with a labeled dataset of binary responses and predictors and an unlabeled dataset with only the predictors. Logistic regression is equivalent to an exponential tilt model in the labeled population. For semi-supervised estimation, we develop further analysis and understanding of a statistical approach using exponential tilt mixture (ETM) models and maximum non-parametric likelihood estimation. The class proportions may differ between the labeled and unlabeled data, which is closely related to label-shift transfer learning problems. We derive asymptotic properties of ETM-based estimation and demonstrate improved efficiency over supervised logistic regression in a random sampling setup and an outcome-stratified sampling setup previously used. Moreover, we reconcile such efficiency improvement with the existing semiparametric efficiency theory when the class proportions in the labeled and unlabeled data are restricted to be the same. We also provide a simulation study to numerically illustrate our theoretical findings. In the second project, we study the estimation and inference of regression coefficients in conditional mean models in SSL and covariate-shift transfer learning problems, while allowing the condition mean models to be misspecified. We develop an augmented inverse probability weighted (AIPW) estimating method, where we use regularized calibrated estimators for both propensity score (PS) and outcome regression (OR) nuisance models. We demonstrate that if the PS model is correctly specified, our estimator achieves asymptotic normality, and valid confidence intervals can be obtained, with possible OR model misspecification and high-dimensional data. We also show that by suppressing detailed technical choices, previous methods can be unified by our AIPW framework. We verify our theoretical analysis through a simulation study and a real-world data application.Ph.D.Includes bibliographical reference
Investigation into the regulation of meristem formation and development by the REL2 family of transcriptional corepressors in Zea mays
No full textMaize (Zea mays L.) is a monoecious cereal crop that serves as one of the four pillars of human caloric sources. This foundational status is the result of several thousand years of artificial selection and breeding which turned a highly tillered progenitor with small ears of 5 – 12 encased kernels into a large, apically dominant plant with an ear of over 300 or more naked kernels. The genetic reprogramming of developmental pathways that yielded modern maize targeted the action and size regulation of meristems, organized structures containing plant stem cells. The post-embryonic formation of the plant body proceeds in a sequential manner through the action of meristems, and tightly coordinated meristematic regulation is required for proper development and reproductive success, eventually determining yield. A major goal of my research was to understand the role of transcriptional co-repression and related transcriptional machinery in regulating maize reproductive growth and in particular the development of the ear. I focused on the RAMOSA ENHANCER LOCUS2 (REL2) family of transcriptional corepressor proteins which includes four members, REL2, RELK1 (REL2-LIKE1), RELK2, and RELK3.In the first chapter of my thesis, my research focused on the molecular characterization of small-upright, a double mutant identified in an unbiased genetic screen for enhancers of the rel2 mutant that bore fewer and shorter internodes and enlarged female inflorescence meristems (IMs) carrying
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mutations in RELK1. I performed RNA-seq analysis on IM tips and showed that REL2 and RELK1 cooperatively regulate IM development by regulating genes involved in redox balance, hormone catabolism, and differentiation ultimately tipping the meristem toward a molecular environment favorable to expanded expression of ZmWUS1, encoding a stem-cell promoting transcription factor. To further investigate the function and relationship among the various family members CRISPR-Cas9 induced mutations in RELK2 and RELK3 were generated. My analysis shows that RELK genes have largely redundant functions in the development and maintenance of various meristem types through the plant life cycle. I also showed that the loss of one functional copy of REL2 can promote an increase in kernel row number across a diverse set of F1 hybrid combinations, indicating that tinkering with the REL2 corepressor family has the potential to increase seed yield. These data are currently incorporated in a bioRxiv preprint and a manuscript is under review for publication in Plant Physiology.
In the second chapter of my thesis, I explored upstream cis-regulation, and downstream targets of REL2. Using ATAC-seq and DAP-seq data, I defined two cis-regulatory modules (CRMs) upstream of REL2. By employing CRISPR- Cas9 to induce edits, I found deletions in CRM1 and CRM2 that decreased expression levels of REL2. In order to identify direct gene targets of REL2 complexes, I designed and validated the specificity of an anti-REL2 C terminal antibody for use in ChIP-seq experiments in immature inflorescences to identify direct targets of REL2 regulation. One putative target of REL2 repression is CLE8, an uncharacterized CLE peptide which is upregulated in inflorescence meristem tips of rel2;relk1. To functionally characterize this peptide, I performed peptide feeding assays on embryos and germinating seedling. I found that CLE8 neither affected SAM width nor root length.
In the third chapter of my thesis, we provided new insight into ZmWUS1 activity in the inflorescence meristem by performing single cell ASSAY FOR TRANSPOSASE-ACCESSIBLE CHROMATIN (ATAC)-seq analysis in inflorescence meristem tips of Bif3, a semidominant mutant caused by overexpression of WUS1. This works has been done in collaboration with Prof.
iv Robert Schmitz and Sohyun Bang at the University of Georgia Athens, as part of a joint NSF grant. Enrichment of the homeodomain recognition CAATAATGC motif was found in genomic regions of increased chromatin accessibility suggesting that ZmWUS1 functions as an activator in the central zone. Conversely, genomic regions of decreased chromatin accessibility in Bif3 inflorescence meristem tips were often adjacent to AUXIN RESPONSE FACTOR (ARF) genes suggesting auxin signaling is repressed in the central zone of the inflorescence meristem. These data are incorporated into a manuscript on which I am a co-author and has been deposited on bioRxiv. My contribution to this publication was genotyping and harvesting of inflorescences for the scATAC-seq analysis performed by Sohyun Bang. At the same time, I have also collected rel2 and rel2;relk1 inflorescences for generating chromatin accessibility data. These data will be carefully analyzed in the future.In the fourth chapter of my thesis, we provided new insight into the transcription factor binding landscape of the maize genome. By employing DAP- seq, transcription factor binding events for 200 transcription factor belonging to 30 families were mapped in B73 and Mo17 inbreds. Comparative analysis of transcription factor binding events between the inbreds revealed changes in background gene expression is driven by structural variation and presence- absence variation in intergenic cis-regulatory regions/modules (CRMs). The biological relevance of our identified CRMs was validated by CRISPR-Cas9 editing of TSH1 and BIF2 CRMs. Mutations in CRMs altered gene expression and recapitulated reference mutant phenotypes. These data are incorporated into a manuscript on which I am a co-author and has been deposited on bioRxiv. My contribution to this publication was generating the TSH1 CRM1 and CRM2 CRISPR-Cas9 constructs, and genotyping and phenotyping of T0 mutants.
Understanding the developmental biology of the ear inflorescence meristem has important implications for positively fine-tuning meristem size to achieve increases in yield. Given projected population growth, more food will need to be produced on the same amount of land in a rapidly changing climate, so achieving even small yield increases per plant can translate into major
agronomic gains. My research showed that basic understanding of the molecular mechanisms regulating maize meristems can provide new tools to face this daunting challenge.Ph.D.Includes bibliographical reference
Frontiers of sovereignty: an environmental history of law, science, and profit on the French Kerguelen Islands
No full textThe Kerguelen Islands are a remote archipelago with no indigenous population in the far southern Indian Ocean, claimed by France since 1772. “Frontiers of Sovereignty” examines how French administrators, politicians, entrepreneurs, and scientists have worked to translate France’s sovereignty claim into fact from the late nineteenth century until the present. Although the “desert island” is the model for traditional Westphalian sovereignty, study of the Kerguelen Islands reveals the difficulties and uncertainties inherent in trying to claim an actual desert island. I reveal how continuous efforts to renew the French claim to the Kerguelen Islands transformed them into a “permanent frontier” on the fringes of empire, where French administrators, politicians, entrepreneurs, and scientists experimented with different methods of establishing a French presence and generating value. The nature and space of the Kerguelen Islands frontier has changed over time, responding to international developments in science, technology, economics, and law. The frontier has not only moved through space, from the ocean surface to the beaches to the tundra, but also changed in shape, growing to three dimensions as French claims and ideas of value encompassed the upper atmosphere of the islands as well as the seabed around them. The shift from horizontal to volumetric concepts of sovereignty drew from, responded to, and transformed international developments in law, policy, and technology. Today, the frontier of the Kerguelen Islands includes land, sea, and airspace. While French politicians, administrators, entrepreneurs and scientists experimented with many methods of making the Kerguelen Islands valuable, today the forms of value that remain are the ones that involve the least human intervention in the territory. Invoking the value of the Kerguelen Islands as a nature reserve and an island “laboratory,” the French state can claim the maximum amount of national control over the Kerguelen Islands while invoking them to justify plans for international environmental governance on the regional and even the planetary scale. As a permanent frontier at the imagined boundary between “human” and “nature,” the Kerguelen Islands allow France to abstract local and specific landscapes/environments/forms of life in the name of the planetary. At the same time, however, close attention to the local and specific on the Kerguelen Islands reveal the problems inherent in any form of abstracted governance, from the desert island model of Westphalian sovereignty to current efforts at neoliberal or planetary forms of governance today.Ph.D.Includes bibliographical reference
Trauma, disability and insight in African literature
No full textThis dissertation argues that depictions of trauma and disability appear in African literature not only as indexes of damage, but as key sites of critique and utopian thought. In my first chapter, I argue that several major concepts from Frantz Fanon’s revolutionary theory can be traced back to his work as a clinical psychiatrist. To stage this argument, I consider Fanon’s published psychiatric research (which includes work in neuropsychiatry and institutional therapy), as well as the psychiatric case studies found in “Colonial War and Mental Disorders,” the final, fragmentary chapter of The Wretched of the Earth. First, I argue that Wretched puts forth a physicalist theory of revolutionary agency derived from Fanon’s work with patients suffering from degenerative neurological disorders—a chain of influences with surprising ideological effects, figuring disability and colonialism as analogous restrictive forces while simultaneously turning Fanon’s disabled patients into figures for the development of revolutionary agency. From here, I turn to Fanon’s more psychoanalytically-inflected work, arguing that Fanon’s case studies of traumatized combatants in the Algerian War of Independence significantly trouble the Manichaean account of anticolonial struggle found in the early chapters of Wretched. If anticolonial war is thrilling and cathartic in “On Violence,” by “Colonial War and Mental Disorders,” it is structured instead around dynamics of guilt and ambivalence. Furthermore, Fanon’s case studies of traumatized perpetrators of violence suggest that while trauma can act as a source of structural understanding, it has no inherent connection to victim or perpetrator roles, appearing instead as an ethically ambivalent condition. I argue that while theories of trauma have tended to equate it with victimhood and therefore with political right, a view of trauma as a category with no predetermined ethical status is key to understanding the colonial encounter. From here, I turn to a set of texts by postcolonial African novelists—Ousmane Sembène, Rebeka Njau, and Yvonne Vera—which engage the same questions of trauma, disability, structural understanding, and perpetration raised by Fanon. In two novels by Sembène and Njau, crowds of disabled people signify the failure of the liberatory project of decolonization, their damaged bodies and psyches testifying to the ongoing violence of neocolonial capitalism. Reading Sembène’s and Njau’s work through the Marxist category of primitive accumulation, I argue that primitive accumulation appears in these texts as a mass disabling event. Furthermore, the weakening of pre-capitalist social ties associated with primitive accumulation weakens the communal structures which would otherwise have provided care for disabled populations. Ultimately, for both authors, disability acts as an entry point into questions of interdependence and collective life, and disabled characters figure the possibility of collective life outside these processes of violence and exploitation. From here, I turn to Vera’s work, which extends and critiques Fanon’s ideas about postcolonial trauma. Vera, I argue, is centrally concerned with dissociation and dissociative mental states, which hide traumatic histories from view while simultaneously ensuring their survival within the psyche. Thus, trauma and dissociation act as mediating forces between the individual psyche and history. Finally, I consider Vera’s ambiguous portrait of a traumatized perpetrator of violence, arguing that this portrait challenges trauma theory’s typical equation of trauma with victimhood and ethical right. Nonetheless, trauma appears as a means of excavating difficult historical truths, and as a source of utopian vision.Ph.D.Includes bibliographical reference
Random list coloring
No full textFor G=(V,E) a graph on n=|V| vertices and random sets L(v) (for each v in V), what conditions suffice to make G L-colorable with high probability as n goes to infinity? In joint work with Jeff Kahn, in Chapters 1-9, the following conditions are shown to be sufficient. For any d>0, with D equal to the maximum degree of G and S(v) given sets of size D+1 (for each v in V), with L(v) drawn uniformly at random from the (1+d)ln(n)-subsets of S(v) (for each v in V, independently of other choices), the probability that G is L-colorable converges to 1 as n goes to infinity.Ph.D.Includes bibliographical reference
The initial frontier: science fiction between Argentina and the United States
No full textThis dissertation describes how the specific settler-colonial histories of the UnitedStates and Argentina led to similar types of counter-colonial science fiction taking shape
in both countries. In Argentina, as opposed to parts of Latin America where ideas of
racial mestizaje are more dominant, colonial discourse has exalted a “pure” whiteness
that would “civilize” the frontier by murdering indigenous people outright. This idea has
much in common with genocidal notions of Manifest Destiny in the United States. The
dismal commonality of these two colonial discourses led, in turn, to both countries
appropriating the style of European proto-science fiction — which tended to allegorize
and rearrange the key terms of colonial discourse — in parallel ways. While the majority
of this science fiction tended to support the settler-colonial ideology of Argentina and the
U.S., there were also authors in both countries that used the genre to subvert the frontier
ideology of their respective nations. The focus of my analysis is the latter, more
subversive type of writing. In describing the shape this science fiction took in Argentina
and the U.S., I hope to contribute to documenting the prehistory of the anticolonial and
antiracist science fiction that has risen to prominence since the 1990s, as well as to
highlight how certain formal features of the genre become salient in geographically
specific colonial contexts.Ph.D.Includes bibliographical reference