VictorJuiz/thesis huggingface dataset:
Experimental Challenges of Higgs Boson Identification in Vector Boson Fusing Final States at the Large Hadron Collider

While all LHC precision Higgs measurements up to date have been consistent with Standard Model predictions, improvements in Higgs identification and larger datasets can reveal couplings to new particles or evidence of new physics. Using the Higgs boson as a tool for discovery is one of the major physics efforts at the LHC. One of the most common but least well-measured Higgs production modes, Vector Boson Fusion (VBF), tends to leave a distinct signature which is especially useful to identify Higgs events whose decays cannot be triggered on directly. In this thesis, we focus on understanding various processes that affect the reconstruction of a candidate VBF event and on developing novel algorithms to better distinguish VBF from the much more common Gluon-Gluon Fusion (ggF) production mode, benchmarking on the H → γγ decay.

Keywords:  Department of Physics
Higgs
VBF
Vector Boson Fusion
Particle
ATLAS
Physics
LHC
Thesis
Advisor: Schwartzman Ariel
Tompkins Lauren
Exploring dark matter with improved numerical techniques

In this thesis, I discuss several computational physics developments. The context is the study of potential dark matter observables calculated from traditional cosmological N-body simulations. These particle-based simulation techniques often suffer from shot noise when sampling of the density field. Building on the phase space sheet (PSS) interpretation of Abel, Hahn and Kaehler (2012) of cold collisionless fluid, I develop a method for geometrically exact and robust volume- and point-sampling algorithms. These operate on a simplicial tessellation of a 3-manifold embedded in the 6-D phase space, such that the mass is interpolated between particles, which are interpreted as Langrangian flow tracers. This results in a smooth continuous and noise free density field that aids accurate interpretations of cosmological dark matter simulations. I discuss the application of these algorithmic developments to the indirect detection of dark matter (via decay and annihilation), studies of cosmic voids, the cosmic neutrino background, and simulations. I also present recent work on extending these concepts to radiation transport with "adaptive beam tracing." This method extends ray-tracing, which follows 1-dimensional rays along their trajectories, to beam tracing, which instead volume-samples 3-D photon packets called "beams".

Keywords: Physics.
Advisor: Abel Tom G.
Madejski Grzegorz
Wechsler Risa H. (Risa Heyrman)
Exploring social and linguistic diversity across African Americans from Rochester, New York

Linguists have problematized the presentation of African American English (AAE) as a uniform variety (Wolfram 2007; Yaeger-Dror & Thomas 2010). My work advances the discussion by examining social and linguistic diversity across African Americans' speech. I examine how linguistic heterogeneity can arise from differences in identity constructions, which are informed by social changes in the community, Rochester, New York. Specifically, I ask how sound change is enacted through personae like the Mobile Black Professional and the Hood Kid. Results indicate that in comparison to other community speakers, Mobile Black Professionals produce significantly lower TRAP tokens and Hood Kids produce significantly backer BOUGHT tokens. The findings demonstrate that African American language and identity are not monolithic.

Keywords: Linguistics.
Advisor: Eckert Penelope 
Rickford John R.
Podesva Robert 
Sumner Meghan
Exploring the evolution of animal cell adhesion mechanisms : characterization of the cadherin-catenin complex of the sea anemone, nematostella vectensis

This dissertation investigates the evolution of cell-cell adhesion in animals. Cell-cell adhesion is the process by which cells interact and attach to neighboring cells through specialized protein complexes, and it is a fundamental necessity for the formation and integrity of tissues. Cell adhesion is therefore a universal property of all multicellular organisms, and represents a profound novelty that was likely coincident with the origin of animal multicellularity. Yet despite its necessity for the formation of multicellular structures, there is surprising diversity in the mechanisms by which cells adhere to one another across the different lineages of multicellular eukaryotic life (e.g., animals, plants, and fungi). In this dissertation, I test whether one specialized protein complex, the cadherin-catenin complex, is a deeply conserved cell-cell adhesion module in animals. In this work, I focus on the extant non-bilaterian animals, which are the living representatives of some of the earliest branches of the animal tree of life, and thus provide important phylogenetic context for testing hypotheses surrounding the evolution of cell-cell adhesion in early animals. Using a combination of biochemistry and functional genetic approaches, I show that a bonafide cadherin-catenin complex is present in the cnidarian sea anemone, Nematostella vectensis, and demonstrate that many of the properties of the complex known from vertebrates were likely present in the last common bilaterian-cnidarian ancestor. Specifically, I provide evidence that the complex can be reconstituted from its purified components in vitro, and demonstrate that it is necessary for cell-cell adhesion and embryogenesis in the anemone embryo. In another line of evidence, I examine the structure and function of vinculin, a catenin-like adhesion protein, in the sea sponge Oscarella pearsei. I provide evidence that sponge tissues are organized like true epithelial tissues found in other animals with cadherin-catenin-associated junctional complexes, and that many of the properties of vinculin are conserved between sponges and bilaterian animals. Taken together, these data suggest that the properties of the cadherin-catenin complex are deeply conserved in animals, and support the notion that cadherin-catenin-mediated cell-cell adhesion may extend to the earliest periods of animal evolution.

Keywords: Biology.
Advisor: Lowe Christopher (Associate professor of biology) 
Nelson W. J. (W. James)
Simon Michael (Biology professor) 
Weis William I.
Exploring the genetic basis of microbial dehalogenation

The role of microbial dehalogenation in the absence of anthropogenic compounds and its effect on the global halogen cycle is an interesting ecological question in and of itself. Furthermore, answering this question can help us mitigate the significant impact of anthropogenic organohalogens on environmental and human health. Detailed investigation into the acquisition, stability, and propagation of genes related to dehalogenating phenotypes is a key component to exploiting the natural halogen cycle for bioremediation of these contaminants. Through in-depth comparative genomic analyses, this dissertation provides insights into the evolution of organohalide respiration in Dehalococcoides spp. and cometabolic carbon tetrachloride mineralization with Pseudomonas stutzeri KC, providing crucial knowledge that can be applied to the bioremediation of anthropogenic organohalogens.

Advisor: Criddle Craig 
Francis Christopher 
Spormann Alfred M. 
Welander Paula
Exploring the regulatory genome in melanoma innate resistance

Targeted therapy for cancer treatment has been confronted with acquired resistance. In metastatic melanoma, for many years conventional chemotherapy and radiation were the common treatment options. The first generation of targeted therapy against BRAFV600E, a mutation found in about 50% of metastatic melanoma, revolutionized standard treatment. This first generation targeted therapy, Vemurafenib, resulted in > 50% clinical response in the first few months of treatment. Unfortunately, drug resistance to this therapy occurs about six months to a year after treatment. Subsequently, numerous genome sequencing studies on Vemurafenib-resistant melanomas identified extensive acquired DNA mutations that up-regulate components of the MAPK signaling pathway, therefore effectively re-wiring around the initial BRAF inhibition. It is hypothesized that during targeted therapy, cancer cells initially engage an innate resistance program to survive, in order to generate secondary DNA mutations in the same pathway to be resistant to the targeted therapy (acquired resistance). Recent studies have shown that HGF in the tumor microenvironment is important for cell survival on targeted BRAF therapy. This suggest that melanoma cells must have drug response and pro-survival mechanisms, including the MET signaling pathway. Using an integrated genomics approach, we identified a dynamic genomic interaction between the MET TSS and a lineage-specific enhancer 63kb downstream during targeted BRAF inhibition. This dynamic interaction is further mediated by the melanocyte lineage master transcription factor, MITF. MITF pro-differentiation and tumorigenic function can be uncoupled by selective editing of the MET specific enhancer. This initial study showed the importance of looking at distal regulatory elements in dynamic cellular responses such as cellular reprogramming in response to drug treatment. We extended this initial study of the MET locus to look at global dynamic regulatory changes. We assessed the global open chromatin dynamics and transcriptomic changes during acute BRAF inhibition and MITF depletion. Using a statistical framework, we generated a global regulatory network of important transcriptional regulators during targeted BRAF inhibition in melanoma cells treated with vemurafenib (PLX4032). Focusing on the MITF sub-network can help identify putative MITF transcriptional co-regulators and parallel pathways during acute oncogenic signaling inhibition.

Advisor: Khavari Paul A. 
Mallick Parag
Oro Anthony
Sage Julien
Exploring the rheological properties of the upper mantle : from the field to the laboratory

The ductile deformation and flow of the upper mantle controls a wide variety of geologic phenomena, including the flexure of plates below glaciers, the formation of new plate boundaries, and the movement of tectonic plates. Olivine, the main mineral of the upper mantle, controls mantle deformation behavior, responding differently to applied stresses depending on the deformation conditions (including temperature, pressure, and composition). This dissertation provides constraints on the rheological properties of the Earth's upper mantle across multiple deformation regimes. In Chapter 1, I use nanoindentation experiments to show that the strength of olivine deforming at low temperatures and high stresses is controlled by its grain size, with smaller grains being stronger than larger grains. As the lithospheric mantle has a relatively large grain size, the mantle is likely weaker than many previous studies have suggested. Deformation throughout the lithosphere is sensitive to small concentrations of water, down to the parts per million level in olivine. Chapter 2 contains a comprehensive description of the methodology necessary for measuring water in the nominally anhydrous minerals of the upper mantle: olivine, orthopyroxene, and clinopyroxene. Using this methodology, I measured water in samples from ductile shear zones in the Josephine Peridotite. In Chapter 3, I examine the relationship between water content and the lattice preferred orientation (LPO) of olivine. Previous experiments found that olivine LPO, and thus the dominant active slip system, changes with increasing water content. However, my measurements suggest that the olivine LPO in the shear zones does not vary as a function of water content, and I use micromechanical modeling to show that deformation kinematics can drive the observed LPO changes. Chapter 4 then examines the role of water in shear localization in the same set of shear zones. While water concentrations are elevated relative to other peridotite settings like mid-ocean ridges, my geochemical data indicate that melt was the initial factor that led to shear localization.

Keywords: Geological Sciences.
Advisor: Mao Wendy (Wendy Li-wen) 
Warren Jessica
Grove Marty
Pollard David D.
Exploring Visual Memory Formation in Drosophila melanogaster

Visual memories represent fundamental elements of our daily experience. However, the circuit mechanisms underpinning visual learning remain unknown in any system. This work develops a series of behavioral paradigms to determine whether Drosophila melanogaster operant conditioning can be used to train flies to discriminate between different patterns of visual motion. Such visual discrimination would demonstrate that Drosophila have the ability to learn visual cues, a necessary step to dissecting the circuit mechanisms that underpin visual learning using the powerful toolkit available in this animal. However, we were unable to demonstrate visually learning under any of the conditions tested. Thus it remains unclear whether Drosophila are capable of visual learning.

Keywords: Neuroscience
Drosophila melanogaster
Biology
Learning and memory
vision
behavior
Thesis
Advisor: Clandinin Thomas
Luo Liqun
Extracellular matrix mechanical plasticity regulates cancer cell migration through confining microenvironments

Breast cancer cells must invade and migrate through nanoporous basement membranes (BM) and dense stromal tissue to metastasize during ductal carcinoma progression. Studies of cancer cell migration have shown that there are two modes: one that is protease-dependent, involving cells degrading matrix with invadopodia, and one that is protease-independent, requiring micron-sized pores or pre-existing channels for cells to squeeze through. Invasion of the BM is thought to require protease degradation, due to its confining, nanometer-sized pores. However, many studies investigating how pore size limits invasion have utilized rigid or elastic pores. By contrast, many extracellular matrices (ECM) exhibit viscoelasticity and mechanical plasticity, irreversibly deforming in response to force, so that pore size may be malleable. Here, we examined the impact of matrix mechanical plasticity on cancer invasion in confining microenvironments. We developed nanoporous and BM ligand-presenting, interpenetrating network (IPN) hydrogels for 3D culture in which plasticity could be modulated independent of stiffness and ligand concentration. Strikingly, cells in high plasticity IPNs exhibited spread morphologies and carried out protease-independent migration, while cells in low plasticity IPNs stayed rounded and did not migrate. Mechanistically, cells in high plasticity IPNs cyclically extended invadopodia, which were identified by their Tks5 dependence as well as their Tks5-actin and cortactin-actin colocalization. Cells used invadopodia, which were several microns wide and on the order of 20 microns long, to exert contractile and protrusive forces on the matrix and mechanically open up lasting channels within the matrix. These reveal a function of invadopodia in generating force, independent of their function in matrix degradation. Cells migrated only after channels were about 2-3 microns wide, which is the width required for the nucleus to deform through an opening during migration. Rac1 and Arp 2/3 mediated cellular protrusivity, while Rho-mediated actomyosin contractility was additionally required for cells to squeeze through the openings they formed. Finally, cells generated protrusive forces at the leading edge during migration. These findings uncover a new mode of protease-independent migration in which cells can migrate through confining matrix if it exhibits sufficient mechanical plasticity. Human breast cancer tissue, and the biological ECMs reconstituted basement membrane matrix and collagen-1, were all found to exhibit substantial mechanical plasticity, indicating the physiological relevance of this migration mode. Broadly, these results establish plasticity, a mechanical property distinct from stiffness, as an important regulator of cancer cell invasion and metastasis.

Keywords: Mechanical Engineering.
Advisor: Chaudhuri Ovijit 
Heilshorn Sarah 
Levenston Marc Elliot
Extremal Kerr Entropy and the Attractor Mechanism

One of string theory's greatest successes has been its ability to provide a microscopic description for a large class of black holes, such that the thermodynamic entropy of those black holes can be reproduced at weak coupling by counting microstates. However, almost all such black holes exhibit supersymmetry, which does not manifest in our observable universe. On the other hand, non-supersymmetric black holes are usually too un-constrained and complicated to obtain a microscopic description. In between the two ends of the unphysical-complex spectrum lie extremal black holes, which are black holes that saturate the cosmic-censorship-required lower bound on their mass arising from their angular momentum or charge. Such black holes are not supersymmetric, but are constrained enough that a microscopic description in string theory is possible. The extremality condition also leads to attractor behavior, in which the asymptotic moduli of the theory are drawn to fixed values at the event horizon, determined only by the quantized charges of the black hole.
In this thesis, we review the string-theoretic description of the extremal Kerr black hole, and how that description can be used to compute the solution's statistical entropy at weak coupling. We then extend that work by applying the attractor mechanism to explain why the entropy at weak coupling matches the thermodynamic entropy at strong coupling.

Keywords:  Department of Physics
physics
senior thesis
black hole
extremal
Kerr
attractor mechanism
entropy
Thesis
Advisor: Kachru Shamit
Hartnoll Sean
Fabrication of efficient monolithic perovskite tandem solar cells with improved environmental stability

In under an hour and a half, the sun illuminates the world with enough energy to meet our yearly global energy consumption. And yet, while the world's installed solar capacity tripled from 2012 to 2016, only 1.3% of global energy demands are met by solar. Increasing efficiency is one of the most promising paths to lowering system costs and drive further solar adoption in a heavily commoditized energy market. As the record single-junction efficiencies of perovskite solar cells now rival those of CIGS, CdTe, and the incumbent crystalline silicon, they are becoming increasingly attractive for use in tandem solar cells, due to their wide, tunable bandgap and solution processability. Tandems offers a pathway to surpassing fundamental efficiency limits on single-junction solar cells by extracting a portion of photo-generated carriers at a higher voltage and thus enabling the realization of the next generation of low cost photovoltaic cells. However, poor environmental stability presides as the Achilles heel of perovskites as they are susceptible to moisture ingress, methylammonium iodide egress, and corrosion of metal electrodes by reaction with halides in the perovskite. Additionally, while the bandgap of perovskites can be continuously tuned between 1.5 and 2.3eV by the substitution of bromide for iodide, open circuit voltages have not increased linearly with bandgap, largely negating the benefit of bandgap tuning. This dissertation will begin by focusing on the development of transparent and functional barrier layers to achieve efficient semi-transparent solar cells for use in tandems and simultaneously address the notoriously poor thermal and environmental stability of perovskites. I will show how the combination of a functional barrier layer and a transparent indium tin oxide electrode present a holistic solution to suppressing the three fastest degradation mechanisms in perovskite devices. This enables us to package our devices and pass several industry standard IEC solar cell stability tests. Next, I will present how compositional engineering can be employed to mitigate the effects of one of the primary causing of voltage loss -- halide segregation -- and achieve tandem relevant bandgaps of 1.68eV and 1.75eV. By fabricating our optimized 1.68eV bandgap perovskite with the window layer described previously on top of a heterojunction silicon solar cell, we achieve a record 25% efficient perovskite/silicon tandem. This combination of improved efficiency and stability represents an exciting step forward in achieving commercially viable perovskite tandem solar cells.

Keywords: Materials Science and Engineering.
Advisor: Dauskardt R. H. (Reinhold H.) 
McGehee Michael
Bent Stacey
Factorization theory of Thom spectra, twists, and duality

This thesis includes two related projects. The first project determines the factorization homology of Thom spectra of n-fold loop maps, and uses this to study the topological Hochschild cohomology of such Thom spectra. Our description of the factorization homology of Thom spectra can be viewed as a twisted form of the non-abelian Poincare duality theorem of Segal, Salvatore, and Lurie, and permits calculations of factorization homology of cobordism spectra and certain Eilenberg-MacLane spectra. Our description of the Hochschild cohomology of these Thom spectra enables calculations and a description in terms of sections of a parametrized spectrum. This allows us to deduce a duality between topological Hochschild homology and topological Hochschild cohomology, and gives ring structures on a certain family of Thom spectra, which were not previously known to be ring spectra. The second project is joint work with Ralph Cohen in which we import the theory of ``Calabi-Yau" algebras and categories from symplectic topology and topological field theories to the setting of spectra. We define two types of Calabi-Yau structures in the setting of ring spectra: one that applies to compact algebras and one that applies to smooth algebras. We apply this theory to describe, prove, and explain a duality between the manifold string topology of Chas and Sullivan and the Lie group string topology of Chataur-Menichi. Using results from the first project in this thesis, we prove that Thom ring spectra of (virtual) bundles over the loop space of a manifold have a Calabi-Yau structure. In the case when the manifold is a sphere, we use this structure to study Lagrangian immersions of the sphere into its cotangent bundle, recasting work of Abouzaid and Kragh.

Keywords: Mathematics.
Advisor: Cohen Ralph L.
Carlsson G. (Gunnar)
Galatius Søren
Failing feedback : evaluation in residency training

Research on expertise development suggests that feedback is a critical component for effective deliberate practice. In complex domains that require adaptive expertise, the quality and implementation of feedback is understudied. This dissertation examines residency education as a case study for feedback in apprenticeship models. A combination of milestone score, narrative comment, evaluator characteristic, student evaluation, and interview data was collected and analyzed for ten residency programs across three training institutions from 2013-2017. Part 1 describes the low assessment reliability and low feedback quality of end-of-rotation milestone scores and narrative comments. This section also presents a novel set of automated tools for assessing feedback quality in residency programs and documents significant variation among evaluators across these feedback metrics. Part 2 tests explanations for variation among evaluators and concludes that evaluator characteristics such as teaching and training experience are not as important as the motivation and incentive systems built into clinical education programs. Part 3 implements an intervention in three residency programs that improves narrative comment specificity and valence in an eight-week post-intervention period. Despite minimal improvement in milestone scores, this study demonstrates the utility of the feedback metric tools for measuring intervention efficacy. We conclude this dissertation with a discussion of recommendations for residency programs seeking to improve their own feedback along with future research directions.

Keywords: Education.
Advisor: Wieman C. E. (Carl Edwin) 
Schwartz Daniel L. 
Tanaka Pedro Paulo