VictorJuiz/thesis huggingface dataset:
Masters of the post : Northern Italy and European communications networks, 1530-1730

Masters of the Post demonstrates how the postal systems of Northern Italy contributed technology, personnel, and an ethical framework to the formation of the first global communications systems. The Tassis family and other residents of a single Alpine valley wielded disproportionate power as the agents of private and public correspondence. This dynasty of postmasters and postmistresses rose to Imperial titles as the House of Thurn und Taxis, but also served the Papacy, Venetian republic, and Spanish monarchy. Using archives in Italy, Spain, Germany and the United Kingdom, I retrace the systems that carried the correspondence of the early modern world. Scholarship on early modern communications has emphasized the technological improvements brought by postal waystations and roads. I reintroduce agents of infrastructure, exploring how the professionalization of mail carrying fit into a burgeoning bureaucracy and changing notions of public service. From diplomatic espionage to attacks on couriers, control over the mail saw the early modern state articulating new powers of surveillance, policing, and information security. Even the apparent failures of these efforts provide key insights into shifting expectations of the state in society, and the highly contingent development of a state postal system. Masters of the Post advances scholarship on the history of early modern commerce and statecraft. The postmaster was one of many quasi-state actors who traded in "intelligencing, " or the handling of politically sensitive information. While a confidante for princes, the postmaster was nonetheless frequently suspected of being a spy. Professional necessity drove the representation of state agents as impartial public servants. From the diplomatic fallout resulting from the 1556 political imprisonment of the Tassis postmaster in Rome, to the 1619 audit of the Tassis postmistress of Milan, accused of serving powerful Genoese businessmen before the state, the distinction between private and public interest was in constant negotiation. Consequently, professionalization of the postmaster adds important nuance to traditional models of bureaucratization in early modern Europe.The real and imagined worlds of long-distance communication overlapped, interacted, and diverged in literature and cartography. The public accessibility of the post raised new concerns about its potential for radical social impact. Like the mailbag, postal coaches, roads, and inns provided new settings for cross-cultural encounter. I turn to dictionaries, guidebooks, journals and other popular works to demonstrate how postal systems shaped commerce, communication, and tourism. Modern travelers and correspondent brought high expectation to postal systems as a utility that mediated between state power and commercial society. By following postal development into the eighteenth century, I demonstrate the reinvention of postal history as domestic infrastructural achievement and the Tassis as nonpartisan patrons

Keywords: History.
Advisor: Findlen Paula
Como David R.
Stokes Laura
De Vivo Filippo
Matrix estimation with adaptive samples

Datasets commonly have missing values, and in many applications, such as recommendation systems, supervised learning, and causal inference, the data can be modeled as a partially observed matrix and the missing values are imputed via a matrix estimation procedure. Most prior literature focuses on the case when samples are missing uniformly at random. However, in certain applications, the decision-maker can choose which entries of the matrix are observed. In the first part of this dissertation, we show theoretical guarantees on column space recovery of a matrix that is growing in one dimension (new columns are added), where the decision-maker can observe a small number of entries of each column, using either random or active sampling. We demonstrate that the theoretically-motivated active sampling strategy can empirically lead to better estimation of not only the column space, but of the entire matrix. In the second part of this dissertation, we study a related problem where the decision of which entries of each new column to observe is modeled as a multi-armed semi-bandit problem, where we allow the decision-maker to choose multiple actions in each round. We use our matrix estimation techniques to provide regret guarantees when the arm selection is performed via the well-known Thompson sampling framework

Advisor: Bayati Mohsen 
Leskovec Jurij
Baiocchi Michael
Brunskill Emma
Mean field limit in neural network learning : autoencoders and multilayer networks

A major outstanding theoretical challenge in deep learning is the understanding of the learning dynamics of neural networks. The difficulty arises from the highly nonlinear and large-scaled structure of the network architecture, usually involving a large number of neurons at each layer, and the non-convex nature of the optimization problem, typically solved by convexity-inspired gradient-based learning rules without any strong guarantees. This begs two questions: Given such complex nature, is it possible to obtain a succinct description of the network's behavior over the course of training? If so, could it be used to shed light on properties of the learning process of neural networks? We explore these questions in a scaling limit regime that gives rise to one such description: the mean field limit. In this regime, the number of neurons is taken to infinity, and yet the network's behavior under gradient descent training converges to a nontrivial and nonlinear dynamical limit. The literature of the mean field limit for neural networks is fairly recent and has focused on two-layer feedforward networks. In this thesis, we analyze the mean field limit for two other important classes of models: weight-tied two-layer autoencoders and multilayer networks. The class of autoencoders constitutes a unique example of two-layer neural networks for unsupervised learning. It is among the rare instances known till date that we can derive an explicit solution to the mean field limit. This allows us to gain in-depth understanding of what the model learns about the high-dimensional data. The derived theory offers a striking match with empirical simulations on real life data. This example also gives rise to a challenging mathematical problem that deviates from previous analyses and inspires a new proof technique, as well as an open conjecture. The class of multilayer neural networks is the main thrust behind the recent breakthrough of deep learning. Being fundamentally different from the two-layer counterpart, it requires completely new ideas and insights. We show the existence of the mean field limit for this class of models via two approaches. In the first approach, we develop a formalism with a new idea on the operational meaning of the neurons, which is a priori unobservable but allows to reason for the existence of a mean field limit. In the second approach, we develop a mathematically rigorous framework which is used to prove properties of multilayer networks under training, with a new idea on a continuum that interpolates from finiteness to infinitude. In both of these approaches, we see a complete departure from the convex paradigm and welcome new insights that are uniquely of neural networks

Keywords: Electrical Engineering.
Advisor: Montanari Andrea
Özgür Ayfer 
Tse David
Mean field model for knowledge propagation and economic growth

My dissertation research is on the mathematical analysis of systems of partial differential equations that arise in modeling the equilibrium of mean filed games. I study the existence of traveling wave solutions of such systems and the large time behavior of the associated time dependent problem. Mean field models are used in optimal decision making based on stochastic games with a very large population of agents that are statistically the same. The main advantage of such models is that the overall effect of the other agents on a single one can be replaced by an averaged effect. Hence, the dynamics of a single agent can be determined as a solution of an optimal control problem that depends on the overall distribution of the agents. These models are governed by two partial differential equations, a forward Kolmogorov equation that keeps track of the distribution of agents in the model, and a backward Hamilton Jacobi Bellman (HJB) equation for the value function of the optimal stochastic control problem for each agent. An equilibrium solution to this mean field problem is a solution of the coupled system of the two equations. In my study I focus on an a mean field model for knowledge propagation and economic growth in which interaction between agents is represented by collisions and has diffusion added, in order to get a more realistic model for knowledge propagation. The equilibrium solution of such a mean field model is the solution of a Boltzmann equation for the agent distribution coupled to an HJB equation for the optimal strategy for the control problem. I have studied the existence of a BGP solution of the mean field learning model with diffusion in logarithmic variables. Such a solution can be considered as a generalization of traveling wave solutions of a system of Fisher-KPP (Fisher- Kolmogorov, Petrovsky, Piskunov) type of equation and an HJB equation. In Chapter 2 I prove that a traveling wave solution of the mean field learning model with diffusion exists and I have explored it numerically. The method that is used to construct traveling wave solutions is a variation of a well known method for the construction of traveling wave solutions of Fisher-KPP type equations. The numerical results that I have obtained in Chapter 4 support and extend the theory as many features observed numerically can be proved analytically. I have also studied analytically and numerically the forward-backward system, supplemented by an initial condition for the Fisher-KPP type of equation and a terminal condition for the HJB equation. In chapter 3 I have proved existence of solutions for a fixed terminal time T . In Chapter 4 I have tested the stability of the traveling wave numerically, by using perturbed traveling wave profiles for the initial value and I found that as time increases the solution of the time dependent problem tends to the traveling wave profiles

Keywords: Mathematics.
Advisor: Papanicolaou George 
Ryzhik Leonid 
Ying Lexing
Measurement of the polarization of the cosmic microwave background with BICEP3 and the keck array telescopes

The Cosmic Microwave Background (CMB) shows the afterglow image of the Big Bang, providing a window to probe the very early Universe. The CMB encodes the information in the temperature and polarization fluctuations. BICEP3 and the Keck Array telescopes are small aperture refracting telescopes at the South Pole to measure the B-mode polarization of the CMB at the degree angular scales, which holds a key to probe inflation theory. This dissertation presents the progress of the BICEP/Keck Array telescopes on measuring the B modes and the recent test of low elevation observation with BICEP3 to expand its sky coverage at the South Pole. The BICEP/Keck Array telescopes produced the tightest constraint to the power of primordial B-modes, parameterized by the tensor-to-scalar ratio, r, to be less than 0.07 at 95% confidence with the one sigma uncertainty in r about 0.02, using polarization data up to 2015 observing season. BICEP3 was fully deployed for 2016 observing season and has been operating since. Together with the Keck Array telescopes operating at higher frequencies, we expect to achieve the one sigma uncertainty in r about 0.01 from data up to 2018 observing season. During the austral summer of 2018-19, we tested the feasibility of using BICEP3 to observe the CMB at a low elevation at the South Pole. Due to operational constraints, we had to use a flat mirror to direct the beams to the low elevation range. We obtained additional data at the end of the 2019 winter observing season. We present the temperature and polarization maps from this data set, which clearly shows the detection of the E mode polarization. This potentially opens an opportunity to cover an extended patch of the sky at the South Pole. If the primordial B-mode is detected at the main observing field, probing larger areas will reduce sample variance. Larger observing field is also important to study the non-Gaussianity and decorrelation of the foregrounds. An interesting patch in this extended region is the CMB Cold Spot, whose origin is still in question. The possibility of testing polarization anomaly deviating from the standard Gaussian fluctuation around the Cold Spot is discussed

Keywords: Physics.
Advisor: Kuo Chao-Lin (Physics professor) 
Allen Steven W. (Steven Ward) 
Church Sarah Elizabeth
Measuring the catalytic impact of nonresonant, pulsed radiation on reactions in the gas and solution phases

Light exists as a propagating wave of electric and magnetic fields. Exploration of the interactions between resonant light and matter has provided us with a wealth of structural and dynamical information. Largely overlooked, however, is the impact of nonresonant radiation which, when introduced into a reaction system from an intense, pulsed laser beam, may induce changes in the system through its associated strong electric field. At field strengths of 10 MV/cm, off-resonant radiation can influence the course of a reaction by interacting with the molecular system's polarizability, α, to lower an activation barrier directly. Because there is no net consumption of nonresonant photons, they behave as catalysts rather than reactants in a process referred to as "laser-field catalysis, " or "photon catalysis." In the experimental work presented in this dissertation, I investigate the impact(s) of a nonresonant IR field (1064 nm) on photoreactions in both the gas and solution phases: the photodissociation of deuterium iodide (gas), the photodissociation of phenol (gas), and the photoisomerization of cis-stilbene to trans-stilbene (solution). Two possible roles of the electric field, alignment of reagent molecules and dynamic Stark shifting of potential energy surfaces, are considered. Theoretical calculations are used to support experimental interpretation of results

Keywords: Chemistry.
Advisor: Martinez Todd J. (Todd Joseph)
Zare Richard N. 
Bent Stacey
Mechanics of thin film systems and the impact of external factors on underlying function

Thin films surround us in more ways than one. From the devices in our phones to the skin on our bodies, thin films are everywhere. In my PhD work, I delved deep into the critical roles that these films play in our everyday life. First, I look at how our skin can effect our perception through tactile interactions with ourselves and the world around us. By applying cosmetic treatments, we can explore how changing biomechanical properties affect these neurological perceptions. Next, I demonstrate how thin film measurement methods used for inorganic films can be useful tools for exploring questions relevant to medicine and biomechanics. Finally, I apply similar methods to in situ characterization of novel solar absorbing films showing how applicable these thin film techniques can be to a wide range of material systems. In exploring skin mechanics, I will show how moisturizing and cleanser treatments can cause measurable changes in comfort for users. Then, I compare these results were compared to ex-vivo peak drying stress measurements and correlations of r(9) = -.88, p < .01 for moisturizers and r(6) = -.99, p < .01 for cleansers are shown. Finally, I develop a computational model was to demonstrate the transmission of SC drying stresses as strain fields to the lower receptor-laden layers of skin. These strain distributions suggest heightened mechanoreceptor activation correlated with stresses in the SC. Next, I show in different cardiovascular systems how bulge testing can be a useful tool for evaluating recovery of tissue. I demonstrate how mouse heart regeneration can be demonstrated from a functional perspective by measuring the modulus with bulge testing post infarction. Next, I am able to demonstrate key empirical evidence of heightened leaflet degradation in porcine leaflets when subjected to ex vivo testing modeling the Ross procedure. Finally, I will demonstrate the importance of thermomechanics when evaluating solar absorber behavior. Novel mechanisms for efficiency improvements are all the rage, but without proper controls, the results can often be misleading. By leveraging thin film systems developed for studying drying, Im able to show that key findings related to light induced expansion are fully explainable by thermal effects

Keywords: Materials Science and Engineering.
Advisor: Dauskardt R. H. (Reinhold H.)
The mechanism of helix-based docking between cyclin D-Cdk4,6 and the retinoblastoma protein

The cyclin-dependent kinases Cdk4 and Cdk6 form complexes with D-type cyclins to drive cell proliferation. A well-known target of cyclin D-Cdk4,6 is the retinoblastoma protein, Rb, which inhibits cell cycle progression until its inactivation by phosphorylation. However, the role of Rb phosphorylation by cyclin D-Cdk4,6 in cell-cycle progression is unresolved because Rb can be phosphorylated by other cyclin-Cdks and cyclin D-Cdk4,6 has other targets involved in cell division. In this dissertation, I describe the work and discoveries that I, the Skotheim lab, and many collaborators have made. We first examine the Rb protein for unique cyclin docking interactions (Chapter 2) and show that cyclin D-Cdk4,6 docks one side of an alpha helix in the Rb C-terminus, which is not recognized by cyclins E, A, and B. This helix-based docking mechanism is shared by the p107 and p130 Rb-family members across metazoans. Mutation of the Rb C-terminal helix prevents its phosphorylation, promotes G1 arrest, and enhances Rb's tumor suppressive function. We then examined the role of cyclin D in helix-based docking (Chapter 3) and identified the region on cyclin D1 responsible for helix-based docking of Rb. When helix-based docking is disrupted by mutation of the C-terminal cyclin box fold alpha2' helix on cyclin D1, Rb phosphorylation is lost and cells arrest in G1. This discovery identifies a role for the cyclin D C-terminal cyclin box fold substrate docking and another mechanism to potentially inhibit cyclin D-Cdk4,6 activity in cancer. More broadly, this work conclusively demonstrates that the cyclin D-Rb interaction drives cell division and expands the diversity of known cyclin-based protein docking mechanisms

Advisor: Skotheim Jan
Cyert Martha S.
Lipsick Joseph Steven
Sage Julien
Mechanism of smoothened regulation by the hedgehog receptor patched

The Hedgehog (Hh) signaling pathway plays a central role in controling cell growth, survival, fate, and patterning during embryogenesis. The primary receptor for the Hedgehog signal in mammals is the twelve-pass transmembrane protein Patched (PTCH1). In the absence of Hedgehog ligand, PTCH1 constitutively suppresses a downstream seven-pass transmembrane protein Smoothened (SMO), thereby maintaining the quiescence of the pathway. When Hedgehog binds to PTCH1, it blocks its activity, lifting its suppression of SMO and allowing SMO to activate downstream signaling events. Although the genetic relationship between Hh pathway components has been known for over two decades, the fundamental mechanism by which PTCH1 regulates SMO has remained a central question in the Hedgehog signaling field. Based on the observations that PTCH1 is homologous to the Resistance, Nodulation and Division (RND) family of chemiosmotically-driven bacterial transporters, which transport hydrophobic substrates, that SMO is modulated by a series of lipid- and sterol-like ligands, and that PTCH1 suppresses SMO sub-stoichiometrically and does not appear to form a stable complex with SMO, it has been proposed that PTCH1 may regulate SMO by acting as a chemiosmotically driven transmembrane transporter of a lipidic Smo modulator. In this thesis, I investigated the underlying mechanism by which PTCH1 regulates SMO through two parallel strands of research, enabled by novel structures of PTCH1 and SMO: (i) investigating the functional importance of transporter-like structural features of the PTCH1 protein, and (ii) determining how PTCH1-mediated changes in the level of cholesterol in the inner leafet lead to SMO activation

Keywords: Developmental Biology.
Advisor: Beachy Philip Arden 
Nusse Roel
Villeneuve Anne
Wysocka Joanna
Mechanistic metabolic interactions between gut microbiota and host

The trillions of bacteria inhabiting the mammalian gastrointestinal tract, known as the gut microbiota, comprise a diverse community and exert wide-ranging systemic effects on the host. Members of the microbiota harbor diverse metabolic capability, are able to consume substrates unavailable to the host, and produce molecules that are not encoded by the human genome. This biochemical cross-talk between microbes and host constitutes an important avenue for signaling between the microbiota and host and coevolution of the mutualistic relationship. As such, metabolism is a valuable lens through which to explore the host-microbe relationship. This work presents four mechanisms by which metabolic interactions shape the ways in which members of the gut microbiota and the host interact: 1) A new understanding for the ways in which the enteric pathogen Clostridium difficile leverages inflammation to alter its metabolic activity in the gut as well as 2) persist during homeostatic conditions. 3) A prebiotic that shapes the microbiota in ways beneficial to the host, and 4) a previously unidentified mechanism for host detoxification of microbially-produced metabolites

Keywords: Microbiology and Immunology.
Advisor: Sonnenburg Justin
Huang Kerwyn Casey
Monack Denise M. 
Spormann Alfred M.
Media production behavior on smartphones : time, content, structure, and context

People are producing lots of media. Digital media technology makes it easy for users to produce all sorts of content conveniently, anytime and anywhere. Understanding media production behavior is more pertinent than ever as more people produce different media in ways not possible even ten years ago. Although production behavior is a critical concept of communication research that interests many media scholars, we surprisingly know little about its specifics—how much production behavior is there? And how should it be described? This study explored production on the quintessential digital media device, the smartphone. Four aspects of production behavior on smartphones were examined: (1) patterns of production behavior over time; (2) content characteristics of production behavior; (3) the structure of production behavior; and (4) the context of production behavior. Using a novel framework for measuring moment-by-moment changes in digital behavior, this study looked into production behavior in different time domains and employed computational methods to generate behavioral measures and media categories. This study employed an inductive research strategy to describe patterns of use that should be important across a range of theories about digital life. A wide array of statistical modeling and testing techniques were used to identify intra- and inter-individual patterns of media production behavior. The results of this study help theorizing about digital communication processes, about patterns and functions of digital media use, and about digital media interaction

Keywords: Communication.
Advisor: Reeves Byron
Hamilton James
Hancock Jeff 
Robinson Thomas (Thomas N.)