VictorJuiz/thesis huggingface dataset:
Dens of tyranny and oppression [electronic resource] : the politics of imprisonment for debt in seventeenth-century London

This dissertation provides the first archival account of England's seventeenth-century prisons, uncovering their internal social structures, their place within wider society and their role in political conflict. As inmate populations swelled with debtors due to dramatic economic shifts and growing strain placed upon credit relations, prisons became hubs of social and political activity. In ever-closer quarters, prisoners lived, petitioned, rioted, participated in self-government and developed novel political arguments. Reacting against what they perceived as oppressive legal and prison systems, inmates proposed more equitable means of maintaining credit networks, and developed radical new models of social relations. This was particularly significant during the English Revolution, when imprisonment was increasingly equated with royal absolutism. Arguments against imprisonment for debt were first developed within inmate societies, but in the mid-seventeenth century entered into broader debates over authority and tyranny, intersecting with a radical political milieu that included John Lilburne and the Levellers during the English Revolution. These developments were contingent upon (and reactions against) both economic turbulence and experiences of the participatory processes that constituted the early modern state. Inmates were the casualties of new levels of economic instability and the increasing activity of an agonistic legal system, left at the mercy of gaolers whose offices operated at the intersection of self-interest and state power. Within this context, inmates developed novel critiques of legal systems (particularly imprisonment for debt) and the social order. Thus, this dissertation considers how direct engagements with the ligatures of the early modern state precipitated by rapid economic change and dislocation could produce friction and contention that was not simply a by-product of growing participation in governance and negotiation with authority, but a key experience in generating political dissent and opposition. In short, it explores how straining credit networks, swelling inmate populations and civil war reshaped early modern prisons and their social worlds, and the political resonances this had within and beyond the prison walls.

Keywords: History.
Advisor: Como David R.
Findlen Paula advisor. Thesis advisor
Stokes Laura
Depth perception in holography [electronic resource]

According to the holographic principle, information about our world can be encoded in a projection of one less dimension, similar to a hologram. This principle has culminated in the discovery of the AdS/CFT duality, an explicit example of holography where, miraculously, the lower-dimensional projection is a theory of familiar local fields. But how is the extra dimension encoded in this holographic theory? The equivalence between a gravitational theory and a lower-dimensional theory implies a radical reorganization of the degrees of freedom: the fundamental building blocks of a gravitational theory are likely extended, not point-like, objects. In this thesis, I describe progress towards formulating both sides of the duality in terms of extended probes -- objects which naturally possess the ability of "holographic depth perception.".

Keywords: Physics.
Advisor: Silverstein Eva
Hartnoll Sean
Kachru Shamit
Design and analysis of loyalty reward programs [electronic resource]

This thesis provides an in-depth analysis of two major components in the design of loyalty reward programs. First, we discuss the design of coalition loyalty programs - schemes where customers can earn and spend reward points across multiple merchant partners. And second, we conduct a model based comparison of a standalone loyalty reward program against traditional pricing - we theoretically characterize the conditions under which it is better to run a reward program within a competitive environment. Coalition loyalty programs are agreements between merchants allowing their customers to exchange reward points from one merchant to another at agreed upon exchange rates. Such exchanges lead to transfer of liabilities between merchant partners, which need to be frequently settled using payments. We first conduct an empirical investigation of existing coalitions, and formulate an analytical model of bargaining for merchant partners to agree upon the exchange rate and payment parameters. We show that our bargaining model produces networks that are close to optimal in terms of social welfare, in addition to cohering with empirical observations. Then, we introduce a novel alternate methodology for settling the transferred liabilities between merchants participating in a coalition. Our model has three interesting properties -- it is decentralized, arbitrage-proof, and fair against market power concentration -- which make it a real alternative to how settlements happen in coalition loyalty programs. Finally, we investigate the design of an optimal reward program for a merchant competing against a traditional pricing merchant, for varying customer populations, where customers measure their utility in rational economic terms. We assume customers are either myopic or strategic, and have a prior loyalty bias toward the reward program merchant, drawn from a known distribution. We show that for the reward program to perform better, it is necessary for a minimum fraction of the customer population to be strategic, and the loyalty bias distribution to be within an optimal range. This thesis is a useful read for marketers building promotional schemes within retail, researchers in the field of marketing and behavioral science, and companies investigating the intersection of customer behavior, loyalty, and virtual currencies.

Keywords: Management Science and Engineering.
Advisor: Goel Ashish primary advisor. Thesis advisor
Iancu Dan advisor. Thesis advisor
Johari Ramesh
Design and control of series elastic actuators for disturbance rejection [electronic resource]

Control abstractions allow robotic control systems to be built up layer upon layer. Each subsystem is considered independent, enforcing modularity, hierarchy, and clarity. At the foundation lie actuators, the source of force and motion. Ideally, actuators produce precisely the force or motion commanded, with no knowledge of the control layer above. But in reality, joints with elasticity couple the robot link dynamics to the actuator dynamics. In this thesis, we present the design and control of series elastic actuators (SEA) for disturbance rejection, in order to better realize uncoupled behavior. This thesis is presented in five parts. First, we introduce the concept of SEA, and show the importance of disturbance rejection for actuator abstraction. Current design and control practices have shortcomings with regard to multi-joint robotic systems. In order to treat actuators as ideal sources of commanded torque, we consider both the force response and disturbance response. Second, we review existing SEA controller design for torque control, and present a modification which simplifies control parameter tuning by reshaping the system's dynamics. The controller is validated on an experimental setup. Third, we describe the relevance and implications of disturbance rejection of SEA under closed-loop control. A new design and control methodology based on disturbance rejection is presented. One application of this methodology is ensuring hybrid actuation design and control synergy. Fourth, we present new mathematical models for reactive SEA dynamics, and an accompanying controller design. Reactive SEAs can produce higher bandwidth torque and can be easier to build. Four configuration of reactive SEA are compared to traditional SEA, in force response, disturbance response, and force measurement. The proposed controller reshapes the dynamics, similar to that proposed for traditional SEA. The methods proposed throughout this thesis for design and control of SEA provide tools for shaping SEA's interaction with external forces, and characterizing each actuators' behavior as an independent subsystem.

Keywords: Mechanical Engineering.
Advisor: Delp Scott primary advisor. Thesis advisor
Khatib Oussama advisor. Thesis advisor
The design, evaluation, and application of ultrasensitive nanoparticle contrast agents for high resolution functional in vivo imaging studies and preclinical diagnostics [electronic resource]

In this dissertation, I explore the use of noble metal nanoparticles called large gold nanorods (LGNRs) as exogenous contrast agents in conjunction with optical coherence tomography (OCT), a high-resolution biomedical imaging modality. First, I study surface chemical properties and modifications of LGNRs to adapt them for in vivo use and demonstrate their optical enhancements relative to nanorods of conventional proportions. Along with colleagues, I proceed to characterize concentration-dependent trends in OCT contrast produced by LGNRs (and scattering media in general); demonstrate spectrally-encoded detection of LGNRs in vivo to improve visualization of microvasculature in tumor models and enable functional mapping of lymphatic capillary networks; and leverage the porosity of intratumoral blood vessels to deliver LGNRs to the tumor stroma, whereupon they accumulate in tumor-associated leukocytes, effectively enabling immune cell tracking studies in solid tumors. In addition to contrast agent development and applications for in vivo imaging, I and colleagues report a method based on hyperspectral microscopy to explore the interactions between nanoparticles and mammalian tissues in ex vivo settings. The method, called HSM-AD, is proposed as a new approach for characterizing nanoparticle biodistribution. The research component of this dissertation concludes with the use of HSM-AD in conjunction with traditional biodistribution methods to yield data that may compel preclinical exploration of nanoparticle contrast agents in judiciously selected diagnostic instances. I conclude with a brief perspective on future directions of the reported work and a small reflection.

Advisor: De la Zerda Adam
Brandman Onn
Chu Steven
Moerner William
Designing crowdsourcing techniques based on expert creative practice [electronic resource]

Platforms like Amazon Mechanical Turk have made it possible for hundreds of people to come together to produce creative work at massive scale. Complex work is often managed by breaking down a large task into smaller subtasks; the sub-results produced by these subtasks are combined to create the final result. Projects like the Johnny Cash Project, for example, asked workers to draw individual frames which were combined to create a reinterpretation of a music video. Another commonly used technique to manage crowdsourced work is to build a workflow that connects individual tasks through concretely defined inputs and outputs. By splitting a larger work into smaller parts that can be completed independently, these crowdsourced workflows can often accomplish work more quickly or accurately than an individual. However, these techniques can only be applied to certain kinds of work: the task must be divisible into independent subtasks, which often means that subtasks are designed to help accomplish a predetermined desired outcome. As a result, crowds have difficulty completing tasks with complex interdependent parts (such as writing stories or composing music), because modifying one section may require changes in other sections of the work. Rather than splitting complex work into independent steps, what if we could enable the crowd to engage in a creative process that looks more like that of an expert? By doing this, we may expand the crowd's ability to work together on complex creative projects. This dissertation takes inspiration from expert creative practices to design new crowdsourcing and social computing techniques for accomplishing complex creative work online. These techniques are developed through three systems: Ensemble, Mechanical Novel, and Mosaic. In Ensemble, I use the practice of developing and revising constraints to split the task of writing a short fiction between a leader (who defines constraints and goals for a story) and the crowd (who executes works based on these goals). Mechanical Novel expands on this by studying how crowds can define high-level goals for themselves, without needing a central leader to coordinate work. Lastly, Mosaic generalizes this idea of designing collaborative systems based on expert practices by exploring design affordances for an online community that values non-traditional success outcomes such as early work, failure, and experimentation. These systems demonstrate how expert creative practices can be built into the design of collaborative creativity support tools, and show how designing for exploration can result in better creative outcomes than just focusing on success.

Advisor: Bernstein Michael S.
Agrawala Maneesh advisor. Thesis advisor
Dontcheva Mira
Determining rare state populations in nucleic acid ensembles [electronic resource]

Several features of nucleic acid behavior including RNA folding, protein-nucleic acid binding, and assembly of large nucleoprotein complexes (such as the ribosome or splicesosome) are dictated by the dynamic properties of nucleic acid molecules in solution. Understanding the properties of nucleic acids which influence their conformational landscape, and thereby their ability to engage in a multitude of functions, is an important biophysical challenge. While the methods of small angle X-ray scattering, Au-Au X-ray interferometry and nuclear magnetic resonance have enabled a characterization of the nucleic acid energy landscape, they do not allow for the characterization of low-populated states in the energy landscape. Low-populated states in nucleic acid energy landscapes play an important role because they represent intermediates in the molecules' folding pathway, and hence their identification and characterization could enable an understanding of higher order nucleic acid binding or assembly processes. In this work, a crosslinking approach has been employed to derive an understanding of low-populated states in the energy landscape of a nucleic acid. The crosslinking approach relies on using nucleic acid conjugated with a disulfide on one hand and a thiol modification on the other, which upon reaction result in the formation of nucleic acids crosslinked via a disulfide bridge. With this approach, the kinetics of disulfide bridge formation is measured and the populations in low-populated states, inferred. The crosslinking approach was applied to a number of nucleic acid motifs in order to provide a proof-of-principle that it can be employed to resolve differences in dynamics between them. The approach was extended to measure populations of molecules in low-populated states within nucleic acid ensembles, through estimations of an Effective Molarity (EM). The approach applied to a double-stranded DNA duplex showed that a large variation in EM for crosslink tether positions on the dsDNA duplex could be observed. When applied to double-stranded DNA duplexes linked by a polyethylene glycol (PEG) junction, relative populations within different subspaces of the molecule could be determined. The approach was also utilized to determine the dynamic circularization behavior of an RNA motif. The experiments described in this work indicate that the crosslink approach may indeed be useful to probe low-populated state populations in nucleic acid ensembles. It permits us to further our understanding of nucleic acid folding and higher order binding and assembly processes, since it opens us the possibility of isolating and characterizing low-populated states, which serve as intermediates in these processes.

Keywords: Chemical Engineering.
Advisor: Herschlag Daniel advisor. Thesis advisor
Khosla Chaitan
Spakowitz Andrew James advisor. Thesis advisor
Developing an instrumented mouthguard to study human mild traumatic brain injury [electronic resource]

Mild traumatic brain injury has been recognized as a silent epidemic, with seemingly transient acute symptoms but potential long-term irreversible brain changes. In more recent years, with increasing awareness of the dangers of concussive and subconcussive trauma, the condition is becoming less and less silent, but still remains invisible. It is known that external forces on the head cause injury, yet their exact effects on the brain are unknown. Although animal studies have helped uncover potential biomechanical mechanisms of injury, there is a lack of human data to confirm any hypotheses. In the current thesis work, an instrumented mouthguard was developed to optimize for kinematic accuracy and impact detection accuracy for the collection of high quality human data in contact sports. It was found that a mouthguard form factor provided tighter skull-coupling than soft tissue-mounted or headgear-mounted sensors. In addition, we identified sensor bandwidth requirements to ensure head impact kinematics are sufficiently captured for computing injury risk criteria. We also designed and validated a head impact detection system in both laboratory and field scenarios to accurately detect helmet contacts from other field activities. Applying the instrumented mouthguard in field studies helped to provide the first evidence of directional dependence of injury from human data, and linked subconcussive head impact exposure with neurological deficit. In the near future, human data gathered using the instrumented mouthguard can help better understand the mechanisms of mild traumatic brain injury, enable on-field real-time injury screening, and aid in the design of better preventative equipment.

Keywords: Bioengineering.
Advisor: Camarillo David primary advisor. Thesis advisor
Altman Russ advisor. Thesis advisor
Fan Jonathan Albert advisor. Thesis advisor
Grant Gerald
Kuhl Ellen
Developing modern tools for metabolic engineering in a non-traditional host [electronic resource] : fine-tuned protein production in Methanosarcina acetivorans C2A

New energy solutions are needed that are carbon independent or carbon neutral to curb the effects of global warming caused by burning fossil fuels to carbon dioxide. One carbon neutral energy technology that is gaining interest involves C1 fermentations using anaerobic microorganisms. In this process, hydrogen or carbon monoxide produced from clean, renewable technologies is mixed with carbon dioxide and transformed by anaerobic microorganisms into multi-carbon products, such as acetate and butanol. This process has the advantage to operate at high product specificity and yield at ambient temperature and pressures, which reduces the energy requirements for the process. In addition, there is opportunity for improved product yield and for tailored end product selection using metabolic engineering. However, metabolic engineering in these hosts has been challenging due to the lack of genetic tools available. This work developed tools for fine-tuned protein production that can be used for metabolic engineering in Methanosarcina acetivorans C2A, an Archaea capable of respiring carbon monoxide to produce acetate. First, a wide range of protein production was demonstrated through manipulation of basal transcription and translation regulation. In addition, the protein production range was further expanded by identifying new regulatory sequences in the 5' untranslated region. Finally, a CRIPSRi system was introduced for tunable repression of any gene in the genome. While the major protein components of the CRIPSRi system were functional in M. acetivorans C2A, further optimization is required to apply this system for metabolic engineering applications. The tools developed in this work for fine-tuned protein production will allow for the construction of more complex genetic circuits in M. acetivorans C2A and will be useful for metabolic engineering.

Advisor: Spormann Alfred M. primary advisor. Thesis advisor
Sattely Elizabeth advisor. Thesis advisor
Welander Paula advisor. Thesis advisor
Development and application of high-throughput sequencing based methods to explore human variation and disease [electronic resource]

In-depth studies of human disease and variation have been greatly enabled by a variety of high-throughput sequencing methods. Efforts that integrate genomic, transcriptomic and protein/nucleic acid binding genome-wide further expand our understanding of the genome and the regulatory information that governs it. In this work we present three efforts centered on the use of integrated high-throughput sequencing methods to unravel questions of human disease and variation. The first describes a novel method for simultaneous DNA and RNA sequencing library preparation (Simul-seq), which provides comprehensive data from small quantities of cells or tissue in a streamlined workflow. Single assay integration provides opportunities for analysis of regulatory variation, RNA editing and allele-specific expression, in addition to genotype and phenotype information. Applying Simul-seq to a laser-capture microdissected esophageal adenocarcinoma, we reveal a highly aneuploid genome with corresponding increases in allele specific expression and both novel and known expressed, nonsynomous mutations. The next work uses ChIP-seq, RNA-seq and Hi-C among other data types to enumerate the effects of genetic variation on chromatin state and RNA levels. Among the findings, we show that long-range interactions govern the effects of QTLs on distal chromatin variation. Finally we profile a diverse panel of 25 cell lines using an improved ChIA-PET method along with RNA-seq to better understand the role chromosomal looping plays in genetic and epigenetic regulation. Enabled by the modified protocol, we find evidence for differential looping between cell types. Taken together we have shown that integration of sequencing methods, or their data provide the best possible foundation for genome interpretation and personalized medicine.

Keywords: Genetics.
Advisor: Snyder Michael
Altman Russ advisor. Thesis advisor
Bustamante Carlos (Carlos D.) advisor. Thesis advisor
Urban Alexander E.