VictorJuiz/thesis huggingface dataset:
An RNA-based framework for cellular dynamic controls - towards building a genetic operational amplifier [electronic resource]
Keywords: Bioengineering.

Biological systems maintain functioning in dynamic environments by performing complex computations to determine proper responses. These "computation" processes can be decomposed and implemented by fundamental genetic controllers, such as amplifiers and differential sensors. Despite a growing number of examples of synthetic control systems, limited effort has been directed toward building a generalizable controller for such dynamic regulations. We proposed to design a genetic operational amplifier (gen-opamp), which can serve as a fundamental component for electronic circuit systems. This gen-opamp consists of three stages: a differential sensor, an amplifier, and an output stage. The differential sensor contains a molecular transducer that maps the inputs to mRNA levels, and an RNA antisense subtractor to perform differential calculation. The genetic differential signal is further amplified by a transcriptional device, which subsequently regulates the expression of an enzymatic output to form feedback loops. The non-feedback configuration of the gen-opamp functions simply as a comparator; whereas its feedback configuration acts as a level-setter that keeps the ratio of the inputs constant by actively adjusting one to the other. We designed a prototype gen-opamp in budding yeast, using theophylline and tetracycline as the inputs. The corresponding aptamer-coupled ribozymes (i.e., RNA switches) are used as molecular transducers to regulate mRNAs at 3' UTR, together with a mutual complementary sense-antisense pair (at 5' UTR) to achieve differential sensing. partially implemented this Two amplifiers are implemented using synthetic LexA- and TetR-based transcriptional devices, driving either an activator (caffeine demethylase) or deactivator (theophylline demethylase) to form enzymatic feedback loops targeting the theophylline level. We began by engineering and verifying biological parts in each stage of the gen-opamp, and further developed a model-facilitated approach to facilitate the assembly process of each stage (i.e., level-matching). We also built a multi-chamber chemostat that enables continuous growth and sampling for characterizing the dynamic regulations under closed-loop controls. We were able to partially assemble the gen-opamp (as an input-controlled amplifier) and achieved a gain on the order of 200. We further demonstrated how to this partially assembled amplifier to form closed-loop feedback, and were able to observe hysteresis effect on theophylline production (positive feedback) and relaxation effect (negative feedback). This thesis presented a strong groundwork for the full assembly of the designed gen-opamp, which is currently still in the process. Future work involves putting both feedback loops into a single system together with the RNA antisense to implement the gen-opamp.
The role of frontoparietal cortex in intertemporal choice [electronic resource]
Keywords: Psychology.

We often have to make decisions in which we need to choose between immediate satisfaction and an objectively better but also more delayed benefit. These decisions are not only pervasive. They determine our well being in major aspects of life, including health, education and finance. The goal of this dissertation is to clarify the cognitive and neural mechanisms that enable us to make this kind of decisions. To this end, two fundamental questions are addressed. First, how can our behavior be influenced by the subjective values that we place on future outcomes? Second, how are we able to forgo temptations that may bring greater pleasure on the short run, but impede the receipt of greater future rewards? The overall thesis defended over six chapters is that the cognitive processes by which we solve both of these problems are implemented by a functionally integrated network of frontoparietal regions in the cerebral cortex.
The role of joint visual attention in collaborative learning [electronic resource]
Keywords: Education.

It is a well-known fact that increased levels of joint attention are associated with interactions of higher quality among individuals of all ages: for instance between babies and their caregivers (Stern, 1977), students (Barron, 2003) and adults (Richardson & Dale, 2005). In this dissertation, I describe three original contributions to the study of joint visual attention (JVA) using eye-tracking technology. In the first study (Schneider & Pea, 2013), I demonstrate that pairs of students who were able to see the gaze of their partner in real-time on a screen collaborated better and learned more than their peers in a control group (who could not see the gaze of their partner). By doing so, I show that levels of JVA can be manipulated and increased to support collaborative learning in dyads of students. In the second study (Schneider & Pea, 2014), I further analyze this eye-tracking dataset by building networks where nodes represent moments of JVA and edges saccades between regions of interest; I then show how features of those networks have predictive value for differentiating between productive and unproductive collaborative groups. Finally, in the third study (Schneider, Sharma, Cuendet, Zufferey, Dillenbourg & Pea, accepted) I extend those results to a more challenging setting and describe a methodology to extract JVA measures in an in-situ collaboration (i.e., when students interacted with a Tangible User Interface; TUI): half of the students worked with a 2D, abstract-looking interface while the other half used a 3D, realistic-looking system. I found that students who were looking at the 3D version of the system had more moments of JVA, and that JVA measures were correlated with outcomes of interest (students' learning gains, their task performance and quality of collaboration). These findings suggest features of a learning environment (i.e., 2D vs. 3D) can be manipulated to affect students' level of JVA. In the last section of this dissertation, I discuss the aforementioned results and mention implications for designing new technologies to support small group interactions.
The saw and the seed [electronic resource] : Japanese forestry in colonial Korea, 1895-1945
Keywords: History.

This dissertation examines Japanese efforts to understand, rehabilitate, exploit, modernize, and showcase Korea's forests during the period of colonial rule (1910-1945). As a source of natural resources, a space of habitation, and a repository of rural traditions, Korea's woodlands formed a dynamic and highly contentious site of colonial governance. And yet, save for Korean- and Japanese-language studies on forestry policy, Korea's mountains and forests, which comprise more than 70 percent of the peninsula, remain a historiographical hinterland. Building on the growing body of comparative literature on the tangled roots of colonialism, scientific forestry, and conservationism, I argue that the forestry enterprise in colonial Korea was as concerned with the seed as it was with the saw: it placed afforestation and forest conservation at the heart of the colonial project to reform the Korean landscape and the ecological sensibilities of its inhabitants. Driven by utilitarian concerns about resource scarcity, a growing empire-wide demand for Korea's forest products, and fears of cascading environmental degradation, Japanese foresters set out in Korea to reclaim a peninsula routinely described as "a land of bald mountains and red earth." But forest reclamation in Korea was far from benevolent or benign: it siphoned off forestland to Japanese corporations and capitalists, cut off local communities from woodlands that had long sustained them, and placed vast tracts of commercially viable forests (especially those in the Yalu and Tumen River basins) under state control. Afforestation, in other words, was a process rife with conflict and fraught with contradiction. By chronicling the vicissitudes of this intensive, contested, and largely forgotten forestry project, I offer a case study in the promise and perils of natural resource management as it took shape in Japan's empire. Three principle lines of inquiry sustain my analysis. First, by surveying how, where, and when Korea's forests (and the range of resources therein) were utilized during the colonial period, I examine the materiality of modernization and the ecological implications of colonial rule. Second, through an examination of the mechanics and implementation of forestry policy, I map the contours of the politics of sustainability: a term that connotes the often-conflicting interests inherent to forest management and the myriad forces shaping forestry reforms (including bureaucratic conflict, geopolitics, peasant protest, and global markets). Third, by drawing attention to the interpenetration of forestry and everyday life, I explore the emergence in Korea of colonial ecological modernity: a concept that highlights how colonial forestry was not simply a process of modernization, but a far reaching and contested public campaign that touched the lives, values, and sensory experiences of residents across the peninsula.
Scalable software tools and methods for smart grid modeling and optimization [electronic resource]
Keywords: Electrical Engineering.

The electric grid in its current incarnation-- comprising utility companies, power system operators, market players and other agents-- is undergoing rapid change. Increasing adoption of distributed energy resources, electric vehicles, and demand response programs are adding further stress to the aging grid infrastructure. In order to realize the benefits of these new technologies, engineers need new tools to model and optimize the complex interactions. We address this need with GridSpice, a software framework with the computational scale and the modeling capability to represent diverse scenarios in large interconnected grid systems. GridSpice leverages existing best-in-class point tools and fuses them together in a modular architecture. The GridSpice framework is designed to run on the cloud, giving researchers and engineers the ability to elastically utilize many machines to perform complex simulations. After describing the GridSpice framework, we introduce a method to optimize centralized storage in wholesale markets. Specifically, this method maximizes the expected present value (PV) of an independently operated electric energy storage (EES) unit cooptimized to perform both energy arbitrage (EA) and regulation service (RS). The method is particularly suitable for fast-ramping EES units with a high power-to-capacity ratio, such as a grid-scale battery. The method is applied to two sample battery technologies using market data from the Independent Service Operator of New England (ISONE), illustrating how the cost and performance of storage technologies translates to financial returns. Next, we present a method for optimizing energy storage on a low voltage distribution grid with high penetrations of renewable distributed generation (RDGs). The method shows how intelligently storage can alleviate local volt/var violations, increase the maximum safe RDG penetration level, and simultaneously reduce the average cost of energy by shifting aggregate load from peak to off-peak hours (i.e., energy arbitrage). Finally, we show how to characterize the return on investment of storage and solar installations as a function of the technology parameters, penetration level, and limitations on the communication network.
Scalar transport in channel networks [electronic resource] : development of a particle tracking model to study the movement of scalars in the Sacramento - San Joaquin Delta
Keywords: Civil and Environmental Engineering.

A three dimensional particle tracking model (PTM) is developed to study the transport of scalars in a branched network of channels. The PTM is used to quantify the effects of different transport mechanisms in the Sacramento-San Joaquin delta (henceforth, the Delta) for various hydrological conditions. The paths taken by scalars and crucial branching points are identified. The different transport and mixing mechanisms are quantified by successively applying the PTM with tidal and cross-sectional flow structure removed and computing the differences between the results. Channel junctions are implemented using a streamline following mechanism of particle movements. It is found that the bifurcating and recombining junctions are critical to the transport of scalars in the Delta. The streamline following junction model produces more accurate results than the randomizing model. Secondly, in-channel transport and mixing mechanisms, which are strongly influenced by the upstream history of mixing along transport pathways do not contribute significantly to the transport of scalars in the Delta. The most important transport mechanism in the Delta is found to be the significantly increased dispersion through the junctions. Thirdly, tides dominate throughout the West, Central and North Delta, and hence the tidal flows and the mixing mechanisms induced by the tides are at least as important as mean river flows and mixing mechanisms due to mean flows. Lastly, parameters which incorporate the transport pathways are better able to quantify bulk Delta processes. Scalar fate is quantified using by developing and using new parameters such as cloud volume growth, particle pathway based residence times and dispersion coefficients and Delta mass balance. The Delta is defined as a set of simply connected interacting geographic regions with dominant transport mechanisms. Applications of the project include pollution mitigation, ecosystem restoration and habitat management, and the design of water quality standards.
Science in popular television [electronic resource] : comparing perspectives of middle school students, university students, and media makers
Keywords: Education.

Popular media influences the ideas about science constructed by the public, affecting outcomes such as scientific knowledge, the pipeline of future scientists, and the public engagement with science. A growing recognition of the impact of entertainment media has resulted in public policy organizations promoting the use of science consultants to influence television and film. Yet, even as the overall connection from consultants to popular media to public outcomes can be broadly inferred, the specifics of this chain of influence are not well understood. This study contributes to building this understanding though an integrated examination of the messages and plot intended by the media makers and consultants for one show and how these were 'read' and received by a range of audiences. To achieve this goal, focus groups were conducted with middle school students and non-science university students watching selected clips of Eleventh Hour -- a television show about a fictional scientist. Interviews were also conducted with both the creator and the consulting scientist of the show. Analysis of the data showed that the show creator and university students discussed the cultural contexts of science, whereas the consultant and middle school students did not. This suggests the consulting scientist missed an opportunity to influence the portrayal of these aspects. It also suggests middle school students may be reading the cultural aspects of media uncritically, a deficiency educators could address in the classroom. In contrast, all groups discussed the science content and practices of the show, indicating that the scientific facts of the program were salient to both media makers and audiences. This suggests that popular media may be influencing public scientific knowledge, supporting the concerns of scientists and science consultants about the accuracy of science in television and film.
Screening for Novel Colon Cancer Oncogenes in Primary Intestinal Organoid Culture
Keywords:  Department of Biology
Molecular Biology
methylation
organoids
ELF5
CRC
Thesis

Online databases like TCGA are useful sources for finding an enormous amount of information about specific cancers; unfortunately, there is a lack of tools capable of traversing such large datasets. MethylMix is one answer to this problem. The algorithm correlates differential methylation patterns with relevant transcriptional elevation or depletion and has the potential to discover new oncogenes. Differential methylation is a novel mechanism of cancer initiation and this MethylMix has yielded a list of potential candidates displaying oncogenic behavior. This list shows a clear correlation of alternate methylation and transcriptional aberration with cancer, but there is a need to screen these genes in order to determine whether they are merely passenger mutations, or if they’re actually contributing to the oncogenic phenotype. One of the genes, ELF5, is significantly hypomethylated and overexpressed in a subset of CRCs. Using in vitro analysis in three dimensional organoid culture, ELF5 is shown to induce hyperproliferation and dysplasia. Furthermore, clinical samples with increased ELF5 expression show a decrease in ELF5 promoter methylation, confirming the correlation found by MethylMix and supporting ELF5’s clinical significance. The mechanism for ELF5-overexpression tumorigenesis is unknown and does not follow the canonical mechanism in breast cancers with the ELF5 mutation; however, the data presented here suggests that ELF5 interacts with the Wnt-signaling pathway to initiate oncogenic behavior.
Search for low-mass dark matter with superCDMS Soudan and study of shorted electric field configurations in CDMS detectors [electronic resource]
Keywords: Physics.

The area of dark matter is one of the most interesting and exciting topics in physics today. Experiments such as SuperCDMS are built to detect dark matter in the lab by looking for low-energy nuclear recoils produced by collisions between dark matter particles and atoms in terrestrial detectors. SuperCDMS Soudan is particularly well-suited to follow up on possible hints of low-mass dark matter seen by other recent experiments because of its low thresholds and excellent background discrimination. Analyzing SuperCDMS Soudan data to look for low-mass dark matter comes with particular challenges because of the low signal-to-noise very near threshold. However, with a detailed background model developed by scaling high-energy events down into the low-energy signal region, SuperCDMS Soudan produced world-leading limits on the existence of low-mass dark matter. However, a few SuperCDMS Soudan detectors experienced cold hardware problems that can affect the data collected. Of particular interest is one detector considered for the low-mass WIMP search that has one of its charge electrodes shorted to chassis ground. The data collected by the shorted detector may have been compromised since an electrode shorted to ground will modify the electric field in the detector. A new model of the expected backgrounds in the low-mass WIMP search is developed using the SuperCDMS Detector Monte Carlo to try to explain how the short may have affected the data collected. Finally, the consequences of a new effective field theory of dark matter-nucleon scattering are examined in the context of current and future dark matter direct detection experiments.
A search for non-standard model Higgs bosons produced in association with b-quarks at the ATLAS experiment [electronic resource]
Keywords: Physics.

With the discovery of a Standard-Model-like Higgs boson at the LHC in 2012, the particle content of the Standard Model has been fully verified experimentally, and the focus turns even more fully to searches for physics beyond the Standard Model. One interesting class of theories, supersymmetry, predicts (at least) 4 additional Higgs bosons. This is a search for two of those SUSY Higgs particles, A0 and H0, in production states including additional b-quarks and in final states where A0 and H0 are decaying to a b-bbar final state. Using data-driven estimations to understand and model the large multi-b-quark QCD backgrounds at the LHC, we set limits on the production cross section times b-bbar branching ratio of 1.79-0.25 pb in the range 450 GeV < mA0 < 800 GeV. No statistically significant excess is observed in the data relative to the background-only expectations. This is the first resonance search in this final state at ATLAS, and the highest-mass search for A0 and H0 decaying to b-bbar that has yet been performed.
Searching for the QCD axion with black holes and gravitational waves [electronic resource]
Keywords: Physics.

Advanced LIGO may be the first experiment to detect gravitational waves. Through superradiance of stellar black holes, it may also be the first experiment to discover the QCD axion with decay constant above the grand unification scale. When an axion's Compton wavelength is comparable to the size of a black hole, the axion binds to the black hole, forming a ``gravitational atom.'' Through the superradiance process, the number of axions occupying the bound levels grows exponentially, extracting energy and angular momentum from the black hole. Axions transitioning between levels of the gravitational atom and axions annihilating to gravitons can produce observable gravitational wave signals. The signals are long-lasting, monochromatic, and can be distinguished from ordinary astrophysical sources. We estimate up to order one transition events at aLIGO and up to ten thousand annihilation events. In the event of a null search, aLIGO can constrain the axion mass for a range of rapidly spinning black hole formation rates. Axion annihilations are also promising for much lighter masses at future lower-frequency gravitational wave observatories; the rates have large uncertainties, dominated by supermassive black hole spin distributions. Our projections for aLIGO are robust against perturbations from the black hole environment and account for our updated exclusion on the QCD axion suggested by stellar black hole spin measurements.
Security empire [electronic resource] : building the secret police in communist Eastern Europe, 1944-1952
Keywords: History.

This dissertation explores how and why three countries with different histories and political cultures—Poland, Czechoslovakia, and East Germany—came to adopt communist political systems in the period following the Second World War. Through a comparative study of one institution, the communist secret police, it explores the people, sentiments, debates, and motivations that turned post-war chaos into centrally organized communist states. It argues that secret police forces in Poland, Czechoslovakia, and East Germany were never as homogenous and unified as historians have commonly assumed. In fact, Eastern European secret police forces developed different institutional forms depending on the social conditions, geography, and experiences of war of each country.