VictorJuiz/thesis huggingface dataset:
Building the roads [electronic resource] : expertise, labor, and politics in provincial France, 1675-1791

I capture a turning point in territorial development when public works outgrew medieval organizational methods, and provincial leaders sought to establish new controls over land and labor. In their approach to public works, leaders of the French province of Brittany took older compulsory labor and estate management practices and shaped them into enlightenment-era administrative methods. Breton nobles, urban magistrates, engineers, and villagers reshaped their political and professional identities at eighteenth-century highway construction sites. Road construction introduced a new kind of political interaction between country and city. My study of provincial highway construction brings to light long overlooked connections between early modern people, their local built environment, and their political sensibilities. "Public" once meant royal, but the road construction experience was key in broadening the word's definition to include civic engagement and provincial administration. Use of the corvée to build highways introduced rural communities to the idea of provincial public administration. The experience of highway construction offered the Breton Estates an opportunity to rise in political and administrative prominence. With the corvée, the provincial population participated in the transfer of technological information among experts, estate owners and managers, and local practitioners. While social and economic reform in Old Regime France is usually discussed in terms of orders or classes, a person's perception of his responsibilities to village, province, and kingdom was spatial. The highway -- part of the royal domain -- was culturally transformed by the act of construction into an active, communal space. The experiences of workers in this space, combined with debates about corvée reforms, laid the groundwork for thinking about roads and other parts of the public domain as democratic spaces.

Keywords: History.
Advisor: Baker Keith
Daughton J. P. (James Patrick) advisor. Thesis advisor
Edelstein Dan advisor. Thesis advisor
Findlen Paula advisor. Thesis advisor
Calcineurin regulates the yeast synaptojanin Inp53/Sjl3 to promote membrane recovery during hyperosmotic stress [electronic resource]

In response to hyperosmotic shock, cells of the budding yeast Saccharomyces cerevisiae lose up to 50% of their volume. This drastic decrease in cell size results in excess plasma membrane, which forms large infoldings that must be quickly removed. How these plasma membrane invaginations are resolved to restore the cell surface is not well understood. We show that hyperosmotic shock activates calcineurin, the Ca2+/calmodulin-dependent protein phosphatase, leading to restoration of normal membrane morphology. During hyperosmotic stress, actin patches (sites of endocytosis) become depolarized; we find that under these conditions calcineurin accumulates at sites of polarized growth and promotes actin patch repolarization. Hyperosmotic stress causes calcineurin to bind to the yeast synaptojanin Inp53/Sjl3 and dephosphorylate its proline rich tail. Dephosphorylation by calcineurin activates Inp53, which in turn dephosphorylates PI(4,5)P2 at the plasma membrane and promotes repolarization of the actin cytoskeleton. Consistently, cells lacking the partially redundant synaptojanins Inp51/Sjl1 and Inp52/Sjl2 require calcineurin for growth even in the absence of hyperosmotic stress, and display abnormal plasma membrane morphology when calcineurin activation of Inp53 is blocked. Finally, we find that calcineurin binding to Inp53 stimulates its association with the yeast amphiphysin Rvs167, suggesting model where calcineurin stimulates Inp53 and Rvs167 mediated membrane scission, promoting recovery from excess membrane stress and allowing resumption of polarized growth. In neurons, periods of intense synaptic vesicle release also result in excess membrane, and calcineurin stimulates association of synaptojanin with amphiphysin to promote synaptic vesicle endocytosis. Our findings in yeast suggest that stimulation of endocytic complex formation by Ca2+/calcineurin is a fundamental and conserved feature of the eukaryotic response to excess plasma membrane.

Keywords: Biology.
Advisor: Cyert Martha S.
Frommer Wolf B.
Nelson W. J. (W. James) advisor. Thesis advisor
Skotheim Jan
Calibration ADC and algorithm for adaptive predistortion of high-speed DACs [electronic resource]

In this thesis, the design and implementation of circuits and signal processing algorithms required for digital predistortion of a digital-to-analog converter (DAC) with an open-loop driver is presented. On the circuit design side, the implementation of a high precision, high acquisition-bandwidth calibration analog-to-digital converter (ADC) for sampling the DAC output is discussed. The ADC has a cyclic core and a variant of the switched-RC sampling network suitable for high frequency operation. It is implemented in 90-nm CMOS and achieves an SFDR of higher than 72 dB for input frequencies under 500 MHz. On the signal processing side, a calibration algorithm is presented that uses the input/output data of the DAC to identify its nonlinearity and cancel it through digital predistortion. The algorithm represents a novel technique for the linearization of Hammerstein systems with low computational cost and is suitable for hardware realization. Overall, this calibration architecture improves the SFDR of the DAC by close to 30 dB to achieve a final linearity of 53 dB for input frequencies up to 400 MHz and peak-to-peak differential output swing of 800 mV.

Keywords: Electrical Engineering.
Advisor: Murmann Boris primary advisor. Thesis advisor
Poon Ada Shuk Yan
Wooley Bruce A.
Cancer gene fusion discovery through integrative genomic analysis [electronic resource]

Recurrent gene fusions and chromosomal translocations have long been recognized for their roles in oncogenesis. This dissertation employs genomic approaches to discover and characterize novel gene fusions in several cancer types. First we developed a "breakpoint analysis" pipeline for gene fusion discovery and applied this method to a collection of nearly 1,000 human cancer samples profiled on DNA microarrays. This approach led to the discovery and characterization of twelve new gene fusions in diverse cancer types including angiosarcoma, pancreatic cancer, and colon cancer. Separately, we performed RNA Sequencing on a series of 36 breast cancer specimens and used a suite of computational tools developed in-house to discover ~350 candidate gene rearrangements. Notably, we discovered recurrent fusions of the sterile 20 (STE20)-like kinase TAOK1, and functional studies suggest that these fusions encode potent oncoproteins that drive breast carcinogenesis. Many of the alterations discovered in this dissertation represent the first gene fusions reported to date in the corresponding cancer type, and many represent potentially druggable targets with therapeutic implications for patients.

Advisor: Pollack Jonathan D.
Kuo Calvin Jay advisor. Thesis advisor
Lipsick Joseph Steven
West Robert advisor. Thesis advisor
Capital allocation strategy for commercial banks [electronic resource]

This dissertation analyzes the capital allocation problem for commercial banks with the objective of maximizing long-term growth rate of wealth. In particular, a bank is faced with the problem of deciding how to allocate its capital into the available multi-period commercial loan products. Under common financial regulations and mild assumptions concerning the bank's internal policies, we prove the existence of a policy that yields the near-optimal long-term growth rate almost surely. The almost sure property implies that it is the best policy for policy makers, regardless of their risk tolerance levels, who wish to maximize the bank's long-term growth rate of wealth. Since the exact algorithms for this problem usually have an impractical computational complexity, we provide an efficient approximate algorithm to solve for an approximated policy and demonstrate its effectiveness in a numerical example.

Keywords: Management Science and Engineering.
Advisor: Luenberger David G.
Primbs James primary advisor. Thesis advisor
Weyant John P. (John Peter) advisor. Thesis advisor
Cast aside [electronic resource] : boredom and homelessness in post-communist Bucharest, Romania

Based on 30 months of ethnographic fieldwork with Romania's new homeless population, this dissertation details the experience of being cast aside in an era of radical economic reform by foregrounding the felt reality of boredom. Central to this dissertation is the historical novelty of homelessness in Romania. Prior to 1989, Communist-era employment and housing guarantees ensured most every Romanian's material subsistence. It was only after the fall of Communism, and in the wake of liberalization, that Romanians started living on the streets. Labeled "homeless" by western aid workers, a new shelter system quickly codified their status. This dissertation traces how the newly minted homeless experience and manage life on the streets through boredom. While boredom is typically thought of as a temporal phenomenon associated with privilege, this study draws upon ethnographic research that moves between homeless shelters, squatter camps, public parks and black labor markets to highlight boredom's spatial dimensions. Boredom, the homeless insist, is a marginal space lacking purposeful things to do. In this sense, the language of boredom captures homeless people's alienation from work and family but also from the pleasures of consumption. Once stuck in a space of boredom, homeless persons struggle to find relief by moving towards certain places and away from others in search of opportunity and excitement. This ethnography of boredom, in the end, provides empirical depth and analytical insight into how people make sense of contracting economic possibilities -- a reality for many in Bucharest, but also the world over following the 2008 Global Financial Crisis.

Keywords: Anthropology.
Advisor: Ferguson James
Caldwell Melissa L.
Malkki Liisa H. (Liisa Helena) advisor. Thesis advisor
Catalysis on platinum surfaces probed using synchrotron-based core-level spectroscopies [electronic resource]

Probing chemical reactions on solid surfaces in situ remains a major challenge in heterogeneous catalysis, because most methods of surface characterization require ultrahigh vacuum (UHV) conditions. In addition, the effects of morphology, particle size, and chemical composition are frequently difficult to disentangle due to sample heterogeneity. This work addresses these limitations by applying synchrotron-based core-level spectroscopies to well-defined systems based on single crystals. With a view to developing improved electrocatalysts for the oxygen reduction reaction (ORR) in fuel cells, the behavior of oxygenated species on the Pt(111) and Pt/Rh(111) surfaces was examined in situ under both electrochemical and ambient-pressure conditions using high-energy-resolution fluorescence-detection x-ray absorption spectroscopy (HERFD XAS) and ambient-pressure x-ray photoelectron spectroscopy (APXPS), respectively.

Keywords: Chemistry.
Advisor: Nilsson Anders
Chidsey Christopher E. D. (Christopher Elisha Dunn)
Dai Hongjie
Catalytic promiscuity in the alkaline phosphatase superfamily [electronic resource] : identifying specificity determinants in the diesterase family leads to a hypothesis of a "generalist" core bimetallo site found throughout the superfamily

Catalytic promiscuity, the property of enzymes possessing low levels of activity toward non-cognate reactions, can be exploited as a functional tool to investigate conserved and non-conserved mechanism of enzyme specificity and catalysis between members in the same superfamily. Members of the main branch of the Alkaline Phosphatase (AP) superfamily have a structurally conserved core and active site bimetallo site. Other active site features that confer specificity for a given reaction differ between the families. Families within this superfamily catalyze a wide range of reactions, and enzymes within different families show catalytic promiscuity toward reactions catalyzed by other families within this branch. Structural comparisons and phylogenetic analysis suggests that all of the families in the superfamily arose from a common ancestor whose active site consisted of the bimetallo site alone, absent of peripheral, specificity determining features. Experimental data with a member of the nucleotide pyrophosphatase/phosphodiesterase (NPP) family suggests that a "minimal" mutant version of this enzyme that lacks peripheral, specificity determining features, has equal activity toward the two major reactions catalyzed by the AP superfamily, phosphate monoester and phosphate diester hydrolysis reactions. Together, the structural comparisons, phylogenic analysis, and experimental results lead to the hypothesis that the common ancestor of the AP superfamily is a "generalist." By using a variety of techniques, we provide support for a mechanism of evolution in which a "generalist" enzyme may give rise to multiple enzymes specific for, related, but individual reactions. Support for this mechanism, first proposed in 1976, has, until, now been limited. We suggest that this "generalist" mechanism is a valid mechanism for the evolution of ancient enzymes, present in the early evolution of life, into diverse superfamilies in which each family possesses specificity for one given reaction.

Keywords: Biochemistry.
Advisor: Herschlag Daniel primary advisor. Thesis advisor
Harbury Pehr advisor. Thesis advisor
Krasnow Mark
Cavity nonlinear optics with a cold atom ensemble on an atom chip [electronic resource] : all-optical latching, modulation, and amplification

I present the setup, the procedure, and the result of the experiment in which I probed nonlinear optical phenomena at very low optical power (femtojoule energy scales) in a multi-atom cavity quantum electrodynamical (cavity QED) system. I also explain the semiclassical model of this system in detail that explicitly treats heterogeneous coupling of atoms to the cavity mode, which I use to analyze the experimental data presented in this thesis. The nonlinear behaviors I demonstrated can be exploited in the design of all-optical memory, modulation, and signal amplification devices. These results highlight the interest of cavity QED systems for ultra-low power photonic signal processing as well as for fundamental studies of mesoscopic nonlinear dynamics.

Keywords: Physics.
Advisor: Mabuchi Hideo primary advisor. Thesis advisor
Bucksbaum Philip H. advisor. Thesis advisor
Miller D. A. B. advisor. Thesis advisor
CD14-expressing bladder cancer cells establish tumor-promoting inflammation and drive tumor cell proliferation [electronic resource]

Keratin 14 (KRT14) expression marks the most primitive differentiation state in bladder cancer (BC) cells. However, the mechanisms by which KRT14-expressing cells promote tumorigenicity remain undefined. We found that KRT14-expressing cells express higher levels of CD14 and inflammatory factors such as IL6 and IL8. Using a syngeneic mouse BC model, we isolated CD14 high BC cells and show that this population is more tumorigenic compared to CD14 low cells and forms tumors that are more highly vascularized with higher myeloid cell infiltration. Inflammatory factors produced by CD14 high BC cells directly drive the recruitment and polarization of monocytes and macrophages to acquire immune-suppressive characteristics. In contrast, CD14 low BC cells have higher relative proliferation, which is markedly increased when stimulated by factors produced by CD14 high cells. Collectively, we demonstrate that CD14 high BC cells orchestrate tumor-promoting inflammation and drive tumor cell proliferation to promote tumor growth.

Advisor: Weissman Irving L. primary advisor. Thesis advisor
Hsieh Michael Harrison advisor. Thesis advisor
Shortliffe Linda advisor. Thesis advisor
Sunwoo John B.
Characterizing multiple roles for ubiquitination and sumoylation in the DNA damage tolerance pathways [electronic resource]

Accurate maintenance and transmission of DNA from one cell to another is crucial for the propagation of a species, as accumulation of random mutations can result in loss of critical cellular functions. During DNA replication, DNA lesions encountered by the replication machinery cannot be repaired, as unwinding of the parental DNA separates the damaged DNA from the undamaged template which would normally be used for repair. These replication-blocking lesions can be seriously detrimental to the cell, as stalled replication forks can collapse into double-stranded DNA breaks and lead to genomic rearrangements. To prevent the accumulation of stalled and collapsed forks, the cell uses DNA damage tolerance (DDT) pathways to bypass the DNA lesion and complete replication. There are two known DDT pathways -- translesion synthesis, which uses specialized translesion synthesis polymerases to replicate directly over a DNA lesion, and template switching, which promotes invasion into the sister chromatid and extrusion of the newly synthesized strand for use as a template. These processes rely on a series of E3 ubiquitin ligases in mammalian cells, including Rad18, SHPRH, and HLTF. As a result, we wished to examine the role of ubiquitin modification, and ubiquitin-related SUMO modification, on the control of DDT. Together, the data presented here provide important new insight into how cells control the response to DNA damage and, importantly, how this response is repressed in the absence of damage. As misregulation of Rad18 and SHPRH, as well as several other DDT components, has been implicated in cancer development and progression, knowing more about this regulation may help us understand how cells avoid the generation of mutations, and ultimately the development of disease.

Advisor: Cimprich Karlene primary advisor. Thesis advisor
Attardi Laura advisor. Thesis advisor
Villeneuve Anne
Wysocka Joanna
Characterizing physicochemical properties of organic aerosol mixtures [electronic resource]

The presence of anthropogenic organic compounds in atmospheric aerosols has the potential to contribute to global climate change by altering the hygroscopic behavior and surface tension of the aerosols. Since the hygroscopicity and surface tension of aerosols are related to their sizes, albedos, and tendencies to form clouds, characterizing these two key parameters is important in understanding the effect of atmospheric aerosols on global climate change. Although real atmospheric aerosols are composed of complex mixtures of inorganic and/or organic compounds, the hygroscopicity and surface tension of various aerosol mixtures are still poorly understood. Laboratory experiments were designed to provide a better understanding of the physicochemical properties of various dicarboxylic acid mixtures. Dicarboxylic acids are frequently measured water-soluble organic compounds in atmospheric aerosols. The major focus was on whether the water uptake or surface tension altering property of one organic solute was affected by the presence of another compound in solution. First, to understand the hygroscopicity of dicarboxylic acid aerosol mixtures, water vapor pressure was measured at 12 °C over aqueous bulk solutions containing dicarboxylic acids using both a quadrupole mass spectrometer and a Baratron pressure transducer. Our water vapor pressure measurements for mixtures were compared with predictions made using Zdanovskii-Stokes-Robinson (ZSR) method and the modified UNIQUAC Functional-group Activity Coefficients (UNIFAC) model. Second, to understand the surface tension of dicarboxylic acid aerosol mixtures, surface tension was measured at 20 °C over dicarboxylic acid solutions using a tensiometer. The surface tension of two-, three-, and four-dicarboxylic acid solutions was measured to see how the overall surface tension depends on the number of dicarboxylic acids added to the solution. Our surface tension measurements were then utilized in Kohler's equation to examine the atmospheric impact of the organic aerosol mixtures. Due to surface tension-lowering effects, aerosols containing organic compounds can be more easily activated into cloud droplets. Lastly, the surface tension of solutions containing dicarboxylic acids plus a second category of water-soluble compounds was measured at 20 °C. Ammonium sulfate, D-glucose, and humic acid sodium salts were chosen to represent other categories of water-soluble compounds. Taken together, our results suggest that the physicochemical properties of organic aerosol mixtures cannot be accurately predicted using a linear combination of single component properties. Instead, the interactions between various components must be included for better predictions of physicochemical properties. More studies are needed to accurately quantify and model aerosol effects on global climate changes.

Keywords: Civil and Environmental Engineering.
Advisor: Hildemann Lynn M. (Lynn Mary) primary advisor. Thesis advisor
Jacobson Mark Z. (Mark Zachary) advisor. Thesis advisor
Reinhard Martin
Characterizing the physicochemical properties of organic matter in atmospheric aerosols [electronic resource] : effects of humic-like substances on hygroscopic growth and cloud activation

Organic matter may have a significant impact on the hygroscopic growth and cloud activation of atmospheric aerosols, thus affecting human health, atmospheric chemistry, and Earth's climate. The work presented in this dissertation characterizes the physicochemical properties of organic matter in atmospheric aerosols with the aim of improving current aerosol knowledge, and better informing global climate and chemistry models. To this end, I performed water activity and surface tension measurements on bulk solutions analogous to organic aerosol composition, using an in-house vapor pressure apparatus and a tensiometer. Experiments conducted focused on humic-like substances (HULIS), an important category of water-soluble organic compounds (WSOC), through the use of fulvic and humic acids as analogs. I have demonstrated the use of bulk water vapor pressure measurements coupled with thermodynamic calculations as an effective method to study the hygroscopic growth of organic aerosols. This method is a simple, inexpensive and reliable way to obtain accurate water activity data, and has several advantages over particle measurement instruments. Water activity parameterizations, and their variation with temperature and Kelvin effects, were reported for several pure and mixed WSOC particles. Hygroscopic growth versus relative humidity curves, individual hygroscopic growth factors and deliquescence measurements were also presented for these systems. The surface tensions of solutions representing HULIS and its mixtures were measured and parameterized for concentration ranges relevant to cloud droplet activation. These data suggest that the depression effects of the organic surfactant govern the surface tension behavior of aqueous solutions of HULIS and its mixtures. Water activity and surface tension parameterizations were input into the Köhler theory to predict cloud droplet activations for various mixed organic aerosol systems. Comparing these predictions with measured data highlighted the importance of considering both effects on modeling cloud formation accurately. Lastly, the critical supersaturations predicted for multicomponent mixtures representing biomass burning and continental polluted aerosol may provide an upper and lower bound for the cloud droplet activation of HULIS particles from biomass burning and urban origin.

Advisor: Jacobson Mark Z. (Mark Zachary) primary advisor. Thesis advisor
Golden David
Hildemann Lynn M. (Lynn Mary) advisor. Thesis advisor