VictorJuiz/thesis huggingface dataset:
Characterizing the mechanism of sensorial perception of biomechanical changes in human skin

The mechanism by which humans perceive biomechanical changes in the outer layer of their skin, the stratum corneum (SC), has not been previously described. The SC, consisting of a network of lipids and corneocytes, interacts with the external environment and its mechanical behavior is sensitive to these interactions. Solar damage, low relative humidity, and damaging topical treatments cause water loss and shrinkage of the SC. Volume changes in the SC result in the development of tensile stresses in the SC, which are perceived as skin tightness. This dissertation first elucidates the mechanism by which SC stresses are transduced by cutaneous mechanoreceptors and their corresponding neurons by demonstrating computationally how stresses in the SC cause the propagation of strains to underlying skin where cutaneous mechanoreceptors reside. A relationship between strain and firing rate of slowly adapting type I (SAI) neurons is used to predict neural activity from computed strains in various skin morphologies. The effects of SC stresses induced by cleansers and moisturizers, which are quantified experimentally, are simulated to predict neural activity specific to each cleanser and moisturizer. A strong linear trend is observed between predicted SAI activity from each topical treatment and skin tightness perception scores reported in a large clinical survey. Next, this dissertation explores the effect of skin layer mechanical properties, skin layer thicknesses, and skin surface topographies on the magnitudes of computed SAI neuron firing rates. Each of these parameters is found to influence the predicted SAI neuron firing rates. Additionally, parameters affecting sensitivity in SAI neuron firing rates to distinct SC contraction amounts are investigated. The topography of the skin surface was found to be especially influential in these studies of sensitivity. Finally, this dissertation evaluates whether it is expected that an individual would maintain the ability to distinguish the unique effects of cleanser and moisturizer treatments when a full thickness skin tensile strain is combined with the SC contractions induced by the topical treatments. This is studied in three distinct skin regions, and it is concluded that the perceptual acuity would be maintained with a stretching of the skin for skin sections with a topography that is not relatively flat. This additional scenario strengthens the conclusion that individuals are capable of perceiving biomechanical changes in the SC through activation of SAI neurons. Overall, this dissertation details the mechanism by which mechanical changes in the SC are perceived and describes relevant parameters for this perception. This provides novel information for the perception of skin tightness, which is not characterized in detail in literature

Keywords: Mechanical Engineering.
Advisor: Dauskardt R. H. (Reinhold H.)
Chaudhuri Ovijit
Goodman Miriam Beth
Charitable Giving and the Housing Market after Hurricane Sandy in New York City

Extreme weather events often have consequences not only economically and financially,
but also in terms of more complex social changes. How people respond to
disasters in their risk-taking, prosociality, and other social behaviors dependent on
group membership is stilla a somewhat open question. This paper explores changes
in charitable giving among New York area neighborhoods with significant exposure
to flood damages from Hurricane Sandy after the storm. While the existence of any
major shift in giving levels is unlikely, there is the possibility of a differential effect
between Republicans and Democrats, with the former increasing contributions while
the latter see no change. Additionally, I provide further evidence to suggest a strong
price discount on single family homes in the Sandy flood zone following the hurricane,
but do not find evidence of changes in rents.

Keywords: Housing
Climatic changes
Flood damage
Hurricane Sandy (2012)
Elections
Economics
Text
Thesis
Advisor: Bernheim B. Douglas
Chiral algebras in physics and mathematics

Chiral algebras and vertex algebras are ubiquitous structures in physics and mathematics. They form the symmetry algebras of two-dimensional conformal field theories, they describe the universal long-distance physics of statistical systems near second order phase transitions, they arise on the world-sheets of string theories, they encode information about protected sectors in higher-dimensional quantum field theories, and they constitute an important mathematical bridge between various subjects in pure mathematics, like number theory and finite group theory. This thesis collects a few vignettes from my research on chiral algebras: it explores classification, exceptional objects, and some hints from mathematics that there are beautiful new structures waiting to be discovered

Keywords: Physics.
Advisor: Kachru Shamit
Hartnoll Sean
Shenker Stephen Hart
Chromatin activity identifies differential gene regulation across human ancestries

Current evidence suggests that cis-regulatory elements controlling gene expression may be the predominant target of natural selection in humans and other species. Detecting selection acting on these elements is critical to understanding evolution but remains challenging because we do not know which mutations will affect gene regulation. To address this, I co-devised an approach to search for lineage-specific selection on three critical steps in transcriptional regulation: chromatin activity, transcription factor binding, and chromosomal looping. Applying this approach to lymphoblastoid cells from 831 individuals of either European or African descent, I find strong signals of differential chromatin activity linked to gene expression differences between ancestries in numerous contexts, but no evidence of functional differences in chromosomal looping. Moreover, I show that enhancers rather than promoters display the strongest signs of selection associated with sites of differential transcription factor binding. Overall, this work indicates that some cis-regulatory adaptation may be more easily detected at the level of chromatin than DNA sequence. This thesis provides a vast resource of genomic interaction data from diverse human populations and establishes a novel selection test that will benefit future study of regulatory evolution in humans and other species

Keywords: Biology.
Advisor: Fraser Hunter B.
Greenleaf William James
Morrison Ashby J.
Chromatin-mediated regulation of neighboring genes in mammalian synthetic circuits

In mammalian cells, genes that are in close proximity can be transcriptionally coupled: silencing or activating one gene can affect its neighbors. Understanding the dynamics of this transcriptional regulation is important for natural processes, such as heterochromatin spreading during development, aging, and disease, and for designing synthetic gene regulation circuits. In this work, we systematically dissect this spreading behavior in single cells by recruiting and releasing repressive chromatin regulators at dual-gene synthetic reporters and measuring how fast gene silencing and reactivation spread as a function of intergenic distance and configuration of insulator elements. We find that with the Kruppel associated box (KRAB), a repressive domain associated with histone methylation, silencing spreads between two genes within hours, with a time delay that increases with distance. This fast KRAB-mediated spreading is not blocked by the classical cHS4 insulators. Silencing by histone deacetylase HDAC4 of the upstream gene can also facilitate background silencing of the downstream gene by polycomb repressive complex 2, but with a days-long delay that does not change with distance. This slower silencing can sometimes be stopped by insulators. We find that gene reactivation of neighboring genes is also coupled, with strong promoters and insulators determining the order of reactivation. Lastly, our data can be described by a model of multi-gene regulation that builds upon previous knowledge of heterochromatin spreading, where both gene silencing and gene reactivation can act at a distance, allowing for coordinated dynamics via chromatin regulator recruitment

Keywords: Bioengineering.
Advisor: Bintu Lacramioara
Covert Markus
Qi Lei (Professor of Bioengineering)
Chronic Smoke Exposure Burden: Impact on the Immune System of Firefighters

Firefighters are exposed to significant levels of smoke during their careers. Long-term smoke exposure has been associated with chronic diseases and cancers in firefighters. Furthermore, smoke exposure has been associated with the long-term accumulation of heavy metals (e.g., lead, arsenic), which have toxic effects. Despite these known risk factors, the impact of this pollutant burden on the immune system of firefighters remains largely unknown. The goal of this study was to characterize the immune dysfunction caused by chronic smoke exposure and identify possible associations with heavy metals in firefighters versus controls.
We profiled peripheral blood mononuclear cells (PBMCs) utilizing cytometry time of flight (CyTOF) and measured heavy metal levels in the cells during CyTOF by utilizing available heavy metal channels in a cohort of San Francisco firefighters (n=9; 21-52 years;) and healthy controls (n=9; 26-58 years) with a similar level of baseline pollution exposure. FlowJo was used to identify cell populations.
The firefighter group had a lower frequency of CD45- CCR7+CD27- NK cells in the live cell population (p<0.02) and in the NK cell population (p=0.016). Lower cell counts (p<0.05) were found in the firefighter group compared to control in B cells that were positive for Cd 106, Pb 204, and W 182 and CD4+ cells that were positive for Pb 204 and Pb 208. These results suggest chronic smoke exposure may alter the frequency of CD45- CCR7+CD27- NK cells and accumulation of certain heavy metals compared to healthy controls.
This study expands our current knowledge of potential mechanisms of immune dysfunction associated with smoke exposure and heavy metals in firefighters.

Keywords:  Department of Biology
Biology
Firefighter
Wildfire
Environmental Pollution
Heavy Metals
Air Pollution
Occupational Health
Immunology
Text
Thesis
Advisor: Nadeau Kari
Jones Patricia
Civil rights and nation building in a multiethnic borderland : Lwów and Galicia 1918-1939

This dissertation is a microhistory of civil rights in the newly founded Polish Republic, as seen through the lens of violence between the state and its citizens during the twenty-year period between the world wars. Focusing on the city of Lwów and the surrounding Eastern Galicia, this dissertation focuses on Poland's two largest minorities, Jews and Ukrainians (who together represented a quarter of the country's population) and employs an approach merging comparisons and connections to analyze the mechanisms of the conflict between the state and the citizens whose civil rights were denied. The chapters of this dissertation are focused on four distinct episodes of violence: the 1918 pogrom of Lwów's Jews by the Polish Army and local Polish population, the 1922 trial of Józef Piłsudski's failed Ukrainian assassin Stepan Iaroslav Fedak, the 1930 "pacification" of Galicia's Ukrainian countryside, and the 1936 workers' protest where fourteen Lwowians of all three ethnicities were shot and killed by the Polish State Police. This work defines the four crucial elements of the conflict between the state and its minority citizens for full civil rights: the gap between the letter of the law and the willingness of state organs to enforce it; the existence of a clearly defined root of the majority group's supposed superiority (discourses on culture, civilization, race); a projection of the dominant group's (by extension, the state's) own entitlement onto the minority groups and the condemnation of their demands for rights as demands for supposed privileges; and defining the non-dominant identities as inherently "political" and therefore anti-state. The proposed model is applicable in wider contexts regarding minorities and civil rights and is the work's contribution towards a global history of civil rights, now including East Central Europe

Keywords: History.
Advisor: Naimark Norman M.
Weiner Amir
Zipperstein Steven J.
The civil-military politics of war termination

Civilian leaders interpret the value of war in terms of political ends, while military leaders often pursue victory itself as war's object. An empowered military can therefore make war harder to end. Estimates from international conflict data show that termination of a war short of victory is more likely when civilian leaders become more politically dominant. However, civil-military consequences for war termination arise from more than outright shocks to political power. Survey experimental evidence demonstrates that senior U.S. military leaders can use typical political activities to recruit public support for persisting in wars and create costs for elected leaders who want to end them. Finally, qualitative analysis of the U.S. post-9/11 wars and text analysis of a new data set of congressional testimony yield evidence of military dissent and its influence on presidential policy decisions. Altogether, this dissertation moves beyond war termination's civil-military problem, which is about whether and how to stop fighting, and sheds light on the problem of its civil-military politics, which is about how to define war's end but also how to resolve competing claims

Keywords: Political Science.
Advisor: Sagan Scott Douglas
Schultz Kenneth A.
Tomz Michael
Climate resilience in the coastal zone : coral survival and regrowth in the Hawaiian archipelago

Coral reefs are essential to marine life throughout the tropics, yet corals are under severe threat from climate change and other human activities. Rising ocean temperatures have caused large-scale bleaching and mortality in corals worldwide, jeopardizing marine biodiversity, coastal infrastructure, and livelihoods in fishing and tourism. This dissertation seeks to understand the conditions under which nearshore corals survive and rebound after heatwaves in the Hawaiian Islands and local management strategies for protecting reefs threatened by climate change. I use a combination of high-resolution remote sensing and field methods to analyze coastal interactions that affect coral survival during, and recovery after, ocean heatwaves. I first analyze the effect of sediment runoff on coral bleaching. I use high-resolution satellite imagery to map sediment runoff across five islands during an ocean heatwave in Hawaiʻi, and measure the effect of turbidity on coral bleaching under different coastal land-use classes. Next, I analyze larval flow and juvenile coral growth in the coastal zone to identify conditions for coral regrowth after bleaching events. Finally, I assess drivers of coastal business participation in a possible "coral insurance" program that is designed to engage the private sector in funding coral restoration in Hawaiʻi. The outcomes of this research indicate specific actions that local communities can take to improve coral reef resilience and recovery under climate change

Advisor: Asner Gregory P.
Crowder Larry B.
Daily Gretchen C.
Micheli Fiorenza
Climate, social order and social protection : mechanisms and moderators in climate-related violent conflict

Do higher temperatures or droughts lead to more conflict? If so, why and under what conditions? And what can we do about it? If warming is increasing the likelihood of violence, two approaches will be necessary to mitigate climate change's most hostile effects. First, we need to understand the causal mechanisms, identifying links in the causal chain that connect climate to conflict. Policymakers can then craft effective interventions that block one or more of those links. Second, we need to identify the moderators that enhance or suppress the influence of climate on conflict. Policymakers and administrators can then more effectively determine the countries, regions or individuals that are most vulnerable to climate-related violence. Together, they can optimally target such interventions towards the most vulnerable areas or individuals. Effective policy, informed by greater knowledge of causal mechanisms, and effective targeting, informed by increased understanding of effect moderators, can reduce the overall likelihood of climate change leading to violence. My dissertation, is composed of three separate but thematically related studies. It seeks to better elucidate both moderators and mechanisms in the climate-conflict relationship, particularly those involving local-level social relations and institutions, and national-level social insurance policies. Specifically, my dissertation explores 1) whether trust and social capital moderate temperature's influence on conflict across 33 countries in Africa, 2) whether climate stress is more likely to lead to conflict or cooperation in northern Namibia and 3) whether a programmatic social safety net policy in Ethiopia can block links in the causal chain from climatic stress, to economic hardship, to violence. Collectively, these studies provide novel empirical tests of a set of notable factors -- suggested by the existing scholarship on political and economic development, social capital, economic influences on conflict and climate resilience -- that may moderate or explain the influence of climatic factors on conflict in developing countries

Advisor: Burke Marshall
Schultz Kenneth A.
Mach Katharine J.
Weinstein Jeremy M.
Clock atom interferometry for precision measurements in fundamental physics

Recent technological advances have enabled the development of new precision atomic sensors for tests of fundamental physics. In this thesis, I will introduce the concept of clock atom interferometry, a hybrid of atomic clocks and atom interferometry that is particularly suited for gravitational wave detection and ultralight dark matter searches. I outline the experiment we built to cool and trap strontium atoms for prototyping this concept and demonstrating our initial atom interferometric results. I will then discuss the first realization of large momentum transfer (LMT) clock atom interferometry using single-photon interactions on the strontium 689 nm transition, implementing Mach-Zehnder interferometers and gradiometers with state-of-the-art momentum separation to enhance their sensitivity. Furthermore, using amplitude modulated pulses, I demonstrate Floquet atom optics as a tool to allow symmetric evolution of two states at equal and opposite detuning and allows high pulse efficiencies greater than 99% for all detunings, in particular even when the detuning is on the order of the Rabi frequency. Applying this technique, I extend the visibility of an atom interferometer out to a record momentum transfer in excess of 400 photon momenta. I conclude by demonstrating how this technique can be further advanced to allow for 601 photon momenta of separation, as well as a discussion of the new measurement opportunities made possible with these techniques in the fields of high-precision inertial sensing and fundamental physics detection

Keywords: Physics.
Advisor: Hogan Jason
Graham Peter (Peter Wickelgren)
Kasevich Mark A.
Coherent control of Angstrom-wavelength laser pulses for ultrafast physics

In 2009, the Linac Coherent Light Source (LCLS) generated Angstrom wavelength x-ray pulses with femtosecond pulse duration. This marked the advent of the first Angstrom wavelength x-ray laser in history. The ultrafast, ultrabright and highly coherent x-ray pulses opened up new opportunities to catch a glimpse of the bizarre and fascinating world of atom dynamics. To explore these dynamics at the natural spatial and temporal scale of atoms and molecules, new x-ray optics systems are required to precisely manipulate the x-ray laser pulse. This is the focus of my research. In this thesis, I summarize my effort of developing an efficient numerical simulation platform for the time-dependent behavior of Bragg crystal optics, and the design and experimental demonstration of a dispersion-free ultra-stable optical system to split, delay and recombine hard x-rays in a manner that will enable a new generation of high sensitivity ultrafast measurements. In the end, I present a future-oriented conceptual study that applies these techniques to the well-known chirped pulse amplification (CPA) process that has revolutionized high power optical lasers and show how this could be achieved at Angstrom wavelengths to deliver over a terawatt of x-ray power

Keywords: Physics.
Advisor: Dunne Mike
Huang Zhirong
Reis David A.
Collaborative artificial intelligence (AI) for idea generation in design teams

Engineering design teams are critical for innovation and in solving the increasingly complex problems we encounter. As Artificial Intelligence (AI) systems are providing capabilities that enable humans to perform well beyond what they might have been able to, an understanding of how engineering design teams can leverage AI systems is critical. We have seen these AI capabilities for example in human-AI art generation; software development where computers write a significant portion of code; and even in radiology where AI identifies patterns that humans cannot. This work takes the position that collaborative human-AI teams are the next frontier, and explores this in two studies. The first one involved a voice/text AI collaborator by developing, then testing various vocabularies. It concluded by highlighting gaps in the current models and datasets, which need to be resolved in order to implement such voice/text AI collaborators. The second involved a sketching AI, and used an open source app. Though it worked well as a divergent ideation collaborator, we identified gaps in the variety of suggestions that the AI presented. In addition to this, it demonstrated that when given a prompt to design for, human-AI teams generated more ideas on average, as well as more that were rated higher by two trained research assistants. By demonstrating that Human-AI teams can outperform Human-Human teams on a design task, we provide empirical evidence of AI's potential in design teams. As we enter to the next phase of human-machine collaboration, this work contributes towards a conceptual design of a new class of AI systems that observe humans and come up with suggestions in real time, enabling researchers to design and test new concepts. Others can apply the methods we have demonstrated to explore different environmental contexts such as distributed teams or mixed reality; as well as other modes of interactions during collaboration such as gestures and non-verbal cues

Keywords: Mechanical Engineering.
Advisor: Leifer Larry J.
Cockayne William R.
Landay James A.