VictorJuiz/thesis huggingface dataset:
Natural and synthetic mechanisms for emergent multicellular patterning [electronic resource] : delayed signaling dynamics and bacterial self-assembly

Natural multicellular organisms are capable of self-organizing intricate spatiotemporal patterns, often with single-cell precision. In contrast, our ability to understand and engineer multicellular spatial organization remains incredibly limited. In my thesis I approach this problem in two ways: (1) through a theoretical analysis of natural checkerboard patterns formed through lateral inhibition; and (2) by engineering the first 100% genetically encoded system for self-assembly of bacterial microstructures. For the first project, I noted that the delay in signal transduction between neighboring cells in lateral inhibition had not been explored. I developed a theoretical model including this delay explicitly, and found surprisingly that this delay precludes defects from forming within a differentiating tissue. In the second project, I noted that synthetic biologists have engineered a number of systems for differentiation and cell-cell signaling, but none for cell-cell adhesion. However, all three tools are crucial for multicellularity. I therefore developed a set of tunable, orthogonal, composable adhesins for cell-cell adhesion in Escherichia coli. The resulting tool enabled me to produce strains of bacteria that bind to one another to form cluster-, mesh-, and lattice-like arrangements, even while growing and dividing. Both projects help shed light on principles of self-organization. The adhesion system in particular will enable future development of synthetic multicellular systems for use in consortia-based metabolic engineering, in living materials, in tissue engineering, and in controlled study of minimal multicellular systems.

Keywords: Bioengineering.
Advisor: Riedel-Kruse Hans
Endy Andrew D. advisor. Thesis advisor
Huang Kerwyn Casey
Spormann Alfred M. advisor. Thesis advisor
A natural history of literary time [electronic resource] : temporality and environment in nineteenth-century American literature

A Natural History of Literary Time argues for the determining force of conceptions of time—both literary and scientific—on the shape of environmental knowledge and representation. It does so by investigating three temporalities central to environmental representation in nineteenth-century American literature: geologic time, regressive time, and static time. As forms of aesthetic time management, these temporal modes resist the progressive logic of national time even as they often serve to authorize national progress in a century that witnessed dramatic changes in the country's shape and size, as well as its "natural" spaces. Balancing historical and theoretical claims, this dissertation argues that the temporalized forms for representing the "natural" world that developed during the republic's first century established strategies for American environmental representation whose effects resonate in contemporary environmental culture and politics. In chapters on geologic time, regressive time, and static time, I uncover how literary and scientific ideas about time inform knowledge of human and nonhuman agency, causality, and affect, while simultaneously inflecting formal literary techniques such as genre, description, and style. The first chapter interlinks James Fenimore Cooper, Herman Melville, Frank Norris, and William Dean Howells to uncover theories of regressive time in the neglected genre of the natural resource novel. The second chapter juxtaposes transcendentalists, such as Emerson and Thoreau, with John Kirk Townsend and Stephen Crane—two very different kinds of naturalist—to find concepts of static time at work in techniques of literary description and in a questioning of the human/nonhuman binary. The final chapter on geologic time brings the sentimentalism of Harriet Beecher Stowe, Louisa May Alcott, Elizabeth Stoddard, and Harriet Jacobs into conversation with the pioneering environmental science of George Perkins Marsh, revealing the challenges to intentional human agency posed by the expansive timeframes of geology.

Advisor: Jones Gavin Roger
Ngai Sianne
Saldívar Ramón
Negotiation in war [electronic resource]

What role do negotiations play in the midst of interstate wars? Lacking detailed intra-war data, extant scholarship has largely treated negotiations as an activity that mirrors hostilities on the battlefield. This view of negotiations as a reflection of war is not well-supported by the historical record, particularly for contemporary conflicts. To address these gaps, I gather new daily level data on 1,700 battles and 10,000 diplomatic acts during all interstate wars since 1816. These new resources reveal new insights on the calculated and intertwined relationship between fighting and bargaining. I find that pre-1945 wars are so costly in signaling weakness that tend to be very infrequent but quickly end wars. But after 1945, diplomatic bargaining becomes much more common, irregular, and less predictive of war termination. I contend that international actors and beleaguered war targets use these negotiations to moderate the battlefield, regroup militarily, and mitigate an initiator's first-mover advantage. Negotiations are used as an instrument of war. In addition, a computational analysis of negotiation transcripts and United Nations military reports from the Korean War demonstrates that the costs of war should not be viewed as exogenous information, but rather choices that are endogenous to the stakes of the conflict. These original data and analyses establish a new and dynamic intra-war framework that enables a more policy-relevant study of conflict management, and speaks to the utility of viewing diplomacy as an equal partner to---not a mere consequence of---fighting in understanding war.

Keywords: Political Science.
Advisor: Fearon James D. primary advisor. Thesis advisor
Grimmer Justin advisor. Thesis advisor
Schultz Kenneth
Tomz Michael advisor. Thesis advisor
The neural circuits underlying valence-guided decision making [electronic resource]

This thesis presents two separate but related bodies of work. In the first half, I discuss the development of a new technology, frame-projected independent-fiber photometry (FIP), that allows simultaneous Ca2+ imaging of up to 7 different brain regions or axonal projections in awake behaving mice. I used this technique to reveal the different activation patterns of ventral tegmental area dopamine (VTA-DA) neurons during reward and punishment. One of my key findings was that the VTA-DA projection to the mPFC responds preferentially to shock rather than reward, suggesting that this region may be especially important in processing punishment in addition to its known role in decision making. This work led to the second half of my thesis where I used FIP along with two-photon Ca2+ imaging, optogenetics, and activity-dependent labeling to study projection-specific subpopulations of the mPFC during aversive experiences. I address how the mPFC projection to NAc (mPFC→NAc) encodes aversive outcomes to suppress reward-seeking in the face of a foot shock. By contrast, I found that the mPFC projection to VTA -- the brain's primary reward center -- does not play a role in the suppression of reward-seeking. First I used cellular resolution two-photon Ca2+ imaging to identify the specific subpopulation of mPFC projection neurons that encode the suppression of reward-seeking. I found that ensembles of mPFC→NAc neurons could robustly predict trial-by-trial suppression of reward-seeking, and that neurons predicting suppression also responded to foot shock. When looking at the activity of all shock-encoding mPFC→NAc neurons, these neurons were more active immediately prior to the suppression of reward-seeking. I then used an activity-dependent labeling strategy to specifically target mPFC→NAc neurons that respond to foot shock, and found that stimulation of this sparse projection could suppress reward-seeking. The work in this thesis suggests a highly specific designation for the mPFC neurons engaged in valence-guided decision making, depending both on projection targeting and functional activity during behavior.

Keywords: Neurosciences.
Advisor: Deisseroth Karl primary advisor. Thesis advisor
Giocomo Lisa advisor. Thesis advisor
Hestrin Shaul
Huguenard John advisor. Thesis advisor
Neural coding of cutaneous temperature in the spinal cord and its modulation under persistent pain condition [electronic resource]

Temperature has a profound influence on all biochemical processes in an organism. In most animals, the nervous system enables them to detect environmental temperature. In this case, animals actively control over their metabolism by adjusting their body temperature. In the past two decades, scientists have discovered various molecular detectors of cutaneous temperature in the primary sensory neurons. Temperature above (or below) their activation thresholds triggers ion influx through these channels, thus converting temperature information into nerve impulses. Despite a growing body of literature on the molecular and cellular mechanisms of temperature detection in the peripheral nervous system, little is known about how temperature is encoded in the central nervous system. The initial stage of integration of somatosensory information occurs the spinal cord. Here, I developed an in vivo calcium imaging system to investigate the coding of cutaneous temperature in the spinal cord. In contrast to the primary sensory neurons in the DRG that encode temperature in a modality-specific manner, the spinal cord uses a population intensity code to encode temperature intensity. Once spinal neurons reach their thresholds, responses to heat faithfully reflect the absolute temperature whereas responses to cold selectively signal the change of temperature. Heat-responsive spinal neurons receive major inputs from TRPV1+ DRG neurons, while cold-responsive neurons receive TRPM8+ DRG inputs as well as novel TRPV1+ DRG inputs that are selectively activated by strong cold. The thermosensory system is adaptable to change. Upon tissue injury, the thermosensory system adjust its sensitivity so that animals can better attend to the injured area. This plasticity is hijacked under chronic pain condition, making it a debilitating disease in human. To understand the change of the neural coding of cutaneous temperature, I examined the representations of temperature in the spinal cord by combining in vivo calcium imaging and various persistent pain models. I show that formalin- or prostaglandin E2-induced inflammation dramatically increases spinal responses to heating and decreases responses to cooling. The reduction of cold response is largely eliminated upon ablation of TRPV1-expressing primary sensory neurons, indicating a crossover inhibition of cold response from heat inputs in the spinal cord. Interestingly, the increase in sensitivity to heat and decrease in sensitivity to cold largely occur in a group of dually tuned neurons that respond to both cold and heat, providing a neural substrate that mediate the altered sensitivity in inflammatory pain. By contrast, oxaliplatin, a chemotherapy medication, increases spinal responses to cooling and suppresses responses to heating. Together, our results provide the first comprehensive examination of the neural coding of heat and cold in the spinal cord and its plasticity under pathological conditions.

Keywords: Biology.
Advisor: Chen Xiaoke
Luo Liqun
Barres Ben
Malenka Robert C.
NGO Family Planning Programs and Indigenous Women's Motivations for Collective Action: A Case Study of Solola, Guatemala

Women’s collective action can lead to fundamental social and political change, yet the factors that encourage such phenomenon are not fully understood. Using Solola as a case study, this research intends to answer the question: How, if at all, can Non-Governmental Organization (NGO) family planning programs motivate Guatemalan rural indigenous women’s collective action-specifically towards demanding accountability from the public sector in the field of reproductive health? Current literature and empirical research pose conflicting mechanisms to explain the impact of NGOs on generating motivations for collective action. This qualitative context-specific field study, using protests and women’s groups as proxies for collective action, aims to both further elucidate this debate and test the hypothesis: Indigenous women who participate in NGO family planning programs are likely to be more motivated to join collective action movements than non-participants due to a) exposure to accurate information about family planning methods and their benefits, b) increased awareness of reproductive rights and government obligations and c) participation in advocacy training. This study’s data set consists of 53 semi-structured interviews with indigenous women in rural communities of Solola, both participants and non-participants of three different NGO programs, as well as community health workers (CHWs) and comadronas (CHW+Cs). Data is analyzed through a three-pass qualitative coding process, using internal and external code types. Main findings of this study are that NGO family planning programs, despite not playing a determinant role in originating motivations to join protests or women’s groups, can leverage indigenous women’s motivations rooted in personal experiences by holding discussion spaces, generating role models and using rights language to refer to family planning. These mechanisms can encourage indigenous women’s collective involvement in their community, which, in turn, can contribute to ensuing motivations for collective action that involve interactions in the public sphere to demand accountability from the government.

Keywords:  Fisher Family Honors Program in Democracy
Guatemala
indigenous women
family planning
collective action
NGO
qualitative research
center on democracy development and the rule of law
Thesis
Advisor: Wise Paul
Nitrification and Microbial Activity in Response to Wastewater Effluent in the Sacramento/San Joaquin River Delta

Nitrification, the oxidation of ammonium (NH4+) to nitrate (NO3-) by ammonia-oxidizing bacteria (AOB) and archaea (AOA), is a crucial step in removing nitrogen from marine ecosystems. NO3- is converted to N2 gas in a subsequent transformation and exit, freeing the ecosystem of a nutrient that in excess can lead to excessive productivity, hypoxia, and other downstream consequences. The Sacramento/San Joaquin River delta receives NH4+-laden effluent from the Sacramento Regional Wastewater Treatment Plant (SRWTP). The system provides freshwater to irrigate the Central Valley and drinking water for many millions of people. Studying the rate of nitrification and the composition of the microbial community will further elucidate how nutrient loading has impacted this ecosystem. Nitrification rates were calculated from water samples collected in the Sacramento River starting upstream of the SRWTP then moving downstream below its outfall. DNA and RNA were extracted from filtered water at each site and qPCR assays were used targeting the amoA gene, which encodes the α-subunit of ammonia monooxygenase, the enzyme catalyzing the oxidation of ammonium to nitrite (NO2-). AOA transcripts predominated among AOA and AOB. Nitrifying microbes provide an ecological service in reducing ammonium concentration, a goal of wastewater regulation. Future monitoring of the activity of the Sacramento River’s nitrifying microorganisms will be important for analyzing how this ecosystem responds to future changes that will impact both people and wildlife.

Keywords:  Department of Biology
Biology
river
nitrification
microbes
Thesis
Advisor: Francis Christopher
Peay Kabir
Nitrous oxide production in coupled aerobic-anoxic nitrous decomposition operation (CANDO) bioreactors [electronic resource] : microbial community structure and metabolic pathways

Much as humans respire oxygen, so do microorganisms, but, unlike humans, microorganisms can also respire other electron acceptors for energy. In the nitrogen cycle, microbial respiration of nitrogen species involves reduction of nitrite (NO3−) to NO2-, NO2- to nitrous oxide (N2O), and N2O to N2. Of particular interest is the N2O-producing step due to its adverse impacts as a greenhouse gas, and its potential beneficial use as a renewable source of energy. Interest in N2O for energy production has increased with introduction of a new process for short-cut nitrogen removal and energy recovery - the coupled aerobic-anoxic nitrous decomposition operation (CANDO). CANDO comprises three steps: (1) ammonia (NH4+) oxidation to NO2−; (2) anoxic NO2− reduction to N2O; and (3) energy generation by N2O conversion to N2. For the anoxic step, reduction of nitrite to N2O is coupled to oxidation of intracellular polyhydroxybutyrate (PHB) - an intracellular biopolymer that is produced upon acetate addition. For energy generation, N2O is used as a co-oxidant with air of methane, yielding more energy than combustion with air alone. It is currently unclear why microorganisms produce N2O, and efforts to address that question have largely focused on characterizing and minimizing N2O emissions in conventional wastewater treatment plants. Maximizing N2O production and monitoring and characterization of CANDO communities provides a new window on the pathways and required functional genes. Enrichment communities and isolated pure cultures that efficiently removed NO2− (95-98%) and converted the majority to N2O (60-78%) providing insights into factors affecting physiology and ecology of N2O production. Under selection conditions favorable for N2O production (alternating exposure to acetate and nitrite), CANDO communities were dominated by strains of Comamonadaceae. Pure culture isolates were sequenced, and the likely pathway of N2O production was identified in which quinol-dependent nitric oxide reductase (qnor) produces N2O using reducing equivalents derived from the oxidation of intracellular PHB. One isolate, Alicycliphilus sp. CD02, contains polyphosphate kinase (ppk), the enzyme required for polyphosphate synthesis and production of PHB in Polyphosphate-Accumulating Organisms (PAOs) that are commonly used for soluble P removal in enhanced biological phosphorus removal (EBPR) systems. An unexpected observation was the lack of glycogen synthesis genes in CANDO isolates. This was surprising because conventional PAOs and GAOs use glycogen as a source of reducing equivalents for PHB synthesis. The ppk gene sequence in the CANDO isolate was also significantly different from those of conventional PAOs, suggesting a different role for polyphosphate (Poly-P) synthesis in Comamonadaceae.

Advisor: Criddle Craig primary advisor. Thesis advisor
Francis Christopher advisor. Thesis advisor
Spormann Alfred M. advisor. Thesis advisor
Noise governance and the hearing subject in urban Taiwan [electronic resource]

Noise Governance and the Hearing Subject in Urban Taiwan investigates the social perception of sound and the technological, political, and historical inflections that modulate the meaning and materiality of noise in urban Taiwan. As an abstract, ephemeral phenomenon, sound resists efforts toward stabilization, a characterization that contradicts the objectification of noise as unwanted sound. The dissertation utilizes a combined historical and ethnographic approach to understand how individuals, communities, and the state contend with the elusiveness of sound through the circumscribing technologies of written petitions, quantitative measurements, and homemade audio recordings. Based upon 16 months of archival research and ethnographic fieldwork with urban residents and environmental protection officials in the capital city Taipei, the dissertation draws attention to the fraught positionality of hearing subjects in perceiving noise as "matter out of place." Divergent beliefs of noise as an acceptable, naturalized part of the urban environment and noise as a socially and historically constructed object in need of elimination are reflective of distinct epistemologies of hearing that inform the making of differentiated auditory publics. The dissertation descries the inter-connected network of civil servants, environmental inspectors, social critics, and urban residents, all of whom participate in separate knowledge practices and value systems that push the limits of noise as a private experience and a state-level problem. By relating acoustic continuities between Taiwan's postwar authoritarian history and contemporary Taiwan, the dissertation brings together a study of urban subjectivity, the historical construction of a modern state, and an acoustemology of urban Taiwan.

Keywords: Anthropology.
Advisor: Inoue Miyako
Ebron Paulla A.
Helmreich Stefan advisor. Thesis advisor
Mullaney Thomas S. (Thomas Shawn) advisor. Thesis advisor
Noncoherent communications with large antenna arrays [electronic resource]

This thesis proposes noncoherent communications as an alternative to coherent communications for massive MIMO systems. In contrast to coherent communications, noncoherent communications does not require information about the rapidly varying wireless channel. Instead it only uses in- formation about the slow changing properties of the channel, both at the transmitter and at the receiver. This thesis proposes two specific noncoherent system architectures: one based on average energy across all the antenna elements, and another based on energy detection in the beamspace, which is obtained by taking a spatial Fourier transform across the antenna elements. We consider one-shot communication and show that, under different conditions, these architectures are optimal in terms of the scaling behavior either of achievable multiuser rates or of error probability with the number of antennas. We also present simulation results to demonstrate the performance of noncoherent communication with these architectures. These architectures allow theoretically unbounded spectral efficiencies and multiuser interference suppression (depending on the number of users) even with no instantaneous information about the wireless channel. Moreover, as demonstrated through simulations in this thesis, due to their dependence only on the slowly changing properties of the wireless channel, the noncoherent architectures retain their good performance even in systems with high mobility or high carrier frequencies, whereas coherent communication breaks down completely in these environments.

Keywords: Electrical Engineering.
Advisor: Goldsmith Andrea
Arbabian Amin advisor. Thesis advisor
Özgür Ayfer advisor. Thesis advisor
Paulraj Arogyaswami advisor. Thesis advisor
Nonequilibrium dynamics and spectroscopies in quantum matter [electronic resource]

Quantum many-body systems have attracted considerable attention because of their emergent properties, which have a wide range of applications such as superconductors for lossless power transmission, high-efficiency photovoltaic devices, and novel transistors for ultrafast switching. In addition, their interactions with light and associated metastable states have further extended the potential applications to quantum control, ultracold matter and quantum computing. Understanding the underlying physics and manipulating emergent properties will be key to an energy-sustainable future. However, due to the complexity of electronic and atomic degrees of freedom, numerical simulations using high-performance computers are usually required. With the help of high-performance computers, complicated microscopic models can be simulated numerically. This enhances our understanding, as well as directs the exploration of novel materials. In this light, this thesis lies in the study of quantum many-body physics utilizing massively parallel computational techniques, with focus on spectroscopy simulations, nonequilibrium problems and novel materials with intertwined orders.

Keywords: Applied Physics.
Advisor: Devereaux Thomas Peter
Shen Zhi-Xun primary advisor. Thesis advisor
Qi Xiaoliang advisor. Thesis advisor