VictorJuiz/thesis huggingface dataset:
Nanoparticle-based emulsions for droplet microfluidics and applications [electronic resource]
Keywords: Materials Science and Engineering.

Emulsions are a biphasic system with one liquid dispersed as droplets in a second immiscible liquid. They are an important class of materials found in many commercial products. They also play a critical role in emerging microfluidics applications for high throughput screening assays and material design. The objective of my thesis dissertation is to develop nanoparticle-based emulsion systems. My thesis covers two major application areas. The first addresses a key challenge in using emulsion drops as micro-reactors in droplet microfluidics, and the second uses emulsion without stabilizer towards the fabrication of nanocomposites. In the first part of my dissertation, I show that the use of amphiphilic nanoparticles (NPs) as a droplet stabilizer enhances the fidelity of droplet-based biochemical assays with the following advantages. 1) The use of NPs mitigates undesired cross-contamination of molecules between droplets. 2) NP-laden interfaces provide a rigid, solid-like surface to promote the growth of adherent cells, which cannot be achieved in surfactant systems. 3) NP-stabilized drops are more stable against break-up than surfactant-stabilized drops. Such stability increases the throughput of droplet interrogation process by at least three-fold. 4) The covalent conjugation of various molecules on droplet-stabilizing NP surfaces is simple, which opens up opportunities for creating customized fluid-fluid interfaces. In the second part of my dissertation, I present a stabilizer-free emulsion system to prevent the agglomeration of NPs during nanocomposite synthesis. I show that the single encapsulation of NP in the emulsion drop is critical for the fine dispersability of NPs in the nanocomposite. I also demonstrate an application of our method in improving the efficiency of photocatalytic nanocomposite for solar water splitting reactions.
Nanostraw platform for nondestructive intracellular sampling and precise delivery [electronic resource]
Keywords: Materials Science and Engineering.

Nanotechnology has shown great potential in biological, medical and clinical applications. In this thesis, I will describe two novel bio-applications based on a recently-developed nanostraw platform. In the first part of the thesis, I will describe a method for time-resolved, longitudinal extraction and quantitative measurement of intracellular proteins and mRNA from a variety of cell types. Cytosolic contents were repeatedly sampled from the same cell or population of cells for more than 5 days through a cell-culture substrate, incorporating hollow 150-nm-diameter nanostraws (NS) within a defined sampling region. Once extracted, the cellular contents were analyzed with conventional methods, including fluorescence, enzymatic assays (ELISA), and quantitative real-time PCR. This process was nondestructive with > 95% cell viability after sampling, enabling long-term analysis. It is important to note that the measured quantities from the cell extract were found to constitute a statistically significant representation of the actual content within the cells. Of 48 mRNA sequences analyzed from a population of cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs), 41 were accurately quantified. The NS platform samples from a select subpopulation of cells within a larger culture, allowing native cell-to-cell contact and communication even during vigorous activities such as cardiomyocyte beating. This platform was applied both to cell lines and to primary cells, including CHO cells, hiPSC-CMs, and human astrocytes derived in 3D cortical spheroids. By tracking the same cell or group of cells over time, this method offers an avenue to have a sight into the dynamic cell behavior, including processes such as induced pluripotency and differentiation. In the second part, I will elaborate a controlled quantitative intracellular delivery by electroporation-assisted alumina NS system (NES). The cell populations that form intimate contact with NS experience localized electric field during delivery and are porated on the tip of the NS. We achieved a quantitative and high uniform delivery of mRNAs and proteins by controlling three variables: (1) delivery duration, (2) electric pulse intensity, and (3) delivery reagent concentration. Fast protein transcription was observed soon after delivery. We also demonstrated ratiometric co-transfection of mRNAs, and showed this system allows high rate transfection to multiple cell lines and difficult-to-transfect primary cells. The NES transfection efficiency is independent of cell density. In addition, we monitored protein delivery and subsequent biological activity, including STIM1 and antibodies. We observed STIM1 peptide binding to cell expressed ORAI protein, immune antibody staining on histone and actin filaments.
Natural and synthetic mechanisms for emergent multicellular patterning [electronic resource] : delayed signaling dynamics and bacterial self-assembly
Keywords: Bioengineering.

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.
Negotiation in war [electronic resource]
Keywords: Political Science.

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.
The neural circuits underlying valence-guided decision making [electronic resource]
Keywords: Neurosciences.

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.
Neural coding of cutaneous temperature in the spinal cord and its modulation under persistent pain condition [electronic resource]
Keywords: Biology.

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.
Next generation thin film photovoltaics [electronic resource] : study and application of surface modification and atomic layer deposition
Keywords: Chemical Engineering.

Solar energy is the most abundant renewable energy resource and is compatible with both utility scale and distributed power applications. Silicon photovoltaics are well established and dominate the market today; however, as silicon technology approaches practical efficiency limitations, we must look toward the next generation of photovoltaic materials. Two promising candidates are quantum dots and metal halide perovskites that have advantages such as low-cost solution processing, a direct and tunable band gap with a high absorption coefficient, and tolerance to defects and impurities. These materials offer the potential to not only reduce the levelized cost of electricity through low-cost manufacturing, but also to increase efficiency through tandem or multi-junction architectures. However, improvements to the stability and efficiency of these devices are required for commercialization. The surfaces and interfaces are critically important to the recombination and charge transport properties that dictate the operation of these thin film devices. In this research, we work to better understand the effects of organic surface species and atomic layer deposition (ALD) processing applied to quantum dot and metal halide perovskite materials. The knowledge gained from these studies is applied to improve thin film photovoltaic devices. Herein, we demonstrate a method to fabricate a graded band structure in colloidal quantum dot photovoltaics through ligand dipole tuning. Proper choice of quantum dot surface ligands creates a favorable alignment between quantum dot layers in order to improve charge separation and device performance. We also present a study of tin oxide ALD on metal halide perovskite thin films and the effects of fullerene layers at the perovskite surface. A low-temperature ALD tin oxide method is developed that enables the sputtering of a transparent indium-tin-oxide electrode on wide-gap perovskite solar cells with high optical transmission in the infrared. This device architecture is shown to have impressive stability, passing the International Electrotechnical Commission (IEC) 61215 accelerated lifetime testing protocol applied to silicon modules. Furthermore, the semitransparent perovskite device is fabricated on top of an infrared-optimized silicon heterojunction solar cell to form a monolithic perovskite/silicon tandem device with a high open circuit voltage of 1.65 V and a certified solar conversion efficiency of 23.6 %, the highest reported monolithic tandem perovskite solar cell efficiency to date. The high photovoltage of this device is sufficient to drive photoelectrochemical water splitting, enabling the conversion of solar energy to chemical bonds for energy storage in the form of hydrogen gas. ALD TiO2 and polymer coatings were applied to demonstrate perovskite-based PEC device operation in aqueous electrolyte for 1 hour and an unassisted initial solar-to-hydrogen conversion efficiency of 4 %.
NGO Family Planning Programs and Indigenous Women's Motivations for Collective Action: A Case Study of Solola, Guatemala
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

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.
Nitrification and Microbial Activity in Response to Wastewater Effluent in the Sacramento/San Joaquin River Delta
Keywords:  Department of Biology
Biology
river
nitrification
microbes
Thesis

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.
Noise governance and the hearing subject in urban Taiwan [electronic resource]
Keywords: Anthropology.

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.