VictorJuiz/thesis huggingface dataset:
Harmonizing conservation and agricultural production across tropical countryside [electronic resource]

One of humanity's greatest challenges will be increasing yields and achieving food security while at the same time safeguarding biodiversity and Earth's life support systems. This thesis examines interactions between biodiversity, ecosystem services, and agriculture in tropical farming landscapes. Across the world, many crop species were originally cultivated together and with patches of native vegetation. Now, industrial agriculture is expanding, with vast monocultures replacing diversified farming systems. In chapter 1, I briefly review our state of knowledge concerning the consequences of such land-use intenficiation on biodiversity and ecosystem services. In chapters 2 and 3, I use one of the most comprehensive datasets available for any tropical vertebrate taxa to show that bird communities are more resilient, both locally and at large spatial scales, to low-intensity agricultural systems than high-intensity systems. How these changes in biodiversity will translate into changes in ecosystem processes and services is largely unknown. Of particular concern is the impact on agricultural pests. In chapter 4, I develop a theoretical model to predict the consequences of predator species loss on pest abundance. I find that the rate of pest-control decline is highly dependent on which predator species are lost. In chapter 5, I use a large-scale exclusion experiment to examine interactions between birds, bats, predatory arthropods, and pests in Costa Rican coffee plantations. I find that birds consume pest arthropods, while bats consume predatory arthropods. These different functional roles affect coffee differentially-- I report that birds, but not bats, prevent leaf damage. Harmonizing conservation and agricultural production is clearly possible, but requires understanding the cascading consequences of land-use decisions. In chapter 6, I demonstrate a case study for how coffee plantations could be managed to enhance biodiversity and production. I provide the first ever evidence that maintaining rainforest may provide an economic benefit to farmers through enhancing the control of crop pests, in this case coffee's most damaging insect pest, the coffee berry borer (Hypothenemus hampei). These results indicate that adjusting production practices to conserve rainforest and associated biodiversity may limit infestation from the most damaging pest of one of the world's most economically important crops.

Keywords: Biology.
Advisor: Daily Gretchen C.
Dirzo Rodolfo advisor. Thesis advisor
Fukami Tadashi
Hadly Elizabeth Anne
Mooney Harold
Header space analysis [electronic resource]

In many engineering disciplines, such as digital design or software engineering, there is an abundance of theoretical foundations and practical tools for verification and debugging. In sharp contrast, the field of networking mostly relies on rudimentary tools such as ping and traceroute, together with the accrued wisdom and intuition of network administrators, for verification and debugging of networks. The verification and debugging of networks is difficult because (1) the forwarding state—the set of rules that determines how an incoming packet is processed and forwarded by network boxes—is distributed across multiple boxes, expressed in vendor dependent command line interface (CLI) formats, and is defined by the forwarding tables, filter rules, and other configuration parameters. As a result it is hard to observe and analyze the forwarding state and understand the overall system behavior. (2) The forwarding state is written by multiple independent programs, protocols, and humans. This may result in complex and unpredictable interactions between these independently generated forwarding states. Therefore, the first step in making tools for network verification and debugging is to create a simple model for the forwarding functionality of the network that abstracts away the complexities of understanding the forwarding state. One observation is that packet headers, despite carrying multiple protocols, are just sequences of bits, and networking boxes, despite all their complexities, simply rewrite and forward packet headers. Therefore, in our analytical framework, called the Header Space Analysis (HSA), a packet header is viewed as a flat sequence of bits and is modeled as a point in a {0,1}^L space, called the Header Space, where L is the length of the header. Each dimension in the header space corresponds to one bit in the packet header. Also, networking boxes are modeled as Transfer Functions, transforming packets from one point in the header space to another point or set of points. This easy-to-use formalism abstracts away the complexity of the protocols and vendor-specific semantics of network boxes and gives us a model to analytically prove properties about networks that are otherwise hard to ensure. In this dissertation, after introducing the header space analysis, I will describe three set of techniques and tools for network verification and testing based on HSA: 1) Hassel, a static and offline verification tool for verifying properties such as reachability of end hosts and finding loops and black holes 2) NetPlumber, a real time policy and invariant checking tool for networks and 3) Automatic Test Packet Generation (ATPG) framework for maximally testing network with the optimal number of test packets.

Keywords: Electrical Engineering.
Advisor: McKeown Nick primary advisor. Thesis advisor
Prabhakar Balaji
Varghese George
Hermetically encapsulated fully differential breathe-mode ring resonators for timing applications [electronic resource]

As modern electronic devices continue to miniaturize and integrate more functionality, silicon-based MEMS timing references are gaining more and more attention and are replacing quartz crystals in the

Keywords: Electrical Engineering.
Advisor: Kenny Thomas William primary advisor. Thesis advisor
Howe Roger Thomas advisor. Thesis advisor
Solgaard Olav advisor. Thesis advisor
Heuristics for large scale dynamic programming [electronic resource]

Dynamic programming algorithms are used to solve problems in a diverse variety of fields, including Decision Analysis, Control Systems, Communication Systems, Dynamic Pricing and Bidding, Networking, Supply Chain Management, and Planning. These applications can be challenging, with exponential complexity, so exact solutions are rarely tractable. Therefore, improvements in the efficiency and quality of approximate dynamic programming algorithms can provide significant benefit. One promising approach is on-line Reinforcement Learning, algorithms which balance exploration and exploitation on Markov decision process applications. In practice, however, these algorithms are usually applied off-line to generate a control policy which is then fixed and used on-line. This work focuses on improving off-line policy generation on both discrete and continuous state-space processes, without the distraction of exploitation. It introduces a variety of modifications to existing algorithms and replacements for those algorithms including backtracking, exact and approximate Kalman filter value modeling, variance feedback, visitation allocation, and particle filter optimization. Backtracking re-orders the update calculations to accelerate the learning process for value iteration. Exact Kalman filter value modeling develops a Bayesian dynamic linear Gaussian representation of value using basis functions. Approximate Kalman filter value modeling is a simplified version that appears to be both higher-performance and more robust than exact Kalman filter value modeling. Variance feedback is an adaptive method for updating a value model that exploits prior knowledge while avoiding overconfidence. Visitation allocation is a heuristic to better manage the exploration process. Particle filter optimization is a stochastic optimization technique that can be applied to many policy search problems, including those that are non-convex. These techniques are demonstrated on a variety of benchmark problems, including both discrete and continuous, discounted and undiscounted, and finite and infinite horizon processes.

Keywords: Electrical Engineering
Advisor: Shachter Ross D. primary advisor. Thesis advisor
Howard Ronald A. (Ronald Arthur)
Van Roy Benjamin advisor. Thesis advisor
Hierarchy maintenance and in-group rejection [electronic resource] : when hierarchy concerns drive rejection of highly identified in-group members

We examine the possibility that Whites might reject high racial identity Whites' bids for political positions in order to avoid upsetting minorities. In Experiment 1, we observed that Whites were more supportive of low White identity White candidates. Additionally, the relationship between racial identity and political support among Whites was mediated by assumptions that high identity White candidates would upset the status hierarchy. In Experiment 2, we found that Whites were less supportive of high White identity White candidates when the hierarchy was said to be unstable as opposed to stable. In Experiment 3, we observed that pro-hierarchy Whites expressed a strong preference for high over low racial identity White candidates when they believed that the hierarchy was stable but this preference disappeared when the hierarchy was said to be unstable.

Keywords: Business.
Advisor: Gruenfeld Deborah H. primary advisor. Thesis advisor
Lowery Brian
Neale Margaret Ann
High bandwith AFM imaging in fluid using interdigitated probes [electronic resource]

High speed imaging of local material properties of soft materials such as biological cells using the Atomic Force Microscope (AFM) is an area of active research. An understanding of nanomechanical properties and local adhesive forces on cell surfaces would greatly improve our understanding of fundamental cellular processes. The interaction force between the probe tip and the sample surface contains rich information about the properties of the sample. However, due to the limited bandwidth of traditional AFM cantilevers, a significant portion of this rich information is lost. Interdigitated AFM probes overcome this limitation by incorporating a high bandwidth diffraction grating based force sensor on the cantilever to measure the time-varying interaction forces with adequately high bandwidth while operating in AC mode AFM. In this work, a new design for interdigitated AFM probes is presented. The new probes have been optically redesigned such that they can be easily operated in both air as well as liquid environments by making small adjustments to manner in which they are used. The mechanical design of the probes allows for simpler fabrication processes which brings them closer to standard probe manufacturing. A new analytical model is presented which allows greater insight into the mechanical properties of the probes. Furthermore, the system design, characterization and signal processing that go along with the use of these probes are discussed. The ability of these probes to map local material properties with high resolution is demonstrated by imaging a wide range of samples in fluid.

Keywords: Electrical Engineering.
Advisor: Solgaard Olav primary advisor. Thesis advisor
Khuri-Yakub Butrus T.
Melosh Nicholas A. advisor. Thesis advisor
High fidelity optimization of flapping airfoils and wings [electronic resource]

Flapping wings are interesting in many ways from both a scientific and an engineering perspective. They are also challenging to design and analyze due to the inherent complexity of both the kinematic motion of the wing and the resulting vortex-dominated fluid dynamics. One way to study flapping wings is to use an optimization approach to find kinematic motions that lead to efficient flight under various conditions. We use this approach, coupling high-fidelity 2D and 3D Navier-Stokes solvers with a gradient-based optimization algorithm. Results are presented for several optimizations of 2D airfoils and 3D wings undergoing periodic, flapping-type motions. In 2D the pitching and plunging NACA0012 airfoil case is considered, with optimizations being carried out to maximize propulsive efficiency and also to minimize input power given a target thrust constraint. In 3D rectangular and semi-elliptic wings of varying thickness that are hinged at the root are considered. The motion of the 3D wing is parameterized by spline control points that allow span-wise variation of twist, dihedral and sweep, allowing complex wing motions and deformations with relatively few parameters. Propulsive efficiency is maximized for the 3D wing in a non-twisting case as well as using one, two and four of these span-wise twist control points, and a case with one each of twist, dihedral and sweep control points. Wing thickness and planform effects are also considered, with optimizations being carried out for both

Keywords: Aeronautics and Astronautics.
Advisor: Jameson Antony
Alonso Juan José
Pulliam T. H. (Thomas H.)
High throughput methods for functional genomics in saccharomyces cerevisiae [electronic resource]

The Saccharomyces cerevisiae deletion collection has revolutionized yeast genetics by allowing genome-wide deletion screens to be performed in pooled cultures. The inclusion of unique, 20-bp DNA sequences known as "tags" or "barcodes" in each strain allows all ~6000 yeast deletion mutants to be analyzed in a single culture by using a microarray to detect changes in tag abundance. Here we discuss improvements and extensions made to the pooled-yeast-deletion assay. This includes a redesign of the barcode array that is used for detecting the tags included in the deletion collection. Our analysis of this barcode array examines whether it is better to use available microarray surface area on a single feature for each probe, or to instead include multiple smaller features. It also covers aspects of data analysis such as the correction of hybridization defects and array saturation, tag-sequence repairs, and estimation of background hybridization. In addition to these microarray changes, we also examine the impact of experimental design on the quality of pooled growth data. Each step in both the experimental protocol and the data-analysis pipeline is examined for possible improvement. Finally, we discuss preliminary experiments testing the application of pooled fitness profiling to the study of epistasis. Data are shown that demonstrate the feasibility of a pooled-double-mutant fitness assay that is compatible with existing barcode array technology. This assay has the potential to become a valuable functional-genomics tool that may provide an improved understanding of pathway relationships in yeast.

Keywords: Genetics.
Advisor: Davis Ronald
Kim Stuart
Pringle John
Stearns Tim advisor. Thesis advisor
High-speed pipelined ADC using a bucket brigade front-end [electronic resource]

Advanced wireless technologies, such as LTE and LTE advanced, require low-power, high-speed, and high-resolution analog-to-digital converters (ADCs). At present, only the pipelined ADC architecture is capable of meeting the stringent bandwidth, linearity, and resolution requirements for this application. However, in current products, the power efficiency of this architecture is limited by the use of operational amplifiers as inter-stage gain elements. This research investigates an approach where the critical operational amplifiers are replaced by a pulsed-based bucket brigade amplifier, which achieves voltage gain by redistributing charge form a large sampling capacitor to a small load capacitor. This circuit performs the residue amplification with lower power, but is weakly nonlinear and therefore requires digital linearization. Since the power overhead for digital arithmetic in modern CMOS technologies is low, this approach has the potential to yield large overall power savings. To evaluate this concept, a prototype ADC was implemented in 65-nm CMOS. The converter operates at 200 MS/s, consumes 11.5 mW from a 1-V supply, and occupies 0.26 mm2. It achieves an SNDR of 65 dB at low input frequencies and 57.6 dB near Nyquist, which corresponds to an SNDR-based Schreier FOM of 164.5 dB and 157 dB, respectively. These results validate the concept of the proposed pulse-based bucket brigade amplification, and the achieved performance compares favorably with the state of the art.

Keywords: Electrical Engineering.
Advisor: Murmann Boris primary advisor. Thesis advisor
Arbabian Amin advisor. Thesis advisor
Wooley Bruce A.
Histone titration by DNA sets the threshold for the mid-blastula transition in Xenopus [electronic resource]

During early development, animal embryos depend upon maternally deposited RNA until zygotic genes become transcriptionally active. Prior to this maternal-to-zygotic transition (MZT), many species execute rapid and synchronous cell divisions without growth phases or cell cycle checkpoints. In Xenopus laevis embryos, the MZT coincides with cell cycle lengthening, cellular motility onset, and the addition of cell cycle checkpoints at a stage termed the mid-blastula transition (MBT). A long standing model is that the timing of the MBT is controlled by a maternally loaded inhibitory factor that is titrated against the exponentially increasing amount of DNA(Newport and Kirschner, 1982b). To identify the inhibitory factor(s), we developed an assay using Xenopus egg extract that recapitulates the activation of transcription only above the DNA-to-cytoplasm ratio found in embryos at the MBT. We used this system to biochemically purify the factor responsible for inhibiting transcription below the threshold DNA-to-cytoplasm ratio. This unbiased approach identified histones H3 and H4 as inhibitory factors. Addition of exogenous H3/H4 tetramers to the extract increased the threshold concentration of DNA required for transcriptional activation. Non-specific removal of endogenous histones reduced the threshold DNA concentration required for transcription, and the addition of histone H3/H4 tetramers was sufficient to restore the threshold in depleted extracts. Finally, reduction of H3 protein in embryos induced a premature MBT. Our observations support a model for MBT regulation by a maternally loaded titratable factor and provide an identity for this long-sought molecule. More broadly, our work demonstrates how a constant concentration DNA binding molecule can be used to measure the amount of cytoplasm per genome, a surrogate for cell size.

Keywords: Biology.
Advisor: Skotheim Jan
Simon Michael (Biology professor) advisor. Thesis advisor
Stearns Tim advisor. Thesis advisor
Historical Consciousness and Ethnicity Among Latino/a Students in a Spanish-for-Native-Speakers Course

In 2010, the Arizona legislature banned any program that promoted ethnic solidarity in high school classrooms. This ban was primarily aimed at ridding middle and high schools of Chicano Studies programs, calling them subversive and racist. In light of such accusations, this thesis sought to explore the effect of a Chicano Studies high school class unit on a predominately Latino classroom. Specifically, this thesis explored the effects of the class unit on students’ historical consciousness, ethnic identification, and future interest in Chicano Studies. Tools employed in this case study included structured interviews, the Multigroup Ethnic Identity Measurement (MEIM), and classroom observations. Students were interviewed and given the MEIM before they were exposed to the material, and again afterwards. It was found that students benefited tremendously from learning Mexican American history. At a minimum, students gained a framework through which they could discuss topics of identity, race, and ethnicity. Additionally, some students developed an elevated sense of historical consciousness, which also manifested itself in the form of critical questioning of their surroundings. All students enjoyed the material and shared that they would be interested in pursuing further work in Chicano Studies. One major finding was the students’ development of historical pride concerning the challenges of Mexican Americans in addition to a renewed sense of purpose in the classroom. Additionally, students developed a new framework through which to interpret and articulate their own history. Ultimately, this study suggests that the introduction and use of Chicano Studies in mainstream history classrooms could prove an effective method of addressing student disinterest and insecurity in the classroom setting.

Keywords: Latino
Latina
Chicano
Chicana
history
historical consciousness
historical thinking
ethnicity
ethnic studies
Chicano Studies
multicultural education
Thesis
Advisor: LaFromboise Teresa
Willinsky John
Horizontal dispersion within the stratified interior of coastal shelf waters [electronic resource]

Horizontal transport and dispersion on the continental shelf are important for understanding the distributions of nutrients, contaminants, biological aggregates, and other scalars in the coastal environment. The hydrodynamic mechanisms leading to transport and dispersion are often not well understood, owing to variability in forcing conditions and scale-dependent behavior. The main goal of this dissertation is to address how complex shelf dynamics lead to horizontal dispersion. To this end, we conducted several field, analytical, and numerical experiments. Field research involved autonomous underwater vehicle measurements to quantify horizontal dispersion of a continuously released Rhodamine WT dye plume within the stratified interior of northern Monterey Bay, CA. The observed spreading of the dye plume provides evidence for scale-dependent dispersion. An analytical shear-flow dispersion model and a numerical particle-tracking model also provide estimates of the lateral dispersion and agree with the field measurements. Another goal of this dissertation is to assess and quantify the effects of shear flow dispersion in steady, oscillatory, and combined shear fields. We demonstrate that the horizontal variance of a point source release is a function of three contributions: a steady shear term responsible for time-cubed growth, an oscillatory shear term subject to long-term linear in time growth, and an interaction term accountable for increasingly negative oscillations in time. A primary finding of this work is that dispersion is strongly related to the ratio of the steady and oscillatory shear amplitudes, and the time non-dimensionalized by the oscillatory shear frequency. When oscillatory shear dominates, the interaction term is particularly important to determine the variance growth behavior. Additionally, temporal variability in vertical turbulent diffusivity generates long-term effects on variance growth. The particle-tracking model is used to evaluate horizontal shear dispersion over the summer upwelling season. Shear within the stratified interior is generally characterized by dominantly diurnal to semi-diurnal oscillations and high frequency oscillations (~15-30 minutes) due to internal waves. The modeled dispersion over 2, 6, and 12 hours is scale-dependent and sensitive to both the time of release relative to the shear phase and the integration time. Additionally, we find that the dispersion is well modeled using the measured vertical shear structure with a constant vertical turbulent diffusivity over the sampling time.

Keywords: Civil and Environmental Engineering.
Advisor: Monismith Stephen Gene primary advisor. Thesis advisor
Fong Derek advisor. Thesis advisor
Fringer Oliver B. (Oliver Bartlett) advisor. Thesis advisor
Koseff Jeffrey Russell advisor. Thesis advisor