Analyses of the white seabass commercial fishery and the regulations governing it revealed that management techniques in use since 1931 have probably affected the yield. Values from catch-per-unit-of-effort, weight-length, age-growth, and population parameters were utilized in an equation to determine the best possible equilibrium yield under existing environmental, biological, and socio-economic conditions. Results indicate that under present fishery practices (namely, fishing on only a portion of the resource) the yield in weight per recruit could be increased if actual harvesting were to begin at age 5 (28 inches TL). Current regulations have sufficient latitude to permit the fishery, on its own volition, to harvest younger fish, namely 5- to 8-year-olds rather than 8- to 11-year-olds.

This thesis aims to make progress on the problem of using dynamic information flow control for computer security at the application level, specifically using Faceted Values. This technique involves augmenting program data values so that each one is a pair of two primitive values:

one high-security version that is visible only to high-security observers, and one low-security version that is visible to everyone else. These augmented values are called faceted values, and the various versions are called facets. This technique allows very precise tracking of information flow through a program, allowing programmers to increase confidence in the security of their systems.

This thesis helps to increase the maturity of research on the ``Faceted Values'' technique, bringing it in line with research on the prior techniques ``No Sensitive Upgrades'' and ``Secure Multi Execution.'' Specifically, we have formalized a new semantics (called Multef) and proved that it satisfies a strong (``termination sensitive'') security property, we have implemented the technique as a Haskell library (called FIO) using two monads, and we have tested it in a prototype social network application (called FacetBook).

Translation of cancer genomic data into cancer therapies and companion

diagnostics remains a primary challenge in personalized medicine. Much of this

challenge is due to the difficulty of identifying genetic co-dependencies that lead to

clinically actionable drug targets. Targeting many of the known essential gene

products are not always selectively efficacious because these targets may be

common to both malignant and benign cells. However, essential genes that are

associated with particular genomic alterations in cancer cells, like those from

synthetic lethality, can potentially provide a source of tumor-specific drug targets.

To help aid novel drug discovery, I developed a computational approach called

CLOvE, a multi-omic approach that identifies co-dependencies in pairs of genes.

These co-dependencies are inferred from context-dependent changes in

expression, where CLOvE assigns high scores to those genes with the greatest

compensatory change in expression. These scores may suggest synthetic lethal

interactions, which may uncover clinically actionable essential genes. These

methods were developed in CCLE cell lines and validated with RNAi and CRISPR

viability data. CLOvE identifies meaningful expression changes, assigns high scores

to known essentials, reveals known synthetic lethal connections, and implicates

many possible new connections. This approach could provide a tool to accelerate

both target discovery and biomarker discovery, to develop drugs suitable for a

specific cancer, and identify and stratify patients who may benefit from these

treatments.

The total synthesis and synthetic efforts towards several diterpene natural products are described. The syntheses of the furanocembranoids coralloidolide B and coralloidolide C were both achieved in a single step from coralloidolide E. The furanocembranoid bipinnatin J was used in a model system to explore the conditions necessary to effect a transannular [2+2] cycloaddition in assembling the pentacyclic core of bielschowskysin. Two distinct strategies were evaluated as part of this model system for their effectiveness in synthesizing the cyclobutane ring of bielschowskysin. Progress was also made towards synthesizing a macrocyclic precursor of bielschowskysin. Numerous selective oxidations of the furanocembranoid carbon framework were discovered which should find utility in the synthesis of other members of this family of diterpenes. Several novel transformations of furanocembranoid derivatives are described, along with a synthesis of the furanocembranoid intricarene through photochemical means.

Determining the composition of dark matter is at the forefront of modern scientific research. There is compelling evidence for the existence of vast quantities of dark matter throughout the universe, however it has so-far eluded all direct detection efforts and its identity remains a mystery. Weakly interacting massive particles (WIMPs) are a favored dark matter candidate and have been the primary focus of direct detection for several decades. The Cryogenic Dark Matter Search (CDMS) has developed the Z-dependent Ionization and Phonon (ZIP) detector to search for such particles. Typically made from germanium, these detectors are capable of distinguishing between electromagnetic background and a putative WIMP signal through the simultaneous measurement of ionization and phonons produced by scattering events. CDMS has operated several arrays of these detectors at the Soudan Underground Laboratory (Soudan, MN, USA) resulting in many competitive (often world-leading) WIMP exclusion limits.

This dissertation focuses on ionization collection in these detectors under the sub-Kelvin, low electric field, and high crystal purity conditions unique to CDMS. The design and performance of a fully cryogenic HEMT-based amplifier capable of achieving the SuperCDMS SNOLAB ionization energy resolution goal of 100 eVee is presented. The experimental apparatus which has been used to record electron and hole properties under CDMS conditions is described. Measurements of charge transport, trapping, and impact ionization as a function of electric field in two CDMS detectors are shown, and the ionization collection efficiency is determined. The data is used to predict the error in the nuclear recoil energy scale under both CDMSlite and iZIP operating modes. A two species, two state model is developed to describe how ionization collection and space charge generation in CDMS detectors are controlled by the presence of ``overcharged'' $D^-$ donor and $A^+$ acceptor impurity states. The thermal stability of these states is exclusive to sub-Kelvin operation, explaining why ionization collection in CDMS detectors differs from similar semiconductor detectors operating at higher temperature. This work represents a solid foundation for the understanding ionization collection in CDMS detectors.

The Washington State Department of Transportation (WSDOT) creates, restores, and enhances wetlands to mitigate for impacts that occur during highway construction projects. Monitoring data provides information on the development and success of these wetland mitigation sites. Valid monitoring data is critical to the adaptive management of site remediation and maintenance activities. In 2000, biologists surveyed wetland vegetation using two different sampling strategies on four mitigation sites in western Washington. Vegetative aerial cover data were collected using both the agency’s historical, standardized monitoring approach, and an alternative method that combines changes in sampling design with new methods of data collection. Cover estimates were calculated for each data set and compared. Post-monitoring data analysis shows the alternate methods generate more reliable aerial cover estimates for target plant populations.

Social groups shape societal dynamics and individual identities, so it is important to have a clear understanding of the metaphysics of these groups. This dissertation offers insights into the metaphysics of social groups and corporate moral responsibility. In the first chapter, I propose and employ criteria to evaluate contemporary metaphysical views of groups, such as the set view, the robust set view, the stage view, the structuralist view, and the constitution view. In the second chapter, I propose a new typology to distinguish organized groups from other types of groups. In the third chapter, I present a novel perspective, arguing that organized groups are abstract artifacts. This idea comes from examples where groups persist without members, leading to the conclusion that these groups are not constantly dependent on their material instantiations. The final chapter shifts focus to metaphysic views of corporate and how to understand corporate moral responsibility. Considering corporations through different metaphysical lenses can give us a clearer understanding of potential instances where a corporation could be morally responsible independent of its individual members. This dissertation offers significant insights into the metaphysical nature of social groups and their moral responsibility.

Proton-exchange-membrane fuel cells (PEMFCs) show promise in automotive applications because of their high efficiency, high power density, and potentially low emissions. To be successful in automobiles, PEMFCs must permit rapid startup with minimal energy from subfreezing temperatures, known as cold-start. In a PEMFC, reduction of oxygen to water occurs in the cathode catalyst layer (CL). Under subfreezing conditions, water generated during startup solidifies and hinders access of gaseous oxygen to the catalytic sites in the cathode CL, severely inhibiting cell performance and potentially causing cell failure. Achieving cold-start is difficult in practice, due to potential flooding, sluggish reaction kinetics, durability loss, and rapid ice crystallization. Currently, however, few studies focus on the fundamentals of ice crystallization during cold-start. Elucidation of the mechanisms and kinetics of ice formation within PEMFC porous media is, therefore, critical to successful cell startup and high performance at low temperatures.

First, an experimental method is presented for obtaining isothermal ice-crystallization kinetics in water-saturated gas-diffusion layers (GDLs). Ice formation is initially studied in the GDL because this layer retains a significant amount of product water during cold-start. Isothermal ice-crystallization and ice-nucleation rates are obtained in commercial Toray GDLs as functions of subcooling using differential scanning calorimetry (DSC). A nonlinear ice-crystallization rate expression is developed using Johnson-Mehl-Avrami-Kolmogorov (JMAK) theory, in which the heat-transfer-limited growth rate is determined from the moving-boundary Stefan problem. Predicted ice-crystallization rates are in excellent agreement with experiment. A validated rate expression is thus available for predicting ice-crystallization kinetics in GDLs.

Ice-crystallization kinetics is also considered under experimental settings similar to real PEMFC operating conditions where ice invariably forms non-isothermally. Non-isothermal ice-crystallization rates and ice-crystallization temperatures are obtained in water-saturated GDLs as a function of cooling rate. Our previously developed ice-crystallization rate expression is extended to non-isothermal crystallization to predict ice-crystallization kinetics at various cooling rates. For non-isothermal ice formation, we find that cooling rate has a negligible effect on the crystallization rate when crystallization times are much faster than the time to decrease the sample temperature by the subcooling. Therefore, a pseudo-isothermal method is proposed for non-isothermal crystallization kinetics using isothermal crystallization kinetics evaluated at the non-isothermal crystallization temperature.

Catalyst layers also retain a significant amount of product water during cold-start. Accordingly, ice nucleation and growth in PEMFC CLs are investigated using isothermal DSC and compared to isothermal galvanostatic membrane-electrode assembly (MEA) cold-starts. Measured ice-crystallization and ice-nucleation rates follow expected trends from classical nucleation theory. Following our previous approach, a quantitative nonlinear ice-crystallization rate expression is developed from the JMAK framework. To validate ice-crystallization kinetics within PEMFCs, we further measure and predict MEA cell-failure time during isothermal galvanostatic cold-start. Using a simplified PEMFC isothermal cold-start continuum model, MEA cell-failure times predicted using the newly obtained rate expression are compared to that predicted using a traditional thermodynamics-based approach. From this comparison, conditions are identified under which including ice-crystallization kinetics is critical and to elucidate the impact of freezing kinetics on low-temperature PEMFC operation.

During cold-start, the time for recovering cell performance strongly depends on the rate of melting residual ice by reactive heat generation. Non-isothermal ice melting in water-saturated GDLs is investigated using DSC with various heating rates. In all cases, ice-melting times decrease nonlinearly with increasing heating rate, whereas melting temperatures remain near the equilibrium melting temperature of bulk ice, demonstrating that melting is thermodynamic-based with a rate limited by heat transfer. Ice-melting endotherms are predicted from overall DSC energy balances coupled with a moving-boundary Stefan problem, where an ice-melting front within a GDL propagates with volume-averaged properties through an effective medium. Agreement between theory and experiment is excellent. Furthermore, an analytical expression is obtained for ice-melting time. Significantly, the new expression elucidates parameters controlling ice melting and allows for better design of both GDL materials and heating strategies to enhance the success of PEMFC cold-start.