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  • Development of New Organic Photoredox Catalysis Driven by Visible Light

    Wang, Wei; Zhang, Yueteng; Wondrak, Georg T.; Hulme, Christopher; Njardarson, Jon T. (The University of Arizona., 2020)
    Development of efficient and sustainable synthetic technologies for molecular construction is the central goal in modern organic synthesis. In recent decades, organocatalysis has become one of the viable tools in organic synthesis with notable features including easy manipulation, low cost, and/or less susceptible to air and moisture. Organophotoredox catalysis has merged as a front runner in organocatalysis. My Ph.D. study focuses on the development of novel visible-light mediated organic photoredox catalysis strategies for the construction of structurally diverse molecular architectures in distinct ways. In the first efforts, a metal- and oxidant-free organophotocatalytic method for preparing structurally diverse thioesters from readily accessible, abundant aldehydes, has been realized. Excited by blue light, the simple and cost-effective 9,10-phenanthrenequinone (PQ) promotes hydrogen atom transfer (HAT) to selectively generate acyl radicals from corresponding aldehydes without inducing crossover reactivity of thioesters. In situ formed acyl radicals then react with thiosulfonate S-esters to efficiently produce thioesters. The mild and efficient method exhibits excellent substrate scope and outstanding functional group tolerance. Significantly, it is proved to be useful in a late-stage functionalization of complex molecules. Direct H/D exchange at formyl groups represents the most straightforward approach to C-1 deuterated aldehydes. Along this line, a new photoredox catalytic, visible-light mediated neutral radical approach has been developed via a unique double-HAT process. Selective control of highly reactive acyl radical enables driving the formation of deuterated products when an excess of D2O is employed. The power of H/D exchange process has been demonstrated for both aromatic aldehydes and aliphatic substrates, and more important late-stage deuterium incorporation into complex structures with uniformly high deuteration level (>90%). The direct dearomatization of indoles represents the most straightforward access to indolines. However, the exiting dearomative methods largely restrict to electron-rich indoles or go through an ionic process using strong nucleophiles. Toward this end, an unprecedented organophotocatalytic process by harnessing nucleophilic radicals to react with electron-deficient indoles was developed. The preparative power of this radical-engaged strategy has been demonstrated by direct addition of in situ formed nucleophilic radicals from readily accessible feedstock carboxylic acids, into structurally diverse electrophilic indoles including (thio)ester, amide, ketone, nitrile and thus delivering a series of trans-2,3-disubstituted indolines with uniformly high stereoselectivity (> 20:1 dr). Moreover, this approach has also been successfully applied to other aromatic heterocycles such as pyrroles, benzofurans and benzothiophenes.
  • After Compatibilism: Essays on Freedom and Responsibility

    McKenna, Michael S.; Wallace, Robert Hamilton; Sartorio, Carolina; Timmons, Mark; Horgan, Terence; Nelkin, Dana K. (The University of Arizona., 2020)
    This dissertation is a series of standalone essays. Together, they form a critique of contemporary compatibilist approaches to the problem of free will and determinism, and they offer an alternative methodology for approaching questions about freedom and responsibility. Compatibilist approaches to the free will problem exist on a spectrum from the more normative to the more metaphysical. Views at the metaphysical end of the spectrum typically understand free will in terms of abilities. In Chapter 1, I argue that these views face a powerful dilemma: they either fail to explain these abilities or fail to show that these abilities are compatible with the thesis of physical determinism. Perhaps a commitment to abilities could be given up, but I argue that takes us too far afield from the intuitive way we understand ourselves as free agents. Compatibilist approaches at the normative end of the spectrum have been largely influenced by P.F. Strawson’s responsibility naturalism. Views of this sort begin by carefully attending to the features of our responsibility practices in order to glean the nature of the sort of freedom that grounds apt responsibility ascriptions. In Chapter 2, I defend a version of this view from a decisive objection: Strawsonian compatibilism seems to make evildoers exempt from moral responsibility. Nevertheless, in Chapter 3, I argue that Strawson's program cannot properly insulate itself from metaphysical concerns about abilities. The methodology may actually support a powerful form of incompatibilism about free will and determinism. This casts the entire contemporary project that draws on his work in a suspect light. Drawing lessons from these two failures, in Chapter 4, I offer a practice-based argument for realism about freedom and responsibility—the view that we really are free and responsible— that is neutral with respect to questions about the compatibility of freedom and determinism. The argument does not depend on any particular metaphysical theory of abilities or particular view of our moral practices. I argue in Chapter 5 that, given this realist framework, we have reason to think that whatever ends up being true about the abilities that characterize free and responsible agents, they will be compatible with determinism after all.
  • Immune-Related Adverse Events (irAEs) of Immune Checkpoint Inhibitors (ICIs) in Advanced Melanoma Patients

    Abraham, Ivo; Almutairi, Abdulaali R.; Erstad, Brian; Slack, Marion; Mcbride, Ali (The University of Arizona., 2020)
    Abstract (1): Background: The use of ipilimumab, nivolumab, and pembrolizumab as monotherapies or in combination has transformed the management of advanced melanoma even though these drugs are associated with a new profile of immune-related adverse events (irAEs). The incidence of irAEs from clinical trials of these agents is an important factor for clinicians when treating patients with advanced melanoma. In the current study, we aimed to profile the incidence of potential irAEs of these agents when used as monotherapy and as combination therapy. Methods: We searched the Medline, Embase, and Cochrane databases;; and websites of regulatory agencies in the USA, Europe, Australia, and Japan for phase 1-3 trials of ipilimumab, nivolumab, and pembrolizumab for advanced melanoma. Random effect meta-analysis was utilized to profile the incidence of potential irAEs. Results: A total of 58 reports of 35 trials including 6331 patients with advanced melanoma and reporting irAE data were included in the meta-analyses. We found higher incidences of potential irAEs in combination therapies versus monotherapies for most of the types of irAEs. Among the monotherapies, ipilimumab users had the most frequent incidence of potential irAEs related to the gastrointestinal system (diarrhea, 29%; and colitis, 8%) and skin (rash, 31%; pruritus, 27%; and dermatitis, 10%), with hypophysitis in 4% of the patients. The most frequent potential irAEs among nivolumab users were maculopapular rash (13%), erythema (4%), hepatitis (3%), and infusion-related reactions (3%), while they were arthralgia (12%), hypothyroidism (8%), and hyperglycemia (6%) among pembrolizumab users. Conclusion: Especially the combination therapies tend to elevate the incidence of potential irAEs. Clinicians should be vigilant about irAEs following combination therapy as well as gastrointestinal and skin irAEs following ipilimumab therapy, in addition to being aware of potential irAEs leading to hyperglycemia, thyroid, hepatic, and musculoskeletal disorders following nivolumab and pembrolizumab therapy. Abstract (2): Importance Anti-cytotoxic T-lymphocyte antigen 4 (anti-CTLA4) antibody (ipilimumab) and anti-programmed cell death 1(anti-PD1) antibodies (nivolumab and pembrolizumab), have been shown to have a beneficial effect in treating melanoma but their risk of immune-related hypothyroidism (ir-hypothyroidism) in elderly patients from a real-world setting is limited. Objective To estimate the risk of ir-hypothyroidism in elderly with advanced melanoma treated with anti-CTLA4 or anti-PD1 in real-world setting. Design, Setting, and Participants SEER-Medicare data was used to identify elderly patients (≥65 years) diagnosed with advanced melanoma between 2011 and 2015 who were de novo users of anti-CTLA4 or anti-PD1. We estimated the risk of ir-hypothyroidism between users of anti-PD1 and anti-CTLA4. We used a propensity weighting approach by using the inverse probability of treatment weighting (IPTW) method to adjust for potential confounders. We utilized proportional hazards models to estimate the risk of ir-hypothyroidism and performed several sensitivity analyses to estimate the risk over ranges of follow-up periods as well as including patients with different stages of melanoma. Exposure Anti-CTLA4 or anti-PD1. Main Outcomes and Measures The risk of ir-hypothyroidism between the initiation of the treatment and up to 90 days from the last dose was measured as a hazard ratio (HR) and its 95% confidence interval (95%CI). Results Our sample had 210 elderly patients with advanced melanoma (164 anti-CTLA4, and 46 anti-PD1 (11 nivolumab, 35 pembrolizumab)). There was no statistical difference in the risk of ir-hypothyroidism between anti-PD1 and anti-CTLA4 (HR 2.15, 95%CI 0.83-5.53). Comparing the individual medications to each other showed a lower risk among users of ipilimumab versus nivolumab (HR 0.15, 95%CI 0.06-0.40) and pembrolizumab versus nivolumab (HR 0.13, 95%CI 0.03-0.55). Sensitivity analyses using a cohort of all-stages melanoma did not show a difference in the risk of ir-hypothyroidism between anti-CTLA4 and anti-PD1 and between individual medications. Conclusions and Relevance In our retrospective study of claims data of elderly patients diagnosed with melanoma, there was no statistical difference in the risk of ir-hypothyroidism between users of anti-CTLA4 or anti-PD1. However, advanced melanoma patients treated with ipilimumab or pembrolizumab may have a lower risk of ir-hypothyroidism compared to nivolumab users. Abstract (3): Purpose Melanoma treatment was advanced significantly by the approval of anti-cytotoxic T-lymphocyte antigen 4 (anti-CTLA4) agents (ipilimumab) and anti-programmed cell death 1 (anti-PD1) agents (nivolumab and pembrolizumab). However, these agents have been associated with gastrointestinal immune-related adverse events (irAEs) including colitis, which could lead to treatment discontinuation. We aimed to estimate the incidence and the risk of colitis in elderly patients with advanced melanoma treated with anti-CTLA4 and anti-PD1 in the real-world setting. Patients and Methods Elderly patients (age ≥ 65 years) diagnosed with advanced melanoma between 2011 and 2015 and treated with anti-CTLA4 or anti-PD1 agents were identified from the SEER-Medicare data. We estimated the risk of colitis from starting the treatment up to 90 days from the last dose of therapy. We used the log-rank test and logistic regression with adjustment for potential confounders using the inverse probability of treatment weighting (IPTW) method. Also, we conducted several sensitivity analyses using different follow-up periods and including all-stages of melanoma. Results A total of 274 elderly patients with advanced melanoma were included in our cohort. The risk of colitis was similar between the anti-PD1 users of and anti-CTLA4 groups based on log-rank test (p=0.17) and logistic regression model (OR 2.86, 95%CI 0.36-25). The 12-month cumulative incidence of colitis was 9.27% in the anti-CTLA4 vs. 4.64% in the anti-PD1 group. Sensitivity analyses for patients with all-stage melanoma showed a significantly lower risk of colitis in anti-PD1 compared to anti-CTLA4 treated patients based on a log-rank test (p=0.017) and logistic regression model (OR of 0.21, 95%CI 0.09-0.53). Conclusion Elderly with advanced melanoma who were treated with anti-CTLA-4 or anti-PD1 had a statistically similar risk of developing colitis. However, there was a statistical difference in the risk of colitis between anti-CTLA4 or anti-PD1 users among all-stages melanoma patients.
  • Characterization and Exploitation of Divergent Substrate Binding Within HspA5 for the Development of Selective Inhibitors

    Chapman, Eli; Ambrose, Andrew; Khanna, May; Wang, Jun; Zhang, Donna (The University of Arizona., 2020)
    Hsp70s are among the most highly conserved proteins in all of biology. These molecular machines function through cofactor interaction and ATP binding and hydrolysis. Through iterative binding and release of exposed hydrophobic residues on client proteins, Hsp70s are able to prevent intermolecular aggregation and promote folding progression toward the native sate. The human proteome contains 8 canonical Hsp70 proteins that vary in tissue specificity, inducibility, and organellular localization. Because Hsp70s are relatively promiscuous with regard to client selection, Hsp70s play a significant role in folding a large proportion of the proteome. Hsp70s are implicated in numerous neurodegenerative diseases and cancer because of their ability to regulate protein homeostasis within cells. In recent years, many groups have attempted to develop selective inhibitors of Hsp70 isoforms to better understand the role of individual isoforms in biology. Through rational design, forced localization, and serendipity, inhibitors have been discovered, however discovery of a molecule that interacts with a single isoform remains elusive. Herein lies a report validating the substrate binding domain of Hsp70 as a targetable site for the development of selective inhibitors. Using a fluorescence polarization (FP) peptide binding assay, a pilot screen revealed hexachlorophene as a selective inhibitor of HspA5. While this molecule is not a lead, it serves as a proof a concept that small molecules can be selective towards Hsp70 isoforms through interaction with the substrate binding domain. From here, an expansion of the assay and scale up of the screen revealed 4.8 as a potent (IC50 = 162 nM) and selective HspA5 inhibitor (20-fold for HspA5 vs HspA9 and at least 300-fold for all other Hsp70s). Through the development of the assay used to discover these compounds it was discovered that Hsp70 isoforms appear to interact differently with substrate peptides. From here, the peptide binding pattern of each canonical human Hsp70 isoform was characterized which led to the development of an algorithm for predicting client interactions with specific Hsp70s. These results highlight the functional variance that exists between Hsp70s in their interaction with peptide substrates, and the possibility for exploiting these differences in inhibitor development.
  • Novel Methods For Next-Generation Sequencing Data With Applications in Microbiome Studies

    An, Lingling; Carter, Kyle Matthew; Watkins, Joseph; Zhang, Helen H.; Slack, Donald (The University of Arizona., 2020)
    Humans maintain a symbiotic relationship with the billions of microbes that exist within and upon the body. The collection of microbes within the body can be considered as a second genome, providing a plethora of unique information about their host. High-throughput next generation sequencing technologies have allowed researchers to build microbial profiles based on microbial RNA sequences for individuals/patients, providing a rich avenue of data to be utilized in statistical models in various field including medicine and forensics. In this dissertation, I present three novel projects which utilize next-generation sequencing based microbiome profiles. In the first project, I proposed a new approach based on microbiome dissimilarity measurements, with applications in forensic trace evidence analysis. This approach utilizes bootstrap Aitchison distances between communities to identify groups of microbial samples and improve current source tracking applications for evidence analysis by removing samples that are highly dissimilar to the evidence. The last two projects focus on detection of mediation effects when the microbes are treated as mediators in clinical mediation models. The second project aims to identify mediation of immune response genes on human gut inflammation non-parametrically by applying information theory concepts from machine learning. The third project expands the scope of mediation modeling by considering time series data in conjunction with mediation. Comprehensive simulation experiments show a drastic improvement in the detection of mediation effects compared to current standard methods for models which utilize microbiome as a mediator.
  • Voltage-Controlled Effects in Magnetic Tunnel Junctions

    Wang, Weigang; Xu, Meng; LeRoy, Brian; Zhang, Shufeng; Schaibley, John R.; Kong, Tai (The University of Arizona., 2020)
    Spintronics, different from traditional electronics, explores additional routes to manipulate electrons through its spin degree of freedom. During its development, magnetic tunnel junctions (MTJs) have been playing a significant role. This is partially due to their fantastic properties such as symmetry-conserving tunneling, which leads to very large magnetoresistance (TMR) and sensitive detection of spin configuration. The relatively simple core structure of the ferromagnet/tunneling barrier/ferromagnet makes it possible to incorporate MTJs into the well-developed fabrication process and a large variety of material systems. Moreover, in recent years, the voltage-controlled effects discovered at FM/Oxide interfaces enables researchers to explore magneto-electric properties of MTJ and more functionalities have been proposed and verified especially in magnetic switching. In this work, we focus our attention on the voltage-controlled effects based on the conventional CoFeB/MgO magnetic tunnel junctions. After a brief introduction to the fundamentals of spin-dependent transport and perpendicular magnetic anisotropy (PMA) in the CoFeB/MgO MTJs. We divert our efforts to various voltage-controlled mechanism discovered in recent years. Chapter 2 briefly touches on the basic experimental technique used in this work. In Chapter 3, we will introduce a revised MTJ nanopillar fabrication procedure which dramatically lowers the requirement for fabricating high-quality MTJ and increases the yield significantly. Chapter 4 will involve interfacial engineering at CoFeB/MgO interface in MTJs. By dusting a thin layer of heavy metal (Ir), in addition to controlling the annealing condition, the VCMA coefficient can be significantly enhanced and the voltage induced switching energy can be greatly reduced, which demonstrated the promises to incorporate MTJs into next-generation memory applications. In Chapter 5, a novel voltage-controlled exchange bias (VCEB) effect is reported and its implication on magnetic switching and further enhancement of TMR is discussed. The last chapter will briefly cover the potential improvement of finished work and topics for future research.
  • Social Structure, Body Size, and Sensory Ecology in Hymenoptera Brain Evolution

    Gronenberg, Wulfila; Keating Godfrey, Rebekah; Nighorn, Alan; Papaj, Daniel; Cai, Haijiang (The University of Arizona., 2020)
    Sociality, like the evolution of multicellularity, is considered a major transition in the evolution of biological complexity. While there is strong foundational knowledge about traits that preceed the evolution of cooperative behaviors and complex forms of social structure, relatively little is known about the role of sociality or social life in individual trait evolution, particularly as it relates to the brain. Hymenoptera (sawflies, wasps, bees, and ants) range from solitary to advanced social species, providing ample comparisons for studying sociality and neural trait evolution. However, hypotheses about sociality and brain evolution have developed separate from studies of trait evolution in insects, and the first chapter of this work suggests unification of trait evolution methods with brain evolution theory. We suggest that recent advances in counting cells and synapses, and quantifying neuron phenotypes and circuit identity be used in trait-based studies of brain evolution in social insects. In the fourth chapter we test a method for quantifying total brain cell number and show this may serve as a meaningful trait for comparisons across Hymenopteran clades. While sociality is generally cited as a major evolutionary transition, superorganisms specifically represent a unique level of biological organization because there exists developmental division of reproductive labor; In superorganisms the colony, not the individual, serves as the reproductive unit upon which natural selection acts. This means the expression of traits at the individual level are selected upon at the collective level of the colony. This form of social organization evolved independently in bees, wasps, and the ancestor to all ants. Thus, all ants are superorganisms and ants show the greatest diversity in colony structure, making them a natural experiment to test how social structure drives individual trait evolution. In the second and third chapter of this work we provide evidence that colony size, a measure of social complexity, is associated with behavioral and neural trait evolution in ants. Specifically, we show that colony size scales inversely with measures of exploratory drive and relative investment in the antennal lobes, a sensory region of the brain responsibly for processing olfactory information. Furthermore, we find that closely related Sonoran Desert species that vary in colony size show differences in sensory systems related to social cue processing, particularly those involved in assessing nestmate identity. We find the large-colony species, Dorymyrmex bicolor has a greater density and number of sensilla basiconica and more glomeruli in the T6 cluster of the antennal lobe, sensory structures and regions responsible in part for processing nestmate cuticular hydrocarbons, than the small-colony Dorymyrmex insanus. Our data suggest habitat structure is also an important drivers in brain evolution in ants, as we find that species living in deserts show less investment in visual processing regions than those living in swamp environments of temperate forests.
  • Exploring Long-term Earthquake Deformation in Southern California using Field-based Geologic and Space-based Geodetic Methods

    Bennett, Richard A.; Guns, Katherine; Beck, Susan; Davis, George; Harig, Christopher; Richardson, Randall (The University of Arizona., 2020)
    The San Andreas plate boundary zone in southern California is characterized by a broad network of interlacing faults, working within different provinces of activity to accommodate modern Pacific – North America plate boundary motion. These tectonic provinces vary in their fault morphology from transpressional east-west trending faults of the Transverse Ranges, to transtensional northwest trending faults of the southern Mojave in the Eastern California Shear Zone (ECSZ), to the main dextral Southern San Andreas Fault (SSAF) running through the center of it all. Characterizing how strain accumulation translates to earthquake deformation along different areas of a plate boundary fault system is a critical goal for better understanding how faults can work together to accommodate plate boundary motion and for assessing the seismic hazards along individual faults in the system. Achieving this goal, however, requires integrating different perspectives and evidence from all aspects of the active tectonics field, from field-based measurements of paleoseismic offsets and chronologies through tectonic geomorphology and paleoseismic trenching, to modern space-based observations of crustal velocities and strain rates using Global Positioning System (GPS) and Interferometric Synthetic Aperture Radar (InSAR) measurements, to measurements of crustal seismicity and seismic waveform analysis of recent events, to synthesis modeling studies based on crustal dynamics. In this dissertation, I have endeavored to complete an interdisciplinary analysis of fault motion and crustal deformation in southern California, in order to better characterize the current slip rates of faults in and around San Gorgonio Pass and in particular, to deepen our understanding of the possible mechanisms of slip and strain transfer that must exist between the SSAF system and the southern ECSZ system. In this effort, I have sought to quantify the effect of ongoing viscoelastic postseismic displacements on the modern deformation field in southern California. I have found that postseismic displacements caused by twelve large magnitude earthquakes are measureable with high precision GPS measurements and thus are affecting crustal velocity estimates. Some of these earthquakes occurred over a century ago, revealing a possibility that postseismic deformation and its effect on the deformation field can last longer than we currently assume. Accounting for these postseismic displacements using the method developed in this work leads to a more accurate time-invariant GPS velocity field. We apply our newly created postseismic-reduced velocity field to elastic fault block models of faults in and around San Gorgonio Pass, and find that removing postseismic motions from the deformation field reduces misfit statistics by up to 50%, depending on fault geometry, when compared with our observed (unreduced) GPS velocity field. In addition, removing postseismic displacements also decreases estimated fault slip rates on nearly all faults in our model. Only one of our fifteen model block geometries is able to resolve a persistent slip rate discrepancy along the Mojave and San Bernardino sections of the SSAF system, and it can only do so with the removal of all activity on ECSZ faults. This intriguing result may be further evidence for a possible balancing connection between the SSAF system and the ECSZ system. Lastly, in order to determine whether block rotation may still be a mechanism of slip transfer between the SSAF and ECSZ, and to fill a gap in our knowledge of Eastern Transverse Ranges (ETR) fault slip rates, I conduct the first tectonic-geomorphologic slip rate study along the Blue Cut Fault. Geomorphic mapping and 10Be surface exposure dating indicate an overall time-averaged slip rate of 1.66 ± 0.44 mm/yr (± 2σ uncertainties), however an analysis of individual surface slip rates indicates that rates of slip may have slowed since ~102 – 68 ka. A slowing Blue Cut Fault suggests a slowing rate of possible block rotation, and implies that other mechanisms of slip transfer must be at work in order to enable elastic strain transfer from the SSAF to the recently active ECSZ.
  • Analysis on Nonlinear Emission from Gold Nanoparticles and Advanced Phase Retrieval Techniques for Adaptive Optics Microscopes

    Milster, Thomas D.; Eguchi, Akira; Kieu, Khanh Q.; Takashima, Yuzuru (The University of Arizona., 2020)
    Multiphoton (MP) imaging with short-wave infrared (SWIR) excitation is one of the powerful techniques to achieve deep tissue imaging. Image quality of the MP microscope is improved with adaptive optics (AO) by compensating extrinsic aberration caused by transmission through a sample. However, the AO-MP microscope has issues, such as the requirement of a proper guide star and improvement of the detection and correction techniques of the extrinsic aberration. In this dissertation, three studies are provided to overcome these issues. The first study focuses on characterization of nonlinear emission from aggregated 50 nm gold nanoparticles (GNPs) excited by a femtosecond laser at 1560 nm, which are potentially attractive guide stars for the sensor-less AO microscopy with SWIR excitation. The study clarifies nonlinear emission characteristics of GNP aggregates, including emission spectra, power dependence, polarization properties, and relationships between brightness and morphology. A critical point in the discussion is SWIR fs excitation, because the previously proposed mechanism does not explain observed nonlinear emission properties with this source. Previously unknown results that are characteristics of nonlinear emission from GNPs are explained by plasmon enhanced polarized hot electrons. The second study presents application of phase retrieval for measurement and correction of extrinsic aberrations with random phase diversity and Gerchberg's reconstruction algorithm. Optimum design parameters of the random phase patterns to improve accuracy and convergence are investigated with Fried's parameter applied to Kolmogorov turbulence. A liquid crystal on silicon (LCoS) spatial light modulator (SLM) is used to experimentally generate random diversity as a demonstration of correcting extrinsic aberration. The results provide the first optimization study using an LCoS and the Gerchberg algorithm in a sensor-less AO application. The third study presents a new single-shot phase retrieval technique called complex diversity. Multiple irradiance data are obtained by a computer-generated hologram (CGH) designed to generate multiple diffraction orders with different diversity values. Complex-number pupil filters containing both amplitude and phase values associated with the individual diffraction orders are determined by numerical propagation from the CGH, and they are used for reconstruction of the extrinsic aberration. The complex diversity technique estimates extrinsic Kolmogorov aberration better than conventional single-shot techniques for a distant point object.
  • The Monetized Value of Knowing Genetic Information With Application to BRCA Mutation: Risk Reduction, Better Treatment, and Potential Values

    Abraham, Ivo; Oh, Yeum Mok; McBride, Ali; Bhattacharjee, Sandipan; Slack, Marion; Jeter, Joanne (The University of Arizona., 2020)
    Importance Women with inherited BRCA1/2 mutations have a higher risk of breast cancer morbidity and mortality. Expanding genetic testing for all women could identify additional mutation carriers who may benefit from preventive interventions. While previous studies focused on the cost-effectiveness of BRCA testing in one disease/setting, the value of knowing BRCA information in multiple settings including breast cancer prevention needs further investigation. Objective To assess the incremental lifetime effects, costs, and net-monetary benefit (NMB) of knowing BRCA information to 40-year-old women without breast cancer by comparing two strategies; ‘with BRCA information’ and ‘without BRCA information.’ Design and Settings A decision-analytic model in combination with a Markov model and a decision tree compared lifetime effects and costs of strategy 1: “with BRCA information” versus strategy 2: “not knowing BRCA information” in the general U.S. population of women at age 40. A hypothetical cohort was simulated based on the age-specific incidence of breast cancer. The corresponding cumulative risks obtained from published literature were utilized for mutation carriers. A life-time horizon was used at discount rate of 3.5% for both effect and cost. Results were estimated for both payer and societal perspectives. Probabilistic, deterministic sensitivity analyses and varied scenario analyses assessed model uncertainty. Interventions In strategy 1, all women at the age of 40 were assumed to have undergone BRCA testing. In strategy 2, BRCA information was not available, and only women with multiple family history of breast cancer were assumed to receive same prophylactic surgery as BRCA carriers. A positive and negative result (BRCA testing for “with BRCA information” and family history testing for “without BRCA information”) prompted a different uptake of prophylactic surgery, chemoprevention, or no prevention. Main Outcomes and Measures Incremental NMB (INMB) was calculated as the monetized benefit of knowing BRCA information per person. Components of NMB included direct medical costs in the payer perspective. Indirect health costs and benefits were considered in the societal perspective. A willingness-to-pay (WTP) threshold of $150,000/QALY was utilized in INMB calculation. The net monetized value of knowing BRCA information was estimated by multiplying the INMB with the eligible population. The net monetized value of knowing BRCA information was presented for year 2020 and accumulated over the ensuing 15 years. Results Compared with strategy 2 (without knowing BRCA information), testing all general female populations at the age of 40 provided an additional 0.01 QALYs at a cost of $588, resulting in an INMB of $663 from the payer perspective and $1,006 from the societal perspective, respectively (WTP= $150,000). In a probabilistic sensitivity analysis, BRCA information showed a positive INMB for 60.1% of the simulations. Both deterministic sensitivity and scenario analyses documented the robustness of the finding. Escalated to the U.S. population of women age 40 without breast cancer, knowing BRCA status resulted in net monetized value of $1.3 billion ($2.0 billion) in one year and yielded accumulated monetized value of $18.3 billion ($27.6 billion) over next 15 years in payer (societal) perspective. Conclusions and Relevance This study quantifies the monetized value of knowing BRCA information for the general population of women age 40 without breast cancer and shows that knowing BRCA information is cost saving for payers ($1.3 billion in one year and $18.3 billion over the next 15 years) and society ($2.0 billion in one year and $27.6 billion in 15 year). This provides compelling short-term and long-term evidence for routine BRCA testing of women age 40 without breast cancer as part of wellness screening and disease prevention.
  • Tribal Strategic and Sustainable Climate Change Adaptation: A Case Study of the Confederated Salish and Kootenai Tribes

    Gimblett, Howard R.; Rae, Lynn; Trosper, Ronald L.; Colombi, Benedict J. (The University of Arizona., 2020)
    Native nations are at the forefront of the climate change crisis and one of the most vulnerable populations to the impacts, but they also possess the most knowledge and experience with adaptation. A growing number of Native nations and tribal institutions are preparing for climate change and developing strategies, formal plans, and initiatives to increase the resiliency of their communities. Moreover, many American Indian tribes are considered models for climate change adaptation because they are tackling complex climate change problems across multiple scales with fewer resources to increase the resiliency of their communities. Previously published research shows that Native nations that exercise sovereignty and self-governance while maintaining cultural continuity are having greater success at managing their land and natural resources (Jorgenson 2007). There is, however, limited understanding of tribal climate change adaptation and additional information is needed to understand how tribes are exercising self-governance and approaching climate change issues to advance adaptation planning and implementation. The purpose of this research is to identify and consider some of the challenges of tribal climate change adaptation and the strategic approaches that tribes are using to manage and protect their land, natural resources and communities. This research involves a limited review of the tribal natural resource planning and climate change adaptation literature, and a case study with the Confederated Salish and Kootenai Tribes (CSKT) of the Flathead Reservation to assess the strategies and resources utilized by their communities to support adaptation planning. A total of 11 semi-structured interviews were conducted with CSKT leaders and department representatives to consider tribal perspectives and experiences in the adaptation planning and implementation process. Additionally, a small group discussion was conducted with CSKT Elders to understand how climate change is affecting the Tribes’ communities and cultures. This research and the case study findings demonstrate the transformative potential for tribal community development and climate change adaptation when aspects of tribal sovereignty, self-governance, and strategic and sustainable natural resource management are embedded into tribal planning and decision-making processes. While there are varying challenges and complexities associated with tribal climate change adaptation that must be considered, the findings offer examples and insights that may help other tribes further develop existing strengths, protect cultural and spiritual values, and increase community resilience. This research also considers future research needs and next steps to support tribal climate change adaptation.
  • Representation of Large-Scale Ocean Circulation in the Atlantic and Southern Ocean in Climate Model Simulations and Projected Changes under Increased Warming

    Russell, Joellen L.; Beadling, Rebecca; Goodman, Paul J.; Stouffer, Ronald J.; Cohen, Andrew S.; Harig, Christopher T. (The University of Arizona., 2020)
    The global ocean acts as a mediator of Earth’s climate due to its role in the storage of heat and carbon. Presently, the ocean accounts for the storage of approximately 93% of the anthropogenic heat on our planet and ~27% of the anthropogenic CO2. Two regions in particular, the Southern Ocean and North Atlantic Ocean (SO, NA), act as gateways for the exchange of CO2 and heat between the atmosphere and the interior ocean. This is due to the unique water mass transformation processes that occur in these regions. Despite their disproportionate role in the climate system, large uncertainty exists with respect to understanding how the ocean circulation patterns and properties are projected to change in these regions throughout the 21st century. One pathway toward reducing projection uncertainty in these regions is to use modern observations and observational products to comprehensively diagnose, quantify, and improve upon mean state biases that exist in the climate simulations used to produce future climate projections. The work presented in this dissertation is a comprehensive analysis of the large-scale ocean circulation and properties in historical and 21st century simulations of large-ensembles of fully-coupled climate and Earth System Models contributed to multiple generations of the Coupled Model Intercomparison Project (CMIP). In the subtropical NA, a key region through which properties from the tropics are advected to the subpolar latitudes, the volume transports of the major flow regimes are reasonably represented in many CMIP5 models relative that observed by the Rapid Climate Change (RAPID) instrumental array at 26.5ºN. As the climate warms, all components of the total flow through the subtropical NA, with the exception of the wind-driven surface Ekman transport, are projected to weaken. Particularly, by applying the dynamical theory of Sverdrup balance, this work highlights the fact that the wind-driven NA subtropical gyre itself is projected to spin-down in response to a reduced wind stress curl over the subtropical latitudes. This spin-down, in conjunction with the reduced overturning at high-latitudes, acts as a source of significant additional weakening to the northward western boundary current flow in the upper ocean. In the SO, despite its dominant role in the oceanic uptake of anthropogenic carbon and heat relative to other basins, the large-scale circulation and properties have been poorly represented in climate models, resulting in low confidence ascribed to 21st century projections of the state of the SO. A comprehensive analysis of the simulation of the large-scale circulation and properties is presented for the Southern Ocean (SO) across thirty-one CMIP5 models. The main focus lies in building a framework to understand the major contributors to a model’s ability to represent the Antarctic Circumpolar Current (ACC) transport. Across the CMIP5 ensemble, the models fall into five different categories: 1) models that produce a reasonable ACC transport for approximately the right reasons, 2) models that accurately simulate key metrics, yet produce a too weak ACC, 3) models that simulate the wind stress forcing at the ocean surface accurately, but have errors in the density gradient, 4) models that simulate an accurate density gradient, but exhibit errors in the wind stress forcing, and 5) models that produce errors in all the metrics. Building on the framework presented in the CMIP5 study, a comprehensive assessment of the large-scale circulation and properties as simulated in the SO is performed across ensembles of models contributed to the past three CMIP generations (CMIP3-CMIP6). The CMIP6 models show improved representation of key observable-metrics in the SO including surface wind stress and wind stress curl, strength of the ACC, and meridional density gradients in the region of the ACC. However, some persistent biases have carried over into CMIP6 including an upper ocean that remains too fresh and too warm, significant warm biases at depth in several simulations, and a poor representation of Antarctic sea ice extent (SIE). These biases in observable metrics need to be considered when interpreting projected trends or biogeochemical properties in this region.
  • The Enigmatic Northwestern North American Climate Response to the 1783 Laki Eruption

    Anchukaitis, Kevin; Edwards, Julie; Woodhouse, Connie; Meko, David (The University of Arizona., 2020)
    The 1783 Laki eruption in Iceland was among the largest high-latitude eruptions of the last millennium, but the seasonal and regional climate response was heterogeneous in space and time. In North America, tree-ring maximum latewood density (MXD) chronologies from Alaska suggest that the summer of 1783 was extraordinarily cold, even though the eruption did not begin until early June. In order to resolve the spatial extent and seasonal timing of the climate ffects of the Laki eruption, we use a combination of high-resolution quantitative wood anatomy analyses, climate model simulations, and proxy systems modeling to examine the temperature response over northwestern North America. We measured wood anatomical characteristics of white spruce (Picea glauca) trees from two locations in northern Alaska. Cell characteristics in the earlywood of the 1783 ring are normal while latewood cell wall thickness is significantly and anomalously reduced compared to non-eruption years. Applying complementary evidence from climate model experiments and proxy systems modeling, we interpret these features as indicating an abrupt and premature cessation of cell wall thickening due to an rapid decrease in temperature toward the end of the growing season linked to both forced and internal climate variability. Reconstructions using conventional annual resolution maximum latewood density likely over-estimate total growing season cooling in this year, while ring width data fail to capture this abrupt late summer volcanic signal. Our study has implications not only for the interpretation of the climatic impacts of the Laki eruption in North America, but more broadly demonstrates the importance of considering timing and internal variability when comparing proxy temperature reconstructions and climate model simulations, and demonstrates the value of developing cellular-scale tree-ring proxy measurements for paleoclimatology.
  • Spatiotemporal Peatland Productivity and Climate Relationships Across the Western South American Altiplano

    Anchukaitis, Kevin J.; Anderson, Talia; Christie, Duncan A.; Chávez, Roberto O.; Evans, Tom P. (The University of Arizona., 2020)
    The South American Altiplano is one of the largest, semiarid, high-altitude plateaus in the world. Within the Altiplano, peatlands locally known as ‘bofedales’ provide key water resources and ecosystem services to Andean communities and are important components of regional hydrology. Since bofedales are found near the upper-elevational limits for vegetation growth, they are highly sensitive to climate variability and change. Recent warming trends, changes in snow cover, and shifting atmospheric circulation patterns are among the differences that will likely affect peatland dynamics and regional hydrology. It is therefore urgent to better understand the relationships between climate variability and the spatiotemporal variations in peatland productivity across the Altiplano. Here, we use a recently developed inventory of bofedales, based on 31 years of Landsat data, to explore regional productivity patterns and climate influences on the dynamics of peatland vegetation. We focus specifically on the bofedal network in the Chilean Altiplano, the driest sector of the plateau, and use the satellite-derived NDVI (Normalized Difference Vegetation Index) as an indicator of vegetation activity. We develop temporally continuous NDVI products at the bofedal unit, 1 km2, and 5 km2 scales in order to evaluate relationships with climate variables over the past three decades. We conclude that cumulative precipitation from the current year to two years prior and snow persistence from two years prior are strongly associated growing season productivity, demonstrating the complex lagged relationships between climate and peatland productivity in the Chilean Altiplano. We also show that the recent jump in peatland productivity between 2013–2015 drives the increasing trend in NDVI and is likely a response to consecutive years of anomalously high snow accumulation and rainfall. A significant relationship between productivity and temperature does not emerge at the large-scale. Understanding the large-scale productivity dynamics and characterizing the response of bofedales to climate variability over the last three decades provides a baseline to more effectively monitor the responses of Andean peatlands to climate change.
  • Estimating the Relationships Between Early-Life Air Pollution Exposures and Wheezing From Birth Into Adulthood

    Beamer, Paloma I.; Lothrop, Nathan; O'Rourke, Mary Kay; Canales, Robert; Guerra, Stefano (The University of Arizona., 2020)
    Half of children in the United States experience wheezing incidents before their 6th birthday, and while most outgrow this condition, those who do not are at increased risk for irreversible decrements in lung function and development of asthma. During early life, lungs are more susceptible to environmental insults, however, findings on the association between ambient air pollution exposures in this time and wheezing outcomes are mixed, and effects on later wheezing outcomes have only been studied to age 11. To better understand these relationships, I took advantage of respiratory health data from the Tucson Children’s Respiratory Study (TCRS), one of the oldest on-going, prospective respiratory birth cohorts in the world, with 32 years of follow-up data (enrolled from 1980-1984, n=1246). I also utilized air pollution measures from two independent, spatially-representative air pollution studies in the Tucson, AZ area, the Pima County Workers Study (1987-1991) and the Tucson Air Pollution Study (2015-2016), to build and validate land use regression (LUR) models for NO2, NOx, PM2.5, and PM10, and then estimate exposures for TCRS participants at birth and age 6. Air pollution measurements from the Pima County Workers and Tucson Air Pollution Studies were well below ambient air quality standards, and concentrations decreased between the study periods, owing to regulations and controls enacted during this time. More sampling sites better characterized the relationships among predictors and pollutant concentrations, as shown by external validation, while the opposite was shown by internal validation. Decreased external validation capacity of LUR models can attenuate the effect of estimated air pollution exposures in health models. Despite relatively low concentrations of pollutants, PM2.5 exposures at birth significantly increased the risk of having wheezing in the first 3 years of life, which has been associated with reduced lung function and later development of asthma. Children born to mothers <25 years of age were more susceptible to NO2 and NOx exposures at birth for wheezing by age 3. NO2 exposures at birth also increased the risk of more frequent wheezing from age 8-32 years. Further reducing ambient concentrations of these pollutants through regulations or emissions controls could reduce the risk of these outcomes and future, long-term respiratory health implications.
  • The Ecological Basis of an Emergent Behavioral Trait

    Duckworth, Renee A.; Potticary, Ahva; Badyaev, Alexander V.; Williams, Tony D.; Michod, Richard (The University of Arizona., 2020)
    Organisms develop and evolve in complex and multi-faceted environments. While the development of the phenotype is generally considered to be due to processes internal to the organism, with the environment acting primarily as a source of selection, phenotypes are produced as a result of reciprocal interactions between internal organismal qualities and the environment. Thus, a phenotype encompasses all of the factors that contribute to its ontogeny, such as other individuals and microhabitat, with the consequence that the developmental system of one individual is often different from that of its parents. For this reason, individual development is subject to the vagaries of life experiences across the life cycle, yet despite this enormous variation in local experience, regularity at the population-level, such as population cycles, emerge. Broadly, how do interactions across scales influence evolution? In this dissertation, I investigated how interactions across local and population scales produced variation in behavioral strategies expressed by breeding birds to answer several key questions. First, given that the developmental system producing the phenotype of the parents often differs from that of the offspring, what is the impact of a mismatch between maternal and offspring environment on the trait expression of offspring? How can the incredibly variable experience of individuals produce specific patterns of offspring trait variation relative to environmental context? Why may population cycles emerge from variable individual experience? And lastly, what mechanisms within taxa may produce recurrent behavioral evolution across taxa? I investigated these questions using variation in the parental care strategies of western bluebirds (Sialia mexicana). My first chapter explored how a mismatch between maternal and offspring environment influenced the expression of parental care strategies in offspring. We found that when there was a mismatch between maternal and offspring experience in competition over resource availability, maternal influence on offspring aggression led to offspring pursuing a rare alternative behavioral strategy with lower fitness outcomes, but only when the environmental contexts across generations were not concordant. In this sense, behavioral variation emerged at the individual level when there was disconnect between local experience and conditions at the population level. While the evolution of adaptive maternal effects are thought to require specific, predictable cues to evolve, such specificity necessarily limits the breadth of environments in which maternally-induced traits function. Moreover, female experience is highly variable across ecological contexts, yet across females, maternal influence produces repeatable, specific offspring behavioral phenotypes. What processes allow for local complexity to be translated into specific outcomes? In my second chapter, I tested the hypothesis that the adaptive maternal effects did not evolve to track specific environmental cues, but instead used a general pathway (HPA stress response axis) that integrated maternal experience of multiple environmental factors. By combining long-term data spanning diverse environmental contexts with a large-scale field experiment, we showed that multiple environmental cues can alter maternal stress hormone levels (corticosterone), that variation in maternal corticosterone predicted offspring trait variation in aggression, and that expression of the maternal effect could not be explained by a single cue. Together, these data indicate that this adaptive maternal effect functions because it can accommodate multiple environmental stressors. Maternal stress pathways can respond to a wide variety of environmental stimuli, and thus this maternal effect can produce appropriate dispersal patterns in offspring, despite wide variation in the habitats that females encounter. Offspring behavioral phenotypes result from an interaction between both maternal and offspring environments, which may produce trait variation in many individuals at one time. For this reason, maternal effects are thought to be a potent regulator of population dynamics, because they may mediate feedbacks between offspring phenotype and environmental conditions. In my third chapter, I tested this idea by performing local manipulations of maternal experience across five replicate populations. I found that decreasing female experience of competition increased recruitment of sons. Lastly, in my fourth chapter, I explore the physiological mechanisms that may produce the recurrent emergence of cooperative breeding. Cooperative breeding has evolved across diverse avian taxa residing in very different environments, thus determining how local trait variation interacts with ecology to promote evolution of cooperative breeding strategies is an important question.
  • The Role of Social Stress in Body Composition: Results From the Women’s Health Initiative

    Chen, Zhao; Follis, Shawna; Bea, Jennifer; Hu, Chengcheng; Klimentidis, Yann (The University of Arizona., 2020)
    Introduction: Changes in several body composition systems are responsible for a high burden of chronic conditions among aging adults. Bone loss and obesity are particularly important proximal risk factors of chronic conditions among aging women. There is evidence that psychosocial stress related to socioenvironmental factors is a distal risk factor for both body composition changes and chronic disease outcomes. The overall objective of this dissertation was to establish a temporal association between social stress with body composition factors, fat and bone, to improve understanding of the pathway through which social stress alters chronic disease outcomes among postmenopausal women. Methods: To address the overall objective, this dissertation undertook three studies using data from the Women’s Health Initiative (WHI) health study. The exposure for the studies were three psychosocial constructs related to the social environment: social strain, social functioning, and social support. One study evaluated social stress with time to fracture incidence using data from the WHI main study (N=161,808). The remaining two studies used data from the WHI Bone Mineral Density (BMD) sub-cohort (N=11,020) to evaluate BMD and visceral adipose tissue (VAT) outcomes. Results: High social stress was associated with greater loss of BMD over six years. After adjustment for confounders, each point higher social strain was associated with a 0.082% greater loss of femoral neck BMD, 0.108% loss of total hip BMD, and 0.069% loss of the lumbar spine BMD (P<0.05). In the second study, social stress was associated with greater risk of total and hip fractures. Social functioning had the greatest magnitude of effect with each one SD higher score, representing lower stress, associated with lower risk of total fractures (HR=0.90; 95% CI: 0.89 to 0.91) and hip fractures (HR=0.87; 95% CI: 0.84 to 0.89). In the third study, results from linear mixed models showed that social stress was longitudinally associated with greater VAT area and visceral/subcutaneous adipose tissue ratio. Age and race/ethnicity modified associations between social stress with fractures and VAT outcomes. Conclusion: The findings of this dissertation provide evidence for an association between social stress and detrimental changes in body composition. Women with high social stress were found to have greater longitudinal risk for decreased BMD, fracture incidence, and greater VAT. The results also suggest heterogeneity in the effect of social stress on body composition by race/ethnicity and age. Future research is needed to determine causal effects of social stress in body composition changes.
  • Proximate Sensing and Computer Modeling to Enhance Food and Water Security by Improving Agricultural Water Management

    Slack, Donald C.; Gonzalez Cena, Juan Roberto; Silvertooth, Jeffrey; Waller, Peter; Pessarakli, Mohammad (The University of Arizona., 2020)
    The global population continues to grow in both number and impact per capita on the environment, exerting more pressure on already degraded lands. Moreover, climate emergency impacts on the environment demand immediate actions to preserve our civilization. Agriculture accounts for 69% of total human water withdrawal, ranking first by consumptive water use among major economic sectors. Thus, any improvement to agricultural water management can significantly save water contributing to enhance and secure food production. The consolidation and the emergence of new technologies as computer modeling and remote sensing (RS) allow us to analyze and simulate different strategies, expediting improvements to agricultural water management. In this research, HYDRUS-2D computer model was used to analyze and develop improved water management practices for leaching salts on saline agricultural soils. HYDRUS-2D simulations represented the actual conditions properly, producing similar salinity patterns and flow lines to those of registered on the lab experiments. Those results were further validated by the good agreement when comparing the breakthrough curves, which is a more quantitative way to compare results. HYDRUS-2D models were developed to simulate and test an alternative method to leach salts. Compared to traditional leaching, both improved strategies reduce water consumption, off-site pollution, and save time. Also, aiming to improve agricultural irrigation management, a novel RS approach was proposed, and pilot tested. Using RS data, from UAS and Satellites, a new trapezoidal space was developed from the near-infrared transformed reflectance (NTR) and normalized difference vegetation index (NDVI) data to estimate and map of soil moisture (SM). The estimated SM was evaluated against in situ observations from TDR sensors and a traditional RS approach based on thermal data and NDVI. SM from the novel approach was further compared to SM estimates from the traditional surface temperature-NDVI approach. Also, HYDRUS-2D numerical simulations were conducted to evaluate SM distribution throughout the soil profile. Results indicate that the NTR-NDVI estimation accuracy varies with soil depth, with r between 0.18 and 0.93 and RMSE between 0.02 and 0.18 cm3 cm-3. The best estimations using UAS- and Satellite-based NTR-NDVI approach were obtained for the near surface soil layer. The NTR-NDVI SM estimates were comparable to LST-NDVI SM. Root-zone SM and fractional PEW maps’ spatial variability depended on the resolution of the source data used. The generated high spatial resolution root-zone SM and PEW maps enable crop producers to increase water productivity by applying water more precisely and reducing environmental impacts.
  • Differences in Propagation and Isolation of Wild Type Iowa Strain and Luciferase Iowa Strain Cryptosporidium Parvum

    Riggs, Michael W.; Pottorff, Karissa; Elliott, David; Vedantam, Gayatri (The University of Arizona., 2019)
    Cryptosporidium parvum, a coccidian parasite in the phylum Apicomplexa, is the second leading infectious agent responsible for causing diarrhea in children younger than five years old in resource-limited countries. It also causes disease in calves and other mammals and is a major cause of economic loss in agriculturally important livestock species. There are currently no consistently effective parasite-specific pharmaceuticals available for treating or preventing the infection besides a P23 vaccine. Therefore, Cryptosporidium parvum was genetically modified by others to express the Luciferase gene to help researchers rapidly and efficiently test multiple potential anti-cryptosporidial drugs and therapies. These genetically modified organisms are also aiding in the study of gene expression, with the ability to identify the slightest changes in transcription, and the role(s) of genes thought to be involved in pathogenesis. In the present study the Luciferase Cryptosporidium parvum (Nluc-Cp) or Wild type Iowa strain Cryptosporidium parvum (WT- Cp) were used to infect Holstein bull calves to determine the level of propagation and recoverability of each after isolation procedures. It was hypothesized that the propagation and isolation of Nluc-Cp versus WT-Cp in neonatal calves would be the same. It was found that the Nluc-Cp calves were healthier and propagated fewer oocysts than WT-Cp. Further, Nluc-Cp proved difficult to isolate based on the self-adherent nature of the oocysts which resulted in clumping and reduced recovery.
  • Automated Cyber Vulnerability Analysis using Machine Reasoning

    Hariri, Salim; Sayan, Carla; Akoglu, Ali; Ditzler, Greg; Ball, George L. (The University of Arizona., 2020)
    One of the major cyber security challenges we face today is overcoming the current limits of security information systems ability to improve an organization’s overall security posture and prioritize the security focus of an enterprise-level network. Latest developments in cyber security relating to the vulnerability of national assets, public utilities, and private industry have raised concern about threat response. The basic advantage to the cybercriminal is a reliance on the overwhelming number of attack vectors at their disposal. The amount of information presented to security analysts in large enterprises (e.g. thousands of machines, one million plus security incidents per day) is a challenging problem. This places analysts at a disadvantage of reactive security defense without a systematic approach to prioritize the security focus of a mission critical enterprise level network. Information presented, while abundant, lacks the context for arriving at knowledge to help determine critical node urgency, true priority of response, and the application of best courses of actions. To improve the security posture and assist the cyber defender, a new paradigm called Automated Cyber Vulnerability Analysis using Machine Reasoning has been implemented which captures relationships between security concepts and physical systems. The development of a Cyber Security Ontology and Cyber Security Infrastructure Ontology is outlined and the value of using ontology-based computational artifacts to support information integration and semantically reason about the impact of vulnerability and attacks on actual enterprise physical systems is demonstrated. We also implement scenarios that adopt a rule engine to enhance the machine reasoning ability of the ontology, resulting in new courses of actions and recommendations for the protection of physical enterprise systems. Our implementation is realized, and results show our approach as a powerful construct to improve security posture, offering a systematic approach to enhance cyber security decision support increasing the speed of analysis.

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