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Anomaly Detection in Paleoclimate Records Using Permutation Entropy
Entropy 2018, 20(12), 931; Permutation entropy techniques can be useful in identifying anomalies in paleoclimate data records, including noise, outliers, and post-processing issues. We demonstrate this using weighted and unweighted permutation entropy of water-isotope records in a deep polar ice core. In one region of these isotope records, our previous calculations revealed an abrupt change in the complexity of the traces: specifically, in the amount of new information that appeared at every time step. We conjectured that this effect was due to noise introduced by an older laboratory instrument. In this paper, we validate that conjecture by re-analyzing a section of the ice core using a more-advanced version of the laboratory instrument. The anomalous noise levels are absent from the permutation entropy traces of the new data. In other sections of the core, we show that permutation entropy techniques can be used to identify anomalies in the raw data that are not associated with climatic or glaciological processes, but rather effects occurring during field work, laboratory analysis, or data post-processing. These examples make it clear that permutation entropy is a useful forensic tool for identifying sections of data that require targeted re-analysis---and can even be useful in guiding that analysis
RNA-RNA Interactions in RNP Granule Assembly
Ribonucleoprotein (RNP) granules, which are composed of numerous RNAs and proteins, are ubiquitous features of eukaryotic cells. This thesis investigates the assembly mechanisms of P-bodies and stress granules, two cytoplasmic granules that rely on RNAs unengaged in translation to form. Previous studies in the field have focused on the roles of proteins, and specifically their intrinsically disordered regions (IDRs), in targeting components and driving granule assembly. However, domain analysis of four proteins illustrates that having an IDR is neither sufficient nor necessary for targeting to P-bodies. Although IDRs have been shown to be important in some contexts, these results suggest that IDRs are not solely responsible for RNP granule formation. With this in mind, the assembly roles of RNA were considered. RNAs self-assemble robustly in vitro, aided by crowders and salt. Remarkably, when total yeast RNA is allowed to assemble in vitro, the RNAs that are enriched in these assemblies are the same RNAs that are enriched in stress granules in vivo. This, in addition to observations compiled from the literature, suggests that RNA-RNA interactions may play an important role in the assembly of many RNP granules. Preliminary interrogation into RNA sequences important for RNA localization to stress granules has revealed that the addition of certain sequences can significantly alter RNA localization under stress despite total length being held constant. This argues for the presence of stress granule targeting elements within RNA, although further mechanistic investigation is required. Taken together, this thesis works towards understanding RNP assembly and the mechanisms that target their components
Developmental Fusion: Chinese Investment, Resource Nationalism, and the Distributive Politics of Uranium Mining in Namibia
China’s rising global influence has significant implications for the politics of natural resource extraction and development in sub-Saharan Africa. Focusing on the uranium industry, I analyze how China’s influence operates at global, national, and sub-national scales in relation to natural resource politics in the southern African country of Namibia. Specifically, I draw on multi-methods fieldwork to evaluate 1) how Namibians are engaging with Chinese investments in mining and 2) what implications these engagements have for the politics of mining and development, including natural resource ownership and the distribution of mining-associated benefits and costs. Contrary to portrayals of Africans as passive foreign investment recipients, I find that Namibian elites are leveraging projects like the Husab uranium mine, which is the Chinese government’s largest investment in Africa to date, to pursue their own political goals. These goals include an increased role for the Namibian state in mining. This outcome — a noteworthy achievement for a small African state — suggests that foreign investment and resource nationalism are not necessarily at odds. It also indicates that African leaders can leverage Chinese investments to improve their bargaining positions in relation to both the global economy and their own domestic politics. Within Namibia, however, the distribution of benefits and costs associated with projects like the Husab mine is likely to further marginalize already-marginalized populations. Furthermore, by reinforcing the state as the trustee of development, projects like Husab may also make it more difficult for minority communities to challenge mining-based development. Characterizing projects like the Husab uranium mine as neo-colonial exploitation by China is an over-generalization given the challenges such projects pose to historical uranium geopolitics and mining ownership patterns. It is equally clear, however, that, far from overturning all forms of mining-related exploitation, China’s rising influence can also deepen historical inequalities associated with mining, particularly for politically-marginalized communities
What Motivates Local Governments to Invest in Critical Infrastructure? Lessons from Chile
In this study, we identify institutional factors and processes that foster local government decisions about disaster risk reduction, especially critical infrastructure investments and maintenance. We propose that municipal institutional capacities, organization, leadership, and multilevel governance will affect critical infrastructure investments by local governments. To examine these ideas, we employ qualitative analysis to compare two representative medium–sized cities in Chile. Our results suggest that there are two main institutional factors that constitute the foundation for improvements in critical infrastructure in Chile: municipal institutional context and the local administration’s links with decision makers at higher levels of governance. These results imply that future interventions to strengthen local government efforts for disaster risk reduction in terms of critical infrastructures would benefit from a pre-intervention diagnosis of the target location’s existing institutional context and linkages with external governance actors
Research Practices of Civil and Environmental Engineering Scholars
In fall 2017, the University of Colorado Boulder (CU Boulder) Libraries joined with ten other university libraries to conduct an Ithaka S+R study investigating the research practices and needs of civil and environmental engineering faculty. Ithaka S+R is a not-for-profit organization doing research and strategic guidance for colleges, universities, libraries, museums, scholarly societies and other institutions that support higher education. This study was part of their ongoing research support services program on how the practices of scholars vary by disciplines.
The report shares findings from exploratory semi-structured interviews with civil and environmental engineers from CU Boulder. Themes from the interviews include the diversity of the field, the data practices of scholars, the value of different kinds of sources, and how these scholars communicate their findings and conclusions. Finally, we provide recommendations for improving services and support for civil and environmental engineers
What Do We Know About the Stewardship Gap.
In the 21st century, digital data drive innovation and decision-making in nearly every field. However, little is known about the total size, characteristics, and sustainability of these data. In the scholarly sphere, it is widely suspected that there is a gap between the amount of valuable digital data that is produced and the amount that is effectively stewarded and made accessible. The Stewardship Gap Project (http://bit.ly/stewardshipgap) investigates characteristics of, and measures, the stewardship gap for sponsored scholarly activity in the United States. This paper presents a preliminary definition of the stewardship gap based on a review of relevant literature and investigates areas of the stewardship gap for which metrics have been developed and measurements made, and where work to measure the stewardship gap is yet to be done. The main findings presented are 1) there is not one stewardship gap but rather multiple "gaps" that contribute to whether data is responsibly stewarded; 2) there are relationships between the gaps that can be used to guide strategies for addressing the various stewardship gaps; and 3) there are imbalances in the types and depths of studies that have been conducted to measure the stewardship gap.</p
Approximate Bayesian Computation for Parameter Estimation in Complex Thermal-Fluid Systems
A major challenge in computational fluid dynamics (CFD) simulations of real-world flows is the accurate assignment of boundary, initial, and geometric conditions, as well as fluid and material properties. Despite advances in experimental techniques, however, acquiring the information necessary to simultaneously set each of these conditions and properties remains a considerable challenge. As a potential solution to this difficulty, recent advances in data-driven parameter estimation techniques have provided flexible and increasingly sophisticated methods for improving the fidelity of simulation configurations using experimental data. This dissertation applies, for the first time, a technique called approximate Bayesian computation (ABC) to complex thermal-fluid flows in order to determine numerical simulation parameters from experimental or other reference data. In this dissertation, the ABC approach is demonstrated for several engineering test cases to demonstrate its efficacy at determining unknown parameters in a wide variety of settings. As a simple initial case, the logistics equation is used to demonstrate the technique. This is followed by the case of a two-dimensional turbulent buoyant jet with variable inlet velocity. The jet is modeled using a large eddy simulation (LES), and reference data is obtained from ensembles of both LES (serving as a benchmark for the technique) and direct numerical simulation (DNS) cases. The reference parameters are correctly identified based on either velocity or temperature measurements at various heights. Using a similar setup, but now with a lightly forced helium plume, the puffing frequency of the jet is identified and used to match experimental observations to predict inlet composition.Moving on to industrial engineering applications, a three-dimensional turbulent buoyant jet with unknown temperature conditions is simulated using a Reynolds-averaged Navier Stokes (RANS) simulation. In this application, reference observations come from the same RANS case with known parameters. The ABC procedure correctly identifies the inlet temperature boundary conditions. In the next case, a rotating cylinder above a high-temperature turbulent buoyant jet is investigated. Here the reference observations come from a two-dimensional RANS simulation. In particular, the initial reference case has known jet inflow and cylinder rotational velocities, and the ABC approach is shown to correctly identify the reference values of these parameters using sparse temperature statistics within the domain. In an additional test using the two-dimensional rotating cylinder case, the reference case has known species concentrations at the jet inflow and we show that ABC can correctly identify the reference concentrations using sparse species and temperature measurements within the domain. The ultimate application of ABC in this dissertation uses the technique to determine three-dimensional LES parameters based on comparisons with experimental observations. The experimental temperature data are obtained above an industrially-relevant catalytic burner using laser absorption spectroscopy. This final application identifies parameters that are not able to be measured experimentally, including inlet velocity and heat addition due to continued combustion within the flow field. These successes indicate that ABC can be extended to additional real-world engineering systems, even when only sparse observational data is available. Using ABC and reference data, one can accurately drive the selection of boundary conditions, as well as model parameters, in numerical simulations. Furthermore, ABC can provide insights into quantities that are not easily measured experimentally
Insights into Processes Affecting Greenland Ice Sheet Dynamics in a Changing Climate: Firn Permeability, Interior Thermal State, Subglacial Hydrology, and Heat Transfer Coefficients
Accurate projections of future sea level rise require detailed modeling of the relevant processes affecting glacier and ice sheet dynamics. Although sophisticated high-resolution ice sheet models have been developed in recent years, some processes are still not well understood. Through a combination of field experiments, numerical modeling, and theoretical analyses, this research explores several processes affecting dynamics of the Greenland ice sheet, particularly in a changing climate as melt increases further inland: a) A novel, low-cost in-situ method of inferring firn permeability is presented, which is especially useful in regions of the ice sheet experiencing increased melt and refrozen solid ice layers in the firn. b) Thermo-mechanically coupled flow line modeling of the Greenland ice sheet interior reveals insights about the distribution of temperate ice and sensitivity to different modeling parameters. c) A subglacial hydrology model is introduced (SHAKTI: Subglacial Hydrology and Kinetic, Transient Interactions) that allows for the coexistence of laminar and turbulent flow regimes and flexible geometry configurations that include both sheetlike and channelized drainage systems, while including melt from viscous dissipation. Application of the SHAKTI model to marine-terminating Store Glacier in west Greenland suggests a channelized system develops near the terminus with high meltwater input and collapses to a sheetlike system with low input, with some residual channel structure extending inland from the front. d) Heat transfer coefficients are obtained through modeling of internal viscous and turbulent dissipation (appropriate for subglacial and englacial hydrology) compared to the case of heated walls (the classical experimental case upon which most heat transfer coefficients are based). A difference of about a factor of two is found between the heat transfer coefficients for heated walls and the internal dissipation case
Influence of Traditional and Innovative Liquefaction Mitigation Strategies on the Performance of Soil-Structure Systems, Considering Soil Heterogeneity
Liquefaction mitigation techniques are often used in the field to alleviate liquefaction hazard to the built environment. However, the current practice of designing mitigation techniques ignores the presence of buildings, and depends solely on satisfying the settlement criteria, and constructability. This design practice is due to lack of understanding of the influence of different mitigation strategies on the performance of soil-foundation-structure systems. In this dissertation, centrifuge experiments were designed and conducted to investigate soil-mitigation-foundation-structure systems, considering two potentially inelastic structures (3- and 9-story) placed on a layered liquefiable deposit (with and without a silt cap), with three different mitigation strategies: 1) enhanced drainage through prefabricated vertical drains (PVDs); 2) shear reinforcement using in-ground structural walls (SWs); and 3) enhanced drainage and damping, and shear reinforcement provided by an in-ground gravel-rubber panel wall system. The first set of test results show that PVDs and SWs reduced total foundation settlement compared to the unmitigated case. However, they amplified accelerations on the foundations, which could increase flexural deformations and P-Δ effects, with potentially adverse effects on foundation tilt (particularly for the taller, heavier, more deeply embedded, and weaker 9-story structure). The presence of soil interlayering (due to a silt cap) affected the overall response of unmitigated and PVD-mitigated structures, particularly impacting foundation tilt. Based on the insights gained from the tests with traditional mitigation techniques, we designed and tested a new mitigation strategy for shallow-founded structures: an in-ground gravel-rubber panel wall (GR) system. This system aims to reduce building settlements and tilts, while isolating the structure from the larger acceleration demands expected in mitigated ground. Test results showed that the GRs could be beneficial, roughly satisfying design objectives for the 3-story structure, but amplified tilt on the 9-story structure. Therefore, additional design considerations and shear reinforcement are required in the panel walls to improve total system response. The results presented in this dissertation point to the importance of considering the structure’s dynamic and geometric properties, force-deformation behavior, soil interlayering, and the possible increase in shaking intensity level due to different mitigation strategies, when designing traditional or innovative techniques to mitigate consequences of liquefaction
Climate change beliefs and forest management in eastern Oregon: implications for individual adaptive capacity
The management decisions of private landowners affect forest structure and composition, and may impact the resilience of forested regions. In this case study we assessed barriers to both intentional and incidental climate-adaptive forest management among nonindustrial private forest owners in eastern Oregon, USA. In this context, incidental adaptations result from synergies between climate-adaptive forest management and actions motivated by goals such as wildfire mitigation, which landowners may prioritize regardless of concerns about climate change. Through semistructured interviews we used qualitative analyses to identify barriers to adaptation, including subjective (cognitive and experiential) and structural barriers (social, political, and economic) by comparing individual cases. Overall, we found that intentional climate change adaptation had low salience among participants, though a large majority of forest owners were active managers motivated by other goals, contributing to widespread incidental adaptation. We found that nonindustrial private forest owners who engaged in or considered intentional climate adaptation actions generally believed that anthropogenic climate change is occurring. Many respondents perceived local environmental change, notably reduced snowpack, but this was not associated with adaptive actions or intentions. The few participants who considered or implemented intentional climate adaptation actions generally had written forest management plans containing both forest inventories and specific management goals. Improving access to resources for forest management planning may enhance fire- and climate-smart forest management by facilitating scenario visioning and formalizing intentions. Although climate change beliefs were subjective barriers to intentional climate adaptation, many of the same structural barriers limited intentional and incidental adaptation. Place-based education, reliable funding mechanisms, and cooperative approaches among landowners may enhance adaptive capacity and promote the resilience of these nonindustrial private forestlands