Finding Statistically Significant Interactions between Continuous Features

The search for higher-order feature interactions that are statistically significantly associated with a class variable is of high relevance in fields such as Genetics or Healthcare, but the combinatorial explosion of the candidate space makes this problem extremely challenging in terms of computational efficiency and proper correction for multiple testing. While recent progress has been made regarding this challenge for binary features, we here present the first solution for continuous features. We propose an algorithm which overcomes the combinatorial explosion of the search space of higher-order interactions by deriving a lower bound on the p-value for each interaction, which enables us to massively prune interactions that can never reach significance and to thereby gain more statistical power. In our experiments, our approach efficiently detects all significant interactions in a variety of synthetic and real-world datasets.Comment: 13 pages, 5 figures, 2 tables, accepted to the 28th International Joint Conference on Artificial Intelligence (IJCAI 2019

Current and Historical Drivers of Landscape Genetic Structure Differ in Core and Peripheral Salamander Populations

With predicted decreases in genetic diversity and greater genetic differentiation at range peripheries relative to their cores, it can be difficult to distinguish between the roles of current disturbance versus historic processes in shaping contemporary genetic patterns. To address this problem, we test for differences in historic demography and landscape genetic structure of coastal giant salamanders (Dicamptodon tenebrosus) in two core regions (Washington State, United States) versus the species' northern peripheral region (British Columbia, Canada) where the species is listed as threatened. Coalescent-based demographic simulations were consistent with a pattern of post-glacial range expansion, with both ancestral and current estimates of effective population size being much larger within the core region relative to the periphery. However, contrary to predictions of recent human-induced population decline in the less genetically diverse peripheral region, there was no genetic signature of population size change. Effects of current demographic processes on genetic structure were evident using a resistance-based landscape genetics approach. Among core populations, genetic structure was best explained by length of the growing season and isolation by resistance (i.e. a ‘flat’ landscape), but at the periphery, topography (slope and elevation) had the greatest influence on genetic structure. Although reduced genetic variation at the range periphery of D. tenebrosus appears to be largely the result of biogeographical history rather than recent impacts, our analyses suggest that inherent landscape features act to alter dispersal pathways uniquely in different parts of the species' geographic range, with implications for habitat management

Flow Resistance Dynamics in Step-pool Channels: 2. Partitioning Between Grain, Spill, and Woody Debris Resistance

In step-pool stream channels, flow resistance is created primarily by bed sediments, spill over step-pool bed forms, and large woody debris (LWD). In order to measure resistance partitioning between grains, steps, and LWD in step-pool channels we completed laboratory flume runs in which total resistance was measured with and without grains and steps, with various LWD configurations, and at multiple slopes and discharges. Tests of additive approaches to resistance partitioning found that partitioning estimates are highly sensitive to the order in which components are calculated and that such approaches inflate the values of difficult-to-measure components that are calculated by subtraction from measured components. This effect is especially significant where interactions between roughness features create synergistic increases in resistance such that total resistance measured for combinations of resistance components greatly exceeds the sum of those components measured separately. LWD contributes large proportions of total resistance by creating form drag on individual pieces and by increasing the spill resistance effect of steps. The combined effect of LWD and spill over steps was found to dominate total resistance, whereas grain roughness on step treads was a small component of total resistance. The relative contributions of grain, spill, and woody debris resistance were strongly influenced by discharge and to a lesser extent by LWD density. Grain resistance values based on published formulas and debris resistance values calculated using a cylinder drag approach typically underestimated analogous flume-derived values, further illustrating sources of error in partitioning methods and the importance of accounting for interaction effects between resistance components

MS Environmental Biology Capstone Project

This study aims to provide a deeper understanding of the role of competition in food webs, and more specifically, in trophic cascades induced by biodiversity loss. Trophic cascades are food web disturbances that result from the removal of an important species, often a predator, and lead to dramatic changes in herbivore and plant populations. It is critical to understand the mechanisms that drive and mitigate trophic cascades, because global biodiversity loss is increasing. Previous research suggests that biodiversity, specifically intraguild biodiversity with members in the same trophic level, is an important factor in reducing the negative effects of trophic cascades. High biodiversity increases competition, which limits population growth of individual species. Research on competition in relation to trophic cascades is scarce, prompting the need for more direct study. I plan to test the hypothesis that increased herbivorous insect biodiversity will decrease typical trophic cascade strength, by increasing competition between the herbivores and reducing plant loss. Using microcosm ecosystems in fish tanks, I will study a three-trophic-level food chain where a predator is present, and a two-trophic-level cascade where the predator has been removed. By manipulating herbivore diversity and predator presence in the tanks, I will investigate how herbivore diversity influences competition, and how the effect of changing herbivore diversity differs in food webs with and without predators. I expect that higher herbivore diversity will yield higher average plant biomass compared to herbivore monoculture treatments, and that plant biomass will be greater in tanks where the predator is present. Maintaining high biodiversity within ecosystems ensures that another mechanism, competition, maintains stable levels of herbivores and protects against major plant loss. My study will provide information to aid in management practices to help sustain ecosystems experiencing biodiversity loss

Effects of fish density, identity, and species richness on stream ecosystems.

Stream ecosystem properties and functions are important because they provide services such as water purification, oxygen production, and carbon fixation that help sustain life. Aquatic organisms can affect these properties and functions through different pathways linked to a species trophic and functional characteristics. It is necessary to understand how these ecosystem effects vary among taxa because as aquatic biota change as a result of random, natural, or anthropogenic influences, ecosystems properties and functions are likely to be affected.This research suggests that the population size, the identity of species in the assemblage, as well as the number of species making up the assemblage can be important factors affecting stream ecosystem properties and functions. Chapters 1--3 were conducted in artificial stream mesocosms, and may have limited applicability to natural stream ecosystems where a variety of abiotic factors can influence ecosystems. In Chapter 4, I tested the ecosystem effects of three fish species from different functional groups on PPR, benthic algae biomass (as chlorophyll-a), and benthic invertebrate density in a natural stream ecosystem using field enclosures. Treatments were Blackstripe Topminnow (Fundulus notatus), a surface insectivore; Longear Sunfish (Lepomis megalotis), a watercolumn insectivore; Orangethroat Darter (Etheostoma spectabile), a benthic invertivore; and a fishless control. Primary productivity was greater in all enclosures with fish than in enclosures without fish. Relative to control enclosures, benthic algae biomass was not different in Blackstripe Topminnow treatments, but was greater in Longear Sunfish treatments on both sample days, and was greater in Orangethroat Darter treatments on day 15. Benthic invertebrate abundance was not affected by any of the fish treatments. These data agree with results from previous mesocosm experiments. Thus, despite the limited realism of stream mesocosms, patterns observed in mesocosm experiments are likely to occur in natural stream ecosystems. (Abstract shortened by UMI.)Fishes are important consumers in stream ecosystems, having important regulatory roles for many ecosystem properties and functions. In this dissertation, I addressed the effects of fishes on stream ecosystems from three perspectives. I asked (1) if fish ecosystem effects were dependent on local fish density, (2) if fish effects were caused by different species-specific food web pathways, and (3) if co-occurring fish species had facilitative effects on ecosystems when in more specious assemblages

Flow Resistance Dynamics in Step-pool Stream Channels: 1. Large Woody Debris and Controls on Total Resistance

Flow resistance dynamics in step-pool channels were investigated through physical modeling using a laboratory flume. Variables contributing to flow resistance in step-pool channels were manipulated in order to measure the effects of various large woody debris (LWD) configurations, steps, grains, discharge, and slope on total flow resistance. This entailed nearly 400 flume runs, organized into a series of factorial experiments. Factorial analyses of variance indicated significant two-way and three-way interaction effects between steps, grains, and LWD, illustrating the complexity of flow resistance in these channels. Interactions between steps and LWD resulted in substantially greater flow resistance for steps with LWD than for steps lacking LWD. LWD position contributed to these interactions, whereby LWD pieces located near the lip of steps, analogous to step-forming debris in natural channels, increased the effective height of steps and created substantially higher flow resistance than pieces located farther upstream on step treads. Step geometry and LWD density and orientation also had highly significant effects on flow resistance. Flow resistance dynamics and the resistance effect of bed roughness configurations were strongly discharge-dependent; discharge had both highly significant main effects on resistance and highly significant interactions with all other variables

Organic carbon storage in mountain river valley bottoms of the western United States

2018 Summer.Includes bibliographical references.Valley bottoms, which include river channels and associated floodplains, are important components of the terrestrial carbon sink. Downed wood and floodplain soil in valley bottoms act as transient pools of organic carbon (OC) that can be stored for up to millennial timescales. This dissertation focuses on quantifying OC storage as downed wood and soil in mountain river valley bottoms in four disparate watersheds that span three mountain ranges across the western United States. Across these four basins, I measured wood load, floodplain OC content, morphologic metrics, and/or vegetation metrics at a total of 178 sites. I find that wood load is a function of metrics that relate to river corridor spatial heterogeneity and wood storage patterns (together determining wood trapping efficiency) at the reach scale and, at a broader spatial scale, wood supply. Wood in an undisturbed basin stores twice as much wood OC as a similar but extensively clearcut basin. In examining floodplain soil OC, I find that much of the variability in OC concentration is due to local factors, such as soil moisture, elevation (a proxy for temperature), and valley bottom geometry. From this, I conclude that local factors likely play a dominant role in regulating OC concentration in valley bottoms, and that inter-basin trends in climate or vegetation characteristics may not translate directly to trends in OC storage. I also use analysis of OC concentration and soil texture by depth to infer that OC is input to floodplain soils mainly by decaying vegetation, not overbank deposition of fine, OC-bearing sediment. Valley bottoms store significant OC stocks in floodplain soil and downed wood (ranging from 0 to 998 Mg C/ha) that vary with valley bottom form and geomorphic processes. Valley bottom morphology, soil retention, and vegetation dynamics determine partitioning of valley bottom OC between soil and wood, implying that modern biogeomorphic process and the legacy of past erosion regulate the modern distribution of OC in river networks. Soil burial is essential to preserving old OC, as measured by an extensive sample of 121 radiocarbon ages of floodplain soil OC. These radiocarbon data indicate a median residence time of floodplain soil OC of 185 yr BP. The age of the floodplain soil OC pool and the distribution of OC between wood and soil imply that OC storage in mountain rivers is sensitive over relatively short timescales to alterations in soil and wood retention, which may have both short- and long-term feedbacks with the distribution of OC between the land and atmosphere. Mountain river valley bottoms act as a high magnitude and moderately long-lasting pool of OC stored on land

Soundscape design of water features used in outdoor spaces where road traffic noise is audible

This research focused on the soundscape design of a wide range of small to medium sized water features (waterfalls, fountains with upward jet(s), and streams) which can be used in gardens or parks for promoting peacefulness and relaxation in the presence of road traffic noise. Firstly, the thesis examined the audio-visual interaction and perceptual assessment of water features, including the semantic components and the qualitative categorisation and evocation of water sounds; and secondly, the thesis investigated the effectiveness of the water features tested in promoting relaxation through sound mapping. Different laboratory tests were carried out, and these included paired comparison tests (audio-only, visual-only and audio-visual tests), semantic differential tests, as well as tests aimed at the qualitative categorisation and evocation of water features. Sound maps of the water generated sounds were developed through the use of propagation models based on either point or line sources. Three acoustic zones (‘water sounds dominant zone’, ‘optimum zone’ and ‘RTN dominant zone’ (RTN: road traffic noise)) were defined in the maps as the zones where relaxation/pleasantness can be promoted over a 20 m × 20 m area for different road traffic noise levels. Paired comparisons highlighted the interdependence between uni-modal (audio-only or visual-only) and bi-modal (audio-visual) perception, indicating that equal attention should be given to the design of both stimuli. In general, natural looking features tended to increase preference scores (compared to audio-only paired comparison scores), while manmade looking features decreased them. Semantic descriptors showed significant correlations with preferences and were found to be more reliable design criteria than physical parameters. A principal component analysis identified three components within the nine semantic attributes tested: “emotional assessment,” “sound quality,” and “envelopment and temporal variation.” The first two showed significant correlations with audio-only preferences, “emotional assessment” being the most important predictor of preferences, and its attributes naturalness, relaxation, and freshness also being significantly correlated with preferences. Categorisation results indicated that natural stream sounds are easily identifiable (unlike waterfalls and fountains), while evocation results showed no unique relationship with preferences. The results of sound maps indicated that small to medium sized water features can be used mainly in environments where road traffic noise levels are equal or lower than 65 dBA

Process Attribute Monitoring Approach to Gaseous Centrifuge Enrichment Plant Safeguards

Unattended and remote monitoring systems for the early detection of gas centrifuge enrichment plant (GCEP) misuse have long been sought by the International Atomic Energy Agency (IAEA) safeguards inspectorate, but have yet to be realized for most GCEPs. The primary misuse of concern is high enriched uranium (HEU) production but additionally include excess low enriched uranium (LEU) production and material diversion. The current research is a feasibility study that investigates a process monitoring approach combined with passive gamma spectroscopy techniques to monitor GCEPs. In the current research, a simulated reference cascade and monitoring system is used to demonstrate several techniques to monitor 235U [uranium-235] enrichment, monitor cascade ideality, detect changes in facility operations, and attribute those changes to specific normal, abnormal, or misuse scenarios. In other words, the monitoring system detects misuse and indicates to inspectors where to look for supporting physical evidence. The techniques for the detection of GCEP misuse introduced in the current research are different from all previous efforts in six fundamental ways. First, previous efforts used custom and complex equipment which could not be sustained by the IAEA safeguards inspectorate; the current research only employs existing IAEA equipment and techniques in routine use. Second, previous efforts used radioactive sources and other invasive equipment and techniques; the current research only utilizes passive and non-invasive gamma spectroscopy. Third, previous efforts relied on measurements at a single point that could be bypassed; the current research includes techniques to additionally monitor entire cascades and production units. Fourth, previous efforts used measurements of the 186 keV [kiloelectron volt] gamma line and the UF6 [uranium hexafluoride] gas pressure; the current study utilizes measurements of the 231Th [thorium-231], 234Th [thorium-234], 234U [uranium-234], and 235U [uranium-235] gamma lines. Fifth, no techniques currently exist for the detection of excess LEU production and gas flow stoppage; the current research presents techniques for the detection and attribution of these scenarios. Sixth, no previous techniques utilize the minor isotope safeguards techniques (MIST); the current research utilizes the 234U [uranium-234] gamma lines and the ratio of 235U [uranium-235] to 234U [uranium-234] to detect and attribute GCEP misuse