Water utilities are facing pressure to continue to provide high-quality potable water in an increasingly energy constrained world; managing the ageing infrastructure that exists in many countries is a challenge in and of itself, but recently this has been coupled with political and public attention to the environmental impacts of the distribution system. Utility managers need to take a holistic approach to decision-making in order to determine all of the impacts of their plans. The intention of this thesis is to present a set of considerations for utility planners and managers to provide clarity to the trade-offs associated with any pipe replacement decision. This research has examined the energy relationships between operational energy reduction and the embodied energy tied to replacing deteriorated pipes in water distribution networks. These relationships were investigated through the development and application of a life-cycle energy analysis (LCEA) for three different pipe replacement schedules developed with the intent to reduce leakage in the system. The results showed that the embodied energy for pipe replacement is significant even when compared against the large amount of energy required to operate a large-scale water utility. The annual operational energy savings of between 8.9 and 9.6 million kWh achieved by 2070 through pipe replacement comes at a cost; 0.88-2.05 million kWh/mile for replacement with ductile iron pipes with diameters of 6” to 16” respectively. This imbalance resulted in a maximum energy payback period of 17.6 years for the most aggressive replacement plan in the first decade. Some of the assumptions that were used to complete the LCEA were investigated through a sensitivity analysis; specific factors that were numerically queried in this chapter include the break rate forecasting method, pumping efficiency, the leakage duration and the flow rate per leakage event. Accurate accounting of energy requirements for pipe replacement will become even more important as energy and financial constraints continue to increase for most water utilities, this thesis provides guidance on some of the complex relationships that need to be considered. / Thesis (Master, Civil Engineering) -- Queen's University, 2013-08-21 16:51:18.963

Mammalians process their photoreceptions through lateral eyes; however, non-mammalian vertebrates and invertebrates possess additional extraretinal photoreceptors over their bodies to detect light stimuli. Chromatophores, i.e. dermal specialized pigment cells, play important roles in the regulation of body patterns. Since chromatophores derive from neural crest, they share the common embryonic origin with retina. Recent evidence shows that they are light-sensitive due to opsin expression. In the present study, the expression of seven cone opsins was detected in tilapia caudal fin tissues. Moreover, distinct photoresponses were found in two chromatophore types. Regardless of stimulating wavelengths, melanophores tend to disperse and maintain cell shape at dispersion stage by shuttling pigment granules. Conversely, erythrophores respond to light in a wavelength-dependent manner. The opsin expression profiles of melanophores and erythrophores imply SWS1 and RH2 group genes may play important roles in chromatophore photoresponses. Through measuring photosensitivity, I suggest the two opsins play opposite roles in light-induced translocations of pigment granules within erythrophores: SWS1 for aggregations at UV and short wavelength regions and RH2b for dispersion in middle/long wavelengths. An antagonistic interaction occurs in the overlapping of the absorbance spectra of the two opsins. I also found that the photoresponses take place along with the occurrence of the change of cell membrane potential. In addition, the effect of different light backgrounds (broad spectrum, short wavelength-rich, and red-shifted light conditions) on the photosensitivity of tilapia erythrophores was investigated. I found that the major opsin classes (SWS1 and RH2b) responsible for photoresponses remain constant in three groups of erythrophores. Together, I postulate that melanophores may serve as a light filter in integumentary tissues, and the chromatically antagonistic mechanism enables tilapia erythrophores to sense the subtle change of environmental photic condition and to fine-tune pigmentation. I also investigated the ontogenetic change of photoresponses of rainbow trout melanophores. Distinct photoresponses were found in parrs and smolts. Furthermore, smolt melanophores responded to light in a wavelength-dependent manner. Since the change of coloration and visual system during smoltification of salmonids is regulated by thyroid hormone (TH), I suggest that the development of melanophore photosensitivity is associated to TH as well. / Thesis (Ph.D, Biology) -- Queen's University, 2013-08-27 09:57:22.907

Mammalians process their photoreceptions through lateral eyes; however, non-mammalian vertebrates and invertebrates possess additional extraretinal photoreceptors over their bodies to detect light stimuli. Chromatophores, i.e. dermal specialized pigment cells, play important roles in the regulation of body patterns. Since chromatophores derive from neural crest, they share the common embryonic origin with retina. Recent evidence shows that they are light-sensitive due to opsin expression. In the present study, the expression of seven cone opsins was detected in tilapia caudal fin tissues. Moreover, distinct photoresponses were found in two chromatophore types. Regardless of stimulating wavelengths, melanophores tend to disperse and maintain cell shape at dispersion stage by shuttling pigment granules. Conversely, erythrophores respond to light in a wavelength-dependent manner. The opsin expression profiles of melanophores and erythrophores imply SWS1 and RH2 group genes may play important roles in chromatophore photoresponses. Through measuring photosensitivity, I suggest the two opsins play opposite roles in light-induced translocations of pigment granules within erythrophores: SWS1 for aggregations at UV and short wavelength regions and RH2b for dispersion in middle/long wavelengths. An antagonistic interaction occurs in the overlapping of the absorbance spectra of the two opsins. I also found that the photoresponses take place along with the occurrence of the change of cell membrane potential. In addition, the effect of different light backgrounds (broad spectrum, short wavelength-rich, and red-shifted light conditions) on the photosensitivity of tilapia erythrophores was investigated. I found that the major opsin classes (SWS1 and RH2b) responsible for photoresponses remain constant in three groups of erythrophores. Together, I postulate that melanophores may serve as a light filter in integumentary tissues, and the chromatically antagonistic mechanism enables tilapia erythrophores to sense the subtle change of environmental photic condition and to fine-tune pigmentation. I also investigated the ontogenetic change of photoresponses of rainbow trout melanophores. Distinct photoresponses were found in parrs and smolts. Furthermore, smolt melanophores responded to light in a wavelength-dependent manner. Since the change of coloration and visual system during smoltification of salmonids is regulated by thyroid hormone (TH), I suggest that the development of melanophore photosensitivity is associated to TH as well. / Thesis (Ph.D, Biology) -- Queen's University, 2013-08-27 09:57:22.907

Aging is associated with increased insulin resistance, a condition in which the tissue response to insulin-stimulated glucose uptake is reduced. Insulin resistance is a strong predictor of disease and mortality. Aging is also associated with a decline in physical activity, lower cardiorespiratory fitness (ability to deliver oxygen to active muscles during exercise), and increase in abdominal fat. Both low cardiorespiratory fitness (CRF) and excess abdominal fat are associated with reduced insulin sensitivity in older adults. Improvements in CRF and abdominal obesity through exercise training may be responsible for improvement in insulin sensitivity. Several investigations have reported that changes in CRF and abdominal obesity through exercise are associated with changes in insulin sensitivity. To our knowledge, no prior study has assessed whether change in CRF or abdominal fat alone explains the association between exercise and improvement in insulin sensitivity in older adults. Our findings suggest that improvement in CRF may not explain the exercise-induced change in insulin sensitivity. The improvement in insulin sensitivity from exercise is explained through a decrease abdominal fat that also occurs with exercise. Additionally, improvements in waist circumference, a surrogate measure for abdominal obesity, and body mass index together explained a large portion of exercise-induced change in insulin sensitivity compared to either variable alone. Our findings suggest that exercise combined with a healthy diet will improve insulin resistance, a risk factor for development of type 2 diabetes and cardiovascular disease in older adults. Our findings suggest that the reduction in abdominal obesity is the conduit by which exercise improves insulin sensitivity in older adults. Although CRF is not related to exercise-induced change in insulin sensitivity, change in CRF from exercise has been reported to decrease risk for other health conditions, such as hypertension and all-cause mortality. Our findings suggest that clinicians should measure both waist circumference and body mass index when evaluating the effectiveness of a lifestyle-based treatment strategy for improving insulin resistance and its associated health outcomes in older adults. / Thesis (Master, Kinesiology & Health Studies) -- Queen's University, 2013-09-27 14:53:00.796

Rises in anthropogenic CO2 emissions are now widely acknowledged to be responsible for changes in the global climate, with potentially disastrous consequences if these rises continue unchecked. Although knowledge of ecosystem responses to climate change has improved, there are still large underlying uncertainties regarding their response to warming. Of all the ecosystems with the potential to mitigate rises in CO2, forests are arguably the most important because of their huge land area and store of carbon. A large proportion of the carbon stored in forests is found in the soil, and it is the response of this soil carbon to temperature that is the main determinant of a forest’s ability to act as a carbon sink, or indeed source. Understanding the response of soil carbon flux to temperature, as well as the contribution of soil carbon flux to the carbon balance of forests as a whole is crucial in helping to improve modelling approaches. In this thesis I first examined the temperature response of old and new soil organic carbon from a Sitka spruce plantation under controlled laboratory conditions. Both the old and new soil organic carbon showed similar temperature sensitivities after prolonged incubation at 20 °C, thus implying a similar response to increasing temperatures. Using a variety of different methods (root intensity, meshing and stable isotope analysis) I then studied the responses under field conditions. These methods showed that autotrophic respiration was responsible for up to 50 % of total soil respiration, and was more sensitive to temperature than heterotrophic respiration. Finally, I compared the contributions and determinants (particularly temperature and moisture) of soil respiration fluxes to ecosystem fluxes at a temperate (Sitka spruce) and Mediterranean (Maritime pine) forest. Temperature was found to be the dominant driver of soil respiration fluxes at the temperature forest, whilst soil respiration was limited by moisture at the Mediterranean forest. Statistically significant relationships between net ecosystem productivity and soil respiration (and the stable isotope signature of soil respiration) were found at both forests, indicating a close coupling between above-ground processes and soil respiration.

This study investigated effects of monitoring on correspondence between nonverbal responding and verbal descriptions of those contingencies, when verbal descriptions and contingencies were compatible and when incompatible. In the Nonverbal Component, the contingency for key pressing was either on a 0.8 s IRT or a 3.4 s IRT. In the Verbal Component, subjects made responses to a statement about the contingency for reinforcement in the Nonverbal Component. Shaping was used to establish targets of 0.8 s and 3.4 s in this component. Results indicated that across 7/8 opportunities subjects exhibited nonverbal and verbal behavior that was sensitive to their respective contingencies regardless of compatibility. This sensitivity to contingencies was not affected by the presence of a monitor.

Doctor of Philosophy / Department of Agronomy / Stephen M. Welch / Global crop production must be doubled by 2050 to feed 9 billion people. Novel crop improvement methods and management strategies are the sine qua non for achieving this goal. This requires reliable quantitative methods for predicting the behavior of crop cultivars in novel, time-varying environments. In the last century, two different mathematical prediction approaches emerged (1) quantitative genetics (QG) and (2) ecophysiological crop modeling (ECM). These methods are completely disjoint in terms of both their mathematics and their strengths and weaknesses. However, in the period from 1996 to 2006 a method for melding them emerged to support breeding programs. The method involves two steps: (1) exploiting ECM’s to describe the intricate, dynamic and environmentally responsive biological mechanisms determining crop growth and development on daily/hourly time scales; (2) using QG to link genetic markers to the values of ECM constants (called genotype-specific parameters, GSP’s) that encode the responses of different varieties to the environment. This can require huge amounts of computation because ECM’s have many GSP’s as well as site-specific properties (SSP’s, e.g. soil water holding capacity). Moreover, one cannot employ QG methods, unless the GSP’s from hundreds to thousands of lines are known. Thus, the overall objective of this study is to identify better ways to reduce the computational burden without minimizing ECM predictability. The study has three parts: (1) using the extended Fourier Amplitude Sensitivity Test (eFAST) to globally identify parameters of the CERES-Sorghum model that require accurate estimation under wet and dry environments; (2) developing a novel estimation method (Holographic Genetic Algorithm, HGA) applicable to both GSP and SSP estimation and testing it with the CROPGRO-Soybean model using 182 soybean lines planted in 352 site-years (7,426 yield observations); and (3) examining the behavior under estimation of the anthesis data prediction component of the CERES-Maize model. The latter study used 5,266 maize Nested Associated Mapping lines and a total 49,491 anthesis date observations from 11 plantings. Three major problems were discovered that challenge the ability to link QG and ECM’s: 1) model expressibility, 2) parameter equifinality, and 3) parameter instability. Poor expressibility is the structural inability of a model to accurately predict an observation. It can only be solved by model changes. Parameter equifinality occurs when multiple parameter values produce equivalent model predictions. This can be solved by using eFAST as a guide to reduce the numbers of interacting parameters and by collecting additional data types. When parameters are unstable, it is impossible to know what values to use in environments other than those used in calibration. All of the methods that will have to be applied to solve these problems will expand the amount of data used with ECM’s. This will require better optimization methods to estimate model parameters efficiently. The HGA developed in this study will be a good foundation to build on. Thus, future research should be directed towards solving these issues to enable ECM’s to be used as tools to support breeders, farmers, and researchers addressing global food security issues.

This thesis defends Semantic Pluralism, the view that sentences express sets of propositions in context. It puts forward two arguments against Contextualism, the main opposing view, on which each sentence expresses exactly one proposition in context. It spells out two versions of Pluralism: Flexible Pluralism, which takes most sentences to be context-sensitive, and Strong Pluralism, which denies that context-sensitivity is widespread. And it defends Flexible Pluralism and Strong Pluralism from a number of objections.

Sensitive and accurate detection methods are critical for monitoring and managing the spread of aquatic invasive species, such as invasive Silver Carp (SC; Hypophthalmichthys molitrix) and Bighead Carp (BH; Hypophthalmichthys nobilis) near the Great Lakes. A new detection tool called environmental DNA (eDNA) sampling, the collection and screening of water samples for the presence of the target species’ DNA, promises improved detection sensitivity compared to conventional surveillance methods. However, the application of eDNA sampling for invasive species management has been challenging due to the potential of false positives, from detecting species’ eDNA in the absence of live organisms. In this dissertation, I study the sources of error and uncertainty in eDNA sampling and develop statistical tools to show how eDNA sampling should be utilized for monitoring and managing invasive SC and BH in the United States. In chapter 2, I investigate the environmental and hydrologic variables, e.g. reverse flow, that may be contributing to positive eDNA sampling results upstream of the electric fish dispersal barrier in the Chicago Area Waterway System (CAWS), where live SC are not expected to be present. I used a beta-binomial regression model, which showed that reverse flow volume across the barrier has a statistically significant positive relationship with the probability of SC eDNA detection upstream of the barrier from 2009 to 2012 while other covariates, such as water temperature, season, chlorophyll concentration, do not. This is a potential alternative explanation for why SC eDNA has been detected upstream of the barrier but intact SC have not. In chapter 3, I develop and parameterize a statistical model to evaluate how changes made to the US Fish and Wildlife Service (USFWS)’s eDNA sampling protocols for invasive BH and SC monitoring from 2013 to 2015 have influenced their sensitivity. The model shows that changes to the protocol have caused the sensitivity to fluctuate. Overall, when assuming that eDNA is randomly distributed, the sensitivity of the current protocol is higher for BH eDNA detection and similar for SC eDNA detection compared to the original protocol used from 2009-2012. When assuming that eDNA is clumped, the sensitivity of the current protocol is slightly higher for BH eDNA detection but worse for SC eDNA detection. In chapter 4, I apply the model developed in chapter 3 to estimate the BH and SC eDNA concentration distributions in two pools of the Illinois River where BH and SC are considered to be present, one pool where they are absent, and upstream of the electric barrier in the CAWS given eDNA sampling data and knowledge of the eDNA sampling protocol used in 2014. The results show that the estimated mean eDNA concentrations in the Illinois River are highest in the invaded pools (La Grange; Marseilles) and are lower in the uninvaded pool (Brandon Road). The estimated eDNA concentrations in the CAWS are much lower compared to the concentrations in the Marseilles pool, which indicates that the few eDNA detections in the CAWS (3% of samples positive for SC and 0.4% samples positive for BH) do not signal the presence of live BH or SC. The model shows that >50% samples positive for BH or SC eDNA are needed to infer AC presence in the CAWS, i.e., that the estimated concentrations are similar to what is found in the Marseilles pool. Finally, in chapter 5, I develop a decision tree model to evaluate the value of information that monitoring provides for making decisions about BH and SC prevention strategies near the Great Lakes. The optimal prevention strategy is dependent on prior beliefs about the expected damage of AC invasion, the probability of invasion, and whether or not BH and SC have already invaded the Great Lakes (which is informed by monitoring). Given no monitoring, the optimal strategy is to stay with the status quo of operating electric barriers in the CAWS for low probabilities of invasion and low expected invasion costs. However, if the probability of invasion is greater than 30% and the cost of invasion is greater than $100 million a year, the optimal strategy changes to installing an additional barrier in the Brandon Road pool. Greater risk-aversion (i.e., aversion to monetary losses) causes less prevention (e.g., status quo instead of additional barriers) to be preferred. Given monitoring, the model shows that monitoring provides value for making this decision, only if the monitoring tool has perfect specificity (false positive rate = 0%).

Intrusion systems have been the subject of considerable research during the past 33 years, since the original work of Anderson. Much has been published attempting to improve their performance using advanced data processing techniques including neural nets, statistical pattern recognition and genetic algorithms. Whilst some significant improvements have been achieved they are often the result of assumptions that are difficult to justify and comparing performance between different research groups is difficult. The thesis develops a new approach to defining performance focussed on comparing intrusion systems and technologies. A new taxonomy is proposed in which the type of output and the data scale over which an intrusion system operates is used for classification. The inconsistencies and inadequacies of existing definitions of detection are examined and five new intrusion levels are proposed from analogy with other detection-based technologies. These levels are known as detection, recognition, identification, confirmation and prosecution, each representing an increase in the information output from, and functionality of, the intrusion system. These levels are contrasted over four physical data scales, from application/host through to enterprise networks, introducing and developing the concept of a footprint as a pictorial representation of the scope of an intrusion system. An intrusion is now defined as “an activity that leads to the violation of the security policy of a computer system”. Five different intrusion technologies are illustrated using the footprint with current challenges also shown to stimulate further research. Integrity in the presence of mixed trust data streams at the highest intrusion level is identified as particularly challenging. Two metrics new to intrusion systems are defined to quantify performance and further aid comparison. Sensitivity is introduced to define basic detectability of an attack in terms of a single parameter, rather than the usual four currently in use. Selectivity is used to describe the ability of an intrusion system to discriminate between attack types. These metrics are quantified experimentally for network intrusion using the DARPA 1999 dataset and SNORT. Only nine of the 58 attack types present were detected with sensitivities in excess of 12dB indicating that detection performance of the attack types present in this dataset remains a challenge. The measured selectivity was also poor indicting that only three of the attack types could be confidently distinguished. The highest value of selectivity was 3.52, significantly lower than the theoretical limit of 5.83 for the evaluated system. Options for improving selectivity and sensitivity through additional measurements are examined.