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BCIT Citations Collection

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The effects of gene recruitment on the evolvability and robustness of pattern-forming gene networks
Gene recruitment or co-option is defined as the placement of a new gene under a foreign regulatory system. Such re-arrangement of pre-existing regulatory networks can lead to an increase in genomic complexity. This reorganization is recognized as a major driving force in evolution. We simulated the evolution of gene networks by means of the Genetic Algorithms (GA) technique. We used standard GA methods of point mutation and multi-point crossover, as well as our own operators for introducing or withdrawing new genes on the network. The starting point for our computer evolutionary experiments was a 4-gene dynamic model representing the real genetic network controlling segmentation in the fruit fly Drosophila. Model output was fit to experimentally observed gene expression patterns in the early fly embryo. We compared this to output for networks with more and less genes, and with variation in maternal regulatory input. We found that the mutation operator, together with the gene introduction procedure, was sufficient for recruiting new genes into pre-existing networks. Reinforcement of the evolutionary search by crossover operators facilitates this recruitment, but is not necessary. Gene recruitment causes outgrowth of an evolving network, resulting in redundancy, in the sense that the number of genes goes up, as well as the regulatory interactions on the original genes. The recruited genes can have uniform or patterned expressions, many of which recapitulate gene patterns seen in flies, including genes which are not explicitly put in our model. Recruitment of new genes can affect the evolvability of networks (in general, their ability to produce the variation to facilitate adaptive evolution). We see this in particular with a 2-gene subnetwork. To study robustness, we have subjected the networks to experimental levels of variability in maternal regulatory patterns. The majority of networks are not robust to these perturbations. However, a significant subset of the networks do display very high robustness. Within these networks, we find a variety of outcomes, with independent control of different gene expression boundaries. Increase in the number and connectivity of genes (redundancy) does not appear to correlate with robustness. Indeed, removal of recruited genes tends to give a worse fit to data than the original network; new genes are not freely disposable once they acquire functions in the network., Book chapter, Published.
The effects of global climate change on carbonation induced corrosion of reinforced concrete structures
There is nearly unanimous consensus amongst scientists that increasing greenhouse gas emissions, including CO2 generated by human activity, are affecting the Earth‘s climate. Climate change has the potential to overwhelm existing capacities, as well as durability of concrete infrastructure. Carbonation of concrete occurs due to a reaction between atmospheric CO2 and the hydrated phases of concrete, leading to a drop in its pH and the depassivation of embedded rebar. Therefore, increases in carbonation rates of reinforced concrete structures are expected as a result of increased temperatures and CO2 concentrations, with the enhanced risk of carbonation induced corrosion likely affecting the longevity of our concrete infrastructure. This thesis considered the potential consequences of global climate change on our concrete infrastructure, with the objective being to determine if there is an increased risk of deterioration due to carbonation induced corrosion. A unique numerical model was developed to determine carbonation rates in structures, and verified through experimental tests. The model was applied to a numbers of cities in locations throughout the world to determine where structures were most vulnerable. Additionally, a number of other laboratory experiments were carried out to supplement the numerical model and provide insights as to how carbonation progress can be monitored within a structure. Using the model developed, and inputting forecasts for increases in future atmospheric CO2 concentrations and weather conditions, it was shown that for medium quality, non-pozzolonic concrete in geographic areas where carbonation induced corrosion is a concern, global climate change will affect its progress in our concrete infrastructure. We will see much higher ultimate carbonation depths in the long term. The use of non-destructive testing (NDT) methods, and structural health monitoring (SHM) techniques could be invaluable in monitoring the progress of carbonation in a structure, but the data generated by the methods and techniques used must be analyzed carefully before making any conclusions. For the NDT methods and carbonation pH sensors which were evaluated in this study, it was found that ambient test conditions had a major impact on results., Thesis, Published.
Endogenous TrkB ligands suppress functional mechanosensory plasticity in the deafferented spinal cord
Dorsal root injury (DRI) disrupts the flow of sensory information to the spinal cord. Although primary afferents do not regenerate to their original targets, spontaneous recovery can, by unknown mechanisms, occur after DRI. Here, we show that brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3), but not nerve growth factor or neurotrophin-4, are upregulated in the spinal gray matter after DRI. Because endognous BDNF and NT-3 have well established roles in synaptic and axonal plasticity, we hypothesized that they contributed to spontaneous recovery after DRI. We first developed a model of DRI-induced mechanosensory dysfunction: rat C7/8 DRI produced a deficit in low-threshold cutaneous mechanosensation that spontaneously improved within 10 d but did not recover completely. To determine the effects of endogenous BDNF and NT-3, we administered TrkB-Fc or TrkC-Fc fusion proteins throughout the recovery period. To our surprise, TrkB-Fc stimulated complete recovery of mechanosensation by 6 d after DRI. It also stimulated mechanosensory axon sprouting but prevented deafferentation-induced serotonergic sprouting. TrkC-Fc had no effect on low-threshold mechanosensory behavior or axonal plasticity. There was no mechanosensory improvement with single-bolus TrkB-Fc infusions at 10 d after DRI (despite significantly reducing rhizotomy-induced cold pain), indicating that neuromodulatory effects of BDNF did not underlie mechanosensory recovery. Continuous infusion of the pan-neurotrophin antagonist K252a also stimulated behavioral and anatomical plasticity, indicating that these effects of TrkB-Fc treatment occurred independent of signaling by other neurotrophins. These results illustrate a novel, plasticity-suppressing effect of endogenous TrkB ligands on mechanosensation and mechanosensory primary afferent axons after spinal deafferentation., Peer-reviewed article, Published. Received Oct. 2, 2006; revised March 26, 2007; accepted April 20, 2007.
Enhancing student engagement and learning effectiveness through multi-role contributions and collaborative exams
This project proposes teaching-learning coupling as students take different roles during the course, from being learners, teachers, and proponents; finally, students take exams in a collaborative manner – initially, their exam is done individually followed by a team consultation period for the exam completion., Not peer reviewed, report
Environmental regulation, asymmetric information, and moral hazard
This paper presents a model of environmental regulation in the presence of measurement costs and asymmetric information. Environmental regulation can be viewed as a form of agency problem where the polluting firms may have better information about the true level of their abatement activities than the regulator. If certain aspects of environmental quality are costly to measure, regulators may resort to proxies to infer information about environmental quality. This may allow firms to circumvent the regulatory constraints by maximizing along those margins that are costly to measure. This problem is especially acute when a single firm produces multiple pollutants., Essay, Published.
Environmentally friendly transport
Article, Published.
Evaluating the use of potentially hazardous secondary aggregates in concrete based on life-cycle effects on water pollution
Proceedings from the 28th International Conference on Solid Waste Technology and Management, Philadelphia, PA U.S.A, March 10-13, 2013., Peer reviewed, Conference proceeding
Evaluation of the antiproliferative effects of Essiac on in vitro and in vivo models of prostate cancer compared to paclitaxel
Essiac, a widely consumed, sparsely tested herbal tea, was evaluated for preparation consistency and antiproliferative effects on prostate cancer cells and xenografts. High performance liquid chromatography (HPLC) was used to compare different lots of Essiac and evaluate extraction consistency by comparing peak areas in concentrated preparations. Repeated analysis of one lot showed < 2% RSD between corresponding peaks. Absolute peak areas varied widely between lots, but similarity in relative size of corresponding peaks was observed. Cytotoxic effects of Essiac were tested in vitro by crystal violet assay and analysis of cell cycle distribution by flow cytometry, but no differences between control and treatment groups was observed. Paclitaxel was used as a positive control in cell cycle analysis and was the only treatment which showed significant effects on cell cycle distribution. Toxicity in nude mice was tested, and efficacy in inhibiting PC-3 xenograft growth. No toxicity or tumour size difference was observed dosing up to 240 mg/kg QD, over 28 days, excepting the positive control group treated with paclitaxel. Ki-67 and PCNA expression was analyzed in treated tumors, but no difference in expression of either marker was observed. These evaluations suggest Essiac has no marked antiproliferative effect on the models tested., Peer-reviewed article, Published.
Evidence-based solution to information sharing between criminal justice agencies
This paper originates from a project done for and with the assistance of the Operations Strategy Branch, E Division, Royal Canadian Mounted Police. The aim of this study was to test a technological solution to two traditional limitations of information sharing between criminal justice agencies: data quality and privacy concerns. Entity Analytics Software (EAS) was tested in two studies with North American criminal justice agencies. In the first test, duplicated cases held in a police record system were successfully identified (4.0%) to a greater extent than the traditionally used software program (1.5%). This resulted in a difference of 11,954 cases that otherwise would not have been identified as duplications. In the second test, entity information held separately by police and border officials was shared anonymously between these two organizations. This resulted in 1,827 alerts regarding entities that appeared in both systems; traditionally, this information could not have been shared, given privacy concerns, and neither criminal justice agency would be aware of the relevant information held by the other. Data duplication resulted in an additional 1,041 alerts, which highlights the need to use technological solutions to improve data quality prior to and during information sharing. While only one potential technological solution (EAS) was tested and organizations must consider the potential expense associated with implementing such technology, the implications resulting from both studies for improved awareness and greater efficiency support and facilitate information sharing between criminal justice organizations., Research paper, Published.
Evolutionary design of gene networks
The co-evolution of species with their genomic parasites (transposons) is thought to be one of the primary ways of rewiring gene regulatory networks (GRNs). We develop a framework for conducting evolutionary computations (EC) using the transposon mechanism. We find that the selective pressure of transposons can speed evolutionary searches for solutions and lead to outgrowth of GRNs (through co-option of new genes to acquire insensitivity to the attacking transposons). We test the approach by finding GRNs which can solve a fundamental problem in developmental biology: how GRNs in early embryo development can robustly read maternal signaling gradients, despite continued attacks on the genome by transposons. We observed co-evolutionary oscillations in the abundance of particular GRNs and their transposons, reminiscent of predator-prey or host-parasite dynamics., Peer-reviewed article, Published.
Evolutionary techniques for image processing a large dataset of early drosophila gene expression
Understanding how genetic networks act in embryonic development requires a detailed and statistically significant dataset integrating diverse observational results. The fruit fly (Drosophila melanogaster) is used as a model organism for studying developmental genetics. In recent years, several laboratories have systematically gathered confocal microscopy images of patterns of activity (expression) for genes governing early Drosophila development. Due to both the high variability between fruit fly embryos and diverse sources of observational errors, some new nontrivial procedures for processing and integrating the raw observations are required. Here we describe processing techniques based on genetic algorithms and discuss their efficacy in decreasing observational errors and illuminating the natural variability in gene expression patterns. The specific developmental problem studied is anteroposterior specification of the body plan., Peer-reviewed article, Published.
Experimental investigation of moisture transfer between concrete foundation and sill plate
Precipitation is one of the most common moisture sources on which building designers focus. Water comes from both top down and bottom up. Although foundations are sometimes constructed out of pressure-treated lumber, generally they are constructed from poured concrete. In a wet climate zone, the foundation of a house is often under continuous contact with moisture, which is mainly caused by rundown rainwater, wet soil, a high water table, or a combination of all these factors. This causes rot growth and decay of the wood-frame structure as it sits constantly on the damp foundation concrete. In this research, moisture transfer between concrete and wood is investigated under three different scenarios: a case with direct wood and concrete contact and two cases with different moisture barriers between the two materials. The moisture barrier materials considered in this study are the damp-proofing layer and sill plate gasket. The moisture transfer processes in these three cases are investigated in a field experimental setting using a customized experimental setup for 1 year. The experimental data suggest that using damp proofing and a sill gasket helps restrict moisture transfer., Peer reviewed article, Published. Received: May 29, 2015; Accepted: December 09, 2015; Published online: February 24, 2016.

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