BCIT Citations Collection | BCIT Institutional Repository

BCIT Citations Collection

Description

Collection of published works from BCIT researchers, faculty, and instructors.

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In silico evolution of gene cooption in pattern-forming gene networks
Gene recruitment or cooption occurs when a gene, which may be part of an existing gene regulatory network (GRN), comes under the control of a new regulatory system. Such re-arrangement of pre-existing networks is likely more common for increasing genomic complexity than the creation of new genes. Using evolutionary computations (EC), we investigate how cooption affects the evolvability, outgrowth and robustness of GRNs. We use a data-driven model of insect segmentation, for the fruit fly Drosophila, and evaluate fitness by robustness to maternal variability—a major constraint in biological development. We compare two mechanisms of gene cooption: a simpler one with gene Introduction and Withdrawal operators; and one in which GRN elements can be altered by transposon infection. Starting from a minimal 2-gene network, insufficient for fitting the Drosophila gene expression patterns, we find a general trend of coopting available genes into the GRN, in order to better fit the data. With the transposon mechanism, we find co-evolutionary oscillations between genes and their transposons. These oscillations may offer a new technique in EC for overcoming premature convergence. Finally, we comment on how a differential equations (in contrast to Boolean) approach is necessary for addressing realistic continuous variation in biochemical parameters., Peer-reviewed article, Published. Received 29 September 2012; Accepted 13 November 2012.
In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression
Biological development depends on the coordinated expression of genes in time and space. Developmental genes have extensive cis-regulatory regions which control their expression. These regions are organized in a modular manner, with different modules controlling expression at different times and locations. Both how modularity evolved and what function it serves are open questions. We present a computational model for the cis-regulation of the hunchback (hb) gene in the fruit fly (Drosophila). We simulate evolution (using an evolutionary computation approach from computer science) to find the optimal cis-regulatory arrangements for fitting experimental hb expression patterns. We find that the cis-regulatory region tends to readily evolve modularity. These cis-regulatory modules (CRMs) do not tend to control single spatial domains, but show a multi-CRM/multi-domain correspondence. We find that the CRM-domain correspondence seen in Drosophila evolves with a high probability in our model, supporting the biological relevance of the approach. The partial redundancy resulting from multi-CRM control may confer some biological robustness against corruption of regulatory sequences. The technique developed on hb could readily be applied to other multi-CRM developmental genes., Peer-reviewed article, Published.
Increasing efficiency of enzymatic hemicellulose removal from bamboo for production of high-grade dissolving pulp
To improve the efficiency of enzymatic hemicellulose removal from bamboo pre-hydrolysis kraft pulp, mechanical refining was conducted prior to enzyme treatment. Refining significantly improved the subsequent hemicellulose removal efficiency by xylanase treatment. Results showed that when PFI refining was followed by 3 h xylanase treatment, the xylan content of the bamboo pre-hydrolysis kraft pulp (after first stage oxygen delignification) could be decreased to 2.72% (w/w). After bleaching of enzyme treated pulp, the alpha-cellulose content was 93.4% (w/w) while the xylan content was only 2.38%. The effect of refining on fibre properties was investigated in terms of freeness, water retention value, fibre length and fibrillation characteristics. The brightness, reactivity and viscosity were also determined to characterize the quality of final pulp. Results demonstrated the feasibility of combining refining and xylanase treatment to produce high quality bamboo dissolving pulp., Peer-reviewed article, Published. Received 1 September 2016; Revised 9 October 2016; Accepted 12 October 2016; Available online 24 October 2016.
Insight into the evolution of the proton concentration during autohydrolysis and dilute-acid hydrolysis of hemicellulose
Background: During pretreatment, hemicellulose is removed from biomass via proton-catalyzed hydrolysis to produce soluble poly- and mono-saccharides. Many kinetic models have been proposed but the dependence of rate on proton concentration is not well-defined; autohydrolysis and dilute-acid hydrolysis models apply very different treatments despite having similar chemistries. In this work, evolution of proton concentration is examined during both autohydrolysis and dilute-acid hydrolysis of hemicellulose from green bamboo. An approximate mathematical model, or “toy model”, to describe proton concentration based upon conservation of mass and charge during deacetylation and ash neutralization coupled with a number of competing equilibria, was derived. The model was qualitatively compared to experiments where pH was measured as a function of time, temperature, and initial acid level. Proton evolution was also examined at room temperature to decouple the effect of ash neutralization from deacetylation. Results: The toy model predicts the existence of a steady-state proton concentration dictated by equilibrium constants, initial acetyl groups, and initial added acid. At room temperature, it was found that pH remains essentially constant both at low initial pH and autohydrolysis conditions. Acid is likely in excess of the neutralization potential of the ash, in the former case, and the kinetics of neutralization become exceedingly small in the latter case due to the low proton concentration. Finally, when the hydrolysis reaction proceeded at elevated temperatures, one case of non-monotonic behavior in which the pH initially increased, and then decreased at longer times, was found. This is likely due to the difference in rates between neutralization and deacetylation. Conclusions: The model and experimental work demonstrate that the evolution of proton concentration during hydrolysis follows complex behavior that depends upon the acetyl group and ash content of biomass, initial acid levels and temperature. In the limit of excess added acid, pH varies very weakly with time. Below this limit, complex schemes are found primarily related to the selectivity of deacetylation in comparison to neutralization. These findings indicate that a more rigorous approach to models of hemicellulose hydrolysis is needed. Improved models will lead to more efficient acid utilization and facilitate process scale-up., Peer-reviewed article, Published. Received: 23 July 2016 ; Accepted: 22 September 2016 ; Published: 21 October 2016.
Integrated analysis of whole building heat, air and moisture transfer
There is a continuous dynamic heat, air and moisture (HAM) interaction between the indoor environment, building envelope and mechanical systems. In spite of these interdependences, the current indoor, building envelope and energy analysis tools are used independently. In this paper a holistic HAM model that integrates building envelope enclosures, indoor environment, HVAC systems, and indoor heat and moisture generation mechanisms, and solves simultaneously for the respective design parameters is developed. The model is benchmarked with internationally published test cases that require simultaneous prediction of indoor environmental conditions, building envelope moisture performance and energy efficiency of a building., Peer reviewed article, Published. Received 26 February 2009, Accepted 11 March 2010, Available online 16 April 2010.
Integrated life-cycle design of building enclosures
In spite of the progress in developing methods and tools to support sustainable building design, there is still a lack of a formal approach to bridge the "no man’s land” gap between the traditional building engineering disciplines, and between these and the architecture, to achieve the level of building integration required for sustainability. This paper presents an integration framework that aims at facilitating the inclusion of life-cycle considerations in the design process from the outset, so that materials and systems are selected not only from environmentally friendly resources, but most importantly, to match service life performance expectations. The framework describes an iterative methodology to evaluate these expectations in practice, which is based on an understanding and modeling of the dynamics of the built environment to which materials, components, and systems are exposed. Quantitative methods and test protocols can be incorporated into the framework for assessing function-performance aspects of alternative solutions. Due to its complexity stemming from its inherent exposure to variable environmental loads and its multi-functionality, the framework focuses on addressing the life cycle of the building enclosure system. It is expected that the organization of the underlying principles of building life-cycle performance described in this paper will become a knowledge core that will facilitate a more integrated treatment of buildings in research, education, and practice., Peer reviewed, Peer reviewed article, Received 29 October 2010 ; Revised 13 January 2011 ; Accepted 18 January 2011 ; Available online 27 January 2011., Life-cycle, Service life, Building science, Building enclosure, Building integration
Interaction with an edu-game
We present the results of a study that explored the emotions experienced by students during interaction with an educational game for math (Heroes of Math Island). Starting from emotion frameworks in affective computing and education, we considered a larger set of emotions than in related research. For emotion labeling, we started from a standard methodology that relies on trained judges to report emotions over 20-s intervals, however, we asked judges to report all observed emotions in each interval, as opposed to only choosing one, as is standard practice. This variation allows us to discuss the appropriateness of this interval for emotion labeling. We present a detailed analysis of interrater reliability, both aggregated and over individual students, that considers not only labeling agreement among judges in terms of emotion type, but also with respect to the number of emotions detected. We also provide an analysis based on in-depth one-to-one interviews with judges, to gain insights on the challenges they encountered in labeling emotions., Peer reviewed, Peer reviewed article, First Online: 07 January 2016., Learning, Educational games, Emotion labeling, Interrater agreement, Interviewing judges, Affective states
Interaction with an edu-game: a detailed analysis of student emotions and judges' perceptions
We present the results of a study that explored the emotions experienced by students during interaction with an educational game for math (Heroes of Math Island). Starting from emotion frameworks in affective computing and education, we considered a larger set of emotions than in related research. For emotion labeling, we started from a standard methodology that relies on trained judges to report emotions over 20-s intervals, however, we asked judges to report all observed emotions in each interval, as opposed to only choosing one, as is standard practice. This variation allows us to discuss the appropriateness of this interval for emotion labeling. We present a detailed analysis of interrater reliability, both aggregated and over individual students, that considers not only labeling agreement among judges in terms of emotion type, but also with respect to the number of emotions detected. We also provide an analysis based on in-depth one-to-one interviews with judges, to gain insights on the challenges they encountered in labeling emotions., Not peer reviewed, Article
Introductory mathematics for computer science
4th custom edition., Not peer reviewed, Book, Published.
Introductory mathematics for computer science
3rd custom edition for BCIT., Published., Peer reviewed, Book
Introductory mathematics for computer science
Taken from: Basic technical mathematics : with calculus, metric version, seventh edition by Allyn J. Washington, Logic and computer design fundamentals, second edition, updated by M. Morris Mano and Charles R. Kime. Custom edition for British Columbia Institute of Technology., Book, Published., Peer reviewed
Investigation of the moisture buffering potential of magnesium oxide board
Research report submitted to Peter Francis, President, MAGO Building Products Ltd in April 2016. Passive humidity control in buildings can be achieved by incorporating materials with moisture buffering potential in that these materials absorb moisture at peak times and give off the stored up moisture at low moisture production times thereby stabilizing the interior relative humidity. Some of the advantages of this phenomenon include but are not limited to energy savings, improvement of thermal comfort and perceived air quality. As such, it is necessary to investigate different materials for their moisture buffering capabilities. As part of product development, the moisture buffering characteristics of Magnesium oxide board (Magnesia board) is experimentally investigated. Other considerations such as the impact of surface finishing and ventilation are also assessed. The experiment is done by monitoring twin buildings termed the Whole Building Performance Research Laboratory (WBPRL) while measuring the relative humidity evolution in time. One is set as the reference building and finished with gypsum wallboard owing to its wide industry use. The other is set as the reference building and covered with the Magnesia board. Both buildings are first validated under non-hygroscopic conditions to ensure similar hygrothermal loading and operation of both buildings. Next, four tests are conducted to simulate surface treatments, ventilation effects, and occupancy density. For each test run, four cases are created for different surface treatment configurations. From the test, it is found that magnesia board and gypsum demonstrate similar moisture buffering characteristics. In the as-in service case where the gypsum wallboard is painted with latex paint, as it is the current common practice, and magnesia board with the company specified paint, the later demonstrates slightly better moisture buffering due to the high permeability surface treatment., Research report, Published.
Iterated belief change due to actions and observations
In action domains where agents may have erroneous beliefs, reasoning about the effects of actions involves reasoning about belief change. In this paper, we use a transition system approach to reason about the evolution of an agent's beliefs as actions are executed. Some actions cause an agent to perform belief revision while others cause an agent to perform belief update, but the interaction between revision and update can be non-elementary. We present a set of rationality properties describing the interaction between revision and update, and we introduce a new class of belief change operators for reasoning about alternating sequences of revisions and updates. Our belief change operators can be characterized in terms of a natural shifting operation on total pre-orderings over interpretations. We compare our approach with related work on iterated belief change due to action, and we conclude with some directions for future research., Peer-reviewed article, Published.
Lessons learnt from the shotcrete repair of the Powell River concrete hulks, and their applicability to other marine structures
Background : Concrete structures can be damaged by many chemical or physical processes. Where such damages affect appearance, serviceability or structural integrity, repair may be required. 10 decommissioned concrete ships form a massive floating breakwater on the Malaspina Strait in the City of Powell River in British Columbia, Canada. The ships are subjected to extremely onerous conditions, namely in the salt water splash zone under seasonal freeze-thaw cycling. This paper provides anecdotal evidence based on condition assessments after repairs were car-ried out, on how a well-matched repair concrete can significantly extend the service life of these and similar sorts of marine structures. Methods: Condition assessment was carried out using sounding, visual examination, photo and video documentation, compressive strength testing, splitting tensile strength testing, chloride ion concentration testing, and half-cell potential testing. Results: It was found that the areas which had been repaired had fared very well, with no observable de-terioration. The non-repaired areas of the structures had continued to deteriorate, particularly in non-submerged areas, close to the waterline, along with new impact damage. Conclusion: Durable concrete repairs can be achieved even for concrete exposed to extreme environ-mental conditions. Key conditions for such repairs are: complete removal of the deteriorated portions of the original concrete, removal of all loose corrosion products from exposed reinforcing steel, prepara-tion of a clean, firm, rough, surface dry but partially or fully water saturated, substrate surface, selection of a compatible repair material, use of an application technique which facilitates high bond strength between substrate and repair material, adequate curing, and protection of the repair material while immature., Peer-reviewed article, Published. Received: September 12, 2015; Revised: December 19, 2015; Accepted: June 28, 2016.
Limiting cases for spectrum closure results
The spectrum of a first-order sentence is the set of cardinalities of its finite models. Given a spectrum S and a function f, it is not always clear whether or not the image of S under f is also a spectrum. In this paper, we consider questions of this form for functions that increase very quickly and for functions that increase very slowly. Roughly speaking, we prove that the class of all spectra is closed under functions that increase arbitrarily quickly, but it is not closed under some natural slowly increasing functions., Peer-reviewed article, Published.
Long-term effects of spinal cord injury on sexual function in men
Study Design: Secure, web-based survey. Objectives: Elicit specific information about sexual function from men with spinal cord injuries (SCI). Setting: World-wide web. Methods: Individuals 18 years or older living with SCI obtained a pass-code to enter a secure website and then answered survey questions. Results: The presence of genital sensation was positively correlated with the ability to feel a build up of sexual tension in the body during sexual stimulation and in the feeling that mental arousal translates to the genitals as physical sensation. There was an inverse relationship between developing new areas of arousal above the level of lesion and not having sensation or movement below the lesion. A positive relationship existed between the occurrence of spasticity during sexual activity and erectile ability. Roughly 60% of the subjects had tried some type of erection enhancing method. Only 48% had successfully achieved ejaculation postinjury and the most commonly used methods were hand stimulation, sexual intercourse, and vibrostimulation. The most commonly cited reasons for trying to ejaculate were for pleasure and for sexual intimacy. Less than half reported having experienced orgasm postinjury and this was influenced by the length of time postinjury and sacral sparing. Conclusion: SCI not only impairs male erectile function and ejaculatory ability, but also alters sexual arousal in a manner suggestive of neuroplasticity. More research needs to be pursued in a manner encompassing all aspects of sexual function., Peer-reviewed article, Published.

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