BCIT Citations Collection | BCIT Institutional Repository

BCIT Citations Collection

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

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Shaped 3D singular spectrum analysis for quantifying gene expression, with application to the early zebrafish embryo
Recent progress in microscopy technologies, biological markers, and automated processing methods is making possible the development of gene expression atlases at cellular-level resolution over whole embryos. Raw data on gene expression is usually very noisy. This noise comes from both experimental (technical/methodological) and true biological sources (from stochastic biochemical processes). In addition, the cells or nuclei being imaged are irregularly arranged in 3D space. This makes the processing, extraction, and study of expression signals and intrinsic biological noise a serious challenge for 3D data, requiring new computational approaches. Here, we present a new approach for studying gene expression in nuclei located in a thick layer around a spherical surface. The method includes depth equalization on the sphere, flattening, interpolation to a regular grid, pattern extraction by Shaped 3D singular spectrum analysis (SSA), and interpolation back to original nuclear positions. The approach is demonstrated on several examples of gene expression in the zebrafish egg (a model system in vertebrate development). The method is tested on several different data geometries (e.g., nuclear positions) and different forms of gene expression patterns. Fully 3D datasets for developmental gene expression are becoming increasingly available; we discuss the prospects of applying 3D-SSA to data processing and analysis in this growing field., Peer-reviewed article, Published. Received 8 February 2015; Accepted 1 May 2015.
Shaped singular spectrum analysis for quantifying gene expression, with application to the early drosophila embryo
In recent years, with the development of automated microscopy technologies, the volume and complexity of image data on gene expression have increased tremendously. The only way to analyze quantitatively and comprehensively such biological data is by developing and applying new sophisticated mathematical approaches. Here, we present extensions of 2D singular spectrum analysis (2D-SSA) for application to 2D and 3D datasets of embryo images. These extensions, circular and shaped 2D-SSA, are applied to gene expression in the nuclear layer just under the surface of the Drosophila (fruit fly) embryo. We consider the commonly used cylindrical projection of the ellipsoidal Drosophila embryo. We demonstrate how circular and shaped versions of 2D-SSA help to decompose expression data into identifiable components (such as trend and noise), as well as separating signals from different genes. Detection and improvement of under- and overcorrection in multichannel imaging is addressed, as well as the extraction and analysis of 3D features in 3D gene expression patterns., Peer-reviewed article, Published. Received 4 July 2014; Revised 10 September 2014; Accepted 10 September 2014.
Sharp borders from fuzzy gradients
Critical boundaries in the early Drosophila embryo are set by morphogenetic gradients. A new quantitative study shows that the placement of one such boundary is more accurate than the gradient thought to set it. Genetic analysis of the accuracy of the process implicates a gene not previously thought to be involved., Peer-reviewed article, Published.
Simulation of wind-driven rain effects on the performance of a stucco-clad wall
Thermal Performance of Exterior Envelopes of Whole Buildings X International Conference, Clearwater Beach, Florida, USA, December 02, 2007. This climate sensitivity study studied the effects of wind-driven rain on a stucco-clad wall using the advanced hygrothermal model, hygIRC. Simulations were made for a number of climatic conditions based on the moisture index (MI) and for amounts of water deposited inside a wall. The moisture index was based on the severity of a given climate in respect to wall assemblies and the degree of wetting and drying to which a wall could potentially be subjected. The failure criteria was the concurrent occurrence of temperature and relative humidity above thresholds of 10oC and 95% respectively, for ninety consecutive days at any location of wood-based material in the wall., Conference paper, Published. A version of this document is published in: Thermal Performance of Exterior Envelopes of Whole Buildings X International Conference, Clearwater Beach, FL., Dec. 2-7, 2007, pp. 1-15.
Single-laboratory validation of a method for the detection and/or quantification of select alkaloids in goldenseal supplements and raw materials by reversed-phase high-performance liquid chromatography
Quality of botanical products and raw materials is important to manufacturers, regulators, researchers, and consumers. Many modern botanical quality-assurance schemes set specifications for select phytochemicals and measure against those specifications as one determinant of quality. While numerous publications describe procedures for determining compounds of interest in plant species, few methods have been systematically evaluated for accuracy, precision, or reliability, and often the analysis of finished products is not within the scope of the method. Hydrastis canadensis L., commonly referred to as Goldenseal, is an economically important North American medicinal plant that has been subject to adulteration in commerce. The phytochemicals of interest in the plant are the alkaloids hydrastine, berberine, and canadine. Of interest is also palmatine, an alkaloid found in potential adulterant species but not in goldenseal. In this study, goldenseal materials in raw, capsule, and tablet form, including an Echinacea/ Goldenseal combination product, were extracted with acidified water and acetonitrile and their hydrastine, berberine, canadine, and palmitine content determined by HPLC. The analytical method was optimized and evaluated in a single-laboratory validation study. Calibration curves for hydrastine and berberine were linear from 10 to 150 μ g/mL. The limits of detection for palmatine and canadine were determined to be 0.5 μ g/mL, which translates to detection of levels of 0.004% w/w in test samples. Chromatographic resolution was achieved for all analytes in an isocratic 12.5-min chromatographic run employing a binary mobile phase. Triplicate determinations performed on 10 test materials by two analysts on 3 days resulted in relative standard deviations ranging from 0.9% to 3.4%., Peer-reviewed article, Published.
Smart Grid and ICT's role in its evolution
While there is debate around the real causes of Climate Change, Green House Gas (GHG) emissions as a result of widespread use of fossil-based fuels by major economies around the world has been thought of playing a significant role in perpetuating the negative impacts of the phenomenon known as Climate Change. Regardless of whether GHG emissions is the sole culprit of the unusual, and often devastating changes in the climate patterns around the world, the global understanding has been sought over mitigating further dependence on fossil fuels by the developed countries. What further accentuates that desire, is not only the political and social instability of the regions which have traditionally supplied such fuels, but the fact that such fuel are finite in nature and due to be substantially exhausted in the not too distant future. It is interesting to note that the political and social turmoil associated with traditional sources of fossil fuels has given rise to the justification for many special interest groups in the developed world to call for "drilling closer to home". This view often ignores the fact that fossil fuel in the developed world often lies in "difficult to reach" and technologically challenging areas, which do not lend themselves to relatively risk-free exploration and exploitation. Recent environmental disasters, such as the oil spill in the Gulf of Mexico is a clear and undisputable indication of the dangers associated with "drilling closer to home". Consequently, to get out of our energy conundrum, it seems that our societies have no choice but to review and question the way our economies generate and utilize energy. Most studies of this nature reveal the wasteful and unsustainable processes and approaches which we have so far used in energy production and use. Conversion of one form of energy into another, transmission of energy from one place to another, distribution of energy through our urban and rural communities, and management of energy resources have all been imperfect, to say the least. Such wasteful approaches to energy use have been the hallmark of the last century, which has now come back to haunt us in terms of devastating consequences associated with Climate Change. It is in that light that Smart Grid has been inadvertently positioned as the silver bullet to address the Climate Change and Energy Independence issues. Smart Grid is expected to enable unprecedented degrees of conservation, efficiencies and utilization of alternative sources of energy, thus substantially reducing this century's dependence on fossil fuels. It is notable that regardless of which development category they belong to, the developed countries, as well as the developing countries, have put together ambitious plans for the development of next generation electric grid, also called Smart Grid, as the main engine for the development of their economies and the well-being of their population. However, the fact remains that Smart Grid is still a collection of concepts and ideas, whose full impact cannot be realized until a rich portfolio of innovative technologies, system architectures, integration solutions and social-economic components are available cost-effectively and in concert to address the energy supply and demand issues which individual countries across the world are grappling with. And as such, energy independence should be perceived by the world community as a global problem longing for global solutions. As will be demonstrated in the rest of this chapter, Information and Communication Technologies are poised to play a critical role in bringing about the full spectrum of functionalities which Smart Grid promises. After all, Smart Grid is all about pervasive monitoring and control, which could not be realized without a comprehensive blanket of communication technologies, encompassing all utility assets, and enabling the intelligence implanted in each node to contribute to the overall system capabilities and functionalities which Smart Grid is expected to provide., book chapter, Book published
Smart microgrids
The utility sector's transition to renewable energy and the smart grid has already begun. The first step towards smart grid is microgrid, which is a smaller electricity grid with access to all the essential assets of a larger grid. This book provides a glimpse into an actual microgrid project. It supplies a system-level approach to the design of smart Microgrids, covering the entire design process-from roadmap to realization. Detailing lessons learned and pitfalls to avoid in Microgrid technology, the book provides an interdisciplinary approach to design and problem solving for smart microgrids., Book, Published.
The Smartphone Peer Physical Activity Counseling (SPPAC) program for manual wheelchair users
Physical activity (PA) must be performed regularly to accrue health benefits. However, the majority of manual wheelchair users do not meet PA recommendations. Existing community-based PA programs for manual wheelchair users appear to work, but effect sizes are small and retention is low. Existing PA programs may not fully implement some psychosocial factors that are strongly linked with PA (eg, autonomy). The use of peers and mobile phone technology in the Smartphone Peer PA Counseling (SPPAC) program represents a novel approach to cultivating a PA-supportive environment for manual wheelchair users., Peer-reviewed article, Published.
Sound transmission loss of extensive green roofs
A study was conducted to review the acoustical features and the potential contributions of green roofs to the acoustical environment, to investigate sound transmission theory, and to report on new empirical findings on the transmission loss of green roofs. The results of the study shows that existing sound transmission algorithms do not adequately predict TL of light-weight roof system or green roofs, nor describe the potential effect of moisture content of the substrate. The sound energy is dissipated in the substrate and provides a mass loading and damping effect on to the light-weight roof deck. The study also suggested that green roofs will provide a higher TL than the additional ceiling element and improve TL throughout the full architectural frequency range, specifically desirable in residential and institutional occupancies that are developed below aircraft flight paths., Article, Published.
Spatial bistability generates hunchback expression sharpness in the drosophila embryo
During embryonic development, the positional information provided by concentration gradients of maternal factors directs pattern formation by providing spatially dependent cues for gene expression. In the fruit fly, Drosophila melanogaster, a classic example of this is the sharp on-off activation of the hunchback (hb) gene at midembryo, in response to local concentrations of the smooth anterior-posterior Bicoid (Bcd) gradient. The regulatory region for hb contains multiple binding sites for the Bcd protein as well as multiple binding sites for the Hb protein. Some previous studies have suggested that Bcd is sufficient for properly sharpened Hb expression, yet other evidence suggests a need for additional regulation. We experimentally quantified the dynamics of hb gene expression in flies that were wild-type, were mutant for hb self-regulation or Bcd binding, or contained an artificial promoter construct consisting of six Bcd and two Hb sites. In addition to these experiments, we developed a reaction-diffusion model of hb transcription, with Bcd cooperative binding and hb self-regulation, and used Zero Eigenvalue Analysis to look for multiple stationary states in the reaction network. Our model reproduces the hb developmental dynamics and correctly predicts the mutant patterns. Analysis of our model indicates that the Hb sharpness can be produced by spatial bistability, in which hb self-regulation produces two stable levels of expression. In the absence of self-regulation, the bistable behavior vanishes and Hb sharpness is disrupted. Bcd cooperative binding affects the position where bistability occurs but is not itself sufficient for a sharp Hb pattern. Our results show that the control of Hb sharpness and positioning, by hb self-regulation and Bcd cooperativity, respectively, are separate processes that can be altered independently. Our model, which matches the changes in Hb position and sharpness observed in different experiments, provides a theoretical framework for understanding the data and in particular indicates that spatial bistability can play a central role in threshold-dependent reading mechanisms of positional information., Peer-reviewed article, Published. Received October 16, 2007; Accepted August 13, 2008; Published September 26, 2008.
Spectrum hierarchies and subdiagonal functions
Proceedings of the 18th IEEE Symposium on Logic in Computer Science (LICS-03), Ottawa, ON, 2003. The spectrum of a first-order sentence is the set of cardinalities of its finite models. Relatively little is known about the subclasses of spectra that are obtained by looking only at sentences with a specific signature. In this paper, we study natural subclasses of spectra and their closure properties under simple subdiagonal functions. We show that many natural closure properties turn out to be equivalent to the collapse of potential spectrum hierarchies. We prove all of our results using explicit transformations on first-order structures., Conference paper, Published.
Spinal cord injury influences psychogenic as well as physical components of female sexual ability
Study Design: Secure, web-based survey. Objectives: Elicit specific information about sexual function from women 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: Bladder and/or bowel incontinence during sexual activity and/or sexual intercourse were significant concerns and prevented some women from seeking sexual activity. Autonomic dysreflexia (AD) during sexual activity was interpreted negatively by many and was found to interfere with sexual activity. Most subjects reported difficulty becoming psychologically aroused as well as physically aroused, which were both correlated with feeling that their SCI had altered their sexual sense of self. An inverse relationship existed between developing new areas of arousal above the level of lesion and not having sensation or movement below the lesion. The most commonly reported sexual stimulation leading to the best arousal involved stimulation of the head/neck and torso areas. The majority of subjects reported having experienced intercourse postinjury. Most participants reported difficulty with positioning during foreplay and intercourse, vaginal lubrication, and spasticity during intercourse. Almost half reported experiencing orgasm postinjury and this was positively associated with the presence of genital sensation. Conclusion: SCI significantly impairs psychological and physical aspects of female sexual arousal. In addition, bladder and bowel incontinence as well as AD negatively impact sexual activity and intercourse., Peer-reviewed article, Published.
A state-of-the-art on concrete repairs and some thoughts on ways to achieve durability in repairs
Thee aim of this chapter is to provide the reader with a general overview of the different phenomena and factors involved with durability of repair and suggest the major aspects which the repair design should focus on. However, it is important to keep in mind that any repair problem needs to be addressed as a unique problem first, and the designer, by developing awareness of the several challenges involved, should be able to make mindful choices, adequate to the specific application that is being considered., Book chapter, Published.
Stochastic dynamics of gene expression in developing fly embryos
Proceedings of 2017 International Conference on Noise and Fluctuations (ICNF), Vilnius, Lithuania on 20-23 June 2017. Segmentation of the developing insect body is preceded by cell-specific gene expression. In fruit flies (Drosophila), pair-rule genes are expressed in spatial stripes specifying segment fates. Transcription of the even-skipped (eve) pair-rule gene was recently shown to proceed in noisy bursts. Here, we develop a stochastic model of eve transcription from DNA to mRNA. This indicates that eve transcription proceeds at two rates, with a slow rate providing basal production and a fast rate allowing for high mRNA output. This two-rate transcription may afford more reliability in mRNA output, and therefore the protein levels which specify cell type, than a simple on-off (one-rate) mechanism., Conference paper, Published.
Storage and the shift to low carbon energy
This work looks at the impact of assumptions made regarding efficiency of storage systems used with variable energy resources and how this applies to a solar PV installation. To find the optimal storage system to work with the cyclic solar output, a linear optimization model is implemented using OSeMOSYS. With 100% efficient, free storage, with no capacity restrictions, it is possible to get down to almost 5 GW of required solar installed capacity, but it requires 1.1 TWh of 100% efficient storage. Existing pumped hydro storage facilities have efficiencies between 70 and 80%, which increase these numbers to 7 GW and 1.2 TWh. With a storage model based on the worlds largest pumped hydro facility between 20 and 25 GW of installed solar capacity are required plus between 15 and 30 GWh of storage capacity to meet the 1 GW load. The capital infrastructure required to allow a solar installation to meet that of a baseload plant is therefore around an order of magnitude larger than what is commonly assumed. A shift away from fossil fuels to renewable/variable energy resources will require more infrastructure than indicated by simply considering the capacity factor of the energy source., Peer-reviewed article, Published. Manuscript received September 30, 2014; revised January 18, 2015.
Structured documents
Proceedings of 2012 European Intelligence and Security Informatics Conference (EISIC) in Odense, Denmark 22-24 Aug. 2012. Much of the information exchanged between agents over a network is encapsulated in XML documents. An XML document has a tree structure, and the meaning of the document can be understood in terms of a set of label-value pairs. The content of a document is often secured through digital signatures applied to different sections, while the document is passed between several agents. In this paper, we illustrate that this process is insecure in the sense that a malicious agent can deceive an honest agent to hold beliefs that are untrue. We provide a formal framework for analyzing the security of structured documents, based on the implicit epistemic impact that a signed document will have on a recipient. This kind of analysis can provide significant insight into deception and fraud detection., Conference paper, Published.

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