In early development, genes are expressed in spatial patterns which later define cellular identities and tissue locations. The mechanisms of such pattern formation have been studied extensively in early Drosophila (fruit fly) embryos. The gap gene hunchback (hb) is one of the earliest genes to be expressed in anterior-posterior (AP) body segmentation. As a transcriptional regulator for a number of downstream genes, the spatial precision of hb expression can have significant effects in the development of the body plan. To investigate the factors contributing to hb precision, we used fine spatial and temporal resolution data to develop a quantitative model for the regulation of hb expression in the mid-embryo. In particular, modelling hb pattern refinement in mid nuclear cleavage cycle 14 (NC14) reveals some of the regulatory contributions of simultaneously-expressed gap genes. Matching the model to recent data from wild-type (WT) embryos and mutants of the gap gene Krüppel (Kr) indicates that a mid-embryo Hb concentration peak important in thoracic development (at parasegment 4, PS4) is regulated in a dual manner by Kr, with low Kr concentration activating hb and high Kr concentration repressing hb. The processes of gene expression (transcription, translation, transport) are intrinsically random. We used stochastic simulations to characterize the noise generated in hb expression. We find that Kr regulation can limit the positional variability of the Hb mid-embryo border. This has been recently corroborated in experimental comparisons of WT and Kr- mutant embryos. Further, Kr regulation can decrease uncertainty in mid-embryo hb expression (i.e. contribute to a smooth Hb boundary) and decrease between-copy transcriptional variability within nuclei. Since many tissue boundaries are first established by interactions between neighbouring gene expression domains, these properties of Hb-Kr dynamics to diminish the effects of intrinsic expression noise may represent a general mechanism contributing to robustness in early development., Peer-reviewed article, Published. Received: December 5, 2014; Accepted: December 15, 2014; Published: March 20, 2015.
Agriculture contributes significantly to anthropogenic greenhouse gases (GHGs), with estimates of agriculture's contribution ranging from 10% to 25% of total global GHG emissions per year. The science regarding mitigating (reducing and removing) GHGs through agriculture is conflicting and inconclusive. However, the severity and urgency of climate change and its potential effects on food security demonstrate that we must include mitigation within food system planning frameworks. In British Columbia, Canada, the provincial government has established significant GHG reduction targets for its agencies, and has called on local governments to reduce their carbon footprints through a charter and incentive, as well as through growth management legislation. At the same time, local governments, are giving increased attention to development of local/regional agri-food systems. However, GHG mitigation efforts do not yet seem to factor into local agri-food system discussions. Although frameworks for reporting agriculture GHGs exist, local government measurement of agriculture mitigation is hampered by a lack of agriculture GHG inventories, limited data availability, and the inherent variability in agriculture emissions and removals due to the dynamic nature of farm ecosystems. With the goal of informing local governments and food system planners on the importance of agriculture GHG mitigation, this paper (1) reviews the science of GHGs, (2) describes sources of agriculture GHG emissions and illustrates potential mitigation practices, (3) discusses the variability of agriculture mitigation science, (4) highlights the importance of agriculture GHG inventories, and (5) emphasizes the necessity for local agriculture mitigation strategies., Peer-reviewed article, Published. Submitted 18 April 2011 ; Revised 4 July 2011 and 1 August 2011 ; Accepted 2 September 2011 ; Published online 20 March 2012.
A central question in evolutionary biology concerns the transition between discrete numbers of units (e.g. vertebrate digits, arthropod segments). How do particular numbers of units, robust and characteristic for one species, evolve into another number for another species? Intermediate phases with a diversity of forms have long been theorized, but these leave little fossil or genomic data. We use evolutionary computations (EC) of a gene regulatory network (GRN) model to investigate how embryonic development is altered to create new forms. The trajectories are epochal and non-smooth, in accord with both the observed stability of species and the evolvability between forms., Peer-reviewed article, Published.
Proceedings of the Ninth International Symposium on Logical Formalizations of Commonsense Reasoning, Toronto, ON, June 1-3, 2009. This paper proposes a framework for analysing cryptographic protocols by expressing message passing and possible attacks as a situation calculus theory. While cryptographic protocols are usually quite short, they are nonetheless notoriously difficult to analyse, and are subject to subtle and nonintuitive attacks. Our thesis is that in previous approaches for expressing protocols, underlying domain assumptions and capabilities of agents are left implicit. We propose a declarative specification of such assumptions and capabilities in the situation calculus. A protocol is then compiled into a sequence of actions to be executed by the principals. A successful attack is an executable plan by an intruder that compromises the stated goal of the plan. We argue that not only is a full declarative specification necessary, it is also much more flexible than previous approaches, permitting among other things interleaved runs of different protocols and participants with varying abilities., Conference paper, Published.
Concrete structures are almost certain to contain cracks due to different physiochemical mechanisms. The formation of cracks is sure to affect its durability by altering ion and fluid transport properties. This includes the incursion of CO2 into the structure. There presently exists no consensus on how to model the effects of structural cracking on carbonation progress within concrete structures. This paper first examines the concept of effective diffusion based on simultaneous diffusion of CO2 through sound and cracked concrete and then considers a series diffusion concept where CO2 diffuses first into the crack, and then outwards into the sound concrete. It is concluded that the effective diffusion concept is not valid for structurally cracked concrete. Instead, research efforts should be concentrated on developing a two–phase series diffusion model., Peer-reviewed article, Published.
Building enclosures are subjected to a random climatic loading on the exterior surface and a relatively stable indoor condition on the interior. These loadings result in a transport of heat, air, and moisture across the building enclosure. In this paper, the drying and wetting of sheathing board in two exterior walls, more specifically 2×6 in.2 wood-frame conventional (no strapping between sheathing membrane and cladding) and a rain-screen wall system (with vertical strapping), are investigated through an experimental field study. The experiment is carried out at British Columbia Institute of Technology field exposure test facility, where the test walls are exposed to the coastal climate (Vancouver weather) on the exterior and controlled indoor temperature and relative humidity conditions in the interior. The field experimental results indicate significant moisture accumulation on the exterior sheathing boards (plywood) during the Winter period. During the 9-month monitoring period from March 13 to Dec. 6, 2009, the plywood underwent a process of drying and wetting. In both the conventional and rain-screen wall systems, the plywood dried to a comparable moisture level during the Summer before the wetting process started. For the wall systems considered in this study, the plywood in the rain-screen wall has a tendency of faster drying and wetting in the Spring and Fall seasons, respectively, in comparison to the plywood in the conventional wall, which is attributed to the presence of an air gap in the rain-screen wall between the sheathing membrane and the cladding. A similar trend is observed during the monitoring period from December 7 to June 15, 2010., Peer-reviewed article, Published. Manuscript received January 14, 2010; accepted for publication August 14, 2010; published online October 2010.
In an effort to develop therapies for promoting neurological recovery after spinal cord injury, much work has been done to identify the cellular and molecular factors that control axonal regeneration within the injured central nervous system. This review summarizes the current understanding of a number of the elements within the spinal cord environment that inhibit axonal growth and outlines the factors that influence the neuron’s ability to regenerate its axon after injury. Recent insights in these areas have identified important molecular pathways that are potential targets for therapeutic intervention, raising hope for victims of spinal cord injury., Peer-reviewed article, Published.
The field of Evolutionary Computation (EC) has been inspired by ideas from the classical theory of biological evolution, with, in particular, the components of a population from which reproductive parents are chosen, a reproductive protocol, a method for altering the genetic information of offspring, and a means for testing the fitness of offspring in order to include them in the population. In turn, impressive progress in EC - understanding the reasons for efficiencies in evolutionary searches - has begun to influence scientific work in the field of molecular evolution and in the modeling of biological evolution (Stemmer, 1994a,b; van Nimwegen et al. 1997; 1999; Crutchfield & van Nimwegen, 2001). In this chapter, we will discuss how developments in EC, particularly in the area of crossover operators for Genetic Algorithms (GA), provide new understanding of evolutionary search efficiencies, and the impacts this can have for biological molecular evolution, including directed evolution in the test tube. GA approaches have five particular elements: encoding (the ‘chromosome’); a population; a method for selecting parents and making a child chromosome from the parents' chromosomes; a method for altering the child’s chromosomes (mutation and crossover/recombination); criteria for fitness; and rules, based on fitness, by which offspring are included into the population (and parents retained). We will discuss our work and others’ on each of these aspects, but our focus is on the substantial efficiencies that can be found in the alteration of the child chromosome step. For this, we take inspiration from real biological reproduction mechanisms., Book chapter, Published.
Specification of the anteroposterior (head-to-tail) axis in the fruit fly Drosophila melanogaster is one of the best understood examples of embryonic pattern formation, at the genetic level. A network of some 14 segmentation genes controls protein expression in narrow domains which are the first manifestation of the segments of the insect body. Work in the New York lab has led to a databank of more than 3300 confocal microscope images, quantifying protein expression for the segmentation genes, over a series of times during which protein pattern is developing (http://flyex.ams.sunysb.edu/FlyEx/). Quantification of the variability in expression evident in this data (both between embryos and within single embryos) allows us to determine error propagation in segmentation signalling. The maternal signal to the egg is highly variable, with noise levels more than several times those seen for expression of downstream genes. This implies that error suppression is active in the embryonic patterning mechanism. Error suppression is not possible with the favoured mechanism of local concentration gradient reading for positional specification. We discuss possible patterning mechanisms which do reliably filter input noise., Peer-reviewed article, Published.
In recent years, Smart Grid technologies such as Advanced Metering, Pervasive Control, Automation and Distribution Management have created numerous control and optimization opportunities and challenges for smart distribution networks. Availability of Co-Gen loads and/or Electric Vehicles (EVs) enable these technologies to inject reactive power into the grid by changing their inverter’s operating mode without considerable impact on their active power operation. This feature has created considerable opportunity for distribution network planners to explore if EVs could be used in the distribution network as reliable VAR suppliers. It may be possible for network operators to employ some EVs as VAR suppliers for future distribution grids. This paper proposes an innovative Smart Grid-based Volt-VAR Optimization (VVO) engine, capable of minimizing system power loss cost as well as the operating cost of switched Capacitor Banks, while optimizing the system voltage using an improved Genetic Algorithm (GA) with two levels of mutation and two levels of crossover. The paper studies the impact of EVs with different charging and penetration levels on VVO in different operating scenarios. Furthermore, the paper demonstrates how a typical VVO engine could benefit from V2G’s reactive power support. In order to assess V2G impacts on VVO and test the applicability of the proposed VVO, revised IEEE-123 Node Test Feeder in presence of various load types is used as case study., Article, Published. Received 24 May 2014, Revised 23 July 2015, Accepted 29 July 2015, Available online 8 August 2015.
Vapour barriers were originally intended to keep building assemblies from getting wet, but they can sometimes end up preventing assemblies from drying out. An innovative new product to manage moisture accumulation in the building envelope, however, may be able to address both issues: while the product acts as a vapour barrier under most conditions, it also allows excess moisture to escape. The Canadian Construction Materials Centre (CCMC) set out to determine whether this product can serve as a vapour barrier and an air barrier system and whether it conformed to the intent of applicable building code requirements. In collaboration with NRC-IRC researchers, CCMC developed a testing protocol for its evaluation, which was based on laboratory testing requirements for vapour diffusion, air leakage control and durability., Article, Published.
Study Design: Observational cross-sectional study. Objectives: Body mass index (BMI), measured as a ratio of weight (Wt) to the square of height (Wt/Ht(2)), waist circumference (WC) and waist-to-height ratio (WHtR) are common surrogate measures of adiposity. It is not known whether alternate scaling powers for height might improve the relationships between these measures and indices of obesity or cardiovascular disease (CVD) risk in individuals with spinal cord injury (SCI). We aimed to estimate the values of 'x' that render Wt/Ht(x) and WC/Ht(x) maximally correlated with dual energy x-ray absorptiometry (DEXA) total and abdominal body fat and Framingham Cardiovascular Risk Scores. Setting: Canadian public research institution. Methods: We studied 27 subjects with traumatic SCI. Height, Wt and body fat measurements were determined from DEXA whole-body scans. WC measurements were also obtained, and individual Framingham Risk Scores were calculated. For values of 'x' ranging from 0.0 to 4.0, in increments of 0.1, correlations between Wt/Ht(x) and WC/Ht(x) with total and abdominal body fat (kg and percentages) and Framingham Risk Scores were computed. Results: We found that BMI was a poor predictor of CVD risk, regardless of the scaling factor. Moreover, BMI was strongly correlated with measures of obesity, and modification of the scaling factor from the standard (Wt/Ht(2)) is not recommended. WC was strongly correlated with both CVD risk and obesity, and standard measures (WC and WHtR) are of equal predictive power. Conclusion: On the basis of our findings from this sample, alterations in scaling powers may not be necessary in individuals with SCI; however, these findings should be validated in a larger cohort., Peer-reviewed article, Published. Received 25 February 2014; revised 1 May 2014; accepted 1 August 2014; published online 30 September 2014.