Showing papers by "University of New Brunswick published in 2008"

Lipid corrections in carbon and nitrogen stable isotope analyses: comparison of chemical extraction and modelling methods

Abstract: Summary 1. Lipids have more negative δ 13 C values relative to other major biochemical compounds in plant and animal tissues. Although variable lipid content in biological tissues alters results and conclusions of δ 13 C analyses in aquatic food web and migration studies, no standard correction protocol exists. 2. We compared chemical extraction and mathematical correction methods for freshwater and marine fishes and aquatic invertebrates to better understand impacts of correction approaches on carbon ( δ 13 C) and nitrogen ( δ 15 N) stable isotope data. 3. Fish and aquatic invertebrate tissue δ 13 C values increased significantly following extraction for almost all species and tissue types relative to nonextracted samples. In contrast, δ 15 N was affected for muscle and whole body samples from only a few freshwater and marine species and had a limited effect for the entire data set. 4. Lipid normalization models, using C : N as a proxy for lipid content, predicted lipid-corrected δ 13 C for paired data sets more closely with parameters specific to the tissue type and species to which they were applied. 5. We present species- and tissue-specific models based on bulk C : N as a reliable alternative to chemical extraction corrections. By analysing a subset of samples before and after lipid extraction, models can be applied to the species and tissues of interest that will improve estimates of dietary sources using stable isotopes.

Identifying Canadian Freshwater Fishes through DNA Barcodes

Abstract: Background DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons.

RevLib: An Online Resource for Reversible Functions and Reversible Circuits

Abstract: Synthesis of reversible logic has become an active research area in the last years. But many proposed algorithms are evaluated with a small set of benchmarks only. Furthermore, results are often documented only in terms of gate counts or quantum costs, rather than presenting the specific circuit. In this paper RevLib (www.revlib.org) is introduced, an online resource for reversible functions and reversible circuits. RevLib provides a large database of functions with respective circuit realizations. RevLib is designed to ease the evaluation of new methods and facilitate the comparison of results. In addition, tools are introduced to support researchers in evaluating their algorithms and documenting their results.

Further Notes on the Basic Reproduction Number

Abstract: The basic reproduction number, R0 is a measure of the potential for disease spread in a population. Mathematically, R0 is a threshold for stability of a disease-free equilibrium and is related to the peak and final size of an epidemic. The purpose of these notes is to give a precise definition and algorithm for obtaining R0 for a general compartmental ordinary differential equation model of disease transmission. Several examples of calculating R0 are included, and the epidemiological interpretation of this threshold parameter is connected to the local and global stability of a disease-free equilibrium.

Quantum Circuit Simplification and Level Compaction

Abstract: Quantum circuits are time-dependent diagrams describing the process of quantum computation. Usually, a quantum algorithm must be mapped into a quantum circuit. Optimal synthesis of quantum circuits is intractable, and heuristic methods must be employed. With the use of heuristics, the optimality of circuits is no longer guaranteed. In this paper, we consider a local optimization technique based on templates to simplify and reduce the depth of nonoptimal quantum circuits. We present and analyze templates in the general case and provide particular details for the circuits composed of NOT, CNOT, and controlled-sqrt-of-NOT gates. We apply templates to optimize various common circuits implementing multiple control Toffoli gates and quantum Boolean arithmetic circuits. We also show how templates can be used to compact the number of levels of a quantum circuit. The runtime of our implementation is small, whereas the reduction in the number of quantum gates and number of levels is significant.

Rubisco, Rubisco activase, and global climate change

Abstract: Global warming and the rise in atmospheric CO(2) will increase the operating temperature of leaves in coming decades, often well above the thermal optimum for photosynthesis. Presently, there is controversy over the limiting processes controlling photosynthesis at elevated temperature. Leading models propose that the reduction in photosynthesis at elevated temperature is a function of either declining capacity of electron transport to regenerate RuBP, or reductions in the capacity of Rubisco activase to maintain Rubisco in an active configuration. Identifying which of these processes is the principal limitation at elevated temperature is complicated because each may be regulated in response to a limitation in the other. Biochemical and gas exchange assessments can disentangle these photosynthetic limitations; however, comprehensive assessments are often difficult and, for many species, virtually impossible. It is proposed that measurement of the initial slope of the CO(2) response of photosynthesis (the A/C(i) response) can be a useful means to screen for Rubisco activase limitations. This is because a reduction in the Rubisco activation state should be most apparent at low CO(2) when Rubisco capacity is generally limiting. In sweet potato, spinach, and tobacco, the initial slope of the A/C(i) response shows no evidence of activase limitations at high temperature, as the slope can be accurately modelled using the kinetic parameters of fully activated Rubisco. In black spruce (Picea mariana), a reduction in the initial slope above 30 degrees C cannot be explained by the known kinetics of fully activated Rubisco, indicating that activase may be limiting at high temperatures. Because black spruce is the dominant species in the boreal forest of North America, Rubisco activase may be an unusually important factor determining the response of the boreal biome to climate change.

An Advanced SVPWM-Based Predictive Current Controller for Three-Phase Inverters in Distributed Generation Systems

Abstract: Space vector pulsewidth modulation (SVPWM) has been widely applied in the current control of three-phase voltage source inverters (VSIs). However, for grid-connected VSIs in distributed generation (DG) systems, the performance of current controllers based on SVPWM is compromised by the grid harmonics and the control delay due to computation and sampling. In this paper, an advanced SVPWM-based predictive current controller is proposed and studied. The controller mimics deadbeat control in the synchronous d-q reference frame, and is very simple and robust to implement. With the necessary grid voltage detection in DG systems for protection, grid harmonics disturbance is effectively suppressed through feedforward compensation. Based on a dual-timer sampling scheme, the control delay compensation becomes more simple yet effective. The comprehensive analysis on the proposed predictive current control system is provided. The simulation and experimental test results show that the proposed current controller has an excellent steady-state response as well as an extremely fast dynamic response.

Learning in Computer Conferenced Contexts: The Learners' Perspective

Abstract: Reported here is a study about how adult students learn in an environment that enables group communication only by text-based messaging, that is, computer conferencing (CC). Four questions guided the study: How do students say they learned? What, in their opinion, are the salient features of CC? What, if any, are the effects of those features on their learning? And Do the students' descriptions of how they learned relate to learning strategies as found in cognitive psychology literature? The results were developed from qualitative data collected from in-depth interviews with 21 M.Ed. students and the instructors for the two courses involved. The key categories of learning strategies identified were choice, expression, peer interaction, and organization of information. The salient features were interconnected to the perceived strengths and weaknesses of CC, and all appear to indicate that CC poses as many challenges as it does opportunities for its use in higher education. The results of the study suggest that the taxonomy from cognitive psychology that was used for this study should be expanded to include strategies that focus on the management of the inter-personal and logistical elements of the CC context. Suggestions for improved practice are offered. Lorsque la communication de groupe depend uniquement de messageries textuelles, a savoir les ordinoconferences, comment les etudiants adultes apprennent-ils? Le present article fait etat des resultats d'une enquete orientee par quatre questions: 1) Comment les etudiants affirment-ils avoir appris? 2) Que percoivent-ils comme etant les traits saillants des ordinoconferen-ces? 3) Ces traits ont-ils une incidence sur leur apprentissage? et 4) Les modes d'apprentissage identifies sont-ils conformes aux strategies decrites par la psychologie cognitive? Au cours d'entrevues en profondeur, on a recueilli des donnees qualitatives aupres de 21 etudiants a la maitrise en education et aupres des enseignants des deux cours en cause. Les princi-pales strategies identifiees ont ete le choix, l'expression, l'interaction avec les pairs et l'organisation des informations. Les traits saillants etaient relies aux forces et aux faiblesses percues de tels environnements, et tout porte a croire qu'au niveau des etudes superieures, les ordinoconferences sont porteuses d'autant de defis que de promesses. Les resultats semblent in-diquer que la taxonomie utilisee, tiree de la psychologie cognitive, devrait inclure aussi des strategies orientees par la gestion des elements interper-sonnels et logistiques propres aux ordinoconferences. L'article presente aussi des suggestions d'ordre pratique.

Ethical sensitivity in professional practice: Concept analysis

Abstract: Title. Ethical sensitivity in professional practice: concept analysis Aim. This paper is a report of a concept analysis of ethical sensitivity. Background. Ethical sensitivity enables nurses and other professionals to respond morally to the suffering and vulnerability of those receiving professional care and services. Because of its significance to nursing and other professional practices, ethical sensitivity deserves more focused analysis. Data sources. A criteria-based method oriented toward pragmatic utility guided the analysis of 200 papers and books from the fields of nursing, medicine, psychology, dentistry, clinical ethics, theology, education, law, accounting or business, journalism, philosophy, political and social sciences and women’s studies. This literature spanned 1970 to 2006 and was sorted by discipline and concept dimensions and examined for concept structure and use across various contexts. The analysis was completed in September 2007. Findings. Ethical sensitivity in professional practice develops in contexts of uncertainty, client suffering and vulnerability, and through relationships characterized by receptivity, responsiveness and courage on the part of professionals. Essential attributes of ethical sensitivity are identified as moral perception, affectivity and dividing loyalties. Outcomes include integrity preserving decision-making, comfort and well-being, learning and professional transcendence. Our findings promote ethical sensitivity as a type of practical wisdom that pursues client comfort and professional satisfaction with care delivery. Conclusion. The analysis and resulting model offers an inclusive view of ethical sensitivity that addresses some of the limitations with prior conceptualizations.

Multitrophic Integration for Sustainable Marine Aquaculture

Abstract: The seafood industry is at a crossroads: while capture fisheries are stagnating in volume and decreasing in profitability, they are also falling short of world demand, as the annual consumption of seafood has been rising, doubling over the last three decades. As this trend is expected to persist, the importance of aquaculture, as the solution for providing the difference between the demand and the biomass available, could increase. The majority of aquaculture production still originates from extensive and semi-intensive systems; however, the rapid development of intensive marine fed aquaculture (e.g., carnivorous finfish and shrimp) throughout the world, even though it represents only 11%, is associated with concerns about the environmental, economic, and social impacts these often monospecific practices can have. To continue to grow, the aquaculture sector needs to develop innovative, responsible, sustainable, and profitable practices. This article examines some of the different options available to face these challenges (geographical expansion, intensification of the existing sites, diversification, social acceptance) and recognizes that changes in attitudes are needed and innovative practices have to be developed for further advancement. One of these options is integrated multitrophic aquaculture (IMTA), which combines the cultivation of fed aquaculture species (e.g., finfish) with inorganic extractive aquaculture species (e.g., seaweed) and organic extractive aquaculture species (e.g., shellfish) for a balanced ecosystem management approach. Through IMTA, some of the food and energy considered lost in fed monoculture operations are recaptured and converted into crops of commercial value (extractive plants and animals), while biomitigation takes place. Several examples of IMTA systems in different parts of the world are described to illustrate the concept. For IMTA to develop from the experimental scale to sustainable commercial food production systems, appropriate regulatory and policy frameworks, and financial incentive tools, which recognize the economic value and environmental benefits of biomitigation services by biofilters, need to be put in place.

Macroinvertebrate community response to inter-annual and regional river flow regime dynamics†

Abstract: Spatio-temporal variability in river flow is a fundamental control on instream habitat structure and riverine ecosystem biodiversity and integrity. However, long-term riverine ecological time-series to test hypotheses about hydrology–ecology interactions in a broader temporal context are rare, and studies spanning multiple rivers are often limited in their temporal coverage to less than five years. To address this research gap, a unique spatio-temporal hydroecological analysis was conducted of long-term instream ecological responses (1990–2000) to river flow regime variability at 83 sites across England and Wales. The results demonstrate clear hydroecological associations at the national scale (all data). In addition, significant differences in ecological response are recorded between three ‘regions’ identified (RM1–3*) associated with characteristics of the flow regime. The effect of two major supra-seasonal droughts (1990–1992 and 1996–1997) on inter-annual (IA) variability of the LIFE scores is evident with both events showing a gradual decline before and recovery of LIFE scores after the low flow period. The instream community response to high magnitude flow regimes (1994 and 1995) is also apparent, although these associations are less striking. The results demonstrate classification of rivers into flow regime regions offers a way to help unravel complex hydroecological associations. The approach adopted herein could easily be adapted for other geographical locations, where datasets are available. Such work is imperative to understand flow regime–ecology interactions in a longer term, wider spatial context and so assess future hydroecological responses to climate change and anthropogenic modification of riverine ecosystems. Copyright © 2008 John Wiley & Sons, Ltd.

Stream network modelling using lidar and photogrammetric digital elevation models : a comparison and field verification

Abstract: A conventional, photogrammetrically derived digital elevation model (DEM; 10 m resolution) and a light detection and ranging (lidar)-derived DEM (1 m resolution) were used to model the stream network of a 193 ha watershed in the Swan Hills of Alberta, Canada. Stream networks, modelled using both hydrologically corrected and uncorrected versions of the DEMs and derived from aerial photographs, were compared. The actual network, mapped in the field, was used as verification. The lidar DEM-derived network was the most accurate representation of the field-mapped network, being more accurate even than the photo-derived network. This was likely due to the greater initial point density, accuracy and resolution of the lidar DEM compared with the conventional DEM. Lidar DEMs have great potential for application in land-use planning and management and hydrologic modelling. The network derived from the hydrologically corrected conventional DEM was more accurate than that derived from the uncorrected one, but this was not the case with the lidar DEM. Copyright © 2007 John Wiley & Sons, Ltd.

UNB3m_pack: a neutral atmosphere delay package for radiometric space techniques

Abstract: Several hybrid neutral atmosphere delay models have been developed at the University of New Brunswick. In this paper we are presenting UNB3m_pack, a package with subroutines in FORTRAN and corresponding functions in MatLab which provides neutral atmospheric information estimated using the UNB3m model. The main goal of UNB3m is to provide reliable predicted neutral atmosphere delays for users of global navigation satellite systems (GNSS) and other transatmospheric radiometric techniques. Slant neutral atmosphere delays are the main output of the package, however, it can be used to estimate zenith delays, Niell mapping functions values, delay rates, mapping function rates, station pressure, temperature, relative humidity and the mean temperature of water vapor in the atmospheric column. The subroutines work using day of year, latitude, height and elevation angle as input values. The files of the package have a commented section at the beginning, explaining how the subroutines work and what the input and output parameters are. The subroutines are self-contained, i.e., they do not need any auxiliary files. The user has simply to add to his/her software one or more of the available files and call them in the appropriate way.

Discriminative parameter learning for Bayesian networks

Abstract: Bayesian network classifiers have been widely used for classification problems. Given a fixed Bayesian network structure, parameters learning can take two different approaches: generative and discriminative learning. While generative parameter learning is more efficient, discriminative parameter learning is more effective. In this paper, we propose a simple, efficient, and effective discriminative parameter learning method, called Discriminative Frequency Estimate (DFE), which learns parameters by discriminatively computing frequencies from data. Empirical studies show that the DFE algorithm integrates the advantages of both generative and discriminative learning: it performs as well as the state-of-the-art discriminative parameter learning method ELR in accuracy, but is significantly more efficient.

Aromatic Amino Acid-Dependent Expression of Indole-3-Pyruvate Decarboxylase Is Regulated by TyrR in Enterobacter cloacae UW5

Abstract: The plant growth-promoting rhizobacterium Enterobacter cloacae UW5 synthesizes the plant growth hormone indole-3-acetic acid (IAA) via the indole-3-pyruvate pathway utilizing the enzyme indole-3-pyruvate decarboxylase that is encoded by ipdC. In this bacterium, ipdC expression and IAA production occur in stationary phase and are induced by an exogenous source of tryptophan, conditions that are present in the rhizosphere. The aim of this study was to identify the regulatory protein that controls the expression of ipdC. We identified a sequence in the promoter region of ipdC that is highly similar to the recognition sequence for the Escherichia coli regulatory protein TyrR that regulates genes involved in aromatic amino acid transport and metabolism. Using a tyrR insertional mutant, we demonstrate that TyrR is required for IAA production and for induction of ipdC transcription. TyrR directly induces ipdC expression, as was determined by real-time quantitative reverse transcription-PCR, by ipdC promoter-driven reporter gene activity, and by electrophoretic mobility shift assays. Expression increases in response to tryptophan, phenylalanine, and tyrosine. This suggests that, in addition to its function in plant growth promotion, indolepyruvate decarboxylase may be important for aromatic amino acid uptake and/or metabolism.

Parents’ Reports of Sexual Communication With Children in Kindergarten to Grade 8

Abstract: We examined factors associated with parents’ reports of three aspects of parent-child sexual communication, quality, frequency with which parents encouraged questions, and extent of communication, on each of 10 sexual health topics. Participants were 3,413 mothers and 426 fathers with children in kindergarten to grade 8. Parents’ demographic characteristics, own sexual health education, knowledge and comfort talking about sexuality with their children, and ratings of the importance of comprehensive school-based sex education plus child gender and grade level were uniquely related to their self-reported sexual communication with their children, although different predictors were associated with various topics. These results highlight the need to include characteristics of parents, their children, and the communication itself in research on parent-child sexual communication.

High precision atomic theory for Li and Be+: QED shifts and isotope shifts.

Abstract: High-precision results are presented for calculations of the nonrelativistic energies, relativistic corrections, and quantum electrodynamic corrections for the $2\text{ }^{2}S$, $2\text{ }^{2}P$, and $3\text{ }^{2}S$ states of Li and ${\mathrm{Be}}^{+}$, using nonrelativistic wave functions expressed in Hylleraas coordinates. Bethe logarithms are obtained for the states of ${\mathrm{Be}}^{+}$. Finite mass corrections are calculated with sufficient accuracy to extract the nuclear charge radius from measurements of the isotope shift for the $2\text{ }^{2}S\ensuremath{-}2\text{ }^{2}P$ and $2\text{ }^{2}S\ensuremath{-}3\text{ }^{2}S$ transitions. The calculated ionization potential for ${\mathrm{Be}}^{+}$ is $146\text{ }882.923\ifmmode\pm\else\textpm\fi{}0.005\text{ }\text{ }{\mathrm{cm}}^{\ensuremath{-}1}$.