Showing papers by "University of New Brunswick published in 2010"

Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri

Abstract: The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are well suited for the investigation of the evolution of multicellularity and development. We sequenced the 138-mega-base pair genome of V. carteri and compared its approximately 14,500 predicted proteins to those of its unicellular relative Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similar protein-coding potentials and few species-specific protein-coding gene predictions. Volvox is enriched in volvocine-algal-specific proteins, including those associated with an expanded and highly compartmentalized extracellular matrix. Our analysis shows that increases in organismal complexity can be associated with modifications of lineage-specific proteins rather than large-scale invention of protein-coding capacity.

Using Isoscapes to Trace the Movements and Foraging Behavior of Top Predators in Oceanic Ecosystems

Abstract: The stable isotope composition of animal tissues can provide intrinsic tags to study the foraging and migratory ecology of predators in the open ocean. Chapter 13 (this volume) demonstrated that by comparing the isotope values of an animal and its local prey or environment, the animal’s movements can be estimated, given that isotopic variation exists between habitats. The utility of using geographical variations in stable isotopes values, or isoscapes to study the movements of marine predators has been limited because of our lack of knowledge on the spatial variation of the carbon, nitrogen, and oxygen isotope values in the open ocean.

Beyond taxonomy: a review of macroinvertebrate trait‐based community descriptors as tools for freshwater biomonitoring

Abstract: Summary 1. Species traits have been frequently used in ecological studies in an attempt to develop a general ecological framework linking biological communities to habitat pressures. The trait approach offers a mechanistic alternative to traditional taxonomy-based descriptors. This review focuses on research employing traits as biomonitoring tools for freshwater ecosystems, although the lessons learned have wider application in the assessment of other ecosystem types. 2. We review the support from ecological theory to employ species traits for biomonitoring purposes (e.g. the habitat templet concept, landscape filtering hypothesis), and the subsequent studies that test the hypotheses arising from these theories, and apply this knowledge under real freshwater biomonitoring scenarios. We also include studies that deal with more specific issues such as trait trade-offs and trait syndromes. 3. We highlight the functional trait approach as one of the most promising tools emerging for biomonitoring freshwater ecosystems. Several technical issues are addressed and solutions are proposed. We discuss the need for: a broader unified trait biomonitoring tool; a more accurate understanding of the natural variation of community patterns of trait expression; approaches to diminish the effects of trait trade-offs and trait syndromes; additional life history and ecological requirement studies; and the detection of specific impacts under multiple stressor scenarios. 4. Synthesis and applications. This review provides biologists with the conceptual underpinning for the use of species traits as community descriptors and for freshwater biomonitoring and management. We expect that the functional trait approach will ultimately improve communication to managers and legislators of the importance of protecting freshwater ecosystem functions.

The integration of Six Sigma and lean management

Abstract: Purpose – Lean and Six Sigma are the two most important continuous improvement (CI) methodologies for achieving operational and service excellence in any organization. The purpose of this paper is to explain how lean compares to the Six Sigma and outline the benefits for integrating them. Also, this paper discusses the existing models that describe how Six Sigma and lean fit together. A new detailed description for integrating Six Sigma and lean is developed to provide an improved approach for CI.Design/methodology/approach – The following research included proposals and discussion, which were mainly based on the authors' own findings and experience, in addition to a literature‐based review of some of the most common and traditional lean and Six Sigma models.Findings – The paper proposes a new lean Six Sigma (LSS) approach and provides a detailed description of its phases. The paper also presents the views on the integration benefits as well as on how Six Sigma compares to lean. Six Sigma and lean are rel...

Toward Credible Evaluation of Anomaly-Based Intrusion-Detection Methods

Abstract: Since the first introduction of anomaly-based intrusion detection to the research community in 1987, the field has grown tremendously. A variety of methods and techniques introducing new capabilities in detecting novel attacks were developed. Most of these techniques report a high detection rate of 98% at the low false alarm rate of 1%. In spite of the anomaly-based approach's appeal, the industry generally favors signature-based detection for mainstream implementation of intrusion-detection systems. While a variety of anomaly-detection techniques have been proposed, adequate comparison of these methods' strengths and limitations that can lead to potential commercial application is difficult. Since the validity of experimental research in academic computer science, in general, is questionable, it is plausible to assume that research in anomaly detection shares the above problem. The concerns about the validity of these methods may partially explain why anomaly-based intrusion-detection methods are not adopted by industry. To investigate this issue, we review the current state of the experimental practice in the area of anomaly-based intrusion detection and survey 276 studies in this area published during the period of 2000-2008. We summarize our observations and identify the common pitfalls among surveyed works.

Space-time coordination dynamics in basketball: Part 2. The interaction between the two teams.

Abstract: In this article, we examine the space-time coordination dynamics of two basketball teams during competition. We identified six game sequences at random, from which the movement data of each player were obtained for analysis of team behaviours in both the longitudinal (basket-to-basket) and lateral (side-to-side) directions. The central position of a team was measured using its spatial (geometric) centre and dispersion using a stretch index, obtained from the mean distance of team members from the spatial centre. Relative-phase analysis of the spatial centres demonstrated in-phase stabilities in both the longitudinal and lateral directions, with more stability in the longitudinal than lateral direction. As anticipated, this finding is consistent with the results of an analysis of individual playing dyads (see companion article, this issue), as well as the more general principle of complex systems conforming to similar descriptions at different levels of analysis. Phase relations for the stretch index demonstrated in-phase attraction in the longitudinal direction and no attraction to any values in the lateral direction. Finally, the difference between the two stretch indexes at any instant showed phase transitions between two stable patterns when the difference was represented in binary form. This result is attributed to the reciprocity between teams in their amounts of expansion and contraction when possession of the ball is won and lost.

Multiple Binary Classifications via Linear Discriminant Analysis for Improved Controllability of a Powered Prosthesis

Abstract: This paper describes a novel pattern recognition based myoelectric control system that uses parallel binary classification and class specific thresholds. The system was designed with an intuitive configuration interface, similar to existing conventional myoelectric control systems. The system was assessed quantitatively with a classification error metric and functionally with a clothespin test implemented in a virtual environment. For each case, the proposed system was compared to a state-of-the-art pattern recognition system based on linear discriminant analysis and a conventional myoelectric control scheme with mode switching. These assessments showed that the proposed control system had a higher classification error (p < 0.001) but yielded a more controllable myoelectric control system (p < 0.001) as measured through a clothespin usability test implemented in a virtual environment. Furthermore, the system was computationally simple and applicable for real-time embedded implementation. This work provides the basis for a clinically viable pattern recognition based myoelectric control system which is robust, easily configured, and highly usable.

Changes in denitrifier abundance, denitrification gene mRNA levels, nitrous oxide emissions, and denitrification in anoxic soil microcosms amended with glucose and plant residues.

Abstract: In agricultural cropping systems, crop residues are sources of organic carbon (C), an important factor influencing denitrification. The effects of red clover, soybean, and barley plant residues and of glucose on denitrifier abundance, denitrification gene mRNA levels, nitrous oxide (N2O) emissions, and denitrification rates were quantified in anoxic soil microcosms for 72 h. nosZ gene abundances and mRNA levels significantly increased in response to all organic carbon treatments over time. In contrast, the abundance and mRNA levels of Pseudomonas mandelii and closely related species (nirSP) increased only in glucose-amended soil: the nirSP guild abundance increased 5-fold over the 72-h incubation period (P < 0.001), while the mRNA level significantly increased more than 15-fold at 12 h (P < 0.001) and then subsequently decreased. The nosZ gene abundance was greater in plant residue-amended soil than in glucose-amended soil. Although plant residue carbon-to-nitrogen (C:N) ratios varied from 15:1 to 30:1, nosZ gene and mRNA levels were not significantly different among plant residue treatments, with an average of 3.5 10 7 gene copies and 6.9 10 7 transcripts g 1 dry soil. Cumulative N2O emissions and denitrification rates increased over 72 h in both glucose- and plant-tissue-C-treated soil. The nirSP and nosZ communities responded differently to glucose and plant residue amendments. However, the targeted denitrifier communities responded similarly to the different plant residues under the conditions tested despite changes in the quality of organic C and different C:N ratios.

School Composition and Contextual Effects on Student Outcomes

Abstract: BackgroundFindings from several international studies have shown that there is a significant relationship between literacy skills and socioeconomic status (SES). Research has also shown that school...

Dna barcoding is a powerful tool to uncover algal diversity: a case study of the phyllophoraceae (gigartinales, rhodophyta) in the canadian flora

Abstract: Previous studies have established that the 5′ end of the mitochondrial gene COI (cytochrome oxidase subunit I) is useful for rapid and reliable identification of red algal species and have demonstrated that our understanding of red algal biodiversity and biogeography is fragmentary. In this context, we are completing a thorough sampling along the Canadian coast and using the DNA barcode for the assignment of collections to genetic species to explore algal diversity in the Canadian flora. In the present study, we provide results regarding diversity of members of the red algal family Phyllophoraceae. We have analyzed 354 individuals from the Arctic, Atlantic, and Pacific coasts of Canada, as well as 26 specimens from the USA, Europe, and Australia, resolving 29 species based on the analyses of the DNA barcode. Twenty-three of these genetic species were present in Canada where only 18 species are currently recognized, including Ceratocolax hartzii Rosenv., which was in the same genetic species group as its host Coccotylus truncatus (Pall.) M. J. Wynne et N. J. Heine and is thus transferred to Coccotylus, C. hartzii (Rosenv.) comb. nov., but retained as a distinct species owing to its unique habit and phenology. Our results revealed the presence of cryptic diversity within the genera Coccotylus, Mastocarpus, Ozophora, and Stenogramme, for which we resurrect Coccotylus brodiei (Turner) Kutz. and describe Mastocarpus pachenicus sp. nov., Ozophora lanceolata sp. nov., and Stenogramme bamfieldiensis sp. nov., leaving a multitude of unnamed Mastocarpus spp. in need of further taxonomic study. In addition, we report range extensions into British Columbia of Besa papillaeformis Setch., previously known only from its type and nearby localities in California; Gymnogongrus crenulatus (Turner) J. Agardh, recorded only from the Atlantic; and Stenogramme cf. rhodymenioides Joly et Alveal, previously only known from South America. Finally, the phylogenetic affinities of the Canadian species of Phyllophoraceae characterized in this study were investigated using LSU rDNA, RUBISCO LSU (rbcL), and combined analyses.

Frictional Melting Processes in Planetary Materials: From Hypervelocity Impact to Earthquakes

Abstract: Frictional melting is the result of the conversion of mechanical deformation to heat under adiabatic conditions of slip. Within planetary materials, which are mainly natural ceramics, frictional melting occurs at high strain rates (typically >10 −2 s −1 ) and at slip velocities greater than 0.1 m s −1 .T he pathway to friction melting is controlled by the mechanical properties of a rock’s constituent minerals, especially fracture toughness. Minerals with the lowest fracture toughnesses and breakdown temperatures are preferentially comminuted and fused to form the melt. The product is a polyphase suspension comprising mineral and rock fragments enclosed in a liquid matrix. This cools to form the rock type known as pseudotachylyte, and at even higher strain rates, it forms shock veins in meteorites and in impact craters, which may contain high-pressure mineral polymorphs. The generation of melt on sliding surfaces can lubricate earthquake faults, facilitate the post-shock modification of impact craters, and make landslides more hazardous.

Abortion in Brazil: a household survey using the ballot box technique

Abstract: This study presents the first results of the National Abortion Survey (PNA, Pesquisa Nacional de Aborto), a household random sample survey fielded in 2010 covering urban women in Brazil aged 18 to 39 years. The PNA combined two techniques, interviewer-administered questionnaires and self-administered ballot box questionnaires. The results of PNA show that at the end of their reproductive health one in five women has performed an abortion, with abortions being more frequent in the main reproductive ages, that is, from 18 to 29 years old. No relevant differentiation was observed in the practice of abortion among religious groups, but abortion was found to be more common among people with lower education. The use of medical drugs to induce abortion occurred in half of the abortions, and post-abortion hospitalization was observed among approximately half of the women who aborted. Such results lead to conclude that abortion is a priority in the Brazilian public health agenda.

Structural and functional diversification of the light-harvesting complexes in photosynthetic eukaryotes

Abstract: Eukaryotes acquired photosynthetic metabolism over a billion years ago, and during that time the light-harvesting antennae have undergone significant structural and functional divergence. The antenna systems are generally used to harvest and transfer excitation energy into the reaction centers to drive photosynthesis, but also have the dual role of energy dissipation. Phycobilisomes formed the first antenna system in oxygenic photoautotrophs, and this soluble protein complex continues to be the dominant antenna in extant cyanobacteria, glaucophytes, and red algae. However, phycobilisomes were lost multiple times during eukaryotic evolution in favor of a thylakoid membrane-integral light-harvesting complex (LHC) antenna system found in the majority of eukaryotic taxa. While photosynthesis spread across different eukaryotic kingdoms via endosymbiosis, the antenna systems underwent extensive modification as photosynthetic groups optimized their light-harvesting capacity and ability to acclimate to changing environmental conditions. This review discusses the different classes of LHCs within photosynthetic eukaryotes and examines LHC diversification in different groups in a structural and functional context.

Hemicellulose Removal from Hardwood Chips in the Pre-Hydrolysis Step of the Kraft-Based Dissolving Pulp Production Process

Abstract: A pre-hydrolysis step to remove hemicelluloses from mixed hardwood chips consisting of maple, aspen, and birch with a ratio of 7:2:1 has been carried out. The effects of parameters on the pre-hydrolysis such as time, temperature, acetic acid addition, and raw material species, were determined. Different sugars, acetic acid, and furfural formation in the pre-hydrolysis liquor were quantified. The results showed that the pre-hydrolysis is a dynamic process, in which the removal of hemicelluloses increased with time while the conversion of extracted hemicelluloses to monosaccharides due to acid hydrolysis increased and part of the xylose was converted to furfural. The maximum temperature was the most critical parameter for hemicelluloses extraction and conversion, and a temperature of 170°C was the optimum for hemicelluloses extraction with relatively low conversion of xylose to furfural. About 11% of the xylan (in both monomeric and oligomeric forms) was removed at 170°C. Due to the presence of a h...

Space-time coordination dynamics in basketball: Part 1. Intra- and inter-couplings among player dyads.

Abstract: We examined space–time patterns of basketball players during competition by analysing movement data obtained from six game sequences. Strong in-phase relations in the longitudinal (basket-to-basket) direction were observed for all playing dyads, especially player–opponent dyads matched for playing position, indicating that these movements were very constrained by the game demands. Similar findings for in-phase relations were observed for the most part in the lateral direction, the main exception being dyads comprising the two wing players from the same team. These dyads instead demonstrated strong attractions to anti-phase, a consequence perhaps of seeking to increase and decrease team width in tandem. Single instances from select dyads and game sequences demonstrated further evidence of phase stabilities and phase transitions on some occasions. Together, these findings demonstrate that space–time movement patterns of playing dyads in basketball, while unique, nonetheless conform to a uniform des...

Perceived organizational barriers to women's career advancement in Lebanon

Abstract: Purpose – The purpose of this paper is to address the research gap on Lebanese female managers and to examine female managers' perceptions of their organizations in relation to women's career progression.Design/methodology/approach – The research was quantitative in nature. A survey questionnaire was used to collect data from 450 female managers. Measures included personal and demographic characteristics, organizational culture, organizational practices, organizational networks, mentoring and role modeling, tokenism, and the usage of wasta.Findings – Descriptive statistics and analysis of variance were used to explain the results. The results reveal that female managers perceive their career progression to be affected by organizational culture, practices, and networks, while mentoring and tokenism were shown to be less critical. In addition, the women in this sample perceived wasta to be a powerful determinant.Practical implications – The findings contribute to a wider appreciation of the implicit barrier...

Odin II - An Open-Source Verilog HDL Synthesis Tool for CAD Research

Abstract: In this work, we present Odin II, a framework for Verilog Hardware Description Language (HDL) synthesis that allows researchers to investigate approaches/improvements to different phases of HDL elaboration that have not been previously possible. Odin II’s output can be fed into traditional back-end flows for both FPGAs and ASICs so that these improvements can be better quantified. Whereas the original Odin [1] provided an open source synthesis tool, Odin II’s synthesis framework offers significant improvements such as a unified environment for both front-end parsing and netlist flattening. Odin II also interfaces directly with VPR [2], a common academic FPGA CAD flow, allowing an architectural description of a target FPGA as an input to enable identification and mapping of design features to custom features. Furthermore, Odin II can also read the netlists from downstream CAD stages into its netlist data-structure to facilitate analysis. Odin II can be used for a wide range of experiments; in this paper, we show three specific instances of how Odin II can be used by ASIC and FPGA researchers for more than basic synthesis. Odin II is open source and released under the MIT License.

Examining the adverse effects of limb position on pattern recognition based myoelectric control

Abstract: Pattern recognition of myoelectric signals for the control of prosthetic devices has been widely reported and debated. A large portion of the literature focuses on offline classification accuracy of pre-recorded signals. Historically, however, there has been a semantic gap between research findings and a clinically viable implementation. Recently, renewed focus on prosthetics research has pushed the field to provide more clinically relevant outcomes. One way to work towards this goal is to examine the differences between research and clinical results. The constrained nature in which offline training and test data is often collected compared to the dynamic nature of prosthetic use is just one example. In this work, we demonstrate that variations in limb position after training can have a substantial impact on the robustness of myoelectric pattern recognition.

On the consistency of model, ground‐based, and satellite observations of tidal signatures: Initial results from the CAWSES tidal campaigns

Abstract: [1] Comparisons between tidal wind signatures diagnosed from satellite and ground-based observations and a general circulations model for two (September–October 2005, March–April 2007) of the four Climate and Weather of the Sun-Earth System (CAWSES) Global Tidal Campaign observation periods are presented (CAWSES is an international program sponsored by Scientific Committee on Solar-Terrestrial Physics). Specific comparisons are made between model (extended Canadian Middle Atmosphere Model), satellite (Thermosphere Ionosphere Mesosphere Energetics and Dynamics (TIMED)), meteor, MF and incoherent scatter radar (ISR), and lidar tidal signatures in the mesosphere and lower thermosphere. The satellite and ground-based signatures are in good agreement and demonstrate for the first time that the tidal wind fields observed by both types of observations are consistent with each other. This is the first time that such agreement has been reported and effectively resolves the long-standing issue between ground-based radar and satellite optical measurements of winds. This level of agreement, which has proved elusive in the past, was accomplished by superposing the significant tidal components from the satellite analyses to reconstruct the fields observed by the ground stations. Particularly striking in these comparisons is the extent to which the superposed fields show strong geographic variability. This variability is also seen in the component superpositions generated from the extended Canadian Middle Atmosphere Model (eCMAM), although differences in the geographic patterns are evident.

Vitamin D for the management of multiple sclerosis

Abstract: Background Multiple sclerosis is a disease of the central nervous system characterized by demyelination of the nerve sheaths which can result in varying levels of disability. Disease occurrence and progression are considered by some to be associated with low serum levels of vitamin D. Studies investigating vitamin D supplementation in MS patients have illustrated a noticeable improvement in the course of the disease. Objectives To evaluate the safety and effectiveness of vitamin D in the management of multiple sclerosis. Search methods We searched the Cochrane Multiple Sclerosis Group Trials Register comprising references identified from comprehensive electronic database searches and hand searches of relevant journals and abstract books of conferences. Selection criteria Randomised and quasi-randomised controlled trials comparing vitamin D with placebo or any other treatment for the management of multiple sclerosis. Data collection and analysis Two review authors selected trials for inclusion, assessed the risk of bias and extracted data independently. Disagreements were resolved by consensus. Trialists were contacted for clarification of study details. Main results We included a single trial (49 participants) conducted over 52 weeks, which treated 25 patients with escalating doses of vitamin D compared with control (24). The trial provided some evidence of the potential benefit of the intervention on several outcomes i.e. the annualised relapse rate; EDSS scores; suppression of T-cell proliferation and illustrated a measure of comparative safety in the relative absence of any adverse events or of high serum calcium levels over the study period. This was a low powered trial with a potential high risk of bias which may ultimately impose limits on the applicability of the available evidence to the MS population as a whole. Authors' conclusions The current level of evidence for the effectiveness of vitamin D supplementation in the management of people with MS is based on a single RCT with potential high risk of bias, which does not at present allow confident decision-making about the use of Vitamin D in MS. Therefore, until further high quality evidence is available, clinicians may wish to consider relevant MS guidelines on vitamin D supplementation when making decisions about the care of people with multiple sclerosis. Adequately powered, multi-centred RCTs with a focus on clinical as well as immunological and MRI outcomes that are meaningful to people with MS, and are able to provide insight into the benefits of Vitamin D in people with MS, are still required.

Predictive factors of excessive online poker playing.

Abstract: Despite the widespread rise of online poker playing, there is a paucity of research examining potential predictors for excessive poker playing. The aim of this study was to build on recent research examining motives for Texas Hold'em play in students by determining whether predictors of other kinds of excessive gambling apply to Texas Hold'em. Impulsivity, negative mood states, dissociation, and boredom proneness have been linked to general problem gambling and may play a role in online poker. Participants of this study were self-selected online poker players (N = 179) who completed an online survey. Results revealed that participants played an average of 20 hours of online poker a week and approximately 9% of the sample was classified as a problem gambler according to the Canadian Problem Gambling Index. Problem gambling, in this sample, was uniquely predicted by time played, dissociation, boredom proneness, impulsivity, and negative affective states, namely depression, anxiety, and stress.

GPS TEC, scintillation and cycle slips observed at high latitudes during solar minimum

Abstract: . High-latitude irregularities can impair the operation of GPS-based devices by causing fluctuations of GPS signal amplitude and phase, also known as scintillation. Severe scintillation events lead to losses of phase lock, which result in cycle slips. We have used data from the Canadian High Arctic Ionospheric Network (CHAIN) to measure amplitude and phase scintillation from L1 GPS signals and total electron content (TEC) from L1 and L2 GPS signals to study the relative role that various high-latitude irregularity generation mechanisms have in producing scintillation. In the first year of operation during the current solar minimum the amplitude scintillation has remained very low but events of strong phase scintillation have been observed. We have found, as expected, that auroral arc and substorm intensifications as well as cusp region dynamics are strong sources of phase scintillation and potential cycle slips. In addition, we have found clear seasonal and universal time dependencies of TEC and phase scintillation over the polar cap region. A comparison with radio instruments from the Canadian GeoSpace Monitoring (CGSM) network strongly suggests that the polar cap scintillation and TEC variations are associated with polar cap patches which we therefore infer to be main contributors to scintillation-causing irregularities in the polar cap.

Sorting improves word-aligned bitmap indexes

Abstract: Bitmap indexes must be compressed to reduce input/output costs and minimize CPU usage. To accelerate logical operations (AND, OR, XOR) over bitmaps, we use techniques based on run-length encoding (RLE), such as Word-Aligned Hybrid (WAH) compression. These techniques are sensitive to the order of the rows: a simple lexicographical sort can divide the index size by 9 and make indexes several times faster. We investigate row-reordering heuristics. Simply permuting the columns of the table can increase the sorting efficiency by 40%. Secondary contributions include efficient algorithms to construct and aggregate bitmaps. The effect of word length is also reviewed by constructing 16-bit, 32-bit and 64-bit indexes. Using 64-bit CPUs, we find that 64-bit indexes are slightly faster than 32-bit indexes despite being nearly twice as large.

Social aspects of the sustainability of integrated multi-trophic aquaculture

Abstract: A pilot project in the Bay of Fundy, Canada, is growing kelps, mussels, and salmon in an integrated multi-trophic aquaculture (IMTA) system. Biological and economic results are positive, but social acceptability is also a critical component of aquaculture sustainability. Focus group sessions with several segments of the population (restaurateurs, residents of communities near aquaculture facilities, and the general population) were held and the participants’ knowledge of, and opinions on, IMTA were recorded. Most participants felt that IMTA had the potential to reduce the environmental impacts of salmon farming, benefit community economies, and improve industry competitiveness and sustainability. All felt that seafood produced in IMTA systems would be safe to eat and 50% of the participants were willing to pay 10% more for these products if labelled as such. The participants felt that IMTA appears to be an improvement over current monoculture practices and would be cautiously welcomed in the marketplace. A promotional campaign educating the general public, food distributors, and other industry stakeholders about the positive benefits of IMTA would go a long way in gaining mainstream acceptance of this aquaculture practice.