Showing papers by "University of New Brunswick published in 2012"

Smart cities of the future

Abstract: Here we sketch the rudiments of what constitutes a smart city which we define as a city in which ICT is merged with traditional infrastructures, coordinated and integrated using new digital technologies. We first sketch our vision defining seven goals which concern: developing a new understanding of urban problems; effective and feasible ways to coordinate urban technologies; models and methods for using urban data across spatial and temporal scales; developing new technologies for communication and dissemination; developing new forms of urban governance and organisation; defining critical problems relating to cities, transport, and energy; and identifying risk, uncertainty, and hazards in the smart city. To this, we add six research challenges: to relate the infrastructure of smart cities to their operational functioning and planning through management, control and optimisation; to explore the notion of the city as a laboratory for innovation; to provide portfolios of urban simulation which inform future designs; to develop technologies that ensure equity, fairness and realise a better quality of city life; to develop technologies that ensure informed participation and create shared knowledge for democratic city governance; and to ensure greater and more effective mobility and access to opportunities for urban populations. We begin by defining the state of the art, explaining the science of smart cities. We define six scenarios based on new cities badging themselves as smart, older cities regenerating themselves as smart, the development of science parks, tech cities, and technopoles focused on high technologies, the development of urban services using contemporary ICT, the use of ICT to develop new urban intelligence functions, and the development of online and mobile forms of participation. Seven project areas are then proposed: Integrated Databases for the Smart City, Sensing, Networking and the Impact of New Social Media, Modelling Network Performance, Mobility and Travel Behaviour, Modelling Urban Land Use, Transport and Economic Interactions, Modelling Urban Transactional Activities in Labour and Housing Markets, Decision Support as Urban Intelligence, Participatory Governance and Planning Structures for the Smart City. Finally we anticipate the paradigm shifts that will occur in this research and define a series of key demonstrators which we believe are important to progressing a science of smart cities.

The International Bathymetric Chart of the Arctic Ocean (IBCAO) Version 3.0

Abstract: The International Bathymetric Chart of the Arctic Ocean (IBCAO) released its first gridded bathymetric compilation in 1999. The IBCAO bathymetric portrayals have since supported a wide range of Arc ...

Formal subdivision of the Holocene Series/Epoch: a Discussion Paper by a Working Group of INTIMATE (Integration of ice‐core, marine and terrestrial records) and the Subcommission on Quaternary Stratigraphy (International Commission on Stratigraphy)

Abstract: This discussion paper, by a Working Group of INTIMATE (Integration of ice-core, marine and terrestrial records) and the Subcommision on Quaternary Stratigraphy (SQS) of the International Commission on Stratigraphy (ICS), considers the prospects for a formal subdivision of the Holocene Series/Epoch. Although previous attempts to subdivide the Holocene have proved inconclusive, recent developments in Quaternary stratigraphy, notably the definition of the Pleistocene-Holocene boundary and the emergence of formal subdivisions of the Pleistocene Series/ Epoch, mean that it may be timely to revisit this matter. The Quaternary literature reveals a widespread but variable informal usage of a tripartite division of the Holocene ('early', 'middle' or 'mid', and 'late'), and we argue that this de facto subdivision should now be formalized to ensure consistency in stratigraphic terminology. We propose an Early-Middle Holocene Boundary at 8200 a BP and a Middle-Late Holocene Boundary at 4200 a BP, each of which is linked to a Global Stratotype Section and Point (GSSP). Should the proposal find a broad measure of support from the Quaternary community, a submission will be made to the International Union of Geological Sciences (IUGS), via the SQS and the ICS, for formal ratification of this subdivision of the Holocene Series/Epoch. Copyright# 2012 John Wiley & Sons, Ltd.

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

Abstract: Animals, plants, and fungi—the three traditional kingdoms of multicellular eukaryotic life—make up almost all of the visible biosphere, and they account for the majority of catalogued species on Earth [1]. The remaining eukaryotes have been assembled for convenience into the protists, a group composed of many diverse lineages, single-celled for the most part, that diverged after Archaea and Bacteria evolved but before plants, animals, or fungi appeared on Earth. Given their single-celled nature, discovering and describing new species has been difficult, and many protistan lineages contain a relatively small number of formally described species (Figure 1A), despite the critical importance of several groups as pathogens, environmental quality indicators, and markers of past environmental changes. It would seem natural to apply molecular techniques such as DNA barcoding to the taxonomy of protists to compensate for the lack of diagnostic morphological features, but this has been hampered by the extreme diversity within the group. The genetic divergence observed between and within major protistan groups greatly exceeds that found in each of the three multicellular kingdoms. No single set of molecular markers has been identified that will work in all lineages, but an international working group is now close to a solution. A universal DNA barcode for protists coupled with group-specific barcodes will enable an explosion of taxonomic research that will catalyze diverse applications.

Control of Upper Limb Prostheses: Terminology and Proportional Myoelectric Control—A Review

Abstract: The recent introduction of novel multifunction hands as well as new control paradigms increase the demand for advanced prosthetic control systems. In this context, an unambiguous terminology and a good understanding of the nature of the control problem is important for efficient research and communication concerning the subject. Thus, one purpose of this paper is to suggest an unambiguous taxonomy, applicable to control systems for upper limb prostheses and also to prostheses in general. A functionally partitioned model of the prosthesis control problem is also presented along with the taxonomy. In the second half of the paper, the suggested taxonomy has been exploited in a comprehensive literature review on proportional myoelectric control of upper limb prostheses. The review revealed that the methods for system training have not matured at the same pace as the novel multifunction prostheses and more advanced intent interpretation methods. Few publications exist regarding the choice of training method and the composition of the training data set. In this context, the notion of outcome measures is essential. By definition, system training involves optimization, and the quality of the results depends heavily on the choice of appropriate optimization criteria. In order to further promote the development of proportional myoelectric control, these topics need to be addressed.

Trophic magnification factors: Considerations of ecology, ecosystems, and study design

Abstract: Recent reviews by researchers from academia, industry, and government have revealed that the criteria used by the Stockholm Convention on persistent organic pollutants under the United Nations Environment Programme are not always able to identify the actual bioaccumulative capacity of some substances, by use of chemical properties such as the octanol–water partitioning coefficient. Trophic magnification factors (TMFs) were suggested as a more reliable tool for bioaccumulation assessment of chemicals that have been in commerce long enough to be quantitatively measured in environmental samples. TMFs are increasingly used to quantify biomagnification and represent the average diet-to-consumer transfer of a chemical through food webs. They differ from biomagnification factors, which apply to individual species and can be highly variable between predator–prey combinations. The TMF is calculated from the slope of a regression between the chemical concentration and trophic level of organisms in the food web. The trophic level can be determined from stable N isotope ratios (δ15N). In this article, we give the background for the development of TMFs, identify and discuss impacts of ecosystem and ecological variables on their values, and discuss challenges and uncertainties associated with contaminant measurements and the use of δ15N for trophic level estimations. Recommendations are provided for experimental design, data treatment, and statistical analyses, including advice for users on reporting and interpreting TMF data. Interspecies intrinsic ecological and organismal properties such as thermoregulation, reproductive status, migration, and age, particularly among species at higher trophic levels with high contaminant concentrations, can influence the TMF (i.e., regression slope). Following recommendations herein for study design, empirical TMFs are likely to be useful for understanding the food web biomagnification potential of chemicals, where the target is to definitively identify if chemicals biomagnify (i.e., TMF > or < 1). TMFs may be less useful in species- and site-specific risk assessments, where the goal is to predict absolute contaminant concentrations in organisms in relation to threshold levels. Integr Environ Assess Manag 2012;8:64–84. © 2011 SETAC

Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants

Abstract: The primary endosymbiotic origin of the plastid in eukaryotes more than 1 billion years ago led to the evolution of algae and plants. We analyzed draft genome and transcriptome data from the basally diverging alga Cyanophora paradoxa and provide evidence for a single origin of the primary plastid in the eukaryote supergroup Plantae. C. paradoxa retains ancestral features of starch biosynthesis, fermentation, and plastid protein translocation common to plants and algae but lacks typical eukaryotic light-harvesting complex proteins. Traces of an ancient link to parasites such as Chlamydiae were found in the genomes of C. paradoxa and other Plantae. Apparently, Chlamydia-like bacteria donated genes that allow export of photosynthate from the plastid and its polymerization into storage polysaccharide in the cytosol.

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.

Abstract: Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next‐generation DNA sequencing

Abstract: Biological monitoring has failed to develop from simple binary assessment outcomes of the impacted/unimpacted type, towards more diagnostic frameworks, despite significant scientific effort over the past fifty years. It is our assertion that this is largely because of the limited information content of biological samples processed by traditional morphology-based taxonomy, which is a slow, imprecise process, focused on restricted groups of organisms. We envision a new paradigm in ecosystem assessment, which we refer to as ‘Biomonitoring 2.0’. This new schema employs DNA-based identification of taxa, coupled with high-throughput DNA sequencing on next-generation sequencing platforms. We discuss the transformational nature of DNA-based approaches in biodiversity discovery and ecosystem assessment and outline a path forward for their future widespread application.

The VTR project: architecture and CAD for FPGAs from verilog to routing

Abstract: To facilitate the development of future FPGA architectures and CAD tools -- both embedded programmable fabrics and pure-play FPGAs -- there is a need for a large scale, publicly available software suite that can synthesize circuits into easily-described hypothetical FPGA architectures. These circuits should be captured at the HDL level, or higher, and pass through logical and physical synthesis. Such a tool must provide detailed modelling of area, performance and energy to enable architecture exploration. As software flows themselves evolve to permit design capture at ever higher levels of abstraction, this downstream full-implementation flow will always be required. This paper describes the current status and new release of an ongoing effort to create such a flow - the 'Verilog to Routing' (VTR) project, which is a broad collaboration of researchers. There are three core tools: ODIN II for Verilog Elaboration and front-end hard-block synthesis, ABC for logic synthesis, and VPR for physical synthesis and analysis. ODIN II now has a simulation capability to help verify that its output is correct, as well as specialized synthesis at the elaboration step for multipliers and memories. ABC is used to optimize the 'soft' logic of the FPGA. The VPR-based packing, placement and routing is now fully timing-driven (the previous release was not) and includes new capability to target complex logic blocks. In addition we have added a set of four large benchmark circuits to a suite of previously-released Verilog HDL circuits. Finally, we illustrate the use of the new flow by using it to help architect a floating-point unit in an FPGA, and contrast it with a prior, much longer effort that was required to do the same thing.

A Survey of Visualization Systems for Network Security

Abstract: Security Visualization is a very young term. It expresses the idea that common visualization techniques have been designed for use cases that are not supportive of security-related data, demanding novel techniques fine tuned for the purpose of thorough analysis. Significant amount of work has been published in this area, but little work has been done to study this emerging visualization discipline. We offer a comprehensive review of network security visualization and provide a taxonomy in the form of five use-case classes encompassing nearly all recent works in this area. We outline the incorporated visualization techniques and data sources and provide an informative table to display our findings. From the analysis of these systems, we examine issues and concerns regarding network security visualization and provide guidelines and directions for future researchers and visual system developers.

Postpartum Depression is a Family Affair: Addressing the Impact on Mothers, Fathers, and Children

Abstract: The purpose of this paper is to present research on the effects of postpartum depression (PPD) on mothers, fathers, and children that point to a re-conceptualization of PPD as a mental health condition that affects the whole family. As such, the objectives of this paper are to discuss: (1) the incidence and effects of PPD on mothers and fathers; (2) common predictors of PPD in mothers and fathers, and (3) the effects of PPD on parenting and parent-child relationships, and (4) the effects of PPD on children's health, and their cognitive and social-emotional development. Finally, the implications for screening and intervention if depression is re-conceptualized as a condition of the family are discussed.

Open-water integrated multi-trophic aquaculture: environmental biomitigation and economic diversification of fed aquaculture by extractive aquaculture

Abstract: Integrated multi-trophic aquaculture (IMTA) seeks to biodiversify fed aquaculture (e.g. finfish or shrimps) with extractive aquaculture, recapturing the inorganic (e.g. seaweeds) and organic (e.g. suspension- and deposit-feeders) nutrients from fed aquaculture for their growth. The combination fed ⁄ extractive aquaculture aims to engineer food production systems providing both biomitigative services to the ecosystem and improved economic farm output through the co-cultivation of complementary species. Major rethinking is needed regarding the definition of an ‘aquaculture farm’ and how it works within an ecosystem. The economic values of the environmental ⁄ societal services of extractive species should be recognized and accounted for in the evaluation of the full value of these IMTA components. Seaweeds and invertebrates produced in IMTA systems should be considered as candidates for nutrient ⁄ carbon trading credits. While organic loading from aquaculture has been associated with localized benthic impacts, there have also been occurrences of increased biodiversity and abundance of wild species in response to moderate nutrient enrichment and the use of infrastructures as substrates. To develop efficient food production systems, it will be important to understand and use the duality of nutrients (essential when limiting ⁄ polluting when in excess) to engineer systems producing them in moderation so that they can be partially recaptured while maintaining their concentrations optimal for healthy and productive ecosystems. Measures of species diversity, colonization rates, abundance, growth and ecosystem functions with respect to nutrient partitioning and recycling, species interactions and control of diseases could represent valid indicators for the development of robust performance metrics.

Communicating and Displaying Real-Time Data with WebSocket

Abstract: Internet communication provides a convenient, hyperlinked, stateless exchange of information, but can be problematic when real-time data exchange is needed. The WebSocket protocol reduces Internet communication overhead and provides efficient, stateful communication between Web servers and clients. To determine whether WebSocket communication is faster than HTTP polling, the authors built a Web application to measure the one-way transmission latency of sending real-time wind sensor data at a rate of 4 Hz. They implemented a Jetty servlet to upgrade an HTTP connection to a WebSocket connection. Here, they compare the WebSocket protocol latency to HTTP polling and long polling.

Methods for DNA barcoding photosynthetic protists emphasizing the macroalgae and diatoms.

Abstract: This chapter outlines the current practices used in our laboratory for routine DNA barcode analyses of the three major marine macroalgal groups, viz., brown (Phaeophyceae), red (Rhodophyta), and green (Chlorophyta) algae, as well as for the microscopic diatoms (Bacillariophyta). We start with an outline of current streamlined field protocols, which facilitate the collection of substantial (hundreds to thousands) specimens during short (days to weeks) field excursions. We present the current high-throughput DNA extraction protocols, which can, nonetheless, be easily modified for manual molecular laboratory use. We are advocating a two-marker approach for the DNA barcoding of protists with each major lineage having a designated primary and secondary barcode marker of which one is always the LSU D2/D3 (divergent domains D2/D3 of the nuclear ribosomal large subunit DNA). We provide a listing of the primers that we currently use in our laboratory for amplification of DNA barcode markers from the groups that we study: LSU D2/D3, which we advocate as a eukaryote-wide barcode marker to facilitate broad ecological and environmental surveys (secondary barcode marker in this capacity); COI-5P (the standard DNA barcode region of the mitochondrial cytochrome c oxidase 1 gene) as the primary barcode marker for brown and red algae; rbcL-3P (the 3' region of the plastid large subunit of ribulose-l-5-bisphosphate carboxylase/oxygenase) as the primary barcode marker for diatoms; and tufA (plastid elongation factor Tu gene) as the primary barcode marker for chlorophytan green algae. We outline our polymerase chain reaction and DNA sequencing methodologies, which have been streamlined for efficiency and to reduce unnecessary cleaning steps. The combined information should provide a helpful guide to those seeking to complete barcode research on these and related "protistan" groups (the term protist is not used in a phylogenetic context; it is simply a catch-all term for the bulk of eukaryotic diversity, i.e., all lineages excluding animals, true fungi, and plants).

The Class II KNOX gene KNAT7 negatively regulates secondary wall formation in Arabidopsis and is functionally conserved in Populus

Abstract: • The formation of secondary cell walls in cell types such as tracheary elements and fibers is a defining characteristic of vascular plants. The Arabidopsis transcription factor KNAT7 is a component of a transcription network that regulates secondary cell wall biosynthesis, but its function has remained unclear. • We conducted anatomical, biochemical and molecular phenotypic analyses of Arabidopsis knat7 loss-of-function alleles, KNAT7 over-expression lines and knat7 lines expressing poplar KNAT7. • KNAT7 was strongly expressed in concert with secondary wall formation in Arabidopsis and poplar. Arabidopsis knat7 loss-of-function alleles exhibited irregular xylem phenotypes, but also showed increased secondary cell wall thickness in fibers. Increased commitment to secondary cell wall biosynthesis was accompanied by increased lignin content and elevated expression of secondary cell wall biosynthetic genes. KNAT7 over-expression resulted in thinner interfascicular fiber cell walls. • Taken together with data demonstrating that KNAT7 is a transcriptional repressor, we hypothesize that KNAT7 is a negative regulator of secondary wall biosynthesis, and functions in a negative feedback loop that represses metabolically inappropriate commitment to secondary wall formation, thereby maintaining metabolic homeostasis. The conservation of the KNAT7 regulatory module in poplar suggests new ways to manipulate secondary cell wall deposition for improvement of bioenergy traits in this tree.

Time and a physical Hamiltonian for quantum gravity.

Abstract: We present a nonperturbative quantization of general relativity coupled to dust and other matter fields. The dust provides a natural time variable, leading to a physical Hamiltonian with spatial diffeomorphism symmetry. The surprising feature is that the Hamiltonian is not a square root. This property, together with the kinematical structure of loop quantum gravity, provides a complete theory of quantum gravity, and puts applications to cosmology, quantum gravitational collapse, and Hawking radiation within technical reach.

Wolbachia and DNA Barcoding Insects: Patterns, Potential, and Problems

Abstract: Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region.

Setting an optimal α that minimizes errors in null hypothesis significance tests.

Abstract: Null hypothesis significance testing has been under attack in recent years, partly owing to the arbitrary nature of setting α (the decision-making threshold and probability of Type I error) at a constant value, usually 0.05. If the goal of null hypothesis testing is to present conclusions in which we have the highest possible confidence, then the only logical decision-making threshold is the value that minimizes the probability (or occasionally, cost) of making errors. Setting α to minimize the combination of Type I and Type II error at a critical effect size can easily be accomplished for traditional statistical tests by calculating the α associated with the minimum average of α and β at the critical effect size. This technique also has the flexibility to incorporate prior probabilities of null and alternate hypotheses and/or relative costs of Type I and Type II errors, if known. Using an optimal α results in stronger scientific inferences because it estimates and minimizes both Type I errors and relevant Type II errors for a test. It also results in greater transparency concerning assumptions about relevant effect size(s) and the relative costs of Type I and II errors. By contrast, the use of α = 0.05 results in arbitrary decisions about what effect sizes will likely be considered significant, if real, and results in arbitrary amounts of Type II error for meaningful potential effect sizes. We cannot identify a rationale for continuing to arbitrarily use α = 0.05 for null hypothesis significance tests in any field, when it is possible to determine an optimal α.

Adaptive geographical clines in the growth and defense of a native plant

Abstract: Broad-scale geographical gradients in the abiotic environment and interspecific interactions should select for clinal adaptation. How trait clines evolve has recently received increased attention because of anticipated climate change and the importance of rapid evolution in invasive species. This issue is particularly relevant for clines in growth and defense of plants, because both sets of traits are closely tied to fitness and because such sessile organisms experience strong local selection. Yet despite widespread recognition that growth and defense traits are intertwined, the general issue of their joint clinal evolution is not well resolved. To address heritable clinal variation and adaptation of growth and defense traits of common milkweed (Asclepias syriaca), we planted seed from 22 populations encompassing the species' latitudinal range in common gardens near the range center (New York) and toward the range edges (New Brunswick and North Carolina). Populations were differentiated in 13 traits, and ...

Evaluations of Cellulose Accessibilities of Lignocelluloses by Solute Exclusion and Protein Adsorption Techniques

Abstract: Cellulose accessibilities of a set of hornified lignocellulosic substrates derived by drying the never dried pretreated sample and a set of differently pretreated lodge- pople pine substrates, were evaluated using solute exclusion and protein adsorption methods. Direct measurements of cellulase adsorption onto cellulose surface of the set of pretreated substrates were also carried out using an in situ UV-Vis spectrophotometric technique. The cellulose accessibilities measured by the solute exclusion and a cellu- lose-binding module (CBM)-containing green fluorescent protein (TGC) adsorption methods correlate well for both sets of samples. The substrate enzymatic digestibilities (SEDs) of the hornified substrates are proportional to the measured cellulose accessibilities. Approximately over 90% of the SED was contributed by the accessible pore surfaces of the hornified substrates, suggesting that the substrate exter- nal surface plays a minor role contributing to cellulose accessibility and SED. The cellulose accessibilities of the pretreated substrates correlated well with the amounts of cellulase adsorbed. The SEDs of these substrates directly correlated with the amounts of adsorbed cellulase. Biotechnol. Bioeng. 2012;109: 381-389. 2011 Wiley Periodicals, Inc.