Journal Articles

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Articles. Typically the realization of research papers reporting original research findings published in a journal issue. (URI: http://purl.org/coar/resource_type/c_6501) Item types include:

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YIGSR domain of laminin binds surface receptors of mesenchyme and stimulates migration during gastrulation in sea urchins
(The Company of Biologists, 1994) Crawford, Bryan D.; Burke, Robert D.
During gastrulation in sea urchins, cells at the tip of the archenteron extend filopodia that attach to the blastocoel wall and are thought to assist in the elongation of the archenteron. Upon completion of gastrulation, these cells migrate into the blastocoel. Time-lapse video records were made of preparations from which ectodermal cells have been removed, leaving the archenteron, mesenchyme cells and blastocoelar extracellular matrix (ECM) bounded by the basal lamina. In preparations of late gastrulae, cells at the tip of the archenteron extend filopodia that attach to the basal lamina and pull it inward, collapsing the preparation. This collapse does not occur in preparations made prior to the elongation phase and can be inhibited with cytochalasin B and azide, but not with colchicine. Migratory behavior increased in preparations treated with the laminin-derived peptide Tyr-Ile-Gly-Ser- Arg (YIGSR). Cells extend and retract filopodia, collapse the ECM and migrate out of the preparation. This behavior was not observed in preparations treated with whole laminin, fibronectin or Arg-Gly- Asp-Ser (RGDS) peptides. Cells in preparations treated with YIGSR extend significantly more processes than those incubated in RGDS, laminin, fibronectin or BSA. This effect is titratable between 10–3 and 10–6 M. Whole laminin has a significant inhibitory effect on the number of cell processes observed. Double labelling experiments with biotinylated laminin or biotinylated CDPGYIGSR and a mesenchyme-specific monoclonal antibody (Sp12) reveal that laminin and CDPGYIGSR label mesenchymal and non-mesenchymal cells. A CDPGYIGSR affinity column binds a 125I-labelled cell surface component, which elutes with YIGSR and has an Mr of about 80x103 on SDS-PAGE. We propose that cells at the tip of the archenteron attach to the basal lamina during archenteron elongation, and that domains of laminin containing YIGSR in the basal lamina of the target region stimulate migratory behavior in these cells.
Experiments with the ALPOC theorem prover
(1995) Spencer, Bruce; Horton, J., D.; Francis, Kelsey
A system for selecting and preparing a batch of data files, and running a selected computer program with each data file is described. Another facility collects the experimental results from several different batches and summarizes the results in a tabular form. A theorem prover, ALPOC, is implemented that combines Shostak's C-literal resolution steps with Stickel's PTTP compiler, and uses Spencer's Ordered Clause set restriction. A series of experiments is run that compares ALPOC with PTTP, using the batch system. The results are summarized and compared with Stickel's PTTP implemented in Prolog. The results show that ALPOC is slower than PTTP by a factor of at most 4, but frequently is much faster. On the problems where ALPOC is faster the number of extension steps in the ALPOC proof is less than the PTTP proof, which leads the iterative deepening search method to explore fewer levels.
The impact of information architecture on academic web site usability
(1999) Gullikson, Shelley; Blades, Ruth; Bragdon, Marc; McKibbon, Shelley; Sparling, Marnie; Toms, Elaine, G.
Recent studies of web‐site use indicate that people do not come to the web for an “experience”, they come for information. Yet, to date, web‐site design has been synonymous with the “look and feel” of a site overlooking the significance of a site’s information architecture. In this study, we assessed the effect of the information architecture of an academic web site: how information is categorised, labelled and presented, and how navigation and access are facilitated. Twenty‐four participants from six faculties attempted to answer typical questions often asked within an academic milieu. They were able to find the answers to just over half the questions successfully and, in subjective assessments, gave the site a failing grade. We address how the information architecture affected their ability to negotiate the site and, additionally, make recommendations for the key ingredients: information design, access tools, and navigational aids.
Shuttling of CTP:Phosphocholine cytidylyltransferase between the nucleus and endoplasmic reticulum accompanies the wave of phosphatidylcholine synthesis during the G(0) --> G(1) transition.
(1999) Northwood, Ingrid, C.; Tong, Amy, H. Y.; Crawford, Bryan, D.; Drobnies, Adrienne, E.; Cornell, Rosemary, B.
The transition from quiescence (G(0)) into the cell division cycle is marked by accelerated phospholipid turnover. We examined the rates of phosphatidylcholine (PC) synthesis and the activity, membrane affinity, and intracellular localization of the rate-limiting enzyme in the synthesis of PC, CTP:phosphocholine cytidylyltransferase (CT) during this transition. The addition of serum to quiescent IIC9 fibroblasts resulted in a wave of PC synthesis beginning at approximately 10 min, peaking at approximately 3 h with a >10-fold increase in rate, and declining to near basal rates by 10 h. CT activity, monitored in situ, was elevated approximately 3-fold between 1 and 2 h postserum. Neither CT mass nor its phosphorylation state changed during the surge in PC synthesis and CT activity. On the other hand, the ratio of particulate/soluble CT surged and then receded in concert with the wave of PC synthesis. During quiescence, CT was confined to the nucleus, as assessed by indirect immunofluorescence. Within 10 min after serum stimulation, a portion of the CT fluorescence appeared in the cytoplasm, where it intensified until approximately 4 h postserum. Thereafter, the cytoplasmic CT signal waned, while the nuclear signal increased, and by 8 h CT was once again predominantly nuclear. The dynamics of CT's apparent translocation in and out of the nucleus paralleled the wave of PC synthesis and the solubility changes of CT. Cytoplasmic CT co-localized with BiP, a resident endoplasmic reticulum protein, in a double labeling experiment. These data suggest that the wave of PC synthesis that accompanies the G(0) --> G(1) transition is regulated by the coordinated changes in CT activity, membrane affinity, and intracellular distribution. We describe for the first time a redistribution of CT from the nucleus to the ER that correlates with an activation of the enzyme. We propose that this movement is required for the stimulation of PC synthesis during entry into the cell cycle.
Activity and Distribution of Paxillin, Focal Adhesion Kinase, and Cadherin Indicate Cooperative Roles during Zebrafish Morphogenesis
(2003) Crawford, Bryan, D.; Henry, Clarissa, A.; Clason, Todd, A.; Becker, Amanda, L.; Hille, Merrill, B.
We investigated the focal adhesion proteins paxillin and Fak, and the cell-cell adhesion protein cadherin in developing zebrafish (Danio rerio) embryos. Cadherins are expressed in presomitic mesoderm where they delineate cells. The initiation of somite formation coincides with an increase in the phosphorylation of Fak, and the accumulation of Fak, phosphorylated Fak, paxillin, and fibronectin at nascent somite boundaries. In the notochord, cadherins are expressed on cells during intercalation, and phosphorylated Fak accumulates in circumferential rings where the notochord cells contact laminin in the perichordal sheath. Subsequently, changes in the orienta- tions of collagen fibers in the sheath suggest that Fak-mediated adhesion allows longitudinal expansion of the notochord, but not lateral expansion, resulting in notochord elongation. Novel observations showed that focal adhesion kinase and paxillin concentrate at sites of cell-cell adhesion in the epithelial enveloping layer and may associate with actin cytoskeleton at epithelial junctions containing cadherins. Fak is phosphorylated at these epithelial junctions but is not phosphorylated on Tyr397, implicating a noncanonical mechanism of regulation. These data suggest that Fak and paxillin may function in the integration of cadherin-based and integrin-based cell adhesion during the morphogenesis of the early zebrafish embryo.
Assigning morphological variants of Fucus (Fucales, Phaeophyceae) in Canadian waters to recognized species using DNA barcoding
(Canadian Science Publishing, 2008) Kucera, Hana; Saunders, Gary, W.
The intertidal brown algal genus Fucus (Phaeophyceae) consists of individuals with a generally dichotomously branched habit. Morphological variability within species, combined with morphological similarity between species, renders field identification difficult. In light of recent taxonomic revisions, which reduced 10 taxa traditionally recognized in Canada to four species, we tested the utility of the DNA barcode (mitochondrial cytochrome oxidase 1, 5′) for assigning individuals to these species. We sequenced the DNA barcode for 125 specimens representing all morphologies recognized. We confirmed our results by sequencing the internal transcribed spacer region for 66 specimens. This is the first study to establish that the DNA barcode successfully assigns different morphologies of brown algae to known species as well as other single-gene molecular markers currently used. Furthermore, the results uncovered substantial phenotypic plasticity in Pacific Fucus distichus, from moss-like fragments embedded in estuarine mud, strap-like morphs on exposed rocky coasts, to “spiralis”-like morphs in the upper intertidal whereas phenotypic expression for this species was more restricted in the Atlantic.
The Case for Early French Immersion: A Response to J. Douglas Willms
(2008) Dicks, Joseph
A DNA barcode examination of the red algal family Dumontiaceae in Canadian waters reveals substantial cryptic species diversity. 1. The foliose Dilsea–Neodilsea complex and Weeksia
(Canadian Science Publishing, 2008) Saunders, Gary, W.
The field of DNA barcoding is working towards generating a genetic system for the quick and accurate identification of eukaryotic species. For the more systematic minded, however, DNA barcoding offers a new approach towards screening and uniting large numbers of biological specimens in genetic groups as a first step towards assigning them to species and genera in an approach best termed “molecular-assisted alpha taxonomy”. This approach is particularly amenable in organisms with simple morphologies, a propensity for convergence, extensive phenotypic plasticity, and life histories with an alternation of heteromorphic generations. It is hard to imagine a group of organisms better defined by all of these traits than the marine macroalgae. In an effort to assess the utility of the DNA barcode (COI-5′) for testing the current concepts of biodiversity of marine macroalgae in Canada, a study to assess species diversity in the red algal family, Dumontiaceae, was initiated. Through this work I confirm the presence in Canadian waters of Dilsea californica (J. Agardh) Kuntze, Dilsea integra (Kjellman) Rosenvinge, and Neodilsea borealis (I.A. Abbott) Lindstrom of the Dilsea–Neodilsea complex, and Weeksia coccinea (Harvey) Lindstrom for the genus Weeksia. However, our work has uncovered two additional species of the former complex, Dilsea lindstromiae Saunders sp. nov. and Dilsea pygmaea (Setchell) Setchell, and an additional species of the latter, Weeksia reticulata Setchell, effectively doubling representation of these foliose dumontiacean genera in Canadian waters.
Practice and preservation: Format issues
(2008) Bragdon, Marc; Burk, Alan; Charlong, Lisa; Nugent, Jason; Schreibman, S.; Seimans, R.
Between Community and State: Practicing public health in Cape Breton, 1938-1948
(University of New Brunswick, 2009) Mullally, Sasha
Using the experiences of a Nova Scotia Public health nurse, Phyllis Lyttle, this article shows how practical considerations and local needs largely defined rural public health work in the early years of the provincial system (1938-1948). Examining public health reports and community narratives reveals how Lyttle expanded her role to include primary care and midwifery services – a role similar to that of a late-20th-century nurse practitioner – in response to the needs and expectations of the local population and the local general practitioner, C. Lamont MacMillan.
Counter-insurgency Intelligence: The Evolution of British Theory and Practice
(2009) Charters, David, A.
The centrality of intelligence to counter-insurgency operations and campaigns is now widely acknowledged. But this has not always been the case, even for Great Britain, which is generally regarded as the world leader in counter-insurgency. By examining operational experience, doctrine and training, and professional writing on the subject, this article will show how intelligence emerged as a centerpiece of British counter-insurgency theory and practice in the post-1945 era. It will demonstrate that the British experienced a steep learning curve. Sound theory and practice were no guarantee of success, since victory or defeat was determined largely by local conditions and British political considerations. And some intelligence practices that had been effective in distant conflicts proved problematic when applied in the domestic arena of Northern Ireland. Ultimately, British counter-insurgency theory and practice became “intelligence-driven.”
Appraising lexical bundles in mathematics classroom discourse: obligation and choice
(Springer Verlag, 2010) Herbel-Eisenmann, Beth; Wagner, David
Working from a large corpus of transcripts from secondary mathematics classrooms, we identify patterns of speech that encode interpersonal positioning. We extend our analysis from a previous article (Herbel-Eisenmann, Wagner & Cortes, in review), in which we introduced a concept from corpus linguistics – a “lexical bundle,” which has been defined as a group of three or more words that frequently recur together, in a single group, in a particular register. In that article we noted the prevalence of pervasive stance bundles unique to the mathematics classroom register. Because stance bundles communicate personal feelings, attitudes and values, we noted the importance of positioning in mathematics classrooms. In this article, we interpret the stance bundles as they relate to authority in mathematics classrooms by organizing them into groups that relate to the ways in which students are assumed to have choice in the discourse and to have obligations. Gradations of obligation and choice are important because they can help mathematics educators think about the ways in which they might open up or close down discourse in the classroom. We argue that it is important for university researchers, classroom teachers and even mathematics students to engage in conversations about issues of authority, as they relate to developing mathematical understanding in their classroom discourse.
DNA barcoding reveals multiple overlooked Australian species of the red algal order Rhodymeniales (Florideophyceae), with resurrection of Halopeltis J. Agardh and description of Pseudohalopeltis gen. nov.
(Canadian Science Publishing, 2010) Saunders, Gary, W.; McDonald, Brian
The DNA barcode (COI-5P) was used to investigate cryptic diversity among Rhodymenia spp. in southern Australia. Whereas eight species are currently recognized, we uncovered ca. 20 genetic species groups, phylogenetically assigned to four genera in two families. Procumbent specimens with molecular and anatomical signatures of the Fryeellaceae are assigned to Pseudohalopeltis tasmanensis gen. et sp. nov. Collections from Lord Howe Island recorded in the field as Rhodymenia/Fauchea sp. are assigned to the poorly known genus Microphyllum as Microphyllum robustum sp. nov. A cluster of species with distinct molecular and anatomical attributes is included in a resurrected Halopeltis J.G. Agardh, including Halopeltis australis (J. Agardh) comb. nov. (type species); Halopeltis austrina (Womersley) comb. nov.; Halopeltis cuneata (Harvey) comb. nov. [including Rhodymenia halymenioides (J. Agardh) Womersley]; Halopeltis gracilis sp. nov.; Halopeltis prostrata sp. nov.; and Halopeltis verrucosa (Womersley) comb. nov. Four additional species of Halopeltis from Lord Howe Island (LH1, LH2), Tasmania (TAS), and Western Australia are not characterized further. For Rhodymenia sensu stricto, similar levels of cryptic diversity were noted. Samples tentatively field-identified as “Rhodymenia sonderi,” but having affiliations to Rhodymenia rather than Halopeltis, are referred to Rhodymenia novahollandica sp. nov. Collections field-identified as R. obtusa are genetically distinct from that species and are assigned to Rhodymenia wilsonis (Sonder) comb. nov. Two highly divergent species currently identified as Rhodymenia leptophylla (LH from Lord Howe Island; TAS from Tasmania), as well as two additional cryptic previously unnamed taxa from South Australia (SA) and Victoria (VIC), are not characterized further.
Lexical bundle analysis in mathematics classroom discourse: The significance of stance
(Springer Verlag, 2010) Herbel-Eisenmann, Beth; Wagner, David; Cortes, Viviana
In this article, we introduce the lexical bundle, defined by corpus linguists as a group of three or more words that frequently recur together, in a single group, in a particular register (Biber, Johansson, Leech, Conrad, & Finegan, 2006; Cortes, English for Specific Purposes 23:397–423, 2004). Attention to lexical bundles helps to explore hegemonic practices in mathematics classrooms because lexical bundles play an important role in structuring discourse and are often treated as “common sense” ways of interacting. We narrow our findings and discussion to a particular type of lexical bundle (called a “stance bundle” or bundles that relate to feelings, attitudes, value judgments, or assessments) because it was the most significant type found. Through comparing our corpus from secondary mathematics classrooms with two other corpora (one from university classrooms (not including mathematics classrooms) and one from conversations), we show that most of the stance bundles were particular to secondary mathematics classrooms. The stance bundles are interpreted through the lens of interpersonal positioning, drawing on ideas from systemic functional linguistics. We conclude by suggesting additional research that might be done, discussing limitations of this work, and pointing out that the findings warrant further attention to interpersonal positioning in mathematics classrooms.
A DNA barcode examination of the Laminariaceae (Phaeophyceae) in Canada reveals novel biogeographical and evolutionary insights
(Taylor and Francis, 2010) McDevit, Daniel, C.; Saunders, Gary, W.
DNA barcoding is becoming a widely applied tool for the rapid and accurate identification of eukaryotic species. In this study we used the DNA barcode for large-scale screening of the brown algal family Laminariaceae in Canada. With the examination of 194 COI-5P (5′ end of cytochrome c oxidase 1) sequences (150 newly determined) from representatives of this family, we confirmed the presence of 12 species in Canadian waters (Cymathaere triplicata, Laminaria digitata, L. ephemera, L. setchellii, L. solidungula, L. yezoensis, Macrocystis integrifolia, Nereocystis leutkeana, Postelsia palmaeformis, Saccharina groenlandica, S. latissima and S. sessilis). Saccharina groenlandica, a species with a history of taxonomic confusion, was found in the Pacific, Hudson Bay (subarctic) and Atlantic Canada extending greatly our comprehension of the biogeography of this species. Additionally, COI-5P data from S. latissima, combined with ITS results, provided insights into historical distributional patterns and uncovered a hybridization zone between incipient species in this complex. These discoveries highlight how the growth of a worldwide barcode database for the assignment of individuals to genetic species will uncover new perspectives on biogeography and species diversity on a global scale.
Warm Bodies Using Cold Mathematics
(Faculty of Education, University of New Brunswick, 2011) Wagner, David
Can rural older drivers meet their needs without a car? Stated adaptation responses from a GPS travel diary survey
(Springer, 2011) Hanson, Trevor R.; Hildebrand, Eric D.
Rural seniors are highly dependent on their automobile to meet their trip making needs, yet the effects of aging can make access to the vehicle difficult or impossible over time. The anticipated growth in the older person population, in concert with limited travel data available to support rural transportation planning in Canada suggests a disconnect between what rural older people may require for transportation and the availability of formal alternatives. Many will seek informal alternatives to driving, such as depending on friends and family, to meet their travel needs, but the degree is not well understood in the context of their actual vehicle usage and stated ability to adapt. This paper draws from a Global Positioning System (GPS)-based multi-day travel diary survey of a convenience sample of 60 rural older drivers (29 men, 31 women, average age of 69.6 years) from New Brunswick, Canada. Participants would rely on “friends and family” for 52% of all trips they undertook as driver in the survey, “walk or bike” for 14% of trips, and “not take the trip” in 34% of trips if they did not have access to a vehicle. “Medical trips”, “Shopping” and “Personal Errands” were the least discretionary of all trip types, yet the most difficult for participants to find alternate arrangements. Most participants (70%) believed a solution is needed in rural areas that does not involve depending on friends and family. These findings suggest the need for transportation policies that encourage the development and sustainability of rural alternatives.
Facing the Mathematics: Students’ Critical Awareness of the Elusiveness of Mathematical Objects
(Taylor & Francis, 2011) Wagner, David
What happens when mathematics students are invited to ask questions and make observations about the way discourse works in their classroom? This article describes my extended conversation with a high school mathematics class about a phenomenon that caught the attention of two girls in the class. Together we observed and reflected on the direction of one’s gaze during mathematics conversations. This discussion came about while I co-taught this class, prompting the students daily to become more aware of their language practices in class. This ‘critical language awareness’ effort aimed to address inequities in power relations within the classroom discourse by inviting student perspectives and resulted in drawing two students’ attention to the power of symbols.
A theory-based primary health care intervention for women who have left abusive partners.
(2011) Ford-Gilboe, Marilyn; Merritt-Gray, Marilyn; Varcoe, Colleen; Wuest, Judith
Although intimate partner violence is a significant global health problem, few tested interventions have been designed to improve women's health and quality of life, particularly beyond the crisis of leaving. The Intervention for Health Enhancement After Leaving is a comprehensive, trauma informed, primary health care intervention, which builds on the grounded theory Strengthening Capacity to Limit Intrusion and other research findings. Delivered by a nurse and a domestic violence advocate working collaboratively with women through 6 components (safeguarding, managing basics, managing symptoms, cautious connecting, renewing self, and regenerating family), this promising intervention is in the early phases of testing.
NAD+ Biosynthesis Ameliorates a Zebrafish Model of Muscular Dystrophy
(PLOS, 2012) Goody, Michelle F.; Kelly, Meghan W.; Reynolds, Christine J.; Khalil, Andre; Crawford, Bryan D.; Henry, Clarissa A.
Muscular dystrophies are common, currently incurable diseases. A subset of dystrophies result from genetic disruptions in complexes that attach muscle fibers to their surrounding extracellular matrix microenvironment. Cell-matrix adhesions are exquisite sensors of physiological conditions and mediate responses that allow cells to adapt to changing conditions. Thus, one approach towards finding targets for future therapeutic applications is to identify cell adhesion pathways that mediate these dynamic, adaptive responses in vivo. We find that nicotinamide riboside kinase 2b-mediated NAD+ biosynthesis, which functions as a small molecule agonist of muscle fiber-extracellular matrix adhesion, corrects dystrophic phenotypes in zebrafish lacking either a primary component of the dystrophin-glycoprotein complex or integrin alpha7. Exogenous NAD+ or a vitamin precursor to NAD+ reduces muscle fiber degeneration and results in significantly faster escape responses in dystrophic embryos. Overexpression of paxillin, a cell adhesion protein downstream of NAD+ in this novel cell adhesion pathway, reduces muscle degeneration in zebrafish with intact integrin receptors but does not improve motility. Activation of this pathway significantly increases organization of laminin, a major component of the extracellular matrix basement membrane. Our results indicate that the primary protective effects of NAD+ result from changes to the basement membrane, as a wild-type basement membrane is sufficient to increase resilience of dystrophic muscle fibers to damage. The surprising result that NAD+ supplementation ameliorates dystrophy in dystrophin-glycoprotein complex– or integrin alpha7–deficient zebrafish suggests the existence of an additional laminin receptor complex that anchors muscle fibers to the basement membrane. We find that integrin alpha6 participates in this pathway, but either integrin alpha7 or the dystrophin-glycoprotein complex is required in conjunction with integrin alpha6 to reduce muscle degeneration. Taken together, these results define a novel cell adhesion pathway that may have future therapeutic relevance for a broad spectrum of muscular dystrophies.

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