91,117 results

  • Ecological diversification in habitat use by subtidal triplefin fishes (Tripterygiidae)

    Wellenreuther, Maren; Barrett, Peter; Clements, Kendall (2007)

    Journal article
    The University of Auckland Library

    ABSTRACT: Recent work has shown that habitat specialisation can lead to diversification in lacustrine and marine fish species. Here we investigate specialisation in the New Zealand triplefin fish fauna (Tripterygiidae), which has the greatest diversity and disparity of triplefin species in the world with 26 endemic species. Most species are sympatric throughout coastal New Zealand, showing no obvious latitudinal trends in abundance. We sampled habitat use quantitatively, and microposition qualitatively, in 17 triplefin species at 151 sites representing a geographic range from 35?? 50??? S to 46?? 70??? S. A novel Euclidean-distance non-metric multidimensional scaling (MDS) technique was used to display the quantitative habitat variables (depth, fetch, rock, cobble, gravel, sand, mud, macroalgae, and coralline and turfing algae) of each species. For each species, the positions of these variables were compared to those of all species using Procrustes configural matrix comparison methodology, which resulted in a final 3D spatial representation of species using non-metric MDS. Our results demonstrate that triplefin species have diversified considerably in habitat and microposition use, resulting in species occupying different patches in the same general location. Strong habitat partitioning was shown by 3 distinct clusters of species along a gradient of depth and exposure. Some species showed an even finer sub-partitioning by using different substratum types, in particular rock and mud. Correspondence Analysis of microposition data showed that 5 species differed from all other species, further partitioning habitat use. Thus, our results suggest that habitat use has been important in the diversification of New Zealand triplefin fishes.

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  • Grounded blends and mathematical gesture spaces: Developing mathematical understandings via gestures

    Yoon, C; Thomas, Michael; Dreyfus, T (2011)

    Journal article
    The University of Auckland Library

    This paper examines how a person???s gesture space can become endowed with mathematical meaning associated with mathematical spaces and how the resulting mathematical gesture space can be used to communicate and interpret mathematical features of gestures. We use the theory of grounded blends to analyse a case study of two teachers who used gestures to construct a graphical anti-derivative while working on a professional development task in a calculus modelling activity. Results indicate that mathematical gesture spaces can encourage mathematical experimentation, lighten the cognitive load for students and can be limited by a person???s physical constraints.

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  • Eigenvalues and eigenvectors: Embodied, symbolic and formal thinking

    Thomas, Michael; Stewart, S (2011)

    Journal article
    The University of Auckland Library

    Many beginning university students struggle with the new approaches to mathematics that they find in their courses due to a shift in presentation of mathematical ideas, from a procedural approach to concept definitions and deductive derivations, and ideas building upon each other in quick succession. This paper highlights this struggle by considering some conceptual processes and difficulties students find in learning about eigenvalues and eigenvectors. We use the theoretical framework of Tall???s three worlds of mathematical thinking, along with perspectives from Dubinsky???s APOS (action, process, object, schema) theory and Thomas???s representational versatility. The results of the study describe thinking about these concepts by several groups of first- and second-year university students. In particular the obstacles they faced, and the emerging links some were constructing between parts of their concept images formed from the embodied, symbolic, and formal worlds are presented. We also identify some fundamental problems with student understanding of the definition of eigenvectors that lead to implementation problems, and some of the concepts underlying such difficulties.

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  • Elastohydrodynamics induced by a rapidly moving microscopic body

    Clarke, Richard; Potnis, S (2011)

    Journal article
    The University of Auckland Library

    The simple model involving a moving rigid particle, separated from a compliant wall by a thin film of viscous fluid, has previously been applied successfully to a number of important problems. For example, transport of blood cells, particle clearance in the lungs and the late stages of particle sedimentation. Considerable fluid forces are generated in the film, causing the compliant surface to deform. Hence, the usual goal is derivation and solution of an appropriate deformation evolution equation. In the applications considered to-date, however, flow inertia is neglected as flow speeds are not especially high. In this study, we are interested in regimes where unsteady flow inertia is significant, such as found in certain microdevices or thermal excitation of light particles. We present a novel model, which for the first time accounts for inertial effects in both the flow, and the deformable surface. The significant role that inertia plays is fully illustrated through surface deformation profiles, computed under a variety of parameter regimes, as well as calculations of associated hydrodynamic loading. Frequency response curves are seen to exhibit distinct shifts in resonant frequency and quality factor under different levels of inertia, a finding which we believe has important practical implications.

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  • Extreme polyploidy in a large bacterium

    Mendell, JE; Clements, Kendall; Choat, John; Angert, ER (2008)

    Journal article
    The University of Auckland Library

    Cells rely on diffusion to move metabolites and biomolecules. Diffusion is highly efficient but only over short distances. Although eukaryotic cells have broken free of diffusion-dictated constraints on cell size, most bacteria and archaea are forced to remain small. Exceptions to this rule are found among the bacterial symbionts of surgeonfish; Epulopiscium spp. are cigar-shaped cells that reach lengths in excess of 600 m. A large Epulopiscium contains thousands of times more DNA than a bacterium such as Escherichia coli, but the composition of this DNA is not well understood. Here, we present evidence that Epulopiscium contains tens of thousands of copies of its genome. Using quantitative, single-cell PCR assays targeting single-copy genes, we have determined that copy number is positively correlated with Epulopiscium cell size. Although other bacteria are known to possess multiple genomes, polyploidy of the magnitude observed in Epulopiscium is unprecedented. The arrangement of genomes around the cell periphery may permit regional responses to local stimuli, thus allowing Epulopiscium to maintain its unusually large size. Surveys of the sequences of single-copy genes (dnaA, recA, and ftsZ) revealed genetic homogeneity within a cell consistent with only a small amount ( 1%) of the parental DNA being transferred to the next generation. The results also suggest that the abundance of genome copies in Epulopiscium may allow for an unstable genetic feature, a long mononucleotide tract, in an essential gene. With the evolution of extreme polyploidy and large cell size, Epulopiscium has acquired some of the advantages of eukaryotic cells.

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  • Three-dimensional elastohydrodynamics of a thin plate oscillating above a wall

    Clarke, Richard; Jensen, OE; Billingham, J (2008)

    Journal article
    The University of Auckland Library

    We consider deflections of a thin rectangular elastic plate that is submerged within a Newtonian fluid. The plate is clamped along one edge and supported horizontally over a plane horizontal wall. We consider both external driving, where the clamped edge is vibrated vertically at high frequencies, and thermal driving, where the plate fluctuates under Brownian motion. In both cases, the amplitude of oscillation is assumed sufficiently small that the resulting flow has little convective inertia, although the oscillation frequency is sufficiently high to generate substantial unsteady inertia in the flow, a common scenario in many nano- and microdevices. We exploit the plate???s thinness to develop an integral-equation representation for the three-dimensional flow a so-called thin-plate theory which offers considerable computational savings over a full boundary-integral formulation. Limiting cases of high oscillation frequencies and small wall-plate separation distances are studied separately, leading to further simplified descriptions for the hydrodynamics. We validate these reduced integral representations against full boundary-integral computations, and identify the parameter ranges over which these simplified formulations are valid. Addressing the full flow-structure interaction, we also examine the limits of simpler two-dimensional hydrodynamic models. We compare the responses of a narrow plate under two- and three-dimensional hydrodynamic loading, and report differences in the frequency response curves that occur when the plate operates in water, in contrast to the excellent agreement observed in air.

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  • Developing Web Searching Skills in Translator Training

    Enriquez Raido, Vanessa (2011)

    Journal article
    The University of Auckland Library

    This paper focuses on the development of online information literacy in translator training. First, it highlights the important role that information skills, especially web searching skills, play in translation as a cognitive activity requiring information and constant decision making, among others. Second, it argues that if we are to train translation students to work in different subject areas, text types and topics, our focus needs to shift from the acquisition of specialized knowledge in several domains to the development of information skills that can be used for problem solving in any field of expertise. Third, given that the need to seek, use and generate translation-related information depends on the type of users and translation tasks performed, it emphasizes the need for empirical studies that focus on real users and learning contexts. To illustrate the potential benefits of such an approach, this paper draws on the results obtained in a multiple-case study of the web search behaviours of a small cohort of postgraduate translation trainees in their first year of studies.

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  • Clinical implications of a molecular genetic classification of monogenic beta-cell diabetes

    Murphy, Rinki; Ellard, S; Hattersley, AT (2008)

    Journal article
    The University of Auckland Library

    Monogenic diabetes resulting from mutations that primarily reduce ??-cell function accounts for 1???2% of diabetes cases, although it is often misdiagnosed as either type 1 or type 2 diabetes. Knowledge of the genetic etiology of diabetes enables more-appropriate treatment, better prediction of disease progression, screening of family members and genetic counseling. We propose that the old clinical classifications of maturity-onset diabetes of the young and neonatal diabetes are obsolete and that specific genetic etiologies should be sought in four broad clinical situations because of their specific treatment implications. Firstly, diabetes diagnosed before 6 months of age frequently results from mutation of genes that encode Kir6.2 (ATPsensitive inward rectifier potassium channel) or sulfonylurea receptor 1 subunits of an ATP-sensitive potassium channel, and improved glycemic control can be achieved by treatment with high-dose sulfonylureas rather than insulin. Secondly, patients with stable, mild fasting hyperglycemia detected particularly when they are young could have a glucokinase mutation and might not require specific treatment. Thirdly, individuals with familial, young-onset diabetes that does not fit with either type 1 or type 2 diabetes might have mutations in the transcription factors HNF-1?? (hepatocyte nuclear factor 1-??) or HNF-4??, and can be treated with lowdose sulfonylureas. Finally, extrapancreatic features, such as renal disease (caused by mutations in HNF-1??) or deafness (caused by a mitochondrial m.3243A>G mutation), usually require early treatment with insulin.

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  • Three-dimensional flow due to a microcantilever oscillating near a wall: an unsteady slender-body analysis.

    Clarke, Richard; Jensen, OE; Billingham, J; Williams, PW (2006)

    Journal article
    The University of Auckland Library

    We compute the drag on a slender rigid cylinder, of uniform circular cross-section, oscillating in a viscous fluid at small amplitude near a horizontal wall. The cylinder???s axis lies at an angle a to the horizontal and the cylinder oscillates in a vertical plane normal to either the wall or its own axis. The flow is described using an unsteady slender-body approximation, which we treat both numerically and using an iterative scheme that extends resistive-force theory to account for the leading-order effects of unsteady inertia and the wall. When a is small, two independent screening mechanisms are identified which suppress end-effects and produce approximately two-dimensional flow along the majority of the cylinder; however, three-dimensional effects influence the drag at larger tilt angles

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  • Stochastic elastohydrodynamics of a microcantilever oscillating near a wall

    Clarke, Richard; Jensen, OE; Billingham, J; Pearson, A; Williams, P (2006)

    Journal article
    The University of Auckland Library

    We consider the thermally driven motion of a microcantilever in a fluid environment near a wall, a configuration characteristic of the atomic force microscope. A theoretical model is presented which accounts for hydrodynamic interactions between the cantilever and wall over a wide range of frequencies and which exploits the fluctuation-dissipation theorem to capture the Brownian dynamics of the coupled fluid-cantilever system. Model predictions are tested against experimental thermal spectra for a cantilever in air and water. The model shows how, in a liquid environment, the effects of non- -correlated Brownian forcing appear in the power spectrum, particularly at low frequencies. The model also predicts accurately changes in the spectrum in liquid arising through hydrodynamic wall effects, which we show are strongly mediated by the angle at which the cantilever is tilted relative to the wall.

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  • Suicide Online: Portrayal of website-related suicide by the New Zealand media

    McKenna, BG; Thom, Katey; Edwards, G; O'Brien, Anthony; Nairn,, RGR; Nakarada-Kordic, Ivana (2011-12)

    Journal article
    The University of Auckland Library

    Media reporting can impact negatively or positively on suicidal behaviour. Specific reporting methods such as the use of sensationalism can influence suicidal behaviour. This paper presents the findings from a study that aimed to provide an in-depth examination of New Zealand mainstream news items in which websites played a role in suicide. We used framing analysis to interpret the role online technology plays in the reporting of the suicide event. The findings indicate that news items were primarily framed in such a way so that the role of online technology was often overemphasised at the expense of the suicide events themselves. While websites were characteristically framed as ???enablers??? or ???preventers??? of suicide, the contribution of mental wellbeing to suicide was largely marginalised in the news media reports. The paper concludes by considering the implications of these framings for existing media studies of suicide and the media???s role in suicide prevention.

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  • Glucokinase, the pancreatic glucose sensor is not the gut glucose sensor

    Murphy, Rinki; Tura, A; Clark, P; Holst, JJ; Mari, A; Hattersley, AT (2009)

    Journal article
    The University of Auckland Library

    The incretin hormones glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotrophic peptide (GIP) are released from intestinal endocrine cells in response to luminal glucose. Glucokinase is present in these cells and has been proposed as a glucose sensor. The physiological role of glucokinase can be tested using individuals with heterozygous glucokinase gene (GCK) mutations. If glucokinase is the gut glucose sensor, GLP-1 and GIP secretion during a 75 g OGTT would be lower in GCK mutation carriers compared with controls.

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  • An Investigation into FOXE1 polyalanine tract length in premature ovarian failure

    Watkins, WJ; Harris, SE; Craven, MJ; Vincent, Andrea; Winship, IM; Gersak, K; Shelling, Andrew (2006)

    Journal article
    The University of Auckland Library

    Premature ovarian failure (POF) is a common condition affecting 1% of women worldwide. There is strong evidence for genetic involvement in POF as many cases are familial, and mutations in several genes have been associated with POF. We investigated variation in FOXE1 polyalanine tract length, following the observation that polyalanine tract deletions are seen in the closely related FOXL2 in patients with POF. In addition, polyalanine tract expansions in FOXL2 are often seen in patients with blepharophimosis???ptosis???epicanthus inversus syndrome (BPES), a rare eyelid disorder often associated with POF. The FOXE1 polyalanine tract shows marked variation in its length between POF patients and normal controls, existing as an allele of 12, 14, 16, 17 or 19 alanine residues. We found evidence to suggest that variation in FOXE1 polyalanine tract length predisposes to POF.

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  • Isolated nocturnal desaturation in COPD: prevalence and impact on quality of life and sleep.

    Lewis, C; Fergusson, W; Eaton, T; Zheng, I; Kolbe, John (2009)

    Journal article
    The University of Auckland Library

    Background and aims: The clinical impact of nocturnal desaturation on health related quality of life (HRQL) and sleep in chronic obstructive pulmonary disease (COPD) has been little studied. The aim of this study was to evaluate the prevalence and clinical impact of nocturnal desaturation in a typical outpatient population with COPD. Patients and methods: Between 2002 and 2005, consecutive patients with COPD attending outpatient services at the study centre underwent resting oximetry if they were not on domiciliary oxygen therapy. If their resting saturations were less than 95%, overnight pulse oximetry was performed. Significant nocturnal desaturation was defined as spending more than 30% of at least one of two nights with a saturation of less than 90%. The Chronic Respiratory Questionnaire (CRQ) and Short Form 36 (SF36) were used to assess HRQL, and the Pittsburgh Sleep Quality Index (PSQI), Epworth Sleepiness Score (ESS) and Functional Outcomes of Sleep (FOSQ) questionnaires were used to assess sleep quality and daytime function. Results: Of 1104 patients, 803 underwent resting oximetry and 79 had resting oxygen saturations of less than 95%. Of these, 59 agreed to undergo overnight oximetry (mean age 70 years, forced expiratory volume in 1 s 37.2% predicted, resting PO2 on air 8.9 kPa). Significant nocturnal desaturation was seen in 29 (49.2%) of the 59 subjects. Assuming the less hypoxic patients do not have nocturnal desaturation, the prevalence of nocturnal desaturation in the whole clinic population could be estimated at 4.8%. There were no significant differences in CRQ, SF36, PSQI, ESS or FOSQ scores for desaturators compared with non-desaturators. Conclusion: Significant nocturnal desaturation was common in patients with COPD with resting saturations of less than 95%, but was estimated to have a prevalence of less than 5% in the whole outpatient population. Nocturnal desaturation was not associated with impairment of HRQL, sleep quality or daytime function.

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  • Exclusion of known corneal dystrophy genes in an autosomal dominant pedigree of a unique anterior membrane corneal dystrophy

    Vincent, Andrea; Markie, D; De Karolyi, B; Patel, Dipika; Wheeldon, CE; Grupcheva, CN; McGhee, Charles (2009)

    Journal article
    The University of Auckland Library

    Purpose: With advances in phenotyping tools and availability of molecular characterization, an increasing number of phenotypically and genotypically diverse inherited corneal dystrophies are described. We aimed to determine the underlying causative genetic mechanism in a three-generation pedigree affected with a unique anterior membrane corneal dystrophy characterized by early onset recurrent corneal erosions, small discrete focal opacities at the level of Bowman layer and anterior stroma, anterior stromal flecks, and prominent corneal nerves. Methods: Twenty affected and unaffected members of a three-generation family were examined and extensively clinically characterized including corneal topography and in vivo confocal microscopy, and biological specimens were collected for DNA extraction. Mutational analysis of two corneal genes (TGFBI [Transforming Growth factor-beta induced] and ZEB1 [zinc finger E box-binding homeobox 1]) was undertaken, in addition to testing with the Asper Corneal Dystrophy gene chip (Asper Ophthalmics, Tartu, Estonia). Subsequent Genotyping To 11 Known Corneal Gene Loci (COL8A2 [Collagen, Type VIII, Alpha-2], TACSTD2 [Tumor-Associated Calcium Signal Transducer 2], PIP5K3 [Phosphatidylinositol-3-Phosphate 5-Kinase, Type III], GSN [Gelsolin], KERA [Keratocan], VSX1 [Visual System Homeobox Gene 1], COL6A1 [Collagen, Type VI, Alpha-1], MMP9 [Matrix Metalloproteinase 9], KRT3 [Keratin 3]), and two putative loci, 3p14-q13 and 15q22.33???24) was undertaken using polymorphic markers, and haplotypes constructed. Multipoint linkage analysis was performed to generate LOD scores and produce LOD plots across the candidate intervals. Results: No pathogenic sequence variations were detected in TGFBI or ZEB1 of the proband nor on the Asper Corneal Dystrophy gene chip (302 mutations in 12 genes). Multipoint linkage analysis of 11 known corneal genes and loci generated negative LOD plots and was able to exclude all genes tested including PIP5K3. Conclusions: Exclusion of linkage to candidate corneal loci combined with an absence of pathogenic mutations in known corneal genes in this pedigree suggest a different genetic causative mechanism in this dystrophy than the previously documented corneal genes. This unique phenotype of an anterior membrane dystrophy may therefore provide an opportunity to identify a new gene responsible for corneal disease.

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  • Alstr??m syndrome - An uncommon cause of early childhood retinal dystrophy

    Sheck, L; Al-Taie, R; Sharp, D; Vincent, Andrea (2011)

    Journal article
    The University of Auckland Library

    Alstr??m syndrome (AS) is a ciliopathy and an uncommon cause of syndromic retinal dystrophy. This case reports findings in a 5-year-old boy with severe early onset retinal dystrophy, and how the recognition of extraocular features with genetic analysis led to the correct diagnosis of AS after 4 years of investigation.

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  • Developing Maintainable Software: The READABLE Approach

    Chua, Cecil; Purao, S; Storey, V (2006)

    Journal article
    The University of Auckland Library

    Software maintenance is expensive and difficult because software is complex and maintenance requires the understanding of code written by someone else. A prerequisite to maintainability is program understanding, specifically, understanding the control flows between software components. This is especially problematic for emerging software technologies, such as the World Wide Web, because of the lack of formal development practices and because web applications comprise a mix of static and dynamic content. Adequate representations are therefore necessary to facilitate program understanding. This research proposes an approach called Readable (Readable, Executable, Augmentable Database-Linked Environment) that generates executable, tabular representations that can be used to both understand and manipulate software applications. A controlled laboratory experiment carried out to test the efficacy of the approach demonstrates that the representations significantly enhance program understanding. The results suggest that the approach and the corresponding environment may be useful to alleviate problems associated with the software maintainability of new web applications.

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  • Significance of SSI and non-uniform near-fault ground motions in bridge response II: Effect on response with modular expansion joint

    Chouw, Nawawi; Hao, H (2008)

    Journal article
    The University of Auckland Library

    This is the second part of the study of soil-structure interaction (SSI) and ground motion spatial variation effects on bridge pounding responses. The first part [1] concentrated on studying the responses of bridges with a traditional expansion joint between adjacent girders. The main objective of this second paper is to investigate the influence of spatial variation of ground motions and SSI on the minimum total gap that a modular expansion joint system (MEJS) between two bridge frames must have to prevent any pounding between the adjoined girders. This minimum total gap is critical in a MEJS design because it ensures intact expansion joint and adjacent girders. Additional investigations of pounding response with a large total gap of a MEJS are performed to study the characteristics of pounding responses when collision does occur e.g. due to unintended underestimation of the ground excitation magnitude, which may be different from the pounding responses between bridge girders with a small gap of a conventional expansion joint. The spatially varying ground excitations are simulated stochastically based on an empirical near-source response spectrum and an empirical coherency loss function. The investigation reveals that neglecting spatial variation of ground motions and SSI can significantly underestimate the total gap of a MEJS required to avoid pounding between the adjacent bridge girders. The results also show that pounding between girders with a large gap of a MEJS in general causes stronger impact forces. Compared with the results reported in the first part of this study, using a MEJS with a large gap is likely to completely preclude bridge girder pounding, and consequently to prevent local damage at the girder ends. However, a large girder movement results in large bending moment in bridge piers, which compensates the advantages of using MEJS in bridges to resist earthquake loading.

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  • Influence of ground motion spatial variation, site condition and SSI on the required separation distances of bridge structures to avoid seismic pounding

    Bi, K; Hao, H; Chouw, Nawawi (2011)

    Journal article
    The University of Auckland Library

    It is commonly understood that earthquake ground excitations at multiple supports of large dimensional structures are not the same. These ground motion spatial variations may significantly influence the structural responses. Similarly, the interaction between the foundation and the surrounding soil during earthquake shaking also affects the dynamic response of the structure. Most previous studies on ground motion spatial variation effects on structural responses neglected soil???structure interaction (SSI) effect. This paper studies the combined effects of ground motion spatial variation, local site amplification and SSI on bridge responses, and estimates the required separation distances that modular expansion joints must provide to avoid seismic pounding. It is an extension of a previous study (Earthquake Engng Struct. Dyn. 2010; 39(3):303???323), in which combined ground motion spatial variation and local site amplification effects on bridge responses were investigated. The present paper focuses on the simultaneous effect of SSI and ground motion spatial variation on structural responses. The soil surrounding the pile foundation is modelled by frequency-dependent springs and dashpots in the horizontal and rotational directions. The peak structural responses are estimated by using the standard random vibration method. The minimum total gap between two adjacent bridge decks or between bridge deck and adjacent abutment to prevent seismic pounding is estimated. Numerical results show that SSI significantly affects the structural responses, and cannot be neglected.

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  • Significance of SSI and nonuniform near-fault ground motions in bridge response I: Effect on response with conventional expansion joint

    Chouw, Nawawi; Hao, H (2008)

    Journal article
    The University of Auckland Library

    This paper studies the influence of spatially varying near-source ground motions and soil-structure interaction (SSI) on the relative response of two bridge frames. The spatial ground motions are simulated according to a near-fault ground motion model with different wave apparent velocity and a coherency loss function. Numerical calculations of bridge structure responses including pounding and SSI effect to a number of simulated spatially varying ground motions are carried out. The study reveals that the assumption of uniform ground excitation and fixed base in the analysis and design might not provide a realistic estimation of the pounding responses of bridge frames. The consequence of adjusting bridge fundamental frequency ratio towards unity to minimize relative response and consequently girder pounding potential as recommended by current design regulations is also evaluated.

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