1,044 results for The University of Auckland Library, Use commercially

  • Data fitness for use in research on alien and invasive species

    McGeoch, M; Groom, QJ; Pagad, Shyama; Petrosyan, V; Wilson, J; Ruiz, G (2016)

    Report
    The University of Auckland Library

    The discovery, access and appropriate use of primary biodiversity data are critical for alien and invasive species (A&IS) research at continental, regional, country and subnational scales. Sustainable, reliable, timely, and accessible data on A&IS is essential to the long-term management of this key threat to biodiversity, including the ability of countries to meet the Honolulu Challenge and to achieve Aichi Target 9 of the CBD Strategic Plan for Biodiversity 2011-2020. GBIF provides a range of essential information services for A&IS researchers, including but not limited to taxonomic and occurrence information. After broad consultation with the research and A&IS community, a suite of recommendations were identified under five broad topic areas: 1) Strategic approaches, 2) Improving existing data, 3) Expanding information content, 4) Functionality, and 5) Communication and engagement. Several recommendations are relevant for other data users, but the availability, quality and timeliness of these data are especially critical for A&IS because of the real-world consequences resulting from the negative impacts of biological invasions. Alien species occurrence includes taxonomically verified species presence records or absence information at a locality with a geographic coordinate, or in a prescribed area, such as a management or geopolitical unit or site (Latombe et al. 2016). Alien species occurrence information is the single most important variable necessary to support research, monitoring and management of A&IS.

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  • Consistency of the Neighbor-Net Algorithm

    Bryant, David; Moulton, Vincent; Spillner, Andreas (2007)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. BACKGROUND:Neighbor-Net is a novel method for phylogenetic analysis that is currently being widely used in areas such as virology, bacteriology, and plant evolution. Given an input distance matrix, Neighbor-Net produces a phylogenetic network, a generalization of an evolutionary or phylogenetic tree which allows the graphical representation of conflicting phylogenetic signals.RESULTS:In general, any network construction method should not depict more conflict than is found in the data, and, when the data is fitted well by a tree, the method should return a network that is close to this tree. In this paper we provide a formal proof that Neighbor-Net satisfies both of these requirements so that, in particular, Neighbor-Net is statistically consistent on circular distances.

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  • Hollow viscus injury in children: Starship Hospital experience

    Abbas, Saleh; Upadhyay, Vipul (2007)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. Starship Children's Hospital in Auckland, New Zealand, serves a population of 1.2 million people and is a tertiary institution for pediatric trauma. This study is designed to review all cases of abdominal injury (blunt and penetrating) that resulted in injury of a hollow abdominal viscus including the stomach, duodenum, small intestine, large intestine and urinary bladder. The mechanism of injury; diagnosis and outcome were studied. This was done by retrospective chart review of patients admitted from January 1995 to December 2001. Thirty two injuries were found in 29 children. The age ranged from 7 months to 15 years with boys represented more commonly. Small bowel was the most frequently injured hollow viscus. Computerized Tomography (CT scan) is an extremely useful tool for the diagnosis of HVI.

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  • Novel rat Alzheimer's disease models based on AAV-mediated gene transfer to selectively increase hippocampal Aß levels

    Lawlor, Patricia; Bland, Ross; Das, Pritam; Price, Robert; Holloway, Vallie; Smithson, Lisa; Dicker, Bridget; During, Matthew; Young, Deborah; Golde, Todd (2007)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. BACKGROUND:Alzheimer's disease (AD) is characterized by a decline in cognitive function and accumulation of amyloid-ß peptide (Aß) in extracellular plaques. Mutations in amyloid precursor protein (APP) and presenilins alter APP metabolism resulting in accumulation of Aß42, a peptide essential for the formation of amyloid deposits and proposed to initiate the cascade leading to AD. However, the role of Aß40, the more prevalent Aß peptide secreted by cells and a major component of cerebral Aß deposits, is less clear. In this study, virally-mediated gene transfer was used to selectively increase hippocampal levels of human Aß42 and Aß40 in adult Wistar rats, allowing examination of the contribution of each to the cognitive deficits and pathology seen in AD.RESULTS:Adeno-associated viral (AAV) vectors encoding BRI-Aß cDNAs were generated resulting in high-level hippocampal expression and secretion of the specific encoded Aß peptide. As a comparison the effect of AAV-mediated overexpression of APPsw was also examined. Animals were tested for development of learning and memory deficits (open field, Morris water maze, passive avoidance, novel object recognition) three months after infusion of AAV. A range of impairments was found, with the most pronounced deficits observed in animals co-injected with both AAV-BRI-Aß40 and AAV-BRI-Aß42. Brain tissue was analyzed by ELISA and immunohistochemistry to quantify levels of detergent soluble and insoluble Aß peptides. BRI-Aß42 and the combination of BRI-Aß40+42 overexpression resulted in elevated levels of detergent-insoluble Aß. No significant increase in detergent-insoluble Aß was seen in the rats expressing APPsw or BRI-Aß40. No pathological features were noted in any rats, except the AAV-BRI-Aß42 rats which showed focal, amorphous, Thioflavin-negative Aß42 deposits.CONCLUSION:The results show that AAV-mediated gene transfer is a valuable tool to model aspects of AD pathology in vivo, and demonstrate that whilst expression of Aß42 alone is sufficient to initiate Aß deposition, both Aß40 and Aß42 may contribute to cognitive deficits.

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  • Classification in Psychiatry: Does it deliver in schizophrenia and depression?

    Mellsop, Graham; Menkes, David; El-Badri, Selim (2007)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. BACKGROUND:In the context of ongoing work to develop the next iteration of psychiatric classification systems, we briefly review the performance of current systems against their own stated objectives, for two major diagnostic groupings.DISCUSSION:In the major groupings of schizophrenia and depression, experience over the last 50 years has highlighted particular inadequacies in the utility and validity of available classifications.SUMMARY:Advances in psychiatric knowledge and practice notwithstanding, present classification systems would be enhanced by the incorporation of dimensional components. Minor tinkering with current systems will reflect only a missed opportunity. Improving classification will facilitate quality improvement of mental health systems.

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  • Tangata whaiora/consumers perspectives on current psychiatric classification systems

    Moeke-Maxwell, Tess; Wells, Debra; Mellsop, Graham (2008)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. BACKGROUND:A number of studies have been undertaken with the aim of considering the utility of mental health classification systems from the perspective of a variety of stakeholders. There is a lack of research on how useful consumers/tangata whaiora think these are in assisting them in their recovery.METHODS:Seventy service users were involved in seven focus groups in order to consider this question.RESULTS AND DISCUSSION:While for clinicians diagnosing someone might be a discrete event and easily forgotten as a moment in a busy schedule, most people in this study remembered the occasion and aftermath very clearly. The overall consensus was that whether being 'diagnosed' was helpful or not, in large part, depended on how the process happened and what resulted from being 'labeled' in the person's life.CONCLUSION:Overall, people thought that in terms of their recovery, the classification systems were tools and their utility depended on how they were used. They suggested that whatever tool was used it needed to help them make sense of their distress and provide them with a variety of supports, not just medication, to assist them to live lives that were meaningful to them.

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  • Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1

    Edwards, Charles; Holmes, Edward; Wilson, Daniel; Viscidi, Raphael; Abrams, Elaine; Phillips, Rodney; Drummond, Alexei James (2006)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. BACKGROUND:Genetic diversity of the human immunodeficiency virus type 1 (HIV-1) population within an individual is lost during transmission to a new host. The demography of transmission is an important determinant of evolutionary dynamics, particularly the relative impact of natural selection and genetic drift immediately following HIV-1 infection. Despite this, the magnitude of this population bottleneck is unclear.RESULTS:We use coalescent methods to quantify the bottleneck in a single case of homosexual transmission and find that over 99% of the env and gag diversity present in the donor is lost. This was consistent with the diversity present at seroconversion in nine other horizontally infected individuals. Furthermore, we estimated viral diversity at birth in 27 infants infected through vertical transmission and found there to be no difference between the two modes of transmission.CONCLUSION:Assuming the bottleneck at transmission is selectively neutral, such a severe reduction in genetic diversity has important implications for adaptation in HIV-1, since beneficial mutations have a reduced chance of transmission.

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  • Milk allergy and bottles over the back fence: two single patient trials

    Arroll, Bruce; Pert, Harry; Guyatt, Gordon (2008)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. OBJECTIVE:To determine if allergy to cows milk was responsible for symptoms in two children.DESIGN:Single patient trial.SETTING:General Practice in New Zealand.PARTICIPANTS:Two children aged about 6 monthsINTERVENTION:Alternating bottles of soya-based milk and cow's milk provided by neighbours over their back fence.MAIN OUTCOME MEASURES:Presence of diarrhea, irritability, rash and wheeze.RESULTS:After 4 cycles of soya-based milk and cows milk one child proved to have a milk allergy and one did not.CONCLUSION:A systematic approach enabled conclusive diagnoses in both children.

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  • Magnetic resonance imaging in psoriatic arthritis: a review of the literature

    McQueen, Fiona; Lassere, Marissa; Ostergaard, Mikkel (2006)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. Psoriatic arthritis is a diverse condition that may be characterized by peripheral inflammatory arthritis, axial involvement, dactylitis and enthesitis. Magnetic resonance imaging (MRI) allows visualization of soft tissue, articular and entheseal lesions, and provides a unique picture of the disease process that cannot be gained using other imaging modalities. This review focuses on the literature on MRI in psoriatic arthritis published from 1996 to July 2005. The MRI features discussed include synovitis, tendonitis, dactylitis, bone oedema, bone erosions, soft tissue oedema, spondylitis/sacroiliitis and subclinical arthropathy. Comparisons have been drawn with the more extensive literature describing the MRI features of rheumatoid arthritis and ankylosing spondylitis.

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  • What is MRI bone oedema in rheumatoid arthritis and why does it matter?

    McQueen, Fiona; Ostendorf, Benedikt (2006)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. MRI bone oedema occurs in various forms of inflammatory and non-inflammatory arthritis and probably represents a cellular infiltrate within bone. It is common in early rheumatoid arthritis and is associated with erosive progression and poor functional outcome. Histopathological studies suggest that a cellular infiltrate comprising lymphocytes and osteoclasts may be detected in subchondral bone and could mediate the development of erosions from the marrow towards the joint surface. There is emerging evidence from animal models that such an infiltrate corresponds with MRI bone oedema, pointing towards the bone marrow as a site for important pathology driving joint damage in rheumatoid arthritis.

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  • Multilocus analysis of GAW15 NARAC chromosome 18 case-control data

    Browning, Sharon; Thomas, Jessica (2007)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. The Genetic Analysis Workshop 15 rheumatoid arthritis data included a set of 460 cases and 460 controls genotyped at 2300 closely spaced markers on a 10 megabase region of chromosome 18q. We conducted a multilocus analysis of these data using a localized haplotype clustering method that adapts to linkage disequilibrium structure and can be applied to large, densely genotyped data sets such as this one. We found a protective haplotype carried by 33 individuals that was significantly associated with rheumatoid arthritis in these data after adjusting for multiple testing. This haplotype was located less than 500 base pairs upstream of the CCBE1 gene. The association was not detected using single-marker tests, but could be found using a variety of multilocus tests.

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  • A yeast model for target-primed (non-LTR) retrotransposition

    Goodwin, Timothy; Busby, Jason; Poulter, Russell (2007)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. BACKGROUND:Amino acid mutations in a large number of human proteins are known to be associated with heritable genetic disease. These disease-associated mutations (DAMs) are known to occur predominantly in positions essential to the structure and function of the proteins. Here, we examine how the relative perpetuation and conservation of amino acid positions modulate the genome-wide patterns of 8,627 human disease-associated mutations (DAMs) reported in 541 genes. We compare these patterns with 5,308 non-synonymous Single Nucleotide Polymorphisms (nSNPs) in 2,592 genes from primary SNP resources.RESULTS:The abundance of DAMs shows a negative relationship with the evolutionary rate of the amino acid positions harboring them. An opposite trend describes the distribution of nSNPs. DAMs are also preferentially found in the amino acid positions that are retained (or present) in multiple vertebrate species, whereas the nSNPs are over-abundant in the positions that have been lost (or absent) in the non-human vertebrates. These observations are consistent with the effect of purifying selection on natural variation, which also explains the existence of lower minor nSNP allele frequencies at highly-conserved amino acid positions. The biochemical severity of the inter-specific amino acid changes is also modulated by natural selection, with the fast-evolving positions containing more radical amino acid differences among species. Similarly, DAMs associated with early-onset diseases are more radical than those associated with the late-onset diseases. A small fraction of DAMs (10%) overlap with the amino acid differences between species within the same position, but are biochemically the most conservative group of amino acid differences in our datasets. Overlapping DAMs are found disproportionately in fast-evolving amino acid positions, which, along with the conservative nature of the amino acid changes, may have allowed some of them to escape natural selection until compensatory changes occur.CONCLUSION:The consistency and predictability of genome-wide patterns of disease- associated and neutral amino acid variants reported here underscores the importance of the consideration of evolutionary rates of amino acid positions in clinical and population genetic analyses aimed at understanding the nature and fate of disease-associated and neutral population variation. Establishing such general patterns is an early step in efforts to diagnose the pathogenic potentials of novel amino acid mutations.

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  • Genetic characterization of psp encoding the DING protein in Pseudomonas fluorescens SBW25

    Zhang, Xue-Xian; Scott, Ken; Meffin, Rebecca; Rainey, Paul (2007)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. BACKGROUND:DING proteins constitute a conserved and broadly distributed set of proteins found in bacteria, fungi, plants and animals (including humans). Characterization of DING proteins from animal and plant tissues indicated ligand-binding ability suggesting a role for DING proteins in cell signaling and biomineralization. Surprisingly, the genes encoding DING proteins in eukaryotes have not been identified in the eukaryotic genome or EST databases. Recent discovery of a DING homologue (named Psp here) in the genome of Pseudomonas fluorescens SBW25 provided a unique opportunity to investigate the physiological roles of DING proteins. P. fluorescens SBW25 is a model bacterium that can efficiently colonize plant surfaces and enhance plant health. In this report we genetically characterize Psp with a focus on conditions under which psp is expressed and the protein exported.RESULTS:Psp is closely related to the periplasmic Pi binding component of the ABC-type phosphate transporter system (Pst). psp is flanked by a gene cluster predicted to function as a type II protein secretion system (Hxc). Deletion analysis combined with chromosomally integrated 'lacZ fusions showed that both psp and pstC are induced by Pi limitation and that pstC is required for competitive growth of the bacterium in Pi limited medium. hxcR is not regulated by Pi limitation. Psp was detected (using anti-DING serum) in the supernatant of wild-type culture but was greatly reduced in the supernatant of an isogenic strain carrying an hxcR mutation (?hxcR). A promoter fusion between hxcR and a promoterless copy of a gene ('dapB) essential for growth in the plant environment showed that expression of hxcR is elevated during colonization of sugar beet seedlings. A similar analysis of psp showed that it is not induced in the plant environment.CONCLUSION:Psp gene is expressed under conditions of Pi limitation. It is an exoprotein secreted mainly via the Hxc type II secretion system, whose expression is elevated on plant surfaces. We propose that Psp is involved in extracellular scavenging of phosphates, which are subsequently taken up by the cell-bound Pst transport system.

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  • Supporting Symmetric 128-bit AES in Networked Embedded Systems: An Elliptic Curve Key Establishment Protocol-on-Chip

    Duraisamy, R.; Salcic, Zoran; Strangio, M.; Morales-Sandoval, M. (2007)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. The secure establishment of cryptographic keys for symmetric encryption via key agreement protocols enables nodes in a network of embedded systems and remote agents to communicate securely in an insecure environment. In this paper, we propose a pure hardware implementation of a key agreement protocol, which uses the elliptic curve Diffie-Hellmann and digital signature algorithms and enables two parties, a remote agent and a networked embedded system, to establish a 128-bit symmetric key for encryption of all transmitted data via the advanced encryption scheme (AES). The resulting implementation is a protocol-on-chip that supports full 128-bit equivalent security (PoC-128). The PoC-128 has been implemented in an FPGA, but it can also be used as an IP within different embedded applications. As 128-bit security is conjectured valid for the foreseeable future, the PoC-128 goes well beyond the state of art in securing networked embedded devices.

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  • Embedded Systems Design in Intelligent Industrial Automation

    Ferrarini, Luca; Martinez, Lastra J.; Martel, A.; Valentini, Antonio Antonio; Vyatkin, Valeriy (2008)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. Industrial automation (IA) is the vast area of embedded computing devoted to industrial applications. Apart from many tailored solutions (numerical controllers, hardware controllers, etc.) the scene is dominated by programmable logic controllers, widely known by the abbreviation PLC, which represent the most wide-spread class of embedded computing platforms. In the past, the progress in embedded technologies has determined qualitative breakthroughs in the performance of automation systems, their affordability and efficiency of their design.

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  • On Definition of a Formal Model for IEC 61499 Function Blocks

    Dubinin, Victor; Vyatkin, Valeriy (2008)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. Formal model of IEC 61499 syntax and its unambiguous execution semantics are important for adoption of this international standard in industry. This paper proposes some elements of such a model. Elements of IEC 61499 architecture are defined in a formal way following set theory notation. Based on this description, formal semantics of IEC 61499 can be defined. An example is shown in this paper for execution of basic function blocks. The paper also provides a solution for flattening hierarchical function block networks.

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  • SoC Design Approach Using Convertibility Verification

    Sinha, Roopak; Roop, Partha; Basu, Samik (2008)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. Compositional design of systems on chip from preverified components helps to achieve shorter design cycles and time to market. However, the design process is affected by the issue of protocol mismatches, where two components fail to communicate with each other due to protocol differences. Convertibility verification, which involves the automatic generation of a converter to facilitate communication between two mismatched components, is a collection of techniques to address protocol mismatches. We present an approach to convertibility verification using module checking. We use Kripke structures to represent protocols and the temporal logic ACTL to describe desired system behavior. A tableau-based converter generation algorithm is presented which is shown to be sound and complete. We have developed a prototype implementation of the proposed algorithm and have used it to verify that it can handle many classical protocol mismatch problems along with SoC problems. The initial idea for ACTL-based convertibility verification was presented at SLA++P '07 as presented in the work by Roopak Sinha et al. 2008.

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  • Using Visual Specifications in Verification of Industrial Automation Controllers

    Vyatkin, Valeriy; Bouzon, Gustavo (2008)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. This paper deals with further development of a graphical specification language resembling timing-diagrams and allowing specification of partially ordered events in input and output signals. The language specifically aims at application in modular modelling of industrial automation systems and their formal verification via model-checking. The graphical specifications are translated into a model which is connected with the original model under study.

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  • A measure of the variability of revenue in auctions: A look at the revenue equivalence theorem

    Beltran, Fernando; Santamaria, Natalia (2006)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. One not-so-intuitive result in auction theory is the revenue equivalence theorem, which states that as long as an auction complies with some conditions, it will on average generate the same revenue to an auctioneer as the revenue generated by any other auction that complies with them. Surprisingly, the conditions are not defined on the payment rules to the bidders but on the fact that the bidders do not bid below a reserve value—set by the auctioneer—the winner is the one with the highest bidding and there is a common equilibrium bidding function used by all bidders. In this paper, we verify such result using extensive simulation of a broad range of auctions and focus on the variability or fluctuations of the results around the average. Such fluctuations are observed and measured in two dimensions for each type of auction: as the number of auctions grows and as the number of bidders increases.

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  • A Paradox in a Queueing Network with State-Dependent Routing and Loss

    Ziedins, I. (2007)

    Journal article
    The University of Auckland Library

    An open access copy of this article is available and complies with the copyright holder/publisher conditions. Consider a network of parallel finite tandem queues with two stages, where each arrival attempts to minimize its own cost due to loss. It is known that the user optimal and asymptotic system optimal policies may differ—we give examples showing that they may differ for finite systems and that as the service rate is increased at the second stage the user optimal policy may change in such a way that the total expected cost due to loss increases.

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