Classification of index partitions to boost XML query performance

XML query optimization continues to occupy considerable research effort due to the increasing usage of XML data. Despite many innovations over recent years, XML databases struggle to compete with more traditional database systems. Rather than using node indexes, some efforts have begun to focus on creating partitions of nodes within indexes. The motivation is to quickly eliminate large sections of the XML tree based on the partition they occupy. In this research, we present one such partition index that is unlike current approaches in how it determines size and number of these partitions. Furthermore, we provide a process for compacting the index and reducing the number of node access operations in order to optimize XML queries

Pattern based processing of XPath queries

As the popularity of areas including document storage and distributed systems continues to grow, the demand for high performance XML databases is increasingly evident. This has led to a number of research eorts aimed at exploiting the maturity of relational database systems in order to in- crease XML query performance. In our approach, we use an index structure based on a metamodel for XML databases combined with relational database technology to facilitate fast access to XML document elements. The query process involves transforming XPath expressions to SQL which can be executed over our optimised query engine. As there are many dierent types of XPath queries, varying processing logic may be applied to boost performance not only to indi- vidual XPath axes, but across multiple axes simultaneously. This paper describes a pattern based approach to XPath query processing, which permits the execution of a group of XPath location steps in parallel

A node partitioning strategy for optimising the performance of XML queries

For ease of communication between heterogeneous systems, the eXtensible Markup Language (XML) has been widely adopted as a data storage format. However, XML query processing presents issues both in terms of query performance and updatability. Thus, many are choosing to shred XML data into relational databases in order to benet from its mature technology. The problem with this approach is that (often complex and time consuming) data transformation processes are required to transform XML data to relational tables and vice versa. Additionally, many of the benets of XML data can be lost during these processes. In this dissertation, we present a process that partitions nodes within an XML document into disjoint subsets. Briefly, as there are fewer partitions than there are nodes, a more efficient join operation can be performed between partitions, thus reducing the number of inefficient node comparisons. The number and size of partitions varies depending on the structure and layout in the XML document, and the number of partitions impacts query performance. Therefore, we also provide a partition classication process, which signicantly reduces the number of partitions because each partition class represents many equivalent partitions within the XML document. In this dissertation, we will demonstrate that our approach outperforms similar approaches for a large subset of XML queries by eliminating complex join operations (where possible) during the query process

SERS active colloidal nanoparticles for the detection of small blood biomarkers using aptamers

Functionalized colloidal nanoparticles for SERS serve as a promising multifunctional assay component for blood biomarker detection. Proper design of these nanoprobes through conjugation to spectral tags, protective polymers, and sensing ligands can provide experimental control over the sensitivity, range, reproducibility, particle stability, and integration with biorecognition assays. Additionally, the optical properties and degree of electromagnetic SERS signal enhancement can be altered and monitored through tuning the nanoparticle shape, size, material and the colloid's local surface plasmon resonance (LSPR). Aptamers, synthetic affinity ligands derived from nucleic acids, provide a number of advantages for biorecognition of small molecules and toxins with low immunogenicity. DNA aptamers are simpler and more economical to produce at large scale, are capable of greater specificity and affinity than antibodies, are easily tailored to specific functional groups, can be used to tune inter-particle distance and shift the LSPR, and their intrinsic negative charge can be utilized for additional particle stability.1,2 Herein, a "turn-off" competitive binding assay platform involving two different plasmonic nanoparticles for the detection of the toxin bisphenol A (BPA) using SERS is presented. A derivative of the toxin is immobilized onto a silver coated magnetic nanoparticle (Ag@MNP), and a second solid silver nanoparticle (AgNP) is functionalized with the BPA aptamer and a Raman reporter molecule (RRM). The capture (Ag@MNP) and probe (AgNP) particles are mixed and the aptamer binding interaction draws the nanoparticles closer together, forming an assembly that results in an increased SERS signal intensity. This aptamer mediated assembly of the two nanoparticles results in a 100x enhancement of the SERS signal intensity from the RRM. These pre-bound aptamer/nanoparticle conjugates were then exposed to BPA in free solution and the competitive binding event was monitored by the decrease in SERS intensity

Comparison of Fe2O3 and Fe2CoO4 core-shell plasmonic nanoparticles for aptamer mediated SERS assays

Conjugation of oligonucleotides or aptamers and their corresponding analytes onto plasmonic nanoparticles mediates the formation of nanoparticle assemblies: molecularly bound bundles of nanoparticles which cause a measurable change in the colloid's optical properties. Here, we present further optimization of a "SERS off" competitive binding assay utilizing plasmonic and magnetic nanoparticles for the detection of the toxin bisphenol A (BPA). The assay involves 1) a 'target' silver nanoparticle functionalized with a Raman reporter dye and PEGylated BPA-binding DNA aptamers, and 2) a version of the toxin BPA, bisphenol A diglycidyl ether (BADGE), PEGylated and immobilized onto a silver coated magnetic 'probe' nanoparticle. When mixed, these target and probe nanoparticles cluster into magnetic dimers and trimers and an enhancement in their SERS spectra is observed. Upon introduction of free BPA in its native form, target AgNPs are competitively freed; reversing the nanoparticle assembly and causing the SERS signal to "turn-off" and decrease in response to the competitive binding event. The assay particles were housed inside two types of optofluidic chips containing magnetically active nickel pads, in either a straight or spotted pattern, and both Fe2O3 and Fe2CoO4 were compared as magnetic cores for the silver coated probe nanoparticle. We found that the Ag@ Fe2O3 particles were, on average, more uniform in size and more stable than Ag@ Fe2CoO4, while the addition of cobalt significantly improved the collection time of particles within the magnetic chips. Using 3D Raman mapping, we found that the straight channel design with the Ag@ Fe2O3 particles provided the most uniform nanoparticle organization, while the spotted channel design with Ag@ Fe2CoO4 demonstrated a larger SERS enhancement, and thus a lower limit of detection

An ISO/IEC 12207 perspective on software development process adaptation

In their earlier work, the authors had a sustained engagement with situational factors affecting software development, particularly how these factors affect the software development process. Part of this previous engagement involved the development of a situational factors reference framework. As part of an ongoing industrial engagement, the authors are currently examining situational factors and software development processes in a series of case studies. This latest case study is concerned with a small start-up organization. They start by identifying the software development process in this organization. Thereafter, the authors examine the situational context of the company, leading to an analysis of the relationship between the process and the situational context. Their general findings are consistent with their previous related work, supporting the case that a software development process is dependent on the organizational context, perhaps in a highly complex manner. In this particular case study, the authors also find that the role of organizational learning and process adaption is considered to be central to organizational survival

Aptamer conjugated silver nanoparticles for the detection of interleukin 6

The controlled assembly of plasmonic nanoparticles by a molecular binding event has emerged as a simple yet sensitive methodology for protein detection. Metallic nanoparticles (NPs) coated with functionalized aptamers can be utilized as biosensors by monitoring changes in particle optical properties, such as the LSPR shift and enhancement of the SERS spectra, in the presence of a target protein. Herein we test this method using two modified aptamers selected for the protein biomarker interleukin 6, an indicator of the dengue fever virus and other diseases including certain types of cancers, diabetes, and even arthritis. IL6 works by inducing an immunological response within the body that can be either anti-inflammatory or pro-inflammatory. The results show that the average hydrodynamic diameter of the NPs as measured by Dynamic Light Scattering was ∼42 nm. After conjugation of the aptamers, the peak absorbance of the AgNPs shifted from 404 to 408 nm indicating a surface modification of the NPs due to the presence of the aptamer. Lastly, preliminary results were obtained showing an increase in SERS intensity occurs when the IL-6 protein was introduced to the conjugate solution but the assay will still need to be optimized in order for it to be able to monitor varying concentration changes within and across the desired range

Ferric plasmonic nanoparticles, aptamers, and magneto-fluidic chips : toward the development of diagnostic surface-enhanced Raman spectroscopy assays

Conjugation of aptamers and their corresponding analytes onto plasmonic nanoparticles mediates the formation of nanoparticle assemblies: molecularly bound nanoclusters which cause a measurable change in the colloid’s optical properties. In this paper the optimization of a surface enhanced Raman spectroscopy (SERS) competitive binding assay is presented utilizing plasmonic ‘target’ and magnetic ‘probe’ nanoparticles for the detection of the toxin bisphenol-A (BPA). These assay nanoclusters were housed inside three types of optofluidic chips patterned with magnetically-activated nickel pads, in either a straight or array pattern. Both Fe2O3 and Fe2CoO4 were compared as potential magnetic cores for the silver coated probe nanoparticles. We found that the Ag@ Fe2O3 particles were, on average, more uniform in size and more stable than Ag@ Fe2CoO4, whereas the addition of cobalt significantly improved the collection time of particles. Using Raman mapping of the assay housed within the magneto-fluidic chips, it was determined that a 1 x 5 array of 50 µm square nickel pads provided the most uniform SERS enhancement of the assay (coefficient of variation ~25%) within the magneto-fluidic chip. Additionally, the packaged assay demonstrated the desired response to BPA, verifying the technology’s potential to translate magnetic nanoparticle assays into a user-free optical analysis platform

Stimulating Neoblast-Like Cell Proliferation in Juvenile Fasciola hepatica Supports Growth and Progression towards the Adult Phenotype In Vitro

Fascioliasis (or fasciolosis) is a socioeconomically important parasitic disease caused by liver flukes of the genus Fasciola. Flukicide resistance has exposed the need for new drugs and/or a vaccine for liver fluke control. A rapidly improving 'molecular toolbox' for liver fluke encompasses quality genomic/transcriptomic datasets and an RNA interference platform that facilitates functional genomics approaches to drug/vaccine target validation. The exploitation of these resources is undermined by the absence of effective culture/maintenance systems that would support in vitro studies on juvenile fluke development/biology. Here we report markedly improved in vitro maintenance methods for Fasciola hepatica that achieved 65% survival of juvenile fluke after 6 months in standard cell culture medium supplemented with 50% chicken serum. We discovered that this long-term maintenance was dependent upon fluke growth, which was supported by increased proliferation of cells resembling the "neoblast" stem cells described in other flatworms. Growth led to dramatic morphological changes in juveniles, including the development of the digestive tract, reproductive organs and the tegument, towards more adult-like forms. The inhibition of DNA synthesis prevented neoblast-like cell proliferation and inhibited growth/development. Supporting our assertion that we have triggered the development of juveniles towards adult-like fluke, mass spectrometric analyses showed that growing fluke have an excretory/secretory protein profile that is distinct from that of newly-excysted juveniles and more closely resembles that of ex vivo immature and adult fluke. Further, in vitro maintained fluke displayed a transition in their movement from the probing behaviour associated with migrating stage worms to a slower wave-like motility seen in adults. Our ability to stimulate neoblast-like cell proliferation and growth in F. hepatica underpins the first simple platform for their long-term in vitro study, complementing the recent expansion in liver fluke resources and facilitating in vitro target validation studies of the developmental biology of liver fluke

A new shock tube configuration for studying dust-lifting during the initiation of a coal dust explosion

The traditional defence against propagating coal dust explosions is the application of dry stone dust. This proven and effective safety measure is strictly regulated based on extensive international experience. While new products, such as foamed stone dust, offer significant practical benefits, no benchmark tests currently exist to certify their dust lifting performance in comparison to dry stone dust. This paper reviews the coal dust explosion mechanism, and argues that benchmark testing should focus on dust lifting during the initial development of the explosion, prior to arrival of the flame. In a practical context, this requires the generation of shock waves with Mach numbers ranging from 1.05 to 1.4, and test times of the order of 10’s to 100’s of milliseconds. These proposed test times are significantly longer than previous laboratory studies, however, for certification purposes, it is argued that the dust lifting behaviour should be examined over the full timescales of an actual explosion scenario. These conditions can be accurately targeted using a shock tube at length scales of approximately 50 m. It is further proposed that useful test time can be maximised if an appropriately sized orifice plate is fitted to the tube exit, an arrangement which also offers practical advantages for testing. The paper demonstrates this operating capability with proof-of-concept experiments using The University of Queensland’s X3 impulse facility