The use of virtual prototyping to rehearse the sequence of construction work involving mobile cranes

Purpose – Rehearsing practical site operations is without doubt one of the most effective methods for minimising planning mistakes, because of the learning that takes place during the rehearsal activity. However, real rehearsal is not a practical solution for on-site construction activities, as it not only involves a considerable amount of cost but can also have adverse environmental implications. One approach to overcoming this is by the use of virtual rehearsals. The purpose of this paper is to investigate an approach to simulation of the motion of cranes in order to test the feasibility of associated construction sequencing and generate construction schedules for review and visualisation. Design/methodology/approach – The paper describes a system involving two technologies, virtual prototyping (VP) and four-dimensional (4D) simulation, to assist construction planners in testing the sequence of construction activities when mobile cranes are involved. The system consists of five modules, comprising input, database, equipment, process and output, and is capable of detecting potential collisions. A real-world trial is described in which the system was tested and validated. Findings – Feedback from the planners involved in the trial indicated that they found the system to be useful in its present form and that they would welcome its further development into a fully automated platform for validating construction sequencing decisions. Research limitations/implications – The tool has the potential to provide a cost-effective means of improving construction planning. However, it is limited at present to the specific case of crane movement under special consideration. Originality/value – This paper presents a large-scale, real life case of applying VP technology in planning construction processes and activities.

An expressed sequence tag (EST) library for Drosophila serrata, a model system for sexual selection and climatic adaptation studies

The native Australian fly Drosophila serrata belongs to the highly speciose montium subgroup of the melanogaster species group. It has recently emerged as an excellent model system with which to address a number of important questions, including the evolution of traits under sexual selection and traits involved in climatic adaptation along latitudinal gradients. Understanding the molecular genetic basis of such traits has been limited by a lack of genomic resources for this species. Here, we present the first expressed sequence tag (EST) collection for D. serrata that will enable the identification of genes underlying sexually-selected phenotypes and physiological responses to environmental change and may help resolve controversial phylogenetic relationships within the montium subgroup.

Viable chimaeric viruses confirm the biological importance of sequence specific maize streak virus movement protein and coat protein interactions

Background. A variety of interactions between up to three different movement proteins (MPs), the coat protein (CP) and genomic DNA mediate the inter- and intra-cellular movement of geminiviruses in the genus Begomovirus. Although movement of viruses in the genus Mastrevirus is less well characterized, direct interactions between a single MP and the CP of these viruses is also clearly involved in both intra- and intercellular trafficking of virus genomic DNA. However, it is currently unknown how specific these MP-CP interactions are, nor how disruption of these interactions might impact on virus viability. Results. Using chimaeric genomes of two strains of Maize streak virus (MSV) we adopted a genetic approach to investigate the gross biological effects of interfering with interactions between virus MP and CP homologues derived from genetically distinct MSV isolates. MP and CP genes were reciprocally exchanged, individually and in pairs, between maize (MSV-Kom)- and Setaria sp. (MSV-Set)-adapted isolates sharing 78% genome-wide sequence identity. All chimaeras were infectious in Zea mays c.v. Jubilee and were characterized in terms of symptomatology and infection efficiency. Compared with their parental viruses, all the chimaeras were attenuated in symptom severity, infection efficiency, and the rate at which symptoms appeared. The exchange of individual MP and CP genes resulted in lower infection efficiency and reduced symptom severity in comparison with exchanges of matched MP-CP pairs. Conclusion. Specific interactions between the mastrevirus MP and CP genes themselves and/or their expression products are important determinants of infection efficiency, rate of symptom development and symptom severity. © 2008 van der Walt et al; licensee BioMed Central Ltd.

Does teaching sequence matter when teaching high school chemistry with scientific visualisations?

Five Canadian high school Chemistry classes in one school, taught by three different teachers, studied the concepts of dynamic chemical equilibria and Le Chatelier’s Principle. Some students received traditional teacher-led explanations of the concept first and used an interactive scientific visualisation second, while others worked with the visualisation first and received the teacher-led explanation second. Students completed a test of their conceptual understanding of the relevant concepts prior to instruction, after the first instructional session and at the end of instruction. Data on students’ academic achievement (highest, middle or lowest third of the class on the mid-term exam) and gender were also collected to explore the relationship between these factors, conceptual development and instructional sequencing. Results show, within this context at least, that teaching sequence is not important in terms of students’ conceptual learning gains.

Which dissimilarity is to be used when extracting typologies in sequence analysis? A comparative study

Originally developed in bioinformatics, sequence analysis is being increasingly used in social sciences for the study of life-course processes. The methodology generally employed consists in computing dissimilarities between the trajectories and, if typologies are sought, in clustering the trajectories according to their similarities or dissemblances. The choice of an appropriate dissimilarity measure is a major issue when dealing with sequence analysis for life sequences. Several dissimilarities are available in the literature, but neither of them succeeds to become indisputable. In this paper, instead of deciding upon one dissimilarity measure, we propose to use an optimal convex combination of different dissimilarities. The optimality is automatically determined by the clustering procedure and is defined with respect to the within-class variance.

Percutaneous patent foramen ovale closure : outcomes with the Premere and Amplatzer devices

BACKGROUND: Transcatheter closure of patent foramen ovale (PFO) has rapidly evolved as the preferred management strategy for the prevention of recurrent cerebrovascular events in patients with cryptogenic stroke and presumed paradoxical embolus. There is limited outcome data in patients treated with this therapy particularly for the newer devices. METHODS: Data from medical records, catheter, and echocardiography databases on 70 PFO procedures performed was collected prospectively. RESULTS: The cohort consisted of 70 patients (mean age 43.6 years, range 19 to 77 years), of whom 51% were male. The indications for closure were cryptogenic cerebrovascular accident (CVA) or transient ischemic attack (TIA) in 64 (91%) and peripheral emboli in two (2.8%) patients and cryptogenic ST-elevation myocardial infarction in one (1.4%), refractory migraine in one (1.4%), decompression sickness in one (1.4%), and orthodeoxia in one (1.4%) patient, respectively. All patients had demonstrated right-to-left shunting on bubble study. The procedures were guided by intracardiac echocardiography in 53%, transesophageal echocardiography in 39%, and the remainder by transthoracic echo alone. Devices used were the Amplatzer PFO Occluder (AGA Medical) (sizes 18-35 mm) in 49 (70%) and the Premere device (St. Jude Medical) in 21 (30%). In-hospital complications consisted of one significant groin hematoma with skin infection. Echocardiographic follow-up at 6 months revealed that most patients had no or trivial residual shunt (98.6%), while one patient (1.4%) had a mild residual shunt. At a median of 11 months' follow-up (range 1 month to 4.3 years), no patients (0%) experienced further CVA/TIAs or paradoxical embolic events during follow-up. CONCLUSION: PFO causing presumed paradoxical embolism can be closed percutaneously with a low rate of significant residual shunting and very few complications. Recurrent index events are uncommon at medium-term (up to 4 years) follow-up.

Addressing the impediments copyright imposes on the use of patent specifications and prior art documents to improve patent quality

This article considers from an Australian perspective the impediments that copyright law places in the path of those who seek to use patent specifications and non-patent prior art documents in ways that are necessary to the proper functioning of the patent system. Until recently, copyright law in Australia had limited the uses to which members of the public could put patent specifications in that country. Those impediments have been removed as a result of an important legislative change to the way in which copyright in patent specifications can be enforced. The change gives the public a greater freedom to make use of patent specifications than it enjoyed before, and removes unwarranted restrictions upon the ways in which the public can reuse valuable information. However, what the amendment does not address is the impediments copyright imposes on using non-patent prior art documents in ways that advance the public interest.

Copyright in patent specifications and prior art documents: Addressing legitimate rights of user

One of the recent Raising the Bar amendments has removed impediments imposed by copyright law that may have limited the uses to which IP Australia and members of the public could have lawfully put patent specifications without seeking permission from the copyright owner. What the amendment does not do, however, is extend the same protections to those who wish to use prior art documents in ways that benefit the patent system and further the public interest.

Library Research Support in developing, testing and promoting an open cyberinfrastructure

QUT Library continues to rethink research support with eResearch as a primary driver. The support to the development of the Lens, an open global cyberinfrastructure, has been especially important in the light of technology transfer promotion, and partly in the response to researchers’ needs in following the innovation landscapes not only within the scientific but also patent literature. The Lens http://www.lens.org/lens/ project makes innovation more efficient, fair, transparent and inclusive. It is a joint effort between Cambia http://www.cambia.org.au and Queensland University of Technology (QUT). The Lens serves more than 84 million patent documents in the world as open, annotatable digital public goods that are integrated with scholarly and technical literature along with regulatory and business data. Users can link from search results to visualization and document clusters; from a patent document description to its full-text; from there, if applicable, the sequence data can also be found. Figure 1 shows a BLAST Alignment (DNA) using the Lens. A unique feature of the Lens is the ability to embed search and BLAST results into blogs and websites, and provide real-time updates to them. PatSeq Explorer http://www.lens.org/lens/bio/patseqexplorer allows users to navigate patent sequences that map onto the human genome and in the future, many other genomes. PatSeq Explorer offers three level views for the sequence information and links each group of sequences at the chromosomal level to their corresponding patent documents in the Lens. By integrating sequence and patent search and document clustering capabilities, users can now understand the big and small details on the true extent and scope of genetic sequence patents. QUT Library supported Cambia in developing, testing and promoting the Lens. This poster demonstrates QUT Library’s provision of best practice and holistic research support to a research group and how QUT Librarians have acquired new capabilities to meet the needs of the researchers beyond traditional research support practices.

Towards an appropriate fatigue loading sequence for roof claddings in cyclone prone areas

Currently two different fatigue tests are being used to investigate the fatigue susceptibility of roof claddings in the cyclone prone areas of Australia. In order to resolve this issue a detailed investigation was conducted to study the nature of cyclonic wind forces using wind tunnel testing and computer modelling and the fatigue behaviour of metal roof claddings using structural testing. This led to the development of an accurate, but complicated loading matrix for a design cyclone. Based on this matrix, a simplified low-high-low loading sequence has been developed for the testing of roofing systems in cyclone prone areas. This paper first reviews the currently used fatigue loading sequences, then presents details of the cyclonic wind loading matrix and finally the development of the new simplified loading sequence. This simplified sequence should become the only suitable test for most of the cyclone prone areas of Australia covered by Region C which suffers from Category 4 cyclones. For Region D which suffers from Category 5 cyclones, the same loading sequence with 20% increased cycles has been recommended. An experimental programme to validate the new simplified loading sequence has been proposed.

De Novo Transcriptome Sequence Assembly and Analysis of RNA Silencing Genes of Nicotiana benthamiana

Background: Nicotiana benthamiana has been widely used for transient gene expression assays and as a model plant in the study of plant-microbe interactions, lipid engineering and RNA silencing pathways. Assembling the sequence of its transcriptome provides information that, in conjunction with the genome sequence, will facilitate gaining insight into the plant's capacity for high-level transient transgene expression, generation of mobile gene silencing signals, and hyper-susceptibility to viral infection. Methodology/Results: RNA-seq libraries from 9 different tissues were deep sequenced and assembled, de novo, into a representation of the transcriptome. The assembly, of16GB of sequence, yielded 237,340 contigs, clustering into 119,014 transcripts (unigenes). Between 80 and 85% of reads from all tissues could be mapped back to the full transcriptome. Approximately 63% of the unigenes exhibited a match to the Solgenomics tomato predicted proteins database. Approximately 94% of the Solgenomics N. benthamiana unigene set (16,024 sequences) matched our unigene set (119,014 sequences). Using homology searches we identified 31 homologues that are involved in RNAi-associated pathways in Arabidopsis thaliana, and show that they possess the domains characteristic of these proteins. Of these genes, the RNA dependent RNA polymerase gene, Rdr1, is transcribed but has a 72 nt insertion in exon1 that would cause premature termination of translation. Dicer-like 3 (DCL3) appears to lack both the DEAD helicase motif and second dsRNA binding motif, and DCL2 and AGO4b have unexpectedly high levels of transcription. Conclusions: The assembled and annotated representation of the transcriptome and list of RNAi-associated sequences are accessible at www.benthgenome.com alongside a draft genome assembly. These genomic resources will be very useful for further study of the developmental, metabolic and defense pathways of N. benthamiana and in understanding the mechanisms behind the features which have made it such a well-used model plant. © 2013 Nakasugi et al.

Replicating satellite RNA induces sequence-specific DNA methylation and truncated transcripts in plants

Tobacco plants were transformed with a chimeric transgene comprising sequences encoding β-glucuronidase (GUS) and the satellite RNA (satRNA) of cereal yellow dwarf luteovirus. When transgenic plants were infected with potato leafroll luteovirus (PLRV), which replicated the transgene-derived satRNA to a high level, the satellite sequence of the GUS:Sat transgene became densely methylated. Within the satellite region, all 86 cytosines in the upper strand and 73 of the 75 cytosines in the lower strand were either partially or fully methylated. In contrast, very low levels of DNA methylation were detected in the satellite sequence of the transgene in uninfected plants and in the flanking nonsatellite sequences in both infected and uninfected plants. Substantial amounts of truncated GUS:Sat RNA accumulated in the satRNA-replicating plants, and most of the molecules terminated at nucleotides within the first 60 bp of the satellite sequence. Whereas this RNA truncation was associated with high levels of satRNA replication, it appeared to be independent of the levels of DNA methylation in the satellite sequence, suggesting that it is not caused by methylation. All the sequenced GUS:Sat DNA molecules were hypermethylated in plants with replicating satRNA despite the phloem restriction of the helper PLRV. Also, small, sense and antisense ∼22 nt RNAs, derived from the satRNA, were associated with the replicating satellite. These results suggest that the sequence-specific DNA methylation spread into cells in which no satRNA replication occurred and that this was mediated by the spread of unamplified satRNA and/or its associated 22 nt RNA molecules.

Sequence and organization of barley yellow dwarf virus genomic RNA

The nucleotide sequence of the genomic RNA of barley yellow dwarf virus, PAV serotype was determined except for the 5′-terminal base, and its genome organization deduced. The 5,677 nucleotide genome contains five large open reading frames (ORFs). The genes for the coat protein (1) and the putative viral RNA-dependent RNA polymerase were identified. The latter shows a striking degree of similarity to that of carnation mottle virus (CarMV). By comparison with corona- and retrovirus RNAs, it is proposed that a translational frameshift is involved in expression of the polymerase. An ORF encoding an Mr 49,797 protein (50K ORF) may be translated by in-frame readthrough of the coat protein stop codon. The coat protein, an overlapping 17K ORF, and a 3′ 6.7K ORF are likely to be expressed via subgenomic mRNAs. © 1988 IRL Press Limited.