Design and implementation of a windows-based parallel computing environment for large scale optimization

A parallel computing environment to support optimization of large-scale engineering systems is designed and implemented on Windows-based personal computer networks, using the master-worker model and the Parallel Virtual Machine (PVM). It is involved in decomposition of a large engineering system into a number of smaller subsystems optimized in parallel on worker nodes and coordination of subsystem optimization results on the master node. The environment consists of six functional modules, i.e. the master control, the optimization model generator, the optimizer, the data manager, the monitor, and the post processor. Object-oriented design of these modules is presented. The environment supports steps from the generation of optimization models to the solution and the visualization on networks of computers. User-friendly graphical interfaces make it easy to define the problem, and monitor and steer the optimization process. It has been verified by an example of a large space truss optimization. (C) 2004 Elsevier Ltd. All rights reserved.

Dynamic binary translation using run-time feedbacks

Dynamic binary translation is the process of translating, modifying and rewriting executable (binary) code from one machine to another at run-time. This process of low-level re-engineering consists of a reverse engineering phase followed by a forward engineering phase. UQDBT, the University of Queensland Dynamic Binary Translator, is a machine-adaptable translator. Adaptability is provided through the specification of properties of machines and their instruction sets, allowing the support of different pairs of source and target machines. Most binary translators are closely bound to a pair of machines, making analyses and code hard to reuse. Like most virtual machines, UQDBT performs generic optimizations that apply to a variety of machines. Frequently executed code is translated to native code by the use of edge weight instrumentation, which makes UQDBT converge more quickly than systems based on instruction speculation. In this paper, we describe the architecture and run-time feedback optimizations performed by the UQDBT system, and provide results obtained in the x86 and SPARC® platforms.

The interorganizational virtual organization: Defining a Weberian ideal

The concept of the virtual organization (VO) has engendered great interest in the literature, yet there is still little common understanding of the concept, as evidenced by the multitude of labels applied to VOs. In this article, we focus on a “Weberian-ideal-type” definition of the interorganizational VO, posited in our earlier work (Kasper-Fuehrer and Ashkanasy 2001). We argue, however, that this definition left unanswered critical questions relating to the nature and effects of interorganizational VOs. We answer these questions here by explicating the terms in the definition and deriving ten corollaries, or “natural consequences” of our definition. The corollaries posit that interorganizational VOs are temporary in nature, are network organizations, are independent, and are based on swift trust. We suggest further that interorganizational VOs enable small to medium enterprises to exploit market opportunities, and enable VO member organizations to create a value-adding partnership. We also identify information and communication technology (ICT) as the essential enabler of VOs. Finally, we argue that interorganizational VOs act as a single organizational unit and that they therefore constitute a uniquely distinguishable organizational form. We conclude with suggestions for further research, including trust, organizational behavior, transaction economics, virtual HRM, and business strategy.

Gaze angle: a possible mechanism of visual stress in virtual reality headsets

It is known that some Virtual Reality (VR) head-mounted displays (HMDs) can cause temporary deficits in binocular vision. On the other hand, the precise mechanism by which visual stress occurs is unclear. This paper is concerned with a potential source of visual stress that has not been previously considered with regard to VR systems: inappropriate vertical gaze angle. As vertical gaze angle is raised or lowered the 'effort' required of the binocular system also changes. The extent to which changes in vertical gaze angle alter the demands placed upon the vergence eye movement system was explored. The results suggested that visual stress may depend, in part, on vertical gaze angle. The proximity of the display screens within an HMD means that a VR headset should be in the correct vertical location for any individual user. This factor may explain some previous empirical results and has important implications for headset design. Fortuitously, a reasonably simple solution exists.

Evolutionary conservation of the membrane fusion machine

Recent structural studies of proteins mediating membrane fusion reveal intriguing similarities between diverse viral and mammalian systems. Particularly striking is the close similarity between the transmembrane envelope glycoproteins from the retrovirus HTLV-1 and the filovirus Ebola. These similarities suggest similar mechanisms of membrane fusion. The model that fits most currently available data suggests fusion activation in viral systems is driven by a symmetrical conformational change triggered by an activation event such as receptor binding or a pH change. The mammalian vesicle fusion mediated by the SNARE protein complex most likely occurs by a similar mechanism but without symmetry constraints.

Virtual models of the HLA class I antigen processing pathway

Antigen recognition by cytotoxic CD8 T cells is dependent upon a number of critical steps in MHC class I antigen processing including proteosomal cleavage, TAP transport into the endoplasmic reticulum, and MHC class 1 binding. Based on extensive experimental data relating to each of these steps there is now the capacity to model individual antigen processing steps with a high degree of accuracy. This paper demonstrates the potential to bring together models of individual antigen processing steps, for example proteosome cleavage, TAP transport, and MHC binding, to build highly informative models of functional pathways. In particular, we demonstrate how an artificial neural network model of TAP transport was used to mine a HLA-binding database so as to identify H LA-binding peptides transported by TAP. This integrated model of antigen processing provided the unique insight that HLA class I alleles apparently constitute two separate classes: those that are TAP-efficient for peptide loading (HLA-B27, -A3, and -A24) and those that are TAP-inefficient (HLA-A2, -B7, and -B8). Hence, using this integrated model we were able to generate novel hypotheses regarding antigen processing, and these hypotheses are now capable of being tested experimentally. This model confirms the feasibility of constructing a virtual immune system, whereby each additional step in antigen processing is incorporated into a single modular model. Accurate models of antigen processing have implications for the study of basic immunology as well as for the design of peptide-based vaccines and other immunotherapies. (C) 2004 Elsevier Inc. All rights reserved.

A study of the interaction between operator style and machine capability for a hydraulic mining excavator

This paper presents a case study that explores how operator digging style juxtaposes with mechanical capability for a class of hydraulic mining excavators. The relationships between actuator and digging forces are developed and these are used to identify the excavator's capability to apply forces in various directions. Two distinct modes of operation are examined to see how they relate to the mechanical capabilities of the linkage and to establish if one has merit over the other. It is found that one of these styles results in lower loading of the machine.

The assessment of oral cytology utilizing ploidy analysis and virtual microscopy for the early detection of epithelial dysplasia and neoplasia in oral mucosal lesions

Oral squamous cell carcinoma (OSCC) is associated with high morbidity and mortality which is due, at least in part, to late detection. Precancerous and cancerous oral lesions may mimic any number of benign oral lesions, and as such may be left without investigation and treatment until they are well advanced. Over the past several years there has been renewed interest in oral cytology as an adjuvant clinical tool in the investigation of oral mucosal lesions. The purpose of the present study was to compare the usefulness of ploidy analysis after Feulgen stained cytological thin-prep specimens with traditional incisional biopsy and routine histopathological examination for the assessment of the pre-malignant potential of oral mucosal lesions. An analysis of the cytological specimens was undertaken with virtual microscopy which allowed for rapid and thorough analysis of the complete cytological specimen. 100 healthy individuals between 30 and 70 years of age, who were non-smokers, non-drinkers and not taking any medication, had cytological specimens collected from both the buccal mucosa and lateral margin of tongue to establish normal cytology parameters within a control population. Patients with a presumptive clinical diagnosis of lichen planus, leukoplakia or OSCC had lesional cytological samples taken prior to their diagnostic biopsy. Standardised thin preparations were prepared and each specimen stained by both Feuglen and Papanicolau methods. High speed scanning of the complete slide at 40X magnification was undertaken using the Aperio Scanscope TM and the green channel of the resultant image was analysed after threshold segmentation to isolate only nuclei and the integrated optical density of each nucleus taken as a gross measure of the DNA content (ploidy). Preliminary results reveal that ploidy assessment of oral cytology holds great promise as an adjunctive prognostic factor in the analysis of the malignant potential of oral mucosal lesions.

Virtual plants - integrating architectural and physiological models

Recent advances in computer technology have made it possible to create virtual plants by simulating the details of structural development of individual plants. Software has been developed that processes plant models expressed in a special purpose mini-language based on the Lindenmayer system formalism. These models can be extended from their architectural basis to capture plant physiology by integrating them with crop models, which estimate biomass production as a consequence of environmental inputs. Through this process, virtual plants will gain the ability to react to broad environmental conditions, while crop models will gain a visualisation component. This integration requires the resolution of the fundamentally different time scales underlying the approaches. Architectural models are usually based on physiological time; each time step encompasses the same amount of development in the plant, without regard to the passage of real time. In contrast, physiological models are based in real time; the amount of development in a time step is dependent on environmental conditions during the period. This paper provides a background on the plant modelling language, then describes how widely-used concepts of thermal time can be implemented to resolve these time scale differences. The process is illustrated using a case study. (C) 1997 Elsevier Science Ltd.

Asymmetric page split generalized index search trees for formal concept analysis

Formal Concept Analysis is an unsupervised machine learning technique that has successfully been applied to document organisation by considering documents as objects and keywords as attributes. The basic algorithms of Formal Concept Analysis then allow an intelligent information retrieval system to cluster documents according to keyword views. This paper investigates the scalability of this idea. In particular we present the results of applying spatial data structures to large datasets in formal concept analysis. Our experiments are motivated by the application of the Formal Concept Analysis idea of a virtual filesystem [11,17,15]. In particular the libferris [1] Semantic File System. This paper presents customizations to an RD-Tree Generalized Index Search Tree based index structure to better support the application of Formal Concept Analysis to large data sources.