Depicting the future strategic plans of the Royal Australian Navy using a roadmapping framework as a visual composite canvas

Strategic planning can be an arduous and complex task; and, once a plan has been devised, it is often quite a challenge to effectively communicate the principal missions and key priorities to the array of different stakeholders. The communication challenge can be addressed through the application of a clearly and concisely designed visualisation of the strategic plan - to that end, this paper proposes the use of a roadmapping framework to structure a visual canvas. The canvas provides a template in the form of a single composite visual output that essentially allows a 'plan-on-a-page' to be generated. Such a visual representation provides a high-level depiction of the future context, end-state capabilities and the system-wide transitions needed to realise the strategic vision. To demonstrate this approach, an illustrative case study based on the Australian Government's Defence White Paper and the Royal Australian Navy's fleet plan will be presented. The visual plan plots the in-service upgrades for addressing the capability shortfalls and gaps in the Navy's fleet as it transitions from its current configuration to its future end-state vision. It also provides a visualisation of project timings in terms of the decision gates (approval, service release) and specific phases (proposal, contract, delivery) together with how these projects are rated against the key performance indicators relating to the technology acquisition process and associated management activities. © 2013 Taylor & Francis.

Sparse recovery of complex phase-encoded velocity images using iterative thresholding

In this paper we propose a new algorithm for reconstructing phase-encoded velocity images of catalytic reactors from undersampled NMR acquisitions. Previous work on this application has employed total variation and nonlinear conjugate gradients which, although promising, yields unsatisfactory, unphysical visual results. Our approach leverages prior knowledge about the piecewise-smoothness of the phase map and physical constraints imposed by the system under study. We show how iteratively regularizing the real and imaginary parts of the acquired complex image separately in a shift-invariant wavelet domain works to produce a piecewise-smooth velocity map, in general. Using appropriately defined metrics we demonstrate higher fidelity to the ground truth and physical system constraints than previous methods for this specific application. © 2013 IEEE.

Identification of a novel C2 domain factor in ovaries of orange-spotted grouper (Epinephelus coioides)

Follicle consists of an oocyte and a lot of surrounding follicular cells, and significant interactions exist between the oocyte and the somatic cells. In this study, a novel cDNA has been screened from a subtractive cDNA library between tail bud embryos and blastula embryos in the protogynous hermaphrodite orange-spotted grouper (Epinephelus coioides). Its full-length cDNA is 821 bp, and has an ORF of 414 by for encoding a peptide of 137 aa, which shows 38%, 37%, 33%, and 33% homology with 4 putative proteins screened from zebrafish (Danio rerio). Conserved domain search in NCBI reveals a single C2 domain existing in the C2 domain superfamily proteins, and has only 7 beta strands in comparison with 8 beta strands of C2 domains in other C2 domain superfamily proteins. Artificial sex reversal, RT-PCR analysis and Western blot detection demonstrated ovary-specific expression of the C2 domain factor, and therefore the novel gene was designated as E. coioides ovary-specific C2 domain factor, EcOC2 factor. Moreover, predominant expression of EcOC2 factor was further revealed in grouper mature ovary, and its strong immunofluorescence signals were located between granulosa cells and oocyte zona radiata in grouper mature follicles. The data indicate that the novel EcOC2 factor might be a main component that associates between granulosa cells and the oocyte during oocyte maturation, and might play significant roles in regulating oocyte maturation and ovulation. Further studies on its developmental behaviour and physiological functions will elucidate the interactions between oocyte and the surrounding somatic cells and the underlying molecular mechanisms. (C) 2005 Elsevier Inc. All rights reserved.

Zebraflsh z-otu, a novel Otu and Tudor domain-containing gene, is expressed in early stages of oogenesis and embryogenesis

Several studies have suggested that Otu domain had de-ubiquitinating activity and Tudor domain was important for the formation of germ cells. Here, we reported a novel zebrafish ovary-specific gene containing Otu and Tudor domain, z-otu, which was expressed at stages I-III oocytes and embryonic stages from zygotes to early blastula during embryonic cells maintained their totipotency. Therefore, z-otu might link the ubiquitin signaling pathway to early oogenesis and maintaining the totipotency of embryonic cell. (c) 2005 Elsevier B.V. All rights reserved.

PURIFICATION AND CHARACTERIZATION OF A KINASE SPECIFIC FOR THE SERINE-RICH AND ARGININE-RICH PRE-MESSENGER-RNA SPLICING FACTORS

Members of the SR family of pre-mRNA splicing factors are phosphoproteins that share a phosphoepitope specifically recognized by monoclonal antibody (mAb) 104. Recent studies have indicated that phosphorylation may regulate the activity and the intracellular localization of these splicing factors. Here, we report the purification and kinetic properties of SR protein kinase 1 (SRPK1), a kinase specific for SR family members. We demonstrate that the kinase specifically recognizes the SR domain, which contains serine/arginine repeats. Previous studies have shown that dephosphorylated SR proteins did not react with mAb 104 and migrated faster in SDS gels than SR proteins from mammalian cells. We show that SRPK1 restores both mobility and mAB 104 reactivity to a SR protein SF2/ASF (splicing factor 2/alternative splicing factor) produced in bacteria, suggesting that SRPK1 is responsible for the generation of the mAb 104-specific phosphoepitope in vivo. Finally, we have correlated the effects of mutagenesis in the SR domain of SF2/ASF on splicing with those on phosphorylation of the protein by SRPK1, suggesting that phosphorylation of SR proteins is required for splicing.

Haematopoietic lineage cell-specific protein 1 (HS1) promotes actin-related protein (Arp) 2/3 complex-mediated actin polymerization

HS1 (haematopoietic lineage cell-specific gene protein 1), a prominent substrate of intracellular protein tyrosine kinases in haematopoietic cells, is implicated in the immune response to extracellular stimuli and in cell differentiation induced by cytokines. Although HS1 contains a 37-amino acid tandem repeat motif and a C-terminal Src homology 3 domain and is closely related to the cortical-actin-associated protein cortactin, it lacks the fourth repeat that has been shown to be essential for cortactin binding to filamentous actin (F-actin). In this study, we examined the possible role of HS1 in the regulation of the actin cytoskeleton. Immunofluorescent staining demonstrated that HS1 co-localizes in the cytoplasm of cells with actin-related protein (Arp) 2/3 complex, the primary component of the cellular machinery responsible for de novo actin assembly. Furthermore, recombinant HS1 binds directly to Arp2/3 complex with an equilibrium dissociation constant (K-d) of 880 nM. Although HS1 is a modest F-actin-binding protein with a Kd of 400 nM, it increases the rate of the actin assembly mediated by Arp2/3 complex, and promotes the formation of branched actin filaments induced by Arp2/3 complex and a constitutively activated peptide of N-WASP (neural Wiskott-Aldrich syndrome protein). Our data suggest that HS1, like cortactin, plays an important role in the modulation of actin assembly.

Amphi-Eomes/Tbr1: An amphioxus cognate of vertebrate Eomesodermin and T-Brain1 genes whose expression reveals evolutionarily distinct domain in amphioxus development

A cDNA for a novel T-box containing gene was isolated from the amphioxus Branchiostoma belcheri. A molecular phylogenetic tree constructed from the deduced amino acid sequence of the isolated cDNA indicates that this gene belongs to the T-Brain subfamily. In situ hybridization reveals that the expression is first detected in the invaginating archenteron at the early gastrula stage and this expression is down-regulated at the neurula stage. In early larvae, the expression appears again and transcripts are detected exclusively in the pre-oral pit (wheel organ-Hatschek's pit of the adult). In contrast to the vertebrate counterparts, no transcripts are detected in the brain vesicle or nerve cord throughout the development. These results are interpreted to mean that a role of T-Brain products in vertebrate forebrain development was acquired after the amphioxus was split from the lineage leading to the vertebrates. On the other hand, comparison of the tissue-specific expression domain of T-Brain genes and other genes between amphioxus and vertebrates revealed that the pre-oral pit of amphioxus has several molecular features which are comparable to those of the vertebrate olfactory and hypophyseal placode. (C) 2002 Wiley-Liss, Inc.

Cloning and expression analysis of myogenin from flounder (Paralichthys olivaceus) and promoter analysis of muscle-specific expression

Myogenin is a bHLH transcription factor of the MyoD family. It plays a crucial role in myoblast differentiation and maturation. We report here the isolation of flounder myogenin gene and the characterization of its expression patterns. Sequence analysis indicated that flounder myogenin shared a similar structure and the conserved bHLH domain with other vertebrate myogenin genes. Flounder myogenin gene contains 3 exons and 2 introns. Sequence alignment and phylogenetic showed that flounder myogenin was more homologous with halibut (Hippoglossus hippoglossus) myogenin and striped bass (Morone saxatilis) myogenin. Whole-mount embryo in situ hybridization revealed that flounder myogenin was first detected in the medial region of somites that give rise to slow muscles, and expanded later to the lateral region of the somite that become fast muscles. The levels of myogenin transcripts dropped significantly in matured somites at the trunk region. Its expression could only be detected in the caudal somites, which was consistent with the timing of somite maturation. Transient expression analysis showed that the 546 bp flounder myogenin promoter was sufficient to direct muscle-specific GFP expression in zebrafish embryos. (c) 2007 Elsevier Inc. All rights reserved.

Dissection and localization of the immunostimulating domain of Edwardsiella tarda FliC

Bacterial flagellin is known to induce potent immune response in vertebrate systems via the toll-like receptor (TLR) 5. As a result, flagellin has been studied extensively as a vaccine adjuvant. In a previous study, we examined the vaccine and adjuvant potentials of the flagellin (FliC) of the fish pathogen Edwardsiella tarda. We found that E. tarda FliC induced low protective immunity by itself but could function as a molecular adjuvant and potentiate the specific immune response induced by the E. tarda antigen Eta6. Since FliC is a large protein and organized into distinct structural domains, we wondered whether the immunostimulating effect observed with the full-length protein could be localized to a certain region. To investigate this question, we in the present study dissected the FliC protein into several segments according to its structural features: (i) N163, which consists of the conserved N-terminal 163 residues of FliC; (ii) M160, which consists of the variable middle 160 residues; (iii) C94, which consists of the conserved C-terminal 94 residues; (iv) NC257, which is an artificial fusion of N163 and C94. To examine the adjuvanticity of the FliC fragments, DNA vaccine plasmids expressing FliC fragments in fusion with Eta6 were constructed and used to immunize Japanese flounder. The results showed that N163 produced the best adjuvant effect, which, in respect to improvement in the relative percent survival of the vaccinated fish, was comparable to that of the full-length FliC. None of the other FliC fragments exhibited apparent immunopotentiating effect. Further analysis showed that N163 enhanced the production of serum specific antibodies and, like full-length FliC, significantly upregulated the expression of the genes that are possibly involved in innate and adaptive immunity. These results indicate that N163 is the immunodominant region of FliC and suggest that E. tarda FliC may induce immune responses in Japanese flounder via mechanisms alternative to that involving TLR5. (C) 2010 Elsevier Ltd. All rights reserved.

Identification, expression, function and localization of a DUF985 domain-containing hypothetical gene from amphioxus Branchiostoma belcheri

The progress in genome sequencing has led to an increasing submission of uncharacterized hypothetical genes with the domain of unknown function, DUF985, in GenBank, and none of these genes is related to a known protein. We therefore underwent an experimental study to identify the function of a DUF985 domain-containing hypothetical gene BbDUF985 (GenBank Accession No. AY273818) isolated from amphioxus Branchiostoma belcheri (B. belcheri). BbDUF985 was successfully expressed in both prokaryotic and eukaryotic systems, and its recombinant proteins expressed in both systems definitely exhibited an activity of phosphoglucose isomerase (PGI). Both tissue-section in situ hybridization and immunohistochemistry demonstrated that BbDUF985 was expressed in a tissue-specific manner, with most abundant levels in the hepatic caecum and ovary. In CHO cells transfected with the expression plasmid pEGFP-N1/BbDUF985, the fusion protein was targeted in the cytoplasm of CHO cells, suggesting that BbDUF985 is a cytosolic protein. In contrast, Western blotting indicated that BbDUF985 was also present in amphioxus humoral fluids, suggesting that it exists as a secreted protein as well. Our study provided a framework for further understanding the biochemical properties and physiological function of DUF985-containing hypothetical proteins in other species. (c) 2008 Elsevier Inc. All rights reserved.

Fast Perceptual Learning in Visual Hyperacuity

In many different spatial discrimination tasks, such as in determining the sign of the offset in a vernier stimulus, the human visual system exhibits hyperacuity-level performance by evaluating spatial relations with the precision of a fraction of a photoreceptor"s diameter. We propose that this impressive performance depends in part on a fast learning process that uses relatively few examples and occurs at an early processing stage in the visual pathway. We show that this hypothesis is plausible by demonstrating that it is possible to synthesize, from a small number of examples of a given task, a simple (HyperBF) network that attains the required performance level. We then verify with psychophysical experiments some of the key predictions of our conjecture. In particular, we show that fast timulus-specific learning indeed takes place in the human visual system and that this learning does not transfer between two slightly different hyperacuity tasks.

Supporting Dynamic Languages on the Java Virtual Machine

In this note, I propose two extensions to the Java virtual machine (or VM) to allow dynamic languages such as Dylan, Scheme and Smalltalk to be efficiently implemented on the VM. These extensions do not affect the performance of pure Java programs on the machine. The first extension allows for efficient encoding of dynamic data; the second allows for efficient encoding of language-specific computational elements.

Sharing visual features for multiclass and multiview object detection

We consider the problem of detecting a large number of different classes of objects in cluttered scenes. Traditional approaches require applying a battery of different classifiers to the image, at multiple locations and scales. This can be slow and can require a lot of training data, since each classifier requires the computation of many different image features. In particular, for independently trained detectors, the (run-time) computational complexity, and the (training-time) sample complexity, scales linearly with the number of classes to be detected. It seems unlikely that such an approach will scale up to allow recognition of hundreds or thousands of objects. We present a multi-class boosting procedure (joint boosting) that reduces the computational and sample complexity, by finding common features that can be shared across the classes (and/or views). The detectors for each class are trained jointly, rather than independently. For a given performance level, the total number of features required, and therefore the computational cost, is observed to scale approximately logarithmically with the number of classes. The features selected jointly are closer to edges and generic features typical of many natural structures instead of finding specific object parts. Those generic features generalize better and reduce considerably the computational cost of an algorithm for multi-class object detection.

The Role of Knowledge in Visual Shape Representation

This report shows how knowledge about the visual world can be built into a shape representation in the form of a descriptive vocabulary making explicit the important geometrical relationships comprising objects' shapes. Two computational tools are offered: (1) Shapestokens are placed on a Scale-Space Blackboard, (2) Dimensionality-reduction captures deformation classes in configurations of tokens. Knowledge lies in the token types and deformation classes tailored to the constraints and regularities ofparticular shape worlds. A hierarchical shape vocabulary has been implemented supporting several later visual tasks in the two-dimensional shape domain of the dorsal fins of fishes.

An integrated firewall policy validation tool.

Security policies are increasingly being implemented by organisations. Policies are mapped to device configurations to enforce the policies. This is typically performed manually by network administrators. The development and management of these enforcement policies is a difficult and error prone task. This thesis describes the development and evaluation of an off-line firewall policy parser and validation tool. This provides the system administrator with a textual interface and the vendor specific low level languages they trust and are familiar with, but the support of an off-line compiler tool. The tool was created using the Microsoft C#.NET language, and the Microsoft Visual Studio Integrated Development Environment (IDE). This provided an object environment to create a flexible and extensible system, as well as simple Web and Windows prototyping facilities to create GUI front-end applications for testing and evaluation. A CLI was provided with the tool, for more experienced users, but it was also designed to be easily integrated into GUI based applications for non-expert users. The evaluation of the system was performed from a custom built GUI application, which can create test firewall rule sets containing synthetic rules, to supply a variety of experimental conditions, as well as record various performance metrics. The validation tool was created, based around a pragmatic outlook, with regard to the needs of the network administrator. The modularity of the design was important, due to the fast changing nature of the network device languages being processed. An object oriented approach was taken, for maximum changeability and extensibility, and a flexible tool was developed, due to the possible needs of different types users. System administrators desire, low level, CLI-based tools that they can trust, and use easily from scripting languages. Inexperienced users may prefer a more abstract, high level, GUI or Wizard that has an easier to learn process. Built around these ideas, the tool was implemented, and proved to be a usable, and complimentary addition to the many network policy-based systems currently available. The tool has a flexible design and contains comprehensive functionality. As opposed to some of the other tools which perform across multiple vendor languages, but do not implement a deep range of options for any of the languages. It compliments existing systems, such as policy compliance tools, and abstract policy analysis systems. Its validation algorithms were evaluated for both completeness, and performance. The tool was found to correctly process large firewall policies in just a few seconds. A framework for a policy-based management system, with which the tool would integrate, is also proposed. This is based around a vendor independent XML-based repository of device configurations, which could be used to bring together existing policy management and analysis systems.