Stochastic models for regulatory networks of the genetic toggle switch

Bistability arises within a wide range of biological systems from the λ phage switch in bacteria to cellular signal transduction pathways in mammalian cells. Changes in regulatory mechanisms may result in genetic switching in a bistable system. Recently, more and more experimental evidence in the form of bimodal population distributions indicates that noise plays a very important role in the switching of bistable systems. Although deterministic models have been used for studying the existence of bistability properties under various system conditions, these models cannot realize cell-to-cell fluctuations in genetic switching. However, there is a lag in the development of stochastic models for studying the impact of noise in bistable systems because of the lack of detailed knowledge of biochemical reactions, kinetic rates, and molecular numbers. In this work, we develop a previously undescribed general technique for developing quantitative stochastic models for large-scale genetic regulatory networks by introducing Poisson random variables into deterministic models described by ordinary differential equations. Two stochastic models have been proposed for the genetic toggle switch interfaced with either the SOS signaling pathway or a quorum-sensing signaling pathway, and we have successfully realized experimental results showing bimodal population distributions. Because the introduced stochastic models are based on widely used ordinary differential equation models, the success of this work suggests that this approach is a very promising one for studying noise in large-scale genetic regulatory networks.

Propagation of low power low divergence Gaussian fields in unbiased self-defocusing photorefractive media and their interactions

Many optical networks are limited in speed and processing capability due to the necessity for the optical signal to be converted to an electrical signal and back again. In addition, electronically manipulated interconnects in an otherwise optical network lead to overly complicated systems. Optical spatial solitons are optical beams that propagate without spatial divergence. They are capable of phase dependent interactions, and have therefore been extensively researched as suitable all optical interconnects for over 20 years. However, they require additional external components, initially high voltage power sources were required, several years later, high power background illumination had replaced the high voltage. However, these additional components have always remained as the greatest hurdle in realising the applications of the interactions of spatial optical solitons as all optical interconnects. Recently however, self-focusing was observed in an otherwise self-defocusing photorefractive crystal. This observation raises the possibility of the formation of soliton-like fields in unbiased self-defocusing media, without the need for an applied electrical field or background illumination. This thesis will present an examination of the possibility of the formation of soliton-like low divergence fields in unbiased self-defocusing photorefractive media. The optimal incident beam and photorefractive media parameters for the formation of these fields will be presented, together with an analytical and numerical study of the effect of these parameters. In addition, preliminary examination of the interactions of two of these fields will be presented. In order to complete an analytical examination of the field propagating through the photorefractive medium, the spatial profile of the beam after propagation through the medium was determined. For a low power solution, it was found that an incident Gaussian field maintains its Gaussian profile as it propagates. This allowed the beam at all times to be described by an individual complex beam parameter, while also allowing simple analytical solutions to the appropriate wave equation. An analytical model was developed to describe the effect of the photorefractive medium on the Gaussian beam. Using this model, expressions for the required intensity dependent change in both the real and imaginary components of the refractive index were found. Numerical investigation showed that under certain conditions, a low powered Gaussian field could propagate in self-defocusing photorefractive media with divergence of approximately 0.1 % per metre. An investigation into the parameters of a Ce:BaTiO3 crystal showed that the intensity dependent absorption is wavelength dependent, and can in fact transition to intensity dependent transparency. Thus, with careful wavelength selection, the required intensity dependent change in both the real and imaginary components of the refractive index for the formation of a low divergence Gaussian field are physically realisable. A theoretical model incorporating the dependence of the change in real and imaginary components of the refractive index on propagation distance was developed. Analytical and numerical results from this model are congruent with the results from the previous model, showing low divergence fields with divergence less than 0.003 % over the propagation length of the photorefractive medium. In addition, this approach also confirmed the previously mentioned self-focusing effect of the self-defocusing media, and provided an analogy to a negative index GRIN lens with an intensity dependent focal length. Experimental results supported the findings of the numerical analysis. Two low divergence fields were found to possess the ability to interact in a Ce:BaTiO3 crystal in a soliton-like fashion. The strength of these interactions was found to be dependent on the degree of divergence of the individual beams. This research found that low-divergence fields are possible in unbiased self-defocusing photorefractive media, and that soliton-like interactions between two of these fields are possible. However, in order for these types of fields to be used in future all optical interconnects, the manipulation of these interactions, together with the ability for these fields to guide a second beam at a different wavelength, must be investigated.

A Virtual Evaluation Track for Cross Language Link Discovery

The Wikipedia has become the most popular online source of encyclopedic information. The English Wikipedia collection, as well as some other languages collections, is extensively linked. However, as a multilingual collection the Wikipedia is only very weakly linked. There are few cross-language links or cross-dialect links (see, for example, Chinese dialects). In order to link the multilingual-Wikipedia as a single collection, automated cross language link discovery systems are needed – systems that identify anchor-texts in one language and targets in another. The evaluation of Link Discovery approaches within the English version of the Wikipedia has been examined in the INEX Link the-Wiki track since 2007, whilst both CLEF and NTCIR emphasized the investigation and the evaluation of cross-language information retrieval. In this position paper we propose a new virtual evaluation track: Cross Language Link Discovery (CLLD). The track will initially examine cross language linking of Wikipedia articles. This virtual track will not be tied to any one forum; instead we hope it can be connected to each of (at least): CLEF, NTCIR, and INEX as it will cover ground currently studied by each. The aim is to establish a virtual evaluation environment supporting continuous assessment and evaluation, and a forum for the exchange of research ideas. It will be free from the difficulties of scheduling and synchronizing groups of collaborating researchers and alleviate the necessity to travel across the globe in order to share knowledge. We aim to electronically publish peer-reviewed publications arising from CLLD in a similar fashion: online, with open access, and without fixed submission deadlines.

The HarmonyGrid : music, space and performance in grid music systems

This research explores music in space, as experienced through performing and music-making with interactive systems. It explores how musical parameters may be presented spatially and displayed visually with a view to their exploration by a musician during performance. Spatial arrangements of musical components, especially pitches and harmonies, have been widely studied in the literature, but the current capabilities of interactive systems allow the improvisational exploration of these musical spaces as part of a performance practice. This research focuses on quantised spatial organisation of musical parameters that can be categorised as grid music systems (GMSs), and interactive music systems based on them. The research explores and surveys existing and historical uses of GMSs, and develops and demonstrates the use of a novel grid music system designed for whole body interaction. Grid music systems provide plotting of spatialised input to construct patterned music on a two-dimensional grid layout. GMSs are navigated to construct a sequence of parametric steps, for example a series of pitches, rhythmic values, a chord sequence, or terraced dynamic steps. While they are conceptually simple when only controlling one musical dimension, grid systems may be layered to enable complex and satisfying musical results. These systems have proved a viable, effective, accessible and engaging means of music-making for the general user as well as the musician. GMSs have been widely used in electronic and digital music technologies, where they have generally been applied to small portable devices and software systems such as step sequencers and drum machines. This research shows that by scaling up a grid music system, music-making and musical improvisation are enhanced, gaining several advantages: (1) Full body location becomes the spatial input to the grid. The system becomes a partially immersive one in four related ways: spatially, graphically, sonically and musically. (2) Detection of body location by tracking enables hands-free operation, thereby allowing the playing of a musical instrument in addition to “playing” the grid system. (3) Visual information regarding musical parameters may be enhanced so that the performer may fully engage with existing spatial knowledge of musical materials. The result is that existing spatial knowledge is overlaid on, and combined with, music-space. Music-space is a new concept produced by the research, and is similar to notions of other musical spaces including soundscape, acoustic space, Smalley's “circumspace” and “immersive space” (2007, 48-52), and Lotis's “ambiophony” (2003), but is rather more textural and “alive”—and therefore very conducive to interaction. Music-space is that space occupied by music, set within normal space, which may be perceived by a person located within, or moving around in that space. Music-space has a perceivable “texture” made of tensions and relaxations, and contains spatial patterns of these formed by musical elements such as notes, harmonies, and sounds, changing over time. The music may be performed by live musicians, created electronically, or be prerecorded. Large-scale GMSs have the capability not only to interactively display musical information as music representative space, but to allow music-space to co-exist with it. Moving around the grid, the performer may interact in real time with musical materials in music-space, as they form over squares or move in paths. Additionally he/she may sense the textural matrix of the music-space while being immersed in surround sound covering the grid. The HarmonyGrid is a new computer-based interactive performance system developed during this research that provides a generative music-making system intended to accompany, or play along with, an improvising musician. This large-scale GMS employs full-body motion tracking over a projected grid. Playing with the system creates an enhanced performance employing live interactive music, along with graphical and spatial activity. Although one other experimental system provides certain aspects of immersive music-making, currently only the HarmonyGrid provides an environment to explore and experience music-space in a GMS.

Locating 'Agency' Within Ubiquitous Computing Systems

The final shape of the "Internet of Things" ubiquitous computing promises relies on a cybernetic system of inputs (in the form of sensory information), computation or decision making (based on the prefiguration of rules, contexts, and user-generated or defined metadata), and outputs (associated action from ubiquitous computing devices). My interest in this paper lies in the computational intelligences that suture these positions together, and how positioning these intelligences as autonomous agents extends the dialogue between human-users and ubiquitous computing technology. Drawing specifically on the scenarios surrounding the employment of ubiquitous computing within aged care, I argue that agency is something that cannot be traded without serious consideration of the associated ethics.

Fault isolation in distributed generation connected distribution networks

Protection of a distribution network in the presence of distributed generators (DGs) using overcurrent relays is a challenging task due to the changes in fault current levels and reverse power flow. Specifically, in the presence of current limited converter interfaced DGs, overcurrent relays may fail to isolate the faulted section either in grid connected or islanded mode of operation. In this paper, a new inverse type relay is presented to protect a distribution network, which may have several DG connections. The new relay characteristic is designed based on the measured admittance of the protected line. The relay is capable of detecting faults under changing fault current levels. The relay performance is evaluated using PSCAD simulation and laboratory experiments.

What happened to the education revolution? : new media technologies and the Australian curriculum : constraints and possibilities

This chapter investigates the place of new media in Queensland in the light of the Australian curriculum. ‘Multimodal texts’ in English are being defined as largely electronically ‘created’ and yet restricted access to digital resources at the chalkface may preclude this work from happening. The myth of the ‘digital native’ (Prensky, 2007), combined with the reality of the ‘digital divide’ coupled with technophobia amongst some quite experienced teachers, responsible for implementing the curriculum, paints a picture of constraints. These constraints are due in part to protective state bans in Queensland on social networking sites and school bans on mobile phone use. Some ‘Generation next’ will have access to digital platforms for the purpose of designing texts at home and school, and others will not. Yet without adequate Professional Development for teachers and substantially increased ICT infrastructure funding for all schools, the way new media and multimodal opportunities are interpreted at state level in the curriculum may leave much to be desired in schools. This chapter draws on research that I recently conducted on the professional development needs of beginning teachers, as well as a critical reading of the ACARA policy documents.

Free software as a democratic principle

Software forms an important part of the interface between citizens and their government. An increasing amount of government functions are being performed, controlled, or delivered electronically. This software, like all language, is never value-neutral, but must, to some extent, reflect the values of the coder and proprietor. The move that many governments are making towards e-governance, and the increasing reliance that is being placed upon software in government, necessitates a rethinking of the relationships of power and control that are embodied in software.

Design for Manufacturing (DFM) – A case study of repetitive measures

Design for Manufacturing (DFM) is a highly integral methodology in product development, starting from the concept development phase, with the aim of improving manufacturing productivity and maintaining product quality. While Design for Assembly (DFA) is focusing on elimination or combination of parts with other components (Boothroyd, Dewhurst and Knight, 2002), which in most cases relates to performing a function and manufacture operation in a simpler way, DFM is following a more holistic approach. During DFM, the considerable background work required for the conceptual phase is compensated for by a shortening of later development phases. Current DFM projects normally apply an iterative step-by-step approach and eventually transfer to the developer team. Although DFM has been a well established methodology for about 30 years, a Fraunhofer IAO study from 2009 found that DFM was still one of the key challenges of the German Manufacturing Industry. A new, knowledge based approach to DFM, eliminating steps of DFM, was introduced in Paul and Al-Dirini (2009). The concept focuses on a concurrent engineering process between the manufacturing engineering and product development systems, while current product realization cycles depend on a rigorous back-and-forth examine-and-correct approach so as to ensure compatibility of any proposed design to the DFM rules and guidelines adopted by the company. The key to achieving reductions is to incorporate DFM considerations into the early stages of the design process. A case study for DFM application in an automotive powertrain engineering environment is presented. It is argued that a DFM database needs to be interfaced to the CAD/CAM software, which will restrict designers to the DFM criteria. Consequently, a notable reduction of development cycles can be achieved. The case study is following the hypothesis that current DFM methods do not improve product design in a manner claimed by the DFM method. The critical case was to identify DFA/DFM recommendations or program actions with repeated appearance in different sources. Repetitive DFM measures are identified, analyzed and it is shown how a modified DFM process can mitigate a non-fully integrated DFM approach.

An analytical tool that quantifies cellular morphology changes from three-dimensional fluorescence images

The most common software analysis tools available for measuring fluorescence images are for two-dimensional (2D) data that rely on manual settings for inclusion and exclusion of data points, and computer-aided pattern recognition to support the interpretation and findings of the analysis. It has become increasingly important to be able to measure fluorescence images constructed from three-dimensional (3D) datasets in order to be able to capture the complexity of cellular dynamics and understand the basis of cellular plasticity within biological systems. Sophisticated microscopy instruments have permitted the visualization of 3D fluorescence images through the acquisition of multispectral fluorescence images and powerful analytical software that reconstructs the images from confocal stacks that then provide a 3D representation of the collected 2D images. Advanced design-based stereology methods have progressed from the approximation and assumptions of the original model-based stereology(1) even in complex tissue sections(2). Despite these scientific advances in microscopy, a need remains for an automated analytic method that fully exploits the intrinsic 3D data to allow for the analysis and quantification of the complex changes in cell morphology, protein localization and receptor trafficking. Current techniques available to quantify fluorescence images include Meta-Morph (Molecular Devices, Sunnyvale, CA) and Image J (NIH) which provide manual analysis. Imaris (Andor Technology, Belfast, Northern Ireland) software provides the feature MeasurementPro, which allows the manual creation of measurement points that can be placed in a volume image or drawn on a series of 2D slices to create a 3D object. This method is useful for single-click point measurements to measure a line distance between two objects or to create a polygon that encloses a region of interest, but it is difficult to apply to complex cellular network structures. Filament Tracer (Andor) allows automatic detection of the 3D neuronal filament-like however, this module has been developed to measure defined structures such as neurons, which are comprised of dendrites, axons and spines (tree-like structure). This module has been ingeniously utilized to make morphological measurements to non-neuronal cells(3), however, the output data provide information of an extended cellular network by using a software that depends on a defined cell shape rather than being an amorphous-shaped cellular model. To overcome the issue of analyzing amorphous-shaped cells and making the software more suitable to a biological application, Imaris developed Imaris Cell. This was a scientific project with the Eidgenössische Technische Hochschule, which has been developed to calculate the relationship between cells and organelles. While the software enables the detection of biological constraints, by forcing one nucleus per cell and using cell membranes to segment cells, it cannot be utilized to analyze fluorescence data that are not continuous because ideally it builds cell surface without void spaces. To our knowledge, at present no user-modifiable automated approach that provides morphometric information from 3D fluorescence images has been developed that achieves cellular spatial information of an undefined shape (Figure 1). We have developed an analytical platform using the Imaris core software module and Imaris XT interfaced to MATLAB (Mat Works, Inc.). These tools allow the 3D measurement of cells without a pre-defined shape and with inconsistent fluorescence network components. Furthermore, this method will allow researchers who have extended expertise in biological systems, but not familiarity to computer applications, to perform quantification of morphological changes in cell dynamics.

What do current planning students and recent graduates think planners do?

A planner’s view of the purpose of their actions, the role they play, the focus of their work and in whose interest they operate greatly influence their approach to planning and the outcome of their work. However there is no common and established understanding within the profession on these themes. Contemporary planning theory, practice and education is characterised by the parallel existence of multiple, often contradictory schools of thought. What values and perspectives are held by the next generation of planning professionals as they emerge from contemporary planning programs? This preliminary investigation seeks to identify the views and perspectives of early career planners on the purpose and role of planning, the degree to which planning is oriented on the future and the nature of the public interest, using various schools of planning thought as a thematic framework. In the current phase of a larger project, extant students and recent graduates from planning courses at three Queensland universities were surveyed electronically to ascertain their views, with plans to undertake a broader study of similar populations across Australia. Within the current pilot, students and graduates did not identify strongly with a single school of planning thought, but favoured contrasting rational and collaborative definitions of the role and purpose of planning and the public interest and pragmatic concepts of partial knowledge of the future and the value of experience in managing present issues.

Family-based programmes for preventing smoking by children and adolescents

BACKGROUND: There is evidence that children's decisions to smoke are influenced by family and friends. OBJECTIVES: To assess the effectiveness of interventions to help family members to strengthen non-smoking attitudes and promote non-smoking by children and other family members. SEARCH STRATEGY: We searched 14 electronic bibliographic databases, including the Cochrane Tobacco Addiction Group specialized register, MEDLINE, EMBASE, PsycINFO and CINAHL. We also searched unpublished material, and the reference lists of key articles. We performed both free-text Internet searches and targeted searches of appropriate websites, and we hand-searched key journals not available electronically. We also consulted authors and experts in the field. The most recent search was performed in July 2006. SELECTION CRITERIA: Randomized controlled trials (RCTs) of interventions with children (aged 5-12) or adolescents (aged 13-18) and family members to deter the use of tobacco. The primary outcome was the effect of the intervention on the smoking status of children who reported no use of tobacco at baseline. Included trials had to report outcomes measured at least six months from the start of the intervention. DATA COLLECTION AND ANALYSIS: We reviewed all potentially relevant citations and retrieved the full text to determine whether the study was an RCT and matched our inclusion criteria. Two authors independently extracted study data and assessed them for methodological quality. The studies were too limited in number and quality to undertake a formal meta-analysis, and we present a narrative synthesis. MAIN RESULTS: We identified 19 RCTs of family interventions to prevent smoking. We identified five RCTs in Category 1 (minimal risk of bias on all counts); nine in Category 2 (a risk of bias in one or more areas); and five in Category 3 (risks of bias in design and execution such that reliable conclusions cannot be drawn from the study).Considering the fourteen Category 1 and 2 studies together: (1) four of the nine that tested a family intervention against a control group had significant positive effects, but one showed significant negative effects; (2) one of the five RCTs that tested a family intervention against a school intervention had significant positive effects; (3) none of the six that compared the incremental effects of a family plus a school programme to a school programme alone had significant positive effects; (4) the one RCT that tested a family tobacco intervention against a family non-tobacco safety intervention showed no effects; and (5) the one trial that used general risk reduction interventions found the group which received the parent and teen interventions had less smoking than the one that received only the teen intervention (there was no tobacco intervention but tobacco outcomes were measured). For the included trials the amount of implementer training and the fidelity of implementation are related to positive outcomes, but the number of sessions is not. AUTHORS' CONCLUSIONS: Some well-executed RCTs show family interventions may prevent adolescent smoking, but RCTs which were less well executed had mostly neutral or negative results. There is thus a need for well-designed and executed RCTs in this area.

Civil Procedure : Commentary and Materials (5th ed.)

This book provides a comprehensive analysis of the practical and theoretical issues encountered in Australian civil procedure, including alternative dispute resolution. Each chapter features in-depth questions and notes together with lists of further reading to aid understanding of the issue. It also examines and discusses each substantive and procedural step in the trial process. Topics include jurisdiction of a court to consider a matter, alternative dispute resolution. limitations of actions, commencing proceedings, pleading, gathering evidence, trial and appeal, costs and practice directions. Each of the state, territory and federal procedures is covered.

Advanced battery storage control for an autonomous microgrid

A new control method for battery storage to maintain acceptable voltage profile in autonomous microgrids is proposed in this article. The proposed battery control ensures that the bus voltages in the microgrid are maintained during disturbances such as load change, loss of micro-sources, or distributed generations hitting power limit. Unlike the conventional storage control based on local measurements, the proposed method is based on an advanced control technique, where the reference power is determined based on the voltage drop profile at the battery bus. An artificial neural network based controller is used to determine the reference power needed for the battery to hold the microgrid voltage within regulation limits. The pattern of drop in the local bus voltage during power imbalance is used to train the controller off-line. During normal operation, the battery floats with the local bus voltage without any power injection. The battery is charged or discharged during the transients with a high gain feedback loop. Depending on the rate of voltage fall, it is switched to power control mode to inject the reference power determined by the proposed controller. After a defined time period, the battery power injection is reduced to zero using slow reverse-droop characteristics, ensuring a slow rate of increase in power demand from the other distributed generations. The proposed control method is simulated for various operating conditions in a microgrid with both inertial and converter interfaced sources. The proposed battery control provides a quick load pick up and smooth load sharing with the other micro-sources in a disturbance. With various disturbances, maximum voltage drop over 8% with conventional energy storage is reduced within 2.5% with the proposed control method.