Open access and scholarly books : Australian perspectives

This three-hour workshop tackles the crucial question of whether globally coordinated, market based approaches to funding open access monographs can support the unique needs of Australian research communities. The workshop takes place in the context of the release in August 2013 of the Book Industry Collaborative Council (BICC) report and especially the recommendations included in the chapter on scholarly book publishing in the humanities and social sciences. This workshop, with expert speakers from the BICC Committee and from across the scholarly publishing industry, will discuss the policy issues most likely to ensure that Australian scholarly communities and audiences are best served in an era of digital technology and globalisation. Australia must think globally and support developments that enhance the accessibility of publicly-funded research. Speakers will outline recent developments in scholarly monograph publishing including new Open Access initiatives and developments. Knowledge Unlatched, is one example of an attempt to create an internationally coordinated, market-based route to open access for Humanities, Arts and Social Sciences (HASS) monographs. Knowledge Unlatched, a not-for-profit London-based company is piloting a global library consortium approach to funding open access monographs and released its pilot program in early October with 28 titles from 13 publishers. The workshop invites discussion and debate from librarians, publishers, researchers and research funders on the role of international coordination and markets in securing a more open future for Australian HASS scholarship.

A multiscale road map of cancer spheroids : incorporating experimental and mathematical modelling to understand cancer progression

Computational models represent a highly suitable framework, not only for testing biological hypotheses and generating new ones but also for optimising experimental strategies. As one surveys the literature devoted to cancer modelling, it is obvious that immense progress has been made in applying simulation techniques to the study of cancer biology, although the full impact has yet to be realised. For example, there are excellent models to describe cancer incidence rates or factors for early disease detection, but these predictions are unable to explain the functional and molecular changes that are associated with tumour progression. In addition, it is crucial that interactions between mechanical effects, and intracellular and intercellular signalling are incorporated in order to understand cancer growth, its interaction with the extracellular microenvironment and invasion of secondary sites. There is a compelling need to tailor new, physiologically relevant in silico models that are specialised for particular types of cancer, such as ovarian cancer owing to its unique route of metastasis, which are capable of investigating anti-cancer therapies, and generating both qualitative and quantitative predictions. This Commentary will focus on how computational simulation approaches can advance our understanding of ovarian cancer progression and treatment, in particular, with the help of multicellular cancer spheroids, and thus, can inform biological hypothesis and experimental design.

Exploring pedestrian accessibility and walkability : insight from public place observations in inner-urban higher density Brisbane, Australia

As planners work to create more sustainable and liveable urban environments, a priority is to transition away from prioritising the automobile and towards enhancing the pedestrian experience. Thus, this research explores the experience of pedestrian accessibility in inner-urban higher-density Brisbane in Australia, drawing on findings from semi-structured in-depth interviews with 24 residents and over 100 hours of public place observations in three case-study neighbourhoods. The interviews took place in residents homes and explored their experience of higher density living and their neighbourhood, whilst observations were recorded through a combination of methods including photographs, sketch maps, recordings and field journals. Observation locations included retail and commercial space, roads, parkland and open space, with multiple observations at each location. A thematic analysis identified common themes in both interviews and the observations, with this paper focusing on residents’ lived experience in urban built environments. This analysis revealed that pedestrian accessibility is linked to access to local amenities and direct routes, aesthetics, sense of community, ownership of space and safety. In particular, observations revealed how pedestrian accessibility and route-taking works with, against or in spite of the design features of urban environments, as well as the importance of the social use of the built environment. Residents spoke about although walking quick and preferred for local amenities, the decision to walk was moderated by factors such as time of day and perceived safety. Measures to ensure and improve the pedestrian accessibility of urban areas needs to take into account the propensity for people to prefer and improvise direct routes (often to the detriment of traffic safety considerations), the importance of ongoing maintenance and upgrading of walking infrastructure and the importance of aesthetically pleasing and safe walking environments. By combining interviews and observations, this research highlights the current dominance of the automobile culture in Brisbane and the layers of meaning, experiences and complexity hidden within the pedestrian experience.

Phagocytosis of bacteria by olfactory ensheathing cells and Schwann cells

Opportunistic bacterial infections of the nasal cavity could potentially lead to infection of the brain if the olfactory or trigeminal nerves are colonised. The olfactory nerve may be a more susceptible route because primary olfactory neurons are in direct contact with the external environment. Peripheral glia are known to be able to phagocytose some species of bacteria and may therefore provide a defence mechanism against bacterial infection. As the nasal cavity is frequently exposed to bacterial infections, we hypothesised that the olfactory and trigeminal nerves within the nasal cavity could be subjected to bacterial colonisation and that the olfactory ensheathing cells and Schwann cells may be involved in responding to the bacterial invasion. We have examined the ability of mouse OECs and Schwann cells from the trigeminal nerve and dorsal root ganglia to phagocytose Escherichia coli and Burkholderia thailandensis in vitro. We found that all three sources of glia were equally able to phagocytose E. coli with 75-85% of glia having phagocytosed bacteria within 24h. We also show that human OECs phagocytosed E. coli. In contrast, the mouse OECs and Schwann cells had little capacity to phagocytose B. thailandensis. Thus subtypes of peripheral glia have similar capacities for phagocytosis of bacteria but show selective capacity for the two different species of bacteria that were examined. These results have implications for the understanding of the mechanisms of bacterial infections as well as for the use of glia for neural repair therapies.

Colonizing while migrating : how do individual enteric neural crest cells behave?

Background Directed cell migration is essential for normal development. In most of the migratory cell populations that have been analysed in detail to date, all of the cells migrate as a collective from one location to another. However, there are also migratory cell populations that must populate the areas through which they migrate, and thus some cells get left behind while others advance. Very little is known about how individual cells behave to achieve concomitant directional migration and population of the migratory route. We examined the behavior of enteric neural crest-derived cells (ENCCs), which must both advance caudally to reach the anal end and populate each gut region. Results The behaviour of individual ENCCs was examined using live imaging and mice in which ENCCs express a photoconvertible protein. We show that individual ENCCs exhibit very variable directionalities and speed; as the migratory wavefront of ENCCs advances caudally, each gut region is populated primarily by some ENCCs migrating non-directionally. After populating each region, ENCCs remain migratory for at least 24 hours. Endothelin receptor type B (EDNRB) signaling is known to be essential for the normal advance of the ENCC population. We now show that perturbation of EDNRB principally affects individual ENCC speed rather than directionality. The trajectories of solitary ENCCs, which occur transiently at the wavefront, were consistent with an unbiased random walk and so cell-cell contact is essential for directional migration. ENCCs migrate in close association with neurites. We showed that although ENCCs often use neurites as substrates, ENCCs lead the way, neurites are not required for chain formation and neurite growth is more directional than the migration of ENCCs as a whole. Conclusions Each gut region is initially populated by sub-populations of ENCCs migrating non-directionally, rather than stopping. This might provide a mechanism for ensuring a uniform density of ENCCs along the growing gut.

Design of an integrated platform for V2X wireless communications and positioning supporting C-ITS safety applications

In this paper, an integrated inter-vehicles wireless communications and positioning system supporting alternate positioning techniques is proposed to meet the requirements of safety applications of Cooperative Intelligent Transportation Systems (C-ITS). Recent advances have repeatedly demonstrated that road safety problems can be to a large extent addressed via a range of technologies including wireless communications and positioning in vehicular environments. The novel communication stack utilizing a dedicated frequency spectrum (e.g. at 5.9 GHz band), known as Dedicated Short-Range Communications (DSRC), has been particularly designed for Wireless Access in Vehicular Environments (WAVE) to support safety applications in highly dynamic environments. Global Navigation Satellite Systems (GNSS) is another essential enabler to support safety on rail and roads. Although current vehicle navigation systems such as single frequency Global Positioning System (GPS) receivers can provide route guidance with 5-10 meters (road-level) position accuracy, positioning systems utilized in C-ITS must provide position solutions with lane-level and even in-lane-level accuracies based on the requirements of safety applications. This article reviews the issues and technical approaches that are involved in designing a vehicular safety communications and positioning architecture; it also provides technological solutions to further improve vehicular safety by integrating the DSRC and GNSS-based positioning technologies.

The acetal concept : regioselective access toortho,ortho-diphenols via dibenzo-1,3-dioxepines

Traditional methods are ill-suited for the synthesis of ortho,ortho-biphenols, a structural motif found in many polyphenolic natural products, as well as synthetically useful compounds such as the chiral ligands binol, vapol, and vanol. The new route consists of a radical-based reaction of an acetal-tethered biphenyl ether substrate and subsequent hydrolytic cleavage of the dibenzo-1,3-dioxepine intermediate.

Co-thought gestures : supporting students to successfully navigate map tasks

This study considers the role and nature of co-thought gestures when students process map-based mathematics tasks. These gestures are typically spontaneously produced silent gestures which do not accompany speech and are represented by small movements of the hands or arms often directed toward an artefact. The study analysed 43 students (aged 10–12 years) over a 3-year period as they solved map tasks that required spatial reasoning. The map tasks were representative of those typically found in mathematics classrooms for this age group and required route finding and coordinate knowledge. The results indicated that co-thought gestures were used to navigate the problem space and monitor movements within the spatial challenges of the respective map tasks. Gesturing was most influential when students encountered unfamiliar tasks or when they found the tasks spatially demanding. From a teaching and learning perspective, explicit co-thought gesturing highlights cognitive challenges students are experiencing since students tended to not use gesturing in tasks where the spatial demands were low.

Synthesis and spectroscopic characterization of copper zinc aluminum nanoferrite particles

Copper doped zinc aluminium ferrites are synthesized by the solid-state reaction route is cubic crystalline with unit cell parameter varying from 8.39 to 8.89 Å. TEM pictures clearly indicating that fundamental unit is composed of octahedral and tetrahedral blocks and joined strongly shown in (a). EPR spectra is compositional dependent at lower Al/Cu concentration EPR spectra is due to Fe3+ and at a higher content of Al/Cu the EPR spectra is due to Cu2+. Absence of EPR spectra at room temperature indicates that the sample is perfectly ferromagnetic. EPR results at low temperature indicate that the sample is paramagnetic, and that copper is placed in the tetragonal elongation (B) site with magnetically non-equivalent ions in the unit cell having strong exchange coupling between them. This is shown in (b). (a) TEM image of ferrite with x = 0.15. (b) EPR spectrum of ferrite with x = 0.75.

Optimising offsets and bandwidths in vehicle traffic networks

Bandwidths and offsets are important components in vehicle traffic control strategies. This article proposes new methods for quantifying and selecting them. Bandwidth is the amount of green time available for vehicles to travel through adjacent intersections without the requirement to stop at the second traffic light. The offset is the difference between the starting-time of ``green'' periods at two adjacent intersections, along a given route. The core ideas in this article were developed during the 2013 Maths and Industry Study Group in Brisbane, Australia. Analytical expressions for computing bandwidth, as a function of offset, are developed. An optimisation model, for selecting offsets across an arterial, is proposed. Arterial roads were focussed upon, as bandwidth and offset have a greater impact on these types of road as opposed to a full traffic network. A generic optimisation-simulation approach is also proposed to refine an initial starting solution, according to a specified metric. A metric that reflects the number of stops, and the distance between stops, is proposed to explicitly reduce the dissatisfaction of road users, and to implicitly reduce fuel consumption and emissions. Conceptually the optimisation-simulation approach is superior as it handles real-life complexities and is a global optimisation approach. The models and equations in this article can be used in road planning and traffic control.

A multi-genome analysis approach enables tracking of the invasion of a single Russian wheat aphid (Diuraphis noxia) clone throughout the New World

This study investigated the population genetics, demographic history and pathway of invasion of the Russian wheat aphid (RWA) from its native range in Central Asia, the Middle East and Europe to South Africa and the Americas. We screened microsatellite markers, mitochondrial DNA and endosymbiont genes in 504 RWA clones from nineteen populations worldwide. Following pathway analyses of microsatellite and endosymbiont data, we postulate that Turkey and Syria were the most likely sources of invasion to Kenya and South Africa, respectively. Furthermore, we found that one clone transferred between South Africa and the Americas was most likely responsible for the New World invasion. Finally, endosymbiont DNA was found to be a high resolution population genetic marker, extremely useful for studies of invasion over a relatively short evolutionary history time frame. This study has provided valuable insights into the factors that may have facilitated the recent global invasion by this damaging pest.

Mechanism‐based selection of a potent kallikrein‐related peptidase 7 inhibitor from a versatile library based on the sunflower trypsin inhibitor SFTI‐1

Potent and specific enzyme inhibition is a key goal in the development of therapeutic inhibitors targeting proteolytic activity. The backbone-cyclized peptide, Sunflower Trypsin Inhibitor (SFTI-1) affords a scaffold that can be engineered to achieve both these aims. SFTI-1's mechanism of inhibition is unusual in that it shows fast-on/slow-off kinetics driven by cleavage and religation of a scissile bond. This phenomenon was used to select a nanomolar inhibitor of kallikrein-related peptidase 7 (KLK7) from a versatile library of SFTI variants with diversity tailored to exploit distinctive surfaces present in the active site of serine proteases. Inhibitor selection was achieved through the use of size exclusion chromatography to separate protease/inhibitor complexes from unbound inhibitors followed by inhibitor identification according to molecular mass ascertained by mass spectrometry. This approach identified a single dominant inhibitor species with molecular weight of 1562.4 Da, which is consistent with the SFTI variant SFTI-WCTF. Once synthesized individually this inhibitor showed an IC50 of 173.9 ± 7.6 nM against chromogenic substrates and could block protein proteolysis. Molecular modeling analysis suggested that selection of SFTI-WCTF was driven by specific aromatic interactions and stabilized by an enhanced internal hydrogen bonding network. This approach provides a robust and rapid route to inhibitor selection and design.

Public transport travel time variability definitions and monitoring

Public Transport Travel Time Variability (PTTV) is essential for understanding the deteriorations in the reliability of travel time, optimizing transit schedules and route choices. This paper establishes the key definitions of PTTV in which firstly include all buses, and secondly include only a single service from a bus route. The paper then analyzes the day-to-day distribution of public transport travel time by using Transit Signal Priority data. A comprehensive approach, using both parametric bootstrapping Kolmogorov-Smirnov test and Bayesian Information Creation technique is developed, recommends Lognormal distribution as the best descriptor of bus travel time on urban corridors. The probability density function of Lognormal distribution is finally used for calculating probability indicators of PTTV. The findings of this study are useful for both traffic managers and statisticians for planning and analyzing the transit systems.

All-environment visual place recognition with SMART

This paper presents Sequence Matching Across Route Traversals (SMART); a generally applicable sequence-based place recognition algorithm. SMART provides invariance to changes in illumination and vehicle speed while also providing moderate pose invariance and robustness to environmental aliasing. We evaluate SMART on vehicles travelling at highly variable speeds in two challenging environments; firstly, on an all-terrain vehicle in an off-road, forest track and secondly, using a passenger car traversing an urban environment across day and night. We provide comparative results to the current state-of-the-art SeqSLAM algorithm and investigate the effects of altering SMART’s image matching parameters. Additionally, we conduct an extensive study of the relationship between image sequence length and SMART’s matching performance. Our results show viable place recognition performance in both environments with short 10-metre sequences, and up to 96% recall at 100% precision across extreme day-night cycles when longer image sequences are used.

STI-GMaS : an open-source environment for simulation of sexually-transmitted infections

Background Sexually-transmitted pathogens often have severe reproductive health implications if treatment is delayed or absent, especially in females. The complex processes of disease progression, namely replication and ascension of the infection through the genital tract, span both extracellular and intracellular physiological scales, and in females can vary over the distinct phases of the menstrual cycle. The complexity of these processes, coupled with the common impossibility of obtaining comprehensive and sequential clinical data from individual human patients, makes mathematical and computational modelling valuable tools in developing our understanding of the infection, with a view to identifying new interventions. While many within-host models of sexually-transmitted infections (STIs) are available in existing literature, these models are difficult to deploy in clinical/experimental settings since simulations often require complex computational approaches. Results We present STI-GMaS (Sexually-Transmitted Infections – Graphical Modelling and Simulation), an environment for simulation of STI models, with a view to stimulating the uptake of these models within the laboratory or clinic. The software currently focuses upon the representative case-study of Chlamydia trachomatis, the most common sexually-transmitted bacterial pathogen of humans. Here, we demonstrate the use of a hybrid PDE–cellular automata model for simulation of a hypothetical Chlamydia vaccination, demonstrating the effect of a vaccine-induced antibody in preventing the infection from ascending to above the cervix. This example illustrates the ease with which existing models can be adapted to describe new studies, and its careful parameterisation within STI-GMaS facilitates future tuning to experimental data as they arise. Conclusions STI-GMaS represents the first software designed explicitly for in-silico simulation of STI models by non-theoreticians, thus presenting a novel route to bridging the gap between computational and clinical/experimental disciplines. With the propensity for model reuse and extension, there is much scope within STI-GMaS to allow clinical and experimental studies to inform model inputs and drive future model development. Many of the modelling paradigms and software design principles deployed to date transfer readily to other STIs, both bacterial and viral; forthcoming releases of STI-GMaS will extend the software to incorporate a more diverse range of infections.