J-Circos : an interactive Circos plotter

Circos plots are graphical outputs that display three dimensional chromosomal interactions and fusion transcripts. However, the Circos plot tool is not an interactive visualization tool, but rather a figure generator. For example, it does not enable data to be added dynamically, nor does it provide information for specific data points interactively. Recently, an R-based Circos tool (RCircos) has been developed to integrate Circos to R, but similarly, Rcircos can only be used to generate plots. Thus, we have developed a Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into JCircos using flat data formats, as well as from the GUI. J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data.

Is there a potential relationship between prior h amstring strain injury and increased risk for future a nterior cruciate ligament injury?

Hamstring strain injuries (HSIs) are the most prevalent injury in a number of sports, and while anterior cruciate ligament (ACL) injuries are less common, they are far more severe and have long-term implications, such as an increased risk of developing osteoarthritis later in life. Given the high incidence and severity of these injuries, they are key targets of injury preventive programs in elite sport. Evidence has shown that a previous severe knee injury (including ACL injury) increases the risk of HSI; however, whether the functional deficits that occur after HSI result in an increased risk of ACL injury has yet to be considered. In this clinical commentary, we present evidence that suggests that the link between previous HSI and increased risk of ACL injury requires further investigation by drawing parallels between deficits in hamstring function after HSI and in women athletes, who are more prone to ACL injury than men athletes. Comparisons between the neuromuscular function of the male and female hamstring has shown that women display lower hamstring-to-quadriceps strength ratios during isokinetic knee flexion and extension, increased activation of the quadriceps compared with the hamstrings during a stop-jump landing task, a greater time required to reach maximal isokinetic hamstring torque, and lower integrated myoelectrical hamstring activity during a sidestep cutting maneuver. Somewhat similarly, in athletes with a history of HSI, the previously injured limb, compared with the uninjured limb, displays lower eccentric knee flexor strength, a lower hamstrings-to-quadriceps strength ratio, lower voluntary myoelectrical activity during maximal knee flexor eccentric contraction, a lower knee flexor eccentric rate of torque development, and lower voluntary myoelectrical activity during the initial portion of eccentric contraction. Given that the medial and lateral hamstrings have different actions at the knee joint in the coronal plane, which hamstring head is previously injured might also be expected to influence the likelihood of future ACL. Whether the deficits in function after HSI, as seen in laboratory-based studies, translate to deficits in hamstring function during typical injurious tasks for ACL injury has yet to be determined but should be a consideration for future work.

Grateful fateful sunshine rain

Grateful Fateful Sunshine Rain is a permanent public artwork commissioned by Aria Property Group through a competitive process for the Austin apartment building in South Brisbane. Artist Statement: Residents of Brisbane have a complex relationship with weather. As the capital of the Sunshine State, weather is an integral part of the city’s cultural identity. Weather deeply affects the mood of the city – from the excitement of scantily clad partygoers on balmy December evenings and late February’s lethargy, to the deepening anxiety that emerges after 100 days of rain (or more commonly, 100 days without rain). With a brief nod to the city’s – now decommissioned – iconic MCL weather beacon, Grateful Fateful Sunshine Rain taps into this aspect of Brisbane’s psyche with poetic, illuminated visualisations of real-time weather forecasts issued by the Bureau of Meteorology. Each evening, the artwork downloads tomorrow’s forecast from the Bureau of Meteorology website. Data including, current local temperature, humidity, wind speed & direction, precipitation (rain, hail etc), are used to generate a lighting display that conveys how tomorrow will feel. The artwork’s background colour indicates the expected temperature – from cold blues through mild pastel pinks and blues to bright hot oranges and reds. White fluffy clouds roll across the artwork if cloud is predicted. The density of these clouds indicates the level of cover whilst movement indicates expected wind speed and direction. If rain is predicted, sparkles of white light will appear on top of whichever background colour is chosen for the next day’s temperature. Sparkles appear constantly before wet, drizzly days, and intermittently if scattered showers are predicted. Intermittent, but more intense sparkles appear before rain storms or thunderstorms. Research Contribution: The work has made contributions to the field in the way it rethinks approaches to the conceptualization, design and realization of illuminated urban media. This has led to new theorizations of urban media, which consider light and illumination can be used to convey meaningful data. The research has produced new methods for controlling illumination systems using tools and techniques typically employed in computation arts. It has also develop methods and processes for the design and production of illuminated urban media architectures that are connected to real time data sources, and do which not follow the assumed logics of screen based media and displays.

Social network resilience following organisational change

This paper presents two key findings from a longitudinal study examining the dynamics of social networks during organisational change. One, the degree to which users seek new sources of information while adapting to the change. Two, the degree to which social networks display structural resilience when undergoing significant structural and technological change. Users reported an increase in advice ties post-implementation, however a proportionally higher increase in ties within their work group compared to the wider network was identified. The results also supported the supposition that while IT driven change may initially disrupt social networks some networks possess a high degree of resilience, with key players reasserting their original positions of influence following the initial phase of change related disruption.

Playful interactions for people with intellectual disabilities

For people with intellectual disabilities, there are significant barriers to inclusion in socially cooperative endeavors. This paper investigates the effectiveness of Stomp, a tangible user interface (TUI) designed to provide new participatory experiences for people with intellectual disability. Results from an observational study reveal the extent to which the Stomp system supports social and physical interaction. The tangible, spatial, and embodied qualities of Stomp result in an experience that does not rely on the acquisition of specific competencies before interaction and engagement can occur.

A generalised deficit can account for problems in facial emotion recognition in schizophrenia

Neuroimaging research has shown localised brain activation to different facial expressions. This, along with the finding that schizophrenia patients perform poorly in their recognition of negative emotions, has raised the suggestion that patients display an emotion specific impairment. We propose that this asymmetry in performance reflects task difficulty gradations, rather than aberrant processing in neural pathways subserving recognition of specific emotions. A neural network model is presented, which classifies facial expressions on the basis of measurements derived from human faces. After training, the network showed an accuracy pattern closely resembling that of healthy subjects. Lesioning of the network led to an overall decrease in the network’s discriminant capacity, with the greatest accuracy decrease to fear, disgust and anger stimuli. This implies that the differential pattern of impairment in schizophrenia patients can be explained without having to postulate impairment of specific processing modules for negative emotion recognition.

Memory and Epileptogenesis in Complex Biological and Simulated Systems

Oscillations of neural activity may bind widespread cortical areas into a neural representation that encodes disparate aspects of an event. In order to test this theory we have turned to data collected from complex partial epilepsy (CPE) patients with chronically implanted depth electrodes. Data from regions critical to word and face information processing was analyzed using spectral coherence measurements. Similar analyses of intracranial EEG (iEEG) during seizure episodes display HippoCampal Formation (HCF)—NeoCortical (NC) spectral coherence patterns that are characteristic of specific seizure stages (Klopp et al. 1996). We are now building a computational memory model to examine whether spatio-temporal patterns of human iEEG spectral coherence emerge in a computer simulation of HCF cellular distribution, membrane physiology and synaptic connectivity. Once the model is reasonably scaled it will be used as a tool to explore neural parameters that are critical to memory formation and epileptogenesis.

DNA molecules and human therapeutics

Nucleic acid molecules are championing a new generation of reverse engineered biopharmaceuticals. In terms of potential application in gene medicine, plasmid DNA (pDNA) vectors have exceptional therapeutic and immunological profiles as they are free from safety concerns associated with viral vectors, display non-toxicity and are simpler to develop. This review addresses the potential applications of pDNA molecules in vaccine design/development and gene therapy via recombinant DNA technology as well as a staged delivery mechanism for the introduction of plasmid-borne gene to target cells via the nasal route.

Three dimensional in-vitro models for studying cancer angiogenesis

Introduction Hydrogels prepared from star-shaped poly(ethylene glycol) (PEG) and maleimide-functionalized heparin provide a potential matrix for use in developing three dimensional (3D) models. We have previously demonstrated that these hydrogels support the cultivation of human umbilical vein endothelial cells (HUVECs). We extend this body of work to study the ability to create an extracellular matrix (ECM)-like model to study breast and prostate cancer cell growth in 3D. Also, we investigate the ability to produce a tri-culture mimicking tumour angiogenesis with cancer spheroids, HUVECs and mesenchymal stem cells (MSCs). Materials and Methods The breast cancer cell lines, MCF-7 and MDA-MB-231, and prostate cancer cell lines, LNCaP and PC3, were seeded into starPEG-heparin hydrogels and grown for 14 Days to analyze the effects of varying hydrogel stiffness on spheroid development. Resulting hydrogel constructs were analyzed via proliferation assays, light microscopy, and immunostaining. Cancer cell lines were then seeded into starPEG-heparin hydrogels functionalized with growth factors as spheroids with HUVECs and MSCs and grown as a tri-culture. Cultures were analyzed via immunostaining and observed using confocal microscopy. Results Cultures prepared in MMP-cleavable starPEG-heparin hydrogels display spheroid formation in contrast to adherent growth on tissue culture plastic. Small differences were visualized in cancer spheroid growth between different gel stiffness across the range of cell lines. Cancer cell lines were able to be co-cultivated with HUVECs and MSC. Interaction was visualized between tumours and HUVECs via confocal microscopy. Further studies intend to further optimize and mimic the ECM environment of in-situ tumour angiogenesis. Discussion Our results confirm the suitability of hydrogels constructed from starPEG-heparin for HUVEC and MSC co-cultivation with cancer cell lines to study cell-cell and cell-matrix interactions in a 3D environment. This represents a step forward in the development of 3D culture models to study the pathomechanisms of breast and prostate cancer.

Developing a three-dimensional in-vitro cell culture model for studying breast and prostate cancer using starPEG-heparin hydrogels

Introduction Hydrogels prepared from poly(ethylene glycol) (PEG) and maleimide-functionalized heparin provide a potential matrix for use in developing three dimensional (3D) models. We have previously demonstrated that these hydrogels support the cultivation of human umbilical vein endothelial cells (HUVECs) (1). We extend this body of work to study the ability to create an extracellular matrix (ECM)-like model to study breast and prostate cancer cell growth in 3D. Also, we investigate the ability to produce a tri-culture mimicking tumour angiogenesis with cancer spheroids, HUVECs and mesenchymal stem cells (MSC). Materials and Methods The breast cancer cell lines, MCF-7 and MDA-MB-231, and prostate cancer cell lines, LNCaP and PC3, were seeded into starPEG-heparin hydrogels and grown for 14 Days to analyse the effects of varying hydrogel stiffness on spheroid development. Resulting hydrogel constructs were analyzed via Alamar Blue assays, light microscopy, and immunofluorescence staining for cytokeratin 8/18, Ki67 and E-Cadherin. Cancer cell lines were then pre-grown in hydrogels for 5-7 days and then re-seeded into starPEG-heparin hydrogels functionalised with RGD, SDF-1, bFGF and VEGF as spheroids with HUVECs and MSC and grown for 14 days as a tri-culture in Endothelial Cell Growth Medium (ECGM; Promocell). Cell lines were also seeded as a single cell suspension into the functionalised tri-culture system. Cultures were fixed in 4% paraformaldehyde and analysed via immunostaining for Von Willebrand Factor and CD31, as well as the above mentioned markers, and observed using confocal microscopy. Results Cultures prepared in MMP-cleavable starPEG-heparin hydrogels display spheroid formation in contrast to adherent growth on tissue culture plastic. Small differences were visualised in cancer spheroid growth between different gel stiffness across the range of cell lines. Cancer cell lines were able to be co-cultivated with HUVECs and MSC. HUVEC tube formation and cancer line spheroid formation occured after 3-4 days. Interaction was visualised between tumours and HUVECs via confocal microscopy. Slightly increased interaction was seen between cancer tumours and micro-vascular tubes when seeded as single cells compared with the pre-formed spheroid approach. Further studies intend to utilise cytokine gradients to further optimise the ECM environment of in situ tumour angiogenesis. Discussion and Conclusions Our results confirm the suitability of hydrogels constructed from starPEG-heparin for HUVECs and MSC co-cultivation with cancer cell lines to study cell-cell and cell-matrix interactions in a 3D environment. This represents a step forward in the development of 3D culture models to study the pathomechanisms of breast and prostate cancer. References 1. Tsurkan MV, Chwalek K, Prokoph S, Zieris A, Levental KR, Freudenberg U, Werner C. Advanced Materials. 25, 2606-10, 2013. Disclosures The authors declare no conflicts of interest

Suppression of cluster ions during rapidly increasing particle number concentration events in the environment

We show that the cluster ion concentration (CIC) in the atmosphere is significantly suppressed during events that involve rapid increases in particle number concentration (PNC). Using a neutral cluster and air ion spectrometer, we investigated changes in CIC during three types of particle enhancement processes – new particle formation, a bushfire episode and an intense pyrotechnic display. In all three cases, the total CIC decreased with increasing PNC, with the rate of decrease being greater for negative CIC than positive. We attribute this to the greater mobility, and hence the higher attachment coefficient, of negative ions over positive ions in the air. During the pyrotechnic display, the rapid increase in PNC was sufficient to reduce the CIC of both polarities to zero. At the height of the display, the negative CIC stayed at zero for a full 10 min. Although the PNCs were not significantly different, the CIC during new particle formation did not decrease as much as during the bushfire episode and the pyrotechnic display. We suggest that the rate of increase of PNC, together with particle size, also play important roles in suppressing CIC in the atmosphere.

When an eco-feedback system joins the family

The dynamic, chaotic, intimate and social nature of family life presents many challenges when designing interactive systems in the household space. This paper presents findings from a whole-of-family approach to studying the use of an energy awareness and management system called “Ecosphere”. Using a novel methodology of inviting 12 families to create their own self-authored videos documenting their energy use, we report on the family dynamics and nuances of family life that shape and affect this use. Our findings suggest that the momentum of existing family dynamics in many cases obstructs behaviour change and renders some family members unaware of energy consumption despite the presence of an energy monitor display in the house. The implication for eco-feedback design is that it needs to recognise and respond to the kinds of family relations into which the system is embedded. In response, we suggest alternative ways of sharing energy-related information among families and incentivising engagement among teenagers.

Using augmented video to test in-car user experiences of context analog HUDs

Automotive interactive technologies represent an exemplar challenge for user experience (UX) designers, as the concerns for aesthetics, functionality and usability add up to the compelling issues of safety and cognitive demand. This extended abstract presents a methodology for the user-centred creation and evaluation of novel in-car applications, involving real users in realistic use settings. As a case study, we present the methodologies of an ideation workshop in a simulated environment and the evaluation of six design idea prototypes for in-vehicle head up display (HUD) applications using a semi-naturalistic drive. Both methods rely on video recordings of real traffic situations that the users are familiar with and/or experienced themselves. The extended abstract presents experiences and results from the evaluation and reflection on our methods.

If you're going to be a leader, at least act like it! Prejudice towards women who are tentative in leader roles

Role congruity theory predicts prejudice towards women who meet the agentic requirements of the leader role. In line with recent findings indicating greater acceptance of agentic behaviour from women, we find evidence for a more subtle form of prejudice towards women who fail to display agency in leader roles. Using a classic methodology, the agency of male and female leaders was manipulated using assertive or tentative speech, presented through written (Study 1, N = 167) or verbal (Study 2, N = 66) communications. Consistent with predictions, assertive women were as likeable and influential as assertive men, while being tentative in leadership reduced the likeability and influence of women, but not of men. Although approval of agentic behaviour from women in leadership reflects progress, evidence that women are quickly singled out for disapproval if they fail to show agency is important for understanding how they continue to be at a distinct disadvantage to men in leader roles.

DNA molecules and future blockbuster therapeutics

Deoxyribonucleic acid molecules are heralding a new generation of reverse - engineered biopharmaceuticals. In terms of potential application in gene medicine, plasmid DNA (pDNA) vectors have exceptional therapeutic and immunological profiles as they are free from safety concerns associated with viral vectors, display non-toxicity and are simpler to develop. This presentation will discuss the potential applications of pDNA molecules in vaccine development and gene therapy, pilot-scale production of pDNA-based biopharmaceuticals and the controlled delivery of therapeutic sequences in biodegradable polymers to different target cells via the nasal route.