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.

Gone Girl and the mediatization of crime

Gone Girl (David Fincher, 2014) will not be remembered for its representation of journalists, although both lead characters are, as the narrative opens in 2012, magazine writers made redundant in the wake of the 2008 global financial crisis. To this extent they personify the “death of journalism” narrative of recent years in the United States, but we never see them in a newsroom or doing journalistic work. The marriage of Nick and Amy Dunne (Ben Affleck and Rosamund Pike) is cast as a victim of, among other things, the downturn in the US economy which accompanied the credit crunch. But this is not the subject of Gone Girl, so much as a context for the marital dysfunctionality at the heart of its plot...

Investigation into chemistry of new particle formation and growth in subtropical urban environment

The role of different chemical compounds, particularly organics, involved in the new particle formation (NPF) and its consequent growth are not fully understood. Therefore, this study was conducted to investigate the chemistry of aerosol particles during NPF events in an urban subtropical environment. Aerosol chemical composition was measured along with particle number size distribution (PNSD) and several other air quality parameters at five sites across an urban subtropical environment. An Aerodyne compact Time-of-Flight Aerosol Mass Spectrometer (c-TOF-AMS) and a TSI Scanning Mobility Particle Sizer (SMPS) measured aerosol chemical composition and PNSD, respectively. Five NPF events, with growth rates in the range 3.3-4.6 nm, were detected at two sites. The NPF events happened on relatively warmer days with lower humidity and higher solar radiation. Temporal percent fractions of nitrate, sulphate, ammonium and organics were modelled using the Generalised Additive Model (GAM), with a basis of penalised spline. Percent fractions of organics increased after the NPF events, while the mass fraction of ammonium and sulphate decreased. This uncovered the important role of organics in the growth of newly formed particles. Three organic markers, factors f43, f44 and f57, were calculated and the f44 vs f43 trends were compared between nucleation and non-nucleation days. f44 vs f43 followed a different pattern on nucleation days compared to non-nucleation days, whereby f43 decreased for vehicle emission generated particles, while both f44 and f43 decreased for NPF generated particles. It was found for the first time that vehicle generated and newly formed particles cluster in different locations on f44 vs f43 plot and this finding can be used as a tool for source apportionment of measured particles.

Social media, audiences, and audience co-creativity in contemporary performance: Restoring balance?

Producers, technicians, performers, audiences and critics are all critical components of the performing arts ecology – critical components of an ecosystem that have to come together into some sort of productive relationship if the performing arts are to be vital, viable and successful. Different performance practices developed in different times, spaces and places do, of course, connect these players in different ways as part of their attempt to achieve their own definition of success, be it based on entertainment, educational, expression, empowerment, or something else. In some contemporary performance practices, social media platforms, applications and processes are seen to have significant potential to restore balance to the relationship between performer and audience, providing audiences with more power to participate in a performance event. In this paper, I investigate prevailing assumptions about social media’s power to democratise performance practice, or, at least, develop more co-creative performance practices in which producers, performers and audiences participate actively before, during and after the event. I focus, in particular, on the use of social media as a means of developing a participatory aesthetic in which an audience member is asked to contribute to the cast of characters, plot or progression of a performance. Although diverse – from performances streamed online, to performances that offer transmedia components the audience can use to learn more about character, context and plot online, to performances that incorporate online voting, liking or linking, to performances that unfold fully online on websites, blogs, microblogs or other social media platforms – what a lot of uses of social media in contemporary performance today share is a desire to encourage audiences to reflect on their role in making, and making meaning, of the event. In this paper I interrogate if, and if so how, this democratises or develops deeper levels of co-creativity in the relationship between producers, performers and audiences.

A new constraint handling method for wind farm layout optimization with lands owned by different owners

For wind farm optimizations with lands belonging to different owners, the traditional penalty method is highly dependent on the type of wind farm land division. The application of the traditional method can be cumbersome if the divisions are complex. To overcome this disadvantage, a new method is proposed in this paper for the first time. Unlike the penalty method which requires the addition of penalizing term when evaluating the fitness function, it is achieved through repairing the infeasible solutions before fitness evaluation. To assess the effectiveness of the proposed method on the optimization of wind farm, the optimizing results of different methods are compared for three different types of wind farm division. Different wind scenarios are also incorporated during optimization which includes (i) constant wind speed and wind direction; (ii) various wind speed and wind direction, and; (iii) the more realisticWeibull distribution. Results show that the performance of the new method varies for different land plots in the tested cases. Nevertheless, it is found that optimum or at least close to optimum results can be obtained with sequential land plot study using the new method for all cases. It is concluded that satisfactory results can be achieved using the proposed method. In addition, it has the advantage of flexibility in managing the wind farm design, which not only frees users to define the penalty parameter but without limitations on the wind farm division.

Plain packaging for the Pacific Rim: The Trans-Pacific Partnership and tobacco control

Big Tobacco has been engaged in a dark, shadowy plot and conspiracy to hijack the Trans-Pacific Partnership Agreement (TPP) and undermine tobacco control measures – such as graphic health warnings and the plain packaging of tobacco products... In the context of this heavy lobbying by Big Tobacco and its proxies, this chapter provides an analysis of the debate over trade, tobacco, and the TPP. This discussion is necessarily focused on the negotiations of the free trade agreement – the shadowy conflicts before the finalisation of the text. This chapter contends that the trade negotiations threaten hard-won gains in public health – including international developments such as the WHO Framework Convention on Tobacco Control, and domestic measures, such as graphic health warnings and the plain packaging of tobacco products. It maintains that there is a need for regional trade agreements to respect the primacy of the WHO Framework Convention on Tobacco Control. There is a need both to provide for an open and transparent process regarding such trade negotiations, as well as a due and proper respect for public health in terms of substantive obligations. Part I focuses on the debate over the intellectual property chapter of the TPP, within the broader context of domestic litigation against Australia’s plain tobacco packaging regime and associated WTO disputes. Part II examines the investment chapter of the TPP, taking account of ongoing investment disputes concerning tobacco control and the declared approaches of Australia and New Zealand to investor-state dispute settlement. Part III looks at the discussion as to whether there should be specific text on tobacco control in the TPP, and, if so, what should be its nature and content. This chapter concludes that the plain packaging of tobacco products – and other best practices in tobacco control – should be adopted by members of the Pacific Rim.

Provisioning a 3.3 MW PhotoVoltaic generation system onto a distribution authority’s 11 kV rural feeder

This paper describes part of an engineering study that was undertaken to demonstrate that a multi-megawatt Photovoltaic (PV) generation system could be connected to a rural 11 kV feeder without creating power quality issues for other consumers. The paper concentrates solely on the voltage regulation aspect of the study as this was the most innovative part of the study. The study was carried out using the time-domain software package, PSCAD/EMTDC. The software model included real time data input of actual measured load and scaled PV generation data, along with real-time substation voltage regulator and PV inverter reactive power control. The outputs from the model plot real-time voltage, current and power variations throughout the daily load and PV generation variations. Other aspects of the study not described in the paper include the analysis of harmonics, voltage flicker, power factor, voltage unbalance and system losses.

Damned to fame: The moral rights of the Beckett estate

The Company B production of Samuel Beckett's Waiting for Godot raises important questions about copyright law, moral rights, and dramatic works. The playwright's nephew and executor, Edward Beckett, threatened to bring a legal action against the Sydney company for breach of contract on the grounds that unauthorised music appeared in the production. The Company B production denied that the contract made any such express provisions. The director Neil Armfield complained: 'In coming here with its narrow prescriptions, its dead controlling hand, the Beckett estate seems to me to be the enemy of art'. In the biography Damned to fame, James Knowlson documents a number of other proceedings taken by Beckett and his agents to control the productions of his work: 'He was often represented as a tyrannical figure, an arch-controller of his work, ready to unleash fiery thunderbolts onto the head of any bold, innovative director, unwilling to follow his text and stage directions to the last counted dot and precisely timed pause.' However, Knowlson notes that Beckett was inconsistent in his willingness to use legal action: 'It made a tremendous difference if he liked and respected the persons involved or if he had been able to listen to their reasons for wanting to attempt something highly innovative or even slightly different'. Famously, in 1988, Beckett brought legal action against a Dutch theatre company, which wanted to stage a production of Waiting for Godot, with women acting all the roles. His lawyer argued that the integrity of the text was violated because actresses were substituted for the male actors asked for in the text. The judge in the Haarlem court ruled that the integrity of the play had not been violated, because the performance showed fidelity to the dialogue and the stage directions of the play. By contrast, in 1992, a French court held a stage director was liable for an infringement of Beckett's moral right of integrity because the director had staged Waiting for Godot with the two lead roles played by women. In 1998, a United States production of Waiting for Godot with a racially mixed cast attracted legal threats amid accusations it had 'injected race into the play'. In the 2000 New York Fringe Festival, a company made light of this ongoing conflict between the Beckett estate and artistic directors. The work was entitled: The complete lost works of Samuel Beckett as found in an envelope (partially burned) in a dustbin in Paris labelled 'Never to be performed. Never. Ever. EVER! Or I'll sue! I'LL SUE FROM THE GRAVE!'. The plot concerned a fight between three producers and the Beckett estate. In the wake of such disputes, Beckett and later his estate sought to tighten production contracts to state that no additions, omissions or alterations should be made to the text of the play or the stage directions and that no music, special effects or other supplements should be added without prior consent.

When Japanese law goes pop

Japanese law is going ‘pop’. Since the turn of the century, Japanese popular culture, especially prime-time television, has dedicated more time to legal themes, characters and settings. Lawyers, overwhelmingly women, are the heroes in both dramatic and comedic television series (Nakamura, 2007). Courtroom battles are the scene for plot developments (Ishikawa, 2004). Practising lawyers are the new celebrities, joining actors and singers on the light entertainment talk show circuit. To be sure, law is not a new thematic preoccupation on Japanese network television. Nor is it one that has become so dominant that it overshadows more traditional genres such as workplace romantic comedies, coming-of-age dramas or family soap operas (eg, Dissanayake, 2012, p._194). But, its growing presence on the silver screen in twenty-first-century Japan is a trend that merits analysis. The purpose of this chapter is to explore that socio-legal significance. This presents theoretical and empirical challenges. Theoretically, is there explanatory potential in the link between law and popular culture in Japan? Empirically, does the greater embrace of law-related characters, plots and scenes in prime-time television series since 2001 provide compelling evidence of changing popular attitudes to law and legal process among Japanese viewers? The inspiration for both the title and theme of this chapter comes from Sherwin’s When Law Goes Pop (2000). But it departs from Sherwin in how it defines and analyses the issues. For Sherwin, ‘pop’ means ‘implosion’.

Electrochemical detection of benzo(a)pyrene and related DNA damage using DNA/hemin/nafion-graphene biosensor

A novel electrochemical biosensor, DNA/hemin/nafion–graphene/GCE, was constructed for the analysis of the benzo(a)pyrene PAH, which can produce DNA damage induced by a benzo(a)pyrene (BaP) enzyme-catalytic product. This biosensor was assembled layer-by-layer, and was characterized with the use of cyclic voltammetry, electrochemical impedance spectroscopy (EIS) and atomic force microscopy. Ultimately, it was demonstrated that the hemin/nafion–graphene/GCE was a viable platform for the immobilization of DNA. This DNA biosensor was treated separately in benzo(a)pyrene, hydrogen peroxide (H2O2) and in their mixture, respectively, and differential pulse voltammetry (DPV) analysis showed that an oxidation peak was apparent after the electrode was immersed in H2O2. Such experiments indicated that in the presence of H2O2, hemin could mimic cytochrome P450 to metabolize benzo(a)pyrene, and a voltammogram of its metabolite was recorded. The DNA damage induced by this metabolite was also detected by electrochemical impedance and ultraviolet spectroscopy. Finally, a novel, indirect DPV analytical method for BaP in aqueous solution was developed based on the linear metabolite versus BaP concentration plot; this method provided a new, indirect, quantitative estimate of DNA damage.

Excess water storage depth - A water management practice to control simetryn and thiobencarb runoff from paddy fields

Experiments were carried out to verify the effectiveness of the excess water storage depth (EWSD) in reducing runoff losses of simetryn and thiobencarb from paddy fields upon appreciable rainfall events. A paddy plot having an EWSD of 2 cm was effective in controlling runoff with the herbicide losses of less than 1% of the applied herbicides. Meanwhile, a plot with 0-cm EWSD lost 18.1 and 3.7% of the applied mass of simetryn and thiobencarb, respectively. Therefore, an appropriate EWSD is essential during the recommended 7-day water holding period in order to completely hold the water inside the field in case of rainfall.

Applicability of ELISA in pesticide monitoring to control runoff of bensulfuron-methyl and simetryn from paddy fields

The applicability of ELISA kits was evaluated as an alternative to monitor bensulfuron-methyl and simetryn behavior in paddy water under intermittent (Plot 1) and continuous (Plot 2) irrigation schemes. Simetryn concentrations in both plots decreased exponentially from the peak of the first day. However, the simetryn kit systematically underestimated by a factor of 0.79 as compared to the GC method. Bensulfuron-methyl concentrations exhibited similar dissipation kinetics in paddy water and the drainage water. The bensulfuron-methyl kit was capable of distinguishing spatial variations of concentrations in the paddy field. The ELISA kits clearly indicated differences in the loss of both herbicides between the two plots and therefore may be useful for evaluating the water management practice of pesticide runoff control in paddy fields.

Simulation of pesticide behavior in a paddy block by a pesticide fate and transport model

A simulation model (PCPF-B) was developed based on the PCPF-1 model to predict the runoff of pesticides from paddy plots to a drainage canal in a paddy block. The block-scale model now comprises three modules: (1) a module for pesticide application, (2) a module for pesticide behavior in paddy fields, and (3) a module for pesticide concentration in the drainage canal. The PCPF-B model was first evaluated by published data in a single plot and then was applied to predict the concentration of bensulfuron-methyl in one paddy block in the Sakura river basin, Ibaraki, Japan, where a detailed field survey was conducted. The PCPF-B model simulated well the behavior of bensulfuron-methyl in individual paddy plots. It also reflected the runoff pattern of bensulfuron-methyl at the block outlet, although overestimation of bensulfuronmethyl concentrations occurred due to uncertainty in water balance estimation. Application of water management practice such as water-holding period and seepage control also affected the performance of the model. A probabilistic approach may be necessary for a comprehensive risk assessment in large-scale paddy areas.

The atmospheric extinction of light

An experiment is described that enables students to understand the properties of atmospheric extinction due to Rayleigh scattering. The experiment requires the use of red, green and blue lasers attached to a traveling microscope or similar device. The laser beams are passed through an artificial atmosphere, made from milky water, at varying depths, before impinging on either a light meter or a photodiode integral to a Picotech Dr. DAQ ADC. A plot of measured spectral intensity verses depth reveals the contribution Rayleigh scattering has to the extinction coefficient. For the experiment with the light meter, the extinction coefficient for red, green and blue light in the milky sample of water were 0.27, 0.36 and 0.47 cm-1 respectively and 0.032, 0.037 and 0.092 cm-1 for the Picotech Dr. DAQ ADC.

Modelling growth rate of Penaeus monodon Fabricius in intensively managed ponds: effects of temperature, pond age and stocking density

Records of shrimp growth and water quality made during 12 crops from each of 48 ponds, over a period of 6.5 years, were provided by a Queensland, Australia, commercial shrimp farm, These data were analysed with a new growth model derived from the Gompertz model. The results indicate that water temperature, mortality and pond age significantly affect growth rates. After 180 days, shrimp reach 34 g at constant 30 degrees C, but only 15 g after the same amount of time at 20 degrees C. Mortality, through thinning the density of shrimp in the ponds, increased the growth rate, but the effect is small. With continual production, growth rates at first remained steady, then appeared to decrease for the sixth and seventh crop, after which they have increased steadily with each crop. It appears that conservative pond management, together with a gradual improvement in husbandry techniques, particularly feed management, brought about this change. This has encouraging implications for the long-term sustainability of the farming methods used. The growth model can be used to predict productivity, and hence, profitability, of new aquaculture locations or new production strategies.