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.

Recycling concrete: An undiscovered source of ultrafine particles

While concrete recycling is practiced worldwide, there are many unanswered questions in relation to ultrafine particle (UFP; Dp<100nm) emissions and exposure around recycling sites. In particular: (i) Does recycling produce UFPs and in what quantities? (ii) How do they disperse around the source? (iii) What impact does recycling have on ambient particle number concentrations (PNCs) and exposure? (iv) How effective are commonly used dust respirators to limit exposure? We measured size-resolved particles in the 5-560 nm range at five distances from a simulated concrete recycling source and found that: (i) the size distributions were multimodal, with up to ~93% of total PNC in the UFP size range; and (ii) dilution was a key particle transformation mechanism. UFPs showed a much slower decay rate, requiring ~62% more distance to reach 10% of their initial concentration compared with their larger counterparts. Compared with typical urban exposure during car journeys, exposure decay profiles showed up to ~5 times higher respiratory deposition within 10 m of the source. Dust respirators were found to remove half of total PNC; however the removal factor for UFPs was only ~57% of that observed in the 100-560 nm size range. These findings highlight a need for developing an understanding of the nature of the particles as well as for better control measures to limit UFP exposure.

Moving from outsider to insider : peer status and partnerships between electricity utilities and residential consumers

An electricity demand reduction project based on comprehensive residential consumer engagement was established within an Australian community in 2008. By 2011, both the peak demand and grid supplied electricity consumption had decreased to below pre-intervention levels. This case study research explored the relationship developed between the utility, community and individual consumer from the residential customer perspective through qualitative research of 22 residential households. It is proposed that an energy utility can be highly successful at peak demand reduction by becoming a community member and a peer to residential consumers and developing the necessary trust, access, influence and partnership required to create the responsive environment to change. A peer-community approach could provide policymakers with a pathway for implementing pro-environmental behaviour for low carbon communities, as well as peak demand reduction, thereby addressing government emission targets while limiting the cost of living increases from infrastructure expenditure.

Dense plasmas in magnetic traps : generation of focused ion beams with controlled ion-to-neutral flux ratios

Customized magnetic traps were developed to produce a domain of dense plasmas with a narrow ion beam directed to a particular area of the processed substrate. A planar magnetron coupled with an arc discharge source created the magnetic traps to confine the plasma electrons and generate the ion beam with the controlled ratio of ion-to-neutral fluxes. Images of the plasma jet patterns and numerical vizualizations help explaining the observed phenomena.

Novel use of faecal sterols to assess human faecal contamination in Antarctica : a likelihood assessment matrix for environmental monitoring

Wastewater containing human sewage is often discharged with little or no treatment into the Antarctic marine environment. Faecal sterols (primarily coprostanol) in sediments have been used for assessment of human sewage contamination in this environment, but in situ production and indigenous faunal inputs can confound such determinations. Using gas chromatography with mass spectral detection profiles of both C27 and C29 sterols, potential sources of faecal sterols were examined in nearshore marine sediments, encompassing sites proximal and distal to the wastewater outfall at Davis Station. Faeces from indigenous seals and penguins were also examined. Faeces from several indigenous species contained significant quantities of coprostanol but not 24-ethylcoprostanol, which is present in human faeces. In situ coprostanol and 24-ethylcoprostanol production was identified by co-production of their respective epi isomers at sites remote from the wastewat er source and in high total organic matter sediments. A C 29 sterols-based polyphasic likelihood assessment matrix for human sewage contamination is presented, which distinguishes human from local fauna faecal inputs and in situ production in the Antarctic environment. Sewage contamination was detected up to 1.5 km from Davis Station.

The path to stoichiometric composition of III–V binary quantum dots through plasma/ion-assisted self-assembly

Semiconductor III-V quantum dots (QDs) are particularly enticing components for the integration of optically promising III-V materials with the silicon technology prevalent in the microelectronics industry. However, defects due to deviations from a stoichiometric composition [group III: group V = 1] may lead to impaired device performance. This paper investigates the initial stages of formation of InSb and GaAs QDs on Si(1 0 0) through hybrid numerical simulations. Three situations are considered: a neutral gas environment (NG), and two ionized gas environments, namely a localized ion source (LIS) and a background plasma (BP) case. It is shown that when the growth is conducted in an ionized gas environment, a stoichiometric composition may be obtained earlier in the QD as compared to a NG. Moreover, the stoichiometrization time, tst, is shorter for the BP case compared to the LIS scenario. A discussion of the effect of ion/plasma-based tools as well as a range of process conditions on the final island size distribution is also included. Our results suggest a way to obtain a deterministic level of control over nanostructure properties (in particular, elemental composition and size) during the initial stages of growth which is a crucial step towards achieving highly tailored QDs suitable for implementation in advanced technological devices.

Relating urban airborne particle concentrations to shipping using carbon based elemental emission ratios

This study demonstrates a novel method for testing the hypothesis that variations in primary and secondary particle number concentration (PNC) in urban air are related to residual fuel oil combustion at a coastal port lying 30 km upwind, by examining the correlation between PNC and airborne particle composition signatures chosen for their sensitivity to the elemental contaminants present in residual fuel oil. Residual fuel oil combustion indicators were chosen by comparing the sensitivity of a range of concentration ratios to airborne emissions originating from the port. The most responsive were combinations of vanadium and sulfur concentration ([S], [V]) expressed as ratios with respect to black carbon concentration ([BC]). These correlated significantly with ship activity at the port and with the fraction of time during which the wind blew from the port. The average [V] when the wind was predominantly from the port was 0.52 ng.m-3 (87%) higher than the average for all wind directions and 0.83 ng.m-3 (280%) higher than that for the lowest vanadium yielding wind direction considered to approximate the natural background. Shipping was found to be the main source of V impacting urban air quality in Brisbane. However, contrary to the stated hypothesis, increases in PNC related measures did not correlate with ship emission indicators or ship traffic. Hence at this site ship emissions were not found to be a major contributor to PNC compared to other fossil fuel combustion sources such as road traffic, airport and refinery emissions.

Standing surface waves in a dust-contaminated large-area planar plasma source

The effect of charged particulates or dusts on surface wave produced microwave discharges is studied. The frequencies of the standing electromagnetic eigenmodes of large-area flat plasmas are calculated. The dusts absorb a significant amount of the plasma electrons and can lead to a modification of the electromagnetic field structure in the discharge by shifting the originally excited operating mode out of resonance. For certain given proportions of dusts, mode conversion is found to be possible. The power loss in the discharge is also increased because of dust-specific dissipations, leading to a decrease of the operating mode quality factor.

Effective control of ion fluxes over large areas by magnetic fields : from narrow beams to highly uniform fluxes

An effective control of the ion current distribution over large-area (up to 103 cm2) substrates with the magnetic fields of a complex structure by using two additional magnetic coils installed under the substrate exposed to vacuum arc plasmas is demonstrated. When the magnetic field generated by the additional coils is aligned with the direction of the magnetic field generated by the guiding and focusing coils of the vacuum arc source, a narrow ion density distribution with the maximum current density 117 A m-2 is achieved. When one of the additional coils is set to generate the magnetic field of the opposite direction, an area almost uniform over the substrate of 103 cm2 ion current distribution with the mean value of 45 A m-2 is achieved. Our findings suggest that the system with the vacuum arc source and two additional magnetic coils can be effectively used for the effective, high throughput, and highly controllable plasma processing.

Performance evaluation of three-level Z-source inverters under semiconductor-failure conditions

This paper evaluates and proposes various compensation methods for three-level Z-source inverters under semiconductor-failure conditions. Unlike the fault-tolerant techniques used in traditional three-level inverters, where either an extra phase-leg or collective switching states are used, the proposed methods for three-level Z-source inverters simply reconfigure their relevant gating signals so as to ride-through the failed semiconductor conditions smoothly without any significant decrease in their ac-output quality and amplitude. These features are partly attributed to the inherent boost characteristics of a Z-source inverter, in addition to its usual voltage-buck operation. By focusing on specific types of three-level Z-source inverters, it can also be shown that, for the dual Z-source inverters, a unique feature accompanying it is its extra ability to force common-mode voltage to zero even under semiconductor-failure conditions. For verifying these described performance features, PLECS simulation and experimental testing were performed with some results captured and shown in a later section for visual confirmation.

Modulation and control of three-phase paralleled Z-source inverters for distributed generation applications

This paper presents a modulation and controller design method for paralleled Z-source inverter systems applicable for alternative energy sources like solar cells, fuel cells, or variablespeed wind turbines with front-end diode rectifiers. A modulation scheme is designed based on simple shoot-through principle with interleaved carriers to give enhanced ripple reduction in the system. Subsequently, a control method is proposed to equalize the amount of power injected by the inverters in the grid-connected mode and also to provide reliable supply to sensitive loads onsite in the islanding mode. The modulation and controlling methods are proposed to have modular independence so that redundancy, maintainability, and improved reliability of supply can be achieved. The performance of the proposed paralleled Z-source inverter configuration is validated with simulations carried out using Matlab/Simulink/Powersim. Moreover, a prototype is built in the laboratory to obtain the experimental verifications.

Evaluation of resonant damping techniques for Z-source current-type inverter

For the renewable energy sources whose outputs vary continuously, a Z-source current-type inverter has been proposed as a possible buck-boost alternative for grid-interfacing. With a unique X-shaped LC network connected between its dc power source and inverter topology, Z-source current-type inverter is however expected to suffer from compounded resonant complications in addition to those associated with its second-order output filter. To improve its damping performance, this paper proposes the careful integration of Posicast or three-step compensators before the inverter pulse-width modulator for damping triggered resonant oscillations. In total, two compensators are needed for wave-shaping the inverter boost factor and modulation ratio, and they can conveniently be implemented using first-in first-out stacks and embedded timers of modern digital signal processors widely used in motion control applications. Both techniques are found to damp resonance of ac filter well, but for cases of transiting from current-buck to boost state, three-step technique is less effective due to the sudden intermediate discharging interval introduced by its non-monotonic stepping (unlike the monotonic stepping of Posicast damping). These findings have been confirmed both in simulations and experiments using an implemented laboratory prototype.

Dual Z-source inverter with three-level reduced common mode switching

This paper presents the design of a dual Z-source inverter that can be used with either a single dc source or two isolated dc sources. Unlike traditional inverters, the integration of a properly designed Z-source network and semiconductor switches to the proposed dual inverter allows buck-boost power conversion to be performed over a wide modulation range with three-level output waveforms generated. The connection of an additional transformer to the inverter ac output also allows all generic wye- or delta-connected loads with three-wire or four-wire configuration to be supplied by the inverter. Modulation-wise, the dual inverter can be controlled using a carefully designed carrier-based pulse-width modulation (PWM) scheme that always will ensure balanced voltage boosting of the Z-source network, while simultaneously achieving reduced common-mode switching. Because of the omission of dead-time delays in the dual inverter PWM scheme, its switched common-mode voltage can be completely eliminated, unlike in traditional inverters where narrow common-mode spikes are still generated. Under semiconductor failure conditions, the presented PWM schemes can easily be modified to allow the inverter to operate without interruption and for cases where two isolated sources are used, zero common-mode voltage can still be ensured. These theoretical findings together with the inverter practicality have been confirmed both in simulations using PSIM with Matlab/Simulink coupler and experimentally using a laboratory implemented inverter prototype.

Dual Z-source inverter with three-level reduced common-mode switching

This paper presents the design of a dual Z-source inverter that can be used with either a single dc source or two isolated dc sources. Unlike traditional inverters, the integration of a properly designed Z-source network and semiconductor switches to the proposed dual inverter allows buck-boost power conversion to be performed over a wide modulation range, with three-level output waveforms generated. The connection of an additional transformer to the inverter ac output also allows all generic wye-or delta-connected loads with three-wire or four-wire configuration to be supplied by the inverter. Modulationwise, the dual inverter can be controlled using a carefully designed carrier-based pulsewidth-modulation (PWM) scheme that will always ensure balanced voltage boosting of the Z-source network while simultaneously achieving reduced common-mode switching. Because of the omission of dead-time delays in the dual-inverter PWM scheme, its switched common-mode voltage can be completely eliminated, unlike in traditional inverters, where narrow common-mode spikes are still generated. Under semiconductor failure conditions, the presented PWM schemes can easily be modified to allow the inverter to operate without interruption, and for cases where two isolated sources are used, zero common-mode voltage can still be ensured. These theoretical findings, together with the inverter practicality, have been confirmed in simulations both using PSIM with Matlab/Simulink coupler and experimentally using a laboratory-implemented inverter prototype.

A pilot study to assess the appropriateness of prescribing from a collaborative pharmacist prescribing study in a surgical pre admission clinic

Background Current evidence to support non-medical prescribing is predominantly qualitative, with little evaluation of appropriateness. This study aims to evaluate the appropriateness of prescribing, and significance of omissions, from a doctor pharmacist collaborative prescribing model in an elective surgery pre admission clinic (PAC). Method A modified version of the Medication Appropriate Index (MAI) was developed, piloted and subsequently used by an expert panel, comprised of a surgeon, anaesthetist, clinical pharmacologist, pharmacist, resident medical officer (RMO) and clinical nurse. The tool was used to rate the appropriateness of prescribing of medications, and the significance of omissions in a 5% sample (N=19) of the total cohort from a randomised, controlled two arm trial of doctor-pharmacist collaborative prescribing. Results When reviewer assessments were combined, 32 out of 294 (10.9%) medications assessed for appropriateness in the control arm were classed as inappropriate, compared to 13 of 266 (4.9%) in the intervention arm. Out of 89 regular medications in the control arm, 25 (28%) were omitted from the medication charts, compared to 1 out of 55 (2%) in the intervention arm (p<0.001, fishers exact) On average, 52% of omissions in the control arm were judged to have potential for patient harm or ward inconvenience. Conclusion For the appropriateness of prescribing, overall results were similar between arms, as judged by individual panel members. Medication charts in the control arm contained significantly more omissions than in the intervention arm, a number of which were rated by the panel members as having the potential for patient harm or ward inconvenience.