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.

Managed livestock grazing is compatible with the maintenance of plant diversity in semidesert grasslands

Even when no baseline data are available, the impacts of 150 years of livestock grazing on natural grasslands can be assessed using a combined approach of grazing manipulation and regional-scale assessment of the flora. Here, we demonstrate the efficacy of this method across 18 sites in the semidesert Mitchell grasslands of northeastern Australia. Fifteen-year-old exclosures (ungrazed and macropod grazed) revealed that the dominant perennial grasses in the genus Astrebla do not respond negatively to grazing disturbance typical of commercial pastoralism. Neutral, positive, intermediate, and negative responses to grazing disturbance were recorded amongst plant species with no single life-form group associated with any response type. Only one exotic species, Cenchrus ciliaris, was recorded at low frequency. The strongest negative response was from a native annual grass, Chionachne hubbardiana, an example of a species that is highly sensitive to grazing disturbance. Herbarium records revealed only scant evidence that species with a negative response to grazing have declined through the period of commercial pastoralism. A regional analysis identified 14 from a total of 433 plant species in the regional flora that may be rare and potentially threatened by grazing disturbance. However, a targeted survey precluded grazing as a cause of decline for seven of these based on low palatability and positive responses to grazing and other disturbance. Our findings suggest that livestock grazing of semidesert grasslands with a short evolutionary history of ungulate grazing has altered plant composition, but has not caused declines in the dominant perennial grasses or in species richness as predicted by the preceding literature. The biggest impact of commercial pastoralism is the spread of woody leguminous trees that can transform grassland to thorny shrubland. The conservation of plant biodiversity is largely compatible with commercial pastoralism provided these woody weeds are controlled, but reserves strategically positioned within water remote areas are necessary to protect grazing-sensitive species. This study demonstrates that a combination of experimental studies and regional surveys can be used to understand anthropogenic impacts on natural ecosystems where reference habitat is not available.

Ultrafine particles in cities

Ultrafine particles (UFP; diameter less than 100 nm) are ubiquitous in urban air, and an acknowledged risk to human health. Globally, the major source for urban outdoor UFP concentrations is motor traffic. Ongoing trends towards urbanisation and expansion of road traffic are anticipated to further increase population exposure to UFPs. Numerous experimental studies have characterised UFPs in individual cities, but an integrated evaluation of emissions and population exposure is still lacking. Our analysis suggest that average exposure to outdoor UFPs in Asian cities is about four-times larger than those in European cities but impacts on human health are largely unknown. This article reviews some fundamental drivers of UFP emissions and dispersion, and highlights unresolved challenges, as well as recommendations to ensure sustainable urban development whilst minimising any possible adverse health impacts.

Guided ionization waves : theory and experiments

This review focuses on one of the fundamental phenomena that occur upon application of sufficiently strong electric fields to gases, namely the formation and propagation of ionization waves-streamers. The dynamics of streamers is controlled by strongly nonlinear coupling, in localized streamer tip regions, between enhanced (due to charge separation) electric field and ionization and transport of charged species in the enhanced field. Streamers appear in nature (as initial stages of sparks and lightning, as huge structures-sprites above thunderclouds), and are also found in numerous technological applications of electrical discharges. Here we discuss the fundamental physics of the guided streamer-like structures-plasma bullets which are produced in cold atmospheric-pressure plasma jets. Plasma bullets are guided ionization waves moving in a thin column of a jet of plasma forming gases (e.g.,He or Ar) expanding into ambient air. In contrast to streamers in a free (unbounded) space that propagate in a stochastic manner and often branch, guided ionization waves are repetitive and highly-reproducible and propagate along the same path-the jet axis. This property of guided streamers, in comparison with streamers in a free space, enables many advanced time-resolved experimental studies of ionization waves with nanosecond precision. In particular, experimental studies on manipulation of streamers by external electric fields and streamer interactions are critically examined. This review also introduces the basic theories and recent advances on the experimental and computational studies of guided streamers, in particular related to the propagation dynamics of ionization waves and the various parameters of relevance to plasma streamers. This knowledge is very useful to optimize the efficacy of applications of plasma streamer discharges in various fields ranging from health care and medicine to materials science and nanotechnology.

Made-to-order nanocarbons through deterministic plasma nanotechnology

Through a combinatorial approach involving experimental measurement and plasma modelling, it is shown that a high degree of control over diamond-like nanocarbon film sp3/sp2 ratio (and hence film properties) may be exercised, starting at the level of electrons (through modification of the plasma electron energy distribution function). Hydrogenated amorphous carbon nanoparticle films with high percentages of diamond-like bonds are grown using a middle-frequency (2 MHz) inductively coupled Ar + CH4 plasma. The sp3 fractions measured by X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy in the thin films are explained qualitatively using sp3/sp2 ratios 1) derived from calculated sp3 and sp2 hybridized precursor species densities in a global plasma discharge model and 2) measured experimentally. It is shown that at high discharge power and lower CH4 concentrations, the sp3/sp2 fraction is higher. Our results suggest that a combination of predictive modeling and experimental studies is instrumental to achieve deterministically grown made-to-order diamond-like nanocarbons suitable for a variety of applications spanning from nano-magnetic resonance imaging to spin-flip quantum information devices. This deterministic approach can be extended to graphene, carbon nanotips, nanodiamond and other nanocarbon materials for a variety of applications

SiC-like phase and room-temperature photoluminescence of low-k SiOCH films

Carbon-doped hydrogenated silicon oxide (SiOCH) low-k films have been prepared using 13.56 MHz discharge in trimethylsilane (3MS) - oxygen gas mixtures at 3, 4, and 5 Torr sustained with RF power densities 1.3 - 2.6 W/cm2. The atomic structure of the SiOCH films appears to be a mixture the amorphous SiO2-like and the partially polycrystalline SiC-like phases. Results of the infra-red spectroscopy reflect the increment in the volume fraction of the SiC-like phase from 0.22 - 0.28 to 0.36 - 0.39 as the RF power increment. Steady-state near-UV laser-excited (364 nm wavelength, 40±2 mW) photoluminescence (PL) has been studied at room temperatures in the visible (1.8 eV - 3.1 eV) subrange of photon spectrum. Two main bands of the PL signal (at the photon energies of 2.5 - 2.6 eV and 2.8 - 2.9 eV) are observed. Intensities of the both bands are changed monotonically with RF power, whereas the bandwidth of ∼0.1 eV remains almost invariable. It is likely that the above lines are dumped by the non-radiative recombination involving E1-like centres in the amorphous-nanocrystalline SiC-like phases. Such explanation of the PL intensity dependences on the RF power density is supported by results of experimental studies of defect states spectrum in bandgap of the SiOCH films.

Web crippling behaviour of C-section beams with web ribs

SupaCee section is one of the cold-formed steel members which is increasingly used in the construction sector. It is characterized by unique ribbed web and curved lip elements, and is claimed to be more economical with extra strength than the traditional channel sections. SupaCee sections are widely used in Australia as floor joists, bearers, purlins and girts. Many experimental and numerical studies have been carried out to evaluate the behaviour and design of conventional channel beams subject to web crippling. To date, however, no investigation has been conducted into the web crippling behaviour and strength of SupaCee sections. Current cold-formed steel design equations do not include any design procedures for SupaCee sections. Hence experimental studies were conducted to assess the web crippling behaviour and strengths of SupaCee sections under ETF and ITF load cases. Thirty six web crippling tests were conducted and the capacity results were compared with the predictions from the AS/NZS 4600 and AISI design rules developed for conventional channel sections. Comparison of ultimate web crippling capacities from tests showed that AS/NZS 4600 and AISI design equations are unconservative for SupaCee sections under ETF load case, but are overly conservative for ITF load case. Hence new equations were proposed to determine the web crippling capacities of SupaCee sections based on the experimental results from this study. Suitable design rules were also developed within the direct strength method format. This paper presents the details of this experimental study of SupaCee sections subject to web crippling and the results.

Reducing bubble defect on the outsole production process in the footwear manufacturing industry

The purpose of this study is to discover the significant factors causing the bubble defect on the outsoles manufactured by the Case Company. The bubble defect occurs approximately 1.5 per cent of the time or in 36 pairs per day. To understand this problem, experimental studies are undertaken to identify various factors such as injector temperature, mould temperature; that affects the production of waste. The work presented in this paper comprises a review of the relevant literature on the Six Sigma DMAIC improvement process, quality control tools, and the design of the experiments. After the experimentation following the Six Sigma process, the results showed that the defect occurred in approximately 0.5 per cent of the products or in 12 pairs per day; this decreased the production cost from 6,120 AUD per month to 2,040 AUD per month. This research aimed to reduce the amount of waste in men’s flat outsoles. Hence, the outcome of research presented in this paper should be used as a guide for applying the appropriate process for each type of outsole.

Short utterance PLDA speaker verification using SN-WLDA and variance modelling techniques

This paper proposes a combination of source-normalized weighted linear discriminant analysis (SN-WLDA) and short utterance variance (SUV) PLDA modelling to improve the short utterance PLDA speaker verification. As short-length utterance i-vectors vary with the speaker, session variations and phonetic content of the utterance (utterance variation), a combined approach of SN-WLDA projection and SUV PLDA modelling is used to compensate the session and utterance variations. Experimental studies have found that a combination of SN-WLDA and SUV PLDA modelling approach shows an improvement over baseline system (WCCN[LDA]-projected Gaussian PLDA (GPLDA)) as this approach effectively compensates the session and utterance variations.

Mathematical Models of Tumor-Immune System Dynamics

"This collection of papers offers a broad synopsis of state-of-the-art mathematical methods used in modeling the interaction between tumors and the immune system. These papers were presented at the four-day workshop on Mathematical Models of Tumor-Immune System Dynamics held in Sydney, Australia from January 7th to January 10th, 2013. The workshop brought together applied mathematicians, biologists, and clinicians actively working in the field of cancer immunology to share their current research and to increase awareness of the innovative mathematical tools that are applicable to the growing field of cancer immunology. Recent progress in cancer immunology and advances in immunotherapy suggest that the immune system plays a fundamental role in host defense against tumors and could be utilized to prevent or cure cancer. Although theoretical and experimental studies of tumor-immune system dynamics have a long history, there are still many unanswered questions about the mechanisms that govern the interaction between the immune system and a growing tumor. The multidimensional nature of these complex interactions requires a cross-disciplinary approach to capture more realistic dynamics of the essential biology. The papers presented in this volume explore these issues and the results will be of interest to graduate students and researchers in a variety of fields within mathematical and biological sciences."--Publisher website

Improving the shear capacities of lipped channel beams with web openings using plate stiffeners

Cold-formed steel lipped channel beams (LCB) are used extensively in residential, industrial and commercial buildings as load bearing structural elements. Their shear capacities are considerably reduced when web openings are included for the purpose of locating building services. Past research has shown that the shear capacities of LCBs were reduced by up to 70% due to the inclusion of these web openings. Hence there is a need to improve the shear capacities of LCBs with web openings. A cost effective way of eliminating the detrimental effects of large web openings is to attach suitable stiffeners around the web openings and restore the original shear strength and stiffness of LCBs. Hence detailed experimental studies were undertaken to investigate the behaviour and strength of LCBs with stiffened web openings subject to shear, and combined bending and shear actions. Both plate and stud stiffeners with varying sizes and thicknesses were attached to the web elements of LCBs using different screw-fastening arrangements. Simply supported test specimens of LCBs with aspect ratios of 1.0 and 1.5 were loaded at mid-span until failure. Numerical studies were also undertaken to investigate the strength of LCBs with stiffened web openings. Finite element models of LCBs with stiffened web openings under shear, combined bending and shear actions were developed to simulate the behaviour of tested LCBs. The developed models were then validated by comparing their results with experimental results and used in further studies. Both experimental and finite element analysis results showed that the stiffening arrangements recommended by past research and available design guidelines are not adequate to restore the original shear strengths of LCBs. Therefore new stiffener arrangements were proposed based on screw fastened plate stiffeners. This paper presents the details of this research study and the results.

The effectiveness of information-sharing interventions to reduce anxiety in families waiting for surgical patients undergoing an elective surgical procedure: A systematic review

Background Whilst waiting for patients undergoing surgery, a lack of information regarding the patient’s status and the outcome of surgery, can contribute to the anxiety experienced by family members. Effective strategies for providing information to families are therefore required. Objectives To synthesize the best available evidence in relation to the most effective information-sharing interventions to reduce anxiety for families waiting for patients undergoing an elective surgical procedure. Inclusion criteria Types of participants All studies of family members over 18 years of age waiting for patients undergoing an elective surgical procedure were included, including those waiting for both adult and pediatric patients.   Types of intervention All information-sharing interventions for families of patients undergoing an elective surgical procedure were eligible for inclusion in the review. Types of studies All randomized controlled trials (RCTs) quasi-experimental studies, case-controlled and descriptive studies, comparing one information-sharing intervention to another or to usual care were eligible for inclusion in the review. Types of outcomes Primary outcome: The level of anxiety amongst family members or close relatives whilst waiting for patients undergoing surgery, as measured by a validated instrument such as the S-Anxiety portion of the State-Trait Anxiety Inventory (STAI). Secondary outcomes: Family satisfaction and other measurements that may be considered indicators of stress and anxiety, such as mean arterial pressure (MAP) and heart rate. Search strategy A comprehensive search, restricted to English language only, was undertaken of the following databases from 1990 to May 2013: Medline, CINAHL, EMBASE, ProQuest, Web of Science, PsycINFO, Scopus, Dissertation and Theses PQDT (via ProQuest), Current Contents, CENTRAL, Google Scholar, OpenGrey, Clinical Trials, Science.gov, Current Controlled Trials and National Institute for Clinical Studies (NHMRC). Methodological quality Two independent reviewers critically appraised retrieved papers for methodological quality using the standardized critical appraisal instruments for randomized controlled trials and descriptive studies from the Joanna Briggs Institute Meta Analysis of Statistics Assessment and Review Instruments (JBI-MAStARI). Data extraction Two independent reviewers extracted data from included papers using a customized data extraction form. Data synthesis Statistical pooling was not possible, mainly due to issues with data reporting in two of the studies, therefore the results are presented in narrative form. Results Three studies with a total of 357 participants were included in the review. In-person reporting to family members was found to be effective in comparison with usual care in which no reports were provided. Telephone reporting was also found to be effective at reducing anxiety, in comparison with usual care, although not as effective as in-person reporting. The use of paging devices to keep family members informed were found to increase, rather than decrease anxiety. Conclusions Due to the lack of high quality research in this area, the strength of the conclusions are limited. It appears that in-person and telephone reporting to family members decreases anxiety, however the use of paging devices increases anxiety.

Improving out-domain PLDA speaker verification using unsupervised inter-dataset variability compensation approach

Experimental studies have found that when the state-of-the-art probabilistic linear discriminant analysis (PLDA) speaker verification systems are trained using out-domain data, it significantly affects speaker verification performance due to the mismatch between development data and evaluation data. To overcome this problem we propose a novel unsupervised inter dataset variability (IDV) compensation approach to compensate the dataset mismatch. IDV-compensated PLDA system achieves over 10% relative improvement in EER values over out-domain PLDA system by effectively compensating the mismatch between in-domain and out-domain data.

The moderating role of task characteristics in determining responses to a stressful work simulation

Two experimental studies were conducted to examine whether the stress-buffering effects of behavioral control on work task responses varied as a function of procedural information. Study 1 manipulated low and high levels of task demands, behavioral control, and procedural information for 128 introductory psychology students completing an in-basket activity. ANOVA procedures revealed a significant three-way interaction among these variables in the prediction of subjective task performance and task satisfaction. It was found that procedural information buffered the negative effects of task demands on ratings of performance and satisfaction only under conditions of low behavioral control. This pattern of results suggests that procedural information may have a compensatory effect when the work environment is characterized by a combination of high task demands and low behavioral control. Study 2 (N=256) utilized simple and complex versions of the in-basket activity to examine the extent to which the interactive relationship among task demands, behavioral control, and procedural information varied as a function of task complexity. There was further support for the stress-buffering role of procedural information on work task responses under conditions of low behavioral control. This effect was, however, only present when the in-basket activity was characterized by high task complexity, suggesting that the interactive relationship among these variables may depend on the type of tasks performed at work.

Shear tests of hollow flange channel beams with real support conditions

This paper presents the details of experimental studies on the effect of real support conditions on the shear strength of hollow flange channel beams, known as LiteSteel beams (LSB). The LSB has a unique shape of a channel beam with two rectangular hollow flanges, made using a unique manufacturing process. In many applications in the building industry LSBs are used with only one web side plate (WSP) at their supports. The WSPs are also often not full height plates. Past research studies showed that these real support connections did not provide the required simply supported conditions. Many studies have been carried out to evaluate the behaviour and design of LSBs with simply supported conditions subject to pure bending and predominant shear actions. To date, however, no investigation has been conducted into the effect of real support conditions on the shear strength of LSBs. Hence a detailed experimental study based on 25 shear tests was undertaken to investigate the shear behaviour and strength of LSBs with real support conditions. Simply supported test specimens of LSBs with aspect ratios of 1.0 and 1.5 were loaded at mid-span until failure. It was found that the effect of using one WSP on the shear behaviour of LSB is significant and there is about 25% shear capacity reduction due to the lateral movement of the bottom flange at the supports. Shear capacity of LSB was also found to decrease when full height WSPs were not used. Suitably improved support connections were developed to improve the shear capacity of LSBs based on test results. Details of the recommended support connections and shear capacity results are given in this paper.