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.

Overexpression of the kiwifruit SVP3 gene affects reproductive development and suppresses anthocyanin biosynthesis in petals, but has no effect on vegetative growth, dormancy, or flowering time

SVP-like MADS domain transcription factors have been shown to regulate flowering time and both inflorescence and flower development in annual plants, while having effects on growth cessation and terminal bud formation in perennial species. Previously, four SVP genes were described in woody perennial vine kiwifruit (Actinidia spp.), with possible distinct roles in bud dormancy and flowering. Kiwifruit SVP3 transcript was confined to vegetative tissues and acted as a repressor of flowering as it was able to rescue the Arabidopsis svp41 mutant. To characterize kiwifruit SVP3 further, ectopic expression in kiwifruit species was performed. Ectopic expression of SVP3 in A. deliciosa did not affect general plant growth or the duration of endodormancy. Ectopic expression of SVP3 in A. eriantha also resulted in plants with normal vegetative growth, bud break, and flowering time. However, significantly prolonged and abnormal flower, fruit, and seed development were observed, arising from SVP3 interactions with kiwifruit floral homeotic MADS-domain proteins. Petal pigmentation was reduced as a result of SVP3-mediated interference with transcription of the kiwifruit flower tissue-specific R2R3 MYB regulator, MYB110a, and the gene encoding the key anthocyanin biosynthetic step, F3GT1. Constitutive expression of SVP3 had a similar impact on reproductive development in transgenic tobacco. The flowering time was not affected in day-neutral and photoperiod-responsive Nicotiana tabacum cultivars, but anthesis and seed germination were significantly delayed. The accumulation of anthocyanin in petals was reduced and the same underlying mechanism of R2R3 MYB NtAN2 transcript reduction was demonstrated.

The extended context of career : families negotiating education and career decisions

In families, decisions about parents’ and children’s education and career require an ongoing negotiation to reconcile the goals of all family members. This paper describes a project which investigates these decisions within families experiencing whole family relocation based on one adult’s work. Semi-structured interviews were conducted with professional workers with school-aged children living in six Australian rural and remote communities. The interview sample included four doctors, 10 teachers, four nurses and nine police. This qualitative phase informed the development of an online survey of a larger sample (n¼278) of the same professional groups, which constituted a second quantitative phase of the research. This paper reports on only one aspect of the survey, that is, the participants’ recording of two previous career location moves they had undertaken and the reasons for these. The data emphasise the family project evident in this decision-making process as the respondents deal with a large range of complex individual, family and broader systems’ influences in reconciling their own careers and their children’s educational opportunities.

Universal codes from switching strategies

We discuss algorithms for combining sequential prediction strategies, a task which can be viewed as a natural generalisation of the concept of universal coding. We describe a graphical language based on Hidden Markov Models for defining prediction strategies, and we provide both existing and new models as examples. The models include efficient, parameterless models for switching between the input strategies over time, including a model for the case where switches tend to occur in clusters, and finally a new model for the scenario where the prediction strategies have a known relationship, and where jumps are typically between strongly related ones. This last model is relevant for coding time series data where parameter drift is expected. As theoretical contributions we introduce an interpolation construction that is useful in the development and analysis of new algorithms, and we establish a new sophisticated lemma for analysing the individual sequence regret of parameterised models.

Social engineering in social networking sites : the art of impersonation

Social networking sites (SNSs), with their large number of users and large information base, seem to be the perfect breeding ground for exploiting the vulnerabilities of people, who are considered the weakest link in security. Deceiving, persuading, or influencing people to provide information or to perform an action that will benefit the attacker is known as “social engineering.” Fraudulent and deceptive people use social engineering traps and tactics through SNSs to trick users into obeying them, accepting threats, and falling victim to various crimes such as phishing, sexual abuse, financial abuse, identity theft, and physical crime. Although organizations, researchers, and practitioners recognize the serious risks of social engineering, there is a severe lack of understanding and control of such threats. This may be partly due to the complexity of human behaviors in approaching, accepting, and failing to recognize social engineering tricks. This research aims to investigate the impact of source characteristics on users’ susceptibility to social engineering victimization in SNSs, particularly Facebook. Using grounded theory method, we develop a model that explains what and how source characteristics influence Facebook users to judge the attacker as credible.

Treatment with the vascular disruptive agent OXi4503 induces an immediate and widespread epithelial to mesenchymal transition in the surviving tumor

Epithelial to mesenchymal transition (EMT) is considered an important mechanism in tumor resistance to drug treatments; however, in vivo observation of this process has been limited. In this study we demonstrated an immediate and widespread EMT involving all surviving tumor cells following treatment of a mouse model of colorectal liver metastases with the vascular disruptive agent OXi4503. EMT was characterized by significant downregulation of E-cadherin, relocation and nuclear accumulation of b-catenin as well as significant upregulation of ZEB1 and vimentin. Concomitantly, significant temporal upregulation in hypoxia and the pro-angiogenic growth factors hypoxia-inducible factor 1-alpha, hepatocyte growth factor, vascular endothelial growth factor and transforming growth factor-beta were seen within the surviving tumor. The process of EMT was transient and by 5 days after treatment tumor cell reversion to epithelial morphology was evident. This reversal, termed mesenchymal to epithelial transition (MET) is a process implicated in the development of new metastases but has not been observed in vivo histologically. Similar EMT changes were observed in response to other antitumor treatments including chemotherapy, thermal ablation, and antiangiogenic treatments in our mouse colorectal metastasis model and in a murine orthotopic breast cancer model after OXi4503 treatment. These results suggest that EMT may be an early mechanism adopted by tumors in response to injury and hypoxic stress, such that inhibition of EMT in combination with other therapies could play a significant role in future cancer therapy.

Human single-stranded DNA binding protein 1 (hSSB1/NABP2) is required for the stability and repair of stalled replication forks

Aberrant DNA replication is a primary cause of mutations that are associated with pathological disorders including cancer. During DNA metabolism, the primary causes of replication fork stalling include secondary DNA structures, highly transcribed regions and damaged DNA. The restart of stalled replication forks is critical for the timely progression of the cell cycle and ultimately for the maintenance of genomic stability. Our previous work has implicated the single-stranded DNA binding protein, hSSB1/NABP2, in the repair of DNA double-strand breaks via homologous recombination. Here, we demonstrate that hSSB1 relocates to hydroxyurea (HU)-damaged replication forks where it is required for ATR and Chk1 activation and recruitment of Mre11 and Rad51. Consequently, hSSB1-depleted cells fail to repair and restart stalled replication forks. hSSB1 deficiency causes accumulation of DNA strand breaks and results in chromosome aberrations observed in mitosis, ultimately resulting in hSSB1 being required for survival to HU and camptothecin. Overall, our findings demonstrate the importance of hSSB1 in maintaining and repairing DNA replication forks and for overall genomic stability.

Supporting process model validation through natural language generation

The design and development of process-aware information systems is often supported by specifying requirements as business process models. Although this approach is generally accepted as an effective strategy, it remains a fundamental challenge to adequately validate these models given the diverging skill set of domain experts and system analysts. As domain experts often do not feel confident in judging the correctness and completeness of process models that system analysts create, the validation often has to regress to a discourse using natural language. In order to support such a discourse appropriately, so-called verbalization techniques have been defined for different types of conceptual models. However, there is currently no sophisticated technique available that is capable of generating natural-looking text from process models. In this paper, we address this research gap and propose a technique for generating natural language texts from business process models. A comparison with manually created process descriptions demonstrates that the generated texts are superior in terms of completeness, structure, and linguistic complexity. An evaluation with users further demonstrates that the texts are very understandable and effectively allow the reader to infer the process model semantics. Hence, the generated texts represent a useful input for process model validation.

Corporate sustainability reporting for water : water footprint, global reporting initiative and the water accounting framework

Three initiatives with respect to water reporting in the mining sector are compared in this paper to understand the quantities that are asked for by each initiative and the guidelines of those initiatives through means of a case study. The Global Reporting Initiative (GRI) was chosen because it has achieved widespread acceptance amongst mining companies and its water-related indicators are widely reported in corporate sustainability reporting. In contrast, the Water Footprint Network, which has been an important initiative in food and agricultural industries, has had low acceptance in the mining industry. The third initiative is the Water Accounting Framework, a collaboration between The Minerals Council of Australia and the Sustainable Minerals Institute of the University of Queensland. A water account had previously been created according to the Water Accounting Framework for the case study site, an open pit coal mine in the Bowen Basin. The resulting account provided consistent data for the Global Reporting Initiative (GRI) and the Water Footprint attributable to mining but in particular, a deficiency in the GRI indicator of EN10 reuse and recycling efficiency was illustrated quantitatively. This has far-reaching significance due to the widespread use of GRI indicators in mining corporate reports.

Effect of plasma environment on synthesis of vertically aligned carbon nanofibers in plasma-enhanced chemical vapor deposition

We present a theoretical model describing a plasma-assisted growth of carbon nanofibers (CNFs), which involves two competing channels of carbon incorporation into stacked graphene sheets: via surface diffusion and through the bulk of the catalyst particle (on the top of the nanofiber), accounting for a range of ion- and radical-assisted processes on the catalyst surface. Using this model, it is found that at low surface temperatures, Ts, the CNF growth is indeed controlled by surface diffusion, thus quantifying the semiempirical conclusions of earlier experiments. On the other hand, both the surface and bulk diffusion channels provide a comparable supply of carbon atoms to the stacked graphene sheets at elevated synthesis temperatures. It is also shown that at low Ts, insufficient for effective catalytic precursor decomposition, the plasma ions play a key role in the production of carbon atoms on the catalyst surface. The model is used to compute the growth rates for the two extreme cases of thermal and plasma-enhanced chemical vapor deposition of CNFs. More importantly, these results quantify and explain a number of observations and semiempirical conclusions of earlier experiments.

Effect of ion current density on the properties of vacuum arc-deposited TiN coatings

The influence of ion current density on the thickness of coatings deposited in a vacuum arc setup has been investigated to optimize the coating porosity. A planar probe was used to measure the ion current density distribution across plasma flux. A current density from 20 to 50 A/m2 was obtained, depending on the probe position relative to the substrate center. TiN coatings were deposited onto the cutting inserts placed at different locations on the substrate, and SEM was used to characterize the surfaces of the coatings. It was found that lowdensity coatings were formed at the decreased ion current density. A quantitative dependence of the coating thickness on the ion current density in the range of 20-50 A/m2 were obtained for the films deposited at substrate bias of 200 V and nitrogen pressure 0.1 Pa, and the coating porosity was calculated. The coated cutting inserts were tested by lathe machining of the martensitic stainless steel AISI 431. The results may be useful for controlling ion flux distribution over large industrial-scale substrates.

Predicting movie ratings from audience behaviors

We propose a method of representing audience behavior through facial and body motions from a single video stream, and use these features to predict the rating for feature-length movies. This is a very challenging problem as: i) the movie viewing environment is dark and contains views of people at different scales and viewpoints; ii) the duration of feature-length movies is long (80-120 mins) so tracking people uninterrupted for this length of time is still an unsolved problem, and; iii) expressions and motions of audience members are subtle, short and sparse making labeling of activities unreliable. To circumvent these issues, we use an infrared illuminated test-bed to obtain a visually uniform input. We then utilize motion-history features which capture the subtle movements of a person within a pre-defined volume, and then form a group representation of the audience by a histogram of pair-wise correlations over a small-window of time. Using this group representation, we learn our movie rating classifier from crowd-sourced ratings collected by rottentomatoes.com and show our prediction capability on audiences from 30 movies across 250 subjects (> 50 hrs).

A unique battery/supercapacitor direct integration scheme for hybrid electric vehicles

Battery/supercapacitor hybrid energy storage systems have been gaining popularity in electric vehicles due to their excellent power and energy performances. Conventional designs of such systems require interfacing dc-dc converters. These additional dc-dc converters increase power loss, complexity, weight and cost. Therefore, this paper proposes a new direct integration scheme for battery/supercapacitor hybrid energy storage systems using a double ended inverter system. This unique approach eliminates the need for interfacing converters and thus it is free from aforementioned drawbacks. Furthermore, the proposed system offers seven operating modes to improve the effective use of available energy in a typical drive cycle of a hybrid electric vehicle. Simulation results are presented to verify the efficacy of the proposed system and control techniques.

Battery clamped three-level inverter for renewable energy systems

This paper presents a novel battery direct integration scheme for renewable energy systems. The idea is to replace ordinary capacitors of a three-level flying-capacitor inverter by three battery banks to alleviate power fluctuations in renewable generation. This approach eliminates the need for interfacing dc-dc converters and thus considerably improves the overall efficiency. However, the major problem with this approach is the uneven distribution of space vectors which is due to unavoidable unbalance in clamping voltages. A detailed analysis on the effects of this issue and a novel carrier based pulse width modulation method, which can generate undistorted currents even in the presence of unevenly distributed space vectors, are presented in this paper. A charge/discharge controller is also proposed for power sharing and state of charge balancing of battery banks. Simulation results are presented to verify the efficacy of the proposed system, modulation method and power sharing controller.

An acoustically enhanced gold film Raman sensor on a lithium niobate substrate

The surface enhanced Raman scattering effect has shown immense potential for detecting trace amounts of explosive vapor molecules. To date, efforts to produce a commercially available, reliable SERS sensor have been impeded by an inability to separate the electromagnetic enhancement produced by the metallic nanostructure from other signal enhancing effects. Here, we show a new Raman sensor that uses surface acoustic waves (SAWs) to produce controllable surface structures on gold films deposited on LiNbO3 substrates that modulate the Raman signal of a target compound (thiophenol) adsorbed on the films. We demonstrate that this sensor can dynamically control the Raman signal simply by changing the SAW’s amplitude, allowing the Raman signal enhancement factor to be directly measured with no variation in the concentration of the target compound. The physically adsorbed molecules can be removed from the sensor without physical cleaning or damage, making it possible to reuse it for real-time Raman detection.