High-yeld RNA-extraction method for saliva

BACKGROUND: The use of salivary diagnostics is increasing because of its noninvasiveness, ease of sampling, and the relatively low risk of contracting infectious organisms. Saliva has been used as a biological fluid to identify and validate RNA targets in head and neck cancer patients. The goal of this study was to develop a robust, easy, and cost-effective method for isolating high yields of total RNA from saliva for downstream expression studies. METHODS: Oral whole saliva (200 mu L) was collected from healthy controls (n = 6) and from patients with head and neck cancer (n = 8). The method developed in-house used QIAzol lysis reagent (Qiagen) to extract RNA from saliva (both cell-free supernatants and cell pellets), followed by isopropyl alcohol precipitation, cDNA synthesis, and real-time PCR analyses for the genes encoding beta-actin ("housekeeping" gene) and histatin (a salivary gland-specific gene). RESULTS: The in-house QIAzol lysis reagent produced a high yield of total RNA (0.89 -7.1 mu g) from saliva (cell-free saliva and cell pellet) after DNase treatment. The ratio of the absorbance measured at 260 nm to that at 280 nm ranged from 1.6 to 1.9. The commercial kit produced a 10-fold lower RNA yield. Using our method with the QIAzol lysis reagent, we were also able to isolate RNA from archived saliva samples that had been stored without RNase inhibitors at -80 degrees C for >2 years. CONCLUSIONS: Our in-house QIAzol method is robust, is simple, provides RNA at high yields, and can be implemented to allow saliva transcriptomic studies to be translated into a clinical setting.

A rapid and cost-effective method of producing recombinant proBNP and NT-proBNP variants in Escherichia coli for immunoassay of heart failure

The measurements of plasma natriuretic peptides (NT-proBNP, proBNP and BNP) are used to diagnose heart failure but these are expensive to produce. We describe a rapid, cheap and facile production of proteins for immunoassays of heart failure. DNA encoding N-terminally His-tagged NT-proBNP and proBNP were cloned into the pJexpress404 vector. ProBNP and NT-proBNP peptides were expressed in Escherichia coli, purified and refolded in vitro. The analytical performance of these peptides were comparable with commercial analytes (NT-proBNP EC50 for the recombinant is 2.6 ng/ml and for the commercial material is 5.3 ng/ml) and the EC50 for recombinant and commercial proBNP, are 3.6 and 5.7 ng/ml respectively). Total yield of purified refolded NT-proBNP peptide was 1.75 mg/l and proBNP was 0.088 mg/l. This approach may also be useful in expressing other protein analytes for immunoassay applications. To develop a cost effective protein expression method in E. coli to obtain high yields of NT-proBNP (1.75 mg/l) and proBNP (0.088 mg/l) peptides for immunoassay use.

A two-stage item recommendation method using probabilistic ranking with reconstructed tensor model

In a tag-based recommender system, the multi-dimensional correlation should be modeled effectively for finding quality recommendations. Recently, few researchers have used tensor models in recommendation to represent and analyze latent relationships inherent in multi-dimensions data. A common approach is to build the tensor model, decompose it and, then, directly use the reconstructed tensor to generate the recommendation based on the maximum values of tensor elements. In order to improve the accuracy and scalability, we propose an implementation of the -mode block-striped (matrix) product for scalable tensor reconstruction and probabilistically ranking the candidate items generated from the reconstructed tensor. With testing on real-world datasets, we demonstrate that the proposed method outperforms the benchmarking methods in terms of recommendation accuracy and scalability.

Stochastic ranking method for thermostatically controllable appliances to provide regulation services

Demand response can be used for providing regulation services in the electricity markets. The retailers can bid in a day-ahead market and respond to real-time regulation signal by load control. This paper proposes a new stochastic ranking method to provide regulation services via demand response. A pool of thermostatically controllable appliances (TCAs) such as air conditioners and water heaters are adjusted using direct load control method. The selection of appliances is based on a probabilistic ranking technique utilizing attributes such as temperature variation and statuses of TCAs. These attributes are stochastically forecasted for the next time step using day-ahead information. System performance is analyzed with a sample regulation signal. Network capability to provide regulation services under various seasons is analyzed. The effect of network size on the regulation services is also investigated.

A new ambiguity acceptance test threshold determination method with controllable failure rate

The ambiguity acceptance test is an important quality control procedure in high precision GNSS data processing. Although the ambiguity acceptance test methods have been extensively investigated, its threshold determine method is still not well understood. Currently, the threshold is determined with the empirical approach or the fixed failure rate (FF-) approach. The empirical approach is simple but lacking in theoretical basis, while the FF-approach is theoretical rigorous but computationally demanding. Hence, the key of the threshold determination problem is how to efficiently determine the threshold in a reasonable way. In this study, a new threshold determination method named threshold function method is proposed to reduce the complexity of the FF-approach. The threshold function method simplifies the FF-approach by a modeling procedure and an approximation procedure. The modeling procedure uses a rational function model to describe the relationship between the FF-difference test threshold and the integer least-squares (ILS) success rate. The approximation procedure replaces the ILS success rate with the easy-to-calculate integer bootstrapping (IB) success rate. Corresponding modeling error and approximation error are analysed with simulation data to avoid nuisance biases and unrealistic stochastic model impact. The results indicate the proposed method can greatly simplify the FF-approach without introducing significant modeling error. The threshold function method makes the fixed failure rate threshold determination method feasible for real-time applications.

Dialogicality in Focus : Challenges to Theory, Method and Application

The phenomenon which dialogism addresses is human interaction. It enables us to conceptualise human interaction as intersubjective, symbolic, cultural, transformative and conflictual, in short, as complex. The complexity of human interaction is evident in all domains of human life, for example, in therapy, education, health intervention, communication, and coordination at all levels. A dialogical approach starts by acknowledging that the social world is perspectival, that people and groups inhabit different social realities. This book stands apart from the proliferation of recent books on dialogism, because rather than applying dialogism to this or that domain, the present volume focuses on dialogicality itself to interrogate the concepts and methods which are taken for granted in the burgeoning literature.

Correlation based method for phase identification in a three phase LV distribution network

Low voltage distribution networks feature a high degree of load unbalance and the addition of rooftop photovoltaic is driving further unbalances in the network. Single phase consumers are distributed across the phases but even if the consumer distribution was well balanced when the network was constructed changes will occur over time. Distribution transformer losses are increased by unbalanced loadings. The estimation of transformer losses is a necessary part of the routine upgrading and replacement of transformers and the identification of the phase connections of households allows a precise estimation of the phase loadings and total transformer loss. This paper presents a new technique and preliminary test results for a method of automatically identifying the phase of each customer by correlating voltage information from the utility's transformer system with voltage information from customer smart meters. The techniques are novel as they are purely based upon a time series of electrical voltage measurements taken at the household and at the distribution transformer. Experimental results using a combination of electrical power and current of the real smart meter datasets demonstrate the performance of our techniques.

Indirect effects of phytochemicals on offspring performance of Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae)

Phytochemical lures such as methyl eugenol (ME) and cue-lure are used in the management of Bactrocera fruit flies for monitoring and control. These lures are not just attractants, but also trigger physiological changes in males that lead to enhanced mating success. Additionally, in the cue-lure-responsive Bactrocera tryoni, females mated with lure-fed males exhibit changes in fecundity, remating receptivity and longevity. While the lures show current generation effects, no research has been carried out on possible multigenerational effects, although such effects have been hypothesized within a ‘sexy-son’ sexual selection model. In this study, we test for indirect, cross-generational effects of lure exposure in F1offspring of B. tryoni females mated with cue-lure-fed, zingerone-fed and lure-unfed (=control) males. The F1 attributes we recorded were immature development time, immature survival, adult survival and adult male lure foraging. No significant differences were found between treatments for any of the three life-history measurements, except that the offspring sired by zingerone-fed males had a longer egg development time than cue-lure and control offspring. However, indirect exposure to lures significantly enhanced the lure-foraging ability of F1 adult males. More offspring of cue-lure-fed males arrived at a lure source in both large flight cages and small laboratory cages over a 2-h period than did control males. The offspring of zingerone-fed males were generally intermediate between cue-lure and control offspring. This study provides the first evidence of a next generation effect of fruit fly male lures. While the results of this study support a ‘sexy-son’ sexual selection mechanism for the evolution of lure response in Bactrocera fruit flies, our discussion urges caution in interpreting our results in this way.

Pre-processing for approximate Bayesian computation in image analysis

Most of the existing algorithms for approximate Bayesian computation (ABC) assume that it is feasible to simulate pseudo-data from the model at each iteration. However, the computational cost of these simulations can be prohibitive for high dimensional data. An important example is the Potts model, which is commonly used in image analysis. Images encountered in real world applications can have millions of pixels, therefore scalability is a major concern. We apply ABC with a synthetic likelihood to the hidden Potts model with additive Gaussian noise. Using a pre-processing step, we fit a binding function to model the relationship between the model parameters and the synthetic likelihood parameters. Our numerical experiments demonstrate that the precomputed binding function dramatically improves the scalability of ABC, reducing the average runtime required for model fitting from 71 hours to only 7 minutes. We also illustrate the method by estimating the smoothing parameter for remotely sensed satellite imagery. Without precomputation, Bayesian inference is impractical for datasets of that scale.

Transport and health in China : recent collaborative research relating to vehicle factors and pollution

The nature of the transport system contributes to public health outcomes in a range of ways. The clearest contribution to public health is in the area of traffic crashes, because of their direct impact on individual death and disability and their direct costs to the health system. Other papers in this conference address these issues. This paper outlines some collaborative research between the Centre for Accident Research and Road Safety - Queensland (CARRS-Q) at QUT and Chinese researchers in areas that have indirect health impacts. Heavy vehicle dynamics: The integrity of the road surface influences crash risk, with ruts, pot-holes and other forms of road damage contributing to increased crash risks. The great majority of damage to the road surface from vehicles is caused by heavy trucks and buses, rather than cars or smaller vehicles. In some cases this damage is due to deliberate overloading, but in other cases it is due to vehicle suspension characteristics that lead to occasional high loads on particular wheels. Together with a visiting researcher and his colleagues, we have used both Queensland and Chinese data to model vehicle suspension systems that reduce the level of load, and hence the level of road damage and resulting crash risk(1-5). Toll worker exposure to vehicle emissions: The increasing construction of highways in China has also involved construction of a large number of toll roads. Tollbooth workers are potentially exposed to high levels of pollutants from vehicles, however the extent of this exposure and how it relates to standards for exposure are not well known. In a study led by a visiting researcher, we conducted a study to model these levels of exposure for a tollbooth in China(6). Noise pollution: The increasing presence of high speed roads in China has contributed to an increase in noise levels. In this collaborative study we modelled noise levels associated with a freeway widening near a university campus, and measures to reduce the noise(7). Along with these areas of research, there are many other areas of transport with health implications that are worthy of exploration. Traffic, noise and pollution contribute to a difficult environment for pedestrians, especially in an ageing society where there are health benefits to increasing physical activity. By building on collaborations such as those outlined, there is potential for a contribution to improved public health by addressing transport issues such as vehicle factors and pollution, and extending the research to other areas of travel activity. 1. Chen, Y., He, J., King, M., Chen, W. and Zhang, W. (2014). Stiffness-damping matching method of an ECAS system based on LQG control. Journal of Central South University, 21:439-446. DOI: 10.1007/s1177101419579 2. Chen, Y., He, J., King, M., Feng, Z. and Chang, W. (2013). Comparison of two suspension control strategies for multi-axle heavy truck. Journal of Central South University, 20(2): 550-562. 3. Chen, Y., He, J., King, M., Chen, W. and Zhang, W. (2013). Effect of driving conditions and suspension parameters on dynamic load-sharing of longitudinal-connected air suspensions. Science China Technological Sciences, 56(3): 666-676. DOI: 10.1007/s11431-012-5091-3 4. Chen, Y., He., J., King, M., Chen, W. and Zhang, W. (2013). Model development and dynamic load-sharing analysis of longitudinal-connected air suspensions. Strojniški Vestnik - Journal of Mechanical Engineering, 59(1):14-24. 5. Chen, Y., He, J., King, M., Liu, H. and Zhang, W. (2013). Dynamic load-sharing of longitudinal-connected air suspensions of a tri-axle semi-trailer. Proceedings of Transportation Research Board Annual Conference, Washington DC, 13-17 January 2013, paper no. 13-1117. 6. He, J., Qi, Z., Hang, W., King, M., and Zhao, C. (2011). Numerical evaluation of pollutant dispersion at a toll plaza based on system dynamics and Computational Fluid Dynamics models. Transportation Research Part C, 19(2011):510-520. 7. Zhang, C., He, J., Wang, Z., Yin, R. and King, M. (2013). Assessment of traffic noise level before and after freeway widening using traffic microsimulation and a refined classic noise prediction method. Proceedings of Transportation Research Board Annual Conference, Washington DC, 13-17 January 2013, paper no. 13-2016.

A numerical method for the fractional Fitzhugh–Nagumo monodomain model

A fractional FitzHugh–Nagumo monodomain model with zero Dirichlet boundary conditions is presented, generalising the standard monodomain model that describes the propagation of the electrical potential in heterogeneous cardiac tissue. The model consists of a coupled fractional Riesz space nonlinear reaction-diffusion model and a system of ordinary differential equations, describing the ionic fluxes as a function of the membrane potential. We solve this model by decoupling the space-fractional partial differential equation and the system of ordinary differential equations at each time step. Thus, this means treating the fractional Riesz space nonlinear reaction-diffusion model as if the nonlinear source term is only locally Lipschitz. The fractional Riesz space nonlinear reaction-diffusion model is solved using an implicit numerical method with the shifted Grunwald–Letnikov approximation, and the stability and convergence are discussed in detail in the context of the local Lipschitz property. Some numerical examples are given to show the consistency of our computational approach.

DroplIT, an improved image analysis method for droplet identification in high-throughput crystallization trials

The application of robotics to protein crystallization trials has resulted in the production of millions of images. Manual inspection of these images to find crystals and other interesting outcomes is a major rate-limiting step. As a result there has been intense activity in developing automated algorithms to analyse these images. The very first step for most systems that have been described in the literature is to delineate each droplet. Here, a novel approach that reaches over 97% success rate and subsecond processing times is presented. This will form the seed of a new high-throughput system to scrutinize massive crystallization campaigns automatically. © 2010 International Union of Crystallography Printed in Singapore-all rights reserved.

A novel ambiguity acceptance test threshold determination method with controllable failure rate

Ambiguity validation as an important procedure of integer ambiguity resolution is to test the correctness of the fixed integer ambiguity of phase measurements before being used for positioning computation. Most existing investigations on ambiguity validation focus on test statistic. How to determine the threshold more reasonably is less understood, although it is one of the most important topics in ambiguity validation. Currently, there are two threshold determination methods in the ambiguity validation procedure: the empirical approach and the fixed failure rate (FF-) approach. The empirical approach is simple but lacks of theoretical basis. The fixed failure rate approach has a rigorous probability theory basis, but it employs a more complicated procedure. This paper focuses on how to determine the threshold easily and reasonably. Both FF-ratio test and FF-difference test are investigated in this research and the extensive simulation results show that the FF-difference test can achieve comparable or even better performance than the well-known FF-ratio test. Another benefit of adopting the FF-difference test is that its threshold can be expressed as a function of integer least-squares (ILS) success rate with specified failure rate tolerance. Thus, a new threshold determination method named threshold function for the FF-difference test is proposed. The threshold function method preserves the fixed failure rate characteristic and is also easy-to-apply. The performance of the threshold function is validated with simulated data. The validation results show that with the threshold function method, the impact of the modelling error on the failure rate is less than 0.08%. Overall, the threshold function for the FF-difference test is a very promising threshold validation method and it makes the FF-approach applicable for the real-time GNSS positioning applications.

A Boundary-Oriented Chinese Segmentation Method Using NGram Mutual Information

This paper describes our participation in the Chinese word segmentation task of CIPS-SIGHAN 2010. We implemented an n-gram mutual information (NGMI) based segmentation algorithm with the mixed-up features from unsupervised, supervised and dictionarybased segmentation methods. This algorithm is also combined with a simple strategy for out-of-vocabulary (OOV) word recognition. The evaluation for both open and closed training shows encouraging results of our system. The results for OOV word recognition in closed training evaluation were however found unsatisfactory.