Optimizing I/O cost and managing memory for composition vector method based on correlation matrix calculation in bioinformatics

The generation of a correlation matrix for set of genomic sequences is a common requirement in many bioinformatics problems such as phylogenetic analysis. Each sequence may be millions of bases long and there may be thousands of such sequences which we wish to compare, so not all sequences may fit into main memory at the same time. Each sequence needs to be compared with every other sequence, so we will generally need to page some sequences in and out more than once. In order to minimize execution time we need to minimize this I/O. This paper develops an approach for faster and scalable computing of large-size correlation matrices through the maximal exploitation of available memory and reducing the number of I/O operations. The approach is scalable in the sense that the same algorithms can be executed on different computing platforms with different amounts of memory and can be applied to different bioinformatics problems with different correlation matrix sizes. The significant performance improvement of the approach over previous work is demonstrated through benchmark examples.

Pyridine-incorporated dihexylquaterthiophene : a novel blue emitter for organic light emitting diodes (OLEDs)

The synthesis and characterisation of 2,5-bis(5′-hexyl-[2,2′- bithiophen]-5-yl)pyridine (Th4PY) and its use as a blue emitter in organic light emitting diodes (OLEDs) is reported. Th4PY was synthesised in high yield using a straightforward Suzuki coupling route with commercially available starting materials. As Th4PY is both soluble and has low molecular weight, blue OLEDs were fabricated using both spin-coating and vacuum deposition thin film processing techniques to study the effect of processing on device performance. OLED devices using a spin-coated layer consisting of 4′,4′′- tris(N-carbazolyl)triphenylamine (TCTA) and 2-(4-biphenylyl)-5-(4-tert- butylphenyl)-1,3,4-oxadiazole (PBD) as a host matrix together with Th4PY as emitter exhibited highly efficient sky-blue emission with a low turn-on voltage of 3V, a maximum brightness close to 15000cdm-2 at 8V, and a maximum luminous efficiency of 7.4cdA -1 (6.3lmW -1) with CIE coordinates of x≤0.212, y≤0.320. The device performance characteristics are compared using various matrices and processing techniques. The promising sky-blue OLED performance, solution processability, and ambient stability make Th4PY a promising blue emitter for application in OLEDs.

Investigations of dielectric monitoring on an energised transformer oil–paper insulation system

Frequency domain spectroscopy (FDS) is being used to assess the insulation condition of oil–paper power transformers. However, it has to date only been implemented on de-energised transformers, which requires the transformers to be shut down for an extended period and may cause significant costs. To solve this issue, a newly improved monitoring method based on the FDS principle is proposed to implement the dielectric measurement on energised transformers. Moreover, a chirp waveform excitation and its novel processing method are introduced. Compared with the conventional FDS results, dielectric results from the energised insulation system have higher tanδ values because of the increased losses. To further understand the insulation ageing process, the effects of the geometric capacitance are removed from the measured imaginary admittance of the insulation system to enhance the ageing signature. The resulting imaginary admittance is then shown to correlate well with the central time constant in return voltage measurements results. The proposed methods address the issues on techniques used on energised transformers and provide a clue for on-line FDS diagnostic application.

Engineered microenvironments provide new insights into ovarian and prostate cancer progression and drug responses

Tissue engineering technologies, which have originally been designed to reconstitute damaged tissue structure and function, can mimic not only tissue regeneration processes but also cancer development and progression. Bioengineered approaches allow cell biologists to develop sophisticated experimentally and physiologically relevant cancer models to recapitulate the complexity of the disease seen in patients. Tissue engineering tools enable three-dimensionality based on the design of biomaterials and scaffolds that re-create the geometry, chemistry, function and signalling milieu of the native tumour microenvironment. Three-dimensional (3D) microenvironments, including cell-derived matrices, biomaterial-based cell culture models and integrated co-cultures with engineered stromal components, are powerful tools to study dynamic processes like proteolytic functions associated with cancer progression, metastasis and resistance to therapeutics. In this review, we discuss how biomimetic strategies can reproduce a humanised niche for human cancer cells, such as peritoneal or bone-like microenvironments, addressing specific aspects of ovarian and prostate cancer progression and therapy response.

Experimental investigations of improved dielectric condition monitoring methods on transformer oil-paper insulation system

Frequency Domain Spectroscopy (FDS) is successfully being used to assess the insulation condition of oil filled power transformers. However, it has to date only been implemented on de-energized transformers, which requires the transformers to be shut down for an extended period which can result in significant costs. To solve this issue, a method of implementing FDS under energized condition is proposed here. A chirp excitation waveform is used to replace the conventional sinusoidal waveform to reduce the measurement time in this method. Investigation of the dielectric response under the influence of a high voltage stress at power frequency is reported based on experimental results. To further understand the insulation ageing process, the geometric capacitance effect is removed to enhance the detection of the ageing signature. This enhancement enables the imaginary part of admittance to be used as a new indicator to assess the ageing status of the insulation.

Inspection of pole-like structures using a vision-controlled VTOL UAV and shared autonomy

We present an approach for the inspection of vertical pole-like infrastructure using a vertical take-off and landing (VTOL) unmanned aerial vehicle and shared autonomy. Inspecting vertical structures, such as light and power distribution poles, is a time consuming, dangerous and expensive task with high operator workload. To address these issues, we propose a VTOL platform that can operate at close-quarters, whilst maintaining a safe stand-off distance and rejecting environmental disturbances. We adopt an Image based Visual Servoing (IBVS) technique using only two line features to stabilise the vehicle with respect to a pole. Visual, inertial and sonar data are used, making the approach suitable for indoor or GPS-denied environments. Results from simulation and outdoor flight experiments demonstrate the system is able to successfully inspect and circumnavigate a pole.

Levels and trends of PBDEs and HBCDs in the global environment : status at the end of 2012

In this paper, we have compiled and reviewed the most recent literature, published from January2010 to December 2012, relating to the human exposure, environmental distribution, behaviour, fate and concentration time trends of polybrominated diphenyl ether (PBDE) and hexabromocyclododecane (HBCD) flame retardants, in order to establish their current trends and priorities for future study. Due to the large volume of literature included, we have provided full detail of the reviewed studies as Electronic Supplementary Information and here summarise the most relevant findings. Decreasing time trends for penta-mix PBDE congeners were seen for soils in northern Europe, sewage sludge in Sweden and the USA, carp from a US river, trout from three of the Great Lakes and in Arctic and UK marine mammals and many birds, but increasing time trends continue in Arctic polar bears and some birds at high trophic levels in northern Europe. This is a result of the time delay inherent in long-range atmospheric transport processes. In general, concentrations of BDE209 (the major component of the deca-mix PBDE product) are continuing to increase. Of major concern is the possible/likely debromination of the large reservoir of BDE209 in soils and sediments worldwide, to yield lower brominated congeners which are both more mobile and more toxic, and we have compiled the most recent evidence for the occurrence of this degradation process. Numerous studies reported here reinforce the importance o f this future concern. Time trends for HBCDs are mixed, with both increases and decreases evident in different matrices and locations and, notably, with increasing occurrence in birds of prey.

Corporatizing the 'intellectual machinery' of government : the case of educational policy in Australia

This article analyses what it describes as the corporatization of the ‘intellectual machinery’ of government: the theories, knowledges, research and ‘know how’ utilized by political authorities to render the world thinkable, programmable and subject to intervention. Through an analysis of two key nodal points in national policy on teacher professional standards in Australia over the last decade, the article discloses a shift in the relation between expertise and politics. This is manifested, it is argued, in an increased reliance by policy authorities on corporatized forms of research produced by national and international private consulting firms, Think Tanks, and ‘policy entrepreneurs’ and a concomitant decrease in their reliance on free research produced largely by academics in institutions of higher education. The article seeks to account for this shift in terms of the ‘advanced liberal’ formula for rule which now characterizes government in contemporary Western polities.

Fully validated LC–MS/MS method for quantification of homocysteine concentrations in samples of human serum : a new approach

Reported homocysteine (HCY) concentrations in human serum show poor concordance amongst laboratories due to endogenous HCY in the matrices used for assay calibrators and QCs. Hence, we have developed a fully validated LC–MS/MS method for measurement of HCY concentrations in human serum samples that addresses this issue by minimising matrix effects. We used small volumes (20 μL) of 2% Bovine Serum Albumin (BSA) as surrogate matrix for making calibrators and QCs with concentrations adjusted for the endogenous HCY concentration in the surrogate matrix using the method of standard additions. To aliquots (20 μL) of human serum samples, calibrators or QCs, were added HCY-d4 (internal standard) and tris-(2-carboxyethyl) phosphine hydrochloride (TCEP) as reducing agent. After protein precipitation, diluted supernatants were injected into the LC–MS/MS. Calibration curves were linear; QCs were accurate (5.6% deviation from nominal), precise (CV% ≤ 9.6%), stable for four freeze–thaw cycles, and when stored at room temperature for 5 h or at −80 °C (27 days). Recoveries from QCs in surrogate matrix or pooled human serum were 91.9 and 95.9%, respectively. There was no matrix effect using 6 different individual serum samples including one that was haemolysed. Our LC–MS/MS method has satisfied all of the validation criteria of the 2012 EMA guideline.

Affinity adsorption of plasmid DNA

The development of a protein-mediated dual functional affinity adsorption of plasmid DNA is described in this work. The affinity ligand for the plasmid DNA comprises a fusion protein with glutathione-S-transferase (GST) as the fusion partner with a zinc finger protein. The protein ligand is first bound to the adsorbent by affinity interaction between the GST moeity and gluthathione that is covalently immobilized to the base matrix. The plasmid binding is then enabled via the zinc finger protein and a specific nucleotide sequence inserted into the DNA. At lower loadings, the binding of the DNA onto the Fractogel, Sepharose, and Streamline matrices was 0.0078 ± 0.0013, 0.0095 ± 0.0016, and 0.0080 ± 0.0006 mg, respectively, to 50 μL of adsorbent. At a higher DNA challenge, the corresponding amounts were 0.0179 ± 0.0043, 0.0219 ± 0.0035, and 0.0190 ± 0.0041 mg, respectively. The relatively constant amounts bound to the three adsorbents indicated that the large DNA molecule was unable to utilize the available zinc finger sites that were located in the internal pores and binding was largely a surface adsorption phenomenon. Utilization of the zinc finger binding sites was shown to be highest for the Fractogel adsorbent. The adsorbed material was eluted with reduced glutathione, and the eluted efficiency for the DNA was between 23% and 27%. The protein elution profile appeared to match the adsorption profiles with significantly higher recoveries of bound GST-zinc finger protein.

A meshless method based on Point Interpolation Method (PIM) for the space fractional diffusion equation

This paper aims to develop a meshless approach based on the Point Interpolation Method (PIM) for numerical simulation of a space fractional diffusion equation. Two fully-discrete schemes for the one-dimensional space fractional diffusion equation are obtained by using the PIM and the strong-forms of the space diffusion equation. Numerical examples with different nodal distributions are studied to validate and investigate the accuracy and efficiency of the newly developed meshless approach.

Accounting for management costs in sensitivity analyses of matrix population models

Traditional sensitivity and elasticity analyses of matrix population models have been used to inform management decisions, but they ignore the economic costs of manipulating vital rates. For example, the growth rate of a population is often most sensitive to changes in adult survival rate, but this does not mean that increasing that rate is the best option for managing the population because it may be much more expensive than other options. To explore how managers should optimize their manipulation of vital rates, we incorporated the cost of changing those rates into matrix population models. We derived analytic expressions for locations in parameter space where managers should shift between management of fecundity and survival, for the balance between fecundity and survival management at those boundaries, and for the allocation of management resources to sustain that optimal balance. For simple matrices, the optimal budget allocation can often be expressed as simple functions of vital rates and the relative costs of changing them. We applied our method to management of the Helmeted Honeyeater (Lichenostomus melanops cassidix; an endangered Australian bird) and the koala (Phascolarctos cinereus) as examples. Our method showed that cost-efficient management of the Helmeted Honeyeater should focus on increasing fecundity via nest protection, whereas optimal koala management should focus on manipulating both fecundity and survival simultaneously. These findings are contrary to the cost-negligent recommendations of elasticity analysis, which would suggest focusing on managing survival in both cases. A further investigation of Helmeted Honeyeater management options, based on an individual-based model incorporating density dependence, spatial structure, and environmental stochasticity, confirmed that fecundity management was the most cost-effective strategy. Our results demonstrate that decisions that ignore economic factors will reduce management efficiency. ©2006 Society for Conservation Biology.

Exploiting parallax in panoramic capture to construct light fields

We show that the parallax motion resulting from non-nodal rotation in panorama capture can be exploited for light field construction from commodity hardware. Automated panoramic image capture typically seeks to rotate a camera exactly about its nodal point, for which no parallax motion is observed. This can be difficult or impossible to achieve due to limitations of the mounting or optical systems, and consequently a wide range of captured panoramas suffer from parallax between images. We show that by capturing such imagery over a regular grid of camera poses, then appropriately transforming the captured imagery to a common parameterisation, a light field can be constructed. The resulting four-dimensional image encodes scene geometry as well as texture, allowing an increasingly rich range of light field processing techniques to be applied. Employing an Ocular Robotics REV25 camera pointing system, we demonstrate light field capture,refocusing and low-light image enhancement.

A fast semi-implicit difference method for a nonlinear two-sided space-fractional diffusion equation with variable diffusivity coefficients

In this paper, we derive a new nonlinear two-sided space-fractional diffusion equation with variable coefficients from the fractional Fick’s law. A semi-implicit difference method (SIDM) for this equation is proposed. The stability and convergence of the SIDM are discussed. For the implementation, we develop a fast accurate iterative method for the SIDM by decomposing the dense coefficient matrix into a combination of Toeplitz-like matrices. This fast iterative method significantly reduces the storage requirement of O(n2)O(n2) and computational cost of O(n3)O(n3) down to n and O(nlogn)O(nlogn), where n is the number of grid points. The method retains the same accuracy as the underlying SIDM solved with Gaussian elimination. Finally, some numerical results are shown to verify the accuracy and efficiency of the new method.

Stability and convergence of a new finite volume method for a two-sided space-fractional diffusion equation

In this paper, we consider a two-sided space-fractional diffusion equation with variable coefficients on a finite domain. Firstly, based on the nodal basis functions, we present a new fractional finite volume method for the two-sided space-fractional diffusion equation and derive the implicit scheme and solve it in matrix form. Secondly, we prove the stability and convergence of the implicit fractional finite volume method and conclude that the method is unconditionally stable and convergent. Finally, some numerical examples are given to show the effectiveness of the new numerical method, and the results are in excellent agreement with theoretical analysis.