An ensemble method for predicting subnuclear localizations from primary protein structures

Background Predicting protein subnuclear localization is a challenging problem. Some previous works based on non-sequence information including Gene Ontology annotations and kernel fusion have respective limitations. The aim of this work is twofold: one is to propose a novel individual feature extraction method; another is to develop an ensemble method to improve prediction performance using comprehensive information represented in the form of high dimensional feature vector obtained by 11 feature extraction methods. Methodology/Principal Findings A novel two-stage multiclass support vector machine is proposed to predict protein subnuclear localizations. It only considers those feature extraction methods based on amino acid classifications and physicochemical properties. In order to speed up our system, an automatic search method for the kernel parameter is used. The prediction performance of our method is evaluated on four datasets: Lei dataset, multi-localization dataset, SNL9 dataset and a new independent dataset. The overall accuracy of prediction for 6 localizations on Lei dataset is 75.2% and that for 9 localizations on SNL9 dataset is 72.1% in the leave-one-out cross validation, 71.7% for the multi-localization dataset and 69.8% for the new independent dataset, respectively. Comparisons with those existing methods show that our method performs better for both single-localization and multi-localization proteins and achieves more balanced sensitivities and specificities on large-size and small-size subcellular localizations. The overall accuracy improvements are 4.0% and 4.7% for single-localization proteins and 6.5% for multi-localization proteins. The reliability and stability of our classification model are further confirmed by permutation analysis. Conclusions It can be concluded that our method is effective and valuable for predicting protein subnuclear localizations. A web server has been designed to implement the proposed method. It is freely available at http://bioinformatics.awowshop.com/snlpr​ed_page.php.

Kinetic energy of He atoms in liquid He-4-He-3 mixtures

Deep inelastic neutron scattering measurements on liquid 3He-4He mixtures in the normal phase have been performed on the VESUVIO spectrometer at the ISIS pulsed neutron source at exchanged wave vectors of about q≃120.0Å-1. The neutron Compton profiles J(y) of the mixtures were measured along the T=1.96K isotherm for 3He concentrations, x, ranging from 0.1 to 1.0 at saturated vapor pressures. Values of kinetic energies 〈T〉 of 3He and 4He atoms as a function of x, 〈T〉(x), were extracted from the second moment of J(y). The present determinations of 〈T〉(x) confirm previous experimental findings for both isotopes and, in the case of 3He, a substantial disagreement with theory is found. In particular 〈T〉(x) for the 3He atoms is found to be independent of concentration yielding a value 〈T〉3(x=0.1)≃12K, much lower than the value suggested by the most recent theoretical estimates of approximately 19 K.

Shahejie−Shahejie/Guantao/Wumishan and Carboniferous/Permian Coal−Paleozoic Total Petroleum Systems in the Bohaiwan Basin, China (based on geologic studies for the 2000 World Energy Assessment Project of the U.S. Geological Survey)

This report discusses the geologic framework and petroleum geology used to assess undiscovered petroleum resources in the Bohaiwan basin province for the 2000 World Energy Assessment Project of the U.S. Geological Survey. The Bohaiwan basin in northeastern China is the largest petroleum-producing region in China. Two total petroleum systems have been identified in the basin. The first, the Shahejie–Shahejie/Guantao/Wumishan Total Petroleum System, involves oil and gas generated from mature pods of lacustrine source rock that are associated with six major rift-controlled subbasins. Two assessment units are defined in this total petroleum system: (1) a Tertiary lacustrine assessment unit consisting of sandstone reservoirs interbedded with lacustrine shale source rocks, and (2) a pre-Tertiary buried hills assessment unit consisting of carbonate reservoirs that are overlain unconformably by Tertiary lacustrine shale source rocks. The second total petroleum system identified in the Bohaiwan basin is the Carboniferous/Permian Coal–Paleozoic Total Petroleum System, a hypothetical total petroleum system involving natural gas generated from multiple pods of thermally mature coal beds. Low-permeability Permian sandstones and possibly Carboniferous coal beds are the reservoir rocks. Most of the natural gas is inferred to be trapped in continuous accumulations near the center of the subbasins. This total petroleum system is largely unexplored and has good potential for undiscovered gas accumulations. One assessment unit, coal-sourced gas, is defined in this total petroleum system.

A pre-treatment verification tool for IMRT based on EPID measurements and a GEANT4 back projection application

The aim of this work is to develop software that is capable of back projecting primary fluence images obtained from EPID measurements through phantom and patient geometries in order to calculate 3D dose distributions. In the first instance, we aim to develop a tool for pretreatment verification in IMRT. In our approach, a Geant4 application is used to back project primary fluence values from each EPID pixel towards the source. Each beam is considered to be polyenergetic, with a spectrum obtained from Monte Carlo calculations for the LINAC in question. At each step of the ray tracing process, the energy differential fluence is corrected for attenuation and beam divergence. Subsequently, the TERMA is calculated and accumulated to an energy differential 3D TERMA distribution. This distribution is then convolved with monoenergetic point spread kernels, thus generating energy differential 3D dose distributions. The resulting dose distributions are accumulated to yield the total dose distribution, which can then be used for pre-treatment verification of IMRT plans. Preliminary results were obtained for a test EPID image comprised of 100 9 100 pixels of unity fluence. Back projection of this field into a 30 cm9 30 cm 9 30 cm water phantom was performed, with TERMA distributions obtained in approximately 10 min (running on a single core of a 3 GHz processor). Point spread kernels for monoenergetic photons in water were calculated using a separate Geant4 application. Following convolution and summation, the resulting 3D dose distribution produced familiar build-up and penumbral features. In order to validate the dose model we will use EPID images recorded without any attenuating material in the beam for a number of MLC defined square fields. The dose distributions in water will be calculated and compared to TPS predictions.

Phantom Scatter and the A-SI EPID

Introduction: The use of amorphous-silicon electronic portal imaging devices (a-Si EPIDs) for dosimetry is complicated by the effects of scattered radiation. In photon radiotherapy, primary signal at the detector can be accompanied by photons scattered from linear accelerator components, detector materials, intervening air, treatment room surfaces (floor, walls, etc) and from the patient/phantom being irradiated. Consequently, EPID measurements which presume to take scatter into account are highly sensitive to the identification of these contributions. One example of this susceptibility is the process of calibrating an EPID for use as a gauge of (radiological) thickness, where specific allowance must be made for the effect of phantom-scatter on the intensity of radiation measured through different thicknesses of phantom. This is usually done via a theoretical calculation which assumes that phantom scatter is linearly related to thickness and field-size. We have, however, undertaken a more detailed study of the scattering effects of fields of different dimensions when applied to phantoms of various thicknesses in order to derive scattered-primary ratios (SPRs) directly from simulation results. This allows us to make a more-accurate calibration of the EPID, and to qualify the appositeness of the theoretical SPR calculations. Methods: This study uses a full MC model of the entire linac-phantom-detector system simulated using EGSnrc/BEAMnrc codes. The Elekta linac and EPID are modelled according to specifications from the manufacturer and the intervening phantoms are modelled as rectilinear blocks of water or plastic, with their densities set to a range of physically realistic and unrealistic values. Transmissions through these various phantoms are calculated using the dose detected in the model EPID and used in an evaluation of the field-size-dependence of SPR, in different media, applying a method suggested for experimental systems by Swindell and Evans [1]. These results are compared firstly with SPRs calculated using the theoretical, linear relationship between SPR and irradiated volume, and secondly with SPRs evaluated from our own experimental data. An alternate evaluation of the SPR in each simulated system is also made by modifying the BEAMnrc user code READPHSP, to identify and count those particles in a given plane of the system that have undergone a scattering event. In addition to these simulations, which are designed to closely replicate the experimental setup, we also used MC models to examine the effects of varying the setup in experimentally challenging ways (changing the size of the air gap between the phantom and the EPID, changing the longitudinal position of the EPID itself). Experimental measurements used in this study were made using an Elekta Precise linear accelerator, operating at 6MV, with an Elekta iView GT a-Si EPID. Results and Discussion: 1. Comparison with theory: With the Elekta iView EPID fixed at 160 cm from the photon source, the phantoms, when positioned isocentrically, are located 41 to 55 cm from the surface of the panel. At this geometry, a close but imperfect agreement (differing by up to 5%) can be identified between the results of the simulations and the theoretical calculations. However, this agreement can be totally disrupted by shifting the phantom out of the isocentric position. Evidently, the allowance made for source-phantom-detector geometry by the theoretical expression for SPR is inadequate to describe the effect that phantom proximity can have on measurements made using an (infamously low-energy sensitive) a-Si EPID. 2. Comparison with experiment: For various square field sizes and across the range of phantom thicknesses, there is good agreement between simulation data and experimental measurements of the transmissions and the derived values of the primary intensities. However, the values of SPR obtained through these simulations and measurements seem to be much more sensitive to slight differences between the simulated and real systems, leading to difficulties in producing a simulated system which adequately replicates the experimental data. (For instance, small changes to simulated phantom density make large differences to resulting SPR.) 3. Comparison with direct calculation: By developing a method for directly counting the number scattered particles reaching the detector after passing through the various isocentric phantom thicknesses, we show that the experimental method discussed above is providing a good measure of the actual degree of scattering produced by the phantom. This calculation also permits the analysis of the scattering sources/sinks within the linac and EPID, as well as the phantom and intervening air. Conclusions: This work challenges the assumption that scatter to and within an EPID can be accounted for using a simple, linear model. Simulations discussed here are intended to contribute to a fuller understanding of the contribution of scattered radiation to the EPID images that are used in dosimetry calculations. Acknowledgements: This work is funded by the NHMRC, through a project grant, and supported by the Queensland University of Technology (QUT) and the Royal Brisbane and Women's Hospital, Brisbane, Australia. The authors are also grateful to Elekta for the provision of manufacturing specifications which permitted the detailed simulation of their linear accelerators and amorphous-silicon electronic portal imaging devices. Computational resources and services used in this work were provided by the HPC and Research Support Group, QUT, Brisbane, Australia.

Smart coordination of energy storage units (ESUs) for voltage and loading management in distribution networks

This paper proposes a distributed control approach to coordinate multiple energy storage units (ESUs) to avoid violation of voltage and thermal constraints, which are some of the main power quality challenges for future distribution networks. ESUs usually are connected to a network through voltage source converters. In this paper, both ESU converters active and reactive power are used to deal with the above mentioned power quality issues. ESUs' reactive power is proposed to be used for voltage support, while the active power is to be utilized in managing network loading. Two typical distribution networks are used to apply the proposed method, and the simulated results are illustrated in this paper to show the effectiveness of this approach.

BoP and MNCs: where is the market and where the source of innovation?

ln 2004 Prahalad made managers aware of the great economic opportunity that the population at the BoP (Base of the Pyramid) could represent for business in the tom of new potential consumers. However, MNCs (Multi-National Corporations) have continued to fail in penetrating low income markets, arguably because applied strategies are often the same adopted at the top of the pyramid. Even in those few cases where products get re-envisioned, theie introduction in contexts of extreme poverty only induces new needs and develops new dependencies. At best the rearrangement of business models by MNCs has meant the realization of CSR (Corporate Social Responsibly) schemes that have validity from a marketing perspective, but still lack the crucial element of social embeddedness (London & Hart, 2004). Today the challenge is lo reach the lowest population tier with reinvented business models based on principles of value co-creation. Starting from a view of the potential consumer at the BoP as a ring of continuity in the value chain process – a resource that can itself produce value - this paper concludes proposing an alternative innovative approach to operate in developing markets that overturns the roles of MNCs and the BoP. The proposed perspective of ‘reversed' source of innovation and primary target market builds on two fundamental tenets: traditional knowledge is rich and greatly unexploded, and markets at the lop of the pyramid are saturated with unnecessary products / practices that have lost contact with the natural environment.

BoP and MNCs: where is the market and where the source of innovation?

ln 2004 Prahalad made managers aware of the great economic opportunity that the population at the BoP (Base of the Pyramid) could represent for business in the tom of new potential consumers. However, MNCs (Multi-National Corporations) have continued to fail in penetrating low income markets, arguably because applied strategies are often the same adopted at the top of the pyramid. Even in those few cases where products get re-envisioned, theie introduction in contexts of extreme poverty only induces new needs and develops new dependencies. At best the rearrangement of business models by MNCs has meant the realization of CSR (Corporate Social Responsibly) schemes that have validity from a marketing perspective, but still lack the crucial element of social embeddedness (London & Hart, 2004). Today the challenge is lo reach the lowest population tier with reinvented business models based on principles of value co-creation. Starting from a view of the potential consumer at the BoP as a ring of continuity in the value chain process – a resource that can itself produce value - this paper concludes proposing an alternative innovative approach to operate in developing markets that overturns the roles of MNCs and the BoP. The proposed perspective of ‘reversed' source of innovation and primary target market builds on two fundamental tenets: traditional knowledge is rich and greatly unexploded, and markets at the lop of the pyramid are saturated with unnecessary products / practices that have lost contact with the natural environment.

The influence of cellular source on periodontal regeneration using calcium phosphate coated polycaprolactone scaffold supported cell sheets

Cell-based therapy is considered a promising approach to achieving predictable periodontal regeneration. In this study, the regenerative potential of cell sheets derived from different parts of the periodontium (gingival connective tissue, alveolar bone and periodontal ligament) were investigated in an athymic rat periodontal defect model. Periodontal ligament (PDLC), alveolar bone (ABC) and gingival margin-derived cells (GMC) were obtained from human donors. The osteogenic potential of the primary cultures was demonstrated in vitro. Cell sheets supported by a calcium phosphate coated melt electrospun polycaprolactone (CaP-PCL) scaffold were transplanted to denuded root surfaces in surgically created periodontal defects, and allowed to heal for 1 and 4 weeks. The CaP-PCL scaffold alone was able to promote alveolar bone formation within the defect after 4 weeks. The addition of ABC and PDLC sheets resulted in significant periodontal attachment formation. The GMC sheets did not promote periodontal regeneration on the root surface and inhibited bone formation within the CaP-PCL scaffold. In conclusion, the combination of either PDLC or ABC sheets with a CaP-PCL scaffold could promote periodontal regeneration, but ABC sheets were not as effective as PDLC sheets in promoting new attachment formation.

Vehicle energy throughput analysis as a drivetrain motor design aid

There are many variables to consider in the design of an electric motor. However, meeting the performance requirements for an electric vehicle drive may cause a designer to loose focus on its typical operation and hence fail to optimise the motor in the region where it processes the most power. This paper investigates operating requirements of electric vehicle motor drives using the University concept vehicle as an example. The paper outlines a methodology for determining primary operating region of a vehicle drive. The methodology is applied to standard driving cycles that are commonly used in the design and testing of vehicles.

Food in an Australian primary school curriculum : a critical sociological study

Food is a multidimensional construct. It has social, cultural, economic, psychological, emotional, biological, and political dimensions. It is both a material object and a catalyst for a range of social and cultural action. Richly implicated in the social and cultural milieu, food is a central marker of culture and society. Yet little is known about the messages and knowledges in the school curriculum about food. Popular debates around food in schools are largely connected with biomedical issues of obesity, exercise and nutrition. This is a study of the sociological dimensions of food-related messages, practices and knowledge formations in the primary school curriculum. It uses an exploratory, qualitative case study methodology to identify and examine the food activities of a Year 5 class in a Queensland school. Data was gathered over a twoyear period using observation, documentation and interviews methods. Food was found to be an integral part of the primary school's activity. It had economic, symbolic, pedagogic, and instrumental value. Messages about food were found in the official, enacted and hidden curricular which were framed by a food governance framework of legislation, procedures and norms. In the school studied, food knowledge was commodified as a part of a political economy that centred on an 'eat more' message. Certain foods were privileged over others while myths about energy, fruit, fruit juice and sugar shaped student dispositions, values, norms and action. There was little engagement with the cognitive and behavioural dimensions of food and nutrition. The thesis concludes with recommendations for a whole scale reconsideration of food in schools as curricular content and knowledge.

Towards a dignified and sustainable electricity generation sector in Australia : a comparative review of three models

Electricity is the cornerstone of modern life. It is essential to economic stability and growth, jobs and improved living standards. Electricity is also the fundamental ingredient for a dignified life; it is the source of such basic human requirements as cooked food, a comfortable living temperature and essential health care. For these reasons, it is unimaginable that today's economies could function without electricity and the modern energy services that it delivers. Somewhat ironically, however, the current approach to electricity generation also contributes to two of the gravest and most persistent problems threatening the livelihood of humans. These problems are anthropogenic climate change and sustained human poverty. To address these challenges, the global electricity sector must reduce its reliance on fossil fuel sources. In this context, the object of this research is twofold. Initially it is to consider the design of the Renewable Energy (Electricity) Act 2000 (Cth) (Renewable Electricity Act), which represents Australia's primary regulatory approach to increase the production of renewable sourced electricity. This analysis is conducted by reference to the regulatory models that exist in Germany and Great Britain. Within this context, this thesis then evaluates whether the Renewable Electricity Act is designed effectively to contribute to a more sustainable and dignified electricity generation sector in Australia. On the basis of the appraisal of the Renewable Electricity Act, this thesis contends that while certain aspects of the regulatory regime have merit, ultimately its design does not represent an effective and coherent regulatory approach to increase the production of renewable sourced electricity. In this regard, this thesis proposes a number of recommendations to reform the existing regime. These recommendations are not intended to provide instantaneous or simple solutions to the current regulatory regime. Instead, the purpose of these recommendations is to establish the legal foundations for an effective regulatory regime that is designed to increase the production of renewable sourced electricity in Australia in order to contribute to a more sustainable and dignified approach to electricity production.

Primary stability of two uncemented acetabular components of different geometry : hemispherical or peripherally enhanced?

Objective This study compared the primary stability of two commercially available acetabular components from the same manufacturer, which differ only in geometry; a hemispherical and a peripherally enhanced design (peripheral self-locking (PSL)). The objective was to determine whether altered geometry resulted in better primary stability. Methods Acetabular components were seated with 0.8 mm to 2 mm interference fits in reamed polyethylene bone substrate of two different densities (0.22 g/cm3 and 0.45 g/cm3). The primary stability of each component design was investigated by measuring the peak failure load during uniaxial pull-out and tangential lever-out tests. Results There was no statistically significant difference in seating force (p = 0.104) or primary stability (pull-out p = 0.171, lever-out p = 0.087) of the two components in the low-density substrate. Similarly, in the high-density substrate, there was no statistically significant difference in the peak pull-out force (p = 0.154) or lever-out moment (p = 0.574) between the designs. However, the PSL component required a significantly higher seating force thanthe hemispherical cup in the high-density bone analogue (p = 0.006). Conclusions Higher seating forces associated with the PSL design may result in inadequate seating and increased risk of component malpositioning or acetabular fracture in the intra-operative setting in high-density bone stock. Our results, if translated clinically, suggest that a purely hemispherical geometry may have an advantage over a peripherally enhanced geometry in high density bone stock.

Atmospheric particles as a pollutant source in the urban water environment in Sri Lanka – current research trends and future directions

Human and ecosystem health impacts imposed by water pollution are a major problem in the urban areas of Sri Lanka. A primary source of pollutants to urban water sources is atmospheric particles. Hence, it is important to develop a detailed understanding of atmospheric particle characteristics, their sources of origin and the transport pathways. Several research studies have been conducted in Sri Lanka on atmospheric pollution and these studies have tended to differ in their scope, study region and the investigated pollutants. The objectives of this paper are: (1) to report the outcomes of a detailed state-of-art literature review of atmospheric pollution related studies in Sri Lanka to understand the current trends and (2) to discuss the future research activities necessary to generate the important knowledge required for the development of effective strategies to control the adverse impacts of atmospheric pollution on urban waterways.

The influence of Monte Carlo source parameters on detector design and dose perturbation in small field dosimetry

To obtain accurate Monte Carlo simulations of small radiation fields, it is important model the initial source parameters (electron energy and spot size) accurately. However recent studies have shown that small field dosimetry correction factors are insensitive to these parameters. The aim of this work is to extend this concept to test if these parameters affect dose perturbations in general, which is important for detector design and calculating perturbation correction factors. The EGSnrc C++ user code cavity was used for all simulations. Varying amounts of air between 0 and 2 mm were deliberately introduced upstream to a diode and the dose perturbation caused by the air was quantified. These simulations were then repeated using a range of initial electron energies (5.5 to 7.0 MeV) and electron spot sizes (0.7 to 2.2 FWHM). The resultant dose perturbations were large. For example 2 mm of air caused a dose reduction of up to 31% when simulated with a 6 mm field size. However these values did not vary by more than 2 % when simulated across the full range of source parameters tested. If a detector is modified by the introduction of air, one can be confident that the response of the detector will be the same across all similar linear accelerators and the Monte Carlo modelling of each machine is not required.