Modelling Human-Fire Interactions: Combining Alternative Perspectives and Approaches

Although it has long been recognised that human activities affect fire regimes, the interactions between humans and fire are complex, imperfectly understood, constantly evolving, and lacking any kind of integrative global framework. Many different approaches are used to study human-fire interactions, but in general they have arisen in different disciplinary contexts to address highly specific questions. Models of human-fire interactions range from conceptual local models to numerical global models. However, given that each type of model is highly selective about which aspects of human-fire interactions to include, the insights gained from these models are often limited and contradictory, which can make them a poor basis for developing fire-related policy and management practices. Here, we first review different approaches to modelling human-fire interactions and then discuss ways in which these different approaches could be synthesised to provide a more holistic approach to understanding human-fire interactions. We argue that the theory underpinning many types of models was developed using only limited amounts of data and that, in an increasingly data-rich world, it is important to re-examine model assumptions in a more systematic way. All of the models are designed to have practical outcomes but are necessarily simplifications of reality and as a result of differences in focus, scale and complexity, frequently yield radically different assessments of what might happen. We argue that it should be possible to combine the strengths and benefits of different types of model through enchaining the different models, for example from global down to local scales or vice versa. There are also opportunities for explicit coupling of different kinds of model, for example including agent-based representation of human actions in a global fire model. Finally, we stress the need for co-production of models to ensure that the resulting products serve the widest possible community

Prediction of backbone dihedral angles and protein secondary structure using support vector machines

<p>Abstract</p> <p>Background</p> <p>The prediction of the secondary structure of a protein is a critical step in the prediction of its tertiary structure and, potentially, its function. Moreover, the backbone dihedral angles, highly correlated with secondary structures, provide crucial information about the local three-dimensional structure.</p> <p>Results</p> <p>We predict independently both the secondary structure and the backbone dihedral angles and combine the results in a loop to enhance each prediction reciprocally. Support vector machines, a state-of-the-art supervised classification technique, achieve secondary structure predictive accuracy of 80% on a non-redundant set of 513 proteins, significantly higher than other methods on the same dataset. The dihedral angle space is divided into a number of regions using two unsupervised clustering techniques in order to predict the region in which a new residue belongs. The performance of our method is comparable to, and in some cases more accurate than, other multi-class dihedral prediction methods.</p> <p>Conclusions</p> <p>We have created an accurate predictor of backbone dihedral angles and secondary structure. Our method, called DISSPred, is available online at <url>http://comp.chem.nottingham.ac.uk/disspred/</url>.</p

TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences

Protein backbone torsion angles (Phi) and (Psi) involve two rotation angles rotating around the Cα-N bond (Phi) and the Cα-C bond (Psi). Due to the planarity of the linked rigid peptide bonds, these two angles can essentially determine the backbone geometry of proteins. Accordingly, the accurate prediction of protein backbone torsion angle from sequence information can assist the prediction of protein structures. In this study, we develop a new approach called TANGLE (Torsion ANGLE predictor) to predict the protein backbone torsion angles from amino acid sequences. TANGLE uses a two-level support vector regression approach to perform real-value torsion angle prediction using a variety of features derived from amino acid sequences, including the evolutionary profiles in the form of position-specific scoring matrices, predicted secondary structure, solvent accessibility and natively disordered region as well as other global sequence features. When evaluated based on a large benchmark dataset of 1,526 non-homologous proteins, the mean absolute errors (MAEs) of the Phi and Psi angle prediction are 27.8° and 44.6°, respectively, which are 1% and 3% respectively lower than that using one of the state-of-the-art prediction tools ANGLOR. Moreover, the prediction of TANGLE is significantly better than a random predictor that was built on the amino acid-specific basis, with the p-value<1.46e-147 and 7.97e-150, respectively by the Wilcoxon signed rank test. As a complementary approach to the current torsion angle prediction algorithms, TANGLE should prove useful in predicting protein structural properties and assisting protein fold recognition by applying the predicted torsion angles as useful restraints. TANGLE is freely accessible at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/TANGLE/

NetTurnP – Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features

UNLABELLED: β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino acid sequence. The individual β-turn types I, I', II, II', VIII, VIa1, VIa2, VIba and IV have been predicted based on classifications by PROMOTIF, and the two-class prediction of β-turn or not is a superset comprised of all β-turn types. The performance is evaluated using a golden set of non-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC=0.50, Qtotal=82.1%, sensitivity=75.6%, PPV=68.8% and AUC=0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17-0.47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively. CONCLUSION: The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences

Coordinated parallelizing compiler optimizations and high-level synthesis

We present a high-level synthesis methodology that applies a coordinated set of coarse-grain and fine-grain parallelizing transformations. The transformations are applied both during a presynthesis phase and during scheduling, with the objective of optimizing the results of synthesis and reducing the impact of control flow constructs on the quality of results. We first apply a set of source level presynthesis transformations that include common sub-expression elimination (CSE), copy propagation, dead code elimination and loop-invariant code motion, along with more coarse-level code restructuring transformations such as loop unrolling. We then explore scheduling techniques that use a set of aggressive speculative code motions to maximally parallelize the design by re-ordering, speculating and sometimes even duplicating operations in the design. In particular, we present a new technique called "Dynamic CSE" that dynamically coordinates CSE and code motions such as speculation and conditional speculation during scheduling. We implemented our parallelizing high-level synthesis in the SPARK framework. This framework takes a behavioral description in ANSI-C as input and generates synthesizable register-transfer level VHDL. Our results from computationally expensive portions of three moderately complex design targets, namely, MPEG-1, MPEG-2 and the GIMP image processing too], validate the utility of our approach to the behavioral synthesis of designs with complex control flows

Efficacy of customised foot orthoses in the treatment of achilles tendinopathy : study protocol for a randomised trial

BACKGROUND: Achilles tendinopathy is a common condition that can cause marked pain and disability. Numerous non-surgical treatments have been proposed for the treatment of this condition, but many of these treatments have a poor or non-existent evidence base. The exception to this is eccentric calf muscle exercises, which have become a standard non-surgical intervention for Achilles tendinopathy. Foot orthoses have also been advocated as a treatment for Achilles tendinopathy, but the long-term efficacy of foot orthoses for this condition is unknown. This manuscript describes the design of a randomised trial to evaluate the efficacy of customised foot orthoses to reduce pain and improve function in people with Achilles tendinopathy. METHODS: One hundred and forty community-dwelling men and women aged 18 to 55 years with Achilles tendinopathy (who satisfy inclusion and exclusion criteria) will be recruited. Participants will be randomised, using a computer-generated random number sequence, to either a control group (sham foot orthoses made from compressible ethylene vinyl acetate foam) or an experimental group (customised foot orthoses made from semi-rigid polypropylene). Both groups will be prescribed a calf muscle eccentric exercise program, however, the primary difference between the groups will be that the experimental group receive customised foot orthoses, while the control group receive sham foot orthoses. The participants will be instructed to perform eccentric exercises 2 times per day, 7 days per week, for 12 weeks. The primary outcome measure will be the total score of the Victorian Institute of Sport Assessment - Achilles (VISA-A) questionnaire. The secondary outcome measures will be participant perception of treatment effect, comfort of the foot orthoses, use of co-interventions, frequency and severity of adverse events, level of physical activity and health-related quality of life (assessed using the Short-Form-36 questionnaire - Version two). Data will be collected at baseline, then at 1, 3, 6 and 12 months. Data will be analysed using the intention to treat principle. DISCUSSION: This study is the first randomised trial to evaluate the long-term efficacy of customised foot orthoses for the treatment of Achilles tendinopathy. The study has been pragmatically designed to ensure that the study findings are generalisable to clinical practice. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry Number: ACTRN12609000829213

Heterogeneous and opportunistic wireless networks

Recent years have witnessed the evolution of a large plethora of wireless technologies with different characteristics, as a response of the operators' and users' needs in terms of an efficient and ubiquitous delivery of advanced multimedia services. The wireless segment of network infrastructure has penetrated in our lives, and wireless connectivity has now reached a state where it is considered to be an indispensable service as electricity or water supply. Wireless data networks grow increasingly complex as a multiplicity of wireless information terminals with sophisticated capabilities get embedded in the infrastructure. © 2012 Springer Milan. All Right Reserved