Developments in texture-based vector field visualisation techniques

Vector field visualisation is one of the classic sub-fields of scientific data visualisation. The need for effective visualisation of flow data arises in many scientific domains ranging from medical sciences to aerodynamics. Though there has been much research on the topic, the question of how to communicate flow information effectively in real, practical situations is still largely an unsolved problem. This is particularly true for complex 3D flows. In this presentation we give a brief introduction and background to vector field visualisation and comment on the effectiveness of the most common solutions. We will then give some examples of current development on texture-based techniques, and given practical examples of their use in CFD research and hydrodynamic applications.

Decentralised particle filtering for multiple target tracking in wireless sensor networks

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Range sensor pose estimation

This paper presents a method of recovering the 6 DoF pose (Cartesian position and angular rotation) of a range sensor mounted on a mobile platform. The method utilises point targets in a local scene and optimises over the error between their absolute position and their apparent position as observed by the range sensor. The analysis includes an investigation into the sensitivity and robustness of the method. Practical results were collected using a SICK LRS2100 mounted on a P&H electric mining shovel and present the errors in scan data relative to an independent 3D scan of the scene. A comparison to directly measuring the sensor pose is presented and shows the significant accuracy improvements in scene reconstruction using this pose estimation method.

Secure data aggregation in wireless sensor networks

A Wireless Sensor Network (WSN) is a set of sensors that are integrated with a physical environment. These sensors are small in size, and capable of sensing physical phenomena and processing them. They communicate in a multihop manner, due to a short radio range, to form an Ad Hoc network capable of reporting network activities to a data collection sink. Recent advances in WSNs have led to several new promising applications, including habitat monitoring, military target tracking, natural disaster relief, and health monitoring. The current version of sensor node, such as MICA2, uses a 16 bit, 8 MHz Texas Instruments MSP430 micro-controller with only 10 KB RAM, 128 KB program space, 512 KB external ash memory to store measurement data, and is powered by two AA batteries. Due to these unique specifications and a lack of tamper-resistant hardware, devising security protocols for WSNs is complex. Previous studies show that data transmission consumes much more energy than computation. Data aggregation can greatly help to reduce this consumption by eliminating redundant data. However, aggregators are under the threat of various types of attacks. Among them, node compromise is usually considered as one of the most challenging for the security of WSNs. In a node compromise attack, an adversary physically tampers with a node in order to extract the cryptographic secrets. This attack can be very harmful depending on the security architecture of the network. For example, when an aggregator node is compromised, it is easy for the adversary to change the aggregation result and inject false data into the WSN. The contributions of this thesis to the area of secure data aggregation are manifold. We firstly define the security for data aggregation in WSNs. In contrast with existing secure data aggregation definitions, the proposed definition covers the unique characteristics that WSNs have. Secondly, we analyze the relationship between security services and adversarial models considered in existing secure data aggregation in order to provide a general framework of required security services. Thirdly, we analyze existing cryptographic-based and reputationbased secure data aggregation schemes. This analysis covers security services provided by these schemes and their robustness against attacks. Fourthly, we propose a robust reputationbased secure data aggregation scheme for WSNs. This scheme minimizes the use of heavy cryptographic mechanisms. The security advantages provided by this scheme are realized by integrating aggregation functionalities with: (i) a reputation system, (ii) an estimation theory, and (iii) a change detection mechanism. We have shown that this addition helps defend against most of the security attacks discussed in this thesis, including the On-Off attack. Finally, we propose a secure key management scheme in order to distribute essential pairwise and group keys among the sensor nodes. The design idea of the proposed scheme is the combination between Lamport's reverse hash chain as well as the usual hash chain to provide both past and future key secrecy. The proposal avoids the delivery of the whole value of a new group key for group key update; instead only the half of the value is transmitted from the network manager to the sensor nodes. This way, the compromise of a pairwise key alone does not lead to the compromise of the group key. The new pairwise key in our scheme is determined by Diffie-Hellman based key agreement.

Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

Background The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

Cardiac health diagnosis using higher order spectra and support vector machine

The Electrocardiogram (ECG) is an important bio-signal representing the sum total of millions of cardiac cell depolarization potentials. It contains important insight into the state of health and nature of the disease afflicting the heart. Heart rate variability (HRV) refers to the regulation of the sinoatrial node, the natural pacemaker of the heart by the sympathetic and parasympathetic branches of the autonomic nervous system. The HRV signal can be used as a base signal to observe the heart's functioning. These signals are non-linear and non-stationary in nature. So, higher order spectral (HOS) analysis, which is more suitable for non-linear systems and is robust to noise, was used. An automated intelligent system for the identification of cardiac health is very useful in healthcare technology. In this work, we have extracted seven features from the heart rate signals using HOS and fed them to a support vector machine (SVM) for classification. Our performance evaluation protocol uses 330 subjects consisting of five different kinds of cardiac disease conditions. We demonstrate a sensitivity of 90% for the classifier with a specificity of 87.93%. Our system is ready to run on larger data sets.

Overcoming the complexity of diagnostic problems due to sensor network architecture

In fault detection and diagnostics, limitations coming from the sensor network architecture are one of the main challenges in evaluating a system’s health status. Usually the design of the sensor network architecture is not solely based on diagnostic purposes, other factors like controls, financial constraints, and practical limitations are also involved. As a result, it quite common to have one sensor (or one set of sensors) monitoring the behaviour of two or more components. This can significantly extend the complexity of diagnostic problems. In this paper a systematic approach is presented to deal with such complexities. It is shown how the problem can be formulated as a Bayesian network based diagnostic mechanism with latent variables. The developed approach is also applied to the problem of fault diagnosis in HVAC systems, an application area with considerable modeling and measurement constraints.

Pseudoseeds : investigating long-distance, ocean seed dispersal with wireless sensors

Recent theoretical research has shown that ocean currents and wind interact to disperse seeds over long distances among isolated landmasses. Dispersal of seeds among isolated oceanic islands, by birds, oceans and man, is a well-known phenomenon, and many widespread island plants have traits that facilitate this process. Crucially, however, there have been no mechanistic vector-based models of long-distance dispersal for seeds among isolated oceanic islands based on empirical data. Here, we propose a plan to develop seed analogues, or pseudoseeds, fitted with wireless sensor technology that will enable high-fidelity tracking as they disperse across the ocean. The pseudoseeds will be precisely designed to mimic actual seed buoyancy and morphology enabling realistic and accurate, vector-based dispersal models of ocean seed dispersal over vast geographic scales.

A compact interferometric sensor design using three waveguide coupling

The use of metal stripes for the guiding of plasmons is a well established technique for the infrared regime and has resulted in the development of a myriad of passive optical components and sensing devices. However, the plasmons suffer from large losses around sharp bends, making the compact design of nanoscale sensors and circuits problematic. A compact alternative would be to use evanescent coupling between two sufficiently close stripes, and thus we propose a compact interferometer design using evanescent coupling. The sensitivity of the design is compared with that achieved using a hand-held sensor based on the Kretschmann style surface plasmon resonance technique. Modeling of the new interferometric sensor is performed for various structural parameters using finite-difference time-domain and COMSOL Multiphysics. The physical mechanisms behind the coupling and propagation of plasmons in this structure are explained in terms of the allowed modes in each section of the device.

Predicting residue-wise contact orders in proteins by support vector regression

Background The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. Results We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. Conclusion The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.