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    Using supernetworks to distinguish hybridization from lineage-sorting
    (BioMed Central, 2008) Holland BR; Benthin S; Lockhart PJ; Moulton V; Huber KT
    BackgroundA simple and widely used approach for detecting hybridization in phylogenies is to reconstruct gene trees from independent gene loci, and to look for gene tree incongruence. However, this approach may be confounded by factors such as poor taxon-sampling and/or incomplete lineage-sorting.ResultsUsing coalescent simulations, we investigated the potential of supernetwork methods to differentiate between gene tree incongruence arising from taxon sampling and incomplete lineage-sorting as opposed to hybridization. For few hybridization events, a large number of independent loci, and well-sampled taxa across these loci, we found that it was possible to distinguish incomplete lineage-sorting from hybridization using the filtered Z-closure and Q-imputation supernetwork methods. Moreover, we found that the choice of supernetwork method was less important than the choice of filtering, and that count-based filtering was the most effective filtering technique.ConclusionFiltered supernetworks provide a tool for detecting and identifying hybridization events in phylogenies, a tool that should become increasingly useful in light of current genome sequencing initiatives and the ease with which large numbers of independent gene loci can be determined using new generation sequencing technologies.
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    LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites
    (Biomed Central, 2008-11-21) Grievink, Liat Shavit; Penny, David; Hendy, Mike D; Holland, Barbara R
    Background: Commonly used phylogenetic models assume a homogeneous evolutionary process throughout the tree. It is known that these homogeneous models are often too simplistic, and that with time some properties of the evolutionary process can change (due to selection or drift). In particular, as constraints on sequences evolve, the proportion of variable sites can vary between lineages. This affects the ability of phylogenetic methods to correctly estimate phylogenetic trees, especially for long timescales. To date there is no phylogenetic model that allows for change in the proportion of variable sites, and the degree to which this affects phylogenetic reconstruction is unknown. Results: We present LineageSpecificSeqgen, an extension to the seq-gen program that allows generation of sequences with both changes in the proportion of variable sites and changes in the rate at which sites switch between being variable and invariable. In contrast to seq-gen and its derivatives to date, we interpret branch lengths as the mean number of substitutions per variable site, as opposed to the mean number of substitutions per site (which is averaged over all sites, including invariable sites). This allows specification of the substitution rates of variable sites, independently of the proportion of invariable sites. Conclusion: LineageSpecificSeqgen allows simulation of DNA and amino acid sequence alignments under a lineage-specific evolutionary process. The program can be used to test current models of evolution on sequences that have undergone lineage-specific evolution. It facilitates the development of both new methods to identify such processes in real data, and means to account for such processes. The program is available at: http://awcmee.massey.ac.nz/downloads.htm.
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    Acoustic wave and bond rupture based biosensor-- principle and development : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University, Palmerston North, New Zealand
    (Massey University, 2009) Hirst, Evan
    Bond rupture is an experimental methodology that is used to augment a conventional mass balance biosensor. A good point-of-care biosensor is fast, reliable, simple, cost-effective, and detects low concentrations of the target analyte. Biosensor development is a multidisciplinary field and bond rupture testing is of technical interest to many groups. The Bond rupture methodology endows a mass probe with the ability to discern bond strength. The recognition of specific bonds by mass loading is separated from erroneous non-specific binding by a probe of the force between the analyte and the transducer. Bond rupture is achieved by acoustic excitation of the point of attachment. The force is incremented gradually until rupture occurs. The advancement of bond rupture biosensors beyond the lab requires improved understanding of the mechanisms of bond rupture by base excitation, the transducers, and the supporting hardware. Bond rupture has traditionally been used in conjunction with the Quartz Crystal Microbalance (QCM). There exists, however, a variety of sensors and transducers to which the bond rupture methodology could be applied. The time, cost and experience required for comprehensive investigation of all avenues is prohibitive. To further the development of bond rupture characteristic experiments are designed and carried out on the QCM platform. Numerical simulations are constructed which model the current bond rupture approach. This work is limited to the simulation of bond rupture by base excitation. From the results of the experimental investigation a number of improvements to the bond rupture technique are proposed. Improvements are tested by simulation and the Surface Acoustic Wave (SAW) device is selected to advance the bond rupture craft. A prototype SAW bond rupture device is designed. The prototype device is manufactured and tested, confirming the principle of SAW bond rupture. Future work is required to progress the SAW bond rupture methodology before possible integration with other sensor systems. Because of this work, and the evaluation of the SAW bond rupture prototype, much is learned about the advancement of SAW device bond rupture.
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    Studies of fault current limiters for power systems protection : a project report submitted in partial fulfilment of the requirements for the degree of Master of Engineering in Information and Telecommunication Engineering, Institute of Information Sciences and Technology, Massey University, Palmerston North, New Zealand
    (Massey University, 2007) Malhi, Gurjeet Singh
    In today’s technological world, electrical energy is one of the most important forms of energy and is needed directly or indirectly in almost every field. Increase in the demand and consumption of electrical energy leads to increase in the system fault levels. It is not possible to change the rating of the equipment and devices in the system or circuits to accommodate the increasing fault currents. The devices in electronic and electrical circuits are sensitive to disturbance and any disturbance or fault may damage the device permanently so that it must be replaced. The cost of equipment like circuit breakers and transformers in power grids is very expensive. Moreover, replacing damaged equipment is a time and labour consuming process, which also affects the reliability of power systems. It is not possible to completely eliminate the faults but it is possible to limit the current during fault in order to save the equipment and devices in the circuits or systems. One solution to this problem is to use a current limiting device in the system. There are many different types of approaches used for limiting fault currents Two different approaches to limit fault currents have been discussed by the author. One is Passive Magnetic Current Limiter (MCL) and another is High Temperature Superconductor Fault Current Limiter (HTSFCL). Both are passive devices and they do not need any sensor or external sources to perform their current limiting action. The first device consists of two ferrite cores and a permanent magnet which is sandwiched between the two saturated cores and it is called Magnetic Current Limiter. Experimental results with the MCL in circuit are discussed. Both field and thermal models of the MCL have been simulated using finite element software, FEMLAB. The demonstration of the High Temperature Superconductor Fault Current Limiter (HTSFCL) in power systems has been explained. The MATLAB simulation of the HTSFCL has been done and the results with and without the fault are shown. Power System Analysis Toolbox (PSAT) software has been used to locate the optimum or the best location of HTSFCL in a nine bus system. It has been shown that it is possible to find a solution that limits the fault current in power systems. Depending on the size of the system, either the MCL or the HTSFCL can be implemented. The location of the HTSFCL is to be carefully selected to achieve optimum results.