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Yes / Safety and reliability are two important aspects of dependability that are needed to be rigorously evaluated throughout the development life-cycle of a system. Over the years, several methodologies have been developed for the analysis of failure behavior of systems. Fault tree analysis (FTA) is one of the well-established and widely used methods for safety and reliability engineering of systems. Fault tree, in its classical static form, is inadequate for modeling dynamic interactions between components and is unable to include temporal and statistical dependencies in the model. Several attempts have been made to alleviate the aforementioned limitations of static fault trees (SFT). Dynamic fault trees (DFT) were introduced to enhance the modeling power of its static counterpart. In DFT, the expressiveness of fault tree was improved by introducing new dynamic gates. While the introduction of the dynamic gates helps to overcome many limitations of SFT and allows to analyze a wide range of complex systems, it brings some overhead with it. One such overhead is that the existing combinatorial approaches used for qualitative and quantitative analysis of SFTs are no longer applicable to DFTs. This leads to several successful attempts for developing new approaches for DFT analysis. The methodologies used so far for DFT analysis include, but not limited to, algebraic solution, Markov models, Petri Nets, Bayesian Networks, and Monte Carlo simulation. To illustrate the usefulness of modeling capability of DFTs, many benchmark studies have been performed in different industries. Moreover, software tools are developed to aid in the DFT analysis process. Firstly, in this chapter, we provided a brief description of the DFT methodology. Secondly, this chapter reviews a number of prominent DFT analysis techniques such as Markov chains, Petri Nets, Bayesian networks, algebraic approach; and provides insight into their working mechanism, applicability, strengths, and challenges. These reviewed techniques covered both qualitative and quantitative analysis of DFTs. Thirdly, we discussed the emerging trends in machine learning based approaches to DFT analysis. Fourthly, the research performed for sensitivity analysis in DFTs has been reviewed. Finally, we provided some potential future research directions for DFT-based safety and reliability analysis.

This diploma thesis defines the term indexing and in preamble are discussed known indexing algorithms and difference between indexing static and moving objects. The practical part of this diploma thesis is aimed to designing and implementing of indexing algorithm for open source application MaNGOS with respect to generic design pattern and effectiveness of spatial search queries for selection of the objects given properties in the specified area. At the end I present and discuss reached results.

This paper presents an analysis of tree-ring growth patterns of male and female Fraxinus mandshurica trees from 1931 to 2007. The specific object was to study the response of radial growth to climate variables separately for male and female trees. The results show that the growth patterns in the two genders were similar during the mid-1950s to 1970s but different in the periods 1931–1940s and 1980–2007. In the period 1980–2007, the mean sensitivity and mean widths of the tree rings were significantly different between the genders (p < 0.05). The climate-growth response in female and male trees was also different. Female trees are sensitive to precipitation in November of the previous year, whereas male trees respond to mean temperature in November of the previous year. The results confirm that climatic sensitivity in male and female trees of dioecious species is different, yet this difference is not stable through time.

Thesis (M.Sc. (Molecular and Life Sciences)) --University of Limpopo, 2007 / Colophospermum mopane (sensu lato) is currently recognised on morphological and physiological characteristics. To add to the suite of taxonomic characters, the genetic variability of C. mopane (sensu lato) was investigated using the RAPD technique. DNA was extracted from young seedlings and mature leaves using the CTAB method. Initially, the DNA extraction was problematic due to the presence of polysaccharides, making PCR nearly impossible. An additional phenol precipitation step was introduced to purify the DNA used to perform RAPD analyses. Twenty random primers were tested for their suitability and reproducibility to reveal polymorphism in C. mopane (sensu lato). Nine of the primers tested amplified the genomic DNA. Subsequently, three primers (OPA 03, OPA 08 and OPA 09) were selected based on their reproducibility and demonstration of polymorphism. OPA 03 amplified most of the samples tested whereas OPA 08 and OPA 09 amplified 50% of the samples. RAPD bands ranged from 180 bp to 2000 bp. RAPD profiles of C. mopane (sensu lato) with three random primers showed few polymorphisms. Individual trees of different ecotypes show similar RAPD banding pattern, instances were found where trees of the same ecotype showed different bands. The total character difference based on presence and absence of bands revealed both variability and similarity of C. mopane (sensu lato). Phylogenetic trees from individual primers and combined primers were constructed using Neighbour Joining and Parsimony analysis. The phylogenetic tree from the combined primers of bootstrap parsimony generated three clades with low and high parsimony bootstrap values. The first clade receives weak support (61%) while the second and third clades receive support of 90% and 70%, respectively. The other remaining entities collapsed resulting in basal polytomy. The third clade shows some members of Alba (Alba 11 Phala, Alba 1 Phala and Alba 7 Musina) grouped together. The overall results of C. mopane (sensu lato) show high (84.1%) genetic similarity. No ecotypic marker was obtained. Most of the ecotypes have not diverged genetically far from one another or from the parental material (Mopane – sensu stricto). The genetic results partially support the perceived morphological differences. In this study the RAPD technique has established its value as an additional tool to express the genetic variability in C. mopane (sensu lato). / The National Research Foundation

P2P is increasingly gaining its popularity for streaming multimedia contents. The architecture of streaming has shifted from traditional client server architecture to P2P architecture. Although it is scalable and robust it faces its own challenges and problems such as churn. In tree topology frequent joining and leaving of users in search for better quality and reliable streaming makes the P2P network instable. This thesis provides an effective approach to achieve a resilient network for streaming. Relying on a single tree to receive data from single parent may leave the user deprived of getting the data if any of its ancestors leaves the network. Therefore we present an ideal solution to this problem by introducing a backup tree for the existing base tree. The backup tree is constructed based on parameter such as bandwidth and delay. In case of failure of a node, its children along the tree receive the data from the nodes of backup tree. We present an efficient algorithm for the construction of base tree as well as the backup tree which are based on normalization of two entities of nodes: bandwidth and delay. Through mathematical formulation and experimental setups we show that introducing a backup tree for an existing base tree can help provide resilience to the network. / UOIT

Phylogenetic analysis can produce easily tens of thousands of equally plausible evolutionary trees. Consensus trees and topological distance matrices are often used to summarize the evolutionary relationships among the trees of interest. However, current approaches are not designed to analyze very large tree collections. In this dissertation, we present two fast algorithms— HashCS and HashRF —for analyzing large collections of evolutionary trees based on a novel hash table data structure, which provides a convenient and fast approach to store and access the bipartition information collected from the tree collections. Our HashCS algorithm is a fast ( ) technique for constructing consensus trees, where is the number of taxa and is the number of trees. By reprocessing the bipartition information in our hash table, HashCS constructs strict and majority consensus trees. In addition to a consensus algorithm, we design a fast topological distance algorithm called HashRF to compute the × Robinson-Foulds distance matrix, which requires ( ^ 2) running time. A RF distance matrix provides plenty of data-mining opportunities to help researchers understand the evolutionary relationships contained in their collection of trees. We also introduce a series of extensions based on HashRF to provide researchers with more convenient set of tools for analyzing their trees. We provide extensive experimentation regarding the practical performance of our hash-based algorithms across a diverse collection of biological and artificial trees. Our results show that both algorithms easily outperform existing consensus and RF matrix implementations. For example, on our biological trees, HashCS and HashRF are 1.8 and 100 times faster than PAUP*, respectively. We show two real-world applications of our fast hashing algorithms: (i) comparing phylogenetic heuristic implementations, and (ii) clustering and visualizing trees. In our first application, we design novel methods to compare the PaupRat and Rec-I-DCM3, two popular phylogenetic heuristics that use the Maximum Parsimony criterion, and show that RF distances are more effective than parsimony scores at identifying heterogeneity within a collection of trees. In our second application, we empirically show how to determine the distinct clusters of trees within large tree collections. We use two different techniques to identify distinct tree groups. Both techniques show that partitioning the trees into distinct groups and summarizing each group separately is a better representation of the data. Additional benefits of our approach are better consensus trees as well as insightful information regarding the convergence behavior of phylogenetic heuristics. Our fast hash-based algorithms provide scientists with a very powerful tools for analyzing the relationships within their large phylogenetic tree collections in new and exciting ways. Our work has many opportunities for future work including detecting convergence and designing better heuristics. Furthermore, our hash tables have lots of potential future extensions. For example, we can also use our novel hashing structure to design algorithms for computing other distance metrics such as Nearest Neighbor Interchange (NNI), Subtree Pruning and Regrafting (SPR), and Tree Bisection and Reconnection (TBR) distances.

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A volume equation for predicting individual tree volume, and a taper function for describing a stem profile were developed for a little known species, Styrax tonkinensis (Siam benzoin) in northern Laos. The species has high potential commercial value and can make an important contribution to the local economy. It can provide two different types of products, a non-wood product (benzoin resin) and timber. In Laos, the most important product is currently resin, and the use of timber for commercial purposes is rare. One reason is that information about the timber is not available. In Vietnam, on the other hand, the species is an import pulpwood species. Data used in this study came from 73 trees. Trees were purposely selected to ensure coverage of a full range of tree sizes. Measurement was undertaken only on over-bark diameters due to some constraints, limitations and problems during the field data collection. However, due to the importance of under-bark volume for this species, a small available dataset was used to build a bark model as an interim guide to the errors associated with using over-bark models for estimating under-bark volumes. From this bark model, errors in estimating under-bark volumes of trees with diameters at breast height between 10cm and 17 cm were approximately 18%. Nineteen individual volume models, and 7 individual taper functions were compared for bias and precision. Collective names for the volume equations tested include single-entry, double-entry, logarithmic, combined variables. Most volume models had similar bias but a few were clearly biased. The models with similar bias were further evaluated by four common statistics including bias, standard error of estimates, standard deviation of residuals and mean absolute deviation. The results showed that a five parameter model was ranked first, and was the most precise model. However, the magnitudes of difference in prediction errors between this model and other models, particularly the three parameter model were not significant. For practical purposes, the simpler model was preferred. Seven taper functions tested here belong to three different groups including single taper equations, compatible taper equations and segmented taper equations. Evaluation of taper equations used the same residual analysis procedures and criteria as those applied with volume equations. Graphical residual analysis showed that most taper models had similar precision with their errors in diameter predictions being similar in range. However, some models showed obvious bias. The most highly ranked taper model was a compatible taper model of polynomial form. It was the least biased model. The second ranked model was a single, simple model. This latter model is relatively simple to apply, but it is not compatible with the volume model, yielding slightly different estimates of volume if it is integrated and rotated around the longitudinal axis of a tree. However, if the sole purpose is to describe tree taper, it is the best model to use.

The analysis of diverse data sets can yield different phylogenetic estimates that challenge systematists to explain the source of discordance. The Ambystomatidae are a classic example of this phylogenetic conflict. Previous attempts to resolve the ambystomatid species tree using allozymic, morphological, and mitochondrial sequence data have yielded different estimates, making it unclear which data source best approximates ambystomatid phylogeny. We present the first multi-locus DNA sequencebased phylogenetic study of the Ambystomatidae. Because independent loci can contain discordant gene tree histories, concatenating unlinked loci into a single data matrix can lead to strongly supported and erroneous results. Therefore, we utilized a range of analyses, including coalescent-based methods of phylogenetic estimation that account for incomplete lineage sorting and concordance-based methods that estimate the proportion of sampled loci that support a particular clade. We repeated these analyses with the removal of individual loci to determine if any locus has a disproportionate effect on our phylogenetic results. Many deep and relatively shallow clades within Ambystoma were robustly resolved. Analyses that excluded loci produced overlapping posterior distributions, suggesting no disproportionate influence of any particular locus. Our estimates differ from previous hypotheses, although there was greater similarity with previous molecular estimates, relative to morphological estimates.