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1
Manolopoulou, Ioanna. "A Bayesian approach to Nested Clade Analysis." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611441.
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Xiao, Weizhong. "Nested logit model analysis of aggregate sales response." Thesis, Massachusetts Institute of Technology, 1997. http://hdl.handle.net/1721.1/10543.
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Sanders, Elizabeth A. "Multilevel Analysis Methods for Partially Nested Cluster Randomized Trials." UNIVERSITY OF WASHINGTON, 2012. http://pqdtopen.proquest.com/#viewpdf?dispub=3452760.
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Chang, Li-yen. "Nested logit analysis of vehicle occupancy and accident severity /." Thesis, Connect to this title online; UW restricted, 1997. http://hdl.handle.net/1773/10189.
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Bailey, Brittney E. "Data analysis and multiple imputation for two-level nested designs." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1531822703002162.
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Mynhardt, Glene. "Population genetics of the pecan weevil, Curculio caryae Horn (Coleoptera: Curculionidae), inferred from mitochondrial nucleotide data." Texas A&M University, 2006. http://hdl.handle.net/1969.1/4388.
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The pecan weevil, Curculio caryae Horn, is an obligate nut feeder of all North American hickory
(Carya) and a key pest of the pecan, C. illinoinensis Koch. This study investigated population
structure of the pecan weevil. Gene flow and genetic variation was estimated for 90 pecan
weevil specimens sampled from the entire Carya range. Cladistic and nested clade analyses, as
well as an analysis of molecular variance (AMOVA) of mitochondrial DNA cytochrome oxidase
I (mtDNA COI) were performed. The data indicate C. caryae diverged from its sister species, C.
nasicus approximately 4.3 million years before present (mybp). Six-hundred and forty equally
parsimonious trees of 31 haplotypes demonstrated high genetic diversity across all pecan weevil
samples, and significant regional subdivision. Three clades recovered in the parsimony and
nested clade analyses were strongly associated with western, eastern and central localities
sampled within C. caryae's range. The current distribution of C. caryae and population structure
were explained by past glaciation events. Lineage divergence between the western and eastern
populations occurred during the Pleistocene (approx. 1.1 million years ago), and a more recent
divergence occurred between C. caryae populations east and west of the Appalachian mountain
range (870,000 yrs. ago). Haplotypes were segregated by region, but further sampling is
necessary to test for gene flow among these regions.
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Halsey, K. "Nested feedback systems : analysis and design within an H∞-loopshaping framework." Thesis, University of Cambridge, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.603601.
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There are two principle problems to address. Firstly, there is a greater degree of freedom in model approximation within the context on an inner-loop, as something less than closed-loop stability on C+ is required. The standard notions which under-pin the H∞-loopshaping framework, such as coprime factor and graph representations, readily generalise to connected subsets of C. However, to assess the fitness of any candidate approximation regarding inner-loop design we require a generalisation of the v-gap metric. This is obtained by removing the artificial dependence upon the existence of normalised coprime factorisations and working instead with a pointwise normalisation on the boundary. Secondly, we desire a means of synthesising a controller with a nested structure, that preserves the robustness guarantees associated with the conventional case. On the occasion that the inner-loop is implemented in observer form, we obtain a simple inequality relating the stability margins associated with a 2-loop nested feedback system. The guarantee this provides for the sequential approach to design is too weak to be of use. Two new methods are therefore developed which exploit the inequality to achieve a robustness guarantee. To complete this work, the generalised v-gap and a rigorous approach to nested feedback system synthesis are both applied to the design of a full flight control system for the USAF Have Dash II air-air missile.
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Savinov, Alexandr. "Concept-Oriented Model and Nested Partially Ordered Sets." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-140652.
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Concept-oriented model of data (COM) has been recently defined syntactically by means of the concept-oriented query language (COQL). In this paper we propose a formal embodiment of this model, called nested partially ordered sets (nested posets), and demonstrate how it is connected with its syntactic counterpart. Nested poset is a novel formal construct that can be viewed either as a nested set with partial order relation established on its elements or as a conventional poset where elements can themselves be posets. An element of a nested poset is defined as a couple consisting of one identity tuple and one entity tuple. We formally define main operations on nested posets and demonstrate their usefulness in solving typical data management and analysis tasks such as logic navigation, constraint propagation, inference and multidimensional analysis.
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Weaver, Brian Lee. "A methodology for ballistic missile defense systems analysis using nested neural networks." Thesis, Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/24675.
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Panchal, Mahesh. "Evaluating Nested Clade Phylogeographic Analysis Under Models of Random Mating and Restricted Gene Flow." Thesis, University of Reading, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485584.
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Phylogeography is a field that has been constantly developing. Many methods exist that can be used to tease apart the demographic processes and events that affect a species evolution. One method in particular, Nested Clade Phylogeographic Analysis (NCPA), has become a popular method for doing this. It claims that the distance statistics it uses can discriminate between multiple demographic scenarios. However, a major limitation of NCPA is that it does not provide estimates of error. Lack of automation of two stages in NCPA has meant few datasets can be simulated. A fully automated package, ANeCA, is developed, tested and applied to published datasets to recover published inferences. Many inferences are recovered showing that ANeCA is representative of a typical application of NCPA. ANeCA is also applied to data simulated under a model of panmixia. Results show on average 76% of datasets gave rise to at least one inference of an event or process when there was no geographic association. This is due to the generation of multiple statistics per clade, and multiple clades per dataset. It is also shown that the statistics are not independent of each other, making it difficult to correct the multiple tests performed. ANeCA is also applied to simulated data under three models of gene flow; an island model; a stepping stone model; and a lat- , tice model with some long distance dispersal. The results show that NCPA has a tendency to infer Restricted Gene Flow with Isolation By Distance, and Contiguous Range Expansion, under panmixia and the three gene flow models. Unlike the panmictic model where other inferences were rare, many inferences are found in higher frequencies irrespective of the underlying gene flow model. Comparison between the island and stepping stone models show that NCPA is unable to discriminate between long and short distance movements. Three classical summary statistics; AMOVAj Fu's FSj and the Mantel test, were also calculated on each dataset. Results show false positives rates to be around 5% for the AMOVA method and Mantel test, and 3% for Fu's Fs at the deme level. In general the AMOVA method is more sensitive to population structure than NCPA, and the Mantel test is more sensitive to isolation by distance than NCPA. The results that have been obtained in this study suggest that previous publications that have used NCPA have most likely made false inferences and it is recommended that classical, and most probably model-based, methods of inference should be used in preference to NCPA.
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Caesar, Ryan Matthew. "Population structure of Acrotrichis xanthocera (Matthews) (Coleoptera: Ptiliidae) in the Klamath Ecoregion of northwestern California, inferred from mitochondrial DNA sequence variation." Thesis, Texas A&M University, 2004. http://hdl.handle.net/1969.1/459.
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The Klamath-Siskiyou Ecoregion of northern California and southern Oregon has extremely high biodiversity, but conservation centers on the protection of habitat for the northern spotted owl. A network of late successional reserves has been established without consideration of potential for protecting overall biodiversity, including genetic diversity. Mitochondrial DNA sequences are used to examine the population structure of Acrotrichis xanthocera (Coleoptera: Ptiliidae) sampled from five late successional reserves within the Klamath-Siskiyou Ecoregion and five comparison sites from northern California. Measures of gene flow, phylogenetic analysis, and nested clade analysis are employed to infer historical demographic and phylogeographic processes. Results show that A. xanthocera populations have undergone past range expansion, but gene flow is currently limited. Individual late successional reserves do not adequately protect the genetic variation in this species. Although further research is needed, these results are likely to be congruent for other edaphic arthropod species. Improvement of the late successional reserve system is warranted for maximum protection of the genetic diversity of soil arthropod populations.
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Olatoye, Olalere Marcus. "Quantitative genomic analysis of agroclimatic traits in sorghum." Diss., Kansas State University, 2017. http://hdl.handle.net/2097/38251.
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Doctor of PhilosophyDepartment of Agronomy
Geoffrey Morris
Climate change has been anticipated to affect agriculture, with most the profound effect in regions where low input agriculture is being practiced. Understanding of how plants evolved in adaptation to diverse climatic conditions in the presence of local stressors (biotic and abiotic) can be beneficial for improved crop adaptation and yield to ensure food security. Great genetic diversity exists for agroclimatic adaptation in sorghum (Sorghum bicolor L. Moench) but much of it has not been characterized. Thus, limiting its utilization in crop improvement. The application of next-generation sequencing has opened the plant genome for analysis to identify patterns of genome-wide nucleotide variations underlying agroclimatic adaptation. To understand the genetic basis of adaptive traits in sorghum, the genetic architecture of sorghum inflorescence traits was characterized in the first study. Phenotypic data were obtained from multi-environment experiments and used to perform joint linkage and genome-wide association mapping. Mapping results identified previously mapped and novel genetic loci underlying inflorescence morphology in sorghum. Inflorescence traits were found to be under the control of a few large and many moderate and minor effect loci. To demonstrate how our understanding of the genetic basis of adaptive traits can facilitate genomic enabled breeding, genomic prediction analysis was performed with results showing high prediction accuracies for inflorescence traits. In the second study, the sorghum-nested association mapping (NAM) population was used to characterize the genetic architecture of leaf erectness, leaf width, and stem diameter. About 2200 recombinant inbred lines were phenotyped in multiple environments. The obtained phenotypic data was used to perform joint linkage mapping using ~93,000 markers. The proportion of phenotypic variation explained by QTL and their allele frequencies were estimated. Common and moderate effects QTL were found to underlie marker-trait associations. Furthermore, identified QTL co-localized with genes involved in both vegetative and inflorescence development. Our results provide insights into the genetic basis of leaf erectness and stem diameter in sorghum. The identified QTL will also facilitate the development of genomic-enable breeding tools for crop improvement and molecular characterization of the underlying genes Finally, in a third study, 607 Nigerian accessions were genotyped and the resulting genomic data [about 190,000 single nucleotide polymorphisms (SNPs)] was used for downstream analysis. Genome-wide scans of selection and genome-wide association studies (GWAS) were performed and alongside estimates of levels of genetic differentiation and genetic diversity. Results showed that phenotypic variation in the diverse germplasm had been shaped by local adaptation across climatic gradient and can provide plant genetic resources for crop improvement.
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Oatley, Graeme. "Nested clade analysis of geographic structure in the morphologically variable Themeda triandra in South Africa." Bachelor's thesis, University of Cape Town, 2004. http://hdl.handle.net/11427/26314.
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The use of phylogeography in plant systems has been on the increase in recent years with the use of chloroplast DNA to detect sufficient intraspecific variation to reach significant conclusions about plant species histories, both temporally and spatially. In this study, the geographic structure and possible origin of the morphologically variable Themeda triandra is explored. The trnF - trnC and psbD - trnS gene regions of the cpDNA were used to find 12 haplotypes found in 11 populations of T. triandra that encompass the species large distributional range. A haplotype tree was constructed that showed the relationship of the 11 haplotypes (haplotype_H12 was excluded as it fell outside of the 95% confidence limit), with haplotype H6 inferred to be the ancestral haplotype. A nested clade analysis was performed with the results used to infer the geographic structure of T. triandra within South Africa. Significant results showed that there was restricted gene flow with nested clades involving the three Free State populations, indicating that there are barriers to gene flow with other haplotypes. The ancestral haplotype showed long distance colonisation, with a probable root of this colonisation being the Kruger National Park. This is the proposed point of introduction of T. triandra into South Africa, with results from this study supporting this proposal. A substantial amount of gene flow (25.49%; AMOV A) between populations is observed, with this probably being due to the widespread distribution of haplotypes H6 and H10. It is thought that T. triandra followed two migration routes within South Africa: one along the coast, with the other inland above the escarpment where populations became genetically isolated from populations below the escarpment. Further studies may look for a correlation between morphological variants of T. triandra and the cpDNA haplotypes found within the species.
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Kim, Junyeop. "Causal inference in multilevel settings estimating and using propensity scores when treatment is implemented in nested settings /." Diss., Restricted to subscribing institutions, 2006. http://proquest.umi.com/pqdweb?did=1280132651&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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Mair, Patrick. "A Framework to Interpret Nonstandard Log-Linear Models." Austrian Statistical Society, 2007. http://epub.wu.ac.at/5636/1/323%2D1067%2D1%2DSM.pdf.
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The formulation of log-linear models within the framework of
Generalized Linear Models offers new possibilities in modeling categorical
data. The resulting models are not restricted to the analysis of contingency
tables in terms of ordinary hierarchical interactions. Such models are considered
as the family of nonstandard log-linear models. The problem that
can arise is an ambiguous interpretation of parameters. In the current paper
this problem is solved by looking at the effects coded in the design matrix
and determining the numerical contribution of single effects. Based on these
results, stepwise approaches are proposed in order to achieve parsimonious
models. In addition, some testing strategies are presented to test such (eventually
non-nested) models against each other. As a result, a whole interpretation
framework is elaborated to examine nonstandard log-linear models in depth.
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Bert, Daniel G. "A multiscale analysis of nested species subsets of forest birds in agricultural landscapes near Ottawa, Canada." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/MQ57784.pdf.
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Jiang, Sheng. "Application of nested PCR, whole genome amplification and comparative genomic hybridisation for single cell genetic analysis." Thesis, University of Glasgow, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.366140.
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Bert, Daniel G. (Daniel George) Carleton University Dissertation Biology. "A multiscale analysis of nested species subsets of forest birds in agricultural landscapes near Ottawa, Canada." Ottawa, 2001.
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Menard, Katrina Louise. "Population genetic structure of Conophthorus ponderosae Hopkins (Coleoptera: Scolytidae) inferred from mitochondrial DNA haplotypes." Texas A&M University, 2006. http://hdl.handle.net/1969.1/4210.
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Pine cone beetles (Conophthorus sp.) are serious pests of many forest ecosystems
since they burrow into pine cone tissues for egg deposition, causing the death of the
seeds. Management of these beetles in natural and commercial stands of pines has been
problematic due to lack of understanding about species limits and distribution. This study
was conducted to investigate the phylogeography and phylogenetics of the genus. Several
species represented by disjunct populations appear to be monophyletic including
Conophthorus edulis, C. mexicanus, C. coniperda, and C. conicollens, whereas C.
ponderosae is polyphyletic with many distinct clades isolated by geography. This study
explored whether host use or geography has played a greater role in the diversification of
this genus, focusing on the polyphyletic C. ponderosae and the monophyletic C. edulis.
In the first study, 751bp of the mtDNA CO1 gene were sequenced to reconstruct a
phylogeny of the genus, and the distribution and host use were compared to investigate
whether these factors were significantly associated. The second study addressed
population structure and possible historical influences on the C. edulis and C. ponderosae
populations using a nested clade analysis of the mtDNA haplotypes. Despite potential
limitations due to sampling, several conclusions could be drawn. Three separate
haplotype networks were found for the C. ponderosae haplotypes, indicating that there have been at least three lineages that have associated with P. ponderosa. Geography was
significantly associated with the phylogeny at greater distances (>900km), but host use
was not significant. At the species level, association with geography is variable.
Population structure for C. ponderosae at the species level is minimal, and suggests that
there has not been much time for lineage sorting of the haplotypes based on the nested
clade analysis as compared to C. edulis.
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Ling, Yuheng. "Corsican housing market analysis : Applications of bayesian hierarchical model." Thesis, Corte, 2020. http://www.theses.fr/2020CORT0011.
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Ce travail de thèse porte sur le développement de modèles économétriques/statistiques spatiaux pour analyser le marché immobilier en Corse. Concernant les contributions techniques, j'aborde dans ce travail la question de l'autocorrélation spatiale et temporelle dans le résidu de la régression linéaire classique qui peut conduire à des estimations biaisées. Les premières études empiriques utilisant des outils « a-spatiaux », tels que la méthode des moindres carrés ordinaires, ont ainsi probablement produit des estimations biaisées. Grâce à l’adoption de techniques basées sur l'économétrie spatiale, les économistes peuvent désormais gérer de manière plus efficace les problèmes liés à la présence d'autocorrélations dans les données. Cependant, la prise en compte de la dimension temporelle dans ce type de modèles demeure « floue » en raison du recours à des paramètres complexes qu’elle nécessite. Pour faire face à l'autocorrelation spatiale et temporelle, j’ai eu recours à l'application de modèles spatiotemporels hiérarchiques bayésiens. En termes d'économie régionale, j’ai utilisé les modèles hiérarchiques spatiotemporels bayésiens que j’ai développés pour évaluer le marché immobilier en Corse. En particulier, la question de savoir en quoi l’emplacement géographique affecte les caractéristiques du logement (prix, destination principale) constitue le cœur de cette thèse. Les sujets analysés sont complexes car ils traitent de questions allant de la prévision des prix de vente des appartements en Corse, à l'enquête sur les taux des résidences secondaires et à l'évaluation de l'impact de la vue sur mer. En outre, les fondements économiques de ces thématiques reposent sur la méthode des prix hédoniques, la prise en compte d’effets adjacents (adjacent effects) et d’effets d’entrainement (ripple effects). Enfin, j'identifie les points chauds (hot spots) et les points froids (cold spots) en termes de prix des appartements et de taux des résidences secondaires, et j’évalue l’impact de la vue sur mer (la mer Méditerranée dans le cadre de ce travail) et de l'accessibilité à la côte sur les prix des appartements. Ces résultats devraient fournir de précieuses informations pouvant aider à la prise de décision des planificateurs en matière d’urbanisation et des décideurs publicsThis thesis focuses on the development of spatial econometric/statistical models that are used for analyzing the Corsican real estate market.Concerning technical contributions, I address the issue of spatial and temporal autocorrelation in the residual of classical linear regression that may yield biased estimates. Early empirical studies using “spaceless” tools such as OLS probably yield biased estimates. With the acceptance of spatial econometrics, regional scientists can better handle the autocorrelation in data. However, the temporal dimension remains unclear due to its complex settings. To tackle both spatial and temporal autocorrelation, I suggest applying Bayesian hierarchical spatiotemporal models.Regarding the contribution in terms of regional economics, the developed ad-hoc Bayesian spatiotemporal hierarchical models have been used to assess the Corsican housing market. In particular, how locations affect housing is the key issue in this thesis. The topics analyzed are complex because they deal with issues ranging from predicting Corsican apartment sales prices, investigating second home rates to assessing the impact of sea views. Furthermore, the economic underpinnings of these topics include the hedonic price method, the adjacent effects and the ripple effects.Finally, I identify “hot spots” and “cold spots” in terms of apartment prices and second home rates, and I also indicate that both the sea (Mediterranean Sea) view and the coast accessibility affect apartment prices. These findings should provide valuable information for planners and policymakers
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尾関, 美喜, and Miki OZEKI. "集団ごとに収集された個人データの分析 - 多変量回帰分析とMCA（Multilevel covariance structuree analysis）の比較 -." 名古屋大学大学院教育発達科学研究科, 2006. http://hdl.handle.net/2237/9476.
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Lunday, Brian Joseph. "Resource Allocation on Networks: Nested Event Tree Optimization, Network Interdiction, and Game Theoretic Methods." Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/77323.
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This dissertation addresses five fundamental resource allocation problems on networks, all of which have applications to support Homeland Security or industry challenges. In the first application, we model and solve the strategic problem of minimizing the expected loss inflicted by a hostile terrorist organization. An appropriate allocation of certain capability-related, intent-related, vulnerability-related, and consequence-related resources is used to reduce the probabilities of success in the respective attack-related actions, and to ameliorate losses in case of a successful attack. Given the disparate nature of prioritizing capital and material investments by federal, state, local, and private agencies to combat terrorism, our model and accompanying solution procedure represent an innovative, comprehensive, and quantitative approach to coordinate resource allocations from various agencies across the breadth of domains that deal with preventing attacks and mitigating their consequences. Adopting a nested event tree optimization framework, we present a novel formulation for the problem as a specially structured nonconvex factorable program, and develop two branch-and-bound schemes based respectively on utilizing a convex nonlinear relaxation and a linear outer-approximation, both of which are proven to converge to a global optimal solution. We also investigate a fundamental special-case variant for each of these schemes, and design an alternative direct mixed-integer programming model representation for this scenario. Several range reduction, partitioning, and branching strategies are proposed, and extensive computational results are presented to study the efficacy of different compositions of these algorithmic ingredients, including comparisons with the commercial software BARON. The developed set of algorithmic implementation strategies and enhancements are shown to outperform BARON over a set of simulated test instances, where the best proposed methodology produces an average optimality gap of 0.35% (compared to 4.29% for BARON) and reduces the required computational effort by a factor of 33. A sensitivity analysis is also conducted to explore the effect of certain key model parameters, whereupon we demonstrate that the prescribed algorithm can attain significantly tighter optimality gaps with only a near-linear corresponding increase in computational effort. In addition to enabling effective comprehensive resource allocations, this research permits coordinating agencies to conduct quantitative what-if studies on the impact of alternative resourcing priorities.
The second application is motivated by the author's experience with the U.S. Army during a tour in Iraq, during which combined operations involving U.S. Army, Iraqi Army, and Iraqi Police forces sought to interdict the transport of selected materials used for the manufacture of specialized types of Improvised Explosive Devices, as well as to interdict the distribution of assembled devices to operatives in the field. In this application, we model and solve the problem of minimizing the maximum flow through a network from a given source node to a terminus node, integrating different forms of superadditive synergy with respect to the effect of resources applied to the arcs in the network. Herein, the superadditive synergy reflects the additional effectiveness of forces conducting combined operations, vis-Ã -vis unilateral efforts. We examine linear, concave, and general nonconcave superadditive synergistic relationships between resources, and accordingly develop and test effective solution procedures for the underlying nonlinear programs. For the linear case, we formulate an alternative model representation via Fourier-Motzkin elimination that reduces average computational effort by over 40% on a set of randomly generated test instances. This test is followed by extensive analyses of instance parameters to determine their effect on the levels of synergy attained using different specified metrics. For the case of concave synergy relationships, which yields a convex program, we design an inner-linearization procedure that attains solutions on average within 3% of optimality with a reduction in computational effort by a factor of 18 in comparison with the commercial codes SBB and BARON for small- and medium-sized problems; and outperforms these softwares on large-sized problems, where both solvers failed to attain an optimal solution (and often failed to detect a feasible solution) within 1800 CPU seconds. Examining a general nonlinear synergy relationship, we develop solution methods based on outer-linearizations, inner-linearizations, and mixed-integer approximations, and compare these against the commercial software BARON. Considering increased granularities for the outer-linearization and mixed-integer approximations, as well as different implementation variants for both these approaches, we conduct extensive computational experiments to reveal that, whereas both these techniques perform comparably with respect to BARON on small-sized problems, they significantly improve upon the performance for medium- and large-sized problems. Our superlative procedure reduces the computational effort by a factor of 461 for the subset of test problems for which the commercial global optimization software BARON could identify a feasible solution, while also achieving solutions of objective value 0.20% better than BARON.
The third application is likewise motivated by the author's military experience in Iraq, both from several instances involving coalition forces attempting to interdict the transport of a kidnapping victim by a sectarian militia as well as, from the opposite perspective, instances involving coalition forces transporting detainees between interment facilities. For this application, we examine the network interdiction problem of minimizing the maximum probability of evasion by an entity traversing a network from a given source to a designated terminus, while incorporating novel forms of superadditive synergy between resources applied to arcs in the network. Our formulations examine either linear or concave (nonlinear) synergy relationships. Conformant with military strategies that frequently involve a combination of overt and covert operations to achieve an operational objective, we also propose an alternative model for sequential overt and covert deployment of subsets of interdiction resources, and conduct theoretical as well as empirical comparative analyses between models for purely overt (with or without synergy) and composite overt-covert strategies to provide insights into absolute and relative threshold criteria for recommended resource utilization.
In contrast to existing static models, in a fourth application, we present a novel dynamic network interdiction model that improves realism by accounting for interactions between an interdictor deploying resources on arcs in a digraph and an evader traversing the network from a designated source to a known terminus, wherein the agents may modify strategies in selected subsequent periods according to respective decision and implementation cycles. We further enhance the realism of our model by considering a multi-component objective function, wherein the interdictor seeks to minimize the maximum value of a regret function that consists of the evader's net flow from the source to the terminus; the interdictor's procurement, deployment, and redeployment costs; and penalties incurred by the evader for misperceptions as to the interdicted state of the network. For the resulting minimax model, we use duality to develop a reformulation that facilitates a direct solution procedure using the commercial software BARON, and examine certain related stability and convergence issues. We demonstrate cases for convergence to a stable equilibrium of strategies for problem structures having a unique solution to minimize the maximum evader flow, as well as convergence to a region of bounded oscillation for structures yielding alternative interdictor strategies that minimize the maximum evader flow. We also provide insights into the computational performance of BARON for these two problem structures, yielding useful guidelines for other research involving similar non-convex optimization problems.
For the fifth application, we examine the problem of apportioning railcars to car manufacturers and railroads participating in a pooling agreement for shipping automobiles, given a dynamically determined total fleet size. This study is motivated by the existence of such a consortium of automobile manufacturers and railroads, for which the collaborative fleet sizing and efforts to equitably allocate railcars amongst the participants are currently orchestrated by the \textit{TTX Company} in Chicago, Illinois. In our study, we first demonstrate potential inequities in the industry standard resulting either from failing to address disconnected transportation network components separately, or from utilizing the current manufacturer allocation technique that is based on average nodal empty transit time estimates. We next propose and illustrate four alternative schemes to apportion railcars to manufacturers, respectively based on total transit time that accounts for queuing; two marginal cost-induced methods; and a Shapley value approach. We also provide a game-theoretic insight into the existing procedure for apportioning railcars to railroads, and develop an alternative railroad allocation scheme based on capital plus operating costs. Extensive computational results are presented for the ten combinations of current and proposed allocation techniques for automobile manufacturers and railroads, using realistic instances derived from representative data of the current business environment. We conclude with recommendations for adopting an appropriate apportionment methodology for implementation by the industry.Ph. D.
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Monroe, Emy M. "Population Genetics and Phylogeography of Two Large-River Freshwater Mussel Species at Large and Small Spatial Scales." Miami University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=miami1218129323.
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Ahmed, Ejaz. "Monitoring and analysis of internet traffic targeting unused address spaces." Thesis, Queensland University of Technology, 2010. https://eprints.qut.edu.au/34075/1/Ejaz_Ahmed_Thesis.pdf.
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Today’s evolving networks are experiencing a large number of different attacks ranging from system break-ins, infection from automatic attack tools such as worms, viruses, trojan horses and denial of service (DoS). One important aspect of such attacks is that they are often indiscriminate and target Internet addresses without regard to whether they are bona fide allocated or not. Due to the absence of any advertised host services the traffic observed on unused IP addresses is by definition unsolicited and likely to be either opportunistic or malicious. The analysis of large repositories of such traffic can be used to extract useful information about both ongoing and new attack patterns and unearth unusual attack behaviors. However, such an analysis is difficult due to the size and nature of the collected traffic on unused address spaces. In this dissertation, we present a network traffic analysis technique which uses traffic collected from unused address spaces and relies on the statistical properties of the collected traffic, in order to accurately and quickly detect new and ongoing network anomalies. Detection of network anomalies is based on the concept that an anomalous activity usually transforms the network parameters in such a way that their statistical properties no longer remain constant, resulting in abrupt changes. In this dissertation, we use sequential analysis techniques to identify changes in the behavior of network traffic targeting unused address spaces to unveil both ongoing and new attack patterns. Specifically, we have developed a dynamic sliding window based non-parametric cumulative sum change detection techniques for identification of changes in network traffic. Furthermore we have introduced dynamic thresholds to detect changes in network traffic behavior and also detect when a particular change has ended. Experimental results are presented that demonstrate the operational effectiveness and efficiency of the proposed approach, using both synthetically generated datasets and real network traces collected from a dedicated block of unused IP addresses.
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Essebag, Vidal. "Amiodarone and the risk of pacemaker insertion in elderly patients with atrial fibrillation : analysis of time-dependent exposure using nested case-control and survival analysis methodologies." Thesis, McGill University, 2003. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=84242.
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The nested case-control design is an efficient method of sampling from a cohort that is increasingly used in cardiovascular research to study causal relationships. This methodology can be used to analyze data from large administrative databases to evaluate potential cardiovascular adverse effects of medications. Using a nested case-control approach, this study investigated whether amiodarone therapy for atrial fibrillation (AF) was associated with an increased risk of bradyarrhythmia requiring permanent pacemaker insertion. This previously unpublished adverse effect of amiodarone was evaluated in a province-wide database of Quebec residents with AF and a previous myocardial infarction. We found that amiodarone use was associated with a greater than twofold increase in the risk of permanent pacemaker insertion after adjusting for potential confounding factors and exposures to other cardiovascular medications. The effect of amiodarone dose on this risk was then evaluated with survival analysis using Cox regression with time-dependent covariates. The risk of permanent pacemaker insertion was found to be dose-dependent and greatest during the initial months of treatment when higher doses of amiodarone were used. The effect of amiodarone dose was reanalyzed using nested case-control methods in order to compare nested case-control and survival analysis approaches for evaluating time-dependent exposure. Expectedly similar risk estimates were obtained with superior computational efficiency using nested case-control methods. In conclusion, amiodarone is associated with a dose-dependent increased risk of permanent pacemaker insertion that should be taken into consideration when initiating amiodarone therapy for elderly patients with AF. The nested case-control design is a useful alternative for analysis of a cohort with time-dependent exposure, particularly when studying rare outcomes in large databases.
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Carbone, Ignazio. "Population history and process, nested clade and coalescent analysis of multiple gene genealogies in a parasite of agricultural and wild plants." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0023/NQ49824.pdf.
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Brown, Megan R. "Judging Disability by its Cover: A Nested Case Study of Student Perceptions of Normal Childhoods in and on Middle Grade Novels." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1554995588014149.
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Cao, Caihua. "Damage and Failure Analysis of Co-Cured Fiber-Reinforced Composite Joints." Diss., Georgia Institute of Technology, 2003. http://hdl.handle.net/1853/5298.
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Joints represent a design challenge, especially for composite structures. Among the available joining methods, co-curing is an efficient way to integrate parts for some applications. Coates and Armanios have proposed a Single Nested Overlap (SNO) co-cured joint configuration, obtained from a single lap joint through the overlap/interleafing of the adjoining top/bottom adherend plies, respectively. Through a comparative investigation, they have demonstrated joint strength and fatigue life improvements over the single lap joint counterparts for unidirectional and quasi-isotropic adherend lay-ups. This research extends the comparative investigation of Coates and Armanios by focusing upon characterizing and differentiating the damage initiation and progression mechanisms under quasi-static loading. Six specimen configurations are manufactured and tested. It is confirmed that single nested overlap joints show 29.2% and 27.4% average improvement in strength over single lap counterparts for zero-degree unidirectional and quasi-isotropic lay-ups, respectively.
Several nondestructive evaluation techniques are used to observe and analyze damage initiation, damage progression and failure modes of the studied specimens and to monitor their mechanical response. Using X-ray Radiography and Optical Microscopy techniques during quasi-static loading, a physical characterization of damage and failure mechanisms is obtained. The acoustic emission data acquired during monotonic loading could reveal the overall picture of AE activities produced by the damage initiation, development and accumulation mechanisms within the specimen via parametric analysis. Further AE analysis by a selected supervised clustering method is carried out and shown successful in differentiating and clustering the AE data. Correlation with physical observations from other techniques suggests that the resulting clusters may be associated to specific damage modes and failure mechanisms.
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Pontes, Júnior Maurício Duarte. "Sucessão bacteriana durante o desenvolvimento de frutos de café (Coffea arabica L.)." Universidade Federal de Viçosa, 2010. http://locus.ufv.br/handle/123456789/5331.
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Previous issue date: 2010-08-19Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
This work aimed to study the diversity of endophytic bacteria associated to Coffea arabica L. fruit during their development. Seven monthly collections were conducted, following coffee fruit development in homogeneous stand of Catuai Vermelho coffee cultivar plantation. Each sample was processed according to protocol aiming to obtain total DNA from the endophytic bacterial community, associated to each stage of fruit development. The strategy of rDNA16S amplification through the Nested-PCR technique and DGGE discrimination were applied. The total population of endophytic bacteria and the phylos Actinobacteria, Firmicutes and Proteobacteria (alpha, beta and gamma classes) were investigated. The analysis of each gel, representing the evolution of a population along time, was carried out using the program Bionumerics®. The existence of endophytic bacteria associated to coffee fruit since the first month of their development was confirmed, by using the universal primer for Eubacteria. Based on the similarity between the distribution pattern of the OTUs on the rays representing the two final months of fruit development, it was inferred that the populations tend to stabilize. Less similarity between the endophytic populations, present in the different phases of fruit development, was confirmed in the phylo Firmicutes, while the beta-Proteobacteria displayed greater similarity among the different phases of fruit development. Amplification of the rDNA by Nested PCR and DGGE discrimination were found to be adequate to distinguish the alteration dynamics among the phylo populations and the bacterial classes studied.
Neste trabalho foi estudada a diversidade de bactérias endofíticas associadas a frutos de Coffea arabica L. durante o seu desenvolvimento. Foram realizadas sete coletas mensais, acompanhando o desenvolvimento dos frutos em cafeeiros de um talhão homogêneo de lavoura do cultivar Catuaí Vermelho. Cada amostra foi processada seguindo protocolo para obter o DNA total da comunidade bacteriana endofítica, associada a cada estádio de desenvolvimento do fruto. Foi empregada a estratégia de amplificação do rDNA16S pela técnica de Nested-PCR e discriminação em DGGE. A população total de bactérias endofíticas e os filos Actinobacteria, Firmicutes e Proteobacteria (classes alfa, beta e gama) foram investigados. A análise de cada gel, representando a evolução de uma população ao longo do tempo, foi realizada empregando o programa Bionumerics®. Demonstrou-se a existência de populações de bactérias endofíticas associadas aos frutos de café desde o primeiro mês de seu desenvolvimento, com emprego do primer universal para Eubacteria. Pela maior similaridade entre o padrão de distribuição das UTOs nas raias que representam os dois meses finais de desenvolvimento dos frutos inferiu-se que as populações tendem para a estabilização. A menor similaridade entre as populações endofíticas, presentes nas diferentes fases de desenvolvimento dos frutos, foi constatada no filo Firmicutes, enquanto as beta- Proteobacteria exibiram maior similaridade entre as diferentes fases de desenvolvimento dos frutos. A amplificação do rDNA por Nested PCR e discriminação em DGGE mostrou-se adequada para a distinção da dinâmica de alterações nas populações entre os filos e as classes de bactérias estudadas.
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Stutz, Heather Lynn. "Inferring Dispersal of Aquatic Invertebrates from Genetic Variation: A Comparative Study of an Amphipod (Talitridae Hyalella azteca) and Mayfly (Baetidae Callibaetis americanus) in Great Basin Springs." BYU ScholarsArchive, 2009. https://scholarsarchive.byu.edu/etd/2018.
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Whether active or passive, dispersal accompanied by gene flow shapes the population genetics and evolutionary divergence of species. Indirect methods which use genetic markers have the ability to assess effective dispersal—that which resulted in gene flow. My objective was to see if an aquatic insect and an obligate aquatic invertebrate show similar phylogeographic patterns and genetic uniqueness. Hyalella azteca and Callibaetis americanus were collected from 4-5 springs in each of six basins in the Great Basin of western North America. No dispersal or genetic studies of C. americanus have been conducted to date. However, several studies focusing on mtDNA diversity of H. azteca have revealed a tremendous degree of cryptic diversity in the desert springs of the Great Basin. Nested clade phylogeographical analysis (NCPA), FST values, AMOVA, and Mantel tests were used to examine geographical associations. I also used traditional phylogenetic approaches including maximum parsimony (MP) and likelihood (ML) analyses using cytochrome c oxidase subunit I (COI), 28S, and 16S as genetic markers. The mitochondrial COI sequence divergences in C. americanus were higher than H. azteca COI divergences within springs but lower among springs. FST values were very high in H. azteca reaching near fixation for certain alleles. C. americanus FST values were lower suggesting greater gene flow and, consequently, greater dispersal rates. Even though Mantel tests did not detect significant isolation by distance when evaluating all haplotypes together, nested clade analysis was able to examine smaller networks of related haplotypes and detect significant isolation by distance. Whereas the genetic structure in C. americanus was dominated by restricted gene flow with isolation by distance, H. azteca was characterized more by gradual range expansion followed by fragmentation. Mayflies likely showed more gene flow than amphipods because of their flight capabilities, but movement was still restricted by long distances between isolated springs.
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Reece, Joshua. "HISTORICAL RESPONSES OF MARINE TURTLES TO GLOBAL CLIMATE CHANGE AND JUVENILE LOGGERHEAD RECRUITMENT IN FLORIDA." Master's thesis, University of Central Florida, 2005. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/3223.
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Marine turtle conservation is most successful when it is based on sound data incorporating life history, historical population stability, and gene flow among populations. This research attempts to provide that information through two studies. In chapter I, I identify historical patterns of gene flow, population sizes, and contraction/expansion during major climatic shifts. In chapter II, I reveal a life history characteristic of loggerhead turtles previously undocumented. I identify a pattern of juvenile recruitment to foraging grounds proximal to their natal nesting beach. This pattern results in a predictable recruitment pattern from juvenile foraging ground aggregations to local rookeries. This research will provide crucial information to conservation managers by demonstrating how sensitive marine turtles are to global climate change. In the second component of my research, I demonstrate how threats posed to juvenile foraging grounds will have measurable effects on rookeries proximal to those foraging grounds. The addition of this basic life history information will have dramatic effects on marine turtle conservation in the future, and will serve as the basis for more thorough, forward-looking recovery plans.M.S.
Department of Biology
Arts and Sciences
Biology
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Jackson, Nathan D. "Phylogenetic History, Morphological Parallelism, and Speciation in a Complex of Appalachian Salamanders (Genus: Desmognathus)." BYU ScholarsArchive, 2005. https://scholarsarchive.byu.edu/etd/358.
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Understanding the mechanisms that generate shared morphologies across closely related taxa is important when identifying distinct evolutionary lineages using morphological characters. Desmognathus salamanders are an ideal group for testing hypotheses concerning the correlation between morphological similarity and genetic exchange within and among nominal species due to a pattern of high discordance between the two. Phylogeographic hypotheses are tested for populations of the D. quadramaculatus species complex throughout southern Appalachia by combining phylogenetic and population genetic methods with geographical information. Phylogenetic and phylogeographic inferences are then assessed in conjunction with morphological characteristics that have traditionally diagnosed taxonomic entities to understand the genetic basis of shared morphology in this complex, and to assess species boundaries. A history of fragmentation followed by range expansion is suggested as a recurrent pattern that has shaped the current population structure within this complex. The current taxonomy is found to unite populations that share similar morphologies due to parallel evolution rather than ancestry. We suggest revisions in taxonomy that will better reflect the evolutionary history of these lineages. Appreciation of the hidden genetic variation and homoplasious morphological variation often present in and among salamander species can foster the implementation of more appropriate methods for detecting and recognizing the complex history of these organisms.
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Engelbrecht, Adriaan. "Phylogeography of the southern African vlei rat, Otomys irroratus, inferred from chromosomal and DNA sequence data." Thesis, Stellenbosch : University of Stellenbosch, 2010. http://hdl.handle.net/10019.1/5476.
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Thesis (MSc)--University of Stellenbosch, 2010.ENGLISH ABSTRACT: This study examines the phylogeography of the southern African vlei rat, Otomys irroratus using the mtDNA cyt b gene and chromosomal data derived using G-, and C-banding, Ag-NOR staining and fluorescence in situ hybridization (FISH using flow sorts of Myotomys unisulcatus). A total of N = 102 specimens were used from the Western Cape, Eastern Cape, Northern Cape, Free State, Mpumalanga and KwaZulu-Natal provinces of South Africa. Of the N = 102, N = 55 comprised fresh material while N = 47 comprises museum material obtained from the Durban Natural Science Museum of South Africa. Cytogentic analysis of N = 55 specimens collected from seven localities in South Africa revealed intra-specific variation resulting from two rearrangements, namely pericentric inversions and heterochromatin variation. Of the 55 specimens that were analyzed 47% contained inversions or centromeric shifts on four autosomes (OIR1, OIR4, OIR6 and OIR10) which were present singly in specimens (i.e. none of the specimens contained all four inversions concurrently). These inversions were present in both homozygous and heterozygous state over a wide geographic range suggesting that they are floating polymorphisms. Given the potential role of inversions in post-mating isolation (through production of aneuploid gametes), the prevalence of inversions as floating polymorphisms in the vlei rats suggest that they are probably retained in the population through suppression of recombination in the inverted regions of the chromosomes. In addition, differences between populations is due to the presence or absence of heterochromatic arms (and not inversions), which cause variation in the NFa (40 – 49) and supernumerary B chromosomes, resulting in the variation in diploid number (2n = 28 – 32). Analysis of N = 55 specimens revealed Ag-NORs on 7 autosomal pairs 1, 2, 5, 7, 8 and 9 proximal to the centromere on the short arm of the chromosome. Pair 8 also displayed Ag-NOR at the distal end of the long arm of the chromosome in individuals from the Free State province. Pair 3 showed two Ag- NORs occurring proximal to the centromere on the short arm and on the terminal end of the long arm, respectively. I obtained 953bp of mtDNA cyt b from fresh material and 400bp from museum material. Using maximum parsimony and Bayesian inference two main clades were retrieved. Clade A specimens occur mainly in the Western and Eastern Cape provinces of South Africa. Clade B specimens occur in the Eastern Cape, Free State, KwaZulu-Natal, Northern Cape and Mpumalanga provinces of South Africa. The mean sequence divergence between the main clades (A and B) is 7.0% and between sub-clades comprising clade B is 4.8%, while within clade A the sequence divergence was 1.91%. Nested clade analysis revealed allopatric fragmentation within O. irroratus. Chromosomal characters also support the two evolutionary lineages as clade A has pericentric inversions which occur as floating polymorphisms which are absent in clade B. Clade B in turn is fixed for a complex tandem fusion rearrangement which is absent from clade A. Divergence date estimates indicate that the two clades separated around 1.1 MYA, which coincides with climate changes since the late Pliocene/Pleistocene epochs. Cladogenesis within this species complex could therefore have been influenced by habitat fragmentation. A full taxonomic review of O. irroratus is therefore warranted by this study.
AFRIKAANSE OPSOMMING: Die suider Afrikaanse vlei rot, Otomys irroratus word gekenmerk deur fenotipiese konservatisme regoor die spesie se verspreiding en het groot chromosomale variasie met diploied chromosoom getalle wat reeks vanaf 2n = 23 tot 2n = 32. Hierdie variasie binne O. irroratus het gelei tot die beskrywing van drie chromosomale groupe naamlik die A sitotipe wat gekenmerk word deur 'n akrosentriese komplement. Die tweede groep wat die B sitotipe genoem word besit ten minste agt chromosoom pare met heterokromatiese kort arms, onderwyl die derde group (die C sitotipe) vier chromosoom pare het met heterokromatiese kort arms. Hierdie studie bestudeer die bevolkings genetika struktuur van O. irroratus deur 102 monsters te analiseer wat gekollekteer was regoor die spesie se verspreiding binne Suid-Afrika en die mitochondriale merker sitokroom b sowel as chromosoom fluoressent hibridisasie te gebruik. Ek het 55 monsters van sewe lokaliteite binne Suid-Afrika sitogeneties geanaliseer deur gebruik te maak van G- en C-bandbepaling asook die hibridisasie patrone geproduseer deur die vloeisorteerde chromosoome van Myotomys unisulcatus. Die analise het gewys dat 47% van die monsters perisentromeriese inversies besit het, wat slegs aangetref was of die outosome OIR1, OIR4, OIR6 en OIR10. Hierdie inversies was nooit almal teenwoordig binne dieselfde monster nie en was gevind in beide heterosigotiese en homosigotiese vorm. Die inversies kom ook voor oor 'n wye verspreiding wat daarop aandui dat dit swerwende polymorfisme is. Omdat inversies lei tot die produksie van aneuploiede gamete speel hulle 'n belangrike rol in post-parings reproduktiewe isolasie, die verskyning van swerwende inversies binne vlei rotte dui dus daarop dat hulle onderhou word binne populasie verband deur die onderdrukking van rekombinasie in die gedeeltes van die chromosoom. Verdere verskille tussen populasies behels die voorkoms of afwesigheid van heterochromatiese kort arms wat (nie inversies) wat lei tot die variasies in die Nfa (40 – 49). Die variasie in diploied getal (2n = 28 – 32) is eksklusief as gevolg van B chromosoome. Ag-NOR banding het ook gewys dat daar twee evolusionêre lyne binne O. irroratus voorkom. Verder het filogenetiese analise van al die monsters verkryg deur volgorde-bepaling met behulp van maksimale parsimonie en Bayesian afleiding twee klades geidentifiseer. Klade A diere kom voor in die Wes en Oos-Kaap provinsies van Suid-Afrika terwyl klade B diere voorkom in die Oos-Kaap, Vrystaat, KwaZulu-Natal, Noord-Kaap en Mpumalanga provinsies onderskeidelik van Suid-Afrika. Die gemiddelde volgorde-bepalings verskille beloop 7% tussen die twee hoof klades (A en B) en tussen sub-klades 4.8%, terwyl binne klade A die verskille slegs 1.91% beloop het. Analise van die verwantskap tussen die klades het gewys dat allopatriese fragmentasie heel waarskynlik gelei het tot die populasie genetiese struktuur binne O. irroratus. Chromosoom karakters onderskraag die twee evolusionêre lyne waar klade A slegs perisentriese inversies besit wat swerwend wat ontbreek in klade B. Klade B op sy beurt besit 'n komplekse tandemme fusie wat glad nie voorkom in klade A nie. Molekulêre datering het verder gewys dat die twee klades omtrent 1.1 miljoen jaar gelede versprei het, wat ooreenstem met die klimaats veranderinge wat sedert die Peioceen en Pleistoceen plaasgevind het. Klade vorming binne die spesies komples kan daarom as gevolg van habitat fragmentasie plaasgevind het. Hierdie studie dus noodsaak 'n volle taksonomiese ondersoek van O. irroratus ten einde vas te stel hoeveel spesies binne die komplex voorkom.
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SILVA, Hugo Delleon da. "Detecção molecular e monitoramento sazonal de adenovírus em águas fluviais no município de Goiânia, Goiás-Brasil: correlação com parâmetros físico-químicos, bacteriológicos e Metanálise avaliativa de metodologias." Universidade Federal de Goiás, 2009. http://repositorio.bc.ufg.br/tede/handle/tde/1700.
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Previous issue date: 2009-05-27Although water is of vital importance for living beings, due to antropic action it becomes a way of dissemination of several microorganisms, which reach aquatic environments through the faeces of man and other animals and can cause several illnesses, especially for immunocompromised individuals. During routine environmental monitoring, coliform bacteria are normally used as a microbiological parameter of water quality, which does not evidence its contamination by viruses. Several researchers have proposed the detection of adenovirus (AdVs) by PCR as a molecular index to monitor other enteric viruses. AdVs are among the most persistent and ubiquitous enteric viruses present in water and associated with a variety of clinical manifestations. This study aimed to evaluate the quality of water collected from lakes and rivers in Goiânia as to the occurrence of AdVs. Water samples were collected monthly, from December 2007 to November 2008, at five different points in Goiânia (lakes of Bosque dos Buritis and Vaca Brava park, João Leite and Meia Ponte rivers downstream and upstream the municipal sewage treatment plant). The analyses were carried out at the Laboratório de Diagnóstico Genético e Molecular and Laboratório de Genética Molecular e Citogenética, Universidade Federal de Goiás. All the samples were filtered in a positively-charged nylon membrane followed by molecular detection using PCR and semi-nested PCR. Also, we performed physical-chemical and bacteriological tests to correlate these results with the occurrence of AdVs. Simultaneously, the Núcleo de Pesquisas em Agentes Emergentes e Re-emergentes carried out a meta-analysis to evaluate three methods of concentration of AdVs coupled to molecular detection in samples of untreated water. Since 29 out of the 54 water samples collected were positive for AdVs (39.2%), our results suggest the use of the methodology proposed in the present study for the detection of these pathogens in water. We observed statistically significant difference between nitrites, phosphates, fixed residues, total residues and the occurrence of AdVs, whereas no correlation was observed between fecal coliforms and AdVs. Furthermore, the occurrence of AdVs in the state of Goiás shows a seasonal trend. Based on the 33 studies selected for the meta-analysis, it was possible to get to the following interpretations: the most effective method to detect AdVs in samples from rivers or lakes was ultracentrifugation combined with nested-PCR; it is advisable to use a combination of microfiltration membrane and ultrafugation with the subsequent diagnosis using qPCR to detect AdVs in samples of treated and untreated sewage. This has been the first study carried out for the detection and monitoring of AdVs in water bodies in the Midwestern Region of Brazil and the present results may be useful to propose the eco-epidemiological profile of AdVs or even the routes of some neglected diseases, which points out the need to define a virus indicator
Embora a água seja de vital importância para os seres vivos, em decorrência da ação antrópica torna-se meio de disseminação de inúmeros microrganismos, que chegam aos ambientes aquáticos por meio das fezes do homem e de outros animais, podendo desencadear diversas doenças, sobretudo em indivíduos imunocomprometidos. Em rotina de monitoramento ambiental, normalmente são utilizadas bactérias do grupo dos coliformes fecais como parâmetro microbiológico de qualidade das águas, o que não evidencia sua contaminação por vírus. Alguns pesquisadores têm proposto a detecção de adenovírus (AdVs) por PCR como indexação no monitoramento de outros vírus entéricos. AdVs estão entre os mais persistentes e ubíquos vírus entéricos presentes em águas e associados com uma variedade de manifestações clínicas. Objetivou-se avaliar a qualidade da água de rios e lagos da cidade de Goiânia em relação à ocorrência de AdVs. Amostras de água foram coletadas mensalmente, entre dezembro de 2007 e novembro de 2008, em cinco diferentes pontos de Goiânia (lagos do Bosque dos Buritis e parque Vaca Brava e rios João Leite e Meia Ponte a jusante e montante da estação de tratamento de esgoto municipal). As análises laboratoriais foram realizadas pelo Laboratório de Diagnóstico Genético e Molecular e Laboratório de Genética Molecular e Citogenética, Universidade Federal de Goiás. Inicialmente, as amostras foram filtradas em membrana de nylon carregada positivamente e, em seguida, submetidas a detecção molecular por PCR e semi-nested PCR. Também foram realizados testes físico-químicos e bacteriológicos para correlacionar estes resultados com a ocorrência de AdVs. Concomitantemente, o Núcleo de Pesquisas em Agentes Emergentes e Re-emergentes conduziu uma metanálise avaliativa de três metodologias de concentração de AdVs acopladas à detecção molecular em amostras de águas não tratadas. Das 54 amostras coletas, 29 foram positivas para AdVs (39,2%), sugerindo o uso da metodologia proposta neste estudo para detectar estes patógenos em água. Foi observada diferença estatisticamente significativa entre nitritos, fosfatos, resíduos fixos, resíduos totais e a ocorrência de AdVs, mas não foi observada correlação entre coliformes fecais e AdVs. Além disso, a ocorrência de AdVs no estado de Goiás exibiu tendência à sazonalidade. Na metanálise, a partir dos 33 artigos selecionados foi possível fazer as seguintes interpretações: para detectar AdVs em amostras de rios ou lagos, o método mais eficiente foi a ultracentrifugação em combinação com nested-PCR; para a detecção de AdVs em amostras de esgoto tratado e não tratado é aconselhável utilizar uma combinação de microfiltração em membrana e ultrafiltração com subsequente diagnóstico por qPCR. Este foi o primeiro estudo a detectar e monitorar AdVs em cursos de água na Região Centro-Oeste do Brasil e os presentes resultados podem ser úteis para propor o perfil eco-epidemiológico dos AdVs ou até mesmo das rotas de algumas doenças que são negligenciadas, o que demonstra a necessidade de definir um indicador viral
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Singh, Sanchit. "Modeling, Analysis, and Algorithmic Development of Some Scheduling and Logistics Problems Arising in Biomass Supply Chain, Hybrid Flow Shops, and Assembly Job Shops." Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/91466.
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In this work, we address a variety of problems with applications to `ethanol production from biomass', `agile manufacturing' and `mass customization' domains. Our motivation stems from the potential use of biomass as an alternative to non-renewable fuels, the prevalence of `flexible manufacturing systems', and the popularity of `mass customization' in today's highly competitive markets. Production scheduling and design and optimization of logistics network mark the underlying topics of our work. In particular, we address three problems, Biomass Logistics Problem, Hybrid Flow Shop Scheduling Problem, and Stochastic Demand Assembly Job Scheduling Problem.
The Biomass Logistics Problem is a strategic cost analysis for setup and operation of a biomass supply chain network that is aimed at the production of ethanol from switchgrass. We discuss the structural components and operations for such a network. We incorporate real-life GIS data of a geographical region in a model that captures this problem. Consequently, we develop and demonstrate the effectiveness of a `Nested Benders' based algorithm for an efficient solution to this problem.
The Hybrid Flow Shop Scheduling Problem concerns with production scheduling of a lot over a two-stage hybrid flow shop configuration of machines, and is often encountered in `flexible manufacturing systems'. We incorporate the use of `lot-streaming' in order to minimize the makespan value. Although a general case of this problem is NP-hard, we develop a pseudo-polynomial time algorithm for a special case of this problem when the sublot sizes are treated to be continuous. The case of discrete sublot sizes is also discussed for which we develop a branch-and-bound-based method and experimentally demonstrate its effectiveness in obtaining a near-optimal solution.
The Stochastic Demand Assembly Job Scheduling Problem deals with the scheduling of a set of products in a production setting where manufacturers seek to fulfill multiple objectives such as `economy of scale' together with achieving the flexibility to produce a variety of products for their customers while minimizing delivery lead times. We design a novel methodology that is geared towards these objectives and propose a Lagrangian relaxation-based algorithm for efficient computation.Doctor of Philosophy
In this work, we organize our research efforts in three broad areas - Biomass Supply Chain, Hybrid Flow Shop, and Assembly Job Shop, which are separate in terms of their application but connected by scheduling and logistics as the underlying functions. For each of them, we formulate the problem statement and identify the challenges and opportunities from the viewpoint of mathematical decision making. We use some of the well known results from the theory of optimization and linear algebra to design effective algorithms in solving these specific problems within a reasonable time limit. Even though the emphasis is on conducting an algorithmic analysis of the proposed solution methods and in solving the problems analytically, we strive to capture all the relevant and practical features of the problems during formulation of each of the problem statement, thereby maintaining their applicability. The Biomass Supply Chain pertains to the production of fuel grade ethanol from naturally occurring biomass in the form of switchgrass. Such a system requires establishment of a supply chain and logistics network that connects the production fields at its source, the intermediate points for temporary storage of the biomass, and bio-energy plant and refinery at its end for conversion of the cellulosic content in the biomass to crude oil and ethanol, respectively. We define the components and operations necessary for functioning of such a supply chain. The Biomass Logistics Problem that we address is a strategic cost analysis for setup and operation of such a biomass supply chain network. We focus our attention to a region in South Central Virginia and use the detailed geographic map data to obtain land use pattern in the region. We conduct survey of existing literature to obtain various transportation related cost factors and costs associated with the use of equipment. Our ultimate aim here is to understand the feasibility of running a biomass supply chain in the region of interest from an economic standpoint. As such, we represent the Biomass Logistics Problem with a cost-based optimization model and solve it in a series of smaller problems. A Hybrid Flow Shop (HFS) is a configuration of machines that is often encountered in the flexible manufacturing systems, wherein a particular station of machines can execute processing of jobs/tasks simultaneously. In our work, we approach a specific type of HFS, with a single machine at the first stage and multiple identical machines at the second stage. A batch or lot of jobs/items is considered for scheduling over such an HFS. Depending upon the area of application, such a batch is either allowed to be split into continuous sections or restricted to be split in discrete sizes only. The objective is to minimize the completion time of the last job on its assigned machine at the second stage. We call this problem, Hybrid Flow Shop Scheduling Problem, which is known to be a hard problem in literature. We aim to derive the results which will reduce the complexity of this problem, and develop both exact as well as heuristic methods in order to obtain near-optimal solution to this problem. An Assembly Job Shop is a variant of the classical Job Shop which considers scheduling a set of assembly operations over a set of assembly machines. Each operation can only be started once all the other operations in its precedence relationship are completed. Assembly Job Shop are at the core of some of the highly competitive manufacturing facilities that are principled on the philosophy of Mass Customization. Assuming an inherent nature of demand uncertainty, this philosophy aims to achieve ‘economy of scale’ together with flexibility to produce a variety of products for the customers while minimizing the delivery lead times simultaneously. We incorporate some of these challenges in a concise framework of production scheduling and call this problem as Stochastic Demand Assembly Job Scheduling Problem. We design a novel methodology that is geared towards achieving the set objectives and propose an effective algorithm for efficient computation.
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Jin, Yan. "Bayesian Solution to the Analysis of Data with Values below the Limit of Detection (LOD)." University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1227293204.
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López-Linares, Karen. "Image analysis and deep learning to support endovascular repair of abdominal aortic aneurysms." Doctoral thesis, Universitat Pompeu Fabra, 2019. http://hdl.handle.net/10803/667102.
Full textAbstract:
An abdominal aortic aneurysm (AAA) is a focal dilation of the aorta that may lead to its rupture. The most common treatment for AAAs is endovascular aneurysm repair (EVAR). EVAR implies lifelong postoperative surveillance using Computed Tomography Angiography (CTA), due to the potential appearance of complications. This thesis sets the basis for intelligent CTA image analysis to support post-operative follow-up of AAAs, providing clinicians with valuable information to prognose the behavior of the aneurysm.
First, novel pre-operative and post-operative AAA segmentation approaches are developed, based on Convolutional Neural Networks (CNN). Initially, 2D AAA detection and segmentation CNNs are proposed. Then, segmentation is extended to 3D to increase segmentation accuracy. Precise AAA segmentation is the basis for a good AAA follow-up. It allows to measure aneurysm volume, which is thought to be a better indicator for
aneurysm rupture than the current AAA diameter measurements. Furthermore, it enables more complex analyses of AAA morphology and deformations.
Subsequently, a methodology for post-operative CTA time-series registration and aneurysm biomechanical strain analysis is also proposed. From these strains, quantitative image-based descriptors are extracted and correlated with the long-term patient prognosis. The extracted descriptors are the basis for possible future imaging biomarkers to be used in clinical practice to assess patient prognosis and to enable informed decision making after EVAR.
Finally, the technological developments in the thesis are applied to solve complex segmentation problems in other clinical domains, such as pectoral muscle segmentation from mammograms and pulmonary artery segmentation from CT scans.
Validation of the 3D AAA segmentation approach proposed in this thesis is being carried out with the aim of integrating it in a commercial product.El aneurisma de aorta abdominal (AAA) es una dilatación focal de la aorta que puede provocar su ruptura. El tratamiento habitual es la reparación endovascular (EVAR), que conlleva un seguimiento postoperatorio de por vida en base a imágenes de angiografía por tomografía computarizada (CTA) para detectar posibles complicaciones. Esta tesis establece la base para el análisis inteligente de imágenes CTA para apoyar el seguimiento postoperatorio de los AAA, proporcionando a los profesionales médicos información valiosa para predecir el comportamiento del aneurisma. Primero, se han desarrollado algoritmos de segmentación de AAA a partir de CTA preoperatorias y postoperatorias, basados en redes neuronales convolucionales (CNN). Inicialmente, se han propuesto CNNs 2D para la detección y la segmentación de AAAs. Posteriormente, el algoritmo de segmentación se ha extendido a 3D para mejorar su precisión, ya que ésta es la base para un buen seguimiento. Permite medir el volumen del aneurisma, que se considera un mejor indicador de riesgo de ruptura del AAA que la aproximación actual en base a su diámetro. Además, permite realizar análisis más complejos de la morfología y las deformaciones del AAA. Una vez obtenida la segmentación, se ha propuesto una metodología para el registro de series de CTA postoperatorias y el subsiguiente análisis biomecánico de las deformaciones del aneurisma. Dichas deformaciones se han cuantificado mediante descriptores de imagen y se han correlacionado con el pronóstico del paciente a largo plazo. Los descriptores extraídos establecen la base para el desarrollo de futuros biomarcadores de imagen que puedan ser utilizados en la práctica clínica para evaluar el pronóstico del paciente y para dar soporte al médico en sus decisiones tras una intervención EVAR. Por último, la experiencia adquirida en la tesis ha permitido aplicar algunas de las tecnologías para la resolución de problemas de segmentación complejos en otros ámbitos médicos, como la segmentación del músculo pectoral en mamografías o la segmentación de la arteria pulmonar en CTA. Actualmente, se está llevando a cabo la validación del algoritmo de segmentación de AAA 3D propuesto en esta tesis, con el objetivo de integrarlo en un producto comercial.
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Janetski, David J. "Genetic Considerations for the Conservation and Management of Yellowstone Cutthroat Trout (Oncorhynchus clarkii bouvieri) in Yellowstone National Park." BYU ScholarsArchive, 2006. https://scholarsarchive.byu.edu/etd/945.
Full textAbstract:
A key component to conservation is an accurate understanding of genetic subdivision within a species. Despite their ecological and economic importance, relatively little is understood about the genetic structuring of Yellowstone cutthroat trout in Yellowstone National Park. Here, we use traditional (Fst, Rst, Nm, and AMOVA) and modern (Bayesian assignment tests, coalescent theory, and nested clade analysis) analytical approaches to describe the population genetic subdivision of cutthroat trout spawning populations in Yellowstone Lake and to identify genetically distinct population segments throughout Yellowstone National Park. Evidence for restricted gene flow between spawning populations within Yellowstone Lake was detected using nested clade analysis. This is the first molecular evidence for restricted gene flow between spawning populations in Yellowstone Lake. In contrast, traditional methods such as Fst and Rst as well as the Bayesian clustering program STRUCTURE v2.0 failed to detect evidence for restricted gene flow. Across our sampling range within Yellowstone National Park, eleven genetically distinct cutthroat trout population segments were detected. These showed a general pattern of small, isolated populations with low genetic diversity in headwater streams and wide-spread, genetically diverse populations in higher-order rivers. We recommend populations be managed to maintain current levels of genetic diversity and gene flow. Based on the recent decline of and distinct morphological, behavioral, and genetic nature of cutthroat trout in Yellowstone Lake, we recommend the Yellowstone Lake spawning populations collectively be recognized as an evolutionarily significant unit.
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Kowarz, Andreas. "Advanced Concepts for Automatic Differentiation based on Operator Overloading." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2008. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1206719130404-22306.
Full textAbstract:
Mit Hilfe der Technik des Automatischen Differenzierens (AD) lassen sich für Funktionen, die als Programmquellcode gegeben sind, Ableitungsinformationen rechentechnisch effizient und mit geringem Aufwand für den Nutzer bereitstellen. Eine Variante der Implementierung von AD basiert auf der Überladung von Operatoren und Funktionen, die von vielen modernen Programmiersprachen ermöglicht wird. Durch Ausnutzung des Konzepts der Überladung wird eine interne Funktions-Repräsentation (Tape) generiert, die anschließend für die Ableitungsberechnung herangezogen wird. In der Dissertation werden neue Techniken erarbeitet, die eine effizientere Tape-Erstellung und die parallele Tape-Auswertung ermöglichen. Anhand von Laufzeituntersuchungen für numerische Beispiele werden die Möglichkeiten der neuen Techniken verdeutlichtUsing the technique of Automatic Differentiation (AD), derivative information can be computed efficiently for any function that is given as source code in a supported programming languages. One basic implementation strategy is based on the concept of operator overloading that is available for many programming languages. Due the overloading of operators, an internal representation of the function can be generated at runtime. This so-called tape can then be used for computing derivatives. In the thesis, new techniques are introduced that allow a more efficient tape creation and the parallel evaluation of tapes. Advantages of the new techniques are demonstrated by means of runtime analyses for numerical examples
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Oliveira, Gustavo Castro de. "Variações no gene yolk em moscas das frutas do grupo fraterculus." Universidade Federal de São Carlos, 2009. https://repositorio.ufscar.br/handle/ufscar/5458.
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Previous issue date: 2009-06-30Financiadora de Estudos e Projetos
Species of the fraterculus group are associated to the biggest damages to fruit crops due to the fact that they attack indiscriminately green and ripe fruits, making them pests of great economic importance. These species are hard to tell apart, even showing some potential criptic species. The understanding of the populational structure and biology of this species group is of paramount importance to strategies of management and control of these pests. Here, we investigate variation on the gene yolk em 37 individuals sampled throughout the species distribution in Brazil seeking to better understand the populational structure of this species group in Brazil. Our data indicated existence of recombination, which lead us to analyze three different regions in the gene, 5 , mid, and 3 . These regions show high levels of nucleotide diversity intra and interspecifically for all three gene regions investigated. The use of Nested Clade Phylogenetic Analysis independently used on these regions indicate two main results that occurred more than one throughout our analyses. The first is a range expansion from north-NE populations towards the south, mostly related to specimens of Anastrepha fraterculus. The second common event, detected eight times, is restricted gene flow with isolation by distance (IBD). Dating of such events indicated that they are temporarily congruent which might indicate that the lack of IBD in other levels of the analysis might be caused either by sampling limitations or an excess of local gene flow that tampers out as we move farther in space. Our results of the gene yolk have provided us with a better understanding of the levels of local variation of this marker of for the species that may help us determine the evolutionary processes that shaped the species group current distribution.
Espécies do grupo fraterculus estão relacionadas com os maiores danos a culturas de frutas carnosas por atacar frutos verdes e maduros indistintamente, o que as torna pragas de grande importância econômica. Contudo, estas espécies são de difícil distinção, com a existência potencial de diversas espécies crípticas. Dessa forma, o entendimento da biologia e, particularmente, da estrutura populacional desses insetos-praga tem grande importância para o desenvolvimento de novas estratégias de manejo. Neste trabalho, investigamos a variação no gene yolk em 37 indivíduos ao longo da distribuição do grupo no Brasil para conhecermos melhor o padrão estrutural das espécies do grupo fraterculus. Os dados indicam a existência de recombinação, de forma que analisamos a região amplificada separadamente por regiões distintas: 5 , mid e 3 . Análises de polimorfismos nestas regiões apontaram para altos valores de diversidade nucleotídicas intra e interespecíficas para as três regiões gênicas em questão, sendo estes valores maiores para a região 3 . A metodologia da Análise dos Clados Aninhados (NCPA) foi utilizada para inferências de possíveis relações entre a configuração das redes haplotípicas com o padrão de distribuição geográfica considerando estas três regiões distintas. Através do uso desta metodologia, observamos dois eventos principais que podem estar influenciando a distribuição das espécies do grupo fraterculus no território nacional. A primeira inferência refere-se à expansão populacional no sentido Centro-Sul do Brasil, referente preferencialmente à espécie Anastrepha fraterculus. O segundo evento de inferência indica fluxo gênico restrito com isolamento por distância ao longo da distribuição global dos espécimes amostrados. A datação destes eventos indica uma congruência temporal, o que pode indicar que a não ocorrência de fluxo gênico em clados inferiores possa estar associado a restrições amostrais, uma vez que nossa amostragem é de fato restrita. Além disso, em populações mais próximas, o fluxo gênico pode estar ocorrendo com freqüência suficiente para promover a homogeneização genética das populações. Os resultados obtidos mediante a análise das seqüências do gene yolk nos permitiu um melhor conhecimento àcerca dos níveis de variação referentes a esse marcador, bem como determinar os processos que possam estar envolvidos no padrão de distribuição atual das espécies do grupo fraterculus no território nacional.
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Qi, Cheng. "Systems Analysis for Urban Water Infrastructure Expansion with Global Change Impact under Uncertainties." Doctoral diss., University of Central Florida, 2012. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/5441.
Full textAbstract:
Over the past decades, cost-effectiveness principle or cost-benefit analysis has been employed oftentimes as a typical assessment tool for the expansion of drinking water utility. With changing public awareness of the inherent linkages between climate change, population growth and economic development, the addition of global change impact in the assessment regime has altered the landscape of traditional evaluation matrix. Nowadays, urban drinking water infrastructure requires careful long-term expansion planning to reduce the risk from global change impact with respect to greenhouse gas (GHG) emissions, economic boom and recession, as well as water demand variation associated with population growth and migration. Meanwhile, accurate prediction of municipal water demand is critically important to water utility in a fast growing urban region for the purpose of drinking water system planning, design and water utility asset management. A system analysis under global change impact due to the population dynamics, water resources conservation, and environmental management policies should be carried out to search for sustainable solutions temporally and spatially with different scales under uncertainties. This study is aimed to develop an innovative, interdisciplinary, and insightful modeling framework to deal with global change issues as a whole based on a real-world drinking water infrastructure system expansion program in Manatee County, Florida. Four intertwined components within the drinking water infrastructure system planning were investigated and integrated, which consists of water demand analysis, GHG emission potential, system optimization for infrastructure expansion, and nested minimax-regret (NMMR) decision analysis under uncertainties. In the water demand analysis, a new system dynamics model was developed to reflect the intrinsic relationship between water demand and changing socioeconomic environment. This system dynamics model is based on a coupled modeling structure that takes the interactions among economic and social dimensions into account offering a satisfactory platform. In the evaluation of GHG emission potential, a life cycle assessment (LCA) is conducted to estimate the carbon footprint for all expansion alternatives for water supply. The result of this LCA study provides an extra dimension for decision makers to extract more effective adaptation strategies. Both water demand forecasting and GHG emission potential were deemed as the input information for system optimization when all alternatives are taken into account simultaneously. In the system optimization for infrastructure expansion, a multiobjective optimization model was formulated for providing the multitemporal optimal facility expansion strategies. With the aid of a multi-stage planning methodology over the partitioned time horizon, such a systems analysis has resulted in a full-scale screening and sequencing with respect to multiple competing objectives across a suite of management strategies. In the decision analysis under uncertainty, such a system optimization model was further developed as a unique NMMR programming model due to the uncertainties imposed by the real-world problem. The proposed NMMR algorithm was successfully applied for solving the real-world problem with a limited scale for the purpose of demonstration.ID: 031001428; System requirements: World Wide Web browser and PDF reader.; Mode of access: World Wide Web.; Adviser: Ni-Bin Chang.; Title from PDF title page (viewed June 24, 2013).; Thesis (Ph.D.)--University of Central Florida, 2012.; Includes bibliographical references (p. 120-131).
Ph.D.
Doctorate
Industrial Engineering and Management Systems
Engineering and Computer Science
Industrial Engineering
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Huang, Fang. "Modeling patterns of small scale spatial variation in soil." Link to electronic thesis, 2006. http://www.wpi.edu/Pubs/ETD/Available/etd-011106-155345/.
Full textAbstract:
Thesis (M.S.)--Worcester Polytechnic Institute.Keywords: spatial variations; nested random effects models; semivariogram models; kriging methods; multiple logistic regression models; missing; multiple imputation. Includes bibliographical references (p. 35-36).
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Malekzadeh, Ali. "Measurement of transit network accessibility based on access stop choice behaviour." Thesis, Queensland University of Technology, 2015. https://eprints.qut.edu.au/89767/8/Ali%20Malekzadah%20Thesis.pdf.
Full textAbstract:
This research improved the measurement of public transport accessibility by capturing; travellers' behaviour; diversity of public transport mode; and the subjectivity of travellers' decision in the complex transport networks. The results of this research not only highlighted the importance of considering public transport network characteristics but also, revealed the impact of public transport diversity in the modelling of public transport accessibility. The research developed a hybrid discrete choice model with a nested logit structure to treat the correlation among the public transport mode choices and, a logit correction factor to rectify the correlation among the stop choices.
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Rust, Henning. "Detection of long-range dependence : applications in climatology and hydrology." Phd thesis, Universität Potsdam, 2007. http://opus.kobv.de/ubp/volltexte/2007/1334/.
Full textAbstract:
It is desirable to reduce the potential threats that result from the
variability of nature, such as droughts or heat waves that lead to
food shortage, or the other extreme, floods that lead to severe
damage. To prevent such catastrophic events, it is necessary to
understand, and to be capable of characterising, nature's variability.
Typically one aims to describe the underlying dynamics of geophysical
records with differential equations. There are, however, situations
where this does not support the objectives, or is not feasible, e.g.,
when little is known about the system, or it is too complex for the
model parameters to be identified. In such situations it is beneficial
to regard certain influences as random, and describe them with
stochastic processes. In this thesis I focus on such a description
with linear stochastic processes of the FARIMA type and concentrate on
the detection of long-range dependence. Long-range dependent processes
show an algebraic (i.e. slow) decay of the autocorrelation
function. Detection of the latter is important with respect to,
e.g. trend tests and uncertainty analysis.
Aiming to provide a reliable and powerful strategy for the detection
of long-range dependence, I suggest a way of addressing the problem
which is somewhat different from standard approaches. Commonly used
methods are based either on investigating the asymptotic behaviour
(e.g., log-periodogram regression), or on finding a suitable
potentially long-range dependent model (e.g., FARIMA[p,d,q]) and test
the fractional difference parameter d for compatibility with
zero. Here, I suggest to rephrase the problem as a model selection
task, i.e.comparing the most suitable long-range dependent and the
most suitable short-range dependent model. Approaching the task this
way requires a) a suitable class of long-range and short-range
dependent models along with suitable means for parameter estimation
and b) a reliable model selection strategy, capable of discriminating
also non-nested models. With the flexible FARIMA model class together
with the Whittle estimator the first requirement is
fulfilled. Standard model selection strategies, e.g., the
likelihood-ratio test, is for a comparison of non-nested models
frequently not powerful enough. Thus, I suggest to extend this
strategy with a simulation based model selection approach suitable for
such a direct comparison. The approach follows the procedure of
a statistical test, with the likelihood-ratio as the test
statistic. Its distribution is obtained via simulations using the two
models under consideration. For two simple models and different
parameter values, I investigate the reliability of p-value and power
estimates obtained from the simulated distributions. The result turned
out to be dependent on the model parameters. However, in many cases
the estimates allow an adequate model selection to be established.
An important feature of this approach is that it immediately reveals
the ability or inability to discriminate between the two models under
consideration.
Two applications, a trend detection problem in temperature records and
an uncertainty analysis for flood return level estimation, accentuate the
importance of having reliable methods at hand for the detection of
long-range dependence. In the case of trend detection, falsely
concluding long-range dependence implies an underestimation of a trend
and possibly leads to a delay of measures needed to take in order to
counteract the trend. Ignoring long-range dependence, although
present, leads to an underestimation of confidence intervals and thus
to an unjustified belief in safety, as it is the case for the
return level uncertainty analysis. A reliable detection of long-range
dependence is thus highly relevant in practical applications.
Examples related to extreme value analysis are not limited to
hydrological applications. The increased uncertainty of return level
estimates is a potentially problem for all records from autocorrelated
processes, an interesting examples in this respect is the assessment
of the maximum strength of wind gusts, which is important for
designing wind turbines. The detection of long-range dependence is
also a relevant problem in the exploration of financial market
volatility. With rephrasing the detection problem as a model
selection task and suggesting refined methods for model comparison,
this thesis contributes to the discussion on and development of
methods for the detection of long-range dependence.Die potentiellen Gefahren und Auswirkungen der natürlicher Klimavariabilitäten zu reduzieren ist ein wünschenswertes Ziel. Solche Gefahren sind etwa Dürren und Hitzewellen, die zu Wasserknappheit führen oder, das andere Extrem, Überflutungen, die einen erheblichen Schaden an der Infrastruktur nach sich ziehen können. Um solche katastrophalen Ereignisse zu vermeiden, ist es notwendig die Dynamik der Natur zu verstehen und beschreiben zu können. Typischerweise wird versucht die Dynamik geophysikalischer Datenreihen mit Differentialgleichungssystemen zu beschreiben. Es gibt allerdings Situationen in denen dieses Vorgehen nicht zielführend oder technisch nicht möglich ist. Dieses sind Situationen in denen wenig Wissen über das System vorliegt oder es zu komplex ist um die Modellparameter zu identifizieren. Hier ist es sinnvoll einige Einflüsse als zufällig zu betrachten und mit Hilfe stochastischer Prozesse zu modellieren. In dieser Arbeit wird eine solche Beschreibung mit linearen stochastischen Prozessen der FARIMA-Klasse angestrebt. Besonderer Fokus liegt auf der Detektion von langreichweitigen Korrelationen. Langreichweitig korrelierte Prozesse sind solche mit einer algebraisch, d.h. langsam, abfallenden Autokorrelationsfunktion. Eine verläßliche Erkennung dieser Prozesse ist relevant für Trenddetektion und Unsicherheitsanalysen. Um eine verläßliche Strategie für die Detektion langreichweitig korrelierter Prozesse zur Verfügung zu stellen, wird in der Arbeit ein anderer als der Standardweg vorgeschlagen. Gewöhnlich werden Methoden eingesetzt, die das asymptotische Verhalten untersuchen, z.B. Regression im Periodogramm. Oder aber es wird versucht ein passendes potentiell langreichweitig korreliertes Modell zu finden, z.B. aus der FARIMA Klasse, und den geschätzten fraktionalen Differenzierungsparameter d auf Verträglichkeit mit dem trivialen Wert Null zu testen. In der Arbeit wird vorgeschlagen das Problem der Detektion langreichweitiger Korrelationen als Modellselektionsproblem umzuformulieren, d.h. das beste kurzreichweitig und das beste langreichweitig korrelierte Modell zu vergleichen. Diese Herangehensweise erfordert a) eine geeignete Klasse von lang- und kurzreichweitig korrelierten Prozessen und b) eine verläßliche Modellselektionsstrategie, auch für nichtgenestete Modelle. Mit der flexiblen FARIMA-Klasse und dem Whittleschen Ansatz zur Parameterschätzung ist die erste Voraussetzung erfüllt. Hingegen sind standard Ansätze zur Modellselektion, wie z.B. der Likelihood-Ratio-Test, für nichtgenestete Modelle oft nicht trennscharf genug. Es wird daher vorgeschlagen diese Strategie mit einem simulationsbasierten Ansatz zu ergänzen, der insbesondere für die direkte Diskriminierung nichtgenesteter Modelle geeignet ist. Der Ansatz folgt einem statistischen Test mit dem Quotienten der Likelihood als Teststatistik. Ihre Verteilung wird über Simulationen mit den beiden zu unterscheidenden Modellen ermittelt. Für zwei einfache Modelle und verschiedene Parameterwerte wird die Verläßlichkeit der Schätzungen für p-Wert und Power untersucht. Das Ergebnis hängt von den Modellparametern ab. Es konnte jedoch in vielen Fällen eine adäquate Modellselektion etabliert werden. Ein wichtige Eigenschaft dieser Strategie ist, dass unmittelbar offengelegt wird, wie gut sich die betrachteten Modelle unterscheiden lassen. Zwei Anwendungen, die Trenddetektion in Temperaturzeitreihen und die Unsicherheitsanalyse für Bemessungshochwasser, betonen den Bedarf an verläßlichen Methoden für die Detektion langreichweitiger Korrelationen. Im Falle der Trenddetektion führt ein fälschlicherweise gezogener Schluß auf langreichweitige Korrelationen zu einer Unterschätzung eines Trends, was wiederum zu einer möglicherweise verzögerten Einleitung von Maßnahmen führt, die diesem entgegenwirken sollen. Im Fall von Abflußzeitreihen führt die Nichtbeachtung von vorliegenden langreichweitigen Korrelationen zu einer Unterschätzung der Unsicherheit von Bemessungsgrößen. Eine verläßliche Detektion von langreichweitig Korrelierten Prozesse ist somit von hoher Bedeutung in der praktischen Zeitreihenanalyse. Beispiele mit Bezug zu extremem Ereignissen beschränken sich nicht nur auf die Hochwasseranalyse. Eine erhöhte Unsicherheit in der Bestimmung von extremen Ereignissen ist ein potentielles Problem von allen autokorrelierten Prozessen. Ein weiteres interessantes Beispiel ist hier die Abschätzung von maximalen Windstärken in Böen, welche bei der Konstruktion von Windrädern eine Rolle spielt. Mit der Umformulierung des Detektionsproblems als Modellselektionsfrage und mit der Bereitstellung geeigneter Modellselektionsstrategie trägt diese Arbeit zur Diskussion und Entwicklung von Methoden im Bereich der Detektion von langreichweitigen Korrelationen bei.
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Judd, Jason D. "Modeling and Analysis of a Feedstock Logistics Problem." Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/26810.
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Recently, there has been a surge in the research and application of â Green energyâ in the United States. This has been driven by the following three objectives: (1) to reduce the nationâ s reliance on foreign oil, (2) to mitigate emission of greenhouse gas, and (3) to create an economic stimulus within the United States. Switchgrass is the biomass of choice for the Southeastern United States. In this dissertation, we address a feedstock logistics problem associated with the delivery of switchgrass for conversion into biofuel. In order to satisfy the continual demand of biomass at a bioenergy plant, production fields within a 48-km radius of its location are assumed to be attracted into production. The bioenergy plant is expected to receive as many as 50-400 loads of biomass per day. As a result, an industrialized transportation system must be introduced as early as possible in order to remove bottlenecks and reduce the total system cost. Additionally, we assume locating multiple bioenergy plants within a given region for the production of biofuel. We develop mixed integer programming formulations for the feedstock logistics problem that we address and for some related problems, and we solve them either through the use of decomposition-based methods or directly through the use of CPLEX 12.1.0.
The feedstock logistics problem that we address spans the entire system-from the growing of switchgrass to the transporting of bio-crude oil, a high energy density intermediate product, to a refinery for conversion into a final product. To facilitate understanding, we present the reader with a case study that includes a preliminary cost analysis of a real-life-based instance in order to provide the reader appropriate insights of the logistics system before applying optimization techniques for its solution. First, we consider the benefits of active versus passive ownership of the production fields. This is followed by a discussion on the selection of baler type, and then, a discussion of contracts between various business entities. The advantages of storing biomass at a satellite storage location (SSL) and interactions between the operations performed at the production field with those performed at the storage locations are then established. We also provide a detailed description of the operations performed at a SSL. Three potential equipment options are presented for transporting biomass from the SSLs to a utilization point, defined in this study as a Bio-crude Plant (BcP). The details of the entire logistics chain are presented in order to highlight the need for making decisions in view of the entire chain rather than basing them on its segments.
We model the feedstock logistics problem as a combination of a 2-level facility location-allocation problem and a multiple traveling salesmen problem (mATSP). The 2-level facility location-allocation problem pertains to the allocation of production fields to SSLs and SSLs to one of the multiple bioenergy plants. The mATSP arises because of the need for scheduling unloading operations at the SSLs. To this end, we provide a detailed study of 13 formulations of the mATSP and their reformulations as ATSPs. First, we assume that the SSLs are always full, regardless of when they are scheduled to be unloaded. We, then, relax this assumption by providing precedence constraints on the availability of the SSLs. This precedence is defined in two different ways and, is then, effectively modeled utilizing all the formulations for the mATSP and ATSP.
Given the location of a BcP for the conversion of biomass to bio-crude oil, we develop a feedstock logistics system that relies on the use of SSLs for temporary storage and loading of round bales. Three equipment systems are considered for handling biomass at the SSLs, and they are either placed permanently or are mobile, and thereby, travel from one SSL to another. We use a mathematical programming-based approach to determine SSLs and equipment routes in order to minimize the total cost incurred. The mathematical program is applied to a real-life production region in South-central Virginia (Gretna, VA), and it clearly reveals the benefits of using SSLs as a part of the logistics system. Finally, we provide a sensitivity analysis on the input parameters that we used. This analysis highlights the key cost factors in the model, and it emphasizes areas where biggest gains can be achieved for further cost reduction.
For a more general scenario, where multiple BcPs have to be located, we use a nested Bendersâ decomposition-based method. First, we prove the validity of using this method. We, then, employ this method for the solution of a potential real-life instance. Moreover, we successfully solve problems that are more than an order of magnitude larger than those solved directly by CPLEX 12.1.0.
Finally, we develop a Bendersâ decomposition-based method for the solution of a problem that gives rise to a binary sub-problem. The difficulty arises because of the sub-problem being an integer program for which the dual solution is not readily available. Our approach consists of first solving the integer sub-problem, and then, generating the convex hull at the optimal integer point. We illustrate this approach for an instance for which such a convex hull is readily available, but otherwise, it is too expensive to generate for the entire problem. This special instance is the solution of the mATSP (using Bendersâ decomposition) for which each of the sub-problems is an ATSP. The convex hull for the ATSP is given by the Dantzig, Fulkerson, and Johnson constraints. These constraints at a given integer solution point are only polynomial in number. With the inclusion of these constraints, a linear programming solution and its corresponding dual solution can now be obtained at the optimal integer points. We have proven the validity of using this method. However, the success of our algorithm is limited because of a large number of integer problems that must be solved at every iteration. While the algorithm is theoretically promising, the advantages of the decomposition do not seem to outweigh the additional cost resulting from solving a larger number of decomposed problems.Ph. D.
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Vivencio, Diego Pagliarini. "Estudos de técnicas de virtualização de memória em arquiteturas multi-core." Universidade Federal de São Carlos, 2010. https://repositorio.ufscar.br/handle/ufscar/572.
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Previous issue date: 2010-08-29The use of computer virtualization has grown rapidly in recent years, motivating the research for software and hardware improvements to optimize performance and reduce the bottlenecks inherent of virtualization. In the middle of this decade, the processors has added support for CPU virtualization, simplifying the design of virtual machine monitors, but the employed approach had performance limitations when combined with the virtualization of memory using shadow page tables. Adding support for nested paging hardware was the answer to this problem, providing performance closer to the native, ie, without the virtual abstraction. The multicore processors were the solution to keep the microprocessors' performance growth , as the monolithic architectures were close to their limit. The use of virtualization allows exploiting parallelism offered by them through the simultaneous execution of multiple virtual machines. This study evaluates the virtualization of memory subsystem and its interaction with the multicore architectures, to determine the set of features that maximize performance. We evaluated shadow and nested paging, comparing the use of conventional and large pages to map virtualized memory. We also analyzed the influence due to the presence of a level of cache shared among cores. The results showed that in the evaluated scenario the best performance was achieved by using nested paging using large pages to map memory, while the additional level of cache didn't bring any specific benefits to virtualization.
O uso de virtualização de computadores vem crescendo rapidamente nos últimos anos, motivando a pesquisa de melhorias em software e hardware que permitam aumento de desempenho e a redução dos gargalos inerentes à virtualização. Em meados desta década, os processadores adicionaram suporte a virtualização de CPU, simplificando o projeto dos monitores de máquinas virtuais, porém o modelo adotado apresentava restrições de desempenho quando combinado com a virtualização de memória utilizando tabelas de páginas de sombra. A inclusão de suporte a paginação aninhada em hardware foi a resposta a esse problema, oferecendo desempenho mais próximo ao nativo, isto é, sem a abstração virtual. Os processadores com múltiplos núcleos, também conhecidos como multi-core, foram a solução encontrada para manter o aumento de desempenho dos microprocessadores, visto que as arquiteturas monolíticas estavam próximo ao seu limite. A utilização de virtualização permite explorar o paralelismo oferecido por eles através da execução simultânea de múltiplas máquinas virtuais. O presente trabalho avalia o subsistema de virtualização de memória e sua interação com as arquiteturas multi-core, visando determinar o conjunto de características que maximizem o desempenho. Foram avaliadas as paginações de sombra e aninhada, comparando a utilização de páginas convencionais e grandes para o mapeamento da memória virtualizada. Também foi avaliada a influência decorrente da presença de um nível de memória cache compartilhado entre os núcleos de processamento. Os resultados mostraram que no cenário avaliado o melhor desempenho foi obtido através de utilização de paginação aninhada utilizando páginas grandes para o mapeamento da memória, enquanto que o nível adicional de memória cache não trouxe benefícios específicos à virtualização.
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Kowarz, Andreas. "Advanced Concepts for Automatic Differentiation based on Operator Overloading." Doctoral thesis, Technische Universität Dresden, 2007. https://tud.qucosa.de/id/qucosa%3A24055.
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Mit Hilfe der Technik des Automatischen Differenzierens (AD) lassen sich für Funktionen, die als Programmquellcode gegeben sind, Ableitungsinformationen rechentechnisch effizient und mit geringem Aufwand für den Nutzer bereitstellen. Eine Variante der Implementierung von AD basiert auf der Überladung von Operatoren und Funktionen, die von vielen modernen Programmiersprachen ermöglicht wird. Durch Ausnutzung des Konzepts der Überladung wird eine interne Funktions-Repräsentation (Tape) generiert, die anschließend für die Ableitungsberechnung herangezogen wird. In der Dissertation werden neue Techniken erarbeitet, die eine effizientere Tape-Erstellung und die parallele Tape-Auswertung ermöglichen. Anhand von Laufzeituntersuchungen für numerische Beispiele werden die Möglichkeiten der neuen Techniken verdeutlicht.Using the technique of Automatic Differentiation (AD), derivative information can be computed efficiently for any function that is given as source code in a supported programming languages. One basic implementation strategy is based on the concept of operator overloading that is available for many programming languages. Due the overloading of operators, an internal representation of the function can be generated at runtime. This so-called tape can then be used for computing derivatives. In the thesis, new techniques are introduced that allow a more efficient tape creation and the parallel evaluation of tapes. Advantages of the new techniques are demonstrated by means of runtime analyses for numerical examples.
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Benavides, Edgar. "Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal." Diss., CLICK HERE for online access, 2006. http://contentdm.lib.byu.edu/ETD/image/etd1652.pdf.
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Glaman, Ryan. "Comparing Three Approaches for Handling a Fourth Level of Nesting Structure in Cluster-Randomized Trials." Thesis, University of North Texas, 2017. https://digital.library.unt.edu/ark:/67531/metadc1011881/.
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This study compared 3 approaches for handling a fourth level of nesting structure when analyzing data from a cluster-randomized trial (CRT). CRTs can include 3 levels of nesting: repeated measures, individual, and cluster levels. However, above the cluster level, there may sometimes be an additional potentially important fourth level of nesting (e.g., schools, districts, etc., depending on the design) that is typically ignored in CRT data analysis. The current study examined the impact of ignoring this fourth level, accounting for it using a model-based approach, and accounting it using a design-based approach on parameter and standard error (SE) estimates. Several fixed effect and random effect variance parameters and SEs were biased across all 3 models. In the 4-level model, most SE biases decreased as the number of level 3 clusters increased and as the number of level 4 clusters decreased. Also, random effect variance biases decreased as the number of level 3 clusters increased. In the 3-level and complex models, SEs became more biased as the weight level 4 carried increased (i.e., larger intraclass correlation, more clusters at that level). The current results suggest that if a meaningful fourth level of nesting exists, future researchers should account for it using design-based approach; the model-based approach is not recommended. If the fourth level is not practically important, researchers may ignore it altogether.
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Van, Staden Surette. "Reading between the lines : contributing factors that affect Grade 5 learner reading performance." Thesis, University of Pretoria, 2010. http://hdl.handle.net/2263/24944.
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This study aims to identify and explain relationships between some major factors associated with successful reading at Grade 5 level in South African primary schools. In South Africa, grave concerns with regards to low levels of student achievement pervade research initiatives and educational debates. Despite considerable investments in educational inputs (such as policy and resources) and processes (such as curriculum provision and teacher support), outcomes (such as student achievement) remain disappointingly low. The South African population is characterized by great diversity and variation. With 11 official languages, current educational policy in South Africa advocates an additive bilingualism model and students in Grade 1 to 3 are taught in their mother tongue. Thereafter, when these students progress to Grade 4, the language of learning and teaching changes to a second language, which in most cases is English. At this key developmental stage students are also expected to advance from learning to read to a stage where they can use reading in order to learn. With this complexity of issues in mind, Hierarchical Linear Modeling (HLM) was used to determine the effect of a number of explanatory variables at learner and school level on reading achievement as outcome variable, while controlling for language using the South African Progress in International Reading Literacy Study (PIRLS) 2006 data. As an international comparative evaluation of reading literacy involving more than 40 countries, PIRLS 2006 was the second, after PIRLS 2001, in a series of planned five-year cycles of assessment to measure trends in children’s reading literacy achievement, policy and practices related to literacy. Grade 5 learners in South African primary schools who participated in PIRLS 2006 were not able to achieve satisfactory levels of reading competence. The gravity of this finding is exacerbated by the fact that these learners were tested in the language in which they had been receiving instruction during the Foundation Phase of schooling. This study found most significant factors associated with reading literacy at learner-level, but this does not mean that the existence of teacher- and school-level factors is not of importance. While some explanatory factors at learner-level can more easily become the target of reading interventions, the higher level effect of the classroom and school are not diminished by this study. Creemers’ Comprehensive Model of Educational Effectiveness was utilized as theoretical point of departure. Creemers’ model was adapted for the purposes of this study to reflect a South African model of reading effectiveness in contrast with Creemers’ original use of it as a model of school effectiveness. Evidence was provided that the conceptual framework was inadequate in identifying factors affecting reading achievement for all South African language groupings. More specifically, the adapted South African reading effectiveness model was only appropriate in explaining reading achievement scores for the Afrikaans and English language groupings than for those from African language groupings.Thesis (PhD)--University of Pretoria, 2011.
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