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- Title
- Computational Approaches for Binning Metagenomic Reads.
- Creator
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Wang, Ying, Hu, Haiyan, Li, Xiaoman, Zhang, Shaojie, Wu, Annie, Savage, Anna, University of Central Florida
- Abstract / Description
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Metagenomics uses sequencing technologies to study genetic sequences from whole microbial communities. Binning metagenomic reads is the most fundamental step in metagenomic studies, which is essential for the understanding of microbial functions, compositions, and interactions in environmental samples. Various taxonomy-dependent and taxonomy-independent approaches have been developed based on information such as sequence similarity, sequence composition, or k-mer frequency. However, there is...
Show moreMetagenomics uses sequencing technologies to study genetic sequences from whole microbial communities. Binning metagenomic reads is the most fundamental step in metagenomic studies, which is essential for the understanding of microbial functions, compositions, and interactions in environmental samples. Various taxonomy-dependent and taxonomy-independent approaches have been developed based on information such as sequence similarity, sequence composition, or k-mer frequency. However, there is still room for improvement, and it is still challenging to bin reads from species with similar or low abundance or to bin reads from unknown species.In this dissertation, we introduce one taxonomy-independent and three taxonomy-dependent approaches to improve the performance of metagenomic reads binning. The taxonomy-independent method called MBBC, bins reads by considering k-mer frequency in reads without reference genomes. The first two taxonomy-dependent methods both bin reads by measuring the similarity of reads to the trained Markov Chains from different taxa. The major difference between these two methods is that the first one selects the potential taxa with the taxonomical decision tree, while the second one, called MBMC, selects potential taxa using ordinary least squares (OLS) method. The third taxonomy-dependent method bins reads by combining the methods of MBMC with clustering Markov chains from the assembled reads. By testing on both simulated and real datasets, these tools showed superior or comparable performance with various the state of the art methods. We anticipate that our tools can significantly improve the accuracy of metagenomic reads binning and thus be widely applied in real environmental samples.
Show less - Date Issued
- 2016
- Identifier
- CFE0006515, ucf:51380
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006515
- Title
- INFLUENCE MAP METHODOLOGY FOR EVALUATING SYSTEMIC SAFETY ISSUES.
- Creator
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Barth, Timothy, Pet-Armacost, Julia, University of Central Florida
- Abstract / Description
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"Raising the bar" in safety performance is a critical challenge for many organizations. Contributing factor taxonomies organize information on why accidents occur. Therefore, they are essential elements of accident investigations and safety reporting systems. Organizations must balance efforts to identify causes of specific accidents with efforts to evaluate systemic safety issues in order to become more proactive about improving safety. This research successfully addressed two problems: (1)...
Show more"Raising the bar" in safety performance is a critical challenge for many organizations. Contributing factor taxonomies organize information on why accidents occur. Therefore, they are essential elements of accident investigations and safety reporting systems. Organizations must balance efforts to identify causes of specific accidents with efforts to evaluate systemic safety issues in order to become more proactive about improving safety. This research successfully addressed two problems: (1) limited methods and metrics exist to support the design of effective taxonomies, and (2) influence relationships between contributing factors are not explicitly modeled within a taxonomy. The primary result of the taxonomic relationship modeling efforts was an innovative "dual role" contributing factor taxonomy with significant improvements in comprehensiveness and diagnosticity over existing taxonomies. The influence map methodology was the result of a unique graphical and analytical combination of the dual role taxonomy and influence relationship models. Influence maps were developed for several safety incidents at Kennedy Space Center. An independent assessment was conducted by a team of experts using the new dual role taxonomy and influence chain methodology to evaluate the accuracy and completeness of contributing factors identified during the formal incident investigations. One hundred and sixteen contributing factors were identified using the influence map methodology. Only 16% of these contributing factors were accurately identified with traditional tools, and over half of the 116 contributing factors were completely unaddressed by the findings and recommendations of the formal incident reports. The new methodology is being applied to improve spaceport operations and enhance designs of future NASA launch systems.
Show less - Date Issued
- 2006
- Identifier
- CFE0001274, ucf:46928
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0001274
- Title
- Beyond building a tree: Phylogeny of pitvipers and exploration of evolutionary patterns.
- Creator
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Fenwick, Allyson, Parkinson, Christopher, Hoffman, Eric, Crampton, William, Wiens, John, University of Central Florida
- Abstract / Description
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As generic and higher-scale evolutionary relationships are increasingly well understood, systematists move research in two directions: 1) understanding species-level relationships with dense taxon sampling, and 2) evaluating evolutionary patterns using phylogeny. In this study I address both foci of systematic research using pitvipers, subfamily Crotalinae. For direction one, I evaluate the relationships of 96% of pitvipers by combining independent sets of molecular and phenotypic data. I...
Show moreAs generic and higher-scale evolutionary relationships are increasingly well understood, systematists move research in two directions: 1) understanding species-level relationships with dense taxon sampling, and 2) evaluating evolutionary patterns using phylogeny. In this study I address both foci of systematic research using pitvipers, subfamily Crotalinae. For direction one, I evaluate the relationships of 96% of pitvipers by combining independent sets of molecular and phenotypic data. I find the inclusion of species with low numbers of informative characters (i.e. less than 100) negatively impacts resolution of the phylogeny, and the addition of independent datasets has no effect on or a small benefit to confidence in estimated evolutionary relationships. Combined evidence is extremely useful in evaluating taxonomy; I use it with South American bothropoid pitvipers. Previous work found the genus Bothrops paraphyletic, but no study had included enough species to propose a taxonomic resolution. I resolve the relationships of 90% of bothropoid pitvipers, and support the paraphyly of Bothrops as previously defined, but find it consists of three well-supported clades distinguished by distinct habitats and geographic ranges. I propose the division of Bothrops sensu lato into three genera.To address research direction two, I investigate the change in reproductive mode from egg-laying (oviparity) to livebearing (viviparity) in vipers, as well as the expansion of pitvipers through South America. I resolve the phylogeny and the divergence times for subgroups of interest then use model comparison and ancestral character state or geographic range estimation to trace the evolution of reproductive mode or geographic range across evolutionary history. For vertebrates, the predominant explanation for the evolution of reproductive mode is Dollo's Law of unidirectional evolution. This law has been challenged for a number of characters in different systems, but the phylogenetic methods that found those violations were criticized. I find support for unidirectional evolution in two analyses and rejection of it in others, and therefore do not reject Dollo's Law for the evolution of reproductive mode in vipers. In the case of geographic range, dozens of hypotheses have been proposed to explain the great biodiversity in South America, but tests of these hypotheses are lacking. I define specific time- and space-based predictions for seven hypotheses based on geological and climatic events (-) uplift of the Andes Mountains, saltwater inundation of inland areas, change in river flow, and Pleistocene climate changes. I find some support for half of the hypotheses, including one allopatric, one parapatric, and one based on climate change. I conclude that the evolution of South American pitvipers is extremely complex. Through fulfillment of both systematic research directions, I generated new knowledge about pitvipers and evolutionary processes. My methods of evaluating evolutionary patterns provide frameworks for different research questions in these areas, and I suggest that other researchers apply similar techniques to evaluate other portions of the Tree of Life.
Show less - Date Issued
- 2012
- Identifier
- CFE0004535, ucf:49236
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004535
- Title
- A TAXONOMY OF LEAN SIX SIGMA SUCCESS FACTORSFOR SERVICE ORGANIZATIONS.
- Creator
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Hajikordestani, Reza, Geiger, Christopher, University of Central Florida
- Abstract / Description
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ABSTRACT Six Sigma is a business improvement strategy that aims to improve process performance using a structured methodology that identifies and removes the causes of defects in manufacturing and business processes, while implementing the lean concepts attempts to remove wasteful activities from those processes. In practice, the Six Sigma strategy and the Lean philosophy are combined and often viewed as one integrated philosophy, where the philosophy of Lean Six Sigma simultaneously removes...
Show moreABSTRACT Six Sigma is a business improvement strategy that aims to improve process performance using a structured methodology that identifies and removes the causes of defects in manufacturing and business processes, while implementing the lean concepts attempts to remove wasteful activities from those processes. In practice, the Six Sigma strategy and the Lean philosophy are combined and often viewed as one integrated philosophy, where the philosophy of Lean Six Sigma simultaneously removes wasteful activities from a process and reduces the variability of that process. This thesis research reviews the concepts and implementation of Lean thinking, Six Sigma strategy, and the integrated concept of Lean Six Sigma, with emphasis in service organizations. Most importantly, this thesis summarizes the critical success factors for implementing Lean Six Sigma within a service business environment and categorizes them within a proposed multi-level taxonomy that can be used by service business units and service providers to improve the success of Lean Six Sigma implementation.
Show less - Date Issued
- 2010
- Identifier
- CFE0003526, ucf:48966
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0003526
- Title
- IMPROVING BUSINESS PERFORMANCE THROUGH THE INTEGRATION OF HUMAN FACTORS ENGINEERING INTO ORGANIZATIONS USING A SYSTEMS ENGINEERING APPROACH.
- Creator
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Philippart, Monica, Karwowski, Waldemar, University of Central Florida
- Abstract / Description
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Most organizations today understand the valuable contribution employees as people (rather than simply bodies) provide to their overall performance. Although efforts are made to make the most of the human in organizations, there is still much room for improvement. Focus in the reduction of employee injuries such as cumulative trauma disorders rose in the 80's. Attempts at increasing performance by addressing employee satisfaction through various methods have also been ongoing for several...
Show moreMost organizations today understand the valuable contribution employees as people (rather than simply bodies) provide to their overall performance. Although efforts are made to make the most of the human in organizations, there is still much room for improvement. Focus in the reduction of employee injuries such as cumulative trauma disorders rose in the 80's. Attempts at increasing performance by addressing employee satisfaction through various methods have also been ongoing for several years now. Knowledge Management is one of the most recent attempts at controlling and making the best use of employees' knowledge. All of these efforts and more towards that same goal of making the most of people's performance at work are encompassed within the domain of the Human Factors Engineering/Ergonomics field. HFE/E provides still untapped potential for organizational performance as the human and its optimal performance are the reason for this discipline's being. Although Human Factors programs have been generated and implemented, there is still the need for a method to help organizations fully integrate this discipline into the enterprise as a whole. The purpose of this research is to develop a method to help organizations integrate HFE/E into it business processes. This research begun with a review of the ways in which the HFE/E discipline is currently used by organizations. The need and desire to integrate HFE/E into organizations was identified, and a method to accomplish this integration was conceptualized. This method consisted on the generation of two domain-specific ontologies (a Human Factors Engineering/Ergonomics ontology, and a Business ontology), and mapping the two creating a concept map that can be used to integrate HFE/E into businesses. The HFE/E ontology was built by generating two concept maps that were merged and then joined with a HFE/E discipline taxonomy. A total of four concept maps, two ontologies and a taxonomy were created, all of which are contributions to the HFE/E, and the business- and management-related fields.
Show less - Date Issued
- 2008
- Identifier
- CFE0002445, ucf:47716
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0002445
- Title
- INTERACTIVE TEXT-IMAGE CONCEPTUAL MODELS FOR LITERARY INTERPRETATION AND COMPOSITION IN THE DIGITAL AGE.
- Creator
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Weaver, Elizabeth, Saper, Craig, University of Central Florida
- Abstract / Description
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This dissertation focuses on text-image conceptual models for literary interpretation and composition in the digital age. The models investigate an interactive blend of textually-based linear-sequential approaches and visually-based spatial-simultaneous approaches. The models employ Gestalt-inspired figure-ground segregation models, along with other theoretical models, that demonstrate the dynamic capabilities of images as conceptual tools as well as alternate forms of text. The models...
Show moreThis dissertation focuses on text-image conceptual models for literary interpretation and composition in the digital age. The models investigate an interactive blend of textually-based linear-sequential approaches and visually-based spatial-simultaneous approaches. The models employ Gestalt-inspired figure-ground segregation models, along with other theoretical models, that demonstrate the dynamic capabilities of images as conceptual tools as well as alternate forms of text. The models encourage an interpretative style with active participants in open-ended, multi-sensory meaning-making processes. The models use the flexible tools of modern technology as approaches to meaning-making with art strategies used for research strategies as well as a means to appreciate reading and writing in the context of an increasingly visual environment.
Show less - Date Issued
- 2010
- Identifier
- CFE0003008, ucf:48335
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0003008
