+publisher:"University of New Mexico" +contributor:("Moses, Melanie")

University of New Mexico

1. Miles, Edward C. Hopscotch: Robust Multi-agent Search.

Degree: Department of Computer Science, 2013, University of New Mexico

URL: http://hdl.handle.net/1928/23202

► The task of searching a space is critical to a wide range of diverse applications such as land mine clearing and planetary exploration. Because applications… (more)

▼ The task of searching a space is critical to a wide range of diverse applications such as land mine clearing and planetary exploration. Because applications frequently require searching remote or hazardous locations, and because the task is easily divisible, it is natural to consider the use of multi-robot teams to accomplish the search task. An important topic of research in this area is the division of the task among robot agents. Interrelated with subtask assignment is failure handling, in the sense that, when an agent fails, its part of the task must then be performed by other agents. This thesis describes Hopscotch, a multi-agent search strategy that divides the search area into a grid of lots. Each agent is assigned responsibility to search one lot at a time, and upon completing the search of that lot the agent is assigned a new lot. Assignment occurs in real time using a simple contract net. Because lots that have been previously searched are skipped, the order of search from the point of view of a particular agent is reminiscent of the progression of steps in the playground game of Hopscotch. Decomposition of the search area is a common approach to multi-agent search, and auction-based contract net strategies have appeared in recent literature as a method of task allocation in multi-agent systems. The Hopscotch strategy combines the two, with a strong focus on robust tolerance of agent failures. Contract nets typically divide all known tasks among available resources. In contrast, Hopscotch limits each agent to one assigned lot at a time, so that failure of an agent compels re-allocation of only one lot search task. Furthermore, the contract net is implemented in an unconventional manner that empowers each agent with responsibility for contract management. This novel combination of real-time assignment and decentralized management allows Hopscotch to resiliently cope with agent failures. The Hopscotch strategy was modeled and compared to other multi-agent strate- gies that tackle the search task in a variety of ways. Simulation results show that Hopscotch is failure-tolerant and very effective in comparison to the other approaches in terms of both search time and search efficiency. Although the search task modeled here is a basic one, results from simulations show the promise of using this strategy for more complicated scenarios, and with actual robot agents. Advisors/Committee Members: Moses, Melanie E., Moses, Melanie E., Tapia, Lydia, Fierro, Rafael.

Subjects/Keywords: multi-agent; search; coverage; task allocation; mobile robots; cellular decomposition; contract net; swarm robotics

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APA (6^th Edition):

Miles, E. C. (2013). Hopscotch: Robust Multi-agent Search. (Masters Thesis). University of New Mexico. Retrieved from http://hdl.handle.net/1928/23202

Chicago Manual of Style (16^th Edition):

Miles, Edward C. “Hopscotch: Robust Multi-agent Search.” 2013. Masters Thesis, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/23202.

MLA Handbook (7^th Edition):

Miles, Edward C. “Hopscotch: Robust Multi-agent Search.” 2013. Web. 01 Mar 2021.

Vancouver:

Miles EC. Hopscotch: Robust Multi-agent Search. [Internet] [Masters thesis]. University of New Mexico; 2013. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/23202.

Council of Science Editors:

Miles EC. Hopscotch: Robust Multi-agent Search. [Masters Thesis]. University of New Mexico; 2013. Available from: http://hdl.handle.net/1928/23202

University of New Mexico

2. Brunetti, Tonya. Transcriptional regulation of muscle development in Drosophila melanogaster.

Degree: UNM Biology Department, 2015, University of New Mexico

URL: https://digitalrepository.unm.edu/biol_etds/9

► The transcriptional regulation of muscle development involves several complex processes that must work together in order to form functional, syncytial muscle cells. However, when transcription… (more)

Subjects/Keywords: Drosophila melanogaster; muscle development; genetic algorithm; myocyte enhancer factor-2; myoblast fusion; entropy; transcriptional regulation

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APA (6^th Edition):

Brunetti, T. (2015). Transcriptional regulation of muscle development in Drosophila melanogaster. (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biol_etds/9

Chicago Manual of Style (16^th Edition):

Brunetti, Tonya. “Transcriptional regulation of muscle development in Drosophila melanogaster.” 2015. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. https://digitalrepository.unm.edu/biol_etds/9.

MLA Handbook (7^th Edition):

Brunetti, Tonya. “Transcriptional regulation of muscle development in Drosophila melanogaster.” 2015. Web. 01 Mar 2021.

Vancouver:

Brunetti T. Transcriptional regulation of muscle development in Drosophila melanogaster. [Internet] [Doctoral dissertation]. University of New Mexico; 2015. [cited 2021 Mar 01]. Available from: https://digitalrepository.unm.edu/biol_etds/9.

Council of Science Editors:

Brunetti T. Transcriptional regulation of muscle development in Drosophila melanogaster. [Doctoral Dissertation]. University of New Mexico; 2015. Available from: https://digitalrepository.unm.edu/biol_etds/9

University of New Mexico

3. Burger, Joseph Robert. Macroecology and Sociobiology of Humans and other Mammals.

Degree: UNM Biology Department, 2015, University of New Mexico

URL: https://digitalrepository.unm.edu/biol_etds/11

► Despite being the most studied species on the planet, ecologists typically do not study humans the same way we study other organisms. My Ph.D. thesis… (more)

▼ Despite being the most studied species on the planet, ecologists typically do not study humans the same way we study other organisms. My Ph.D. thesis contributes to scientific development in two ways: i) synthesizing our understand of the inter and intraspecific variation in social behavior in an understudied rodent lineage, the caviomorphs, providing a comparative context to understand social evolution in general, and 2) developing a macroecological approach to understand the metabolic trajectory of the human species. Through comparative analysis, chapter 2 synthesizes the available information on the diversity of sociality in the caviomorph rodents, both within and across species. Studies and theory derived from better-studied mammalian taxa establish an integrative and comparative framework from which to examine social systems in caviomorphs. We synthesize the literature to evaluate variation in space use, group size, mating systems, and parental care strategies in caviomorphs in the context of current hypotheses. We highlight unique aspects of caviomorph biology and offer potentially fruitful lines for future research both at the inter and intraspecific levels. We can gain unique insights into the ecological drivers and evolutionary significance of diverse animal societies by studying this diverse taxon. Chapter 3 outlines core ecological principles that should be integral to a science of sustainability: 1) physical conservation laws govern the flows of energy and materials between human systems and the environment, 2) smaller systems are connected by these flows to larger systems in which they are embedded, 3) global constraints ultimately limit flows at smaller scales. Over the past few decades, decreasing per-capita rates of consumption of petroleum, phosphate, agricultural land, fresh water, fish, and wood indicate that the growing human population has surpassed the capacity of the Earth to supply enough of these essential resources to sustain even the current population and level of socioeconomic development. Chapter 4 applies a socio-metabolic perspective of the urban transition coupled with empirical examination of cross-country data spanning decades. It highlights the central role of extra-metabolic energy in global urbanization and the coinciding transition from resource extraction to industrial and service economies. The global urban transition from resource producers in rural areas, to industrial and service employment in urban systems is fuelled by supplementing extra-metabolic energy in the form of fossil fuels for decreasing human and animal labor. Collectively, I hope this work demonstrates the utility of comparative analysis and synthesis in understanding the evolutionary ecology of sociality and the power of a macroecological approach in understanding the metabolic ecology and trajectory of the human species. Advisors/Committee Members: Brown, James, Smith, Felisa, Moses, Melanie, Milne, Bruce.

Subjects/Keywords: Human Ecology; Macroecology; Metabolic Ecology; Sociality; Sustainability; Cities

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APA (6^th Edition):

Burger, J. R. (2015). Macroecology and Sociobiology of Humans and other Mammals. (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biol_etds/11

Chicago Manual of Style (16^th Edition):

Burger, Joseph Robert. “Macroecology and Sociobiology of Humans and other Mammals.” 2015. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. https://digitalrepository.unm.edu/biol_etds/11.

MLA Handbook (7^th Edition):

Burger, Joseph Robert. “Macroecology and Sociobiology of Humans and other Mammals.” 2015. Web. 01 Mar 2021.

Vancouver:

Burger JR. Macroecology and Sociobiology of Humans and other Mammals. [Internet] [Doctoral dissertation]. University of New Mexico; 2015. [cited 2021 Mar 01]. Available from: https://digitalrepository.unm.edu/biol_etds/11.

Council of Science Editors:

Burger JR. Macroecology and Sociobiology of Humans and other Mammals. [Doctoral Dissertation]. University of New Mexico; 2015. Available from: https://digitalrepository.unm.edu/biol_etds/11

University of New Mexico

4. Burnside, William. Pattern and process in metabolic ecology : from biotic interactions to cultural diversity gradients.

Degree: UNM Biology Department, 2012, University of New Mexico

URL: https://digitalrepository.unm.edu/biol_etds/12

► Many ecological patterns and processes are functions of metabolism (Brown 2004), meaning the acquisition, transformation, and allocation of energy, materials, and information within the bodies… (more)

▼ Many ecological patterns and processes are functions of metabolism (Brown 2004), meaning the acquisition, transformation, and allocation of energy, materials, and information within the bodies of individuals and among members of human and other animal societies. Individual metabolic rate should influence behavior by determining the energy available for action as well as the rate at which the body requires fuel. First, I test a key prediction of the metabolic theory of ecology (MTE), that biotic interaction rates are characteristic functions of temperature. Findings support this prediction and suggest that herbivory, predation, parasitism, parasitoidy, and competition increase exponentially with temperature and that this increase echoes that of individual metabolic rates. Second, I extend a metabolic framework to foraging patterns and space use of traditional human societies. Together with colleagues, I build on Hamilton (2007) to offer a model that formally incorporates hypothesized mechanisms affecting population sizes and densities and territory sizes: temperature, productivity, seasonality, and trophic level (degree of carnivory). We test this model on a dataset of 333 traditional foraging societies using multiple linear regression. Interactions between explanatory variables were important, and the influence of temperature, productivity, and seasonality often depended on trophic level. In addition, coastal productivity allowed marine foragers to disassociate themselves from terrestrial energetic constraints and maintain high population densities, small territory sizes, and thus high levels of cultural diversity. A metabolic perspective is useful for interpreting patterns in large scale human ecology and suggesting underlying mechanisms. Third, I argue for a macroecological approach to human ecology and suggest the value of a metabolic perspective using examples from human foraging ecology, life history, space use, population structure, disease ecology, cultural and linguistic diversity patterns, and industrial and urban systems. The ability of a metabolic framework to inform our understanding of behavior, from the interaction rates of small ectotherms to cultural diversity and urban activity patterns in Homo sapiens, suggests the power and promise of this approach. Advisors/Committee Members: Brown, James, Moses, Melanie, Kaplan, Hillard, Hamilton, Marcus.

Subjects/Keywords: metabolic ecology macroecology

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APA (6^th Edition):

Burnside, W. (2012). Pattern and process in metabolic ecology : from biotic interactions to cultural diversity gradients. (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biol_etds/12

Chicago Manual of Style (16^th Edition):

Burnside, William. “Pattern and process in metabolic ecology : from biotic interactions to cultural diversity gradients.” 2012. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. https://digitalrepository.unm.edu/biol_etds/12.

MLA Handbook (7^th Edition):

Burnside, William. “Pattern and process in metabolic ecology : from biotic interactions to cultural diversity gradients.” 2012. Web. 01 Mar 2021.

Vancouver:

Burnside W. Pattern and process in metabolic ecology : from biotic interactions to cultural diversity gradients. [Internet] [Doctoral dissertation]. University of New Mexico; 2012. [cited 2021 Mar 01]. Available from: https://digitalrepository.unm.edu/biol_etds/12.

Council of Science Editors:

Burnside W. Pattern and process in metabolic ecology : from biotic interactions to cultural diversity gradients. [Doctoral Dissertation]. University of New Mexico; 2012. Available from: https://digitalrepository.unm.edu/biol_etds/12

University of New Mexico

5. Okie, Jordan G. Allometric scaling and metabolic ecology of microorganisms and major evolutionary transitions.

Degree: UNM Biology Department, 2011, University of New Mexico

URL: https://digitalrepository.unm.edu/biol_etds/89

► My dissertation centers around investigating big-picture questions related to understanding the consequences of metabolism and energetics on the evolution, ecology, and physiology of life. The… (more)

▼ My dissertation centers around investigating big-picture questions related to understanding the consequences of metabolism and energetics on the evolution, ecology, and physiology of life. The evolutionary transitions from prokaryotes to unicellular eukaryotes to multicellular organisms were accompanied by major innovations in metabolic design. In my first chapter, I show that the scaling of metabolic rate, population growth rate, and production efficiency with body size have changed across these transitions. Metabolic rate scales with body mass superlinearly in prokaryotes, linearly in protists, and sublinearly in metazoans, so Kleibers 3/4 power scaling law does not apply universally across organisms. This means that major changes in metabolic processes during the early evolution of life overcame existing physical constraints, exploited new opportunities, and imposed new constraints on organism physiology. Surface areas of physiological structures of organisms impose fundamental constraints on metabolic rate. In my second chapter, I demonstrate that organisms have a variety of options for increasing the scaling of the area of their metabolic surfaces with body sizes. I develop models and examples illustrating the role of cell membrane elaborations, mitochondria, vacuoles, vesicles, inclusions, and shape-shifting in the architectural design, evolution, and ecology of unicellular microbes. I demonstrate how these surface-area scaling adaptations have played important roles in the evolution of major biological designs of cells and the physiological ecology of organisms. In my third and final chapter, I integrate and synthesize findings from the previous two chapters with important developments in geochemistry, microbiology, and astrobiology in order to identify the fundamental physical and biological dimensions that characterize a metabolic theory of ecology of microorganisms. These dimensions are thermodynamics, chemical kinetics, physiological harshness, cell size, and levels of biological organization. I show how addressing these dimensions can inform understanding of the physical and biological factors governing the metabolic rate, growth rate, and geographic distribution of cells. I propose a unifying theory to understand how the major ecological and evolutionary transitions that led to increases in levels of organization of life, such as endosymbiosis, multicellularity, eusociality, and multi-domain complexes, influences the metabolism and growth and the metabolic scaling of these complexes. Advisors/Committee Members: Brown, James H., Michod, Richard, Moses, Melanie, Sinsabaugh, Robert.

Subjects/Keywords: Major evolutionary transitions; Metabolic theory of ecology; Microbial ecology; Thermodynamics; Kinetics; Allometric scaling; Unicellular organisms; Body size; Cell physiological ecology

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APA (6^th Edition):

Okie, J. G. (2011). Allometric scaling and metabolic ecology of microorganisms and major evolutionary transitions. (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biol_etds/89

Chicago Manual of Style (16^th Edition):

Okie, Jordan G. “Allometric scaling and metabolic ecology of microorganisms and major evolutionary transitions.” 2011. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. https://digitalrepository.unm.edu/biol_etds/89.

MLA Handbook (7^th Edition):

Okie, Jordan G. “Allometric scaling and metabolic ecology of microorganisms and major evolutionary transitions.” 2011. Web. 01 Mar 2021.

Vancouver:

Okie JG. Allometric scaling and metabolic ecology of microorganisms and major evolutionary transitions. [Internet] [Doctoral dissertation]. University of New Mexico; 2011. [cited 2021 Mar 01]. Available from: https://digitalrepository.unm.edu/biol_etds/89.

Council of Science Editors:

Okie JG. Allometric scaling and metabolic ecology of microorganisms and major evolutionary transitions. [Doctoral Dissertation]. University of New Mexico; 2011. Available from: https://digitalrepository.unm.edu/biol_etds/89

University of New Mexico

6. Bezerra, George. Energy consumption in networks on chip : efficiency and scaling.

Degree: Department of Computer Science, 2012, University of New Mexico

URL: http://hdl.handle.net/1928/21020

► Computer architecture design is in a new era where performance is increased by replicating processing cores on a chip rather than making CPUs larger and… (more)

Subjects/Keywords: multi-core; many-core; energy consumption; communicaiton locality; scaling

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Bezerra, G. (2012). Energy consumption in networks on chip : efficiency and scaling. (Doctoral Dissertation). University of New Mexico. Retrieved from http://hdl.handle.net/1928/21020

Chicago Manual of Style (16^th Edition):

Bezerra, George. “Energy consumption in networks on chip : efficiency and scaling.” 2012. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/21020.

MLA Handbook (7^th Edition):

Bezerra, George. “Energy consumption in networks on chip : efficiency and scaling.” 2012. Web. 01 Mar 2021.

Vancouver:

Bezerra G. Energy consumption in networks on chip : efficiency and scaling. [Internet] [Doctoral dissertation]. University of New Mexico; 2012. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/21020.

Council of Science Editors:

Bezerra G. Energy consumption in networks on chip : efficiency and scaling. [Doctoral Dissertation]. University of New Mexico; 2012. Available from: http://hdl.handle.net/1928/21020

University of New Mexico

7. Villalon, Ricardo. Fault-tolerant wireless sensor networks using evolutionary games.

Degree: Department of Computer Science, 2012, University of New Mexico

URL: http://hdl.handle.net/1928/22075

► This dissertation proposes an approach to creating robust communication systems in wireless sensor networks, inspired by biological and ecological systems, particularly by evolutionary game theory.… (more)

Subjects/Keywords: Wireless Sensor Networks; Agent-based systems

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Villalon, R. (2012). Fault-tolerant wireless sensor networks using evolutionary games. (Doctoral Dissertation). University of New Mexico. Retrieved from http://hdl.handle.net/1928/22075

Chicago Manual of Style (16^th Edition):

Villalon, Ricardo. “Fault-tolerant wireless sensor networks using evolutionary games.” 2012. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/22075.

MLA Handbook (7^th Edition):

Villalon, Ricardo. “Fault-tolerant wireless sensor networks using evolutionary games.” 2012. Web. 01 Mar 2021.

Vancouver:

Villalon R. Fault-tolerant wireless sensor networks using evolutionary games. [Internet] [Doctoral dissertation]. University of New Mexico; 2012. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/22075.

Council of Science Editors:

Villalon R. Fault-tolerant wireless sensor networks using evolutionary games. [Doctoral Dissertation]. University of New Mexico; 2012. Available from: http://hdl.handle.net/1928/22075

University of New Mexico

8. Levin, Drew. The Environment Constrains Successful Search Strategies in Natural Distributed Systems.

Degree: Department of Computer Science, 2016, University of New Mexico

URL: http://hdl.handle.net/1928/32313

► This dissertation investigates two natural systems that use distributed search algorithms and tests the hypothesis that the searchers' environment is a key constraint on an… (more)

▼ This dissertation investigates two natural systems that use distributed search algorithms and tests the hypothesis that the searchers' environment is a key constraint on an optimal algorithm. Natural instances of distributed autonomous systems of simple components exist in both biology and social systems. These systems have been honed through eons of evolution by natural selection to perform well in their environment. I examine two specific systems that use distributed methods to search and recruit individuals to locations of interest: T cells' search for pathogens in the human body and ants searching for food. Both systems are examples of time-constrained processes that require the distributed coordination of simple autonomous agents and interaction with their environment. Taking common principles from both domains, the dissertation examines three distributed search strategies: uninformed random search, origin-based local recruitment, and chemical-based pheromone recruitment. Using both numerical and agent-based models, it evaluates the effectiveness of these strategies across two environmental factors: the spatial clustering and temporal volatility of resources. The results demonstrate that both recruitment-based strategies (origin-based and chemical-based) suffer in environments of high resources dispersion and volatility. Conversely, uninformed random search performs better in these environments. The results are relevant to certain algorithmic issues in swarm robotics. For example, it is expensive to implement chemical trails in a distributed physical system, and the dissertation shows that strategies using only local recruitment perform similarly in all environments. Also, origin-only algorithms are much easier to implement in a robotics context. Further, because each strategy examined in this dissertation performs best at one extreme of resource spatial distribution, the results establish that the most difficult environments for search are likely those with intermediate levels of clustering. Finally, the dissertation classifies the exact nature of the environmental trade-offs and presents methods to determine the best search strategy given knowledge of the environment. Advisors/Committee Members: Forrest, Stephanie, Moses, Melanie, Tapia, Lydia, Cannon, Judy.

Subjects/Keywords: Distributed Systems; Distributed Search; Computational Biology; Theoretical Biology; Immunology; Virology; Myrmecology

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APA (6^th Edition):

Levin, D. (2016). The Environment Constrains Successful Search Strategies in Natural Distributed Systems. (Doctoral Dissertation). University of New Mexico. Retrieved from http://hdl.handle.net/1928/32313

Chicago Manual of Style (16^th Edition):

Levin, Drew. “The Environment Constrains Successful Search Strategies in Natural Distributed Systems.” 2016. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/32313.

MLA Handbook (7^th Edition):

Levin, Drew. “The Environment Constrains Successful Search Strategies in Natural Distributed Systems.” 2016. Web. 01 Mar 2021.

Vancouver:

Levin D. The Environment Constrains Successful Search Strategies in Natural Distributed Systems. [Internet] [Doctoral dissertation]. University of New Mexico; 2016. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/32313.

Council of Science Editors:

Levin D. The Environment Constrains Successful Search Strategies in Natural Distributed Systems. [Doctoral Dissertation]. University of New Mexico; 2016. Available from: http://hdl.handle.net/1928/32313

University of New Mexico

9. Flynn, Mark. Improving peer review with ACORN : Ant Colony Optimization algorithm for Reviewer's Network.

Degree: Department of Computer Science, 2011, University of New Mexico

URL: http://hdl.handle.net/1928/13085

► Peer review, our current system for determining which papers to accept and which to reject by journals and conferences, has limitations that impair the quality… (more)

Subjects/Keywords: Ant Colony Optimization; Peer review

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APA (6^th Edition):

Flynn, M. (2011). Improving peer review with ACORN : Ant Colony Optimization algorithm for Reviewer's Network. (Masters Thesis). University of New Mexico. Retrieved from http://hdl.handle.net/1928/13085

Chicago Manual of Style (16^th Edition):

Flynn, Mark. “Improving peer review with ACORN : Ant Colony Optimization algorithm for Reviewer's Network.” 2011. Masters Thesis, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/13085.

MLA Handbook (7^th Edition):

Flynn, Mark. “Improving peer review with ACORN : Ant Colony Optimization algorithm for Reviewer's Network.” 2011. Web. 01 Mar 2021.

Vancouver:

Flynn M. Improving peer review with ACORN : Ant Colony Optimization algorithm for Reviewer's Network. [Internet] [Masters thesis]. University of New Mexico; 2011. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/13085.

Council of Science Editors:

Flynn M. Improving peer review with ACORN : Ant Colony Optimization algorithm for Reviewer's Network. [Masters Thesis]. University of New Mexico; 2011. Available from: http://hdl.handle.net/1928/13085

University of New Mexico

10. Stolleis, Karl. The Ant and the Trap: Evolution of Ant-Inspired Obstacle Avoidance in a Multi-Agent Robotic System.

Degree: Department of Computer Science, 2015, University of New Mexico

URL: http://hdl.handle.net/1928/27969

► Interest in swarm robotics, particularly those modeled on biological systems, has been increasing with each passing year. We created the iAnt robot as a platform… (more)

Subjects/Keywords: robot; swarm robotics; ant; genetic algorithm; foraging; obstacle avoidance; biologically inspired; in situ resource utilization; evolution; robot behavior

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APA (6^th Edition):

Stolleis, K. (2015). The Ant and the Trap: Evolution of Ant-Inspired Obstacle Avoidance in a Multi-Agent Robotic System. (Masters Thesis). University of New Mexico. Retrieved from http://hdl.handle.net/1928/27969

Chicago Manual of Style (16^th Edition):

Stolleis, Karl. “The Ant and the Trap: Evolution of Ant-Inspired Obstacle Avoidance in a Multi-Agent Robotic System.” 2015. Masters Thesis, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/27969.

MLA Handbook (7^th Edition):

Stolleis, Karl. “The Ant and the Trap: Evolution of Ant-Inspired Obstacle Avoidance in a Multi-Agent Robotic System.” 2015. Web. 01 Mar 2021.

Vancouver:

Stolleis K. The Ant and the Trap: Evolution of Ant-Inspired Obstacle Avoidance in a Multi-Agent Robotic System. [Internet] [Masters thesis]. University of New Mexico; 2015. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/27969.

Council of Science Editors:

Stolleis K. The Ant and the Trap: Evolution of Ant-Inspired Obstacle Avoidance in a Multi-Agent Robotic System. [Masters Thesis]. University of New Mexico; 2015. Available from: http://hdl.handle.net/1928/27969

University of New Mexico

11. Flanagan, Tatiana. How ants turn information into food.

Degree: UNM Biology Department, 2015, University of New Mexico

URL: https://digitalrepository.unm.edu/biol_etds/37

► Animals constantly process information from their environment. In social organisms, information exchange among individuals allows for behaviors to be finely tuned to local environmental cues.… (more)

Subjects/Keywords: ant foraging; information; colony size

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APA (6^th Edition):

Flanagan, T. (2015). How ants turn information into food. (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biol_etds/37

Chicago Manual of Style (16^th Edition):

Flanagan, Tatiana. “How ants turn information into food.” 2015. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. https://digitalrepository.unm.edu/biol_etds/37.

MLA Handbook (7^th Edition):

Flanagan, Tatiana. “How ants turn information into food.” 2015. Web. 01 Mar 2021.

Vancouver:

Flanagan T. How ants turn information into food. [Internet] [Doctoral dissertation]. University of New Mexico; 2015. [cited 2021 Mar 01]. Available from: https://digitalrepository.unm.edu/biol_etds/37.

Council of Science Editors:

Flanagan T. How ants turn information into food. [Doctoral Dissertation]. University of New Mexico; 2015. Available from: https://digitalrepository.unm.edu/biol_etds/37

University of New Mexico

12. Bezzo, Nicola. Coordination strategies for connected robotic networks.

Degree: Electrical and Computer Engineering, 2013, University of New Mexico

URL: http://hdl.handle.net/1928/22030

► In this dissertation we present theoretical techniques to coordinate multi-robotic systems in cluttered environment considering sensing, manipulation, and communication constraints. We address communication constraints in… (more)

▼ In this dissertation we present theoretical techniques to coordinate multi-robotic systems in cluttered environment considering sensing, manipulation, and communication constraints. We address communication constraints in the context of mobile routers coordination within complex operations. Motivated by real world applications, we present strategies to deploy teams of robotic agents with communication connectivity constraints to keep a user connected to a base station at all times. We consider several aspects about wireless communication to improve the connection quality of mobile robotic systems while performing cooperative missions inspired by real world applications. This dissertation is organized in two main parts. In Part I we study networks of homogeneous robots consisting of agents having the same dynamics, sensing, and communication capabilities. We first present a centralized approach based on disjunctive programming to tether a chain of mobile routers between a base station and a user that is moving in a concave environment. We consider line-of-sight (LOS) communication and use a mixed integer approach to determine the number of required agents and their goal locations. Because centralized approaches have the limitation that a central node has to compute all the operations and everything has to be known a priori, we study decentralized approaches to swarm groups of mobile agents while considering communication constraints. Specifically we introduce a spring-mass virtual interaction between the agents and use artificial potentials to navigate the network in a cluttered environment. Finally we use bit error rate (BER) optimization to maintain a certain quality of communication while keeping the system stable in the sense of Lyapunov. When dealing with connected networks of mobile robots, the problem of detecting variations in the topology is an important area of study. Therefore we present a novel decentralized technique to detect and estimate changes in the topology of mobile robotic networks. In this case we assume that each robot is equipped with a chaotic oscillator whose state is propagated to the other robots through wireless communication. The key idea of our approach is that every node receives an aggregate signal from the surrounding neighbors, which can be used to detect changes in the local network topology. We introduce an adaptive strategy that each robot independently implements to: (i) estimate the net coupling of all the oscillators in its neighborhood, and (ii) synchronize the state of the oscillators onto the same time evolution. We show that by using this strategy, synchronization can be attained and changes of the network topology can be detected. Finally in the last chapter of Part I we exploit antenna diversity in a practical case study to localize and improve the signal quality between a mobile agent and a user. In Part II we focus our attention on heterogeneous systems. With the term heterogeneous we imply the synergy of multiple robotic platforms characterized by different dynamics… Advisors/Committee Members: Fierro, Rafael, Abdallah, Chaouki T., Sorrentino, Francesco, Moses, Melanie.

Subjects/Keywords: Robots – Control systems.; Multiagent systems.; Swarm intelligence.; Bit error rate.; Local area networks (Computer networks); Local area networks (Computer networks); Heterogeneous computing.

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APA (6^th Edition):

Bezzo, N. (2013). Coordination strategies for connected robotic networks. (Doctoral Dissertation). University of New Mexico. Retrieved from http://hdl.handle.net/1928/22030

Chicago Manual of Style (16^th Edition):

Bezzo, Nicola. “Coordination strategies for connected robotic networks.” 2013. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/22030.

MLA Handbook (7^th Edition):

Bezzo, Nicola. “Coordination strategies for connected robotic networks.” 2013. Web. 01 Mar 2021.

Vancouver:

Bezzo N. Coordination strategies for connected robotic networks. [Internet] [Doctoral dissertation]. University of New Mexico; 2013. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/22030.

Council of Science Editors:

Bezzo N. Coordination strategies for connected robotic networks. [Doctoral Dissertation]. University of New Mexico; 2013. Available from: http://hdl.handle.net/1928/22030

University of New Mexico

13. Ericksen, John. Transfuse: A Compile-Time Metaprogramming Solution for Reducing Boilerplate on Google's Android.

Degree: Department of Computer Science, 2016, University of New Mexico

URL: http://hdl.handle.net/1928/32945

► Modern Java application development makes use of metaprogramming to offset and reduce application boilerplate. Unfortunately, metaprogramming techniques typically require a relatively high run-time cost, particularly… (more)

Subjects/Keywords: Dependency Injection; Android; Compile time; Annotation Processing; Metaprogramming; Boilerplate

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APA (6^th Edition):

Ericksen, J. (2016). Transfuse: A Compile-Time Metaprogramming Solution for Reducing Boilerplate on Google's Android. (Masters Thesis). University of New Mexico. Retrieved from http://hdl.handle.net/1928/32945

Chicago Manual of Style (16^th Edition):

Ericksen, John. “Transfuse: A Compile-Time Metaprogramming Solution for Reducing Boilerplate on Google's Android.” 2016. Masters Thesis, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/32945.

MLA Handbook (7^th Edition):

Ericksen, John. “Transfuse: A Compile-Time Metaprogramming Solution for Reducing Boilerplate on Google's Android.” 2016. Web. 01 Mar 2021.

Vancouver:

Ericksen J. Transfuse: A Compile-Time Metaprogramming Solution for Reducing Boilerplate on Google's Android. [Internet] [Masters thesis]. University of New Mexico; 2016. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/32945.

Council of Science Editors:

Ericksen J. Transfuse: A Compile-Time Metaprogramming Solution for Reducing Boilerplate on Google's Android. [Masters Thesis]. University of New Mexico; 2016. Available from: http://hdl.handle.net/1928/32945

University of New Mexico

14. Schulte, Eric. Neutral Networks of Real-World Programs and their Application to Automated Software Evolution.

Degree: Department of Computer Science, 2014, University of New Mexico

URL: http://hdl.handle.net/1928/25819

► The existing software development ecosystem is the product of evolutionary forces, and consequently real-world software is amenable to improvement through automated evolutionary techniques. This dissertation… (more)

▼ The existing software development ecosystem is the product of evolutionary forces, and consequently real-world software is amenable to improvement through automated evolutionary techniques. This dissertation presents empirical evidence that software is inherently robust to small randomized program transformations, or 'mutations. Simple and general mutation operations are demonstrated that can be applied to software source code, compiled assembler code, or directly to binary executables. These mutations often generate variants of working programs that differ significantly from the original, yet remain fully functional. Applying successive mutations to the same software program uncovers large 'neutral networks' of fully functional variants of real-world software projects. These properties of 'mutational robustness' and the corresponding 'neutral networks' have been studied extensively in biology and are believed to be related to the capacity for unsupervised evolution and adaptation. As in biological systems, mutational robustness and neutral networks in software systems enable automated evolution. The dissertation presents several applications that leverage software neutral networks to automate common software development and maintenance tasks. Neutral networks are explored to generate diverse implementations of software for improving runtime security and for proactively repairing latent bugs. Next, a technique is introduced for automatically repairing bugs in the assembler and executables compiled from off-the-shelf software. As demonstration, a proprietary executable is manipulated to patch security vulnerabilities without access to source code or any aid from the software vendor. Finally, software neutral networks are leveraged to optimize complex nonfunctional runtime properties. This optimization technique is used to reduce the energy consumption of the popular PARSEC benchmark applications by 20% as compared to the best available public domain compiler optimizations. The applications presented herein apply evolutionary computation techniques to existing software using common software engineering tools. By enabling evolutionary techniques within the existing software development toolchain, this work is more likely to be of practical benefit to the developers and maintainers of real-world software systems. Advisors/Committee Members: Forrest, Stephanie, Weimer, Westley, Crandall, Jedidiah, Moses, Melanie.

Subjects/Keywords: software engineering; search based software engineering; software mutational robustness; mutational robustness; evolutionary computation; genetic algorithm; genetic programming; optimization; automated program repair; automated software engineering; bug repair; fitness landscape; instruction set architecture; neutral network

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APA (6^th Edition):

Schulte, E. (2014). Neutral Networks of Real-World Programs and their Application to Automated Software Evolution. (Doctoral Dissertation). University of New Mexico. Retrieved from http://hdl.handle.net/1928/25819

Chicago Manual of Style (16^th Edition):

Schulte, Eric. “Neutral Networks of Real-World Programs and their Application to Automated Software Evolution.” 2014. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/25819.

MLA Handbook (7^th Edition):

Schulte, Eric. “Neutral Networks of Real-World Programs and their Application to Automated Software Evolution.” 2014. Web. 01 Mar 2021.

Vancouver:

Schulte E. Neutral Networks of Real-World Programs and their Application to Automated Software Evolution. [Internet] [Doctoral dissertation]. University of New Mexico; 2014. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/25819.

Council of Science Editors:

Schulte E. Neutral Networks of Real-World Programs and their Application to Automated Software Evolution. [Doctoral Dissertation]. University of New Mexico; 2014. Available from: http://hdl.handle.net/1928/25819

University of New Mexico

15. Chang, Michael. Scaling of crop diversity and optimal allocation of foodshed infrastructure.

Degree: UNM Biology Department, 2013, University of New Mexico

URL: https://digitalrepository.unm.edu/biol_etds/14

► Food hubs are organizations that manage the aggregation and distribution of local products, and are a small, but growing means to satisfy high demand… (more)

▼ Food hubs are organizations that manage the aggregation and distribution of local products, and are a small, but growing means to satisfy high demand for diverse, healthy diets. However, economic barriers inhibit small producers and distributors from developing mainstream, local consumer alternatives to industrial-scale products. To build foodshed, distribution hubs could help overcome these challenges by reducing costs through shared refrigeration, processing, and transportation infrastructure. However, there is no theory to help plan them. I present and test theory to allocate foodshed infrastructure based on insight by Dunn, et al. (2011) that Shannon diversity measured relative to a whole set of sites, rather than site-by-site, reveals law-like scaling behavior. I accessed the US Dept of Agricultures 2011 Cropland Data Layer (CDL) for 40 crop cover types at 30 m resolution in New Mexico. I tested two competing hypotheses: 1) a site-specific and 2) a whole-system normalization of crop probabilities interpretable as the information experienced by producers versus a distributor, respectively. Directly edible and marketable crops were differentiated from forage crops for livestock because of the different destinations and infrastructure they require. A distributor with information about the whole foodshed experiences law-like increase in uncertainty with increasing observation scales. Since the distributor uncertainty about an area's crop inventory is an order of magnitude lower than the producers', a distributor should plan infrastructure at a scale that maximizes reduction of a producer's uncertainty. For all crops, I compared their relative contribution to total diversity per unit area so as to compare areas on the landscape with the highest capacity to diversify the foodshed as a whole. Development of a diverse foodshed will require knowledge of which products affect local diversity. This work grounds whole-foodshed planning in ecological theory, and contributes to understanding about how the conventional food system has allocated crop diversity. Advisors/Committee Members: Milne, Bruce, Moses, Melanie, Duvall, Chris, N/A.

Subjects/Keywords: Food; Agriculture; Sustainability; Diversity; Entropy; Cropland Data Layer; Hierarchy; Agrobiodiversity – Economic aspects.; Sustainable agriculture – Planning.; Farms; Small – Management.; Food supply – Social aspects.; Farmers' markets – Planning.; Local foods.; Biology

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APA (6^th Edition):

Chang, M. (2013). Scaling of crop diversity and optimal allocation of foodshed infrastructure. (Masters Thesis). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biol_etds/14

Chicago Manual of Style (16^th Edition):

Chang, Michael. “Scaling of crop diversity and optimal allocation of foodshed infrastructure.” 2013. Masters Thesis, University of New Mexico. Accessed March 01, 2021. https://digitalrepository.unm.edu/biol_etds/14.

MLA Handbook (7^th Edition):

Chang, Michael. “Scaling of crop diversity and optimal allocation of foodshed infrastructure.” 2013. Web. 01 Mar 2021.

Vancouver:

Chang M. Scaling of crop diversity and optimal allocation of foodshed infrastructure. [Internet] [Masters thesis]. University of New Mexico; 2013. [cited 2021 Mar 01]. Available from: https://digitalrepository.unm.edu/biol_etds/14.

Council of Science Editors:

Chang M. Scaling of crop diversity and optimal allocation of foodshed infrastructure. [Masters Thesis]. University of New Mexico; 2013. Available from: https://digitalrepository.unm.edu/biol_etds/14

University of New Mexico

16. Letendre, Kenneth. Variation and organization in social behavior : infectious disease and human intergroup conflict and warfare; and the organization of foraging behavior in harvester ants.

Degree: UNM Biology Department, 2012, University of New Mexico

URL: https://digitalrepository.unm.edu/biol_etds/70

► Social behavior is an important contributor to the success of widely distributed animal taxa, including such distantly related taxa as humans and ants. There is… (more)

▼ Social behavior is an important contributor to the success of widely distributed animal taxa, including such distantly related taxa as humans and ants. There is variation in the features and organization of social systems based on ecological constraints and goals, as these alter the costs and benefits of social behaviors, and select for different optimal behaviors for social groups in different environments. I present two bodies of research: an effort to explain geographic variation in the frequency and intensity of human civil conflict; and an effort to describe and model the foraging behavior of colonies of harvester ants of the genus Pogonomyrmex. First, in an investigation of the geographic variation in the frequency of human civil conflict, I show that cross-nationally, intrastate armed conflicts are predicted positively by variation in the intensity of human infectious disease. I present a theoretical model to explain this variation that proposes that risk of exposure to novel infectious diseases imposes costs on intergroup social interaction, and in regions with high intensity of infectious disease these costs create relative poverty and exacerbate conflict over resources. Second, I show that infectious disease predicts other categories of civil conflict, including clan wars, and revolutions and coups. I present a path analysis of the global peace index to test the plausibility of the hypothesized model, including the various indirect effects linking infectious disease to conflict; this analysis supports the importance of the relationship between infectious disease and conflict cross-nationally. Third, I present the results of a study using a computer model of host-parasite coevolution to examine the mechanisms by which localized host-parasite coevolutionary races impose fitness costs on host intergroup interaction, and lead to the evolution of out-group avoidance in mating decisions. In the fourth chapter I present a field study of the foraging behavior of three sympatric species of harvester ants, and their response to variation in heterogeneity in the distribution of foods. Fifth, I present a computer model of ant colony foraging behavior, which I optimized using genetic algorithms for different distributions of food, and whose resulting foraging behavior I compare to the previous observations of harvester ants in the field. Advisors/Committee Members: Thornhill, Randy, Watson, Paul, Gangestad, Steve, Kodric-Brown, Astrid, Moses, Melanie.

Subjects/Keywords: human warfare; competition; inter-group violence; political values; evolution; behavior; infectious disease; harvester ants; foraging ecology; agent-based modeling

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APA (6^th Edition):

Letendre, K. (2012). Variation and organization in social behavior : infectious disease and human intergroup conflict and warfare; and the organization of foraging behavior in harvester ants. (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biol_etds/70

Chicago Manual of Style (16^th Edition):

Letendre, Kenneth. “Variation and organization in social behavior : infectious disease and human intergroup conflict and warfare; and the organization of foraging behavior in harvester ants.” 2012. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. https://digitalrepository.unm.edu/biol_etds/70.

MLA Handbook (7^th Edition):

Letendre, Kenneth. “Variation and organization in social behavior : infectious disease and human intergroup conflict and warfare; and the organization of foraging behavior in harvester ants.” 2012. Web. 01 Mar 2021.

Vancouver:

Letendre K. Variation and organization in social behavior : infectious disease and human intergroup conflict and warfare; and the organization of foraging behavior in harvester ants. [Internet] [Doctoral dissertation]. University of New Mexico; 2012. [cited 2021 Mar 01]. Available from: https://digitalrepository.unm.edu/biol_etds/70.

Council of Science Editors:

Letendre K. Variation and organization in social behavior : infectious disease and human intergroup conflict and warfare; and the organization of foraging behavior in harvester ants. [Doctoral Dissertation]. University of New Mexico; 2012. Available from: https://digitalrepository.unm.edu/biol_etds/70

University of New Mexico

17. Wenyun, Zuo. From growth to extinction : explored by life history and metabolic theory.

Degree: UNM Biology Department, 2011, University of New Mexico

URL: https://digitalrepository.unm.edu/biol_etds/111

► The laws of energy and material conservation are fundamental principles across various scales and systems. Based on the conservation laws, I derive several theoretical models… (more)

▼ The laws of energy and material conservation are fundamental principles across various scales and systems. Based on the conservation laws, I derive several theoretical models to understand mechanisms behind the energy budget of ontogenetic growth and the pattern of the late Pleistocene extinction of megafauna in the Americas. First, I present a model, empirically grounded in data from birds and mammals, that correctly predicts how growing animals allocate food energy between synthesis of new biomass and maintenance of existing biomass. Previous energy budget models have typically been based on rates of either food consumption or metabolic energy expenditure. The model provides a framework that reconciles these two approaches and highlights the fundamental principles that determine rates of food assimilation and rates of energy allocation to maintenance, biosynthesis, activity, and storage. The model predicts that growth and assimilation rates for all animals should cluster closely around two canonical curves. Second, the previous model, which focuses on endotherms, has been extended to understand effects of temperature on the energy budget of ontogenetic growth of ectotherms. A tendency for ectotherms to develop faster but mature at smaller body sizes in warmer environments has been studied for decades, and is called the temperature size rule (TSR). It can be explained by a simple model in which the rate of growth or biomass accumulation and the rate of development or differentiation have different temperature dependence. The model accounts for both TSR and the less frequently observed reverse-TSR, predicts the fraction of energy allocated to maintenance and synthesis over the course of development, and the temperature independent growth efficiency. It also predicts that less total energy is expended when developing at warmer temperatures for TSR and vice versa for reverse-TSR. It has important implications for effects of climate change on ectothermic animals and also provides how selection may lead to the evolution of both TSR and reverse-TSR. Finally, based on mammalian life history and life history scaling relationships, an exploitation-extinction theory has been developed for the rate of human harvest in the disappearance of the Pleistocene megafauna in the Americas. The theory demonstrates that the added mortality of human harvest on populations need not be selective to produce a size-biased extinction. The variation in the adult natural instantaneous mortality rate and/or the maximum recruitment compensation at any body mass are main components determining the probability of extinction. The theory successfully predicts the shapes of the extinction probability curves for the late Pleistocene extinction in the Americas. It provides a theoretical basis to challenge a major criticism of the "overkill" theory that early Paleoindian hunters had to be extremely selective to have produced the highly size-biased pattern characteristic to the late Pleistocene extinction of megafauna in the Americas. Advisors/Committee Members: Brown, James H., West, Geoffrey B., Moses, Melanie E., Wearing, Helen.

Subjects/Keywords: energy budget; endotherm; ectotherm; late Pleistocene; the effect of temperature

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Wenyun, Z. (2011). From growth to extinction : explored by life history and metabolic theory. (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biol_etds/111

Chicago Manual of Style (16^th Edition):

Wenyun, Zuo. “From growth to extinction : explored by life history and metabolic theory.” 2011. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. https://digitalrepository.unm.edu/biol_etds/111.

MLA Handbook (7^th Edition):

Wenyun, Zuo. “From growth to extinction : explored by life history and metabolic theory.” 2011. Web. 01 Mar 2021.

Vancouver:

Wenyun Z. From growth to extinction : explored by life history and metabolic theory. [Internet] [Doctoral dissertation]. University of New Mexico; 2011. [cited 2021 Mar 01]. Available from: https://digitalrepository.unm.edu/biol_etds/111.

Council of Science Editors:

Wenyun Z. From growth to extinction : explored by life history and metabolic theory. [Doctoral Dissertation]. University of New Mexico; 2011. Available from: https://digitalrepository.unm.edu/biol_etds/111

University of New Mexico

18. Kanigel Winner, Kimberly Rene. Multi-scale models of ovarian cancer.

Degree: UNM Biology Department, 2015, University of New Mexico

URL: https://digitalrepository.unm.edu/biol_etds/58

► In ovarian cancer, disease and treatment can be examined across multiple spatial scales including molecules, cells, intra-tumor vasculature, and body-scale dynamics of circulating drugs.… (more)

▼ In ovarian cancer, disease and treatment can be examined across multiple spatial scales including molecules, cells, intra-tumor vasculature, and body-scale dynamics of circulating drugs. Survival of primary tumor cells and their development into disseminated tumors is related to adhesion between the cells, attachment, and invasion. Growth of new tumors depends on the delivery of nutrients, which depends on the tumor diameter and the tumors vasculature. Drug delivery also depends on tumor diameter and vasculature, and molecular- and gross-scale drug processes. A cellular Potts simulation integrated data at these multiple scales to model microscopic residual disease during relapse after a primary surgery. The model generated new hypotheses about tumor cell behavior, and the effectiveness of drug delivery to tumors disseminated in the peritoneal cavity. First, the model required high intra-tumor adhesion in ovarian tumors, the existence of an unknown factor that drew tumor cells to vessels, a threshold of vascular endothelial growth factor (VEGF) for initiation of endothelial sprouting, and constitutive expression of angiogenic chemical messengers by tumor cells prior to needing oxygen. Alteration of the model incorporated drug delivery by the two standard routes, intraperitoneal and intravenous, from tumor vasculature parameterized from real patient data. Delivery of both small- and large-molecular weight therapies was superior during intraperitoneal therapy. Finally, empirical and theoretical distributions of vessel radii were considered. Samples from tumors with each type of vascular morphology were run as though too distant from the peritoneal cavity to receive peritoneal delivery, with three results: first, intravenous delivery was superior to the secondary delivery into the circulatory system from a primary intraperitoneal delivery. Second, small molecules penetrated homogeneously across all cells, regardless of vascular volume or morphology, while antibodies penetrated heterogeneously, particularly in low-vessel-volume samples. Third, when each of the whole tumors was considered, this heterogeneity resulted in a large sub-population of cells that accumulated non-therapeutic levels of antibody, even during the best delivery scenario (IV). Fourth, delivery of antibodies was poorest in the empirical distribution. Finally, hypotheses were generated about the impact of heterogeneity of drug delivery, to be addressed as future questions. Advisors/Committee Members: Moses, Melanie, Wearing, Helen, Jiang, Yi, Wilson, Bridget S., Wearing, Helen.

Subjects/Keywords: multi-scale; cellular Potts; ovarian cancer; ErbB2; drug delivery; vascularization; tumor modeling; Biology

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APA (6^th Edition):

Kanigel Winner, K. R. (2015). Multi-scale models of ovarian cancer. (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biol_etds/58

Chicago Manual of Style (16^th Edition):

Kanigel Winner, Kimberly Rene. “Multi-scale models of ovarian cancer.” 2015. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. https://digitalrepository.unm.edu/biol_etds/58.

MLA Handbook (7^th Edition):

Kanigel Winner, Kimberly Rene. “Multi-scale models of ovarian cancer.” 2015. Web. 01 Mar 2021.

Vancouver:

Kanigel Winner KR. Multi-scale models of ovarian cancer. [Internet] [Doctoral dissertation]. University of New Mexico; 2015. [cited 2021 Mar 01]. Available from: https://digitalrepository.unm.edu/biol_etds/58.

Council of Science Editors:

Kanigel Winner KR. Multi-scale models of ovarian cancer. [Doctoral Dissertation]. University of New Mexico; 2015. Available from: https://digitalrepository.unm.edu/biol_etds/58

University of New Mexico

19. Malone, Nick D. High-Dimensional Motion Planning and Learning Under Uncertain Conditions.

Degree: Department of Computer Science, 2015, University of New Mexico

URL: http://hdl.handle.net/1928/31730

► Many existing path planning methods do not adequately account for uncertainty. Without uncertainty these existing techniques work well, but in real world environments they struggle… (more)

▼ Many existing path planning methods do not adequately account for uncertainty. Without uncertainty these existing techniques work well, but in real world environments they struggle due to inaccurate sensor models, arbitrarily moving obstacles, and uncertain action consequences. For example, picking up and storing childrens toys is a simple task for humans. Yet, for a robotic household robot the task can be daunting. The room must be modeled with sensors, which may or may not detect all the strewn toys. The robot must be able to detect and avoid the child who may be moving the very toys that the robot is tasked with cleaning. Finally, if the robot missteps and places a foot on a toy, it must be able to compensate for the unexpected consequences of its actions. This example demonstrates that even simple human tasks are fraught with uncertainties that must be accounted for in robotic path planning algorithms. This work presents the first steps towards migrating sampling-based path planning methods to real world environments by addressing three different types of uncertainty: (1) model uncertainty, (2) spatio-temporal obstacle uncertainty (moving obstacles) and (3) action consequence uncertainty. Uncertainty is encoded directly into path planning through a data structure in order to successfully and efficiently identify safe robot paths in sensed environments with noise. This encoding produces comparable clearance paths to other planning methods which are a known for high clearance, but at an order of magnitude less computational cost. It also shows that formal control theory methods combined with path planning provides a technique that has a 95% collision-free navigation rate with 300 moving obstacles. Finally, it demonstrates that reinforcement learning can be combined with planning data structures to autonomously learn motion controls of a seven degree of freedom robot despite a low computational cost despite the number of dimensions. Advisors/Committee Members: Tapia, Lydia, Wood, John, Kapur, Deepak, Moses, Melanie, Oishi, Meeko.

Subjects/Keywords: Path Planning; Uncertainty; Stochastic Reachability; Reinforcement Learning; Modeling Error

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Malone, N. D. (2015). High-Dimensional Motion Planning and Learning Under Uncertain Conditions. (Doctoral Dissertation). University of New Mexico. Retrieved from http://hdl.handle.net/1928/31730

Chicago Manual of Style (16^th Edition):

Malone, Nick D. “High-Dimensional Motion Planning and Learning Under Uncertain Conditions.” 2015. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/31730.

MLA Handbook (7^th Edition):

Malone, Nick D. “High-Dimensional Motion Planning and Learning Under Uncertain Conditions.” 2015. Web. 01 Mar 2021.

Vancouver:

Malone ND. High-Dimensional Motion Planning and Learning Under Uncertain Conditions. [Internet] [Doctoral dissertation]. University of New Mexico; 2015. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/31730.

Council of Science Editors:

Malone ND. High-Dimensional Motion Planning and Learning Under Uncertain Conditions. [Doctoral Dissertation]. University of New Mexico; 2015. Available from: http://hdl.handle.net/1928/31730

University of New Mexico

20. Banerjee, Soumya. Scaling in the immune system.

Degree: Department of Computer Science, 2013, University of New Mexico

URL: http://hdl.handle.net/1928/23083

► How different is the immune system in a human from that of a mouse? Do pathogens replicate at the same rate in different species? Answers… (more)

▼ How different is the immune system in a human from that of a mouse? Do pathogens replicate at the same rate in different species? Answers to these questions have impact on human health since multi-host pathogens that jump from animals to humans affect millions worldwide. It is not known how rates of immune response and viral dynamics vary from species to species and how they depend on species body size. Metabolic scaling theory predicts that intracellular processes are slower in larger animals since cellular metabolic rates are slower. We test how rates of pathogenesis and immune system response rates depend on species body size. We hypothesize that immune response rates are invariant with body size. Our work suggests how the physical architecture of the immune system and chemical signals within it may lead to nearly scale-invariant immune search and response. We fit mathematical models to experimental West Nile Virus (WNV, a multi-host pathogen) infection data and investigate how model parameters characterizing the pathogen and the immune response change with respect to animal mass. Phylogeny also affects pathogenesis and immune response. We use a hierarchical Bayesian model, that incorporates phylogeny, to test hypotheses about the role of mass and phylogeny on pathogen replication and immune response. We observe that: 1) Hierarchical models (informed by phylogeny) make more accurate predictions of experimental data and more realistic estimates of biologically relevant parameters characterizing WNV infection. 2) Rates of WNV production decline with species body mass, modified by a phylogenetic influence. Our work is the first to systematically explore the role of host body mass in pathogenesis using mathematical models and empirical data. We investigate the complex interplay between the physical structure of the immune system and host body mass in determining immune response. The modeling strategies and tools outlined here are likely to be applicable to modeling of other multi-host pathogens. This work could also be extended to understand how drug and vaccine efficacy differ in humans from model organisms like mice where most immunological experiments are conducted. Advisors/Committee Members: Moses, Melanie, Forrest, Stephanie, Perelson, Alan, Koster, Frederick, Lane, Terran.

Subjects/Keywords: scaling; immune system; mathematical modeling; viral dynamics; lymph node scaling

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Banerjee, S. (2013). Scaling in the immune system. (Doctoral Dissertation). University of New Mexico. Retrieved from http://hdl.handle.net/1928/23083

Chicago Manual of Style (16^th Edition):

Banerjee, Soumya. “Scaling in the immune system.” 2013. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/23083.

MLA Handbook (7^th Edition):

Banerjee, Soumya. “Scaling in the immune system.” 2013. Web. 01 Mar 2021.

Vancouver:

Banerjee S. Scaling in the immune system. [Internet] [Doctoral dissertation]. University of New Mexico; 2013. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/23083.

Council of Science Editors:

Banerjee S. Scaling in the immune system. [Doctoral Dissertation]. University of New Mexico; 2013. Available from: http://hdl.handle.net/1928/23083

University of New Mexico

21. Hecker, Joshua Peter. Evolving Efficient Foraging Behavior in Biologically-Inspired Robot Swarms.

Degree: Department of Computer Science, 2015, University of New Mexico

URL: http://hdl.handle.net/1928/31723

► Human beings are driven to explore distant new worlds as we seek to better understand our place in the Universe. Because of the inherent dangers… (more)

▼ Human beings are driven to explore distant new worlds as we seek to better understand our place in the Universe. Because of the inherent dangers of human spaceflight, we often send robots as surrogate explorers, controlled from millions of miles away by teams of capable rover drivers here on Earth. As technology continues to advance, scientists and engineers aspire to build low-cost, durable, fully autonomous rovers to succeed today's tele-operated extraplanetary explorers. Here we aim to advance this goal by designing and programming robots that can successfully navigate unknown and variable environments. We present a swarm robotics system that mimics the foraging behaviors of seed-harvester ants, employing evolutionary computation and machine learning to mitigate the adverse effects of unreliable information, variable environments, congestion bottlenecks, and sparse resources. We describe a central-place foraging algorithm (CPFA) whose parameters are evolved by a genetic algorithm (GA) to maximize foraging performance under different experimental conditions. We find that foraging for resources in heterogeneous clusters requires more complex communication, memory, and environmental sensing than strategies evolved in previous work. Additionally, we observe sub-linear scaling in resources collected per robot as swarm size increases, which we attribute to the 'bottleneck' constraint imposed by central-place foraging. Finally, we augment our foraging robot swarm with machine learning and statistical models, demonstrating that combining our existing biologically-inspired CPFA with a cluster exploitation algorithm produces more efficient total resource collection compared to each algorithm acting alone. While our system is designed to be a demonstration platform for swarm robotics research, this work provides a foundation for designing and implementing autonomous robot swarms that can function outside of the academic research laboratory. The ability of robot swarms to tolerate sensor noise, adapt to variable environments, distribute work across large teams, and identify and exploit heterogeneously-distributed resources are all critical factors for successful remote exploration missions on distant worlds. Advisors/Committee Members: Moses, Melanie E., Tapia, Lydia, Fierro, Rafael, Winfield, Alan F.T..

Subjects/Keywords: Swarm robotics; Biologically-inspired computation; Central-place foraging; Genetic algorithms; Agent-based models

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APA (6^th Edition):

Hecker, J. P. (2015). Evolving Efficient Foraging Behavior in Biologically-Inspired Robot Swarms. (Doctoral Dissertation). University of New Mexico. Retrieved from http://hdl.handle.net/1928/31723

Chicago Manual of Style (16^th Edition):

Hecker, Joshua Peter. “Evolving Efficient Foraging Behavior in Biologically-Inspired Robot Swarms.” 2015. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/31723.

MLA Handbook (7^th Edition):

Hecker, Joshua Peter. “Evolving Efficient Foraging Behavior in Biologically-Inspired Robot Swarms.” 2015. Web. 01 Mar 2021.

Vancouver:

Hecker JP. Evolving Efficient Foraging Behavior in Biologically-Inspired Robot Swarms. [Internet] [Doctoral dissertation]. University of New Mexico; 2015. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/31723.

Council of Science Editors:

Hecker JP. Evolving Efficient Foraging Behavior in Biologically-Inspired Robot Swarms. [Doctoral Dissertation]. University of New Mexico; 2015. Available from: http://hdl.handle.net/1928/31723

University of New Mexico

22. Faust, Aleksandra. Reinforcement Learning and Planning for Preference Balancing Tasks.

Degree: Department of Computer Science, 2014, University of New Mexico

URL: http://hdl.handle.net/1928/24551

► Robots are often highly non-linear dynamical systems with many degrees of freedom, making solving motion problems computationally challenging. One solution has been reinforcement learning (RL),… (more)

Subjects/Keywords: Reinforcement learning; Motion planning; Robotics; Artificial Intelligence; Unmanned Aerial Vehcile; Systems control

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APA (6^th Edition):

Faust, A. (2014). Reinforcement Learning and Planning for Preference Balancing Tasks. (Doctoral Dissertation). University of New Mexico. Retrieved from http://hdl.handle.net/1928/24551

Chicago Manual of Style (16^th Edition):

Faust, Aleksandra. “Reinforcement Learning and Planning for Preference Balancing Tasks.” 2014. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/24551.

MLA Handbook (7^th Edition):

Faust, Aleksandra. “Reinforcement Learning and Planning for Preference Balancing Tasks.” 2014. Web. 01 Mar 2021.

Vancouver:

Faust A. Reinforcement Learning and Planning for Preference Balancing Tasks. [Internet] [Doctoral dissertation]. University of New Mexico; 2014. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/24551.

Council of Science Editors:

Faust A. Reinforcement Learning and Planning for Preference Balancing Tasks. [Doctoral Dissertation]. University of New Mexico; 2014. Available from: http://hdl.handle.net/1928/24551

University of New Mexico

23. Gunning, Christian E. Population and Metapopulation Ecology of Childhood Diseases.

Degree: UNM Biology Department, 2014, University of New Mexico

URL: https://digitalrepository.unm.edu/biol_etds/46

► Researchers have long used mathematical models and empirical data to explore the population ecology of childhood diseases such as measles and whooping cough. These diseases… (more)

▼ Researchers have long used mathematical models and empirical data to explore the population ecology of childhood diseases such as measles and whooping cough. These diseases have proven ideal model systems for studying population dynamics over space and time. Here we present a novel dataset of weekly measles and whooping cough case reports in pre-vaccine era U.S. cities and states, along with a previously- studied dataset of measles in England & Wales. We first estimate per-population disease reporting probabilities. We find that disease reporting is highly variable over space and between diseases, and correlated with socioeconomic covariates including ethnic composition and school attendance. Using these reporting estimates, we infer the long-term, marginal distribution of disease incidence for each population. This describes a probabilistic measure of disease persistence that compares favorably with a classic threshold persistence measure, critical community size (CCS). The U.S. and England & Wales exhibit similar patterns of measles incidence distributions: larger populations show higher mean viincidence and lower variance. The per-time probability of local extinction (conditioned on population size) is higher in the U.S. than in England & Wales, likely due to larger distances between U.S. cities. Finally, we use observed persistence and inferred incidence distributions to estimate the per-time probability of true persistence. Estimated persistence of whooping cough is much higher than persistence of measles (conditioned on population size). We find that cryptic persistence (the difference between observed and estimated persistence) of whooping cough is most common in small populations, while for measles cryptic persistence is most common in medium-sized populations that hover at the edge of extinction. Our results show that variation in disease reporting can significantly affect meta- population estimates of disease persistence, such as CCS. The distributional estimates of incidence presented here explicitly account for incomplete reporting, providing summaries of long-term ecological patterns that are comparable between metapopulations. These measures can provide disease control programs with valuable information on where disease incidence is expected to be higher or lower than expected based on population size alone. Advisors/Committee Members: Wearing, Helen J., Erhardt, Erik B., Moses, Melanie E., Brown, James H..

Subjects/Keywords: population ecology; persistence; extinction; measles; pertussis; dynamical systems; stochastic; metapopulation; disease

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APA (6^th Edition):

Gunning, C. E. (2014). Population and Metapopulation Ecology of Childhood Diseases. (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biol_etds/46

Chicago Manual of Style (16^th Edition):

Gunning, Christian E. “Population and Metapopulation Ecology of Childhood Diseases.” 2014. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. https://digitalrepository.unm.edu/biol_etds/46.

MLA Handbook (7^th Edition):

Gunning, Christian E. “Population and Metapopulation Ecology of Childhood Diseases.” 2014. Web. 01 Mar 2021.

Vancouver:

Gunning CE. Population and Metapopulation Ecology of Childhood Diseases. [Internet] [Doctoral dissertation]. University of New Mexico; 2014. [cited 2021 Mar 01]. Available from: https://digitalrepository.unm.edu/biol_etds/46.

Council of Science Editors:

Gunning CE. Population and Metapopulation Ecology of Childhood Diseases. [Doctoral Dissertation]. University of New Mexico; 2014. Available from: https://digitalrepository.unm.edu/biol_etds/46

24. Semenov, Oleg. Abstract Models of Molecular Walkers.

Degree: Department of Computer Science, 2013, University of New Mexico

URL: http://hdl.handle.net/1928/23579

► Recent advances in single-molecule chemistry have led to designs for artificial multi-pedal walkers that follow tracks of chemicals. The walkers, called molecular spiders, consist of… (more)

▼ Recent advances in single-molecule chemistry have led to designs for artificial multi-pedal walkers that follow tracks of chemicals. The walkers, called molecular spiders, consist of a rigid chemically inert body and several flexible enzymatic legs. The legs can reversibly bind to chemical substrates on a surface, and through their enzymatic action convert them to products. We study abstract models of molecular spiders to evaluate how efficiently they can perform two tasks: molecular transport of cargo over tracks and search for targets on finite surfaces. For the single-spider model our simulations show a transient behavior wherein certain spiders move superdiffusively over significant distances and times. This gives the spiders potential as a faster-than-diffusion transport mechanism. However, analysis shows that single-spider motion eventually decays into an ordinary diffusive motion, owing to the ever increasing size of the region of products. Inspired by cooperative behavior of natural molecular walkers, we propose a symmetric exclusion process (SEP) model for multiple walkers interacting as they move over a one-dimensional lattice. We show that when walkers are sequentially released from the origin, the collective effect is to prevent the leading walkers from moving too far backwards. Hence, there is an effective outward pressure on the leading walkers that keeps them moving superdiffusively for longer times. Despite this improvement the leading spider eventually slows down and moves diffusively, similarly to a single spider. The slowdown happens because all spiders behind the leading spiders never encounter substrates, and thus they are never biased. They cannot keep up with leading spiders, and cannot put enough pressure on them. Next, we investigate search properties of a single and multiple spiders moving over one- and two-dimensional surfaces with various absorbing and reflecting boundaries. For the single-spider model we evaluate by how much the slowdown on newly visited sites, owing to catalysis, can improve the mean first passage time of spiders and show that in one dimension, when both ends of the track are an absorbing boundary, the performance gain is lower than in two dimensions, when the absorbing boundary is a circle; this persists even when the absorbing boundary is a single site. Next, we study how multiple molecular spiders influence one another during the search. We show that when one spider reaches the trace of another spider it is more likely not to follow the trace and instead explore unvisited sites. This interaction between the spiders gives them an advantage over independent random walkers in a search for multiple targets. We also study how efficiently the spiders with various gaits are able to find specific targets. Spiders with gaits that allow more freedom of leg movement find their targets faster than spiders with more restrictive gaits. For every gait, there is an optimal detachment rate that minimizes the time to find all target sites. Advisors/Committee Members: Stefanovic, Darko, Moore, Cristopher, Moses, Melanie, Stojanovic, Milan N., Krapivsky, Pavel L..

Subjects/Keywords: Molecular Motors; Simulation; Kinetic Monte Carlo

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APA (6^th Edition):

Semenov, O. (2013). Abstract Models of Molecular Walkers. (Doctoral Dissertation). University of New Mexico. Retrieved from http://hdl.handle.net/1928/23579

Chicago Manual of Style (16^th Edition):

Semenov, Oleg. “Abstract Models of Molecular Walkers.” 2013. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/23579.

MLA Handbook (7^th Edition):

Semenov, Oleg. “Abstract Models of Molecular Walkers.” 2013. Web. 01 Mar 2021.

Vancouver:

Semenov O. Abstract Models of Molecular Walkers. [Internet] [Doctoral dissertation]. University of New Mexico; 2013. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/23579.

Council of Science Editors:

Semenov O. Abstract Models of Molecular Walkers. [Doctoral Dissertation]. University of New Mexico; 2013. Available from: http://hdl.handle.net/1928/23579

University of New Mexico

25. Scholle, Stacy O'Neil. Temporal dynamics and spatial analysis of competing dengue 2 virus strains in the Americas.

Degree: UNM Biology Department, 2010, University of New Mexico

URL: https://digitalrepository.unm.edu/biol_etds/90

► The dengue virus is the causative agent of an important re-emerging infectious disease that has become increasingly significant in tropical America and the Caribbean… (more)

Subjects/Keywords: Dengue; Biology; Biology

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APA (6^th Edition):

Scholle, S. O. (2010). Temporal dynamics and spatial analysis of competing dengue 2 virus strains in the Americas. (Masters Thesis). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biol_etds/90

Chicago Manual of Style (16^th Edition):

Scholle, Stacy O'Neil. “Temporal dynamics and spatial analysis of competing dengue 2 virus strains in the Americas.” 2010. Masters Thesis, University of New Mexico. Accessed March 01, 2021. https://digitalrepository.unm.edu/biol_etds/90.

MLA Handbook (7^th Edition):

Scholle, Stacy O'Neil. “Temporal dynamics and spatial analysis of competing dengue 2 virus strains in the Americas.” 2010. Web. 01 Mar 2021.

Vancouver:

Scholle SO. Temporal dynamics and spatial analysis of competing dengue 2 virus strains in the Americas. [Internet] [Masters thesis]. University of New Mexico; 2010. [cited 2021 Mar 01]. Available from: https://digitalrepository.unm.edu/biol_etds/90.

Council of Science Editors:

Scholle SO. Temporal dynamics and spatial analysis of competing dengue 2 virus strains in the Americas. [Masters Thesis]. University of New Mexico; 2010. Available from: https://digitalrepository.unm.edu/biol_etds/90

University of New Mexico

26. Letendre, Kenneth. Simulating the evolution of recruitment behavior in foraging Ants.

Degree: Department of Computer Science, 2010, University of New Mexico

URL: http://hdl.handle.net/1928/12049

► Spatial heterogeneity in the distribution of food is an important determinant of species' optimal foraging strategies, and of the dynamics of populations and communities. In… (more)

Subjects/Keywords: Ants; Distributed-Problem Solving; Foraging; Genetic Algorithm; Optimization; Recruitment

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APA (6^th Edition):

Letendre, K. (2010). Simulating the evolution of recruitment behavior in foraging Ants. (Masters Thesis). University of New Mexico. Retrieved from http://hdl.handle.net/1928/12049

Chicago Manual of Style (16^th Edition):

Letendre, Kenneth. “Simulating the evolution of recruitment behavior in foraging Ants.” 2010. Masters Thesis, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/12049.

MLA Handbook (7^th Edition):

Letendre, Kenneth. “Simulating the evolution of recruitment behavior in foraging Ants.” 2010. Web. 01 Mar 2021.

Vancouver:

Letendre K. Simulating the evolution of recruitment behavior in foraging Ants. [Internet] [Masters thesis]. University of New Mexico; 2010. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/12049.

Council of Science Editors:

Letendre K. Simulating the evolution of recruitment behavior in foraging Ants. [Masters Thesis]. University of New Mexico; 2010. Available from: http://hdl.handle.net/1928/12049

University of New Mexico

27. Roy, Sushmita. Learning condition-specific networks.

Degree: Department of Computer Science, 2009, University of New Mexico

URL: http://hdl.handle.net/1928/10331

► Condition-specific cellular networks are networks of genes and proteins that describe functional interactions among genes occurring under different environmental conditions. These networks provide a systems-level… (more)

▼ Condition-specific cellular networks are networks of genes and proteins that describe functional interactions among genes occurring under different environmental conditions. These networks provide a systems-level view of how the parts-list (genes and proteins) interact within the cell as it functions under changing environmental conditions and can provide insight into mechanisms of stress response, cellular differentiation and disease susceptibility. The principle challenge, however, is that cellular networks remain unknown for most conditions and must be inferred from activity levels of genes (mRNA levels) under different conditions. This dissertation aims to develop computational approaches for inferring, analyzing and validating cellular networks of genes from expression data. This dissertation first describes an unsupervised machine learning framework for inferring cellular networks using expression data from a single condition. Here cellular networks are represented as undirected probabilistic graphical models and are learned using a novel, data-driven algorithm. Then several approaches are described that can learn networks using data from multiple conditions. These approaches apply to cases where the condition may or may not be known and, therefore, must be inferred as part of the learning problem. For the latter, the condition variable is allowed to influence expression of genes at different levels of granularity: condition variable per gene to a single condition variable for all genes. Results on simulated data suggest that the algorithm performance depends greatly on the size and number of connected components of the union network of all conditions. These algorithms are also applied to microarray data from two yeast populations, quiescent and non-quiescent, isolated from glucose starved cultures. Our results suggest that by sharing information across multiple conditions, better networks can be learned for both conditions, with many more biologically meaningful dependencies, than if networks were learned for these conditions independently. In particular, processes that were shared among both cell populations were involved in response to glucose starvation, whereas the processes specific to individual populations captured characteristics unique to each population. These algorithms were also applied for learning networks across multiple species: yeast (S. cerevisiae) and fly (D. melanogaster). Preliminary analysis suggests that sharing patterns across species is much more complex than across different populations of the same species and basic metabolic processes are shared across the two species. Finally, this dissertation focuses on validation of cellular networks. This validation framework describes scores for measuring how well network learning algorithms capture higher-order dependencies. This framework also introduces a measure for evaluating the entire inferred network structure based on the extent to which similarly functioning genes are close together on the network. Advisors/Committee Members: Lane, Terran, Werner-Washburne, Margaret, Moses, Melanie, Atlas, Susan.

Subjects/Keywords: Machine learning; Computational Biology; Probabilistic graphical models; Gene expression; Condition-specific response

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APA (6^th Edition):

Roy, S. (2009). Learning condition-specific networks. (Doctoral Dissertation). University of New Mexico. Retrieved from http://hdl.handle.net/1928/10331

Chicago Manual of Style (16^th Edition):

Roy, Sushmita. “Learning condition-specific networks.” 2009. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/10331.

MLA Handbook (7^th Edition):

Roy, Sushmita. “Learning condition-specific networks.” 2009. Web. 01 Mar 2021.

Vancouver:

Roy S. Learning condition-specific networks. [Internet] [Doctoral dissertation]. University of New Mexico; 2009. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/10331.

Council of Science Editors:

Roy S. Learning condition-specific networks. [Doctoral Dissertation]. University of New Mexico; 2009. Available from: http://hdl.handle.net/1928/10331

University of New Mexico

28. Greene, Kshanti. Collective belief models for representing consensus and divergence in communities of Bayesian decision-makers.

Degree: Department of Computer Science, 2010, University of New Mexico

URL: http://hdl.handle.net/1928/10878

► Bayesian belief aggregation is the process of forming a consensus model from the probabilistic beliefs of multiple individuals. Preference aggregation attempts to find an optimal… (more)

Subjects/Keywords: Decision-making; Bayesian reasoning; Social choice theory; Probabilistic reasoning; Bayesian belief aggregation; game theory; diversity; artificial intelligence; social decision-making

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APA (6^th Edition):

Greene, K. (2010). Collective belief models for representing consensus and divergence in communities of Bayesian decision-makers. (Doctoral Dissertation). University of New Mexico. Retrieved from http://hdl.handle.net/1928/10878

Chicago Manual of Style (16^th Edition):

Greene, Kshanti. “Collective belief models for representing consensus and divergence in communities of Bayesian decision-makers.” 2010. Doctoral Dissertation, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/10878.

MLA Handbook (7^th Edition):

Greene, Kshanti. “Collective belief models for representing consensus and divergence in communities of Bayesian decision-makers.” 2010. Web. 01 Mar 2021.

Vancouver:

Greene K. Collective belief models for representing consensus and divergence in communities of Bayesian decision-makers. [Internet] [Doctoral dissertation]. University of New Mexico; 2010. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/10878.

Council of Science Editors:

Greene K. Collective belief models for representing consensus and divergence in communities of Bayesian decision-makers. [Doctoral Dissertation]. University of New Mexico; 2010. Available from: http://hdl.handle.net/1928/10878

University of New Mexico

29. Arora, Tamanna. Using ant colony optimization for routing in microprocesors.

Degree: Department of Computer Science, 2009, University of New Mexico

URL: http://hdl.handle.net/1928/10258

► Power consumption is an important constraint on VLSI systems. With the advancement in technology, it is now possible to pack a large range of functionalities… (more)

Subjects/Keywords: VLSI; Routing; ACO

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APA (6^th Edition):

Arora, T. (2009). Using ant colony optimization for routing in microprocesors. (Masters Thesis). University of New Mexico. Retrieved from http://hdl.handle.net/1928/10258

Chicago Manual of Style (16^th Edition):

Arora, Tamanna. “Using ant colony optimization for routing in microprocesors.” 2009. Masters Thesis, University of New Mexico. Accessed March 01, 2021. http://hdl.handle.net/1928/10258.

MLA Handbook (7^th Edition):

Arora, Tamanna. “Using ant colony optimization for routing in microprocesors.” 2009. Web. 01 Mar 2021.

Vancouver:

Arora T. Using ant colony optimization for routing in microprocesors. [Internet] [Masters thesis]. University of New Mexico; 2009. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/1928/10258.

Council of Science Editors:

Arora T. Using ant colony optimization for routing in microprocesors. [Masters Thesis]. University of New Mexico; 2009. Available from: http://hdl.handle.net/1928/10258

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