Thesis (M.A.)--University of North Carolina at Chapel Hill, 2007.

The rapid replication and high mutation rates of viruses like HIV lead to the formation of a community of highly similar genomes, referred to as a viral quasispecies, in an infected individual. Next-generation sequencing technologies enable researchers to sequence a complete quasispecies community with reduced expense and effort compared to traditional sequencing methods. However, typical sequence assembly software is designed to reconstruct a single genome from sequencing reads rather than a community of highly similar genomes. We describe and implement a de novo assembly method for reconstructing variants from a quasispecies community using de Bruijn graphs and a novel, heuristic path-construction method designed to identify corresponding variations at long distances across the genome. We predict the relative abundance of reconstructed variants using an approach inspired from Markov chains.

The rapid replication and high mutation rates of viruses like HIV lead to the formation of a community of highly similar genomes, referred to as a viral quasispecies, in an infected individual. Next-generation sequencing technologies enable researchers to sequence a complete quasispecies community with reduced expense and effort compared to traditional sequencing methods. However, typical sequence assembly software is designed to reconstruct a single genome from sequencing reads rather than a community of highly similar genomes. We describe and implement a de novo assembly method for reconstructing variants from a quasispecies community using de Bruijn graphs and a novel, heuristic path-construction method designed to identify corresponding variations at long distances across the genome. We predict the relative abundance of reconstructed variants using an approach inspired from Markov chains.

Tübingen, Univ., Diss., 2004.

Our understanding regarding the function of YjeQ, RbfA, RimM and Era in ribosome biogenesis has been derived in part from the study of immature 30S particles that accumulate in bacteria strains lacking one of these factors. However, their mechanistic details are still unknown. Here, we demonstrate that the 30SΔyjeQ and 30SΔrimM immature particles are not dead-end products of assembly, but progress into mature 30S subunits. Mass spectrometry analysis revealed that in vivo the occupancy level of these factors in these immature 30S particles is below 10% and that the concentration of factors does not increase when immature particles accumulate in cells. Analysis of the binding interactions of these assembly factors with mature 30S subunits and the immature particles demonstrated that YjeQ and Era bind to the mature 30S subunit with high affinity, however binding of these factors to the immature particles and of RimM and RbfA to mature or immature particles is weak. This indicates that binding of the assembly factors to the immature particles is not occurring at physiological concentrations. These results suggest that in the absence of these factors, the immature particles evolve into a thermodynamically stable intermediate that exhibits low affinity for the assembly factors and that the true substrates of YjeQ, RbfA, RimM and Era are immature particles that precede the ribosomal particles accumulating in the knockouts strains. We also developed an Era-depletion and ΔrbfA strain, which exhibited slow-growth, cold-sensitivity and an aberrant ribosome profile, which are all characteristic of ribosome assembly defects. Cryo-EM structural analysis of the 30SEra-depleted particles revealed that multiple classes at various stages in the assembly process accumulate upon depletion of Era, suggesting that Era may have a global effect on biogenesis. Ultimately, this thesis provides new insights into the nature of 30S particles that accumulate during assembly factor perturbation and advances our understanding of ribosome biogenesis as a whole. / Dissertation / Doctor of Philosophy (PhD) / One of the most fundamental processes in all living cells is the synthesis of proteins by the ribosome. The ribosome is a massive macromolecular complex that consists of both proteins and RNA, which must be manufactured from its individual components before it can perform its function. There is a myriad of protein factors that assist in the assembly of ribosomes to ensure that biogenesis proceeds rapidly and efficiently. The purpose of this thesis was to gain a better understanding of how the assembly factors YjeQ, Era, RbfA and RimM work by studying the intermediates that accumulate when they are removed or depleted from the cell. Specifically, the fate, binding interactions and structure of the immature particles that accumulate in the assembly factor knockout or depletion strains were investigated. The work here brings new insights into the nature of these immature ribosomal particles and the maturation reactions catalyzed by these factors.

The technologies and methodologies of assembly design and evaluation in the early design stage are highly significant to product development. This paper looks at a promising technology to mix real components (e.g. physical prototypes, assembly tools, machines, etc.) with virtual components to create an Augmented Reality (AR) interface for assembly process evaluation. The goal of this paper is to clarify the methodologies and enabling technologies of how to establish an AR assembly simulation and evaluation environment. The architecture of an AR assembly system is proposed and the important functional modules including AR environment set-up, design for assembly (DFA) analysis and AR assembly sequence planning in an AR environment are discussed in detail. / Singapore-MIT Alliance (SMA)

Thesis (Ph. D.)--University of Texas at Austin, 2006. / Vita. Includes bibliographical references.

Thesis (M.S.)--Virginia Polytechnic Institute and State University, 1992. / Vita. Abstract. Includes bibliographical references (leaves 63-66). Also available via the Internet.

Thesis--Auburn University, 2009. / Abstract. Vita. Includes bibliographical references (p. 49.

In spite of advances in industrial automation, manual assembly tasks continue to be an important feature of many industrial operations. In heavy part assembly, some pieces of raw material or equipment are too heavy to be safely handled by an operator. Material handling devices such as Jib cranes or overhead cranes are employed to help operators work safer and, in some cases, faster. However, during full-load productions, these devices could become limited and insufficient resources and hence, delay or extend the cycle times. Not only may the companies not be able to ship the products on time, but the labor and overhead costs also increase from the workers' increased idle time as they wait for a turn to use the devices. Finding a way to utilize the material handling devices more effectively could significantly reduce the total cycle times and production costs. An assembly task could be separated into three steps: transferring, approaching or positioning, and joining or fixing. The transferring time is principally dependent on the distance. The joining time could be directly reduced by increasing the efficiency of the joining machines. However, the positioning time depends on task difficulties, handling methods, and operators' skills. Therefore, this research focuses on how to specify the task difficulties and improve the efficiency of the handling methods. In this research, metal plates were used to represent heavy parts. Four handling methods were studied including One-person, Two-person team, One person with an overhead crane, and One person with a spring-equipped overhead crane. This study applies Fitts' Index of Difficulty as a guideline to determine task difficulty. The results indicate that, for all methods mentioned above, the relationships between moment time and task difficulty are linear. The results also show that, for a part that weights up to 40 pounds, a two-person team gives the fastest assembly time for every task difficulty. In addition, the assembly performance of one person with an overhead crane could be increased approximately 250% by adding a spring between the hook and the gripper. / Master of Science