http://hdl.handle.net/1903/6626 2013-05-18T06:00:47Z http://hdl.handle.net/1903/13812 Title: TASK SPECIFIC EVALUATION METHODOLOGY FOR CLINICAL FULL FIELD DIGITAL MAMMOGRAPHY Authors: Liu, Haimo Abstract: <bold>Purpose</bold>: The purpose of this dissertation is to evaluate the image quality of clinical Full Field Digital Mammography (FFDM) systems. This is done by evaluating image acquisition performance of clinical FFDM in a comprehensive way that accounts for scatter, focal spot un-sharpness, detector blur and anti-scatter grid performance using an anthropomorphic phantom. Additionally we intend to provide a limited evaluation of the effects that image processing in clinical FFDM has in signal detectability. <bold>Methodology</bold>: We explored different strategies and a variety of mathematical model observers in order to evaluate the performance of clinical FFDM systems under different conditions. To evaluate image acquisition performance, we tested a system-model-based Hotelling observer (SMHO) model on a bench-top system using a uniform anthropomorphic phantom for an signal known exactly background known exactly (SKE/BKE) task. We then applied this concept on two clinical FFDM systems to compare their performance. In a limited study to evaluate the effects of image processing in the detectability of FFDM, we implemented the channelized Hotelling observer (CHO) model on clinically realistic images of an anatomical phantom for an SKE/BKE task. <bold>Results</bold>: Even though the two systems use different detection technologies, there was no significant difference between their image acquisition performances quantified by the Contrast-Detail (CD) curves. We applied the CHO model to investigate the image processing algorithms used in GE Senographe DS FFDM system. For the particular SKE/BKE task with rotationally symmetric signals, the image processing tends to contribute to a non-significant reduction of system detectability. <bold>Conclusion</bold>: We provided a complete description of FFDM system performance including the image acquisition chain and post-acquisition image processing. We demonstrated the simplicity and effectiveness of both the MFHO and CHO methods in a clinical setting. 2012-01-01T00:00:00Z http://hdl.handle.net/1903/13618 Title: Mechanical, Structural and Biological Properties of Biopolymer-Based Hydrogels Authors: Hyland, Laura Abstract: The aim of this dissertation was to begin to understand how biopolymer interactions affect mechanical and structural properties of biomaterials, and how those properties affect stem cell behavior. Polysaccharide, oligopeptide and oligopeptide-polysaccharide composite materials were made and then characterized using a range of techniques. It was found that chondroitin addition to chitosan-alginate networks improved both tensile and compressive strength. Increasing polysaccharide concentration also improved mechanical properties. Also, polysaccharide incorporation into peptide hydrogels increased biomaterial resistance to strain break. Structural analysis supported mechanical data, showing that incorporation of the peptides dramatically changed the morphology of the polysaccharide networks. Biopolymer chirality was also explored in this work. By incorporating polysaccharides and oligosaccharides into both L- and D-forms of peptide hydrogels, we observed differences in mechanical properties not seen in L- and D-oligopeptide hydrogels alone. Greater interactions between L-oligopeptides and D-saccharides lead to stronger materials with distinctively different structural characteristics from hydrogels made from D-oligopeptides and D-saccharides. This phenomenon, known as chiral selectivity, has previously only been seen at the molecular level. Here, we showed that chiral selectivity is another unique property of biopolymers that can be exploited to tune mechanical and structural properties of materials. Chiral selectivity was also observed in terms of stem cell behavior in this work. However another property, hydrogel charge, was used to diminish the effects of chiral selectivity in order to enhance the biocompatibility of D-oligopeptide hydrogels. It was found that negative charges significantly improved human mesenchymal stem cell attachment and proliferation in D-oligopeptide gels but had little effect on their interactions with L-oligopeptide gels. These results suggest that it is possible to use charge and other properties of biopolymers to engineer biomaterials whose chirality is distinct from that of natural biomaterials but whose performance is close to that of natural biomaterials. These oligopeptide-based biomaterials also offer new tools to investigate biohomochirality, an important and unresolved question in biology. 2012-01-01T00:00:00Z http://hdl.handle.net/1903/13387 Title: Complete genomic sequence analysis of infectious bronchitis virus Ark DPI strain and its evolution by recombination Authors: Ammayappan, Arun; Upadhyay, Chitra; Gelb, Jack Jr.; Vakharia, Vikram N Abstract: An infectious bronchitis virus Arkansas DPI (Ark DPI) virulent strain was sequenced, analyzed and compared with many different IBV strains and coronaviruses. The genome of Ark DPI consists of 27,620 nucleotides, excluding poly (A) tail, and comprises ten open reading frames. Comparative sequence analysis of Ark DPI with other IBV strains shows striking similarity to the Conn, Gray, JMK, and Ark 99, which were circulating during that time period. Furthermore, comparison of the Ark genome with other coronaviruses demonstrates a close relationship to turkey coronavirus. Among non-structural genes, the 5'untranslated region (UTR), 3C-like proteinase (3CL pro) and the polymerase (RdRp) sequences are 100% identical to the Gray strain. Among structural genes, S1 has 97% identity with Ark 99; S2 has 100% identity with JMK and 96% to Conn; 3b 99%, and 3C to N is 100% identical to Conn strain. Possible recombination sites were found at the intergenic region of spike gene, 3'end of S1 and 3a gene. Independent recombination events may have occurred in the entire genome of Ark DPI, involving four different IBV strains, suggesting that genomic RNA recombination may occur in any part of the genome at number of sites. Hence, we speculate that the Ark DPI strain originated from the Conn strain, but diverged and evolved independently by point mutations and recombination between field strains. 2008-12-22T00:00:00Z http://hdl.handle.net/1903/13377 Title: Assembly complexity of prokaryotic genomes using short reads Authors: Kingsford, Carl; Schatz, Michael C; Pop, Mihai Abstract: Background: De Bruijn graphs are a theoretical framework underlying several modern genome assembly programs, especially those that deal with very short reads. We describe an application of de Bruijn graphs to analyze the global repeat structure of prokaryotic genomes. Results: We provide the first survey of the repeat structure of a large number of genomes. The analysis gives an upper-bound on the performance of genome assemblers for de novo reconstruction of genomes across a wide range of read lengths. Further, we demonstrate that the majority of genes in prokaryotic genomes can be reconstructed uniquely using very short reads even if the genomes themselves cannot. The non-reconstructible genes are overwhelmingly related to mobile elements (transposons, IS elements, and prophages). Conclusions: Our results improve upon previous studies on the feasibility of assembly with short reads and provide a comprehensive benchmark against which to compare the performance of the short-read assemblers currently being developed. 2010-01-12T00:00:00Z