Optimization under uncertainty with application to data clustering

A new optimization technique with uncertainty that extends the pure nested partition (NP) algorithm is presented in this thesis. This method is called the nested partition with inheritance. The basic idea of a NP algorithm is very simple. At each iteration, the most promising region is partitioned and the performance of the partitioned region is evaluated using sampling. Based on the performance evaluation, the most promising region is chosen for the next iteration. These procedures are repeated until it satisfies the termination condition.;Even though the pure NP method guarantees the convergence to the optimal solution, it has several shortcomings. To handle these shortcomings, two extensions to the pure NP are suggested. To rigorously determine the required sample effort, some statistical selection methods are implemented, which include the Nelson Matejcik procedure, the Rinott procedure, and the Dudewicz and Dalal procedure, as well as a subset procedure. In addition, Genetic Algorithms (GAs) are used to speed convergence and to overcome the difficulty in the backtracking stage of the NP algorithm.;As an application of the new methodology, this work also suggests the methods to be applied to a data clustering problem. This is a very hard problem with two of the main difficulties being lack of scalability with respect to amount of data and problems with high dimensionality. The new algorithms are found to be effective for solving this problem. Random sampling enhances scalability and the iterative partitioning addresses the dimensionality

Proteomic Validation of Multifunctional Molecules in Mesenchymal Stem Cells Derived from Human Bone Marrow, Umbilical Cord Blood and Peripheral Blood

Mesenchymal stem cells (MSCs) are one of the most attractive therapeutic resources in clinical application owing to their multipotent capability, which means that cells can differentiate into various mesenchymal tissues such as bone, cartilage, fat, tendon, muscle and marrow stroma. Depending on the cellular source, MSCs exhibit different application potentials according to their different in vivo functions, despite similar phenotypic and cytological characteristics. To understand the different molecular conditions that govern the different application or differentiation potential of each MSC according to cellular source, we generated a proteome reference map of MSCs obtained from bone marrow (BM), umbilical cord blood (CB) and peripheral blood (PB). We identified approximately 30 differentially regulated (or expressed) proteins. Most up-regulated proteins show a cytoskeletal and antioxidant or detoxification role according to their functional involvement. Additionally, these proteins are involved in the increase of cell viability, engraftment and migration in pathological conditions in vivo. In summary, we examined differentially expressed key regulatory factors of MSCs obtained from several cellular sources, demonstrated their differentially expressed proteome profiles and discussed their functional role in specific pathological conditions. With respect to the field of cell therapy, it may be particularly crucial to determine the most suitable cell sources according to target disease

Quaternary structures of Vac8 differentially regulate the Cvt and PMN pathways.

Armadillo (ARM) repeat proteins constitute a large protein family with diverse and fundamental functions in all organisms, and armadillo repeat domains share high structural similarity. However, exactly how these structurally similar proteins can mediate diverse functions remains a long-standing question. Vac8 (vacuole related 8) is a multifunctional protein that plays pivotal roles in various autophagic pathways, including piecemeal microautophagy of the nucleus (PMN) and cytoplasm-to-vacuole targeting (Cvt) pathways in the budding yeast Saccharomyces cerevisiae. Vac8 comprises an H1 helix at the N terminus, followed by 12 armadillo repeats. Herein, we report the crystal structure of Vac8 bound to Atg13, a key component of autophagic machinery. The 70-angstrom extended loop of Atg13 binds to the ARM domain of Vac8 in an antiparallel manner. Structural, biochemical, and in vivo experiments demonstrated that the H1 helix of Vac8 intramolecularly associates with the first ARM and regulates its self-association, which is crucial for Cvt and PMN pathways. The structure of H1 helix-deleted Vac8 complexed with Atg13 reveals that Vac8[Delta 19-33]-Atg13 forms a heterotetramer and adopts an extended superhelical structure exclusively employed in the Cvt pathway. Most importantly, comparison of Vac8-Nvj1 and Vac8-Atg13 provides a molecular understanding of how a single ARM domain protein adopts different quaternary structures depending on its associated proteins to differentially regulate 2 closely related but distinct cellular pathways

Peptidyl-prolyl cis/trans isomerase Pin1 interacts with hepatitis B virus core particle, but not with HBc protein, to promote HBV replication

Here, we demonstrate that the peptidyl-prolyl cis/trans isomerase Pin1 interacts noncovalently with the hepatitis B virus (HBV) core particle through phosphorylated serine/threonine-proline (pS/TP) motifs in the carboxyl-terminal domain (CTD) but not with particle-defective, dimer-positive mutants of HBc. This suggests that neither dimers nor monomers of HBc are Pin1-binding partners. The 162TP, 164SP, and 172SP motifs within the HBc CTD are important for the Pin1/core particle interaction. Although Pin1 dissociated from core particle upon heat treatment, it was detected as an opened-up core particle, demonstrating that Pin1 binds both to the outside and the inside of the core particle. Although the amino-terminal domain S/TP motifs of HBc are not involved in the interaction, 49SP contributes to core particle stability, and 128TP might be involved in core particle assembly, as shown by the decreased core particle level of S49A mutant through repeated freeze and thaw and low-level assembly of the T128A mutant, respectively. Overexpression of Pin1 increased core particle stability through their interactions, HBV DNA synthesis, and virion secretion without concomitant increases in HBV RNA levels, indicating that Pin1 may be involved in core particle assembly and maturation, thereby promoting the later stages of the HBV life cycle. By contrast, parvulin inhibitors and PIN1 knockdown reduced HBV replication. Since more Pin1 proteins bound to immature core particles than to mature core particles, the interaction appears to depend on the stage of virus replication. Taken together, the data suggest that physical association between Pin1 and phosphorylated core particles may induce structural alterations through isomerization by Pin1, induce dephosphorylation by unidentified host phosphatases, and promote completion of virus life cycle

Improvement of postnatal neovascularization by human embryonic stem cell derived endothelial-like cell transplantation in a mouse model of hindlimb ischemia

BACKGROUND: We established an efficient preparation method to obtain endothelial-like cells (ECs) from human embryonic stem cells (hESCs) and tested whether these hESC-ECs would show therapeutic potential for treatment of hindlimb ischemia. METHODS AND RESULTS: ECs differentiated from hESCs were obtained by mechanical isolation and cell sorting for von Willebrand factor. The isolated hESC-ECs maintained endothelial cell-specific characteristics such as endothelial marker expression and capillary formation. One day after surgical induction of hindlimb ischemia in athymic mice, hESC-ECs were injected intramuscularly into ischemic limbs. Four weeks after treatment, hESC-EC treatment significantly increased limb salvage (36%) compared with treatment with medium (0%). In addition, laser Doppler imaging showed that the ratio of blood perfusion (ischemic to normal limb) was increased significantly (P<0.01) by hESC-EC treatment (0.511+/-0.167) compared with medium injection (0.073+/-0.061). Capillary and arteriole densities were 658+/-190/mm2 and 30+/-11/mm2 in the hESC-EC group, respectively, whereas those in the medium group were 392+/-118/mm2 and 16+/-8/mm2, respectively (P<0.01). Reverse-transcription polymerase chain reaction with human-specific primers revealed mRNA expression of human endothelial markers and human angiogenic factors in ischemic mouse tissues. The transplanted hESC-ECs were localized as capillaries near muscle tissues in ischemic regions or incorporated in the vessels between muscle tissues, as confirmed by human nuclear antigen staining with platelet/endothelial cell adhesion molecule or von Willebrand factor. CONCLUSIONS: This study demonstrates that hESC-EC transplantation improves blood perfusion and limb salvage by facilitating postnatal neovascularization in a mouse model of hindlimb ischemia. Thus, hESC-ECs might be useful as an alternative cell source for angiogenic therapy

Proteomic analysis of pregnancy-related proteins from pig uterus endometrium during pregnancy

Many important molecular events associated with implantation and development occur within the female reproductive tract, especially within the uterus endometrium, during pregnancy periods. The endometrium includes the mucosal lining of the uterus, which provides a suitable site for implantation and development of a fertilized egg and fetus. To date, the molecular cascades in the uterus endometrium during pregnancy periods in pigs have not been elucidated fully. In this study, we compared the functional regulated proteins in the endometrium during pregnancy periods with those in non-pregnant conditions and investigated changes in expression patterns during pregnancy (days 40, 70, and 93) using two-dimensional gel electrophoresis (2-DE) and western blotting. The functional regulated proteins were identified and discovered from differentially expressed proteins in the uterus endometrium during pregnancy. We discovered 820 protein spots in a proteomic analysis of uterus endometrium tissues with 2-DE gels. We identified 63 of the 98 proteins regulated differentially among non-pregnant and pregnant tissues (matched and unmatched spots). Interestingly, 10 of these 63 proteins are development-, cytoskeleton- and chaperon-related proteins such as transferrin, protein DJ-1, transgelin, galectin-1, septin 2, stathmin 1, cofilin 1, fascin 1, heat shock protein (HSP) 90β and HSP 27. The specific expression patterns of these proteins in the endometrium during pregnancy were confirmed by western blotting. Our results suggest that the expressions of these genes involved in endometrium function and endometrium development from early to late gestation are associated with the regulation of endometrium development for maintaining pregnancy

Optimization under uncertainty with application to data clustering

A new optimization technique with uncertainty that extends the pure nested partition (NP) algorithm is presented in this thesis. This method is called the nested partition with inheritance. The basic idea of a NP algorithm is very simple. At each iteration, the most promising region is partitioned and the performance of the partitioned region is evaluated using sampling. Based on the performance evaluation, the most promising region is chosen for the next iteration. These procedures are repeated until it satisfies the termination condition.;Even though the pure NP method guarantees the convergence to the optimal solution, it has several shortcomings. To handle these shortcomings, two extensions to the pure NP are suggested. To rigorously determine the required sample effort, some statistical selection methods are implemented, which include the Nelson Matejcik procedure, the Rinott procedure, and the Dudewicz and Dalal procedure, as well as a subset procedure. In addition, Genetic Algorithms (GAs) are used to speed convergence and to overcome the difficulty in the backtracking stage of the NP algorithm.;As an application of the new methodology, this work also suggests the methods to be applied to a data clustering problem. This is a very hard problem with two of the main difficulties being lack of scalability with respect to amount of data and problems with high dimensionality. The new algorithms are found to be effective for solving this problem. Random sampling enhances scalability and the iterative partitioning addresses the dimensionality.</p

Experiencing Korean pansori as a Western-style singer : a vocal interpretation of Dongjin Kim's operas based on Kim's shin-chang-ak

P’ansori is a unique form of Korean traditional music in the opera genre. It is known for its distinctive rhythm, vocal timbre, key, and texture. Musical pioneer Dongjin Kim (1913-2009) masterfully blended authentic Korean music with Western style music most notably in two operas that retained their p’ansori heritage while also appealing to wider audiences. Kim believed in the importance of accurately portraying Korean culture and history in his vocal music feeling that Korea’s “unique national music” had much to contribute to the rest of the world. Although traditional p’ansori operas are sung with a gritty and husky voice that lacks any sense of resonance, Kim adapted this harsh style for Western singers by introducing what he called “shin-ch’ang-ak” (New Singing Music). The purpose of shinch’ang-ak was to allow singers to retain their normal vocal technique while preserving key elements of traditional p’ansori. Previous studies of shin-ch’ang-ak have focused primarily on its history, purpose, and design and typically have been written in the Korean language. In this study I expound upon this work in English and I provide a vocal interpretation of Kim’s shin-ch’ang-ak as applied to excerpts taken from his two operas. I also offer my own suggestions for performing Kim’s shin-ch’ang-ak provided from the perspective of a performer who has practiced Western music.Thesis (D.A.)School of MusicPansori -- Pansori performance issues -- Shin-chang-ak (new singing music) -- Performing shin-chang-ak -- Conclusion and suggestions for further study