Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 5 uppsatser.

Thesis (M.Sc.). / Written for the Dept. of Microbiology and Immunology. Title from title page of PDF (viewed 2008/05/28). Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (leaves 155-166).

Numerical techniques for linear systems arising from discretization of partial differential equations are nowadays essential for understanding the physical world. Among these techniques, iterative methods and the accompanying preconditioning techniques have become increasingly popular due to their great potential on large scale computation. In this work, we present preconditioning techniques for linear systems built with tensor product basis functions. Efficient algorithms are designed for various problems by exploiting the Kronecker product structure in the matrices, inherited from tensor product basis functions. Specifically, we design preconditioners for mass matrices to remove the complexity from the basis functions used in isogeometric analysis, obtaining numerical performance independent of mesh size, polynomial order and continuity order; we also present a compound iteration preconditioner for stiffness matrices in two dimensions, obtaining fast convergence speed; lastly, for the Helmholtz problem, we present a strategy to `hide' its indefiniteness from Krylov subspace methods by eliminating the part of initial error that corresponds to those negative generalized eigenvalues. For all three cases, the Kronecker product structure in the matrices is exploited to achieve high computational efficiency.

Chan Pui Kwan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (leaves 98-104). / Abstracts in English and Chinese. / TABLE OF CONTENTS --- p.i / LIST OF FIGURES --- p.iv / LIST OF TABLES --- p.vii / ABBREVIATIONS --- p.viii / Chapter Chapter one --- Research Background / Chapter 1.1 --- Carbohydrates --- p.2 / Chapter 1.2 --- Impact of molecular weight of polysaccharides --- p.5 / Chapter 1.3 --- Molecular Weight Determination of polysaccharides --- p.6 / Chapter 1.3.1 --- Laser Scattering --- p.6 / Chapter 1.3.2 --- Gel Permeation Chromatography --- p.7 / Chapter 1.3.3 --- Mass spectrometry --- p.9 / Chapter 1.4 --- Matrix assisted laser desorption/ ionization (MALDI) --- p.10 / Chapter 1.4.1 --- Laser desorption --- p.10 / Chapter 1.4.2 --- Matrix-assisted laser desorption / ionization (MALDI) --- p.11 / Chapter 1.5 --- MALDI-TOFMS analysis of polymers --- p.14 / Chapter 1.6 --- Outline of the present work --- p.16 / Chapter Chapter two --- Experimental and Instrumentation / Chapter 2.1 --- Matrix-assisted laser desorption/ ionization Time of flight Mass Spectrometry (MALDI-TOFMS) --- p.18 / Chapter 2.2 --- Delayed extraction --- p.20 / Chapter 2.3 --- Time of flight mass spectrometry (TOFMS) --- p.20 / Chapter 2.3.1 --- Linear time-of-flight mass spectrometry --- p.20 / Chapter 2.3.2 --- Reflectron --- p.21 / Chapter 2.4 --- Instrumentation --- p.23 / Chapter 2.4.1 --- Laser system --- p.24 / Chapter 2.4.2 --- Ion source --- p.26 / Chapter 2.4.3 --- Ion deflection --- p.26 / Chapter 2.4.4 --- Detection --- p.27 / Chapter 2.4.5 --- Reflector --- p.27 / Chapter 2.4.6 --- Data acquisition --- p.29 / Chapter 2.5 --- Experimental --- p.29 / Chapter 2.5.1 --- Sample preparation --- p.29 / Chapter 2.5.2 --- Calibration --- p.33 / Chapter 2.6 --- Data analysis --- p.33 / Chapter Chapter three --- Use of ammonium fluoride as co-matrix / Chapter 3.1 --- Introduction --- p.35 / Chapter 3.2 --- Results and discussion --- p.37 / Chapter 3.2.1 --- Effect of co-matrix --- p.45 / Chapter 3.2.2 --- Effect of sample preparation --- p.49 / Chapter 3.2.3 --- Analysis of dispersed dextran --- p.52 / Chapter 3.3 --- Conclusion --- p.55 / Chapter Chapter four --- Effect of sample preparation / Chapter 4.1 --- Introduction --- p.57 / Chapter 4.2 --- Experimental --- p.57 / Chapter 4.2.1 --- Sample preparation --- p.57 / Chapter 4.3 --- Results and discussion --- p.59 / Chapter 4.4 --- Conclusion --- p.71 / Chapter Chapter five --- Development of liquid matrix systems / Chapter 5.1 --- Introduction --- p.73 / Chapter 5.2 --- Experimental --- p.75 / Chapter 5.2.1 --- Sample preparation --- p.75 / Chapter 5.3 --- Results and discussion --- p.76 / Chapter 5.3.1 --- Formulation of matrix solutions --- p.76 / Chapter 5.3.2 --- Use of liquid matrix system --- p.87 / Chapter 5.3.3 --- Analysis of dispersed dextran --- p.90 / Chapter 5.4 --- Conclusion --- p.93 / Chapter Chapter six --- Conclusion / Chapter 6.1 --- Conclusion --- p.95 / References --- p.98 / Appendix / Appendix 1 Chemical structure of matrices / Appendix 2 Chemical structure of solubilizing agents / Appendix 3 Chemical structure of liquid supports / Appendix 4 Chemical structure of additives

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 7 uppsatser.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2005. / Härtill 5 uppsatser.

Bien que l'on ne sache pas (encore) quel phénomène unitarise la diffusion WLWL à l'échelle du TeV, les données indirecte actuelles favorise le boson de Higgs. Etant donné que cette particule scalaire pourrait être aussi lourde que la masse de Planck, comment peut-on expliquer sa légèreté ? La supersymmétrie (SUSY), brisée à l'échelle du TeV, peut effectuer cette stabilisation, et permettre du même coup l'existence de Théories de Grande Unifications (GUTs). Ces SUSY GUTs réalisées dans une dimension supplémentaire compactifiée, peuvent être particulièrement simples. De plus, elles peuvent être prises comme limite basse énergie d'une théorie de cordes. Cette thèse est consacrée à l'étude de tels modèles de SUSY GUTs. Nous avons étudié, développé et étendu certains aspects de la classe de modèle d'Unification Jauge-Higgs, et de la classe de modèle d'Unification Holographique. Différents aspects de la physique basse-énergie ont été étudiés, incluant spectre de masses, physique des saveur, matière noire, et phénoménologie au LHC. / Although one does not know (yet) which phenomenon unitarizes WLWL scattering at the TeV scale, indirect data currently favors the Higgs boson. Since such a scalar particle is susceptible to become as heavy as the Planck mass, how can one explain its lightness ? Supersymmetry (SUSY), broken at the TeV scale, can do this stabilization, providing in the same time models of Grand Uni fied Theories (GUTs). These SUSY GUTs, combined with extra spatial dimensions compacti fied on an interval, can be particularly simple. Moreover they can be seen as the low energy limit of some string theory. This thesis is devoted to the study of such models of SUSY GUTs on flat and warped orbifolds, trying to cover the range from models to experimental constraints. We studied, developed and extended certain aspects of two interesting frameworks of this type: a framework with gauge-Higgs uni fication, and the framework of holographic grand uni fication. We investigated several aspects of the low-energy implications, including mass spectra, flavour constraints, dark matter and LHC phenomenology

A especiação de isolados clínicos de Aspergillus ganhou relevância nos últimos anos devido à descrição de espécies crípticas resistentes aos derivados azólicos. A identificação morfológica convencional não é capaz de discriminar as espécies de Aspergillus e o sequenciamento de DNA é uma técnica pouco adaptada a laboratórios clínicos. A espectrometria de massas por ionização/dessorção a laser auxiliada por matriz tempo-devoo (EM MALDI-TOF) é uma metodologia emergente que vem sendo explorada com intuito de fornecer identificação rápida e acurada de microrganismos, incluindo os fungos filamentosos de importância clínica. Entretanto, há poucos estudos avaliando a plataforma VITEK MS® para a identificação de espécies de Aspergillus. O presente estudo teve como objetivo fornecer dados adicionais sobre a performance dos sistemas do VITEK MS® e suas bibliotecas de espectros de referências (ER) In Vitro Diagnostics (IVD) e Research Use Only (RUO) para identificar as espécies de Aspergillus de relevância clínica. Uma biblioteca de ER in-house também foi construída e avaliada. Um total de 106 organismos foram avaliados por EM, incluindo 47 cepas provenientes das coleções de fungos do Westerdijk Fungal Biodiversity Institute (Holanda) e do LEMIUNIFESP, seis isolados ambientais (IMT-USP) e 53 isolados cínicos do HC-FMUSP. Foram utilizados dois protocolos de extração proteica, um recomendado pelo fabricante e outro empregando meio de cultura líquido para os isolados/cepas com baixa esporulação. Trinta e cinco organismos foram selecionadas para construir os ERs, e os 71 restantes foram usados para avaliação de desempenho das bibliotecas IVD, RUO e RUO+in-house. Entre os 71 organismos analisados, 91,5%, 84,5% e 100% tiveram identificação correta de gênero pelos bibliotecas IVD, RUO e RUO+in-house, respectivamente. Enquanto para identificação de espécie, as bibliotecas IVD, RUO e RUO+in-house mostraram 83,1%, 77,4% e 90,1% de identificações de espécie, respectivamente. Para as 16 espécies crípticas de Aspergillus analisadas, a identificação foi correta em 31,2%, 18,7% e 62,5%, pelos sistemas IVD, RUO e RUO+in-house, respectivamente. Entre as espécies crípticas resistentes aos derivados azólicos, o sistema IVD forneceu identificação correta para as espécies Aspergillus lentulus, Aspergillus calidoustus e Aspergillus sydowii. Entretanto, Aspergillus fumigatiaffinis e Neosartorya pseudofischeri foram erroneamente identificadas como Aspergillus fumigatus pelo sistema IVD. A biblioteca in-house demonstrou melhor performance, mas espécies filogeneticamente próximas como A. fumigatiaffinis e A. lentulus tiveram identificações cruzadas. Concluímos que o VITEK® MS demonstrou boa performance para a identificação das espécies de Aspergillus, porém para algumas espécies crípticas, há necessidade de melhoria das bibliotecas de espectro de referência comercializadas. Algumas espécies crípticas filogeneticamente relacionadas apresentaram espectros similares e são de difícil diferenciação por EM MALDI, mesmo com a construção de uma biblioteca de ER in-house com vários representantes de cada espécie / Aspergillus spp. identification has become more relevant in clinical practice since azoleresistant cryptic species have emerged in the last years. Conventional morphologic identification is not able to discriminate Aspergillus species and DNA sequencing is not feasible for clinical laboratories. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is an emergent technology that has been explored to provide fast and accurate identification of microorganisms, including clinically relevant molds. However, only a few studies have explored the platform VITEK MS® for the identification of Aspergillus species. The present study aimed to provide additional data regarding the performance of the In Vitro Diagnostics (IVD) and Research Use Only (RUO) systems for the identification of Aspergillus species, including azoleresistant ones, and also to construct and to evaluate an in-house reference spectrum library. A total of 106 organisms were evaluated by MS, including 47 Aspergillus strains (Westerdijk Fungal Biodiversity Institute and LEMI-UNIFESP collections), six environmental (IMT-USP) and 53 clinical isolates (HC-FMUSP). Two protein extraction protocols were used, one recommended by the manufacturer and another with liquid broth for the organisms with poor sporulation. Thirty-five organisms were selected to construct the in-house reference spectrum library and the remaining 71 were used for the performance evaluation. Correct genus identification was provided in 91.5%, 84.5% and 100% by the IVD, RUO, and RUO+in-house reference spectrum libraries, respectively. Correct species identification was provided in 83.1%, 77.4% and 90.1% by the IVD, RUO, and RUO+in-house reference spectrum libraries, respectively. Among the 16 Aspergillus cryptic species, correct identification was provided in 31.5%, 18.7% and 62.5% by the IVD, RUO, and RUO+in-house reference spectrum libraries, respectively. Among the azole-resistant cryptic species, the IVD system provided correct identification for Aspergillus lentulus, Aspergillus calidoustus and Aspergillus sydowii. However, Aspergillus fumigatiaffinis and Neosartorya pseudofischeri were misidentified as Aspergillus fumigatus by the IVD system. The in-house library had better performance for the identification of Aspergillus cryptic species, but closely related taxa may be difficult to have correct differentiation by MALDI-TOF MS. In conclusion, VITEK® MS showed good performance for the identification of Aspergillus species and some azoleresistant species. However, a more robust reference spectrum library including more representatives of azole-resistant cryptic species may be necessary to achieve better identification performance of closely related taxa

O gênero Trichosporon é composto por leveduras artrosporadas do Filo Basidiomycota e é conhecido agente de infecção fúngica invasiva (IFI) em pacientes imunodeprimidos ou com outros fatores de risco. Em pacientes onco-hematológicos é a principal levedura responsável por IFI depois do gênero Candida. Entre as espécies responsáveis por infecções no homem encontram-se: T. asahii, T. inkin, T. mucoides, T. dermatis, T. jirovecii, T. ovoides, T. cutaneum, T. montevideense, T. domesticum, T. asteroides, T. coremiiforme, T. faecale, T. dohaense, T. lactis, T. japonicum. A tecnologia de identificação de fungos por espectrometria de massa (SM) MALDI-TOF ainda carece de padronização para identificação de fungos do gênero Trichosporon, mas a literatura mostra resultados encorajadores. O objetivo deste estudo é padronizar a técnica de espectrometria de massa MALDI-TOF para a identificação das espécies do gênero Trichosporon de importância médica. O estudo foi realizado em cooperação entre a Divisão de Laboratório Central do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (DLC, HC-FMUSP), Instituto de Medicina Tropical da USP (IMT-USP), Instituto Adolfo Lutz (IAL) e Laboratoire de Parasitologie-Mycologie do Hospital Saint Antoine de Paris, vinculado ao grupo de pesquisa INSERM/UPMC UMR S945 \"Immunité et Infection\" Faculté de Medecine et Université Pierre et Marie Curie de Paris. Noventa e três cepas/isolados foram analisado(a)s, sendo dezenove cepas de referência adquiridas junto à coleção holandesa Centraalbureau Schimmelcultures (CBS), 19 isolados do HC-FMUSP e IAL, e 55 isolados de diferentes hospitais franceses. A identificação molecular foi realizada através do sequenciamento da região IGS1 do rDNA e foi considerada como método de referência. O protocolo de extração de proteínas foi estabelecido através da comparação do desempenho de três metodologias (Bruker®, Cassagne et al., Sendid et al.). Os espectros de massa foram obtidos no laboratório de bacteriologia do Hospital Saint Antoine de Paris através do aparelho Microflex LT®. A interpretação dos resultados qualitativos e quantitativos (logscore) foi realizada através do Software Biotyper 3.0®. O desempenho de identificação do banco de espectros de referência Biotyper 3.0® foi comparado a outros cinco bancos criados a partir de espectros de referência (ERs) derivados de 18 cepas de referência CBS, sete isolados clínicos e 11 ERs do banco Biotyper 3.0. O protocolo de extração de proteínas descrito por Sendid et al. foi escolhido como protocolo de referência pois os espectros produzidos tiveram logscore superiores àqueles obtidos através do método do fabricante. O banco de ERs Biotyper 3.0® apresentou 32,3% de identificações corretas das espécies, sendo que o banco de ERs in house (número 5, constituído cepas CBS e isolados clínicos) apresentou 98,5% de identificações de espécies. Espectros de referência do banco de dados Biotyper 3.0® foram submetidos à identificação com a utilização dos ERs criados a partir de cepas CBS e isolados clínicos e foram evidenciados com erros de identificação: T. mucoides (2), T. ovoides (1) e T. cutaneum (2). Após padronização do protocolo de extração e criação de banco de ERs com cepas CBS e isolados clínicos caracterizados pelo sequenciamento da região IGS, a SM por MALDI-TOF apresentou-se como potente uma ferramenta para a identificação de fungos do gênero Trichosporon. O banco de ERs Biotyper 3.0® apresentou um fraco desempenho, relacionado a ERs que foram criados a partir de cepas mal identificadas / Trichosporon spp. are arthrospored yeasts from the Filum Basidiomycota that are known to produce invasive fungal infection (IFI) in patients with immunosupression or other risk factors. After Candida, Trichosporon is the second genus of yeasts responsible for IFI in patients with onco-hematological diseases. The most important species related to human infection are: T. asahii, T. inkin, T. mucoides, T. dermatis, T. jirovecii, T. ovoides, T. cutaneum, T. montevideense, T. domesticum, T. asteroides, T. coremiiforme, T. faecale, T. dohaense, T. lactis, T. japonicum. The technology of mass spectrometry (MS) for identification of Trichosporon species has not yet been standardized. However, preliminary promising results can be found in the literature. The objective of this study is to analyse and validate MS MALDI-TOF for the identification of Trichosporon species of medical relevance. This was a multicentric study with collaboration from the Central Laboratory Section from Clinics Hospital of the Medical School from the University of São Paulo (DLC-HCFMUSP), Tropical Medicine Institute from the University of São Paulo (IMT-USP), Instituto Adolfo Lutz (IAL) and Laboratoire de Parasitologie-Mycologie from the Hospital Saint Antoine of Paris and INSERM/UPMC UMR S945 \"Immunité et Infection\", Faculté de Medecine et Université Pierre et Marie Curie of Paris. Ninety three strains/isolates belonging to sixteen Trichosporon species were analysed. Nineteen were purchased from Centraalbureau Schimmelcultures (CBS) yeast collection, 19 belonged to HC-FMUSP and IAL collections, 55 belonged to different French collections. The reference identification method was the IGS1 rDNA sequencing. A protein extraction protocol was first established after comparing the performance of three different methodologies (Bruker(TM), Cassagne et al., Sendid et al.). The mass spectra were obtained through a Microflex LT(TM) mass spectrometer located at the bacteriology laboratory from Saint Antoine Hospital, Paris. Mass spectra, qualitative and quantitative results were produced through the software Biotyper 3.0(TM). The performance of the original main spectrum (MSP) library was compared to other 5 in house libraries built with the combination of MSPs derived from CBS strains (18), clinical strains (7) or (Bruker Daltonics/BD, Germany/USA) (11). The extraction protocol described by Sendid et al. showed better performance when compared to the manufacturer\'s one and was chosen for the subsequent extractions. Among the 6 different reference spectra databases tested, a specific one composed of 18 reference strains plus 7 clinical isolates (database 5) allowed the correct identification of 66 amongst 67 clinical isolates (98,5%). Biotyper 3.0 library produced only 32,3% of correct identifications. Biotyper\'s MSPs were submitted to cross-identification with MSPs derived from CBS strains and clinical isolates and misidentified original MSPs were identified: T. mucoides (2), T. ovoides (1) e T. cutaneum (2). While until now less widely applied to basidiomycetous fungi, MALDI-TOF appears to be a valuable tool for identifying clinical Trichosporon isolates at the species level. The MSP library Biotyper 3.0 showed a poorer performance which was due to misidentified strains utilized as reference for the MSPs