Η συσταδοποίηση είναι μία από τις βασικές εργασίες εξόρυξης γνώσης από δεδομένα. Παρουσιάζονται οι κυριότερη αλγόριθμοι συσταδοποίησης και αναλύεται ο αλγόριθμος Xmeans. O Xmeans Επιτρέπει την ομαδοποίηση των δεδομένων χωρίς να χρειάζεται να προσδιοριστεί ακριβώς ο αριθμός των συστάδων. Το Weka είναι ένα λογισμικό μηχανικής μάθησης όπου περιλαμβάνει τον αλγόριθμο X-means. Η φασματομετρία μάζας είναι μία τεχνική για τον προσδιορισμό της σύστασης-φάσματος ενός χημικού δείγματος ή μορίου. Η συσταδοποίηση χρησιμοποιείται στη φασματομετρία μάζας για την ανάδειξη ομάδων όμοιων φασμάτων, όπου έτσι επιτυγχάνεται η καλύτερη κατανόηση του δείγματος αλλά επίσης και της προέλευσης του. Στην εργασία εφαρμόζεται ο αλγόριθμος X-means, μέσω του Weka σε φάσματα μάζας χημικών ουσιών. / The algorithm X-means is used for clustering mass spectra.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18794号 / 理博第4052号 / 新制||理||1583(附属図書館) / 31745 / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)教授 川合 光, 准教授 福間 將文, 教授 田中 貴浩 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

The mass spectra of some monomethylquinolines, dimethylquinolines, monoethylquinolines and monopropylquinolines have been determined. In addition, the spectra of 1,2,3,4-tetrahydroquinoline, 5,6,7,8-tetrahydroquinoline and some monomethyl-1,2,3,4-tetrahydroquinolines have also been studied. Fragmentation mechanisms are proposed to account for the most important peaks in the spectra of these compounds. Deuterium labelled analogues of many of the compounds have been prepared and their spectra support the proposed fragmentation mechanisms. / Thesis / Doctor of Philosophy (PhD)

Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: The aim of this thesis was to study structure-property relationships in porous materials using various adapted analytical techniques and in-house instruments. The thesis is divided into two sections, and the first section of work constitutes the majority of the thesis. The first section of work deals with the theoretical versus experimental classification of sorption selectivity in porous compounds. A transiently porous metallocycle that can adsorb acetylene and carbon dioxide served as a model host for this experiment. A volumetric sorption instrument had to be constructed to carry out sorption with acetylene. Even though the metallocycle should theoretically be selective for acetylene over carbon dioxide based on single-gas sorption isotherms, this was not the case during the sorption of a mixture of the two gases. Furthermore, high-pressure single-crystal diffraction was carried out utilising an in-house environmental gas cell, and structural elucidation indicated that both acetylene and carbon dioxide coexist in a single cavity of the host. Additional complementary techniques are discussed that were used to confirm that both gases are present in a single host cavity. The techniques included infrared spectroscopy as well as high-pressure florescence and Raman spectroscopy, which had to be conducted with a specially designed pressure vessel and with adapted instrumentation. Finally, density functional theory calculations were employed to explain how host-guest and guest-guest interactions lead to the change in adsorption selectivity. It is concluded that researchers need to show experimentally that a compound is selective for the adsorption of a specific gas, because theoretical models are not always accurate. The second part of this work focuses on a fundamental study of the structure-property relationships in a porous hydrogen-bonded organic framework. The section starts off by exploring the activation conditions and thermal stability of the framework. This is followed by an exploration of a possible phase transformation or thermal expansion in the framework, but neither of these occurred. Thereafter, an extended study of the framework’s sorption behaviour with various gases is discussed. Then, a structural study of its solvated phase is used to explain the framework’s stability. Finally, a novel analytical method is introduced, and two examples are used to demonstrate why the instrument is useful in the field of supramolecular chemistry. The chapter is concluded by stating the importance these fundamental studies, as well the development of new analytical techniques. / AFRIKAANSE OPSOMMING: Die doel van hierdie tesis was om die struktuur-afhanklike eienskappe van poreuse materiale te ondersoek. Die studie het gebruik gemaak van verskeie aangepasde analitiese metodes asook instrumente wat spesifiek vir die studie gebou was. Die werk word in twee dele verdeel, en die meerderheid van die tesis word in die eerste deel bevat. In die eerste deel van die tesis word die validiteit van teoretiese- teen eksperimentele adsorpsie selektiwiteit opgeweeg. ʼn Gasheer wat bestaan uit ringvormige koördinasie-verbindings en wat asetileen asook koolstof dioksied kan adsorbeer, dien as ʼn model gasheer vir die studie. ʼn Volumetriese sorpsie instrument was spesiaal vir die studie gebou sodat asetileen sorpsie gedoen kon word. Volgens asetileen en koolstof dioksied se enkel-gas adsorpsie isoterme moet asetileen teoreties met voorkeur geadsorbeer word gedurende ʼn adsorpsie eksperiment waarin beide gasse teenwoordig is, maar eksperimenteel was dit bepaal dat dit nie so is nie, dus is daar ʼn verandering in die gasheer se adsorpsie selektiwiteit. Hierna word strukturele data van die gasheer, onder ʼn hoë druk van die gas mengsel, versamel deur gebruik te maak van enkel-kristal diffraksie en ʼn spesiaal-gemaakde gas sel. Die strukturele data toon dat beide asetileen en koolstof dioksied teenwoordig is binne elke porie van die gasheer. Daar word dan van addisionele analitiese metodes gebruik te maak om die observasie te bevestig. Die analitiese metodes sluit in infrarooi spektroskopie asook hoë-druk fluoressensie en Raman spektroskopie wat geëis het dat ʼn spesiale druk-bestande monster houer gebou moes word en dat analitiese instrumente gemodifiseer moet word. Ten slotte was daar van “density functional theory” gebruik gemaak om te verduidelik dat die interaksie tussen die gasheer en gas sowel as die interaksie tussen twee gasse lei tot die verandering in adsorpsie selektiwiteit. Uit hierdie bevinding word die gevolgtrekking gemaak dat navorsers met meer eksperimentele data vorendag sal moet kom voordat ʼn gevolgtrekking gemaak kan word dat ʼn raamwerk selektief een gas adsorbeer. Die tweede afdeling van die werk fokus op ʼn fundamentele studie van die struktuur-afhanklike eienskappe van ʼn poreuse waterstof-verbinde organies raamwerk. Die afdeling begin deur ʼn ondersoek van die aktivering kondisies sowel as die temperatuur-afhanklike stabiliteit van die raamwerk. Dit word gevolg deur te soek na moontlike fase veranderings of temperatuur-afhanklike uitsetting van die raamwerk, maar nie een van die twee eienskappe word waargeneem nie. Daarna word die deeglike ondersoek van die raamwerk se adsorpsie vermoë met verskeie gasse bespreek. Dit word gevolg deur ʼn strukturele studie van die solvaat van die raamwerk, wat dan gebruik word om die stabiliteit van die raamwerk te verduidelik. Ten slotte word ʼn analitiese metode bekend gestel, en twee voorbeelde word gebruik om te wys hoe nuttig die metode is om ʼn kombinasie van resultate te bekom. Die hoofstuk word saamgevat deur te verduidelik hoekom dit belangrik is om hierdie tipe fundamentele studies te doen asook waarom nuwe analitiese metodes ontwerp moet word.

Le sujet de cette thèse porte sur la recherche de nouvelles résonances massives se désintégrant en une paire d’électrons ou une paire électron-muon avec le détecteur CMS, installé auprès du Grand Collisionneur du Hadrons (LHC) au CERN. Les données analysées correspondent à l’ensemble des collisions proton-proton enregistrées par le détecteur en 2012 à une énergie dans le centre de masse de 8 TeV. Après une brève introduction au modèle standard des particules élémentaires et à quelques unes des théories allant au-delà, le LHC et le détecteur CMS sont présentés. La reconstruction des différentes particules créées lors des collisions, en particulier des électrons et muons de haute énergie, est ensuite discutée. Deux analyses séparées sont menées.<p>La première consiste en la recherche d’une nouvelle résonance étroite, plus massive que le boson Z, dans le spectre de masse invariante des paires d’électrons, dont la principale contribution, dans le modèle standard, provient du processus de Drell–Yan. De telles résonances sont notamment prédites par des modèles dits de grande unification ou à dimensions spatiales supplémentaires. Le bruit de fond provenant des processus du modèle standard étant réduit dans la région étudiée, quelques événements localisés peuvent suffire pour mener à une découverte, et la sélection des électrons est optimisée afin de ne perdre aussi peu d’événements que possible. Les différentes contributions des bruits de fond sont partiellement estimées à partir de simulations. Une méthode basée sur le spectre de masse invariante des paires électron-muon mesuré dans les données est développée pour valider la contribution du second bruit de fond en terme d’importance. Aucun excès n’est observé par rapport aux prédictions du modèle standard et des limites supérieures à 95% de niveau de confiance sont placées sur le rapport entre la section efficace de production multipliée par le rapport de branchement d’une nouvelle résonance et celle au pic du boson Z. Ces limites sont ensuite converties en limites inférieures sur la masse de différentes particules hypothétiques de spin 1 ou de spin 2.<p>La seconde analyse consiste en une recherche de résonances massives et étroites dans le spectre de masse invariante des paires électron-muon. De telles résonances briseraient la conservation du nombre leptonique tel que prédit par le modèle standard. Cette possibilité existe cependant dans certains modèles de nouvelle physique. C’est notamment le cas pour un modèle à dimensions supplémentaires où apparaissent des nouveaux bosons neutres lourds. La sélection des événements demande un électron de haute énergie comme dans l’analyse précédente, et un muon de grande impulsion transverse. La stratégie de recherche est similaire au cas des paires d’électrons :le fait de rechercher un signal étroit rend l’analyse statistique très peu sensible aux erreurs systématiques affectant la normalisation absolue du spectre de masse électron-muon. Comme aucune déviation significative n’est observée par rapport aux prévisions du modèle standard, des limites supérieures sur la section efficace multipliée par le rapport de branchement sont établies pour le modèle à dimensions spatiales supplémentaires. Étant données les faibles valeurs théoriques de la section efficace de production des résonances violant la conservation de la saveur dans ce modèle, la quantité de données analysées ne permet pas d’en déduire une limite inférieure sur leur masse. Cette analyse représente néanmoins la première recherche directe avec l’expérience CMS, de bosons massifs, se désintégrant avec violation du nombre leptonique, en une paire électron-muon.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Mass Spectrometry, especially matrix assisted laser desorption/ionization (MALDI) time of flight (TOF), is emerging as a leading technique in the proteomics revolution. It can be used to find disease-related protein patterns in mixtures of proteins derived from easily obtained samples. In this paper, a novel algorithm for MALDI-TOF MS data processing is developed. The software design includes the application of splines for data smoothing and baseline correction, wavelets for adaptive denoising, multivariable statistics techniques such as clustering analysis, and signal processing techniques to evaluate the complicated biological signals. A MatLab implementation shows the processing steps consecutively including step-interval unification, adaptive wavelet denoising, baseline correction, normalization, and peak detection and alignment for biomarker discovery.

Neste trabalho estudamos a aplicabilidade dos conceitos de autoconsistência de R. Hagedorn e de não-extensividade de acordo com a estatística de Tsallis. Estes dois conceitos podem ser associados de acordo com a teoria autoconsistente não-extensiva. A análise dos dados de distribuição de momento tranversal e do espectro de massa de hádrons permite testar a aplicabilidade desses conceitos, e neste trabalho desenvolvemos esta análise para dados obtidos em colisões pp em energias ultrarelativísticas. Os resultados obtidos nessas análises confirmam a idéia de Hagedorn da existência de uma temperatura limite para sistemas hadrônicos e também é observado uma ótima descrição do espectro de massa hadrônico pela da TACNE. Parte dos resultados deste trabalho está publicada na Physical Review D 87, 114022 (2013). / In this work, we study the applicability of the concepts of self-consistency by R. Hagedorn and non-exntensivity according to the Tsallis statistic. These two concepts can be associeted in accordance with the self-consistency non-extensive theory. The analysis of distribution data of transverse momentum and mass spectrum allows hadron test applicability of these concepts, and in this work we developed this analysis for data obtained from pp collisions at ultrarelativistic energies. The results of these analysis support the ideia of the existence of a Hagedorns temperature threshold for hadronic systems and a very good description of the hadroic mass spectrum by the self-consistency non-extensive theory is also verified. Part of this work is published in Physical Review D 87, 114022 (2013).

Neste trabalho estudamos a aplicabilidade dos conceitos de autoconsistência de R. Hagedorn e de não-extensividade de acordo com a estatística de Tsallis. Estes dois conceitos podem ser associados de acordo com a teoria autoconsistente não-extensiva. A análise dos dados de distribuição de momento tranversal e do espectro de massa de hádrons permite testar a aplicabilidade desses conceitos, e neste trabalho desenvolvemos esta análise para dados obtidos em colisões pp em energias ultrarelativísticas. Os resultados obtidos nessas análises confirmam a idéia de Hagedorn da existência de uma temperatura limite para sistemas hadrônicos e também é observado uma ótima descrição do espectro de massa hadrônico pela da TACNE. Parte dos resultados deste trabalho está publicada na Physical Review D 87, 114022 (2013). / In this work, we study the applicability of the concepts of self-consistency by R. Hagedorn and non-exntensivity according to the Tsallis statistic. These two concepts can be associeted in accordance with the self-consistency non-extensive theory. The analysis of distribution data of transverse momentum and mass spectrum allows hadron test applicability of these concepts, and in this work we developed this analysis for data obtained from pp collisions at ultrarelativistic energies. The results of these analysis support the ideia of the existence of a Hagedorns temperature threshold for hadronic systems and a very good description of the hadroic mass spectrum by the self-consistency non-extensive theory is also verified. Part of this work is published in Physical Review D 87, 114022 (2013).

Tandem mass spectrometry, also known as MS/MS, is an analytical technique to measure the mass-to-charge ratio of charged ions and widely used in genomics, proteomics and metabolomics areas. There are two types of automatic ways to interpret tandem mass spectra: de novo methods and database searching methods. Both of them need to use massive computational resources and complicated comparison algorithms. The real-time peptide-spectrum matching (RT-PSM) algorithm is a database searching method to interpret tandem mass spectra with strict time constraints. Restricted by the hardware and architecture of an individual workstation the RT-PSM algorithm has to sacrifice the level of accuracy in order to provide prerequisite processing speed. The peptide-spectrum similarity scoring module is the most time-consuming part out of four modules in the RT-PSM algorithm, which is also the core of the algorithm. In this study, a multi-core computing algorithm is developed for individual workstations. Moreover, a distributed computing algorithm is designed for a cluster. The improved algorithms can achieve the speed requirement of RT-PSM without sacrificing the accuracy. With some expansion, this distributed computing algorithm can also support different PSM algorithms. Simulation results show that compared with the original RT-PSM, the parallelization version achieves 25 to 34 times speed-up based on different individual workstations. A cluster with 240 CPU cores could accelerate the similarity score module 210 times compare with the single-thread similarity score module and the whole peptide identification process 85 times compare with the single-thread peptide identification process.

Hypertrophic scarring is a common occurrence for severe burn victims leading to major functional, physiological, and aesthetic effects to the patients. Limiting the hypertrophic scarring of the patients alleviates the functional, physiological, and aesthetic effects. Silicone gels, over the past decade, have been widely used to remediate and limit hypertrophic scarring but the mechanism of action is yet to be determined. One explanation has been that hydration of the outermost area of the burn is induced by the silicone gel . However, non-silicone polymers which increase hydration could not mimic the effect. An alternative interpretation is that there may be silicone species that migrate from the silicone gel into the viable tissue to mediate reactions in the extra-cellular matrix that result in a decreased deposition of excessive amounts of collagen - a central feature of the hypertrophic scar. A novel and informative technique to study these species is MALDI-TOF/MS (Matrix Assisted Laser Desorption Ionisation-Time of Flight Mass Spectrometry) in conjunction with gel permeation chromatography. MALDI-TOF/MS, which has allowed the detection of intact molecular species that were not possible with more established mass spectrometric techniques. The mobile species that may migrate from polydimethylsiloxane medical gel sheeting into skin have been identified by MALDI-MS. The bulk gel contains predominantly cyclic oligomers with a mass distribution peaking at n = 19 (number of repeating siloxane units), but in an aqueous environment the species at the surface of the silicone medical gel are predominantly methyl/methylol-terminated linear siloxanes. By using a gelatine matrix as a model substrate, the distribution of silicon after application of the silicone gel for 16 weeks was determined by Energy-dispersive X-Ray mapping of the sectioned gelatine. The association of the linear and cyclic oligomers with proteins relevant in hypertrophic scarring are considered. The mobility of silicone species across stratum corneum was confirmed by Attenuated Total Reflectance Fourier Transform Infrared spectroscopy (ATR-FT/IR). This method confirms our hypothesis that not only are the low molecular weight silicone species mobile, but also that they do traverse the natural barrier, the stratum corneum, to levels that are detectable by ATR after a continuous application over approximately 11 days. Invitro studies of the effects of LMWS on primary line fibroblast cells indicate a response that down regulates the proliferation of fibroblast cells and protein production. Preliminary results indicate that a family of pendant functional LMWS are effective in down regulating hypertrophic-derived fibroblast primary cells. Studies on hypertrophic scar tissue treated with silicone medical gel indicate that LMWS permeate across the stratum corneum into viable scar tissue. In some areas, the LMWS tend to pool as detected by SEM/EDX elemental silicon analysis. These areas of LMWS pooling tend to be composed of highly disorganised collagen nodules.