Rozprawy doktorskie na temat „Synthetic Transformation”

The aqueous chemistry, precipitation, and crystallization of metal-carbonates comprises a vast field of research that underlies the urgency of CO₂ sequestration, ocean-acidification, and biomineralization. The results of recent experimental and computational studies suggest that amorphous calcium and magnesium carbonates are precipitated from supersaturated aqueous conditions by non-classical aggregation of ion pairs, dimers, dynamically-ordered-liquid-likeoxypolymers (DOLLOPS), and prenucleation clusters (PNCs). We present the first high field (20 T) ⁴³Ca and ²⁵Mg NMR studies of amorphous calcium-magnesium carbonates (ACC, ACMC, AMC) materials. Direct integration of computational techniques with experimental NMR provides a novel step forward toward multi-scale integration of computational and experimental techniques. Supporting information is derived from X-ray diffraction (XRD), thermogravimetric/differential thermal analysis (TGA-DTA), and scanning electron microscopy—energy dispersive spectroscopy (SEM-EDS) and provides important comparison to the bulk structures and composition.

High field NMR of amorphous carbonates demonstrates that amorphous carbonates contain various types of local disorder, but does not corroborate the theory of polyamorphism nor nano scale phase separations postulated by other workers. Carbon (¹³C) NMR of ¹³Cenriched materials indicates a degree of Ca-Mg solid solution in ACMCs, as ACMC ¹³C resonances cannot be adequately reconstructed from the pure ACC and AMC ¹³C resonances. However, with increasing Mg-content (and therefore H₂O content) ¹³C NMR resonances are strongly influenced by water-carbonate hydrogen bonding, shifting to lower resonance frequency and broadening. The ¹³C-NMR are well-fit with single Gaussian distributions, suggesting that two-phase models of ACMCs are not required to explain our ¹³C NMR observations. Protoncarbon cross polarization indicates that there is a H population proximal to carbonate groups for all amorphous phases. ⁴³Ca NMR yields line shapes that span the resonance frequency range of all known crystalline calcium carbonate polymorphs and is well fit with a single Gaussian distributions. ⁴³Ca NMR does not support a theory of polyamorphisms, but rather suggests an unstructured, continuous distribution of local environments that is unlike any specific crystalline phase. The mean ⁴³Ca chemical shifts vary 0.77 ppm from compositions x = 0 to 0.5 [x = Mg/(Mg + Ca)], demonstrating that Mg²⁺ has very little influence on the molecular-scale ⁴³Ca environment in ACMCs. Through integration of quantum mechanical calculations, classical MD, and NMR we ascertain a maximum mean Ca-O bond distance in our ACCs/ACMCs of 2.45 ± 1 Å that is independent of composition. Unlike the indistinguishable local calcium environments, ²⁵Mg NMR of amorphous material gives evidence for several distinct overlapping quadrupolar line shapes. These sites do not generate NMR resonances that are perfect matches for known crystalline polymorphs of magnesian carbonates and extend toward lower resonance frequencies far beyond the range of known equilibrium analogs. By comparison to the range of reference phases, the low frequency singularities of ACMC-AMC resonances are consistent with some population of Mg-O bond distances greater than 2.10 Å and/or some fraction of sites with high coordination numbers (up to 8). The local Mg environment of a protodolomite crystallization [x = Mg/(Mg + Ca) = 0.6] exhibits ²⁵Mg NMR parameters most similar to the asymmetric Mg²⁺ coordination environment of lansfordite [Mg(CO₃)2(H₂O)₄]^2– or huntite. Although H-C cross polarization indicates no H-bonding with carbonate the XRD gives not longrange indications of huntite. The large effective radius of strongly hydrated Mg in the protodolomite likely provides a driving force for cation ordering in dolomite.

Aquesta tesi s'ha dut a terme dins del Grup en de Tecnologies Mèdia (GTM) de l'Escola d'Enginyeria i Arquitectura la Salle. El grup te una llarga trajectòria dins del cap de la síntesi de veu i fins i tot disposa d'un sistema propi de síntesi per concatenació d'unitats (US-TTS) que permet sintetitzar diferents estils expressius usant múltiples corpus. De forma que per a realitzar una síntesi agressiva, el sistema usa el corpus de l'estil agressiu, i per a realitzar una síntesi sensual, usa el corpus de l'estil corresponent. Aquesta tesi pretén proposar modificacions del esquema del US-TTS que permetin millorar la flexibilitat del sistema per sintetitzar múltiples expressivitats usant només un únic corpus d'estil neutre. L'enfoc seguit en aquesta tesi es basa en l'ús de tècniques de processament digital del senyal (DSP) per aplicar modificacions de senyal a la veu sintetitzada per tal que aquesta expressi l'estil de parla desitjat. Per tal de dur a terme aquestes modificacions de senyal s'han usat els models harmònic més soroll per la seva flexibilitat a l'hora de realitzar modificacions de senyal. La qualitat de la veu (VoQ) juga un paper important en els diferents estils expressius. És per això que es va estudiar la síntesi de diferents emocions mitjançant la modificació de paràmetres de VoQ de baix nivell. D'aquest estudi es van identificar un conjunt de limitacions que van donar lloc als objectius d'aquesta tesi, entre ells el trobar un paràmetre amb gran impacte sobre els estils expressius. Per aquest fet l'esforç vocal (VE) es va escollir per el seu paper important en la parla expressiva. Primer es va estudiar la possibilitat de transferir l'VE entre dues realitzacions amb diferent VE de la mateixa paraula basant-se en la tècnica de predicció lineal adaptativa del filtre de pre-èmfasi (APLP). La proposta va permetre transferir l'VE correctament però presentava limitacions per a poder generar nivells intermitjos d'VE. Amb la finalitat de millorar la flexibilitat i control de l'VE expressat a la veu sintetitzada, es va proposar un nou model d'VE basat en polinomis lineals. Aquesta proposta va permetre transferir l'VE entre dues paraules qualsevols i sintetitzar nous nivells d'VE diferents dels disponibles al corpus. Aquesta flexibilitat esta alineada amb l'objectiu general d'aquesta tesi, permetre als sistemes US-TTS sintetitzar diferents estils expressius a partir d'un únic corpus d'estil neutre. La proposta realitzada també inclou un paràmetre que permet controlar fàcilment el nivell d'VE sintetitzat. Això obre moltes possibilitats per controlar fàcilment el procés de síntesi tal i com es va fer al projecte CreaVeu usant interfícies gràfiques simples i intuïtives, també realitzat dins del grup GTM. Aquesta memòria conclou presentant el treball realitzat en aquesta tesi i amb una proposta de modificació de l'esquema d'un sistema US-TTS per incloure els blocs de DSP desenvolupats en aquesta tesi que permetin al sistema sintetitzar múltiple nivells d'VE a partir d'un corpus d'estil neutre. Això obre moltes possibilitats per generar interfícies d'usuari que permetin controlar fàcilment el procés de síntesi, tal i com es va fer al projecte CreaVeu, també realitzat dins del grup GTM. Aquesta memòria conclou presentant el treball realitzat en aquesta tesi i amb una proposta de modificació de l'esquema del sistema US-TTS per incloure els blocs de DSP desenvolupats en aquesta tesi que permetin al sistema sintetitzar múltiple nivells d'VE a partir d'un corpus d'estil neutre.
Esta tesis se llevó a cabo en el Grup en Tecnologies Mèdia de la Escuela de Ingeniería y Arquitectura la Salle. El grupo lleva una larga trayectoria dentro del campo de la síntesis de voz y cuenta con su propio sistema de síntesis por concatenación de unidades (US-TTS). El sistema permite sintetizar múltiples estilos expresivos mediante el uso de corpus específicos para cada estilo expresivo. De este modo, para realizar una síntesis agresiva, el sistema usa el corpus de este estilo, y para un estilo sensual, usa otro corpus específico para ese estilo. La presente tesis aborda el problema con un enfoque distinto proponiendo cambios en el esquema del sistema con el fin de mejorar la flexibilidad para sintetizar múltiples estilos expresivos a partir de un único corpus de estilo de habla neutro. El planteamiento seguido en esta tesis esta basado en el uso de técnicas de procesamiento de señales (DSP) para llevar a cabo modificaciones del señal de voz para que este exprese el estilo de habla deseado. Para llevar acabo las modificaciones de la señal de voz se han usado los modelos harmónico más ruido (HNM) por su flexibilidad para efectuar modificaciones de señales. La cualidad de la voz (VoQ) juega un papel importante en diferentes estilos expresivos. Por ello se exploró la síntesis expresiva basada en modificaciones de parámetros de bajo nivel de la VoQ. Durante este estudio se detectaron diferentes problemas que dieron pié a los objetivos planteados en esta tesis, entre ellos el encontrar un único parámetro con fuerte influencia en la expresividad. El parámetro seleccionado fue el esfuerzo vocal (VE) por su importante papel a la hora de expresar diferentes emociones. Las primeras pruebas se realizaron con el fin de transferir el VE entre dos realizaciones con diferente grado de VE de la misma palabra usando una metodología basada en un proceso filtrado de pre-émfasis adaptativo con coeficientes de predicción lineales (APLP). Esta primera aproximación logró transferir el nivel de VE entre dos realizaciones de la misma palabra, sin embargo el proceso presentaba limitaciones para generar niveles de esfuerzo vocal intermedios. A fin de mejorar la flexibilidad y el control del sistema para expresar diferentes niveles de VE, se planteó un nuevo modelo de VE basado en polinomios lineales. Este modelo permitió transferir el VE entre dos palabras diferentes e incluso generar nuevos niveles no presentes en el corpus usado para la síntesis. Esta flexibilidad está alineada con el objetivo general de esta tesis de permitir a un sistema US-TTS expresar múltiples estilos de habla expresivos a partir de un único corpus de estilo neutro. Además, la metodología propuesta incorpora un parámetro que permite de forma sencilla controlar el nivel de VE expresado en la voz sintetizada. Esto abre la posibilidad de controlar fácilmente el proceso de síntesis tal y como se hizo en el proyecto CreaVeu usando interfaces simples e intuitivas, también realizado dentro del grupo GTM. Esta memoria concluye con una revisión del trabajo realizado en esta tesis y con una propuesta de modificación de un esquema de US-TTS para expresar diferentes niveles de VE a partir de un único corpus neutro.
This thesis was conducted in the Grup en Tecnologies M`edia (GTM) from Escola d’Enginyeria i Arquitectura la Salle. The group has a long trajectory in the speech synthesis field and has developed their own Unit-Selection Text-To-Speech (US-TTS) which is able to convey multiple expressive styles using multiple expressive corpora, one for each expressive style. Thus, in order to convey aggressive speech, the US-TTS uses an aggressive corpus, whereas for a sensual speech style, the system uses a sensual corpus. Unlike that approach, this dissertation aims to present a new schema for enhancing the flexibility of the US-TTS system for performing multiple expressive styles using a single neutral corpus. The approach followed in this dissertation is based on applying Digital Signal Processing (DSP) techniques for carrying out speech modifications in order to synthesize the desired expressive style. For conducting the speech modifications the Harmonics plus Noise Model (HNM) was chosen for its flexibility in conducting signal modifications. Voice Quality (VoQ) has been proven to play an important role in different expressive styles. Thus, low-level VoQ acoustic parameters were explored for conveying multiple emotions. This raised several problems setting new objectives for the rest of the thesis, among them finding a single parameter with strong impact on the expressive style conveyed. Vocal Effort (VE) was selected for conducting expressive speech style modifications due to its salient role in expressive speech. The first approach working with VE was based on transferring VE between two parallel utterances based on the Adaptive Pre-emphasis Linear Prediction (APLP) technique. This approach allowed transferring VE but the model presented certain restrictions regarding its flexibility for generating new intermediate VE levels. Aiming to improve the flexibility and control of the conveyed VE, a new approach using polynomial model for modelling VE was presented. This model not only allowed transferring VE levels between two different utterances, but also allowed to generate other VE levels than those present in the speech corpus. This is aligned with the general goal of this thesis, allowing US-TTS systems to convey multiple expressive styles with a single neutral corpus. Moreover, the proposed methodology introduces a parameter for controlling the degree of VE in the synthesized speech signal. This opens new possibilities for controlling the synthesis process such as the one in the CreaVeu project using a simple and intuitive graphical interfaces, also conducted in the GTM group. The dissertation concludes with a review of the conducted work and a proposal for schema modifications within a US-TTS system for introducing the VE modification blocks designed in this dissertation.

Mycoplasma hominis est un pathogène humain opportuniste responsable d’infections génitales et néo-natales. Modifier génétiquement cette bactérie est nécessaire afin de comprendre les mécanismes de virulence et d’infection de ce pathogène. Il n’existe à ce jour aucun outil moléculaire efficace permettant de manipuler le génome de M. hominis, limitant les recherches sur sa pathogénicité et son métabolisme particulier reposant sur l’arginine. De nouvelles technologies rassemblées sous le terme de Biologie de Synthèse (BS) ont récemment émergé, offrant des perspectives inédites pour l’étude des mycoplasmes en permettant de modifier leurs génomes à grande échelle et de produire des souches mutantes. Ces travaux menés au J. Craig Venter Institute (JCVI, USA) ont montré que le génome de mycoplasmes apparentés pouvait être cloné et manipulé dans la levure avant d’être transplanté dans une cellule receveuse. La levure sert d’hôte d’accueil temporaire pour modifier le génome de la bactérie. Cette approche novatrice ouvre de nombreuses perspectives dans le cadre du développement de la génomique fonctionnelle chez les mycoplasmes pour lesquels les outils génétiques efficaces sont peu nombreux. Le but de cette thèse a été d’adapter pour la première fois certains outils de BS à M. hominis dans le but de créer des mutants déficients pour une fonction donnée. Pour cela, le génome de la souche type de M. hominis PG21 (665 kb) a été cloné dans la levure Saccharomyces cerevisiae par « Transformation-Associated Recombination cloning » (TAR-cloning). Deux clones (B3-2 et B3-4) de levure possédant le génome complet de M. hominis ont été validés par analyse en PCR simplex, PCR multiplex et électrophorèse en champs pulsé (PFGE). Ces clones levures ont ensuite été propagés en milieu sélectif durant 180 générations (30 passages), afin d’évaluer la stabilité du génome bactérien dans son hôte. Cette expérience a montré que (i) si la taille du génome de M. hominis ne variait pas au cours des premiers passages, elle diminuait progressivement à partir du dixième passage (≈60 générations), et que (ii) les zones du génome enrichies en séquence répétées étaient préférentiellement perdues. En tenant compte de ces résultats, le génome de M. hominis a été modifié chez le clone B3-4 par la technique « Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 » (CRISPR/Cas9) lors de passages précoces. Des clones de S. cerevisiae possédant un génome de M. hominis PG21 complet délété du gène vaa, codant une protéine d’adhésion majeure, ont été ainsi produits. La dernière étape de cette approche consistait à transplanter le génome modifié dans une cellule receveuse de M. hominis ou de Mycoplasma arthritidis, espèce phylogénétiquement la plus proche de M. hominis. Aucun protocole de transformation de M. hominis n’étant disponible au début de nos travaux, cette étape constituait un verrou majeur dans la mise en place des outils de BS chez cette espèce. Ce verrou a été en partie levé puisqu’une méthode de transformation de M. hominis basée sur du polyéthylène glycol (PEG) et mettant en jeu le plasposon pMT85 (plasmide contenant un transposon conférant la résistance à la tétracycline) a été mise au point au laboratoire. Cette technique de transformation, développée pour la souche de référence M. hominis M132 (745 kb) reste encore peu efficace ; elle est néanmoins reproductible et a permis d’obtenir des mutants d’intérêt de M. hominis. Le transformant n°28-2 a, ainsi, été muté dans le gène Mhom132_2390, codant le précurseur de la protéine P75, une adhésine putative de M. hominis. Le séquençage des génomes complets d’autres transformants a révélé l’insertion de multiples copies du transposon et la présence d’évènements de duplication et d’inversion de larges fragments d’ADN dans au moins deux génomes de M. hominis
Mycoplasma hominis is an opportunistic human pathogen responsible for genital and neonatal infections. Genetically modifying this bacterium is necessary to understand the virulence and infection mechanisms of this pathogen. There is currently no effective molecular tool to engineer the genome of this bacterium, limiting research on its pathogenicity and its peculiar metabolism based on arginine.New technologies have recently emerged in the field of Synthetic Biology (BS), offering new perspectives for the study of mycoplasmas by allowing large scale genome modifications and the production of mutant strains. Work at the J. Craig Venter Institute (JCVI, USA) has shown that the genome of related mycoplasmas can be cloned and manipulated in yeast before being transplanted into a recipient cell. The yeast serves as a temporary host to modify the genome of the bacterium. This innovative approach opens many perspectives in the development of functional genomics in mycoplasmas for which there are few effective genetic tools. The goal of this thesis was to adapt a number of BS tools to M. hominis for the first time, in order to create mutants deficient for a given function. To achieve this goal, the genome of the M. hominis type strain PG21 (665 kb) was cloned into the yeast Saccharomyces cerevisiae by Transformation-Associated Recombination cloning (TAR-cloning). Two yeast clones (B3-2 and B3-4) possessing the complete genome of M. hominis were validated by simplex PCR, multiplex PCR and Pulsed Field Gel Electrophoresis (PFGE) analyses. These yeast clones were then propagated in a selective medium for 180 generations (30 passages) to evaluate the stability of the bacterial genome in its host. This experiment showed that (i) the size of the genome of M. hominis did not change during the first passages, it decreased progressively from the tenth passage (≈60 generations), and (ii) the enriched genome areas in repeated sequence were preferentially lost. Thus, the genome of M. hominis was modified in the B3-4 clone at early passages using the Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 (CRISPR/Cas9) technology. Yeast clones with a complete M. hominis PG21 genome with a deleted vaa gene, encoding a major adhesion protein, were produced using this approach. The final step of this approach was to transplant the modified genome into a recipient cell of M. hominis or Mycoplasma arthritidis, the species phylogenetically closest to M. hominis. As no M. hominis transformation protocol was available at the beginning of our work, this step constituted a major obstacle in the implementation of BS tools in this species. This barrier has been partially lifted since a method of transformation of M. hominis based on polyethylene glycol (PEG) and involving the plasposon pMT85 (plasmid carrying a transposon conferring resistance to tetracycline) has been developed in the laboratory. This transformation technique, developed for the reference strain M. hominis M132 (745 kb) still remains not very efficient; it is nevertheless reproducible and allowed to obtain M. hominis mutants of interest. The Mhom132_2390 gene, encoding the precursor of the P75 protein, a putative adhesin of M. hominis, was effectively mutated in transformant No. 28-2. Complete genome sequencing of other transformants revealed the insertion of multiple copies of the transposon and the presence of duplication and inversion of large DNA fragments within at least two M. hominis genomes.In conclusion, this data has opened the way for the development and transposition of existing genetic modification approaches to M. hominis, previously considered as a genetically intractable bacterium

Thesis (Ph. D.)--Ohio State University, 2003.
Title from first page of PDF file. Document formatted into pages; contains xxiii, 184 p.; also includes graphics (some color). Includes bibliographical references (p. 166-184).

Owing to the growing demand for enantiopurity in biological and chemical processes, tremendous efforts have been devoted to the synthesis of homochiral metal-organic materials (MOMs) because of their potential applications in chiral separation and asymmetric catalysis. In this dissertation, the synthetic strategies for homochiral MOMs are discussed keeping the focus on their applications. Two distinct approaches have been taken to synthesize chiral structures with different topologies and accessible cavities. The chiral MOMs have been utilized in enantioselective separation of racemates. Chiral variants of the prototypal metal-organic framework MOF-5, δ-CMOF-5 and [lambda]-CMOF-5, have been synthesized by preparing MOF-5 in the presence of L-proline or D-proline, respectively. CMOF-5 crystallizes in chiral space group P213 instead of Fm-3m as exhibited by MOF-5. The phase purity of CMOF-5 was validated by single crystal and powder X-ray diffraction, IR spectroscopy, TGA, N2 adsorption, microanalysis and solid-state CD. CMOF-5 undergoes a reversible single crystal to single crystal phase change to MOF-5 when immersed in a variety of organic solvents although N-methyl-2-pyrolidone, NMP, does not induce loss of chirality. Indeed, MOF-5 undergoes chiral induction when immersed in NMP, affording racemic CMOF-5. A pair of homochiral network materials (CNMs), [Co2(S-man)2(bpy)3](NO3)2·guests (1S) and [Co2(R-man)2(bpy)3](NO3)2·guests (1R) based upon S-mendelic acid and R-mendelic acid were synthesized and characterized, respectively. The cationic networks contain 1D homochiral channels with the cross section of 8.0 Å × 8.0 Å. The chiral amphiphilic channel surfaces lined with hydrophilic nitrate anions and hydrophobic phenyl groups are capable for multiple interactions with guest species. Chiral resolution of 1-phenyl-1-propanol (PP) enantiomers was performed utilizing the homochiral porosity of 1S and 1R through different time period at different temperatures with/without additives. The mechanism for enantioselective separation of PP was fully investigated through single crystal structural analysis of guest exchanged 1S and 1R. Chiral resolution of PP revealed enhanced performance with additive, which can significantly improve the ee value from 32% to 60%.

Biotechnology of microalgae is a fast-growing field and several species have become targets for transgenic manipulation. Microalgae provide low-cost and scalable production platforms for manufacturing recombinant proteins and other high value products. However, the exploitation of microalgae as expression systems is restricted by the low yield of recombinant proteins and the limited availability of tools for the genetic manipulation of commercially important species. This thesis explores transgene instability and gene autoregulation as causes for low recombinant protein accumulation in the chloroplast of Chlamydomonas reinhardtii and describes the isolation of a mutant phytoene desaturase (PDS) gene which confers resistance to the herbicide norflurazon for future use as a selection marker for the marine microalga Dunaliella tertiolecta. Recombination between short dispersed DNA repeats (SDR) found in the chloroplast genome of C. reinhardtii was identified as a cause of transgene instability. The genes coding for β-glucuronidase (GUS) and peridinin-chlorophyll binding protein (PCP) were inserted in the chloroplast genome next to the atpB 3' UTR by homologous recombination. Recombination of a 30bp SDR located within the 3' UTR of atpB was identified as the cause of transgene excision in the transplastomic lines. Such transgene instability was tackled by replacing the 3' UTR of atpB with the rbcL 3' UTR from D. tertiolecta. Using this 3'UTR sequence from a different species produced a photosynthetic strain and prevented excision of the transgene by SDR recombination in all transfomants. Very low levels of recombinant GUS and PCP accumulated in chloroplast transformants when using the psbD 5' regulatory region to drive their expression. To address low levels of accumulation caused by regulatory pathways that inhibit transgene expression, I have engineered the chloroplast genome of a non-photosynthetic atpB mutant of C. reinhardtii by replacing the endogenous psbD promoter and 5'UTR with the promoter and 5'UTR of psbA. The engineered strain was subsequently transformed with the wildtype atpB and two different reporter genes driven by the psbD regulatory regions: gusA and kat, which code for GUS and the fluorescent protein Katushka respectively. Analysis of the transformants showed that accumulation of recombinant proteins in our engineered strain was 10 to 20 fold higher than in the nonengineered cells. Most of the selectable markers used in plants and algae are inefficient in Dunaliella, which is naturally resistant to many of the antibiotics used for the selection of transformants. Norflurazon inhibits PDS, an essential enzyme for carotenoid biosynthesis. Using forward genetics I have isolated, sequenced and characterised mutant PDS alleles conferring norflurazon resistance in D. tertiolecta. Independent mutations in pds, leading to substitutions R265C, S472L, S472F and L502F, all result in high resistance to norflurazon but differ in sensitivity to other bleaching herbicides. By mapping the four amino acid substitutions on 3D models of D. tertiolecta PDS I determined that R265C, S472L, S472F and L502F, cluster together in proximity to a Rossman-like domain and to aminoacids F128 and V469, previously reported to confer norflurazon resistance. This suggests that the mode of action of norflurazon is by competition with flavin adenine dinucleotide (FAD) for its binding site. A unique aspect of the R265C substitution is its negative cross-resistance to diflufenican and beflutamid which could be advantageous for its use as a positive/negative selection marker for transformation.

The sea surface microlayer is a millimeter-scale interfacial layer between the atmosphere and the ocean. A number of studies have suggested that there is a unique ecosystem for marine bacteria in the sea surface microlayer, but little information exists on the microbial community composition of this ecosystem due to sampling complexities. In this work, we present an improved method to sample and compare the bacterial diversity of the sea surface microlayer with that of subsurface water at the same site. Bacterial samples were collected from the sea surface microlayer with a sampling method, which minimized sample contamination from the research platform and the subsurface water. Sampling was conducted using a polycarbonate membrane filter to obtain the bacterial community structure at open water and coastal water sites in the Straits of Florida. The microlayer sampling was planned to coincide with synthetic aperture radar satellite overpasses (COSMO SkyMed), which capture a range of fine-scale features on the sea surface. The presence of surfactants affect the synthetic aperture radar imaging process because surfactants in the sea surface microlayer suppress short gravity-capillary ocean surface waves, thereby decreasing the backscatter and allowing the radar to detect surfactant-covered areas. Although sources of surfactants vary, certain marine bacteria are known to produce and transform surfactants, which suggest that these surfactant-related marine bacteria have an important biological influence on fine-scale synthetic aperture radar satellite imagery. Therefore, the comparison between synthetic aperture radar satellite images and in situ field samples may be used for interpreting and studying fine-scale features on the sea surface. The surfactant-associated bacterial composition of the sampling sites was determined using high-throughput, 454 pyrosequencing methods. A total of 61,663 sequences were analyzed and the results indicated the presence of surfactant-associated bacteria such as Moraxellaceae, Halomonadaceae, Enterobacteriaceae, Bacillaceae, and Nocardiaceae. By establishing these bacterial groups that influence the presence of surfactants, remote sensing techniques which involve monitoring the microlayer are expected to be enhanced and may provide additional information on the state of the upper ocean ecosystem.

Brinjal shoot and fruit borer (Leucinodes orbonalis Guenee) is a major limiting factor in commercial cultivation of eggplant in southeast Asia. Extensive use of pesticides as well as the conventional breeding methods have been ineffective in controlling the borer so there is a need for Integrated Pest Management (IPM) strategies for its control. Bacillus thuringiensis (Bt) is known to produce a variety of insecticidal crystal proteins toxic to lepidopteran, dipteran and coleopteran pests. The Cry2Aa protein has been found to be more toxic to brinjal shoot and fruit borer than Cry1Ab. My objective was to develop eggplant cultivars that express a codon-optimized cry2Aa gene, the sequence of which is based on that of an Indian isolate of Bt, with the eventual goal of producing fully resistant cultivars. The cry2Aa gene was modified for optimal expression in eggplant using the codon usage frequencies based on solanaceous sequences (eggplant, tomato and pepper). The GC content was increased from 34.3% in the native gene to 41.3% in the optimized gene, thus removing the AT-rich regions that are typical for Bt cry genes. Also, other mRNA destabilizing and hairpin forming structure sequences were removed. The gene was synthesized in four different parts with complementary restriction sites. A total of 152 oligonucleotides (oligos) was used to assemble the 1.9 kb gene using dual asymmetric (DA) and overlap extension (OE) PCR techniques. The individual parts were subsequently ligated using the complementary restriction sites and inserted into vector pCAMBIA 1302. Also, the transformation efficiency of 12 different eggplant cultivars was tested using plasmid pHB2892 to predict utility for transformation with the synthetic cry2Aa.
Master of Science

The work deals with design of transformation cells suitable for realization of higher orders frequency filters with possibility of cutoff frequency control. At first, there is a common description of frequency filters and active elements like current and voltage conveyors. Furthermore assumptions of cutoff frequency control are defined which result in a convenient characteristical equation. Phylosophy of synthetic elements DP , EP , DS , ES including a possibility of change of cutoff frequency is next in line. By exploitation of synthetic elements theory new circuit’s schemes of transformation cells are searched. The work continues with the choice of appropriate transformation cells for resulting circuit’s solutions of frequency filters with possibility of cutoff frequency control by using transfer coefficients of active elements or with help of passive elements. The work concludes with verification of its proper function based on a simulation executed in OrCAD and with practical implementation of choosen circuit’s solution.

and biological sources. Recent advances in decarboxylative activation has allowed for the application of these reagents as building-blocks in organic synthesis; presenting viable, green alternatives to traditional organometallic or organohalide reagents. This thesis focuses on the development of novel transition metal catalysed decarboxylations, and investigation into the mechanisms of these, and related transformations. In the first part of the thesis, an extensive overview of the latest Carboxylic acids are cheap, shelf-stable reagents readily available from several commercial and biological sources. Recent advances in decarboxylative activation has allowed for the application of these reagents as building-blocks in organic synthesis; presenting viable, green alternatives to traditional organometallic or organohalide reagents. This thesis focuses on the development of novel transition metal catalysed decarboxylations, and investigation into the mechanisms of these, and related transformations. In the first part of the thesis, an extensive overview of the latest decarboxylative methodologies is presented, with discussion of the mechanistic aspects of different metal-catalysed decarboxylations. This is followed by a mechanistic investigation into the silver-catalysed decarboxylation of benzoic acids. In this system, an ortho substituent is required to facilitate decarboxylation. Using DFT, kinetic studies and the Fujita-Nishioka LFER we were able to show that the ortho-effect is a combination of electronic and steric effects, contrary to previous reports. In the second part of the thesis a practical, mild and highly selective protocol for the mono-deuteration of a variety of (hetero)arenes is described. Ag-catalysis was shown to facilitate the deuterodecarboxylation of (hetero)aromatic carboxylic acids in D2O/DMSO. The last two parts of this thesis focus on the formation and activation of carbon-fluorine bonds. Organofluorine compounds are of great importance to the agrochemical and pharmaceutical industries; however, there are limited examples of selective C-F bond formation that do not require stoichiometric metals, harsh conditions or toxic reagents. Using transition metal catalysis, we investigated a fluorodecarboxylation methodology. Initially this was explored in aromatic systems; though no synthetically useful yields were realised. However, aliphatic carboxylic acids were successfully transformed under aqueous conditions. The developed protocol was exploited to access benzylic fluorides. Subsequently, we established unprecedented metal-free conditions to activate their C-F bonds towards nucleophilic displacement; presenting a novel, decarboxylative methodology to furnish carbon-carbon and carbon-heteroatom bonds.

The aim of this diploma thesis is to design active frequency filters based on passive RLC prototype. Three methods of the design of active filters and active functional blocks of electronic circuits working in current or mixed mode are used to this purpose. These blocks allow to process electrical signals with frequencies up to low tens of megahertz. In addition they feature for instance with high slew rate and low supply voltage power. Active high-pass and low-pass 2nd order filters are designed using simulation of inductor by active subcircuit method. Grounded and subsequently floating synthetic inductor is made with the current conveyors in the first case and with the current operational amplifiers with single input and differential output in the second case. This method advantage is relatively simple design and disadvantage is great quantity of active functional blocks. Active filters based on passive frequency ladder 3rd order filter while only one floating inductor is connected, are designed with circuit equation method. In the first design differential input / output current followers are used and in the second case current-differencing buffered amplifiers are used. This method benefits by smaller active blocks number and disadvantage is more complex design of the active filter. Active filter based on passive prototype of low-pass 3rd order filter with two floating inductors is designed with Bruton transformation method. Final active filter uses current operational amplifiers with single input and differential output which together with other passive elements replace frequency depending negative resistor, which arise after previous Bruton transform. This method usage is advantageous if the design consists of larger quantity of inductors and less number of capacitors. High-pass 2nd order filter is simulated by tolerance and parametrical analyses. Physical realisation utilising current feedback operational amplifier which substitute commercially hardly accessible current conveyors is subsequently made. Measurements of constructed active filter show that additional modifications, which allow better amplitude frequency characteristics conformity, are necessary.

Nitrile-containing natural products are rare in Nature, and there have been very few studies on the mechanisms by which they are synthesized and utilized. The biosynthesis of 7-deazapurine containing natural products is a unique case whereby both formation of a nitrile and its conversion to an amide are documented. The overall theme of this work is to interrogate the biosynthesis of the nitrile intermediate in the pathway and its subsequent hydration to an amide. The biosynthesis 7-cyano-7-deazaguanine (preQ₀), the key intermediate in the biosynthesis of the hypermodified base queuosine and the toyocamycin natural product, is accomplished by preQ₀ synthetase through a series of unprecedented reactions whereby the carboxylate moiety of the substrate, 7-carboxy-7-deazaguanine (CDG), is successively activated by adenylation, reacted with ammonia, and dehydrated to produce the nitrile. This one-enzyme synthesis of a nitrile is unique as the only other known route to nitriles proceeds through at least two enzymes. Nitrile hydratases are metalloenzymes that selectively hydrate nitriles to the amide and are used industrially to produce acrylamide and nicotinamide. These enzymes use a trivalent iron or cobalt complex comprised of two backbone amidate ligands and three cysteine thiolate ligands of which two are modified to the sulfenato and sulfinato form. This work describes aspects of a particular nitrile hydratase, toyocamycin nitrile hydratase (TNH). Whereas most nitrile hydratases are heterodimeric, TNH is heterotrimeric, and yet what was discovered is that only the subunit containing the active site metal complex is required for activity. This single subunit analog of the protein was used for single turnover assays in ¹⁸O-labeled water to show with high resolution mass spectrometry that the source of the product amide oxygen is actually the enzyme itself and likely the sulfenato ligand oxygen acting as a nucleophile. The mechanism of the active site complex synthesis is described showing that this is self-catalytic in the presence of cobalt(II) and molecular oxygen.

Simulator models are a type of stochastic model that is often used to approximate a real-life process. Current statistical methods for simulator models are computationally intensive, relying on a large number of model simulations. In this thesis, we develop new, efficient and flexible statistical methods that can be used for complex statistical models, such as simulator models. The new methods are theoretically justified and applied to a variety of simulated and real-life modelling scenarios from ecology and biology.

Le but de cette thèse était de conduire des recherches sur la synthèse et transformation expressive de voix chantée, en vue de pouvoir développer un synthétiseur de haute qualité capable de générer automatiquement un chant naturel et expressif à partir d’une partition et d’un texte donnés. 3 directions de recherches principales peuvent être identifiées: les méthodes de modélisation du signal afin de générer automatiquement une voix intelligible et naturelle à partir d’un texte donné; le contrôle de la synthèse, afin de produire une interprétation d’une partition donnée tout en transmettant une certaine expressivité liée à un style de chant spécifique; la transformation du signal vocal afin de le rendre plus naturel et plus expressif, en faisant varier le timbre en adéquation avec la hauteur, l’intensité et la qualité vocale. Cette thèse apporte diverses contributions dans chacune de ces 3 directions. Tout d’abord, un système de synthèse complet a été développé, basé sur la concaténation de diphones. L’architecture modulaire de ce système permet d’intégrer et de comparer différent modèles de signaux. Ensuite, la question du contrôle est abordée, comprenant la génération automatique de la f0, de l’intensité, et des durées des phonèmes. La modélisation de styles de chant spécifiques a également été abordée par l’apprentissage des variations expressives des paramètres de contrôle modélisés à partir d’enregistrements commerciaux de chanteurs célèbres. Enfin, des investigations sur des transformations expressives du timbre liées à l'intensité et à la raucité vocale ont été menées, en vue d'une intégration future dans notre synthétiseur
This thesis aimed at conducting research on the synthesis and expressive transformations of the singing voice, towards the development of a high-quality synthesizer that can generate a natural and expressive singing voice automatically from a given score and lyrics. Mainly 3 research directions can be identified: the methods for modelling the voice signal to automatically generate an intelligible and natural-sounding voice according to the given lyrics; the control of the synthesis to render an adequate interpretation of a given score while conveying some expressivity related to a specific singing style; the transformation of the voice signal to improve its naturalness and add expressivity by varying the timbre adequately according to the pitch, intensity and voice quality. This thesis provides some contributions in each of those 3 directions. First, a fully-functional synthesis system has been developed, based on diphones concatenations. The modular architecture of this system allows to integrate and compare different signal modeling approaches. Then, the question of the control is addressed, encompassing the automatic generation of the f0, intensity, and phonemes durations. The modeling of specific singing styles has also been addressed by learning the expressive variations of the modeled control parameters on commercial recordings of famous French singers. Finally, some investigations on expressive timbre transformations have been conducted, for a future integration into our synthesizer. This mainly concerns methods related to intensity transformation, considering the effects of both the glottal source and vocal tract, and the modeling of vocal roughness

The present PhD thesis focuses on two main classes of semiconductor colloidal nanocrystals, i.e. lead halide perovskite and copper chalcogenides. The former class of semiconductor NCs are promising materials for many high performance optoelectronics applications, as they exhibit a tunable band gap in the range of 1.4 to 2.9 eV and an efficient photoluminescence characterized by narrow emission linewidths and have been explored the most in the last years. Following the standard hot injection based synthesis and selecting a combination of short chain acid (octanoic acid or hexanoic acid) together with alkyl amines (octylamine and oleylamine) we prepared strongly fluorescent CsPbBr3 perovskite nanowires with tuneable width, in the range from 20 nm (exhibiting no quantum confinement, hence emitting in the green) to 3 nm (in the strong quantum-confinement regime, emitting in the blue) for the first time. However the main limitation of the colloidal synthesis protocols that was followed in aforementioned case including the ligand assisted reprecipitation routes which is the second most frequently used method for preparation of LHPs, is that they employ PbX2 (X= Cl, Br, or I) salts as both lead and halide precursors which consequently limit the precise tunability of the amount of reaction species such as metals or halides precursors and are not applicable to entire family of APbX3 (A=FA, MA and Cs; X=Cl, Br, I). To overcome this issue we developed benzoyl halide based colloidal synthesis route i.e broadly applicable to the entire family of LHP NCs and not only ensures the independent tunability of reaction precursors but also maintain the overall integrity of the NCs such as phase purity and high PLQY. Despite the significant advances in synthesis procedures, the control over size monodispersity, shape and phase purity remains another long standing challenge. This is in fact due to the tendency of primary alkyl amine in the form of alkylammonium ions that could compete with Cs+ ions and leads to the anisotropic growth such as NPLs or their use in excess permotes the Pb-depleted Cs4PbX6 phases. We develop here a strategy to achieve size, shape and phase pure CsPbBr3 nanocubes by substituting primary alkyl amines with secondary alkyl amines. We attributed this excellent control over the shape and phase purity to the inability of secondary amines to find the right steric conditions at the surface of the nanocrystals which consequently limits the formation of low dimensional structures. The shape purity and narrow size distribution leads to their ease of self-assembly in superlattices reaching up to 50 microns in lateral dimensions, which are the largest dimensions reported to date for superlattices of LHP NCs. The second class of materials studied here, i.e. copper chalcogenides, are mainly attractive due to their tunable composition via post synthesis chemical transformations, plasmonic properties, low toxicity and environmental friendliness. Taking the advantage of colloidal synthesis and using Cu2S as a template we develop a strategy to obtain novel AuCuS-Cu2S heterostructure through cation exchange, which cannot be realized through conventional synthesis approaches. We further investigated the stability of Cu2S NCs with different dimensionalities and their thermal evolution subsequent to the metal decoration. Interestingly the presence of additional metallic NCs, such as Au and Pt not only improves their thermal stability but also leads to the formation of bi-metallic alloys semiconductor heterostructure.

This thesis describes the synthesis of highly substituted geminally difluorinated cyclohexenols based on Diels-Alder reactions between a difluorinated dienophile and furans (furan, 2-methyl and 2,3-dimenthyl) in presence of stannic chloride. The dienophile was synthesised in two different ways: a literature procedure, starting from the commercially available trifluoroethanol and new route involving an organometallic reagent.;Sulphur electrophile chemistry applied to the endo and exo cycloadducts gained stereo- and regio- control completely. Full protection of the free hydroxyl group was required before two different ring-opening strategies could be implemented: a carbanionic and a reductive method were attempted to ring-open the 7-oxabicyclo[2.2.1]heptenyl system. The scope of these methodologies was investigated with furan, 2-methyl and 2,3-dimethyl furan cycloadducts. When a stoichiometric amount of the Lewis acid (stannic chloride) was used in the cycloaddition with furan, an interesting bicyclic carbonate was afforded. To understand the mechanism of the reaction and the role of the Lewis acid in binding the cycloadduct, crystals were grown and an interesting complex was obtained.;Useful vinyl bromide products (endo and carbonate) were generated by cycloaddition between the difluorinated alkenoate and 3-bromofuran in the presence of 1.0 equivalents of tin tetrachloride. Suzuki coupling reaction of endoadduct with phenylboronic acid was carried out under Leadbeater's aqueous microwave conditions. Finally, dihydroxylation of the ring opened products and deprotections of the protected hydroxyl groups delivered the required gem- difluorinated polyhydroxy cyclohexane allowing for the first time the synthesis of cyclitol analogues via Diels-Alder reaction.

Due to the rapidly increasing complexity in hardware designs and competitive time to market trends in the industry, there is an inherent need to move designs to a higher level of abstraction. Behavioral Synthesis is the process of automatically compiling such Electronic System Level (ESL) designs written in high-level languages such as C, C++ or SystemC into Register-Transfer Level (RTL) implementation in hardware description languages such as Verilog or VHDL. However, the adoption of this flow is dependent on designers' faith in the correctness of behavioral synthesis tools. Loop pipelining is a critical transformation employed in behavioral synthesis process, and ubiquitous in commercial and academic behavioral synthesis tools. It improves the throughput and reduces the latency of the synthesized hardware. It is complex and error-prone, and a small bug can result in faulty hardware with expensive ramifications. Therefore, it is critical to certify the loop pipelining transformation so that designers can trust the behaviorally synthesized pipelined designs. Certifying a loop pipelining transformation is however, a major research challenge because there is a huge semantic gap between the input sequential design and the output pipelined implementation, making it infeasible to verify their equivalence with automated sequential equivalence checking (SEC) techniques. Complex loop pipelining transformations can be certified by a combination of theorem proving and SEC: (1) creating a certified pipelining algorithm which generates a reference pipeline model by exploiting pipeline generation information from the synthesis flow (e.g. the iteration interval of a generated pipeline) and (2) conduct SEC between the synthesized pipeline and this reference model. However, a key and arguably, the most complex component of this approach is the development of a formal, mechanically verifiable loop pipelining algorithm. We show how to systematically construct such an algorithm, and carry out its verification using the ACL2 theorem prover. We propose a framework of certified pipelining primitives which are essential for designing pipelining algorithms. Using our framework, we build a certified loop pipelining algorithm. We also propose a key invariant in certifying this algorithm, which links sequential loops with their pipelined counterparts. This is unlike other invariants that have been used in proofs of microprocessor pipelines so far. This dissertation provides a framework for creating certified pipelining algorithms utilizing a mechanical theorem prover. Using this framework, we have developed a certified loop pipelining algorithm. This certified algorithm is essential in the overall approach to certify behaviorally synthesized pipelined designs. We demonstrate the scalability and robustness of our algorithm on several ESL designs across various domains.

The work described herein is concerned with Lewis acidic triarylboranes for synthetic and catalytic transformations where the influence of different substitution pattern and substituents were crucial in determining the resulting reactivity. Chapter 1 will provide a general introduction into acidity and will lay the theoretical foundation for the ensuing chapters. Chapter 2 introduces the boranes utilised in this work and will give literature examples describing reactivities of the currently known boranes. Besides providing several crystal structures, this chapter will discuss the Lewis acidity of these boranes. Chapter 3 explores the hydroboration of imines catalysed by tris[3,5-bis(trifluoromethyl)-phenyl]borane. By testing a variety of various Lewis acids further insight into the mechanism of this hydroboration is gained. Chapter 4 further investigates borane imine adducts and the impact of the adduct formation on the electronic transitions within the imines. The photoactive adducts are then explored as vapochromic materials towards various solvent vapours. Chapter 5 focuses on the formation of pyrones, dihydropyrones and isocoumarins catalysed by tris(pentafluorophenyl)borane. A cross over experiment reveals the nature of this cyclisation reaction. Chapter 6 investigates the radical character of a frustrated Lewis pairs and their resulting reactivity. A novel protocol for a radical Heck-type reaction is provided and the mechanism was investigated. Finally, Chapter 7 will show the ambiguity between 1,1-carboboration and 1,3-haloboration in the reaction of propargyl esters with dichlorophenylborane.

The use of gold in organic chemistry is a relatively recent occurrence. In addition to being previously considered too expensive, it was also believed to be chemically inert. Soon after the early reports indicating its rich reactivity, the number of reports on chemical transformations involving gold sky rocketed. One such report by Toste and coworkers demonstrated the intramolecular addition of silyl enol ether onto Au(I) activated alkynes, resulting in a 5-exo dig cyclization. The first part (Chapter 1) of this thesis discusses the development of a Au(I) catalyzed polycyclization reaction inspired by this transformation. The reaction demonstrated the ability of Au(I) to successfully catalyze the formation of multiple C-C bonds and resulted in the synthesis of benzothiophenes, benzofurans, carbazoles and hydrindene. With the current resurgence of photochemical transformations being reported in literature, various opportunities for the use of Au(I) complexes arose. The substantial relativistic effect observed in gold which make it a good soft Lewis acid also has a significant influence on the redox potential of this metal. Chapter 3 of this thesis discusses the development of a Au(I) photocatalyzed process which benefits from having both a strong oxidation and reduction potential for the reduction of carbon-halide bonds. Radical reductions and cyclizations were accessed with the use of polynuclear Au(I) photocatalysts. In depth analysis of catalytically active Au(I) complexes helped elucidate the mechanism by which this photochemical reaction occurs. This part (Chapter 4) also covers serendipitously discovered uncatalyzed photochemical transformations derived from our work with gold. The halogenation reaction of primary alcohols was successfully achieved and a combination of our developed methods resulted in an efficient dehydroxylation protocol.

Lignin is a complex, interlinked, non-repeating, heterogeneous bio-polymer found in wood which consists of phenylpropane subunits. The phenolic monomers of lignin are linked via various ether and carbon-carbon bonds. It is the second most abundant biopolymer after cellulose, accounting for 15-30 % of biomass and it has the potential to be a renewable source of small aromatic feedstock molecules. The synthesis of lignin model compounds plays an important role in both the elucidation of lignin's structure and in modelling the conditions required for the production of valuable feedstock molecules from lignin depolymerisation. The aim of the research presented in this thesis has been to provide an efficient route to multi-gram quantities of lignin model compounds which are more representative of lignin than the low molecular weight models typically employed in previously published work. The syntheses of several hexameric lignin models as well as an octamer, all of which contain three of the most common linkages in the native polymer have been carried out. The synthetic methodology used improves upon existing methods of preparing higher molecular weight lignin models in both overall yield and efficiency as well as practically on a multi-gram scale. Several of these compounds were then subjected to published procedures aimed at the transformation of lignin and model compounds into added value fine chemical intermediates. Extensive analysis of the major products was performed leading to some preliminary mechanistic insights into lignin oxidative and reductive depolymerisation chemistry.

The work presented in this thesis involves new transformations of azacycles, focusing on the introduction of functionality α-to N. α-C-H functionalisation on an azetidine has been a long-standing challenge, with N-protecting/activating groups that work well in the higher and lower azacyclic systems not viable. A recent breakthrough in the Hodgson group showed the rarely used N-thiopivaloyl group was effective for α-deprotonation– electrophile trapping on azetidines, but was not without limitations concerning harsh removal conditions and scope for further substitutions. This thesis describes efforts to overcome these issues by development of a new protecting/activating group for N, t-butoxythiocarbonyl (Botc).

Sampling, as a musical or synthesis technique, is a way to reuse recorded musical expressions. In this dissertation, several ways to expand sampling synthesis are explored, especially mosaicing synthesis, which imitates target signals by transforming and compositing source sounds, in the manner of a mosaic made of broken tile. One branch of extension consists of the automatic control of sound transformations towards targets defined in a perceptual space. The approach chosen uses models that predict how the input sound will be transformed as a function of the selected parameters. In one setting, the models are known, and numerical search can be used to find sufficient parameters; in the other, they are unknown and must be learned from data. Another branch focuses on the sampling itself. By mixing multiple sounds at once, perhaps it is possible to make better imitations, e.g. in terms of the harmony of the target. However, using mixtures leads to new computational problems, especially if properties like continuity, important to high quality sampling synthesis, are to be preserved. A new mosaicing synthesizer is presented which incorporates all of these elements: supporting automatic control of sound transformations using models, mixtures supported by perceptually relevant harmony and timbre descriptors, and preservation of continuity of the sampling context and transformation parameters. Using listening tests, the proposed hybrid algorithm was compared against classic and contemporary algorithms, and the hybrid algorithm performed well on a variety of quality measures.
El mostreig, com a tècnica musical o de síntesi, és una manera de reutilitzar expressions musicals enregistrades. En aquesta dissertació s’exploren estratègies d’ampliar la síntesi de mostreig, sobretot la síntesi de “mosaicing”. Aquesta última tracta d’imitar un senyal objectiu a partir d’un conjunt de senyals font, transformant i ordenant aquests senyals en el temps, de la mateixa manera que es faria un mosaic amb rajoles trencades. Una d’aquestes ampliacions de síntesi consisteix en el control automàtic de transformacions de so cap a objectius definits a l’espai perceptiu. L’estratègia elegida utilitza models que prediuen com es transformarà el so d’entrada en funció d’uns paràmetres seleccionats. En un cas, els models són coneguts, i cerques númeriques es poden fer servir per trobar paràmetres suficients; en l’altre, els models són desconeguts i s’han d’aprendre a partir de les dades. Una altra ampliació es centra en el mostreig en si. Mesclant múltiples sons a la vegada, potser és possible fer millors imitacions, més específicament millorar l’harmonia del resultat, entre d’altres. Tot i així, utilitzar múltiples mescles crea nous problemes computacionals, especialment si propietats com la continuïtat, important per a la síntesis de mostreig d’alta qualitat, han de ser preservades. En aquesta tesi es presenta un nou sintetitzador mosaicing que incorpora tots aquests elements: control automàtic de transformacions de so fent servir models, mescles a partir de descriptors d’harmonia i timbre perceptuals, i preservació de la continuïtat del context de mostreig i dels paràmetres de transformació. Fent servir proves d’escolta, l’algorisme híbrid proposat va ser comparat amb algorismes clàssics i contemporanis: l’algorisme híbrid va donar resultats positius a una varietat de mesures de qualitat.

This thesis is concerned with the synthesis of allenic compounds and their gold-catalyzed isomerization reactions. Its general aim is the development of new reaction methodologies within these topics and the work has been published in two separate articles. After an introductory chapter (covering relevant literature upto 2010) three separate projects are discussed: 1. Development of tandem enzyme/gold-catalyzed reaction where lipase-catalyzed kinetic resolution of alpha-allenic acetates [R1 2CCCH(CHR2OAc)] (R1,R2 = alkyl) leads to the formation of alpha-hydroxyallenes with 86-99% ee and this transformation is followed by the cycloisomerization of the alpha-hydroxyallenes to the corresponding 2,5-dihydrofurans in a one-pot reaction. It is found that the two transformations work well in one pot except in the case where R2 is branched, which are not hydrolysed. 2. A new approach is developed for the synthesis of allenyl acetates [Ar(R1)CCCH(O2CR2)] (R1 = alkyl, R2 = Me, Ph, t-Bu) using cuprate-mediated SN2’nucleophilic substitution to propargylic dicarboxylates. The reaction was successfull with a range of substrates (11 examples). Investigation on a catalytic variant for the synthesis of the above allenyl acetates. Nickel-catalyzed SN2’ nucleophilic substitution to propargylic dicarboxylates gives the highest selectivity of the desired allenic products but the transformation is not very high-yielding. Attempts towards an asymmetric reaction are thwarted by low enantioselectivities (<22% ee). 3. Comparing the reactivity of propargylic acetates and allenyl acetates (prepared in Sections 2-3) in the gold-catalyzed synthesis of indenes. It was discovered that the allenyl acetates prepared earlier yield indenes with up to quantitative yields and high chemoselectivity, whereas propargylic acetates with terminal a alkyne group only yielded a mixture of cyclization and elimination products.

Thesis advisor: James P. Morken
This dissertation details the development of several enantioselective or stereospecific transformations involving organoboronic esters. Chapter one will introduce electrophile-induced boronate rearrangements which underpins much of the reactivity that will be discussed in subsequent chapters. In chapter two the conjunctive cross-coupling reaction is presented. Its development and application to the synthesis of non-racemic boronic esters, along with its application to the synthesis of enantioenriched allylic boronic esters, will be discussed. In chapter three the cross-coupling of geminal bis(boronic) esters is introduced and the development of a method to employ them in cross-coupling with alkenyl bromides, affording enantioenriched substituted allylic boronic esters is outlined. In chapter four we highlight the utility of allylic boronic esters, and detail the development of a cross-coupling reaction that involves the use of these substrates and halide electrophiles to furnish enantiomerically enriched products containing all carbon quaternary stereocenters. Finally, in chapter five we describe the development of a metalfree amination reaction of organoboron compounds, which is able to deliver otherwise difficult-to-access enantiomerically enriched α-tertiary amines
Thesis (PhD) — Boston College, 2018
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Chemistry

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Capes
Ferramentas como ErrorProne, ReSharper e PMD ajudam os programadores a detectar e/ou remover automaticamente vários padrões de códigos suspeitos, possíveis bugs ou estilo de código incorreto. Essas regras podem ser expressas como quick fixes que detectam e reescrevem padrões de código indesejados. No entanto, estender seus catálogos de regras é complexo e demorado. Nesse contexto, os programadores podem querer executar uma edição repetitiva automaticamente para melhorar sua produtividade, mas as ferramentas disponíveis não a suportam. Além disso, os projetistas de ferramentas podem querer identificar regras úteis para automatizarem. Fenômeno semelhante ocorre em sistemas de tutoria inteligente, onde os instrutores escrevem transformações complicadas que descrevem "falhas comuns" para consertar submissões semelhantes de estudantes a tarefas de programação. Nesta tese, apresentamos duas técnicas. REFAZER, uma técnica para gerar automaticamente transformações de programa. Também propomos REVISAR, nossa técnica para aprender quick fixes em repositórios. Nós instanciamos e avaliamos REFAZER em dois domínios. Primeiro, dados exemplos de edições de código dos alunos para corrigir submissões de tarefas incorretas, aprendemos transformações para corrigir envios de outros alunos com falhas semelhantes. Em nossa avaliação em quatro tarefas de programação de setecentos e vinte alunos, nossa técnica ajudou a corrigir submissões incorretas para 87% dos alunos. No segundo domínio, usamos edições de código repetitivas aplicadas por desenvolvedores ao mesmo projeto para sintetizar a transformação de programa que aplica essas edições a outros locais no código. Em nossa avaliação em 56 cenários de edições repetitivas de três grandes projetos de código aberto em C#, REFAZER aprendeu a transformação pretendida em 84% dos casos e usou apenas 2.9 exemplos em média. Para avaliar REVISAR, selecionamos 9 projetos e REVISAR aprendeu 920 transformações entre projetos. Atuamos como projetistas de ferramentas, inspecionamos as 381 transformações mais comuns e classificamos 32 como quick fixes. Para avaliar a qualidade das quick fixes, realizamos uma survey com 164 programadores de 124 projetos, com os 10 quick fixes que apareceram em mais projetos. Os programadores suportaram 9 (90%) quick fixes. Enviamos 20 pull requests aplicando quick fixes em 9 projetos e, no momento da escrita, os programadores apoiaram 17 (85%) e aceitaram 10 delas.
Tools such as ErrorProne, ReSharper, and PMD help programmers by automatically detecting and/or removing several suspicious code patterns, potential bugs, or instances of bad code style. These rules could be expressed as quick fixes that detect and rewrite unwanted code patterns. However, extending their catalogs of rules is complex and time-consuming. In this context, programmers may want to perform a repetitive edit into their code automatically to improve their productivity, but available tools do not support it. In addition, tool designers may want to identify rules helpful to be automated. A similar phenomenon appears in intelligent tutoring systems where instructors have to write cumbersome code transformations that describe “common faults” to fix similar student submissions to programming assignments. In this thesis, we present two techniques. REFAZER, a technique for automatically generating program transformations. We also propose REVISAR, our technique for learning quick fixes from code repositories. We instantiate and evaluate REFAZER in two domains. First, given examples of code edits used by students to fix incorrect programming assignment submissions, we learn program transformations that can fix other students’ submissions with similar faults. In our evaluation conducted on four programming tasks performed by seven hundred and twenty students, our technique helped to fix incorrect submissions for 87% of the students. In the second domain, we use repetitive code edits applied by developers to the same project to synthesize a program transformation that applies these edits to other locations in the code. In our evaluation conducted on 56 scenarios of repetitive edits taken from three large C# open-source projects, REFAZER learns the intended program transformation in 84% of the cases and using only 2.9 examples on average. To evaluate REVISAR, we select 9 projects, and REVISAR learns 920 transformations across projects. We acted as tool designers, inspected the most common 381 transformations and classified 32 as quick fixes. To assess the quality of the quick fixes, we performed a survey with 164 programmers from 124 projects, showing the 10 quick fixes that appeared in most projects. Programmers supported 9 (90%) quick fixes. We submitted 20 pull requests applying our quick fixes to 9 projects and, at the time of the writing, programmers supported 17 (85%) and accepted 10 of them.