In this thesis we exploit piano acoustics to automatically transcribe piano recordings into a symbolic representation: the pitch and timing of each detected note. To do so we use approaches based on non-negative matrix factorisation (NMF). To motivate the main contributions of this thesis, we provide two preparatory studies: a study of using a deterministic annealing EM algorithm in a matrix factorisation-based system, and a study of decay patterns of partials in real-word piano tones. Based on these studies, we propose two generative NMF-based models which explicitly model different piano acoustical features. The first is an attack/decay model, that takes into account the time-varying timbre and decaying energy of piano sounds. The system divides a piano note into percussive attack and harmonic decay stages, and separately models the two parts using two sets of templates and amplitude envelopes. The two parts are coupled by the note activations. We simplify the decay envelope by an exponentially decaying function. The proposed method improves the performance of supervised piano transcription. The second model aims at using the spectral width of partials as an independent indicator of the duration of piano notes. Each partial is represented by a Gaussian function, with the spectral width indicated by the standard deviation. The spectral width is large in the attack part, but gradually decreases to a stable value and remains constant in the decay part. The model provides a new aspect to understand the time-varying timbre of piano notes, but furtherinvestigation is needed to use it effectively to improve piano transcription. We demonstrate the utility of the proposed systems in piano music transcription and analysis. Results show that explicitly modelling piano acoustical features, especially temporal features, can improve the transcription performance.

The performance of peristaltic pumps is mainly governed by their tubing or hose materials. Research and development in this area is therefore very important for peristaltic pump manufacturers to keep in front of the competition and to open up new applications to enable further market penetration. Another aspect of this is of course price; performance and cost have to be in balance. As an approach to fabricate a new tube material, the field of negative Poisson's ratio (or: auxetic) materials is explored. The combined deformations of tensile, compression and shear in a peristaltic pump tube may well benefit from the specific characteristics of auxetic materials. Materials can be designed to keep their dimensions constant in directions perpendicular to an applied load. This is referred to as “auxetic balancing”. Finite element modelling shows that lowering the Poisson's ratio will rapidly decrease the maximum stresses in the cross-section of an occluded tube. Optimum values for the Poisson's ratio are found to be between −0.1 and +0.1, preferentially being 0. The re-entrant honeycomb structure is selected for initial trials, but manufacturing of this structure at the desired dimension proved to be too difficult at this time. Instead, electrospun nanofibre membranes are selected as the reinforcement structure. A liquid silicone elastomer is used as the matrix material. Key characteristics for the new material are derived from baseline test results on existing tubing. Laminates are manufactured from electrospun nylon6 nanofibre membranes coated with a liquid silicone rubber. Compression moulding is used to cure the nylon6-silicone rubber laminate, to give two effects: it ensures impregnation of the membrane and the compression deforms the nanofibre structure in such a way that it will become auxetic through-the-thickness. Flat sheet laminates of 2 mm thickness are manufactured with 14 layers of reinforcement. A reinforcing effect and substantial lowering of the through-the-thickness Poisson's ratio is observed for the laminates at low strains. At higher strains (>50%) the effect of the reinforcement diminishes and the Poisson's ratio of the laminate and pure silicone rubber equalises. Finally, tubular laminates are manufactured and the resulting tubes are tested in a peristaltic pump with some promising results (>1 million occlusions before failure). Tube performance is not yet at the required level, but with further optimisation of the laminating process, mould design and (post-)curing large steps forward can be made.

The rise of antimicrobial resistance (AMR) has culminated in the most pressing problem in modern medicine. The situation is most acute with regards to the management of multi- drug resistant Gram-negative infections (MDRGNB) with common infections increasingly untreatable due to rapidly dwindling therapeutic options. A solution to the problem of AMR is unlikely to be easily found, but revisiting and re-purposing existing antimicrobials is a viable approach in the medium term. This study investigated the use of unorthodox antimicrobial combination therapies for the treatment of MDRGNB, with particular focus on agents of last resort. A systematic review of clinical studies highlighted the potential for polymyxin (colistin) combination therapies (e.g. colistin-rifampicin, colistin-carbapenems), although this could not be supported in a formal meta-analysis. A systematic approach for screening MDRAB for susceptibility to novel colistin combinations using multiple methods was employed and uncovered a number that were more potent than those previously identfied. The most potent combination that was consistently identified was colistin when combined with fusidic acid, despite this drug having no useful activity against MDRGNB on its own. The combination was further evaluated in static time-kill assays against a range of Gram-negative pathogens with defined resistance mechanisms, including to polymyxins and using invertebrate (Galleria mellonella) and murine models of MDRGNB infection. Colistin and fusidic acid combination therapy was subsequently used to successfully treat a case of ventilator-associated pneumonia due to MDR A. baumannii. This work highlights how older drugs can be re-purposed to tackle the problem of AMR using a precision medicine approach. Further studies to elucidate the mechanism of action of the colistin- fusidic acid combination and a formal clinical trial are warranted to investigate the potential utility of this combination in the treatment of MDRGNB with the expressed goal of bridging the current antimicrobial development gap.

Acidithiobacillus ferrooxidans is a gram-negative bacterium that is able to extract energy from oxidation of Fe²⁺ and reduced sulfur compounds and fix carbon dioxide from atmosphere. The facts that A. ferrooxidans thrives in acidic pH (~2), fixes carbon dioxide from the atmosphere and oxidizes Fe²⁺ for energy make it a good candidate in many industrial applications such as electrofuels and biomining. Electrofuels is a new type of bioprocess, which aims to store electrical energy, such as solar power, in the form of chemical bonds in the liquid fuels. Unlike traditional biofuels made from agricultural feedstocks, electrofuels bypass the inefficient photosynthesis process and thus have potentially higher photon-to-fuel efficiency than traditional biofuels. This thesis covers the development of a novel bioprocess involving A. ferrooxidans to make electrofuels, i.e. isobutyric acid and heptadecane. There are four major steps: characterization of wild-type cells, engineering of medium for improved electrochemical performance, genetic modification of A. ferrooxidans and optimization of operating conditions to enhance biofuel production. Each is addressed in one of the chapters in this thesis. In addition, applications of A. ferrooxidans in biomining processes will be briefly discussed. An economic analysis of various applications including electrofuels and biomining is also presented. Wild-type A. ferrooxidans were first characterized in both batch and continuous cultures. A modified 9-K medium suggested by American Type Culture Collection (ATCC) was used as a starting point which has 72 mM Fe²⁺ at pH 1.8. The Fe²⁺ concentration and pH were varied in the experiments to assess their impacts on growth rate, cell yield (g cells/g Fe²⁺) and maintenance (energy used to keep cell viability). Citrate was added to the growth medium to dissolve precipitates which can be problematic in a continuous operation. It was found out that cells exhibited higher cell yield (g cells/g Fe²⁺) and lower maintenance with higher pH and addition of citrate. This indicates that cells grow in a more energy-efficient manner at such conditions since cells spend less energy in maintenance and more energy in biomass formation. Next the growth medium containing 72 mM Fe³⁺ and 70 mM citrate at pH 2.2 was explored during the electrochemical reduction of Fe³⁺. It turned out that electrochemical reduction of Fe³+ could not be carried out effectively due to a low electrolyte conductivity and low energy density of the medium. Citrate was also found to negative affect electrochemical performance due to a strong complexation with Fe³⁺. The conductivity was improved by adding 500 mM Mg²⁺ to the medium. Vanadium was used as an alternative redox mediator that has a much better solubility than Fe³⁺ to improve the energy density. Genetic modification was achieved by introducing genes from two foreign pathways i.e. valine synthesis and fatty acid synthesis into A. ferrooxidans to enable cells to produce either isobutyric acid (IBA) or heptadecane. Transformed cells were characterized based on the findings in wild-type cells. Isobutyric acid production was found to increase with increasing pH and Fe²⁺ concentration and addition of citrate. Further optimization of the growth medium was done by increasing Fe²⁺ to 288 mM, holding pH at 2.2 and using gluconate as the iron chelator instead of citrate. An economic analysis was performed on the electrofuel process and applications of genetically modified A. ferrooxidans in copper biomining processes. At electricity prices of $0.05/kWh, further improvement in biological efficiency needs to be achieved before the electrofuel process may become economically viable. The use of genetically modified cells in copper biomining process could open new opportunities to co-produce valuable chemicals and copper from the reduced material associated with the copper ores. The chemicals co-produced during copper processing could be sold for additional revenue or used on-site.

LITERATURE REVIEW: A systematic review of the associations between effortful control, repetitive negative thinking and depression in adolescence. ABSTRACT: Background: Repetitive negative thinking (RNT) and the self-regulatory temperament, effortful control (EC), have been found to be important risk factors for the development of depressive symptoms. Furthermore, adolescence has been found to be a period of increased risk for developing depressive symptoms. The relationships between these risk pathways are not well understood during this period of development. Objective: This systematic review aimed to evaluate the literature exploring the relationships RNT and EC have in accounting for depressive symptoms in adolescents. In particular, whether RNT and EC are associated with depressive symptoms, and whether EC moderates the effects of RNT on depressive symptoms. Methods: Three databases and key journals were searched for studies measuring EC, RNT and depressive symptoms in 10-20 year olds. Study selection was undertaken by applying inclusion and exclusion criteria. The methodological quality of the included studies was assessed using a validated checklist. Inter-rater reliability was calculated for a random subsample of the search. Results: Thirteen studies were selected for inclusion. There was evidence indicating that RNT was correlated with depressive symptoms both concurrently and prospectively. The evidence for a relationship between lower EC and higher levels of depressive symptoms was mixed. High quality studies concluded that EC and depressive symptoms are associated concurrently, but not over time. There is evidence that lower EC predicts RNT over time, and even spanning over childhood. Some evidence was found for EC as a moderator between RNT and depressive symptoms and this was also found when the relationship was prospective. Conclusions: Whilst the reviewed literature had many strengths, there were large differences in how EC in particular, was measured. This resulted in a challenge synthesising the results and making clear conclusions. Future research would benefit from considering self-report and behavioural measures, and recognising the potential impact of stressful life events. EMPIRICAL PAPER: Investigating associations between repetitive negative thinking, stress, and effortful control, and the development and maintenance of depression in adolescence: A follow-up study. ABSTRACT: Background: Adolescence is a period of increased vulnerability for depressive symptoms (Twenge & Nolen-Hoeksema, 2002). Given the impact of emotional disorders on an individual, it is important to understand risk factors, and conversely, protective factors to inform effective interventions. Repetitive negative thinking (RNT) and the self-regulatory temperament, effortful control (EC), have been found to be important risk factors for the development of depressive symptoms and require further exploration in adolescence. Objective: This study investigated whether RNT predicted changes in later depressive symptoms, and if so, whether this change was moderated by EC. The study examined these associations during emotional reactivity to a stressor (exams), and emotional recovery following the stressor. Methods: Two samples with similar designs and measures were combined in this study. Two-hundred-and-fifty-five females completed Baseline questionnaires measuring life events, RNT, EC, and depressive symptoms. One-hundred-and-ninety-nine participants were followed up prior to their exams (Pre-exam), and 115 participants were followed up after their exams (Post-exam). Results: The study first examined emotional reactivity to stress, finding that contrary to the literature, RNT did not predict depressive symptoms in response to stress, when controlling for Baseline depressive symptoms. EC did not significantly interact with RNT in predicting depressive symptoms. However, RNT was associated with emotional recovery from stress: RNT predicted levels of depressive symptoms following exams, when controlling for Pre-exam depressive symptoms. Furthermore, EC moderated this relationship, however contrary to the literature and predictions, this was not in the expected direction, with high levels of EC associated with high levels of depressive symptoms. Conclusions: These findings suggest that despite the strengths of the study design, including a large sample at Baseline and follow up over a period of stress, hypothesized associations were not found during emotional reactivity to stress, but hypothesized associations were found during emotional recovery from stress. Recommendations are made for future studies, including recruiting sufficient number of males to the study.

by Chin Miu Ling, Nathalie. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1996. / Includes bibliographical references (leaves 130-143). / ABSTRACT --- p.i / ACKNOWLEDGEMENTS --- p.iii / LIST OF TABLES --- p.vii / LIST OF FIGURES --- p.x / INTRODUCTION --- p.1 / Chapter A --- Aminoglycosides --- p.1 / Chapter 1 --- Structure --- p.1 / Chapter 2 --- Classification --- p.1 / Chapter 3 --- Mode of action --- p.2 / Chapter 4 --- Types --- p.9 / Chapter B --- Mechanisms of aminoglycoside-resistance --- p.13 / Chapter C --- Aminoglycoside-modifying enzymes --- p.14 / Chapter 1 --- Classification --- p.19 / Chapter i --- Phosphotransferases --- p.19 / Chapter ii --- Adenylytransferases --- p.21 / Chapter iii --- Acetyltransferases --- p.22 / Chapter 2 --- Genes encoding AMEs --- p.24 / Chapter 3 --- Applications --- p.27 / Chapter D --- Prevalence of aminoglycoside-resistance --- p.28 / Chapter E --- Methods for the determination of aminoglycoside-modifying enzymes --- p.34 / Chapter 1 --- Examination of resistance phenotype --- p.35 / Chapter 2 --- Phosphocellulose paper binding assay --- p.38 / Chapter 3 --- Hybridization with specific gene probes --- p.39 / Chapter 4 --- Antibiotic inactivation --- p.44 / Chapter 5 --- High performance liquid chromatography (HPLC) --- p.44 / Chapter F --- Prevalence of aminoglycoside-modifying enzymes --- p.45 / Chapter G --- Objectives --- p.52 / MATERIALS AND METHODS --- p.53 / Materials --- p.53 / Chapter A --- Bacterial strains --- p.53 / Chapter 1 --- Standard strains --- p.53 / Chapter 2 --- Clinical isolates --- p.53 / Chapter B --- "Antibiotic, media, chemicals and instruments" --- p.55 / Methods --- p.55 / Chapter A --- Orevalence of aminoglycoside-resistance --- p.55 / Chapter B --- Susceptibility testing --- p.55 / Chapter C --- Characterization of aminoglycoside-modifying enzymes (AMEs) --- p.61 / Chapter 1 --- Extraction of enzymes --- p.61 / Chapter 2 --- Substrate profile analysis by the phosphocellulose paper binding assay --- p.62 / Chapter D --- Localization of resistance genes --- p.64 / Chapter 1 --- Genetic study --- p.64 / Chapter 2 --- Molecular studies --- p.67 / Chapter i --- Preparation of crude plasmid extracts --- p.68 / Chapter ii --- Agarose gel electrophoresis --- p.68 / Chapter E --- Plasmid profile analysis --- p.69 / Chapter F --- Plasmid fingerprinting --- p.69 / Chapter 1 --- Preparation of purified plasmid --- p.69 / Chapter 2 --- Restriction endonuclease digestion of plasmid DNA --- p.70 / Plan to achieve objectives --- p.71 / results --- p.73 / Chapter A --- Prevalence of aminoglycoside-resistant Gram-negative bacteria isolated in the Prince of Wales Hospital from 1989 to1992 --- p.73 / Chapter B --- "Susceptibility to 12 aminoglycosides of aminoglycoside-resistant E. coli, K pneumoniae and Ps. aeruginosa" --- p.78 / Chapter C --- "Aminoglycoside-modifying enzymes (AMEs) produced by E. coli, K pneumoniae and Ps. aeruginosa" --- p.88 / Chapter D --- Plasmid profile analysis --- p.93 / Chapter E --- Localization of aminoglycoside-resistance genes --- p.102 / discussion --- p.114 / Chapter A --- Aminoglycoside-resistance --- p.114 / Chapter B --- Mechanisms of aminoglycoside-resistance --- p.118 / Chapter C --- Genetic location of aminoglycoside-resistance and plasmid profiles --- p.122 / Chapter D --- Characterization of AMEs --- p.126 / Chapter E --- Areas for future research --- p.128 / references --- p.130 / appendix --- p.144

No description available.

Doctor of Philosophy / Biochemistry and Molecular Biophysics Interdepartmental Program / Phillip E. Klebba / Siderophore uptake systems are one the most prominent methods of Fe³+-iron acquisition in Gram negative bacteria. The catecholate siderophore enterobactin is synthesized and utilized by many members of Enterobacteriaceae as well as several of the ESKAPE pathogens. The outer membrane (OM) transporter of ferric enterobactin (FeEnt), FepA is a ligand-gated porin (LGP) that requires interaction with the inner membrane (IM) protein TonB in order to accomplish active transport. TonB is thought to transduce the electrochemical energy created by the proton gradient across the IM to LGPs like FepA in the OM, to promote siderophore transport through their occluded channels. However, we do not yet have a clear picture of either how TonB transfers energy to FepA, or what kind of conformational changes occur in the occluding domain of FepA to allow ligand passage. The experiments described herein investigate these two questions, building on previously outlined models and observations. Using fluorescence labeling of strategically substituted cysteines in the surface loops of FepA, we unraveled a hierarchy of loop motion during binding of FeEnt to FepA. Additionally, by rendering parts of the FepA protein immobile as a result of engineered disulfide bonds, I identified residues or regions within its occluding domain that may normally unfold to open a size-specific channel for FeEnt. I also elucidated the role of the peptidoglycan polymer beneath the OM a framework for protein-protein interactions between IM and OM proteins. This includes the proposed interaction between a rotating TonB and FepA, or other LGPs, that may transfer kinetic energy to the OM transporter. The role of iron in microbial survival and pathogenesis makes iron-uptake pathways an attractive target for therapeutic intervention. Using the FeEnt-FepA uptake system as a model, we used a fluorescence based high-throughput screening method to identify novel small molecule inhibitors of TonB action in E. coli. The approach used can be potentially adopted to screen bigger chemical libraries as well as used to find inhibitors of ESKAPE pathogens that use FeEnt such as, Acinetobacter baumannii, Klebsiella pneumoniae or Pseudomonas aeruginosa. Finally, we discoverd a TonB-dependent OM transporter of heme/hemoglobin called HutA in the oligotrophic bacterium Caulobacter crescentus.

Doctor of Philosophy / Department of Kinesiology / Carl Ade / During exercise, muscle blood flow (Q ̇m) increases to match metabolic demand of the active skeletal muscle. In order for this matching to take place, ‘competition’ between local vasodilating metabolites and sympathetically mediated vasoconstriction, termed “functional sympatholysis,” must take place. A key feature of functional sympatholysis is that it is driven largely by metabolic rate (i.e., a higher work rates lead to greater sympatholysis), but may also be largely dependent on nitric oxide bioavailability and oxidative stress in certain disease states (e.g., hypertension). Thus, evaluation of these factors may provide valuable insight into the vascular control mechanisms during exercise in both health and disease. Therefore, the purpose of this dissertation was to 1) determine the role metabolic rate and blood flow on mediating functional sympatholysis, 2) determine the role of nitric oxide bioavailability on functional sympatholysis with high salt intake, a risk factor for primary hypertension, and 3) determine the effect of increases in nitric oxide bioavailability on functional sympatholysis in primary hypertension patients. In the first investigation (Chapter 1), we increased the relaxation phase of the contraction-relaxation cycle to increase active skeletal muscle blood flow (Q ̇m) and see if this would impact vasoconstriction of the active skeletal muscle. We showed that a decreased relaxation time led to greater functional sympatholysis. Interestingly, despite a lower metabolic rate (15% and 20% MVC), we showed that there was no difference in vasoconstriction between the increased relaxation times. These results may show that increases in Q ̇m play a role in functional sympatholysis when mechanical compression is minimized. In the second investigation (Chapter 2), we sought to determine if high dietary sodium (HS) intake would impact functional sympatholysis. We showed that HS intake (15g/day for 7 days) did not impact functional sympatholysis during exercise. Importantly, we show a significant increase in mean arterial pressure (i.e., pressor response) during handgrip exercise. These findings show the deleterious changes in blood pressure, but further work is needed to pinpoint specific mechanisms causing the responses. In the final investigation (Chapter 3), we used an acute nitrate rich (NR) supplement to improve NO bioavailability in hypertensive post-menopausal women (PMW), and observe the impact on functional sympatholysis. We provide novel evidence that functional sympatholysis is improved (~50%) with a NR supplement. The finding that a NR supplement can attenuate vasoconstriction in hypertensive PMW sheds light on the complexities of hypertension, functional sympatholysis and NO bioavailability. The current results indicate that the ‘competition’ between vasodilating metabolites and sympathetically mediated vasoconstriction can be independently modified in health and disease. In individuals with impairment to local vasodilation (e.g., hypertension), the ability to increase functional sympatholysis and muscle blood flow may lead to improvements in cardiovascular health. Taken together, the present results suggest that modifying duty cycle, sodium intake, and NO bioavailability are important factors to be considered with regard to overall cardiovascular health.

No description available.