Performing Near Field Acoustic Holography Scans for the Purpose of Finding the Acoustic Impedance of a Violin

This project aimed to measure the acoustic impedance of the violin so that the violin can be better understood from an acoustic standpoint. Near field acoustic holography scans are to be conducted at the open A string resonance of the violin (440 Hz). Pressure microphones along the back plate of the violin allow pressure and particle velocity to be measured, and with that, the acoustic impedance to be calculated and mapped in 1 cm x 1cm increments. This work presents a guide for this procedure. The set-up method and materials used are detailed and the analysis and computations of values are described in the presentation

Bioprospecting For Genes That Confer Biofuel Tolerance To Escherichia Coli Using A Genomic Library Approach

Microorganisms are capable of producing advanced biofuels that can be used as ‘drop-in’ alternatives to conventional liquid fuels. However, vital physiological processes and membrane properties are often disrupted by the presence of biofuel and limit the production yields. In order to make microbial biofuels a competitive fuel source, finding mechanisms for improving resistance to the toxic effects of biofuel production is vital. This investigation aims to identify resistance mechanisms from microorganisms that have evolved to withstand hydrocarbon-rich environments, such as those that thrive near natural oil seeps and in oil-polluted waters. First, using genomic DNA from Marinobacter aquaeolei, we constructed a transgenic library that we expressed in Escherichia coli. We exposed cells to inhibitory levels of pinene, a monoterpene that can serve as a jet fuel precursor with chemical properties similar to existing tactical fuels. Using a sequential strategy of a fosmid library followed by a plasmid library, we were able to isolate a region of DNA from the M. aquaeolei genome that conferred pinene tolerance when expressed in E. coli. We determined that a single gene, yceI, was responsible for the tolerance improvements. Overexpression of this gene placed no additional burden on the host. We also tested tolerance to other monoterpenes and showed that yceI selectively improves tolerance. Additionally, we used genomic DNA from Pseudomonas putida KT2440, which has innate solvent-tolerance properties, to create transgenic libraries in an E. coli host. We exposed cells containing the library to pinene, selecting for genes that improved tolerance. Importantly, we found that expressing the sigma factor RpoD from P. putida greatly expanded the diversity of tolerance genes recovered. With low expression of rpoDP. putida, we isolated a single pinene tolerance gene; with increased expression of the sigma factor our selection experiments returned multiple distinct tolerance mechanisms, including some that have been previously documented and also new mechanisms. Interestingly, high levels of rpoDP. putida induction resulted in decreased diversity. We found that the tolerance levels provided by some genes are highly sensitive to the level of induction of rpoDP. putida, while others provide tolerance across a wide range of rpoDP. putida levels. This method for unlocking diversity in tolerance screening using heterologous sigma factor expression was applicable to both plasmid and fosmid-based transgenic libraries. These results suggest that by controlling the expression of appropriate heterologous sigma factors, we can greatly increase the searchable genomic space within transgenic libraries. This dissertation describes a method of effectively screening genomic DNA from multiple organisms for genes to mitigate biofuel stress and shows how tolerance genes can improve bacterial growth in the presence of toxic biofuel compounds. These identified genes can be targeted in future studies as candidates for use in biofuel production strains to increase biofuel yields

Separating what is evaluated from what is selected in artificial evolution

In artificial evolution, selection and evaluation are separate and distinct steps. This distinction is rather different in natural evolution, where fitness (corresponding to evaluation) is a direct consequence of selection rather than a precursor to it. This thesis presents a new way of thinking about artificial evolution that separates evaluation and selection and consequently opens up the space of potential evolutionary algorithms beyond the limitations imposed by ignoring this distinction. In Part I of the thesis we explore how varying the level of evaluation and selection impacts evolution. Using novel genetic algorithms (GAs) we show how group level evaluation allows evolution to find solutions to problems that require niching or a division of labour amongst component parts, something that cannot be accomplished using a standard GA. One of the inspirations for testing GAs with group-level evaluation was recent research into bacterial evolution which shows in bacterial colonies, distinguishing between the individual and group is very difficult because of the symbiotic relationship between different bacteria. We find that depending on the task it sometimes makes sense to select the individual while in other cases simply selecting groups is the best choice. Finally, we present a method for evolving the group size in these types of GAs that has the benefit of avoiding the need to know the optimal division of labour ahead of time. In Part II we move away from studying the relationship between evaluation and selection to show how our novel view of evolution can be used to develop GAs that implement horizontal gene transfer which was again inspired by looking at bacterial evolution. By testing these GAs on a variety of different tasks we show how this promiscuous gene swapping is often beneficial to evolution because it can reduce the probability of the population getting stuck on a sub-optimal solution. The thesis demonstrates the benefits of of looking at artificial evolution in terms of both evaluation and selection when it comes to algorithm development, and thus provides the GA community with a new context in which they can choose different algorithms appropriate to different tasks

An Information System's Jabber/XMPP Gateway as a Web Service

Cílem práce je seznámit se s protokolem XMPP a s webovými službami a vytvořit webovou službu, která umožní komunikaci s uživatelem pomocí XMPP zpráv.The objective of this thesis was to learn about XMPP protocol and web services and to create a web service that provides communication with the user through XMPP messages.

Cost-effectiveness analysis of prophylaxis duration following lung transplantation for CMV mismatch and non-mismatch recipients

Survival following lung transplantation is lower than survival following all other solid organ transplants. Chronic rejection, graft failure, and opportunistic infections all contribute to these poor outcomes. One such opportunistic infection is cytomegalovirus (CMV). CMV is one of the most common infections after lung transplant, and can cause direct effects (viremia and disease), and indirect effects including increased risk of acute cellular rejection, and death. Donor CMV serology positive, recipient negative (D+/R-) patients have the highest risk for developing CMV, for which they receive extended valganciclovir prophylaxis. Longer prophylaxis durations, however, may lead to an increased risk of infection due to resistant CMV, and no standardized guidelines exist for prophylaxis duration. To investigate the effect of duration length on survival, a cost-effectiveness analysis of mismatch and non-mismatch patients was performed, where non-mismatch patients received 6 months of prophylaxis and mismatch patients received either 1 or 2 years. A Markov-state transition model was used, with month-long cycles over a five-year time horizon, a 3% discount rate, and took a healthcare system perspective. Health states of no CMV, sensitive and resistant CMV viremia, sensitive and resistant CMV disease, and death are modeled, with possible episodes of acute cellular rejection in each state. Outcomes included life-years gained and quality-adjusted life-years (QALYs). The model showed that increasing prophylaxis duration resulted in gains in both life-years and QALYs. Incremental cost-effectiveness ratios were $110,510 per life-year gained and$150,280 per QALY. Continued prophylaxis for 5 years after transplant increases the ICER to $153,862 per life-year gained, and$203,756 per QALY. These results show that extended valganciclovir prophylaxis for mismatch patients is associated with gains of life-years and QALYs, and is economically reasonable. As only a limited number of lungs are available, and the demand outweighs the supply, extended prophylaxis would result in these organs being used to their greatest benefit, and could decrease the need for re-transplants, showing a clear public health impact