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Digitized by Kansas Correctional Industries

Digitized by Kansas Correctional Industries

Next generation sequencing based methods allow us to identify active genes and potential regulatory elements rapidly across the genome, but an outstanding challenge is to unravel which regulatory elements control which genes. This is problematic because regulatory elements control genes over huge distances (over 1 million base pairs) and they have an unpredictable distribution around the genes they influence. In order to enhance transcription the protein complexes at distal regulatory elements make physical contact with the promoter. These interactions can be detected using Chromosome Conformation Capture (3C) technology and the position of regulatory elements can be deduced from these data. However, these methods are either low throughput or low resolution and they are prone to bias. In this 3C techniques were specifically developed to determine the interactions between regulatory elements and gene promoters promoter. The focus has been the development of Next Generation Capture-C, which allows many genetic loci and samples to be analysed simultaneously, with greater sensitivity and accuracy than has previously been possible. High resolution data can be produced from as few as 100,000 cells, and single-nucleotide polymorphisms can be used to generate allele-specific tracks. Nanostring technology has also been developed for analysis of 3C libraries, as this allows interaction profiles to be determined without PCR or sequencing bias. The Nanostring data show remarkable correlation with the interaction profiles generated by NG Capture-C.

Wong, Pui Shuen. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 92-96). / Abstracts in English and Chinese. / Title Page --- p.i / Abstract (English) --- p.ii / Abstract (Chinese) --- p.iii / Acknowledgements --- p.iv / Table of Contents --- p.V / List of Tables --- p.viii / List of Figures --- p.ix / List of Schemes --- p.xi / Symbols and Abbreviations --- p.xii / Dedication --- p.xiv / Chapter Chapter 1 --- Introduction / Chapter 1.1 --- Mass Spectrometry of peptides/ proteins --- p.1 / Chapter 1.1.1 --- Electrospray ionization of peptides/ proteins --- p.3 / Chapter 1.2 --- Tandem mass spectrometry of peptides/ proteins --- p.4 / Chapter 1.2.1 --- Nomenclature of peptide fragment ions --- p.5 / Chapter 1.2.2 --- Slow heating methods for MSn --- p.6 / Chapter 1.2.2.1 --- Collision induced dissociation --- p.7 / Chapter 1.2.3 --- "Electron based ion activation for MS""" --- p.8 / Chapter 1.3 --- Electron Capture Dissociation --- p.9 / Chapter 1.3.1 --- ECD mechanism for protonated peptide ions --- p.10 / Chapter 1.3.2 --- ECD efficiency --- p.12 / Chapter 1.3.3 --- ECD of metal ions-adducted peptide --- p.13 / Chapter 1.4 --- Overview of present work --- p.14 / Chapter Chapter 2 --- "Instrumentation, Experimental and Calculations" / Chapter 2.1 --- Fourier-transform Ion Cyclotron Resonance Mass Spectrometer --- p.15 / Chapter 2.1.1 --- Basic principle of FTICR-MS --- p.15 / Chapter 2.1.2 --- The instrument --- p.19 / Chapter 2.1.2.1 --- Vacuum system --- p.19 / Chapter 2.1.2.2 --- Nanospray source --- p.24 / Chapter 2.1.2.3 --- Electrostatic ion focusing system --- p.26 / Chapter 2.1.2.4 --- Infinity´ёØ Cell --- p.28 / Chapter 2.1.2.5 --- Electron emission source --- p.29 / Chapter 2.1.2.6 --- Data acquisition system --- p.31 / Chapter 2.2 --- Experimental --- p.31 / Chapter 2.2.1 --- Acquisition pulse program --- p.31 / Chapter 2.2.1.1 --- Simple ESI acquisition pulse program (MS experiment) --- p.31 / Chapter 2.2.1.2 --- ESI-ECD acquisition pulse program (MS experiment) --- p.34 / Chapter 2.2.2 --- Molecular mechanics calculation --- p.36 / Chapter Chapter 3 --- Structural Parameters Affecting Suppression of N-Ca Cleavages of Peptides Ions after Electron Capture / Chapter 3.1 --- Introduction --- p.37 / Chapter 3.2 --- Experimental section --- p.39 / Chapter 3.3 --- Results and Discussion --- p.40 / Chapter 3.3.1 --- Peptides with three arginine residues --- p.40 / Chapter 3.3.1.1 --- General ECD mass spectra features --- p.40 / Chapter 3.3.1.2 --- Comparison of the extent of suppression of triariginated and diarginated model peptides ions --- p.46 / Chapter 3.3.2 --- Peptides with histidine and lysine as proton carriers --- p.47 / Chapter 3.3.2.1 --- General features of ECD mass spectra --- p.47 / Chapter 3.3.2.2 --- Comparison of ECD behavior of peptide ions with different proton carrier --- p.50 / Chapter 3.3.3 --- Peptides with various chain length --- p.53 / Chapter 3.3.3.1 --- General ECD mass spectra features --- p.53 / Chapter 3.3.3.2 --- Reactivation of [M+2H]+* by collision activation --- p.57 / Chapter 3.3.3.3 --- Significance of glutamic acid residues --- p.57 / Chapter 3.3.3.4 --- Results of conformational searches --- p.60 / Chapter 3.4 --- Conclusions --- p.64 / Chapter Chapter 4 --- Investigation of the Role of Conformation of Peptide Ions in Suppression of Backbone fragmentation / Chapter 4.1 --- Introduction --- p.67 / Chapter 4.2 --- Experimental section --- p.69 / Chapter 4.3 --- Results and Discussion --- p.70 / Chapter 4.3.1 --- Peptide with N-methylated amino acid residues --- p.70 / Chapter 4.3.1.1 --- General features of ECD mass spectra --- p.70 / Chapter 4.3.1.2 --- Comparison between normal and N-methylated peptide ions under ECD --- p.72 / Chapter 4.3.2 --- Peptides with proline residues vi --- p.73 / Chapter 4.3.2.1 --- General ECD mass spectra features --- p.73 / Chapter 4.3.2.2 --- Comparison of ECD of peptide ions with and without proline residues --- p.76 / Chapter 4.3.3 --- Transition metal ions as charge carriers --- p.80 / Chapter 4.3.3.1 --- General ECD mass spectra features --- p.80 / Chapter 4.3.3.2 --- Comparison of ECD behavior using proton and metal ions as charge carrier --- p.85 / Chapter 4.4 --- Conclusions --- p.87 / Chapter Chapter 5 --- Conclusions --- p.90 / References --- p.92 / Chapter Appendix I --- Twenty common amino acids --- p.97 / Chapter Appendix II --- Pulse programs for MS and MSn experiments --- p.98

This research investigates the use of a PETtrace cyclotron produced by General Electric (GE) as a neutron source for boron neutron capture therapy (BNCT). The GE PETtrace was chosen for this investigation because this type of cyclotron is popular among nuclear pharmacies and clinics in many countries; it is compact and reliable; it produces protons with energies high enough to produce neutrons with appropriate energy and fluence rate for BNCT and it does not require significant changes in design to provide neutrons. In particular, the standard PETtrace 18O target is considered. The cyclotron efficiency may be significantly increased if unused neutrons produced during radioisotopes production could be utilized for other medical modalities such as BNCT at the same time. The resulting dose from the radiation emitted from the target is evaluated using the Monte Carlo radiation transport code MCNP at several depths in a brain phantom for different scattering geometries. Four different moderating materials of various thicknesses were considered: light water, carbon, heavy water, and FluentalTM. The fluence rate tally was used to calculate photon and neutron dose, by applying fluence rate-to-dose conversion factors. Fifteen different geometries were considered and a 30-cm thick heavy water moderator was chosen as the most suitable for BNCT with the GE PETtrace cyclotron. According to the Brookhaven Medical Research Reactor (BMRR) protocol, the maximum dose to the normal brain is set to 12.5 RBEGy, which for the conditions of using a heavy water moderator, assuming a 60 ??A beam current, would be reached with a treatment time of 258 min. Results showed that using a PETtrace cyclotron in this configuration provides a therapeutic ratio of about 2.4 for depths up to 4 cm inside a brain phantom. Further increase of beam current proposed by GE should significantly improve the beam quality or the treatment time and allow treating tumors at greater depths.

The purpose of this paper is to investigate the possibility of replacing data from highspeed filming (Qualisys motion capture) with data from Inertial Measurement Units (X-io technologies), when used to run a model of torso and pelvis in OpenSim. Qualisys motion capture data is used as the golden standard to validate the result visually and with Bland-Altman plots. In order to obtain comparable data experiments are conducted where both methods of collecting data are used simultaneously. Data from the IMU's then need to be processed in Matlab before it can be used to run the OpenSim modell. Several Matlab programs rotate the IMU data to a static reference frame, filter and integrate it, then create viritual markers that correspond to Qualisys' optical markers. The conclusion is that using IMU as a method for collecting data can replace Qualisys in some applications, but not in ones that require high precision. However, this paper only begins the examination of IMU's and there are most likely improvements to be made.

In a carbon-constrained economy, the decision making process for selecting carbon reducing technologies for existing single power plants, portfolios of power plants, or new power plant technologies must incorporate the monetary impact of reducing CO2 emissions. Cost of electricity and the monetary impacts of reducing criteria pollutants primarily drive power plant decisions. For example, a gas turbine power plant may upgrade its combustion system to a Dry Low NOx combustor if regulations require or provide incentives for reduced NOx emissions. Similarly, in a carbon-constrained economy, the CO2 emissions strategy selected may impact the operating profile and or equipment of the power plant. Given the wide array of CO2 mitigation strategies available for power plants, robust guidelines are needed to consistently compare varying strategies. The purpose of this study is to provide guidelines for comparing currently available and near-term CO2 mitigation strategies, while also providing guidelines for comparing new low CO2 emission technologies. Furthermore, the issue of making a decision for a portfolio of power plants versus a single plant will be explored along with fuel price sensitivity and CO2 credit trading.

This research investigates the use of a PETtrace cyclotron produced by General Electric (GE) as a neutron source for boron neutron capture therapy (BNCT). The GE PETtrace was chosen for this investigation because this type of cyclotron is popular among nuclear pharmacies and clinics in many countries; it is compact and reliable; it produces protons with energies high enough to produce neutrons with appropriate energy and fluence rate for BNCT and it does not require significant changes in design to provide neutrons. In particular, the standard PETtrace 18O target is considered. The cyclotron efficiency may be significantly increased if unused neutrons produced during radioisotopes production could be utilized for other medical modalities such as BNCT at the same time. The resulting dose from the radiation emitted from the target is evaluated using the Monte Carlo radiation transport code MCNP at several depths in a brain phantom for different scattering geometries. Four different moderating materials of various thicknesses were considered: light water, carbon, heavy water, and FluentalTM. The fluence rate tally was used to calculate photon and neutron dose, by applying fluence rate-to-dose conversion factors. Fifteen different geometries were considered and a 30-cm thick heavy water moderator was chosen as the most suitable for BNCT with the GE PETtrace cyclotron. According to the Brookhaven Medical Research Reactor (BMRR) protocol, the maximum dose to the normal brain is set to 12.5 RBEGy, which for the conditions of using a heavy water moderator, assuming a 60 ??A beam current, would be reached with a treatment time of 258 min. Results showed that using a PETtrace cyclotron in this configuration provides a therapeutic ratio of about 2.4 for depths up to 4 cm inside a brain phantom. Further increase of beam current proposed by GE should significantly improve the beam quality or the treatment time and allow treating tumors at greater depths.

Thesis (Ph. D.)--Ohio State University, 2003. / Title from first page of PDF file. Document formatted into pages; contains xiii, 279 p.: ill. (some col.). Includes abstract and vita. Advisor: Todd L. Lowary, Dept. of Chemistry. Includes bibliographical references (p. 150-154).