Abstract Intraoperative surgery has created a need to develop new kinds of surgical tools. Also, the development of imaging techniques and devices has precipitated the need. Robotics plays an increasingly important role in surgery. A robot can yield better accuracy, smaller movements and, as a result, a faster healing process than a normal operation would require for recovering and healing larger cuts in the human body. Magnetic resonance imaging, MRI, is one of the safest imaging techniques, and it has excellent soft tissue contrast. In the last few years, MRI has become a more frequently-used technique in the intraoperative surgery, such as the biopsy. Brain biopsies in particular are easier to perform by the help of MRI. When designing a robot, or any other mechatronic device, for an MR environment, it becomes vital to consider its appropriateness, i.e., electric and magnetic compatibility with MRI. The latter is a notion related to the surgical procedure and the magnetic field being applied. It implies that instrumentation has to be more compatible with MR in higher magnetic fields. In this study, an MR-compatible robot was developed to work inside open MRI equipment. The MR compatibility of the robot was evaluated, using the testing method evolved during the study. The method helps select the suitable material and parts for mechatronic devices operating under MRI. Most notably, this work also devised and introduced new types of sensors to achieve better MR compatibility of the equipment. As a result of this research, a suitable material was developed for the robot's body as well as for the sensors, actuators and tools. Furthermore, it was deduced that some sensors and the control system when powered can not be used in the MR scanner at all. A further result was that the movement of a robotic arm does not disturb image quality in any way. The testing method developed in this research helps address the compatibility issues arising from the use of any device that works in MRI. The testing method can be used for magnetic fields of different strengths. The robot and the control parts constructed in the research were tested under a 0.23-T open MRI scanner. The results show which materials and fibre optics provide a highly MR compatible solution for an MRI environment. The results also show that normal electric motors can not be driven close to the magnetic field while imaging.

Sequence alignment has become one of the most common tasks in bioinformatics. Most of the existing sequence alignment methods use general scoring schemes. But these alignments are sometimes not completely relevant because they do not necessarily provide the desired information. It would be extremely difficult, if not impossible, to include any possible objective into an algorithm. Our goal is to allow a working biologist to augment a given alignment with additional information based on their knowledge and objectives.<p></p>In this thesis, we will formally define constraints and compatible constraint sets for an alignment which require some positions of the sequences to be aligned together. Using this approach, one can align some specific segments such as domains within protein sequences by inputting constraints (the positions of the segments on the sequences), and the algorithm will automatically find an optimal alignment in which the segments are aligned together.<p></p>A necessary prerequisite of calculating an alignment is that the constraints inputted be compatible with each other, and we will develop algorithms to check this condition for both pairwise and multiple sequence alignments. The algorithms are based on a depth-first search on a graph that is converted from the constraints and the alignment. We then develop algorithms to perform pairwise and multiple sequence alignments satisfying these compatible constraints.<p></p>Using straightforward dynamic programming for pairwise sequence alignment satisfying a compatible constraint set, an optimal alignment corresponds to a path going through the dynamic programming matrix, and as we are only using single-position constraints, a constraint can be represented as a point on the matrix, so a compatible constraint set is a set of points. We try to determine a new path, rather than the original path, that achieves the highest score which goes through all the compatible constraint set points. The path is a concatenation of sub-paths, so that only the scores in the sub-matrices need to be calculated. This means the time required to get the new path decreases as the number of constraints increases, and it also varies as the positions of the points change. It can be further reduced by using the information from the original alignment, which can offer a significant speed gain.<p></p>We then use exact and progressive algorithms to find multiple sequence alignments satisfying a compatible constraint set, which are extensions of pairwise sequence alignments. With exact algorithms for three sequences, where constraints are represented as lines, we discuss a method to force the optimal path to cross the constraint lines. And with progressive algorithms, we use a set of pairwise alignments satisfying compatible constraints to construct multiple sequence alignments progressively. Because they are more complex, we leave some extensions as future work.

Sequence alignment has become one of the most common tasks in bioinformatics. Most of the existing sequence alignment methods use general scoring schemes. But these alignments are sometimes not completely relevant because they do not necessarily provide the desired information. It would be extremely difficult, if not impossible, to include any possible objective into an algorithm. Our goal is to allow a working biologist to augment a given alignment with additional information based on their knowledge and objectives.<p></p>In this thesis, we will formally define constraints and compatible constraint sets for an alignment which require some positions of the sequences to be aligned together. Using this approach, one can align some specific segments such as domains within protein sequences by inputting constraints (the positions of the segments on the sequences), and the algorithm will automatically find an optimal alignment in which the segments are aligned together.<p></p>A necessary prerequisite of calculating an alignment is that the constraints inputted be compatible with each other, and we will develop algorithms to check this condition for both pairwise and multiple sequence alignments. The algorithms are based on a depth-first search on a graph that is converted from the constraints and the alignment. We then develop algorithms to perform pairwise and multiple sequence alignments satisfying these compatible constraints.<p></p>Using straightforward dynamic programming for pairwise sequence alignment satisfying a compatible constraint set, an optimal alignment corresponds to a path going through the dynamic programming matrix, and as we are only using single-position constraints, a constraint can be represented as a point on the matrix, so a compatible constraint set is a set of points. We try to determine a new path, rather than the original path, that achieves the highest score which goes through all the compatible constraint set points. The path is a concatenation of sub-paths, so that only the scores in the sub-matrices need to be calculated. This means the time required to get the new path decreases as the number of constraints increases, and it also varies as the positions of the points change. It can be further reduced by using the information from the original alignment, which can offer a significant speed gain.<p></p>We then use exact and progressive algorithms to find multiple sequence alignments satisfying a compatible constraint set, which are extensions of pairwise sequence alignments. With exact algorithms for three sequences, where constraints are represented as lines, we discuss a method to force the optimal path to cross the constraint lines. And with progressive algorithms, we use a set of pairwise alignments satisfying compatible constraints to construct multiple sequence alignments progressively. Because they are more complex, we leave some extensions as future work.

Pulse Pressure Metal-Organic Chemical Vapour Deposition (PP-MOCVD) is a technique for creating thin coatings. It is less dependent on the volatility of precursors than other Chemical Vapour Deposition (CVD) processes as the precursors are introduced into the reaction chamber as an aerosol; therefore sublimation of the precursor is not necessary. This allows solutions of multiple compounds to be created with a known concentration and ratio of precursors. We explored the formation of hydroxyapatite (HAp) coatings for use on bone implants, using a methanolic solution of calcium lactate and trimethyl phosphate (TMP) as a PP-MOCVD precursor solution. The thermal decomposition of the precursors and the reaction between them were investigated using Thermogravimetric Analysis (TGA). Several variables on the PP-MOCVD apparatus were varied to test their effect on the formed coating: deposition temperatures, ratio of precursors, number of pulses, precursor concentration, the use of ambient temperatures and annealing the coatings after formation. All the coatings were analysed using Scanning Electron Microscope (SEM), Energy Dispersive Spectroscopy (EDS) and Fourier Transform Infra-Red spectroscopy (FTIR). These coatings were not uniformly smooth in appearance at the micro level. However, using higher deposition temperatures, an excess ratio of TMP to calcium lactate and annealing the coatings for short periods of time and low temperatures improved the uniformity of the coating. When vigorous annealing was performed it resulted in surface oxidation and the production of titanium dioxide (TiO2 ). The EDS results showed that both calcium and phosphorus were present in the coatings. The use of high deposition temperatures, excess TMP or gentle annealing resulted in calcium to phosphorous ratios similar to the stoichiometry of HAp. These same conditions gave improved coating uniformity.

Pulse Pressure Metal-Organic Chemical Vapour Deposition (PP-MOCVD) is a technique for creating thin coatings. It is less dependent on the volatility of precursors than other Chemical Vapour Deposition (CVD) processes as the precursors are introduced into the reaction chamber as an aerosol; therefore sublimation of the precursor is not necessary. This allows solutions of multiple compounds to be created with a known concentration and ratio of precursors. We explored the formation of hydroxyapatite (HAp) coatings for use on bone implants, using a methanolic solution of calcium lactate and trimethyl phosphate (TMP) as a PP-MOCVD precursor solution. The thermal decomposition of the precursors and the reaction between them were investigated using Thermogravimetric Analysis (TGA). Several variables on the PP-MOCVD apparatus were varied to test their effect on the formed coating: deposition temperatures, ratio of precursors, number of pulses, precursor concentration, the use of ambient temperatures and annealing the coatings after formation. All the coatings were analysed using Scanning Electron Microscope (SEM), Energy Dispersive Spectroscopy (EDS) and Fourier Transform Infra-Red spectroscopy (FTIR). These coatings were not uniformly smooth in appearance at the micro level. However, using higher deposition temperatures, an excess ratio of TMP to calcium lactate and annealing the coatings for short periods of time and low temperatures improved the uniformity of the coating. When vigorous annealing was performed it resulted in surface oxidation and the production of titanium dioxide (TiO2 ). The EDS results showed that both calcium and phosphorus were present in the coatings. The use of high deposition temperatures, excess TMP or gentle annealing resulted in calcium to phosphorous ratios similar to the stoichiometry of HAp. These same conditions gave improved coating uniformity.

No description available.

"This thesis presents the development of a magnetic resonance imaging (MRI) compatible pneumatic actuation test system regulated by piezoelectric valve for image guided robotic intervention. After comparing pneumatic, hydraulic and piezoelectric MRI-compatible actuation technologies, I present a piezoelectric valve regulated pneumatic actuation system consisted of PC, custom servo board driver, piezoelectric valves, sensors and pneumatic cylinder. This system was proposed to investigate the control schemes of a modular actuator, which provides fully MRI-compatible actuation; the initial goal is to control our MRI-compatible prostate biopsy robot, but the controller and system architecture are suited to a wide range of image guided surgical application. I present the mathematical modeling of the pressure regulating valve with time delay and the pneumatic cylinder. Three different sliding mode control (SMC) schemes are proposed to compare the system performance. Simulation results are presented to validate the control algorithm. Practical tests with parameters determined from simulation show that the system performance attained the goal. A novel MRI- compatible locking device for the pneumatic actuator was developed to provide safe lock function as the pneumatic actuator fully stopped."

Cette thèse présente une nouvelle classe de schémas de discrétisation spatiale sur maillages polyédriques, nommée Compatible Discrete Operator (CDO) et en étudie l'application aux équations elliptiques et de Stokes. La préservation au niveau discret des caractéristiques essentielles du système continu sert de fil conducteur à la construction des opérateurs. Les opérateurs de de Rham définissent les degrés de liberté en accord avec la nature physique des champs à discrétiser. Les équations sont décomposées de manière à différencier les relations topologiques (lois de conservation) des relations constitutives (lois de fermeture).Les relations topologiques sont associées à des opérateurs différentiels discrets et les relations constitutives à des opérateurs de Hodge discrets. Une particularité de l'approche CDO est l'utilisation explicite d'un second maillage, dit dual, pour bâtir l'opérateur de Hodge discret. Deux familles de schémas CDO sont ainsi considérées : les schémas vertex-based lorsque le potentiel est discrétisé aux sommets du maillage (primal), et les schémas cell-based lorsque le potentiel est discrétisé aux sommets du maillage dual (les sommets duaux étant en bijection avec les cellules primales).Les schémas CDO associés à ces deux familles sont présentés et leur convergence est analysée. Une première analyse s'appuie sur une définition algébrique de l'opérateur de Hodge discret et permet d'identifier trois propriétés clés : symétrie, stabilité et $mathbb{P}_0$-consistance. Une seconde analyse s'appuie sur une définition de l'opérateur de Hodge discret à l'aide d'opérateurs de reconstruction pour lesquels sont identifiées les propriétés à satisfaire. Par ailleurs, les schémas CDO fournissent une vision unifiée d'une large gamme de schémas de la littérature (éléments finis, volumes finis, schémas mimétiques…).Enfin, la validité et l'efficacité de l'approche CDO sont illustrées sur divers cas tests et plusieurs maillages polyédriques / This thesis presents a new class of spatial discretization schemes on polyhedral meshes, called Compatible Discrete Operator (CDO) schemes and their application to elliptic and Stokes equations. In CDO schemes, preserving the structural properties of the continuous equations is the leading principle to design the discrete operators. De Rham maps define the degrees of freedom according to the physical nature of fields to discretize. CDO schemes operate a clear separation between topological relations (balance equations) and constitutive relations (closure laws).Topological relations are related to discrete differential operators, and constitutive relations to discrete Hodge operators. A feature of CDO schemes is the explicit use of a second mesh, called dual mesh, to build the discrete Hodge operator. Two families of CDO schemes are considered: vertex-based schemes where the potential is located at (primal) mesh vertices, and cell-based schemes where the potential is located at dual mesh vertices (dual vertices being in one-to-one correspondence with primal cells).The CDO schemes related to these two families are presented and their convergence is analyzed. A first analysis hinges on an algebraic definition of the discrete Hodge operator and allows one to identify three key properties: symmetry, stability, and $mathbb{P}_0$-consistency. A second analysis hinges on a definition of the discrete Hodge operator using reconstruction operators, and the requirements on these reconstruction operators are identified. In addition, CDO schemes provide a unified vision on a broad class of schemes proposed in the literature (finite element, finite element, mimetic schemes...).Finally, the reliability and the efficiency of CDO schemes are assessed on various test cases and several polyhedral meshes

International Telemetering Conference Proceedings / October 28-31, 1996 / Town and Country Hotel and Convention Center, San Diego, California / An S-band telemetry transmitter has been developed for Expendable Launch Vehicles (ELV's) that can downlink data through NASA's Tracking and Data Relay Satellite System (TDRSS). The transmitter operates in the 2200 to 2300 MHz range and provides a number of unique features to achieve optimum performance in the launch vehicle environment: · Commandable QPSK or BPSK modulation format. · Data rates up to 10 Mbps. · Commandable concatenated coding provides superior link performance. · Premodulation filtering produces excellent spectral containment characteristics. · Phase noise of less than 3 degrees rms is maintained through launch and ascent vibration profiles. · A 30 watt nominal RF output power provides a robust RF link. · Two RF antenna output ports with commandable selection of all power out to either port or power split evenly between ports. · Operating modes and conditions of the unit can be monitored through a number of bilevel and analog outputs. · A ruggedized mechanical design provides a reliable communications link for launch vehicle environments.

International Telemetering Conference Proceedings / October 25-28, 1993 / Riviera Hotel and Convention Center, Las Vegas, Nevada / NASA's ground telemetry data systems developed by the Microelectronics Systems Branch at the Goddard Space Flight Center, use a generic but expandable architecture known as the "Functional Components Approach." This approach is based on the industry standard VMEbus and makes use of multiple commercial and custom VLSI hardware based cards to provide standard off-the-shelf telemetry processing functions (e.g., frame synchronization, packet processing, etc.) for many telemetry data handling applications. To maintain maximum flexibility and performance of these systems, a special real-time system environment has been developed, the Modular Environment for Data Systems (MEDS). Currently, MEDS comprises over 300,000 lines of tested and operational code based on a non-UNIX real-time commercial operating system. To provide for increased functionality and adherence to industry standards, this software is being transformed to run under a UNIX-compatible real-time environment. This effort must allow for existing systems and interfaces and provide exact duplicates of the system functions now used in the current real-time environment. Various techniques will be used to provide a relatively quick transition to this new real-time operating system environment. Additionally, all standard MEDS card to card and system to system interfaces will be preserved, providing for a smooth transition and allowing for telemetry processing cards that have not yet been converted to reside side-by-side with cards that have been converted. This paper describes this conversion effort.