Revised; Originally Published: 2003 / 2 pp.

Thesis (Ph. D.)--Oregon State University, 2001. / Typescript (photocopy). Includes bibliographical references. Also available on the World Wide Web.

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

Chapter one of this thesis presents the literature pertaining to biological invasions and the different stages of invasions in terms of plant pathogens. The review focuses on determining areas where studying the population genetics of a pathogen might complement the knowledge of the ecology of the pathogen in order to gain a better understanding of their evolutionary and invasive potential. Dothistroma septosporum, which causes Dothistroma needle blight (DNB), is one of the better known examples of an invasive plant pathogen and is the focus of this thesis. After presenting an overview of the pathogen, it is concluded that a thorough knowledge of the ecological aspects of the pathogen has been gained by many intensive studies but that there is a distinct, and perhaps dangerous, lack of knowledge pertaining to the global population genetics of this pathogen. Throughout the years of this study, DNB has become a global concern as more epidemics were being reported, not only in the Southern Hemisphere where the disease has been problematic for over 50 years, but also in the Northern Hemisphere in both native and nonnative forests. An “International Dothistroma Alliance Committee” was established in 2004 among researchers world-wide with the aim being to share and integrate knowledge about the pathogen and the disease it causes. The main focus of this group incorporates aspects such as diagnostics and monitoring, assessing pathogen risk (pest-risk), disease impact, management and pathogen variability as well as population diversity. The research in this thesis greatly assists in the latter two aims of the committee. In the second chapter, multigene phylogenies were constructed from Dothistroma septosporum isolates obtained worldwide. These studies revealed that the disease is not caused by one pathogen with varying morphotypes, but that two, very closely related sibling species are responsible. A thorough description of the two species, named Dothistroma septosporum and D. pini, is provided. It is also shown in Chapter six that both species are capable of infecting the same needle and can co-exist within the same conidioma. There is thus a distinct potential for hybridisation to occur between these two species. Coincident with the initiation of this research is an increase globally in the incidence of DNB. This increased the knowledge base about the pathogens around the world and also made it easier to obtain cultures and isolates for this study from different sources. As a consequence, an understanding of the distribution and occurrence of each species was possible and is documented in Chapters three and six. The molecular techniques developed in this work have enabled the development of a robust technique to distinguish between the two pathogens causing DNB. A combination of the species-specific mating type markers designed by Groenewald et al. (2007), the diagnostic Primer_A, and an effective species-specific RFLP test, provide a quick and effective means of identifying the DNB pathogens, directly or indirectly, from conidiomata on infected needles. In order to study the population diversity of the DNB fungi, twelve microsatellite markers were developed in Chapter three. In Chapter four, the preliminary applications of these markers provide a first glimpse of the global diversity of D. septosporum which has caused the most devastation world-wide. From this research it is also obvious that the pattern of diversity reflects the movement of its host (pine) from its native Northern Hemisphere to various countries within the Southern Hemisphere. Dothistroma septosporum is an important disease of both plantation grown pines and native forests. Climate change and the continual movement of infected plant material pose great threats to existing forests. The fact that a sibling species has been discovered shows the evolutionary potential of the species to adapt to changing environments. Successful quarantine and monitoring will aid in curbing the further spread of the disease into areas where it could, potentially, be more devastating. The chapters in this thesis correspond to different research projects and are represented in the text in the format of a publication. Due to the nature of this style, however, there is some unavoidable repetition in the text, especially within the introduction of each chapter. Three of the chapters within this thesis have been published in internationally recognised ISI rated journals. / Thesis (PhD)--University of Pretoria, 2009. / Genetics / Unrestricted

Background: The liver biopsy technique in dogs that consistently provides samples adequate for accurate histopathologic interpretation and the variability of histopathology among lobes is unknown. Hypothesis:  Liver biopsy specimens obtained via punch, cup biopsy, and 14 gauge needle biopsy would result in similar histopathologic diagnoses to those found on deeply sectioned samples of liver obtained at necropsy and that discordant results would not differ between lobes.   Animals:  Seventy dogs undergoing necropsy. Methods: Liver specimens were obtained from the left lateral liver lobe with an 8 mm punch, a cup, and a 14 gauge needle. Two larger tissue samples were then collected near the center of the left lateral lobe and used as a histologic standard for comparison.  Samples were also obtained from all remaining lobes. Histopathologic features and numbers of portal triads in each sample were compared. Results: The mean number of portal triads were 2.9 in needle biopsies, 3.4 in cup biopsies, 12 in punch biopsies, and 30.7 in the necropsy samples. Sixty-six percent of needle biopsies,  60% of laparoscopic cup samples, and 69% of punch samples were in agreement with the necropsy samples, differences that were not significantly different. The corresponding kappa coefficient were 0.59 for needle biopsies, 0.52 for cup biopsies, and 0.62 for punch biopsies.  Discordant results did not differ between the liver lobes. Conclusions and Clinical Relevance:  A single biopsy using any of the tested techniques is insufficient for reliable diagnosis of liver disease in the dog.  Multiple biopsies from 2 lobes is recommended. / Master of Science

published_or_final_version / abstract / Electrical and Electronic Engineering / Master / Master of Philosophy

Embryonic biopsy routinely involves the removal of one or two blastomeres in the preimplantation genetic diagnosis (PGD) procedure to determine the presence of a specific disease. The rapid development of the PGD technique and stem cell research has led to great demand for highly automated high precision equipment for cellular component micro-extraction. This thesis presents the development of an automated microsurgery system for embryo biopsy. While the ultimate objective of this research is to improve the so called “take-home-baby rate”, the primary focus of this research, however, is devoted to demonstrate the automation of the first two steps in the embryo biopsy procedure: embryo immobilization and embryo perforation with a piezoelectric actuated micro-cutter mounted on a five DOF micromanipulator. A biological embryo holding device incorporating a unique configuration of fluidic channels is designed to increase embryo mobility in order to overcome friction force while maintaining a low suction flow rate and pressure. The validity of this design is demonstrated by good qualitative agreement between the experimental and simulation results. 3D nonlinear equations of motion of a micro-needle driven longitudinally by a piezoelectric actuator are developed based on Kane’s method . The longitudinal vibration of a micro-needle results in excitation of its out-of-plane, lateral eigenmodes at low damping coefficients. The dynamic model is in good agreement with experimental observations. This model is exploited further to describe the response of an immersed glass micropipette with imbedded mercury in piezo-assisted intracytoplasmic sperm injection (ICSI). Furthermore, piezoelectric actuator dynamic nonlinearity introduced by hysteresis is addressed in this research. A new model is proposed to characterize the rate-dependent hysteresis based on Duffing's equation. A nonlinear capacitor element is incorporated into a linear second-order system to predict the relationship between an input state and a hysteretic output. The proposed hysteresis model is verified experimentally. Based on this approach, a new electromechanical piezoelectric actuator model is proposed. A vision-assisted controller for embryo perforation is proposed by implementing a vision tracking and robust autofocusing algorithm using the particle swarm optimization (PSO) method. The performance of the proposed visual-based controller demonstrated experimentally to be effective in providing accurate embryo and micro-needle 3D positioning. Finally, an automated embryo perforation with the proposed mechanical approach was conducted successfully.

Embryonic biopsy routinely involves the removal of one or two blastomeres in the preimplantation genetic diagnosis (PGD) procedure to determine the presence of a specific disease. The rapid development of the PGD technique and stem cell research has led to great demand for highly automated high precision equipment for cellular component micro-extraction. This thesis presents the development of an automated microsurgery system for embryo biopsy. While the ultimate objective of this research is to improve the so called “take-home-baby rate”, the primary focus of this research, however, is devoted to demonstrate the automation of the first two steps in the embryo biopsy procedure: embryo immobilization and embryo perforation with a piezoelectric actuated micro-cutter mounted on a five DOF micromanipulator. A biological embryo holding device incorporating a unique configuration of fluidic channels is designed to increase embryo mobility in order to overcome friction force while maintaining a low suction flow rate and pressure. The validity of this design is demonstrated by good qualitative agreement between the experimental and simulation results. 3D nonlinear equations of motion of a micro-needle driven longitudinally by a piezoelectric actuator are developed based on Kane’s method . The longitudinal vibration of a micro-needle results in excitation of its out-of-plane, lateral eigenmodes at low damping coefficients. The dynamic model is in good agreement with experimental observations. This model is exploited further to describe the response of an immersed glass micropipette with imbedded mercury in piezo-assisted intracytoplasmic sperm injection (ICSI). Furthermore, piezoelectric actuator dynamic nonlinearity introduced by hysteresis is addressed in this research. A new model is proposed to characterize the rate-dependent hysteresis based on Duffing's equation. A nonlinear capacitor element is incorporated into a linear second-order system to predict the relationship between an input state and a hysteretic output. The proposed hysteresis model is verified experimentally. Based on this approach, a new electromechanical piezoelectric actuator model is proposed. A vision-assisted controller for embryo perforation is proposed by implementing a vision tracking and robust autofocusing algorithm using the particle swarm optimization (PSO) method. The performance of the proposed visual-based controller demonstrated experimentally to be effective in providing accurate embryo and micro-needle 3D positioning. Finally, an automated embryo perforation with the proposed mechanical approach was conducted successfully.

This thesis deals with automatic localization and tracking of surgical tools such as needles in Magnetic Resonance Imaging(MRI). The accurate and precise localization of needles is very important for medical interventions such as biopsy, brachytherapy, anaesthesia and many other needle based percutaneous interventions. Needle tracking has to be really precise, because the target may reside adjacent to organs which are sensitive to injury. More over during the needle insertion, Magnetic Resonance Imaging(MRI) scan plane must be aligned such that needle is in the field of view (FOV) for surgeon. Many approaches were proposed for needle tracking and automatic MRI scan plane control over last decade that use external markers, but they are not able to account for possible needle bending. Significant amount of work has already been done by using the image based approaches for needle tracking in Image Guided Therapy (IGT) but the existing approaches for surgical robots under MRI guidance are purely based on imaging information; they are missing the important fact that, a lot of important information (for example, depth of insertion, entry point and angle of insertion) is available from the kinematic model of the robot. The existing approaches are also not considering the fact that the needle insertion results in a time sequence of images. So the information about needle positions from the images seen so far can be used to make an approximate estimate about the needle position in the subsequent images. During the course of this thesis we have investigated an image based approach for needle tracking in real-time MR images that leverages additional information available from robot's kinematics model, supplementing the acquired images. The proposed approach uses Standard Hough Transform(SHT) for needle detection in 2D MR image and uses Kalman Filter for tracking the needle over the sequence of images. We have demonstrated experimental validation of the method on Real MRI data using gel phantom and artificially created test images. The results proved that the proposed method can track the needle tip position with root mean squared error of 1.5 mm for straight needle and 2.5mm for curved needle.

This study was directed to improve our understanding of the ecology of Swiss needle cast (SNC) of Douglas-fir, a disease that produces extensive damage to forests and plantation in the coastal region of Oregon and Washington. A disease prediction model for the coastal area of Oregon was built by establishing the relationship between the distribution of disease severity and the environment. Currently available methods of determining the distribution of SNC were analyzed, and the possibility of mapping the disease using Landsat TM satellite images was explored. Two types of regression approaches were used to study the relationship between disease severity and climate, topography, soil and forest stand characteristics. Although both types provided useful information and insight, the multiple regression approach was chosen over the regression tree analysis to build the model, due to its capacity to produce a continuous prediction response. Fog occurrence, precipitation, temperature, elevation and slope aspect, were the variables that contributed to explain most of the disease severity variability. Findings agree with and formalize our previous understanding of the ecology of SNC: cool and wet conditions in summer appear to increase disease severity. When the model was applied to past climate conditions, retrospective predictions suggest that changes in climate in the last two decades could help to explain the observed recent regional increase in SNC disease severity. The resulting model was used to construct a disease prediction map. This map showed an accuracy equivalent to the currently available SNC aerial survey. The prediction model, however, is able to produce a continuous prediction surface, more suitable for testing and appropriate for assisting in disease management and research. A strong relationship between mature stand canopy defoliation and the Landsat TM indices greenness and brightness, indicates that it is possible to use satellite imagery to map SNC. In contrast, young stands showed high variability, most likely due to the relatively high proportion of exposed understory vegetation. The possibility of mapping stand defoliation is of great importance because this symptom can be directly linked to tree growth and forest productivity. Satellite imagery can be used in future and in retrospective disease mapping. / Graduation date: 2002