3D follicle segmentation in ultrasound image volumes of ex-situ bovine ovaries

Conventional ultrasonographic examination of the bovine ovary is based on a sequence of two-dimensional (2D) cross-section images. Day-to-day estimation of the number, size, shape and position of the ovarian follicles is one of the most important aspects of ovarian research. Computer-assisted follicle segmentation of ovarian volume can relieve physicians from the tedious manual detection of follicles, provide objective assessment of spatial relationships between the ovarian structures and therefore has the potential to improve accuracy. Modern segmentation procedures are performed on 2D images and the three-dimensional (3D) visualization of follicles is obtained from the reconstruction of a sequence of 2D segmented follicles. The objective of this study was to develop a semi-automatic 3D follicle segmentation method based on seeded region growing. The 3D datasets were acquired from a sequence of 2D ultrasound images and the ovarian structures were segmented from the reconstructed ovarian volume in a single step. A “seed” is placed manually in each follicle and the growth of the seed is controlled by the algorithm using a combination of average grey-level, standard deviation of the intensity, newly-developed volumetric comparison test and a termination criterion. One important contribution of this algorithm is that it overcomes the boundary leakage problem of follicles of conventional 2D segmentation procedures. The results were validated against the aspiration volume of follicles, the manually detected follicles by an expert and an existing algorithm.We anticipate that this algorithm will enhance follicular assessment based on current ultrasound techniques in cases when large numbers of follicles (e.g. ovarian superstimulation) obviate accurate counting and size measurement

An Agent-Based Model of Cryoprotectant Equilibration in Secondary Stage Preantral Ovarian Follicles

Young cancer patients have limited options for fertility treatment when facing gonadotoxic treatment. One promising fertility treatment for young cancer patients is the cryopreservation of immature ovarian follicles followed by maturation and subsequent reimplantation. However, preantral ovarian follicles currently have lower post-thaw success rates compared to mature oocytes and embryos. Previous research suggests that damage to vital intercellular connections, Transzonal Projections (TZPs), occurs during the cryopreservation process and may account for the observed lower post-thaw success rate in this tissue. It is likely that cryoprotective agent (CPA) equilibration is the cryopreservation step during which TZP damage occurs. Constructing a biologically relevant model of CPA equilibration and the associated damage may allow for improved protocols as measured by increased post-thaw success rates. Agent-based models are a promising technique to capture steps in the cryopreservation process, such as CPA equilibration. In this thesis, I conducted a series of experiments with typical CPAs and nonpermeating solutes at different temperatures using preantral ovarian follicles from a non-human primate (Rhesus monkeys) to measure TZP damage. In these experiments, I also estimated relevant permeability parameters within the tissue. I found that the majority of TZP damage was likely the result of mechanical forces that occurred during the cell volume reduction phase of CPA equilibration. Furthermore, through these experiments, I demonstrate that for this tissue type, parameters collected either during monolayer or single-cell experiments can be used to construct full tissue models. Using the derived experimental parameters and available literature values, I constructed and validated a 3-D agent-based model to capture CPA equilibration in preantral ovarian follicles. My agent-based model utilizes parallel computing on an average desktop computer and allows for the rapid design and testing of CPA equilibration protocols. The model I constructed can account for both mechanical and toxic damage. Importantly, my model accurately captures the experimental damage to TZPs in the majority of simulations. Lastly, I propose several theoretically improved cryopreservation protocols for preantral ovarian follicles. The research presented in this thesis demonstrates that agent-based models can be utilized to capture steps in the cryopreservation in silico and represents a non-invasive, less costly means to test and improve CPA equilibration protocols

Cellular Automata

Modelling and simulation are disciplines of major importance for science and engineering. There is no science without models, and simulation has nowadays become a very useful tool, sometimes unavoidable, for development of both science and engineering. The main attractive feature of cellular automata is that, in spite of their conceptual simplicity which allows an easiness of implementation for computer simulation, as a detailed and complete mathematical analysis in principle, they are able to exhibit a wide variety of amazingly complex behaviour. This feature of cellular automata has attracted the researchers' attention from a wide variety of divergent fields of the exact disciplines of science and engineering, but also of the social sciences, and sometimes beyond. The collective complex behaviour of numerous systems, which emerge from the interaction of a multitude of simple individuals, is being conveniently modelled and simulated with cellular automata for very different purposes. In this book, a number of innovative applications of cellular automata models in the fields of Quantum Computing, Materials Science, Cryptography and Coding, and Robotics and Image Processing are presented

The role of space in homeostasis and preneoplasia in stratified squamous epithelia

A major subject of study in biological research is the dynamics of stem cells in squamous epithelia. Given that most common human cancers develop from epithelia, understanding the rules of cell fate decision in these systems is key to explaining not only healthy tissue growth and maintenance but also the processes of mutagenesis and cancer. The aim of my project was to investigate the dynamics in squamous epithelial tissues both in homeostasis and preneoplasia, using cellular automata (CA) models. Stem cell dynamics has been shown to be accurately described by a simple mathematical model, the single progenitor (SP) model. Reliable parameterisation of this model would give access to valuable quantitative information on epithelial tissue maintenance and enable investigating how mutations affect tissue dynamics. I initially identified the most appropriate method for accurately parameterising the homeostatic system. I then sought to account for the spatial patterning of cells by implementing the SP model in two-dimensional space. The spatial model was able to reproduce the key signatures of homeostatic dynamics, thus showing that restrictions imposed by tissue organization do not alter the neutral dynamics. Furthermore, I studied non-homeostatic dynamics in stratified squamous epithelial tissues by spatially modelling the growth and competition of non-neutral mutations as well as the effects of wounding in the tissue. The studied dynamics of Notch and p53 mutant clones in mouse epithelia has been found to be highly distinct, with the former fully colonizing the tissue whereas the latter only partially. I demonstrated that the two mutants’ tissue takeover dynamics can be recapitulated by two distinct spatial feedback rules, on the basis of response to crowding, providing a mechanistic explanation of the observed distinct growth modes. Finally, mutant competition was explored. A striking effect resulting from the spatial interaction of the two mutations in a wild-type background is that the p53 mutant cell population was always outcompeted by the Notch mutant population and appeared to shrink. Considering this consistent emergent behaviour in the competition simulations and given the paucity of Notch mutations in human cancer datasets, it is tempting to speculate that the aggressive fitness of Notch may offer a tumour-protective effect

Computational Approaches and Models for Ovarian Ageing: From 2D to 4D

The theme of the work presented in this multi-disciplinary PhD is the development of new computational tools and techniques to study and understand spatio-temporal follicle growth in neonatal mouse ovaries. The female ovary is endowed at birth with a finite, non-renewable supply of oocytes, each enclosed in a layer of supporting somatic (granulosa) cells to form a quiescent follicle. From birth, a steady trickle of follicles initiate growth to maintain a supply of mature oocytes for regular ovulation. Disruption in the regulation of initiation of follicle growth can result in various pathologies, such as premature ovarian failure and polycystic ovary syndrome. The mechanism of regulation of the initiation of follicle growth remains unclear, but may involve inter-follicle signaling via paracrine growth factors. To investigate this hypothesis, a new technique for quantifying and analyzing spatial distributions of quiescent and growing follicles in the adult human has been developed, as an extension of a novel technique previously developed in neonatal mice in our laboratory. As in the mouse study, we have found evidence that in the human ovary neighbouring quiescent follicles inhibit follicle growth, at a small range. This approach has been further extended to cultured neonatal mouse ovaries, which in vitro lack a systemic blood supply, to investigate the relative contributions of inter-follicle paracrine signaling and endocrine growth factor/nutrient signaling to the regulation of initiation of follicle growth. Accurate counts of the numbers of follicles in ovaries are important for a wide variety of studies of ovarian physiology, including investigating the effects of age, toxins, chemotherapeutics, endocrine disruptors and specific genes (knock out/transgenic studies) on follicle formation, endowment and development. Many published studies use frequent sampling of a small number of ovaries (often as few as three) to obtain estimates of the number of follicles. We have tested the validity of this approach by generating 3D spherical simulated ovaries which contain realistic numbers of follicles at different stages and which are realistically positioned within these ovaries. The number and position of follicles is based on real biological data. This model enables us to rapidly ‘virtually’ section the ovary in silico and obtain computer-generated counts of the numbers of follicles in sections at different frequencies, such as one every fifth section (1/5), 1/20 or 1/50. As we know precisely how many follicles each simulated ovary contains, we can compare the accuracy using different sampling frequencies of varying numbers of ovaries. This has enabled us to demonstrate that the error is smaller when infrequent sampling of a large number of ovaries (≥8) is carried out, and that this actually involves analyzing fewer sections overall. We have gone on to generate simulated ovaries from knockout mice, with more or fewer follicles, and can predict how many ovaries are required to make robust comparisons between knockout and control animals. This has shown that biological variability contributes more to counting error than the method of sampling. These simulated ovaries provide a unique resource to model large studies. Currently follicle counts are obtained by fixing and serially sectioning ovaries, and manually counting the follicles in sections. This is laborious and time-consuming. Faster methods of obtaining follicle estimates are required. With the use of confocal microscopy and immunohistochemistry for an oocyte-specific protein, we were able to establish a protocol that allows us to image and computationally reconstruct a whole neonatal mouse ovary in 3D. Follicle number can be estimated rapidly using a stereologic method. The stereologic technique error was estimated using the simulated ovary model, leading to the conclusion that the method can be safely used to obtain rapid estimates of follicle number. The time required can be further reduced by using image processing to detect the stained follicles on the sections. We have developed an algorithmic technique that can instantaneously identify stained oocytes, count them, and calculate their spatial distribution. A fundamental unanswered question is whether follicles move in the ovary, particularly as they grow. This question has arisen from the observation that small follicles tend to be situated close to the ovarian surface, while large ones are closer to the medulla. This question has implications for interfollicle signaling. We have developed a protocol to image the ovary while in culture using timelapse confocal and live lipid stains to visualize the follicles. Results show that small follicles are not moving significantly over a period of 12h. This project can be extended in the future with the use of transgenic mice for GFP tagging, to accurately monitor changes in structures of interest within cultured ovaries

Advancements and Breakthroughs in Ultrasound Imaging

Ultrasonic imaging is a powerful diagnostic tool available to medical practitioners, engineers and researchers today. Due to the relative safety, and the non-invasive nature, ultrasonic imaging has become one of the most rapidly advancing technologies. These rapid advances are directly related to the parallel advancements in electronics, computing, and transducer technology together with sophisticated signal processing techniques. This book focuses on state of the art developments in ultrasonic imaging applications and underlying technologies presented by leading practitioners and researchers from many parts of the world

05. 2009 IMSAloquium Student Investigation Showcase

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2009 IMSAloquium, Student Investigation Showcase

SIR enables students to pursue solutions to problems that challenge our global community through partnerships with distinguished professionals at colleges and universities, research institutions, businesses, and museums.”https://digitalcommons.imsa.edu/archives_sir/1001/thumbnail.jp

Chaos in music: historical developments and applications to music theory and composition

The Doctoral Dissertation submitted by Jonathan R. Salter, in partial fulfillment of the requirements for the degree Doctor of Musical Arts at the University of North Carolina at Greensboro comprises the following: 1. Doctoral Recital I, March 24, 2007: Chausson, Andante et Allegro; Tomasi, Concerto for Clarinet; Bartok, Contrasts; Fitkin, Gate. 2. Doctoral Recital II, December 2, 2007: Benjamin, Le Tombeau de Ravel ; Mandat, Folk Songs; Bolcom, Concerto for Clarinet; Kovacs, Sholem-alekhem, rov Fiedman! 3. Doctoral Recital III, May 3, 2009: Kalliwoda, Morceau du Salon; Shostakovich, Sonata, op. 94 (transcription by Kennan); Tailleferre, Arabesque; Schoen eld, Trio for Clarinet, Violin, and Piano. 4. Dissertation Document: Chaos in Music: Historical Developments and Applications to Music Theory and Composition. Chaos theory, the study of nonlinear dynamical systems, has proven useful in a wide-range of applications to scienti c study. Here, I analyze the application of these systems in the analysis and creation of music, and take a historical view of the musical developments of the 20th century and how they relate to similar developments in science. I analyze several 20th century works through the lens of chaos theory, and discuss how acoustical issues and our interpretation of music relate to the theory. The application of nonlinear functions to aspects of music including organization, acoustics and harmonics, and the role of chance procedures is also examined toward suggesting future possibilities in incorporating chaos theory in the act of composition. Original compositions are included, in both sheet music and recorded form