by Ho, Chi-Kin. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1996. / Includes bibliographical references (leaves 62-64). / Chapter 1 --- Introduction / Chapter 2 --- Previous Work --- p.2-1 / Chapter 2.1 --- Thresholding --- p.2-1 / Chapter 2.2 --- Edge Detection --- p.2-2 / Chapter 2.3 --- Region Growing --- p.2-2 / Chapter 2.4 --- Radial Contour Model --- p.2-3 / Chapter 2.5 --- Regularized Region Contrast --- p.2-3 / Chapter 2.6 --- Deformable Model --- p.2-4 / Chapter 3 --- The ODD-Balloons Model --- p.3-1 / Chapter 3.1 --- Design Rationale --- p.3-1 / Chapter 3.2 --- Overview --- p.3-5 / Chapter 3.3 --- 2-D Deformations --- p.3-8 / Chapter 3.4 --- Orthogonal Cut and Volume Transfer --- p.3-11 / Chapter 3.5 --- Smoothing Operation --- p.3-17 / Chapter 3.6 --- Properties --- p.3-20 / Chapter 3.6.1 --- Conformation to 3-D Shape --- p.3-20 / Chapter 3.6.2 --- Noise Sensitivity --- p.3-20 / Chapter 3.6.3 --- Convergence and Efficiency --- p.3-22 / Chapter 3.6.4 --- Easy-to-Use --- p.3-23 / Chapter 3.7 --- Summary --- p.3-24 / Chapter 4 --- Experiment Results --- p.4-1 / Chapter 4.1 --- Synthetic Data Experiments --- p.4-1 / Chapter 4.2 --- Real Data Experiment --- p.4-3 / Chapter 4.3 --- Discussions --- p.4-6 / Chapter 5 --- Conclusion and Future Work --- p.5-1 / Chapter 5.1 --- Conclusion --- p.5-1 / Chapter 5.2 --- Recommended Future Work --- p.5-2 / Appendix A Discrete Implementation of 2-D Deformation --- p.A-1 / Appendix B Choosing Elasticity and Rigidity Coefficients of 2-D Deformation --- p.B-1 / Bibliography --- p.BIB-1

Le but de notre étude était d'évaluer si les marqueurs moléculaire pourrait détecter de façon sensible et pour aider à un diagnostic précoce et améliorer la survie des patients avec CCR. Dans ce travail, nous avons utilisé les méthodes courantes telles que la spectrométrie, la PCR, l’ELISA et PicoGreen® pour évaluer l’ADN circulant, l’intégrité de l’ADN circulante, l’ARN circulant, l’ARNm CA9 sérique, et la protéine CA9 circulant pour le diagnostic ou le suivi des CCR. Le niveau d’ARN sérique et celui d’ARNm CA9 sérique chez les patients atteints de CRCC sont plus élevés que chez les témoins sains. Chez les patients atteints de CRCC, le niveau de l’ARN circulant est indépendant de l’âge, du sexe, du stade TNM, du grade Fuhrman, et de la taille de la tumeur. Le niveau de l’ARNm CA9 sérique est indépendant de l’âge, du sexe et du grade Fuhrman, mais est corrélé au stade TNM, à la présence de métastases et à la taille de la tumeur. Selon nos résultats, l’ARN circulant et l’ARNm CA9 sérique peuvent être utilisés comme biomarqueurs diagnostiques du CRCC. Par spectrométrie et par la méthode PicoGreen®, la moyenne de l’ADN sérique chez les patients atteints de CRCC était plus élevée que chez les témoins sains, mais cette différence n’était pas significative. Nos résultats indiquent que la sensibilité et la spécificité de l’ADN sérique ne sont pas satisfaisantes pour le diagnostic de CCR. En outre, l’intégrité de l’ADN sérique chez les patients atteints de CRCC était meilleure que chez les patients atteints d’oncocytome rénal et que chez les témoins sains. L’intégrité de l’ADN dans le sérum pourrait constituer un marqueur pour le diagnostic de CRCC. Le niveau de la protéine CA9 chez les patients atteints de CRCC métastatique était plus élevé que chez les patients atteints de CRCC localisé et que chez les témoins sains. Le niveau élevé de la protéine CA9 suggère un risque élevé de récidive. La protéine CA9 sérique pourrait être utilisé pour guider le suivi post opératoire et peut être dans l’avenir indiquer un traitement adjuvant précoce des patients du groupe à haut risque de récidive / The aim of our study was to estimate whether molecular markers could detect significantly and help early diagnosis and improved survival of patients with CCR. In this work, we used some methods such as spectrometry, PCR, ELISA and PicoGreen® to evaluate the circulating DNA, the integrity of circulating DNA, the circulating RNA, the mRNA CA9 of serum and the circulating CA9 protein in the diagnosis or monitoring of CCR. The level of RNA and the mRNA CA9 of serum in patients with CRCC are higher than in healthy controls. In patients with CRCC, the level of circulating RNA is independent of age, gender, TNM stage, Fuhrman grade, and tumor size. The level of mRNA CA9 is independent of age, sexe et Fuhrman grade, but is correlated with TNM stage, presence of metastases and tumor size. According to our results, the circulating RNA and mRNA CA9 of serum can be used as diagnostic biomarkers of CRCC. By the spectrometry and the PicoGreen ® method, the average serum DNA in patients with CRCC was higher than in healthy controls, but this difference was not significant. Our results indicate that the sensitivity and specificity of serum DNA is not satisfactory for the diagnosis of CCR. In addition, the integrity of serum DNA in patients with CRCC was better than in patients with renal oncocytoma and also better than in healthy controls. The integrity of DNA in the serum could be a marker for the diagnosis of CRCC. The level of CA9 protein in patients with metastatic CRCC was higher than in patients with CRCC localized and also higher than in healthy controls. The high level of CA9 protein suggests a high risk of recurrence. The serum CA9 protein could be used to guide post-operative monitoring and may be indicating early adjuvant treatment of patients with high risk of recurrence in the future

Leung Yee Fong. / "August 2002." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (p. 262-287). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

Chiu Hoi Shan Clarissa. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (leaves 110-126). / Abstracts in English and Chinese. / Abstract in English --- p.i / Abstract in Chinese --- p.iii / Acknowledgement --- p.iv / List of Abbreviations --- p.v / List of Tables --- p.vi / List of Figures --- p.viii / Introduction and Objectives / Hepatocellular Carcinoma / Epidemiology --- p.1 / Sex and Age --- p.1 / Geographic distibution --- p.2 / Risk factors of HCC --- p.2 / Mortality from liver cancer --- p.4 / Treatment for HCC --- p.4 / Tumor markers --- p.5 / Alpha-fetoprotein / Structure --- p.5 / Physiological Functions of AFP --- p.7 / Re-expression of AFP in Adult --- p.7 / Re-expression of AFP in HCC --- p.8 / Isoforms of AFP --- p.8 / Specific AFP isoform in HCC --- p.9 / Sialic Acid --- p.11 / Sialyltransferase / "Galβ 1,4GlcnAc α2,6-sialyitransferase" --- p.12 / "Characterization of ST2,6Gal I" --- p.12 / "Expression of ST2,6Gal I" --- p.12 / "General features of ST2,6Gal I Activity" --- p.15 / Relationship Between AFP isoforms and ST2，6Gal in Fetal Mouse Model --- p.15 / "Change in ST2,6GaI I Activity in Transgenic Mouse Models of HCC" --- p.16 / "Study of Activity of ST2,6Gal I in Colon Carcinoma" --- p.16 / Objective of the Project --- p.18 / Chapter Chapter 1 --- Formation of Monosialyated AFP by Hepatoma Cells / Chapter 1.1 --- Introduction --- p.21 / Chapter 1.2 --- Materials and Methods --- p.23 / Chapter 1.3 --- Results / Chapter 1.3.1 --- AFP obtained from cell culture --- p.34 / Chapter 1.3.2 --- IEF for AFP in cell culture medium --- p.34 / Chapter 1.3.3 --- SDS-PAGE analysis of AFP --- p.34 / Chapter 1.3.4 --- Stability of AFP isoforms after secreted to cell culture medium --- p.39 / Chapter 1.3.5 --- Comparison of the AFP isoforms between liver tissues and serum --- p.38 / Chapter 1.4 --- Discussion / Chapter 1.4.1 --- Origin of the extracellular msAFP - in vitro Model --- p.43 / Chapter 1.4.2 --- Origin of circulating msAFP - in vivo Model --- p.44 / Chapter 1.5 --- Conclusion --- p.46 / Chapter Chapter 2 --- "Presence of msAFP in the serum of HCC patient is a Consequence of Decrease in the Activity of ST2, / Chapter 2.1 --- Introduction --- p.47 / Chapter 2.2 --- Materials and Methods --- p.49 / Chapter 2.3 --- Results / Chapter 2.3.1 --- Semi-quantitation of msAFP --- p.61 / Chapter 2.3.2 --- Evaluation of the ST2，6Gal I Assay --- p.65 / Chapter 2.3.3 --- "Measurements and comparisons of the activity of ST2,6Gal I in non-tumor and tumor tissue" --- p.65 / Chapter 2.3.4 --- "Evaluation of the RT-PCR ELISA for semi-quantitation and comparisons of ST2,6Gal I mRNA levels" --- p.75 / Chapter 2.3.5 --- "Semi-quantitation and comparisons of ST2,6Gal I mRNA levels in the non-tumor and tumor tissues" --- p.84 / Chapter 2.3.6 --- Correlations between the markers --- p.87 / Chapter 2.4 --- Discussion / Chapter 2.4.1 --- "Overproduction of AFP, a possible cause for increased msAFP formation" --- p.99 / Chapter 2.4.2 --- "Decrease of ST2,Gal I activity, a possible cause for increased msAFP formation" --- p.100 / Chapter 2.4.3 --- "ST2,6Gal I activity in tumor is not regulated at transcriptional level" --- p.102 / General Discussion / Origin of blood stream msAFP --- p.103 / Physiological Mechanism for the formation of msAFP in HCC --- p.104 / Regulation of ST2，6Gal I activity in HCC --- p.105 / "Comparison between the ST2,6GaI I activities in human HCC and Colon Cancer" --- p.107 / Conclusion and Future studies / Conclusion --- p.108 / Future studies --- p.109 / References --- p.110

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Rotavírus têm sido identificados mundialmente como o mais importante agente etiológico de diarréias agudas não-bacterianas em animais jovens de várias espécies, incluindo a humana. Foi desenvolvido e avaliado um método de ELISA tipo “duplo-sanduíche” para a detecção de rotavírus a partir de material fecal. Para tanto, a amostra NCDV de rotavírus do grupo A foi propagada em cultivo celular com células MA-104. O vírus foi concentrado por ultracentrifugação e inoculado em coelhos e carneiros. Em seguida, as frações IgG, oriundas de amostras de soro dos animais, foram purificadas por cromatografia de troca iônica e absorvidas com soro total de ambas espécies animais, utilizando-se polímero de glutaraldeído, de modo a eliminar reações inespecíficas. A presença do rotavírus foi detectada pela IgG de carneiros e revelada pela IgG de coelho, usando como conjugado IgG de cabra anti-IgG de coelho conjugada à peroxidase. Os valores de diluição dos componentes do ELISA e o valor do ponto-de-corte foram definidos usando-se 26 amostras fecais (13 positivas e 13 negativas) de leitões, tendo como prova padrão a eletroforese em gel de poliacrilamida (PAGE). Aplicado a um painel constituído de 86 amostras fecais diarréicas de leitões, os resultados do ELISA foram: 100% de sensibilidade; 98,79% de especificidade, com uma concordância de 98,83%. A variância entre 86 repetições da mesma amostra foram 0,001 (para a amostra positiva) e 0,0002 (para a amostra negativa). Estes resultados demonstram que este ELISA é um teste sensível e específico para o diagnóstico de rotavírus a partir de material fecal. / Rotaviruses have been identified worldwide as a major etiologic agent of acute nonbacterial diarrhea in the young of many species, including humans. In this investigation was developed and evaluated a “double-sandwich” antibody ELISA method for detection of rotavirus from stool specimens. For that, the NCDV strain of rotavirus group A was serially cultivated in MA-104 cell culture. The virus was concentrated by ultra-centrifugation and inoculated in rabbits and sheeps. After that, the IgG of serum samples of the animals was purified by ion-exchange chromatography and absorbed with whole serum of both animal species using a glutaraldehyde polymer, in order to eliminate inespecific reactions. The presence of rotavirus was detected by the sheep’s IgG and revelated by the rabbit’s IgG, using a anti-rabbit IgG peroxidase conjugate developed in goat. The values of diluition of the components of the ELISA and the cut-off value were defined using 26 fecal samples (13 positive and 13 negative) of piglets. Following this procedure, the test was employed in a panel of 86 fecal samples from piglets with diarrhea, using as standard the polyacrilamide gel electrophoresis (PAGE) test. The results of the ELISA were: 100% of sensivity; 98.79% of specificity, with an agreement of 98.83%. The variance between 86 repetitions of the same sample were 0.001 (for one positive sample) and 0.0002 (for one negative sample). These results showed that this ELISA is an sensitive and specific screening test for rotavirus diagnosis from fecal material.

The purpose of this thesis is to explore methodology concerning Markov Chain Monte Carlo (MCMC), a powerful technique in the Bayesian framework, on binary variables. The primary application of interest in this thesis is applying this methodology to phase haplotypes, a type of categorical variable. Haplotypes are the combination of variants present in an individual’s genome. Phasing refers to estimating the true haplotype. By considering only biallelic and heterozygous variants, the haplotype can be expressed as a vector of binary variables. Accounting for differences in haplotypes is essential for the study of associations between genotype and disease. MCMC is an extremely popular class of statistical methods for simulating autocorrelated draws from target distributions, including posterior distributions in Bayesian analysis. Techniques for sampling categorical variables in MCMC have been developed in a variety of disparate settings. Samplers include Gibbs, Metropolis-Hastings, and exact Hamiltonian based samplers. A review of these techniques is presented and their relevance to the genetic model discussed. An important consideration in using simulated MCMC draws for inference is that they have converged to the distribution of interest. Since the distribution is typically of a non-standard form, convergence cannot generally be proven and, instead, is assessed with convergence diagnostics. The convergence diagnostics developed so far focus on continuous variables and may be inappropriate for binary variables or categorical variables in general. Two convergence diagnostics are proposed that are tailor-made for categorical variables by modeling the data using categorical time series models. Performance of the convergence diagnostics is evaluated under various simulations. The methodology developed in the thesis is applied to estimate haplotypes. There are two main challenges involved in accounting for haplotype differences. One is estimating the true combination of genetic variants on a single chromosome, known as haplotype phasing. The other is the phenomenon of allele-specific expression (ASE) in which haplotypes can be expressed non-equally. No existing method addresses these two intrinsically linked challenges together. Rather, current strategies rely on known haplotypes or family trio data, i.e. having data on subject of interest and their parents. A novel method is presented, named IDP-ASE, which is capable of phasing haplotypes and quantifying ASE using only RNA-seq data. This model leverages the strengths of both Second Generation Sequencing (SGS) data and Third Generation Sequencing (TGS) data. The long read length of TGS data facilitates phasing, while the accuracy and depth of SGS data facilitates estimation of ASE. Moreover, IDP-ASE is capable of estimating ASE at both the gene and isoform level.

Diffusion-weighted image(DWI) and tractography have been developed for decades and are key elements in recent, large-scale efforts for mapping the human brain. The two techniques together provide us a unique possibility to access the macroscopic structure and connectivity of the human brain non-invasively and in vivo. The information obtained not only can help visualize brain connectivity and help segment the brain into different functional areas but also provides tools for understanding some major cognitive diseases such as multiple sclerosis, schizophrenia, epilepsy, etc. There are lots of efforts have been put into this area. On the one hand, a vast spectrum of tractography algorithms have been developed in recent years, ranging from deterministic approaches through probabilistic methods to global tractography; On the other hand, various mathematical models, such as diffusion tensor, multi-tensor model, spherical deconvolution, Q-ball modeling, have been developed to better exploit the acquisition dependent signal of Diffusion-weighted image(DWI). Despite considerable progress in this area, current methods still face many challenges, such as sensitive to noise, lots of false positive/negative fibers, incapable of handling complex fiber geometry and expensive computation cost. More importantly, recent researches have shown that, even with high-quality data, the results using current tractography methods may not be improved, suggesting that it is unlikely to obtain an anatomically accurate map of the human brain solely based on the diffusion profile. Motivated by these issues, this dissertation develops a global approach that incorporates anatomical validated geometric shape prior when reconstructing neuron fibers. The fiber tracts between regions of interest are initialized and updated via deformations based on gradients of the posterior energy defined in this paper. This energy has contributions from diffusion data, shape prior information, and roughness penalty. The dissertation first describes and demonstrates the proposed method on the 2D dataset and then extends it to 3D Phantom data and the real brain data. The results show that the proposed method is relatively immune to issues such as noise, complicated fiber structure like fiber crossings and kissing, false positive fibers, and achieve more explainable tractography results. / A Dissertation submitted to the Department of Statistics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester 2019. / April 16, 2019. / active contours, Bayesian estimation, dMRI fiber tracts, geometric shape analysis, tractography / Includes bibliographical references. / Anuj Srivastava, Professor Directing Dissertation; Eric Klassen, University Representative; Wei Wu, Committee Member; Fred Huffer, Committee Member.

Thesis (MSc.(Med)(Physics))--University of Limpopo, 2010. / Key words: Diagnostic reference levels (DRL), entrance surface dose (ESD), thermoluminescence dosimetry (TLD) Introduction: Diagnostic reference levels (DRL‟s) are defined as a dose level set for standard sized patients or standard phantoms and are not for individual exposures and individual patients and are an efficient standard for optimizing the radiation protection of patients and are practically useful for more common examinations. The International Atomic Energy Agency (IAEA) recommends entrance surface dose (ESD) as DRL‟s in diagnostic radiology and are establish using a TLD on a patient/phantom surface. Aim: To estimate entrance surface dose for different X-ray procedures. Objectives: The objective of this study is to develop the diagnostic reference levels by assessing the dose received by a patient in radiographic exposure. This was achieved using different X-ray techniques to estimate the entrance surface dose for different examinations. Method: The study was conducted at the Dr George Mukhari hospital using 5 different X-ray machines. Before the study commenced quality assurance was done on the machines. The following examinations were considered: Cervical spine (AP), cervical spine (LAT), Skull (AP), Skull (PA), Abdomen (AP), Pelvis (AP), Lumber spine (AP), Lumber spine (LAT), Chest (PA) and Chest (LAT). Thermoluminescence lithium fluoride (LiF) (TLD-100, 3.16 X 3.16 X 0.9 mm3, Harshaw) and the Rando phantom were used to estimate the ESD‟s in mGy. Three TLD‟s were mounted on the top of the phantom in the centre of X-ray beam, external to the organ/tissue being imaged. The average dose was calculated for each radiograph and for each examination. The following technique factors were recorded: tube kilovoltage, focus-to-surface distance, focus-to-film distance, time and mA. vi Results: The mean ESD‟s measured at the centre of X-ray beam on the surface of the phantom for the following examinations are: Cervical spine (AP), 2.99 (± 0.26) mGy; Cervical spine (LAT), 3.23 (± 0.34) mGy; Skull (PA), 3.50 (±0.37) mGy; Skull (LAT), 2.60 (± 0.26) mGy; Abdomen (AP), 4.18 (± 0.40) mGy; Pelvis (AP), 3.96 (± 0.33) mGy; Lumber spine (APS), 4.72 (± 0.39) mGy; Lumber spine (LAT), 8.56 (± 0.67) mGy Chest (PA), 0.72 (± 0.27) mGy and Chest (LAT), 1.03 (± 0.45) mGy. Conclusion: The results of the individual exposure and the overall results of each examination were lower than reported in the literature except for the chest (PA). The determination of patient dose and the comparison with the international DRL‟s are an important factor in the optimization process in diagnostic radiology and it is of special concern for the patient‟s protection. The baseline of diagnostic reference levels for the Dr George Mukhari hospital has been established and the results obtained could be useful for future patient dose measurements in diagnostic radiology Department at the Dr George Mukhari hospital.

Our current ability to identify and appropriately treat infants who are at risk for developing various handicapping conditions is limited. Thus, research aimed at developing early diagnostic techniques and differential intervention programs for infants at risk for handicaps needs further attention. The purpose of this study was to determine if infants who suffered perinatal intraventricular hemorrhage and who received routine medical care plus sensorimotor intervention between 3 and 12 months of age, differed from similar infants who received only routine medical care. Twenty-four subjects (10 experimental and 14 control) who were patients in neonatal intensive care at University of Utah or Primary Children's Medical Centers constituted the study sample. Descriptive data specific to the birth and perinatal period were obtained on the infant and its mother. All infants were evaluated with the Battelle Developmental Inventory at 3 and 12-months corrected age. In addition, the Carey Infant Temperament Questionnaire was completed by the parent when the infant was 6 to 9 months corrected age, and the Parenting Stress Index was completed when the infants was 12 months corrected age. Experimental subjects and their parent(s) participated in an individualized sensorimotor intervention program, directed by a licensed physical therapist, for 1 hour per week on a bi-monthly basis. Parents reported spending an average of 20 minutes per day, 5 days per week, working on exercises with their infant at home throughout the 9- month program. A statistically significant positive relationship was found between developmental outcome and participation in sensorimotor intervention , as measured by the posttest Battelle. No significant differences between groups were found on levels of parenting stress. On each of the measures, stress levels were moderate. Continued enrollment and annual follow-up of subjects in the current study will allow for longitudinal evaluation of the effects of early sensorimotor intervention on development.