Optical scanning holography, which was proposed by Poon[1], is a fascinating technology to record holographic information. The technique is applied in the operation of scanning holographic microscopy to record the entire three-dimensional volume of a biological specimen in the form of a hologram. With the data captured, a digital reconstruction or decoding is used to reconstruct the hologram of that such specimen. An accurate reconstruction of the recorded data provides with an in-depth analysis in the area where random noise and other imperfection effects may occur. In this thesis, three different approaches of reconstruction process are presented to provide in high-resolution a comparison between theoretical and experimental reconstruction a hologram of fluorescent beads. The first approach is to use only the experimental pinhole hologram recorded to correlate with the hologram of the object to give the reconstruction of the section. The second approach is to use the propagated pinhole hologram to reconstruct at an arbitrary depth. Finally, the third approach is to reconstruct without using the experimental pinhole hologram but with diffraction theory. Comparing these results in high-resolution gives us analysis of the reconstruction noise due to optical aberration. / Master of Science

No / The purpose of the research was to examine the practical feasibility of developing a hyperspectral camera from a Zeiss fundus camera and to illustrate its use in imaging diabetic retinopathy and glaucoma patients. The original light source of the camera was replaced with an external lamp filtered by a fast tunable liquid-crystal filter. The filtered light was then brought into the camera through an optical fiber. The original film camera was replaced by a digital camera. Images were obtained in normals and patients (primary open angle glaucoma, diabetic retinopathy) recruited at the Manchester Royal Eye Hospital. A series of eight images were captured across 495- to 720-nm wavelengths, and recording time was less than 1.6s. The light level at the cornea was below the ANSI limits, and patients judged the measurement to be very comfortable. Images were of high quality and were used to generate a pixel-to-pixel oxygenation map of the optic nerve head. Frame alignment is necessary for frame-to-frame comparison but can be achieved through simple methods. We have developed a hyperspectral camera with high spatial and spectral resolution across the whole visible spectrum that can be adapted from a standard fundus camera. The hyperspectral technique allows wavelength-specific visualization of retinal lesions that may be subvisible using a white light source camera. This hyperspectral technique may facilitate localization of retinal and disc pathology and consequently facilitate the diagnosis and management of retinal disease.

Cerca de 10% dos casos de câncer de mama e/ou ovário são caracterizados como hereditários, onde a presença de mutações germinativas no gene de suscetibilidade BRCA1 aumenta o risco de desenvolver esses cânceres durante a vida da mulher. O BRCA1 é um gene supressor tumoral envolvido na resposta de danos ao DNA, controle do ciclo celular, na remodelação da cromatina, ubiquitinação e regulação da transcrição. O presente estudo tem como objetivo central caracterizar as mutações do gene BRCA1 associadas a Síndrome Hereditária do Câncer de Mama e/ou Ovário (HBOC) em pacientes atendidos no Serviço de Aconselhamento Genético do Câncer do Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (HCFMRP/USP). Os vinte e dois éxons codificantes do BRCA1 foram analisados utilizando o método de High Resolution Melting (HRM) para triagem de mutações pontuais, seguido pelo sequenciamento de DNA dos casos selecionados para validação. A técnica de MLPA (Multiplex Ligation-dependent Probe Amplification) também foi usada para detectar grandes deleções e duplicações. Uma vez confirmada a mutação, membros da família considerados de alto risco, serão investigados para a mutação específica, a fim de proporcionar-lhes um aconselhamento genético apropriado para a detecção precoce do câncer. No presente estudo, foram investigados 41 pacientes que preencheram os critérios para o teste genético de acordo com NCCN Clinical Practice Guidelines in Oncology v.1.2010. Um total de 21 mutações foram identificadas, duas das quais são patogênicas: a deleção dos éxons 17-18 e a deleção dos éxon 19. Ambas estão localizadas no domínio BRCT do gene BRCA1, essencial para a ligação de fosfoproteínas críticas para a ativação do complexo de reparo do DNA. Outra mutação, a S616del, foi tratada como patogênica, mas apresenta informações controversas em diferentes estudos. O trabalho também identificou uma nova mutação, Val1117Ile. Um estudo de haplótipos das mutações identificadas nos pacientes foi realizado e revelou que um dos haplótipos, denominado de 6, contendo quatro resíduos mutados (871Leu, 1038Gly, 1183Arg e 1613Gly) estava presente em 50% das pacientes. O estudo de associação com 82 indivíduos saudáveis, mostrou diferença significativa (p=0,026) nos pacientes, sugerindo assim um risco aumentado de HBOC. Adicionalmente, foi analisada a mutação germinativa R337H no gene p53 para os casos suspeitos de Síndrome de Li-Fraumeni. Em síntese, o presente estudo contribui com a identificação de uma nova mutação não-sinônina no gene BRCA1 e sugere que o haplótipo 871Leu-1038Gly-1183Arg-1613Gly possa conferir risco aumentado do câncer de mama e/ou ovário em pacientes diagnosticados com HBOC. / About 10% of cases of breast and/or ovary cancer are characterized as hereditary, where the presence of germline mutations in susceptibility BRCA1 gene increases the risk of developing these cancers during womans lifetime. BRCA1 is a tumor suppressor gene involved in DNA damage response, cell cycle control, chromatin remodeling, ubiquitination and transcriptional regulation. The present study aims to characterize BRCA1 gene mutations associated with Hereditary Breast/Ovary Cancer Syndrome (HBOC) in patients from the Cancer Genetic Counseling Service of the General Hospital of the Medical School of Ribeirão Preto, University of São Paulo (HCFMRP-USP). The twenty two coding exons of BRCA1 were analyzed using High Resolution Melting (HRM) method for the screening of point mutations, followed by DNA sequencing of the cases selected to validation. MLPA (Multiplex Ligation-dependent Probe Amplification) technique was also used to detect gross deletions and duplications. Once confirmed the mutation, family members most at risk will be analyzed for the specific mutation in order to provide them with an appropriate genetic counseling for early detection of cancer. In the present study, we investigated 41 patients that fulfilled the criteria for genetic testing according to NCCN Clinical Practice Guidelines in Oncology v.1.2010. A total of 21 mutations were identified, two of them are pathogenic: a deletion of exons 17-18 and a deletion of exon 19. Both of them are located in the BRCT domain of BRCA1 gene, impairing the binding of essential phosphoproteins critical to the activation of DNA repair complex. Another mutation, S616del, shows controversial information about its pathogenesis in different studies.The present study also describes a new mutation, Val1117Ile. A study of haplotypes of the mutations identified in patients was performed and revealed that one of the haplotypes, called 6, containing four mutated residues (871Leu, 1038Gly, and 1183Arg 1613Gly) was present in 50% of patients. The association study with 82 healthy subjects showed a significant difference (p = 0.026) in patients, thus suggesting an increased risk for HBOC. Additionally, the germline mutation R337H on p53 gene was also analyzed in the present study for suspected cases of Li-Fraumeni Syndrome. In summary, this study contributes to the identification of a new missense mutation in the BRCA1 gene and suggests that the haplotype-871Leu-1038Gly 1183Arg-1613Gly may confer increased risk of breast cancer and / or ovarian cancer in patients diagnosed with HBOC.

Cerca de 10% dos casos de câncer de mama e/ou ovário são caracterizados como hereditários, onde a presença de mutações germinativas no gene de suscetibilidade BRCA1 aumenta o risco de desenvolver esses cânceres durante a vida da mulher. O BRCA1 é um gene supressor tumoral envolvido na resposta de danos ao DNA, controle do ciclo celular, na remodelação da cromatina, ubiquitinação e regulação da transcrição. O presente estudo tem como objetivo central caracterizar as mutações do gene BRCA1 associadas a Síndrome Hereditária do Câncer de Mama e/ou Ovário (HBOC) em pacientes atendidos no Serviço de Aconselhamento Genético do Câncer do Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (HCFMRP/USP). Os vinte e dois éxons codificantes do BRCA1 foram analisados utilizando o método de High Resolution Melting (HRM) para triagem de mutações pontuais, seguido pelo sequenciamento de DNA dos casos selecionados para validação. A técnica de MLPA (Multiplex Ligation-dependent Probe Amplification) também foi usada para detectar grandes deleções e duplicações. Uma vez confirmada a mutação, membros da família considerados de alto risco, serão investigados para a mutação específica, a fim de proporcionar-lhes um aconselhamento genético apropriado para a detecção precoce do câncer. No presente estudo, foram investigados 41 pacientes que preencheram os critérios para o teste genético de acordo com NCCN Clinical Practice Guidelines in Oncology v.1.2010. Um total de 21 mutações foram identificadas, duas das quais são patogênicas: a deleção dos éxons 17-18 e a deleção dos éxon 19. Ambas estão localizadas no domínio BRCT do gene BRCA1, essencial para a ligação de fosfoproteínas críticas para a ativação do complexo de reparo do DNA. Outra mutação, a S616del, foi tratada como patogênica, mas apresenta informações controversas em diferentes estudos. O trabalho também identificou uma nova mutação, Val1117Ile. Um estudo de haplótipos das mutações identificadas nos pacientes foi realizado e revelou que um dos haplótipos, denominado de 6, contendo quatro resíduos mutados (871Leu, 1038Gly, 1183Arg e 1613Gly) estava presente em 50% das pacientes. O estudo de associação com 82 indivíduos saudáveis, mostrou diferença significativa (p=0,026) nos pacientes, sugerindo assim um risco aumentado de HBOC. Adicionalmente, foi analisada a mutação germinativa R337H no gene p53 para os casos suspeitos de Síndrome de Li-Fraumeni. Em síntese, o presente estudo contribui com a identificação de uma nova mutação não-sinônina no gene BRCA1 e sugere que o haplótipo 871Leu-1038Gly-1183Arg-1613Gly possa conferir risco aumentado do câncer de mama e/ou ovário em pacientes diagnosticados com HBOC. / About 10% of cases of breast and/or ovary cancer are characterized as hereditary, where the presence of germline mutations in susceptibility BRCA1 gene increases the risk of developing these cancers during womans lifetime. BRCA1 is a tumor suppressor gene involved in DNA damage response, cell cycle control, chromatin remodeling, ubiquitination and transcriptional regulation. The present study aims to characterize BRCA1 gene mutations associated with Hereditary Breast/Ovary Cancer Syndrome (HBOC) in patients from the Cancer Genetic Counseling Service of the General Hospital of the Medical School of Ribeirão Preto, University of São Paulo (HCFMRP-USP). The twenty two coding exons of BRCA1 were analyzed using High Resolution Melting (HRM) method for the screening of point mutations, followed by DNA sequencing of the cases selected to validation. MLPA (Multiplex Ligation-dependent Probe Amplification) technique was also used to detect gross deletions and duplications. Once confirmed the mutation, family members most at risk will be analyzed for the specific mutation in order to provide them with an appropriate genetic counseling for early detection of cancer. In the present study, we investigated 41 patients that fulfilled the criteria for genetic testing according to NCCN Clinical Practice Guidelines in Oncology v.1.2010. A total of 21 mutations were identified, two of them are pathogenic: a deletion of exons 17-18 and a deletion of exon 19. Both of them are located in the BRCT domain of BRCA1 gene, impairing the binding of essential phosphoproteins critical to the activation of DNA repair complex. Another mutation, S616del, shows controversial information about its pathogenesis in different studies.The present study also describes a new mutation, Val1117Ile. A study of haplotypes of the mutations identified in patients was performed and revealed that one of the haplotypes, called 6, containing four mutated residues (871Leu, 1038Gly, and 1183Arg 1613Gly) was present in 50% of patients. The association study with 82 healthy subjects showed a significant difference (p = 0.026) in patients, thus suggesting an increased risk for HBOC. Additionally, the germline mutation R337H on p53 gene was also analyzed in the present study for suspected cases of Li-Fraumeni Syndrome. In summary, this study contributes to the identification of a new missense mutation in the BRCA1 gene and suggests that the haplotype-871Leu-1038Gly 1183Arg-1613Gly may confer increased risk of breast cancer and / or ovarian cancer in patients diagnosed with HBOC.

Time-lapse fluorescence live cell imaging has been widely used to study various dynamic processes in cell biology. As the initial step of image analysis, it is important to localize and segment cell edges with higher accuracy. However, fluorescence live-cell images usually have issues such as low contrast, noises, uneven illumination in comparison to immunofluorescence images. Deep convolutional neural networks, which learn features directly from training images, have successfully been applied in natural image analysis problems. However, the limited amount of training samples prevents their routine application in fluorescence live-cell image analysis. In this thesis, by exploiting the temporal coherence in time-lapse movies together with VGG-16 [1] pre-trained model, we demonstrate that we can train a deep neural network using a limited number of image frames to segment the entire time-lapse movies. We propose a novel framework, vU-net, which combines the advantages of VGG-16 [1] in feature extraction and U-net [2] in feature reconstruction. Moreover, we design an auxiliary convolutional block at the end of the architecture to enhance edge detection. We evaluate our framework using dice coefficient and the distance between the predicted edge and the ground truth on high-resolution image datasets of an adhesion marker, paxillin, acquired by a Total Internal Reflection Fluorescence (TIRF) microscope. Our results demonstrate that, on difficult datasets: (i) The testing dice coefficient of vU-net is 3.2% higher than U-net with the same amount of training images. (ii) vU-net can achieve the best prediction results of U-net with one third of training images needed by U-net. (iii) vU-net produces more robust prediction than U-net. Therefore, vU-net can be more practically applied to challenging live cell movies than U-net since it requires a small size of training sets and achieved accurate segmentation.

Although significant progress has been made in imaging devices during the past few decades, the photographs acquired by digital cameras are still far from perfection due to the physical limitations of hardware such as aperture, lens and sensor. This fact brings out the demand for study on image enhancement: a computational technique that aims to improve the interpretability or perception of information in photographs for human viewers. The work in this thesis mainly focuses on three tasks in image enhancement. / Finally, since the radiance of the real world spans several orders of magnitude and its dynamic range dramatically exceeds the capability of the current digital cameras, there often exist some undesirable over- or under-exposed regions in a photograph. The third part of this thesis aims at producing one great looking well-exposed image that is virtually impossible with a single exposure by compositing a stack of photos at different exposures taken with a conventional camera. Particularly, a simple but effective method is presented to describe how to take advantage of the gradient information to accomplish exposure composition in both static and dynamic scenes. Compared to conventional high dynamic range (HDR) imaging work, the proposed approach is quite appealing in practice since it is computationally efficient and easy to use, and frees users from the tedious radiometric calibration and tone mapping steps. / Firstly, since the camera sensor has limited resolution, the acquired images cannot capture the scene very detailedly. Hence, people often resort to a postprocessing technique called super-resolution (SR) to enhance the resolution of the captured images. In the first part of this thesis, two approaches are presented to address the challenging single image SR problem, which is to recover a high-resolution (HR) image from one low-resolution (LR) input. Specifically, a novel learning-based framework is designed specifically for face image SR task from the perspective of DCT domain. In addition, an efficient two-step scheme is developed to super-resolve generic image by exploiting the salient edges of the input LR image. / Secondly, due to the limitation of lens and aperture, some cameras cannot produce pleasant photographs with desired focus setting. For example, portrait photography that requires shallow depth of field (DOF) is not allowed when using the compact point-and-shoot cameras. In the second part of this thesis, a new and complete postprocessing-based focus editing system that is able to handle the tasks of focus map estimation, image refocusing and defocusing, is developed to overcome the optical limitations and create different kinds of novel photos with desired focus setting from an imperfect photo. / Throughout this work, extensive experiments on various real and synthetic image data are conducted to evaluate the performance of the proposed algorithms. / Zhang, Wei. / Adviser: Wai-Kuen Chan. / Source: Dissertation Abstracts International, Volume: 73-03, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 116-125). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Yang, Mei. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 73-75). / Abstracts in English and Chinese. / THESIS COMMITTEE --- p.II / ABSTRACT --- p.III / 中文摘要 --- p.V / ACKNOWLEDGENTS --- p.VI / TABLE OF CONTENTS --- p.VII / LIST OF FIGURES --- p.IX / LIST OF TABLES --- p.X / Chapter CHAPTER 1 --- INTRODUCTION --- p.1 / Chapter 1.1 --- Matrix isolation spectroscopy --- p.1 / Chapter 1.2 --- Properties of Molecular Hydrogen： A Review --- p.3 / Chapter 1.3 --- Unique properties of solid hydrogen --- p.8 / Chapter CHAPTER 2 --- THEORETICAL BACKGROUND --- p.12 / Chapter 2.1 --- Multipole moments of molecules --- p.12 / Chapter 2.2 --- POLARIZABILITY --- p.14 / Chapter 2.3 --- Pair intermolecular potential --- p.15 / Chapter 2.4 --- Multipole induced transitions --- p.20 / Chapter CHAPTER 3 --- THEORY OF MATRIX ISOLATED 02 IN SOLID PARAHYDROGEN --- p.24 / Chapter 3.1 --- Structural properties of 1602 --- p.24 / Chapter 3.1.1 --- Group theoretical treatment --- p.24 / Chapter 3.1.2 --- Rovibrational wavefunctions and energies --- p.26 / Chapter 3.2 --- O2 isolated in hcp crystal field of parahydrogen --- p.31 / Chapter 3.2.1 --- Group theory --- p.31 / Chapter 3.2.2 --- Crystal field splitting --- p.37 / Chapter 3.2.3 --- Effect of quadrupolar induction --- p.42 / Chapter 3.2.4 --- Pure vibrational transitions --- p.42 / Chapter 3.2.5 --- Calculation of quadrupole matrix elements --- p.47 / Chapter CHAPTER 4 --- RESULTS AND DISCUSSION --- p.54 / Chapter 4.1 --- Results --- p.55 / Chapter 4.1.1 --- Effect of quadrupolar induction --- p.55 / Chapter 4.1.2 --- Crystal field splitting of rovibrational levels of O2 in p-H2 matrix --- p.57 / Chapter 4.1.3 --- Predicted pure vibrational spectrum --- p.64 / Chapter 4.2 --- Discussion and Conclusion --- p.67 / REFERENCE --- p.73

No description available.

The recent disaster of Fukushima in Japan combined with the high demand to enhance nuclear safety and to minimize personal exposure to radioactive materials has a significant impact on research and development of radiation detection instrumentation. Currently, there is ample effort worldwide in the pursuit of radiation detection to maximize the accuracy and meet international standards in terms of size and specifications to enable radiation protection decision making. Among the requirements is the development of a portable, light-weight gamma-ray isotope identifier to be used by first responders in nuclear accidents as well as for radiation security and identification of illicit material isotopes. From nuclear security perspective, research into advanced screening technologies has become a high priority in all aspects, while for occupational safety, and environmental radiation protection, the regulatory authorities are requiring specific performance of radiation detection and measuring devices. At the applied radiation laboratory of the University of Ontario Institute of Technology, UOIT, the development of a high resolution spectrometer for medium and high energy gamma ray has been conducted. The spectrometer used a newly developed scintillator based on a LaBr3(Ce) crystal. The detector has been modeled using advanced Monte Carlo code (MCNP/X code) for the response function simulation and parameter characterization. The simulation results have been validated by experimental investigations using a wide range of gamma radiation energies. The developed spectrometer has been characterized in terms of resolution and response in different fields. It has also been compared with other crystals such as NaI(TI) and LiI(Eu). / UOIT

Recent episodes of extreme weather and the drastic consequences they can have for ecosystems, societies, and economies, emphasize the need for a better understanding of Earths climate. In order to gain a better understanding of modern and future climate, a more thorough knowledge of past climates at the highest resolution possible from different regions is necessary. To this end, a study of seasonal temperature variability in the waters off the northern coast of Iceland was undertaken. Twenty-six bivalves were selected from marine sediment cores recovered from the northern and northwestern coasts of Iceland. Bivalves were selected from intervals of climatic interest as determined from sedimentological characteristics. Shells were micromilled and the carbonate analysed for stable oxygen and carbon isotope values. Oxygen isotope values are driven principally by the temperature of the water from which the shell was precipitated. These data provide a time-series of discrete climate profiles of seasonal temperature variations from c. 360 cal yr BC to cal yr AD 1660, each recording 2 to 9 consecutive years of temperature variability. Several notable warm and cold periods were identified and characterized in terms of maximum and minimum temperatures. As this period overlaps the Viking Age (c. 790 to 1070) and the establishment of Norse colonies in Iceland and Greenland, the temperature record was compared with historical records and demonstrates the significant impact of variation in temperature seasonality on the establishment, development, and in some cases, collapse of societies in the North Atlantic.