Proxy-based quantitative estimates of Eocene climates can be made from marine isotope records for ocean conditions or fossil plants for terrestrial environment. However, our understanding about Eocene terrestrial climates is derived mainly from North America and Europe, and little is known about East Asia. Previous qualitative paleoclimate studies briefly revealed three climatic regimes across China during the Eocene with a planetary wind-dominated subtropical to tropical arid zone in the central part (i.e., the subtropical highs), which was flanked by the subtropical climate zone in the north and tropical climate zone in the south. But such a pattern of paleoclimatic zonation still requires a test from quantitative study. Based on analyses of 66 plant assemblages, carefully selected from 37 fossil sites throughout China, we here report the first large-scale quantitative climatic results and discuss the Eocene climatic patterns in China. Our results demonstrate that the Eocene monsoonal climate must have been more or less developed over China, judging from the presence of apparent seasonality of both temperature and precipitation revealed by our quantitative estimation. This appears not to support the previously claimed Eocene planetary wind-dominated climate system, at least in the region of eastern China. In addition, the research indicates that, with a slight declining trend of MAT during the Eocene, the winter temperature substantially dropped in tropical southern China during the middle to late Eocene interval. This might be related to the development of a weak Eocene Kuroshio Current in the southwestern Pacific, and/or a significantly enhanced paleo-winter monsoon from Siberia.

A Ultrassonografia é uma ferramenta que vem sendo bastante utilizada pelas equipes médicas para diagnosticar e monitorar diferentes doenças. Isto pode ser explicado pelo fato de ser não invasiva e ser livre de radiação ionizante. A tomografia por ultrassom (USCT), uma das classes de ultrassonografia, é apresentada como uma alternativa promissora, de baixo custo, na avaliação de patologias e tumores nas glândulas mamárias. Apesar disso, a eficiência dos algoritmos desenvolvidos para o USCT depende tanto dos seus parâmetros iniciais como das características dos objetos dentro do meio de propagação (refletividade, tamanho, contraste). Para melhorar os resultados dos algoritmos de USCT é comum inicializar estes algoritmos com informação anatômica da região a ser reconstruída (Priors). Apesar das melhoras, para baixos contrastes, os efeitos das alterações nos Priors sobre estes algoritmos não são claros, e além disso, não existem estudos sobre a geração e uso de Priors para altos contrastes. Neste trabalho foi investigada a reconstrução tomográfica quantitativa por ultrassom, desde informações provenientes da reflexão, transmissão e espalhamento das ondas de ultrassom, com o intuito de diminuir o erro nos algoritmos de USCT e gerar melhores Priors para múltiplos contrastes. Para este propósito, através de simulações, foram estudadas técnicas que usam a reflexão como caminho para conhecer regiões (máscara por reflexão) ou para inferir bordas dos objetos dentro do meio (Abertura Sintética de Transmissão (STA)), técnicas que assumem transmissão linear do som oferecendo uma ideia da velocidade dentro do meio (Técnicas de Reconstrução Algébrica (ART)) e algoritmos que usam a difração do som (Distorted Born Iterative Method (DBIM)) para, segundo certos limites, inferir melhor tanto bordas como velocidade dos objetos dentro do meio. Também foi analisada como esta última técnica se comporta diante de diversas inicializações (Priors). Como resultados e conclusões neste trabalho mostrou-se: como o aumento do contraste no meio gera os piores resultados do DBIM; perante a boas inicializações do meio de propagação, o algoritmo, independentemente do contraste, tende a gerar boas reconstruções; o uso de estratégias que delimitem ou diminuam o número de variáveis a serem encontradas (máscara por reflexão) junto com o DBIM possibilita uma convergência mais rápida e melhora desempenho deste; inicializar os objetos dentro do meio de propagação (Priors) com áreas maiores do que as esperadas, oferece melhores resultados no DBIM do que trabalhar com áreas menores; informações qualitativas provenientes da reflexão (STA) são relevantes e aumentam a sua importância conforme aumenta o contraste estudado; através dos algoritmos ART, é possível uma delimitação inicial dos objetos dentro do meio para certos contrastes. Estas informações quantitativas podem ser melhoradas por meio da execução conjunta do ART com uma variação do Modified Median Filter aqui proposta. / Ultrasonography is a tool that has been used by medical professionals to diagnose and to monitor different kinds of diseases. This can be explained by its characteristics, such as being non-invasive and being free of ionizing radiation. Ultrasound Tomography (USCT) is one of the classes of ultrasonography, and is presented as a promising low cost alternative in the evaluation of pathologies and tumors in the breast. However, the efficiency of the USCT-algorithms depends both on its initial parameters and of the objects characteristics within the propagation medium (reflectivity, size, contrast). To improve the results of the USCT-algorithms it is common to initialize the algorithms with a-priori anatomical information of the region to be reconstructed (Priors). Despite of improving the results of the USCT-algorithms for low contrasts, the effects of the Priors in these algorithms are not clear, and in addition, there are no studies about the generation and the use of Priors for high contrasts. In this work, quantitative reconstruction for ultrasound was investigated based on information from the reflection, transmission and scattering of ultrasound waves, in order to reduce the error in the USCT-algorithms and to generate better Priors for multiple contrasts. For this purpose, it was studied, through simulations, techniques that use reflection to differentiate regions (reflection mask), or to deduce objects borders within the propagation medium (synthetic transmission aperture (STA)), as well as techniques that assume linear sound transmission to get an idea of the velocity inside the propagation medium (algebraic reconstruction technique (ART)) and algorithms that use sound diffraction (Distorted Born Iterative Method (DBIM)) to better infer both edges and velocity of objects within the propagation medium. It was also analyzed how the DBIM behaves due to multiple initializations (Priors). As results and conclusions, it was shown: how the increase of contrast in the propagation medium generates the worse results of the DBIM; in the presence of a good initialization of the propagation medium, the DBIM, regardless of the contrast, tends to generate good reconstructions; the use of strategies that delimit or reduce the number of unknown variables (reflection mask) along with the DBIM enables fast convergence and it improves the DBIM\'s performance; initializing the objects within the propagation medium with areas larger than expected provides better DBIM results than working with smaller areas; qualitative information derived from the reflection (STA) are relevant and increase their importance as the contrast increases; initial delimitation of objects within the propagation medium for certain contrasts is possible via transmission reconstruction. This quantitative information can be improved through the implementation of ART together with a variation of the Modified Median Filter here proposed.

<p>X-ray computed tomography (CT) is a non-destructive medical imaging technique for assessing the cross-sectional images of an object in terms of attenuation. As it is designed based on the physical processes involved in the x-ray and matter interactions, faithfully modeling the physics in the reconstruction procedure can yield accurate attenuation distribution of the scanned object. Otherwise, unrealistic physical assumptions can result in unwanted artifacts in reconstructed images. For example, the current reconstruction algorithms assume the photons emitted by the x-ray source are mono-energetic. This oversimplified physical model neglects the poly-energetic properties of the x-ray source and the nonlinear attenuations of the scanned materials, and results in the well-known beam-hardening artifacts (BHAs). The purpose of this work was to incorporate the poly-energetic nature of the x-ray spectrum and then to eliminate BHAs. By accomplishing this, I can improve the image quality, enable the quantitative reconstruction ability of the single-spectrum CT scanner, and potentially reduce unnecessary radiation dose to patients.</p><p>In this thesis, in order to obtain accurate spectrum for poly-energetic reconstruction, I first presented a novel spectral estimation technique, with which spectra across a large range of angular trajectories of the imaging field of view can be estimated with a single phantom and a single axial acquisition. The experimental results with a 16 cm diameter cylindrical phantom (composition: ultra-high-molecular-weight polyethylene [UHMWPE]) on a clinical scanner showed that the averaged absolute mean energy differences and the normalized root mean square differences with respect to the actual spectra across kVp settings (i.e., 80, 100, 120, 140) and angular trajectories were less than 0.61 keV and 3.41%, respectively</p><p>With the previous estimation of the x-ray spectra, three poly-energetic reconstruction algorithms are proposed for different clinical applications. The first algorithm (i.e., poly-energetic iterative FBP [piFBP]) can be applied to routine clinical CT exams, as the spectra of the x-ray source and the nonlinear attenuations of diverse body tissues and metal implant materials are incorporated to eliminate BHAs and to reduce metal artifacts. The simulation results showed that the variation range of the relative errors of various tissues across different phantom sizes (i.e., 16, 24, 32, and 40 cm in diameter) and kVp settings (80, 100, 120, 140) were reduced from [-7.5%, 17.5%] for conventional FBP to [-0.1%, 0.1%] for piFBP, while the noise was maintained at the same low level (about [0.3%, 1.7%]).</p><p>When iodinated contrast agents are involved and patient motions are not readily correctable (e.g., in myocardial perfusion exam), a second algorithm (i.e., poly-energetic simultaneous algebraic reconstruction technique [pSART]) can be applied to eliminate BHAs and to quantitatively determine the iodine concentrations of blood-iodine mixtures with our new technique. The phantom experiment on a clinical CT scanner indicated that the maximum absolute relative error across material inserts was reduced from 4.1% for conventional simultaneous algebraic reconstruction technique [SART] to 0.4% for pSART.</p><p>Extending the work beyond minimizing BHAs, if patient motions are correctable or negligible, a third algorithm (i.e., poly-energetic dynamic perfusion algorithm [pDP]) is developed to retrieve iodine maps of any iodine-tissue mixtures in any perfusion exams, such as breast, lung, or brain perfusion exams. The quantitative results of the simulations with a dynamic anthropomorphic thorax phantom indicated that the maximum error of iodine concentrations can be reduced from 1.1 mg/cc for conventional FBP to less than 0.1 mg/cc for pDP.</p><p>Two invention disclosure forms based on the work presented in this thesis have been submitted to Office of Licensing & Ventures of Duke University.</p> / Dissertation

A Ultrassonografia é uma ferramenta que vem sendo bastante utilizada pelas equipes médicas para diagnosticar e monitorar diferentes doenças. Isto pode ser explicado pelo fato de ser não invasiva e ser livre de radiação ionizante. A tomografia por ultrassom (USCT), uma das classes de ultrassonografia, é apresentada como uma alternativa promissora, de baixo custo, na avaliação de patologias e tumores nas glândulas mamárias. Apesar disso, a eficiência dos algoritmos desenvolvidos para o USCT depende tanto dos seus parâmetros iniciais como das características dos objetos dentro do meio de propagação (refletividade, tamanho, contraste). Para melhorar os resultados dos algoritmos de USCT é comum inicializar estes algoritmos com informação anatômica da região a ser reconstruída (Priors). Apesar das melhoras, para baixos contrastes, os efeitos das alterações nos Priors sobre estes algoritmos não são claros, e além disso, não existem estudos sobre a geração e uso de Priors para altos contrastes. Neste trabalho foi investigada a reconstrução tomográfica quantitativa por ultrassom, desde informações provenientes da reflexão, transmissão e espalhamento das ondas de ultrassom, com o intuito de diminuir o erro nos algoritmos de USCT e gerar melhores Priors para múltiplos contrastes. Para este propósito, através de simulações, foram estudadas técnicas que usam a reflexão como caminho para conhecer regiões (máscara por reflexão) ou para inferir bordas dos objetos dentro do meio (Abertura Sintética de Transmissão (STA)), técnicas que assumem transmissão linear do som oferecendo uma ideia da velocidade dentro do meio (Técnicas de Reconstrução Algébrica (ART)) e algoritmos que usam a difração do som (Distorted Born Iterative Method (DBIM)) para, segundo certos limites, inferir melhor tanto bordas como velocidade dos objetos dentro do meio. Também foi analisada como esta última técnica se comporta diante de diversas inicializações (Priors). Como resultados e conclusões neste trabalho mostrou-se: como o aumento do contraste no meio gera os piores resultados do DBIM; perante a boas inicializações do meio de propagação, o algoritmo, independentemente do contraste, tende a gerar boas reconstruções; o uso de estratégias que delimitem ou diminuam o número de variáveis a serem encontradas (máscara por reflexão) junto com o DBIM possibilita uma convergência mais rápida e melhora desempenho deste; inicializar os objetos dentro do meio de propagação (Priors) com áreas maiores do que as esperadas, oferece melhores resultados no DBIM do que trabalhar com áreas menores; informações qualitativas provenientes da reflexão (STA) são relevantes e aumentam a sua importância conforme aumenta o contraste estudado; através dos algoritmos ART, é possível uma delimitação inicial dos objetos dentro do meio para certos contrastes. Estas informações quantitativas podem ser melhoradas por meio da execução conjunta do ART com uma variação do Modified Median Filter aqui proposta. / Ultrasonography is a tool that has been used by medical professionals to diagnose and to monitor different kinds of diseases. This can be explained by its characteristics, such as being non-invasive and being free of ionizing radiation. Ultrasound Tomography (USCT) is one of the classes of ultrasonography, and is presented as a promising low cost alternative in the evaluation of pathologies and tumors in the breast. However, the efficiency of the USCT-algorithms depends both on its initial parameters and of the objects characteristics within the propagation medium (reflectivity, size, contrast). To improve the results of the USCT-algorithms it is common to initialize the algorithms with a-priori anatomical information of the region to be reconstructed (Priors). Despite of improving the results of the USCT-algorithms for low contrasts, the effects of the Priors in these algorithms are not clear, and in addition, there are no studies about the generation and the use of Priors for high contrasts. In this work, quantitative reconstruction for ultrasound was investigated based on information from the reflection, transmission and scattering of ultrasound waves, in order to reduce the error in the USCT-algorithms and to generate better Priors for multiple contrasts. For this purpose, it was studied, through simulations, techniques that use reflection to differentiate regions (reflection mask), or to deduce objects borders within the propagation medium (synthetic transmission aperture (STA)), as well as techniques that assume linear sound transmission to get an idea of the velocity inside the propagation medium (algebraic reconstruction technique (ART)) and algorithms that use sound diffraction (Distorted Born Iterative Method (DBIM)) to better infer both edges and velocity of objects within the propagation medium. It was also analyzed how the DBIM behaves due to multiple initializations (Priors). As results and conclusions, it was shown: how the increase of contrast in the propagation medium generates the worse results of the DBIM; in the presence of a good initialization of the propagation medium, the DBIM, regardless of the contrast, tends to generate good reconstructions; the use of strategies that delimit or reduce the number of unknown variables (reflection mask) along with the DBIM enables fast convergence and it improves the DBIM\'s performance; initializing the objects within the propagation medium with areas larger than expected provides better DBIM results than working with smaller areas; qualitative information derived from the reflection (STA) are relevant and increase their importance as the contrast increases; initial delimitation of objects within the propagation medium for certain contrasts is possible via transmission reconstruction. This quantitative information can be improved through the implementation of ART together with a variation of the Modified Median Filter here proposed.

Continental Paleogene climates have been well studied in Europe and North America, but very little is known from Asia because paleoclimatic results have only been reported from particular geological intervals. Here, based on 29 plant assemblages from 8 well age-controlled fossiliferous sites, we quantitatively reconstruct the climates through most of the Paleogene of northeast China and discuss related seasonal variations. Our results demonstrate that the mean annual temperature (MAT) gradient was fairly shallow (0.27 °C/1° latitude) during the Paleocene throughout this region. In the Eocene, seasonality was high in the region, indicated by marked differences in both temperature and precipitation between winters and summers of the sites. The paleo-East Asian monsoon must have had intensified at least in the late mid Eocene, shown by apparent differences in annual precipitation distribution at all the sites. Regarding the Paleogene climatic evolution of northeast China, our quantitative results suggest that MAT overall declined from warm in the Paleocene and Eocene to moderate in the Oligocene, generally consistent with the trend of marine records but with some distinctions. Two significant cooling events are recognized in the early and mid Eocene with MAT 3.4 °C and 3.8 °C lower, and winter temperature 5.8 °C and 4.7 °C lower, respectively, in similar magnitudes to corresponding variations in Europe and North America. Furthermore, the present results show that MAT rebounded in the late mid Eocene and then decreased until the Oligocene, a similar pattern demonstrated in Europe during the mid Eocene to Oligocene interval.

Pollen spectra found in sediments enable the research of quantitative changes in vegetation composition in the past. The fact is conditioned upon assumption of unchangeable linear relationship between abundance of pollen and the vegetation that is responsible for its production. Calibration of this relationship is experimentally performed on modern pollen samples and current vegetation. Relative pollen produktivity etimates (PPEs) represents basic parameters for the conversion of proportional pollen data into the vegetational ones. Their knowledge is indispensible for the quantitative vegetation restoration and for the simulating of the processes of pollen dispersion and deposition. PPEs estimation is performed by ERV model which corrects nonlinear relationship of proportional pollen and vegetation data back to the linear relationship. ERV model estimates PPEs values together with values of pollen background by maximum likelihood method. Knowledge of PPEs of main tree species is crucial for the understanding of processes which takes place on the level of landscape scale. Model area of Křivoklátsko was selected due to its high forest coverage and tree diversity. Twenty-four localities were chosen upon stratified random selection. Moss polsters containing modern pollen loading were taken and detailed...

L'imagerie photoacoustique (IPA) des tissus biologiques permet de combiner les avantages des imageries optique et ultrasonore. Le principal contraste endogène pour l’IPA provient des vaisseaux sanguins en raison de la forte absorption de l'hémoglobine par rapport aux tissus environnants. De plus, les vaisseaux sanguins sont à peu près cylindriques et la concentration d'hémoglobine peut être supposée uniforme à l'intérieur des veines. Comme première contribution, nous avons développé dans cette thèse un modèle analytique de fluence optique pour plusieurs inhomogénéités cylindriques parallèles incorporées dans un milieu turbide. Les modèles analytiques n’existent que pour les cas simples. Pour traiter des situations plus complexes, comme les tissus biologiques, les méthodes numériques sont nécessaires. La deuxième contribution de cette thèse consiste à développer un solveur multigrilles de l'équation de diffusion optique et donc de proposer une méthode numérique efficace pour résoudre la fluence optique. Enfin, notre troisième contribution concerne la reconstruction de la tomographie quantitative photoacoustique (TQPA). Basée sur les modèles efficaces présentées dans les première et seconde contributions, nous avons proposé une méthode de reconstruction basée sur le modèle direct analytique pour les cas simples et une méthode d'inversion basée sur multigrille pour les cas plus réalistes. Les avantages de la méthode d'inversion basée sur multigrille sont présentés à la fois en terme de temps de calcul et de vitesse de convergence. Une validation expérimentale est présentée dans le dernier chapitre de cette thèse, prouvant la validité et l'analyse des performances des méthodes développées. / Photoacoustic imaging (PAI) of biological tissues tries to combine the advantages of optical and acoustical imaging. The main endogenous contrast for PAI is derived from blood vessels due to the strong absorption of hemoglobin compared to the background tissues. Furthermore, blood vessels are roughly cylindrical and hemoglobin concentration can be assumed to be uniform inside the vessel. Therefore, the blood vessels can be considered as “cylindrical inhomogeneities”. As a first contribution, we have developed in this thesis an analytical model of optical fluence for multiple parallel cylindrical inhomogeneities embedded in an otherwise homogeneous turbid medium. Analytical models only exist for simple cases. To deal with more complex situations like biological tissues, numerical methods are required. The second contribution of this thesis is to develop a multigrid solver of optical diffusion equation and therefore to propose an efficient numerical method to resolve the optical fluence. Finally, our third contribution is concerned with quantitative PA tomography (QPAT) reconstruction. Based on the efficient models presented in the first and second contributions, we have proposed an analytic-based reconstruction method for simple cases and a multigrid-based inversion scheme for more realistic cases. The advantages of multigrid-based inversion scheme are shown in both computation and convergence speed. An experimental validation is presented in the last chapter of this thesis, proving the validity and analyzing the performances of the developed methods.