“Improved Feature Extraction and Classification Techniques for Multispectral Brain Magnetic Resonance Images”

Magnetic Resonance Imaging (MRI) is a multi sequence medical imaging technique in which stacks of images are acquired with different tissue contrasts. Simultaneous observation and quantitative analysis of normal brain tissues and small abnormalities from these large numbers of different sequences is a great challenge in clinical applications. Multispectral MRI analysis can simplify the job considerably by combining unlimited number of available co-registered sequences in a single suite. However, poor performance of the multispectral system with conventional image classification and segmentation methods makes it inappropriate for clinical analysis. Recent works in multispectral brain MRI analysis attempted to resolve this issue by improved feature extraction approaches, such as transform based methods, fuzzy approaches, algebraic techniques and so forth. Transform based feature extraction methods like Independent Component Analysis (ICA) and its extensions have been effectively used in recent studies to improve the performance of multispectral brain MRI analysis. However, these global transforms were found to be inefficient and inconsistent in identifying less frequently occurred features like small lesions, from large amount of MR data. The present thesis focuses on the improvement in ICA based feature extraction techniques to enhance the performance of multispectral brain MRI analysis. Methods using spectral clustering and wavelet transforms are proposed to resolve the inefficiency of ICA in identifying small abnormalities, and problems due to ICA over-completeness. Effectiveness of the new methods in brain tissue classification and segmentation is confirmed by a detailed quantitative and qualitative analysis with synthetic and clinical, normal and abnormal, data. In comparison to conventional classification techniques, proposed algorithms provide better performance in classification of normal brain tissues and significant small abnormalities.

Multivariate analysis of the dielectric response of materials modeled using networks of resistors and capacitors

We discuss the modeling of dielectric responses of electromagnetically excited networks which are composed of a mixture of capacitors and resistors. Such networks can be employed as lumped-parameter circuits to model the response of composite materials containing conductive and insulating grains. The dynamics of the excited network systems are studied using a state space model derived from a randomized incidence matrix. Time and frequency domain responses from synthetic data sets generated from state space models are analyzed for the purpose of estimating the fraction of capacitors in the network. Good results were obtained by using either the time-domain response to a pulse excitation or impedance data at selected frequencies. A chemometric framework based on a Successive Projections Algorithm (SPA) enables the construction of multiple linear regression (MLR) models which can efficiently determine the ratio of conductive to insulating components in composite material samples. The proposed method avoids restrictions commonly associated with Archie’s law, the application of percolation theory or Kohlrausch-Williams-Watts models and is applicable to experimental results generated by either time domain transient spectrometers or continuous-wave instruments. Furthermore, it is quite generic and applicable to tomography, acoustics as well as other spectroscopies such as nuclear magnetic resonance, electron paramagnetic resonance and, therefore, should be of general interest across the dielectrics community.

Gamma Knife(A (R)) 3-D Dose Distribution Mapping by Magnetic Resonance Imaging

In medical processes where ionizing radiation is used, dose planning and dose delivery are the key elements to patient safety and treatment success, particularly, when the delivered dose in a single session of treatment can be an order of magnitude higher than the regular doses of radiotherapy. Therefore, the radiation dose should be well defined and precisely delivered to the target while minimizing radiation exposure to surrounding normal tissues [1]. Several methods have been proposed to obtain three-dimensional (3-D) dose distribution [2, 3]. In this paper, we propose an alternative method, which can be easily implemented in any stereotactic radiosurgery center with a magnetic resonance imaging (MRI) facility. A phantom with or without scattering centers filled with Fricke gel solution is irradiated with Gamma Knife(A (R)) system at a chosen spot. The phantom can be a replica of a human organ such as head, breast or any other organ. It can even be constructed from a real 3-D MR image of an organ of a patient using a computer-aided construction and irradiated at a specific region corresponding to the tumor position determined by MRI. The spin-lattice relaxation time T (1) of different parts of the irradiated phantom is determined by localized spectroscopy. The T (1)-weighted phantom images are used to correlate the image pixels intensity to the absorbed dose and consequently a 3-D dose distribution with a high resolution is obtained.

Direct Observation of Millisecond to Second Motions in Proteins by Dipolar CODEX NMR Spectroscopy

We present a site-resolved study of stow (ms to s) motions in a protein in the solid (microcrystalline) state performed with the use of a modified version of the centerband-only detection of exchange (CODEX) NMR experiment. CODEX was originally based on measuring changes in molecular orientation by means of the chemical shift anisotropy (CSA) tensor, and in our modification, angular reorientations of internuclear vectors are observed. The experiment was applied to the study of stow (15)N-(1)H motions of the SH3 domain of chicken a-spectrin. The protein was perdeuterated with partial back-exchange of protons at labile sites. This allowed indirect (proton) detection of (15)N nuclei and thus a significant enhancement of sensitivity. The diluted proton system also made negligible proton-driven spin diffusion between (15)N nuclei, which interferes with the molecular exchange (motion) and hampers the acquisition of dynamic parameters. The experiment has shown that approximately half of the peaks in the 2D (15)N-(1)H correlation spectrum exhibit exchange in a different extent. The correlation time of the slow motion for most peaks is 1 to 3 s. This is the first NMR study of the internal dynamics of proteins in the solid state on the millisecond to second time scale with site-specific spectral resolution that provides both time-scale and geometry information about molecular motions.

CONTRA: Improving the performance of dynamic investigations in natural abundance organic solids by mirror-symmetric constant-time CODEX

We present a minor but essential modification to the CODEX 1D-MAS exchange experiment. The new CONTRA method, which requires minor changes of the original sequence only, has advantages over the previously introduced S-CODEX, since it is less sensitive to artefacts caused by finite pulse lengths. The performance of this variant, including the finite pulse effect, was confirmed by SIMPSON calculations and demonstrated on a number of dynamic systems. (C) 2007 Elsevier Inc. All rights reserved.

Effects of Extrusion on the Emulsifying Properties of Rumen and Soy Protein

Defatted rumen protein and soy protein concentrate were extruded in a 15.5:1 L/D single-screw extruder at the optimum conditions for their expansion (150A degrees C and 35% moisture, and 130A degrees C and 35% moisture, respectively). Emulsions were produced with these proteins and studied by rheology and time domain low-resolution (1)H nuclear magnetic resonance (TD-NMR). Extrusion increased storage modulus of rumen protein emulsions. The opposite was observed for soy protein. Mechanical relaxation showed the existence of three relaxing components in the emulsions whose relative contributions were changed by extrusion. Likewise, spin-spin relaxation time constants (T (2)) measured by TD-NMR also showed three major distinct populations of protons in respect to their mobility that were also altered by extrusion. Extrusion increased surface hydrophobicity of both rumen and soy protein. Solubility of rumen protein increased with extrusion whereas soy protein had its solubility decreased after processing. Extrusion promoted molecular reorganization of protein, increasing its superficial hydrophobicity, affecting its interfacial properties and improving its emulsifying behavior. The results show that extrusion can promote the use of rumen, a by-product waste from the meat industry, in human nutrition by replacing soy protein in food emulsions.

NMR study of styrene-butadiene rubber (SBR) and TiO2 nanocomposites

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Nuclear magnetic relaxation of F-19 in fluoride glasses

Temperature and frequency dependence of the F-19 nuclear spin relaxation of the fluoroindate glass, 40InF(3)-20ZnF(2)- 20SrF(2)-2GaF(3)-2NaF-16BaF(2) and the fluorozirconate glass, 50ZrF(4)-20BaF(2)-21LiF-5LaF(3)-4AlF(3); are reported. Measurements were undertaken on pure and Gd3+ doped samples, in the temperature range of 185-1000 K, covering the region below and above the glass transition temperature, T-g. The temperature and frequency dependence of the spin-lattice relaxation rate, T-1(-1), measured in the glassy state at temperature <300 K, is less than the observed dependence at higher temperatures. At temperatures >T-g, the fluorine mobility increases, leading to a more efficient spins lattice relaxation process. Activation energies, for F- motion, are 0.8 eV for the fluoroindate glass and 1 eV for the fluorozirconate glass. The addition of Gd3+ paramagnetic impurities;at 0.1-wt%, does not alter the temperature and frequency dependence of T-1(-1), but increases its magnitude more than one order of magnitude. At temperatures <400 K, the spin-spin relaxation time, T-2(-1), measured for all samples, is determined by the rigid-lattice nuclear dipole-dipole coupling, and it is temperature independent within the accuracy of the measurements. Results obtained for the pure glass, at temperatures >400 K, show that T-2(-1) decreases monotonically as the temperature increases. This decrease is explained as a consequence of the motional narrowing effect caused by the onset of the diffusive motion of the F- ions, with an activation energy around 0.8 eV. For the doped samples, the hyperfine interaction with the paramagnetic impurities is most effective in the relaxation of the nuclear spin, causing an increase in the T(2)(-1)s observed at temperatures >600 K. (C) 1999 Elsevier B.V. B.V. All rights reserved.

Using state-space techniques to represent frequency dependent single-phase lines directly in time domain

This paper proposes to use a state-space technique to represent a frequency dependent line for simulating electromagnetic transients directly in time domain. The distributed nature of the line is represented by a multiple 1t section network made up of the lumped parameters and the frequency dependence of the per unit longitudinal parameters is matched by using a rational function. The rational function is represented by its equivalent circuit with passive elements. This passive circuit is then inserted in each 1t circuit of the cascade that represents the line. Because the system is very sparse, it is possible to use a sparsity technique to store only nonzero elements of this matrix for saving space and running time. The model was used to simulate the energization process of a 10 km length single-phase line. ©2008 IEEE.

Pesquisa e desenvovimento de novos materiais microporosos e mesoporosos para uso em ressonância magnética nuclear por imagem como agentes de contraste

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Desenvolvimento de um magnetometro a precessão nuclear

O objetivo desta tese foi desenvolver um magnetômetro à precessão nuclear para prospecção geofísica e estações-base magnéticas. O magnetômetro à precessão nuclear mede a intensidade total do campo magnético. Seu funcionamento é baseado na ressonância magnética nuclear. A medida de campo é feita pela de terminação da freqüência de precessão de núcleos de hidrogênio – prótons - de líquidos não viscosos no campo magnético terrestre. O magnetômetro é constituído de duas partes: o sensor e o instrumento de medida. O sensor é uma bobina solenoidal, cujo núcleo é preenchido com o líquido. Três líquidos diferentes foram testados; água, propanol e um querosene sintético. Optou-se pelo uso do querosene porque oferece maior amplitude no sinal de precessão, dando, conseqüentemente, maior relação sinal/ ruído. O sistema de medida contém os circuitos de sintonia e amplificação do sinal e, os circuitos lógicos para a programação da operação e contagem da freqüência de precessão. Cada ciclo de medida tem duração de 3 segundos, sendo 2,3s para a polarização e 0,7s para a recepção do sinal. São possíveis dois modos de operação: manual, reciclando automaticamente e por controle remoto. O sinal de precessão é amplificado seletivamente em uma das 14 faixas de sintonia, que cobrem medidas entre 22000 e 95000 gammas. A freqüência de precessão é multiplicada por um fator de 64 e contada durante um tempo igual a 0,36699s, determinado com base na razão giromagnética do próton. O número de pulsos contados é numericamente igual ao valor do campo magnético em gammas. A resposta pode ser lida em mostradores digitais ou na saída BCD paralela quando operando por controle remoto. A precisão da medida é de 1 gamma. O instrumento foi testado no campo para avaliar a relação sinal/ruído, gradiente suportável e consumo de potência. Nos testes de aplicação do protótipo, foram obtidos dados de variação diurna e realizaram-se levantamentos magnético de reconhecimento e detalhe em um sítio arqueológico na Ilha de Marajó, Pará. As respostas dos testes foram comparados com dois magnetômetros comerciais - o GP-70, McPhar e o G-816, Geometrics e, ainda, com dados do Observatório Magnético de Tatuoca-Pa. Em todos os casos, a comparação dos dados mostrou bom desempenho do magnetômetro em teste.

Caracterização da qualidade e previsão dos parâmetros físico-químicos de gasolinas comerciais brasileiras através da aplicação de métodos quimiométricos em perfis (fingerprintings) espectroscópicos de ressonância magnética nuclear

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Order-Disorder Transitions Govern Kinetic Cooperativity and Allostery of Monomeric Human Glucokinase

Glucokinase (GCK) catalyzes the rate-limiting step of glucose catabolism in the pancreas, where it functions as the body's principal glucose sensor. GCK dysfunction leads to several potentially fatal diseases including maturity-onset diabetes of the young type II (MODY-II) and persistent hypoglycemic hyperinsulinemia of infancy (PHHI). GCK maintains glucose homeostasis by displaying a sigmoidal kinetic response to increasing blood glucose levels. This positive cooperativity is unique because the enzyme functions exclusively as a monomer and possesses only a single glucose binding site. Despite nearly a half century of research, the mechanistic basis for GCK's homotropic allostery remains unresolved. Here we explain GCK cooperativity in terms of large-scale, glucose-mediated disorder-order transitions using 17 isotopically labeled isoleucine methyl groups and three tryptophan side chains as sensitive nuclear magnetic resonance (NMR) probes. We find that the small domain of unliganded GCK is intrinsically disordered and samples a broad conformational ensemble. We also demonstrate that small-molecule diabetes therapeutic agents and hyperinsulinemia-associated GCK mutations share a strikingly similar activation mechanism, characterized by a population shift toward a more narrow, well-ordered ensemble resembling the glucose-bound conformation. Our results support a model in which GCK generates its cooperative kinetic response at low glucose concentrations by using a millisecond disorder-order cycle of the small domain as a "time-delay loop," which is bypassed at high glucose concentrations, providing a unique mechanism to allosterically regulate the activity of human GCK under physiological conditions.

Pancreatic iron stores assessed by magnetic resonance imaging (MRI) in beta thalassemic patients

Purpose: To assess the correlation between MRI findings of the pancreas with those of the heart and liver in patients with beta thalassemia; to compare the pancreas T2* MRI results with glucose and ferritin levels and labile plasma iron (LPI). Materials and methods: We retrospectively evaluated chronically transfused patients, testing glucose with enzymatic tests, serum ferritin with chemiluminescence, LPI with cellular fluorescence, and T2* MRI to assess iron content in the heart, liver, and pancreas. MRI results were compared with one another and with serum glucose, ferritin, and LPI. Liver iron concentration (LIC) was determined in 11 patients' liver biopsies by atomic absorption spectrometry. Results: 289 MRI studies were available from 115 patients during the period studied. 9.4% of patients had overt diabetes and an additional 16% of patients had impaired fasting glucose. Both pancreatic and cardiac R2* had predictive power (p < 0.0001) for identifying diabetes. Cardiac and pancreatic R2* were modestly correlated with one another (r(2) = 0.20, p < 0.0001). Both were weakly correlated with LIC (r(2) = 0.09, p < 0.0001 for both) and serum ferritin (r(2) = 0.14, p < 0.0001 and r(2) = 0.03, p < 0.02, respectively). None of the three served as a screening tool for single observations. There is a strong log-log, or power-law, relationship between ratio of signal intensity (SIR) values and pancreas R2* with an r(2) of 0.91. Conclusions: Pancreatic iron overload can be assessed by MRI, but siderosis in other organs did not correlate significantly with pancreatic hemosiderosis. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

ANTERIOR SHOULDER INSTABILITY: CORRELATION BETWEEN MAGNETIC RESONANCE ARTHROGRAPHY, ULTRASOUND ARTHROGRAPHY AND INTRAOPERATIVE FINDINGS

The purpose of the present study was to determine ultrasound (US) arthrography diagnostic accuracy in patients with recurrent shoulder dislocation by comparing US arthrography and magnetic resonance arthrography (MRA) with intraoperative findings. Fifty-six consecutive patients with diagnosis of chronic anterior instability of the shoulder were evaluated for assessment of bone and soft tissue lesions by three radiologists. Twenty-five cases were confirmed by surgery. Sensitivity, specificity, inter-and intraobserver agreement were calculated. Ultrasound sensitivity ranged from 20% to 100% and specificity from 25% to 90%. MRA sensitivity ranged from 80% to 100% and specificity from 50% to 100%. Interobserver agreement was good for MRA (0.54-0.70) and fair for US arthrography (0.19-0.40). Despite a higher interobserver variability for US arthrography than for MRA, our results indicate that US is capable of demonstrating bone and soft tissue lesions related to chronic instability of the shoulder in the presence of intra-articular fluid. (E-mail: marcelo_simao@hotmail.com) (C) 2012 World Federation for Ultrasound in Medicine & Biology.