Comparison of linear and non-linear 2D+T registration methods for DE-MRI cardiac perfusion studies

A series of motion compensation algorithms is run on the challenge data including methods that optimize only a linear transformation, or a non-linear transformation, or both – first a linear and then a non-linear transformation. Methods that optimize a linear transformation run an initial segmentation of the area of interest around the left myocardium by means of an independent component analysis (ICA) (ICA-*). Methods that optimize non-linear transformations may run directly on the full images, or after linear registration. Non-linear motion compensation approaches applied include one method that only registers pairs of images in temporal succession (SERIAL), one method that registers all image to one common reference (AllToOne), one method that was designed to exploit quasi-periodicity in free breathing acquired image data and was adapted to also be usable to image data acquired with initial breath-hold (QUASI-P), a method that uses ICA to identify the motion and eliminate it (ICA-SP), and a method that relies on the estimation of a pseudo ground truth (PG) to guide the motion compensation.

Packing of atermal polymers in the bulk and under confinement

Polymers constitute a distinct class of anisotropic particles with unique dynamical, rheological and mechanical properties.

Non-Destructive Global and Localized 2D T1/T2 NMR Relaxometry to Resolve Microstructure in Apples Affected by Watercore

Apples can be considered as having a complex system formed by several structures at different organization levels: macroscale (>100 μm) and microscale (<100 μm). This work implements 2D T1/T2 global and localized relaxometry sequences on whole apples to be able to perform an intensive non-destructive and non-invasive microstructure study. The 2D T1/T2 cross-correlation spectroscopy allows the extraction of quantitative information about the water compartmentation in different subcellular organelles. A clear difference is found as sound apples show neat peaks for water in different subcellular compartments, such as vacuolar, cytoplasmatic and extracellular water, while in watercore-affected tissues such compartments appear merged. Localized relaxometry allows for the predefinition of slices in order to understand the microstructure of a particular region of the fruit, providing information that cannot be derived from global 2D T1/T2 relaxometry.

1D and 2D neutral particle patterning by dielectrophoretic forces on z-cut Fe:LiNbO3 crystals

1D and 2D patterning of uncharged micro- and nanoparticles via dielectrophoretic forces on photovoltaic z-cut Fe:LiNbO3 have been investigated for the first time. The technique has been successfully applied with dielectric micro-particles of CaCO3 (diameter d = 1-3 μm) and metal nanoparticles of Al (d = 70 nm). At difference with previous experiments in x- and y-cut, the obtained patterns locally reproduce the light distribution with high fidelity. A simple model is provided to analyse the trapping process. The results show the remarkably good capabilities of this geometry for high quality 2D light-induced dielectrophoretic patterning overcoming the important limitations presented by previous configurations.

Comparative theoretical analysis between parallel and perpendicular geometries for 2D particle patterning in photovoltaic ferroelectric substrates

This paper describes the dielectrophoretic potential created by the evanescent electric field acting on a particle near a photovoltaic crystal surface depending on the crystal cut. This electric field is obtained from the steady state solution of the Kukhtarev equations for the photovoltaic effect, where the diffusion term has been disregarded. First, the space charge field generated by a small, square, light spot where d _ l (being d a side of the square and l the crystal thickness) is studied. The surface charge density generated in both geometries is calculated and compared as their relation determines the different properties of the dielectrophoretic potential for both cuts. The shape of the dielectrophoretic potential is obtained and compared for several distances to the sample. Afterwards other light patterns are studied by the superposition of square spots, and the resulting trapping profiles are analysed. Finally the surface charge densities and trapping profiles for different d/l relations are studied.

Visual attention and perception models for assessing quality in 2D and 3D stereoscopic video

La medida de calidad de vídeo sigue siendo necesaria para definir los criterios que caracterizan una señal que cumpla los requisitos de visionado impuestos por el usuario. Las nuevas tecnologías, como el vídeo 3D estereoscópico o formatos más allá de la alta definición, imponen nuevos criterios que deben ser analizadas para obtener la mayor satisfacción posible del usuario. Entre los problemas detectados durante el desarrollo de esta tesis doctoral se han determinado fenómenos que afectan a distintas fases de la cadena de producción audiovisual y tipo de contenido variado. En primer lugar, el proceso de generación de contenidos debe encontrarse controlado mediante parámetros que eviten que se produzca el disconfort visual y, consecuentemente, fatiga visual, especialmente en lo relativo a contenidos de 3D estereoscópico, tanto de animación como de acción real. Por otro lado, la medida de calidad relativa a la fase de compresión de vídeo emplea métricas que en ocasiones no se encuentran adaptadas a la percepción del usuario. El empleo de modelos psicovisuales y diagramas de atención visual permitirían ponderar las áreas de la imagen de manera que se preste mayor importancia a los píxeles que el usuario enfocará con mayor probabilidad. Estos dos bloques se relacionan a través de la definición del término saliencia. Saliencia es la capacidad del sistema visual para caracterizar una imagen visualizada ponderando las áreas que más atractivas resultan al ojo humano. La saliencia en generación de contenidos estereoscópicos se refiere principalmente a la profundidad simulada mediante la ilusión óptica, medida en términos de distancia del objeto virtual al ojo humano. Sin embargo, en vídeo bidimensional, la saliencia no se basa en la profundidad, sino en otros elementos adicionales, como el movimiento, el nivel de detalle, la posición de los píxeles o la aparición de caras, que serán los factores básicos que compondrán el modelo de atención visual desarrollado. Con el objetivo de detectar las características de una secuencia de vídeo estereoscópico que, con mayor probabilidad, pueden generar disconfort visual, se consultó la extensa literatura relativa a este tema y se realizaron unas pruebas subjetivas preliminares con usuarios. De esta forma, se llegó a la conclusión de que se producía disconfort en los casos en que se producía un cambio abrupto en la distribución de profundidades simuladas de la imagen, aparte de otras degradaciones como la denominada “violación de ventana”. A través de nuevas pruebas subjetivas centradas en analizar estos efectos con diferentes distribuciones de profundidades, se trataron de concretar los parámetros que definían esta imagen. Los resultados de las pruebas demuestran que los cambios abruptos en imágenes se producen en entornos con movimientos y disparidades negativas elevadas que producen interferencias en los procesos de acomodación y vergencia del ojo humano, así como una necesidad en el aumento de los tiempos de enfoque del cristalino. En la mejora de las métricas de calidad a través de modelos que se adaptan al sistema visual humano, se realizaron también pruebas subjetivas que ayudaron a determinar la importancia de cada uno de los factores a la hora de enmascarar una determinada degradación. Los resultados demuestran una ligera mejora en los resultados obtenidos al aplicar máscaras de ponderación y atención visual, los cuales aproximan los parámetros de calidad objetiva a la respuesta del ojo humano. ABSTRACT Video quality assessment is still a necessary tool for defining the criteria to characterize a signal with the viewing requirements imposed by the final user. New technologies, such as 3D stereoscopic video and formats of HD and beyond HD oblige to develop new analysis of video features for obtaining the highest user’s satisfaction. Among the problems detected during the process of this doctoral thesis, it has been determined that some phenomena affect to different phases in the audiovisual production chain, apart from the type of content. On first instance, the generation of contents process should be enough controlled through parameters that avoid the occurrence of visual discomfort in observer’s eye, and consequently, visual fatigue. It is especially necessary controlling sequences of stereoscopic 3D, with both animation and live-action contents. On the other hand, video quality assessment, related to compression processes, should be improved because some objective metrics are adapted to user’s perception. The use of psychovisual models and visual attention diagrams allow the weighting of image regions of interest, giving more importance to the areas which the user will focus most probably. These two work fields are related together through the definition of the term saliency. Saliency is the capacity of human visual system for characterizing an image, highlighting the areas which result more attractive to the human eye. Saliency in generation of 3DTV contents refers mainly to the simulated depth of the optic illusion, i.e. the distance from the virtual object to the human eye. On the other hand, saliency is not based on virtual depth, but on other features, such as motion, level of detail, position of pixels in the frame or face detection, which are the basic features that are part of the developed visual attention model, as demonstrated with tests. Extensive literature involving visual comfort assessment was looked up, and the development of new preliminary subjective assessment with users was performed, in order to detect the features that increase the probability of discomfort to occur. With this methodology, the conclusions drawn confirmed that one common source of visual discomfort was when an abrupt change of disparity happened in video transitions, apart from other degradations, such as window violation. New quality assessment was performed to quantify the distribution of disparities over different sequences. The results confirmed that abrupt changes in negative parallax environment produce accommodation-vergence mismatches derived from the increasing time for human crystalline to focus the virtual objects. On the other side, for developing metrics that adapt to human visual system, additional subjective tests were developed to determine the importance of each factor, which masks a concrete distortion. Results demonstrated slight improvement after applying visual attention to objective metrics. This process of weighing pixels approximates the quality results to human eye’s response.

Structure and function in rhodopsin: Packing of the helices in the transmembrane domain and folding to a tertiary structure in the intradiscal domain are coupled*

A previous study of the retinitis pigmentosa mutation L125R and two designed mutations at this site, L125A and L125F, showed that these mutations cause partial or total misfolding of the opsins expressed in COS cells from the corresponding mutant opsin genes. We now report on expression and characterization of the opsins from the following retinitis pigmentosa mutants in the transmembrane domain of rhodopsin that correspond to six of the seven helices: G51A and G51V (helix A), G89D (helix B), A164V (helix D), H211P (helix E), P267L and P267R (helix F), and T297R (helix G). All the mutations caused partial misfolding of the opsins as observed by the UV/visible absorption characteristics and by separation of the expressed opsins into fractions that bound 11-cis-retinal to form the corresponding mutant rhodopsins and those that did not bind 11-cis-retinal. Further, all the mutant rhodopsins prepared from the above mutants, except for G51A, showed strikingly abnormal bleaching behavior with abnormal metarhodopsin II photointermediates. The results show that retinitis pigmentosa mutations in every one of the transmembrane helices can cause misfolding of the opsin. Therefore, on the basis of these and previous results, we conclude that defects in the packing of the transmembrane helices resulting from these mutations are relayed to the intradiscal domain, where they cause misfolding of the opsin by inducing the formation of a disulfide bond other than the native Cys-110—Cys-187 disulfide bond. Thus, there is coupling between packing of the helices in the transmembrane domain and folding to a tertiary structure in the intradiscal domain.

A general method for determining helix packing in membrane proteins in situ: Helices I and II are close to helix VII in the lactose permease of Escherichia coli

It was previously shown that coexpression of the lactose permease of Escherichia coli in two contiguous fragments leads to functional complementation. We demonstrate here that site-directed thiol crosslinking of coexpressed permease fragments can be used to determine helix proximity in situ without the necessity of purifying the permease. After coexpression of the six N-terminal (N6) and six C-terminal (C6) transmembrane helices, each with a single Cys residue, crosslinking was carried out in native membranes and assessed by the mobility of anti-C-terminal-reactive polypeptides on immunoblots. A Cys residue at position 242 or 245 (helix VII) forms a disulfide with a Cys residue at either position 28 or 29 (helix I), but not with a Cys residue at position 27, which is on the opposite face of helix I, thereby indicating that the face of helix I containing Pro-28 and Phe-29 is close to helix VII. Similarly, a Cys residue at position 242 or 245 (helix VII) forms a disulfide with a Cys residue at either position 52 or 53 (helix II), but not with a Cys residue at position 54. Furthermore, low-efficiency crosslinking is observed between a Cys residue at position 52 or 53 and a Cys residue at position 361 (helix XI). The results indicate that helix VII lies in close proximity to both helices I and II and that helix II is also close to helix XI. The method should be applicable to a number of different polytopic membrane proteins.

Advances in random matrix theory, zeta functions, and sphere packing

Over four hundred years ago, Sir Walter Raleigh asked his mathematical assistant to find formulas for the number of cannonballs in regularly stacked piles. These investigations aroused the curiosity of the astronomer Johannes Kepler and led to a problem that has gone centuries without a solution: why is the familiar cannonball stack the most efficient arrangement possible? Here we discuss the solution that Hales found in 1998. Almost every part of the 282-page proof relies on long computer verifications. Random matrix theory was developed by physicists to describe the spectra of complex nuclei. In particular, the statistical fluctuations of the eigenvalues (“the energy levels”) follow certain universal laws based on symmetry types. We describe these and then discuss the remarkable appearance of these laws for zeros of the Riemann zeta function (which is the generating function for prime numbers and is the last special function from the last century that is not understood today.) Explaining this phenomenon is a central problem. These topics are distinct, so we present them separately with their own introductory remarks.

A cooperative model for receptor recognition and cell adhesion: evidence from the molecular packing in the 1.6-A crystal structure of the pheromone Er-1 from the ciliated protozoan Euplotes raikovi.

The crystal structure of the pheromone Er-1 from the unicellular eukaryotic organism Euplotes raikovi was determined at 1.6 A resolution and refined to a crystallographic R factor of 19.9%. In the tightly packed crystal, two extensive intermolecular helix-helix interactions arrange the Er-1 molecules into layers. Since the putative receptor of the pheromone is a membrane-bound protein, whose extracellular C-terminal domain is identical in amino acid sequence to the soluble pheromone, the interactions found in the crystal may mimic the pheromone-receptor interactions as they occur on a cell surface. Based on this, we propose a model for the interaction between soluble pheromone molecules and their receptors. In this model, strong pheromone-receptor binding emerges as a consequence of the cooperative utilization of several weak interactions. The model offers an explanation for the results of binding studies and may also explain the adhesion between cells that occurs during mating.

Primary and secondary metabolites production in signal grass around the year under nitrogen fertilizer

Plants produce a number of substances and products and primary and secondary metabolites (SM) are amongst them with many benefits but limitation as well. Usually, the fodder are not considered toxic to animals or as a source having higher SM. The Brachiaria decumbens has a considerable nutritional value, but it is considered as a toxic grass for causing photosensitization in animals, if the grass is not harvested for more than 30 days or solely. The absence of detailed information in the literature about SM in Brachiaria, metabolites production and its chemical profile enable us to focus not only on the nutritive value but to get answers in all aspects and especially on toxicity. The study was conducted in the period of december 2013 to december 2014; in greenhouse FZEA-USP. B. decumbens was used with two cutting heights (10 and 20 cm) and nitrogen doses (0, 150, 300 and 450 kg ha-1) in complete randomized block design. The bromatological analysis were carried out on near infrared spectroscopy. Generally, the application of 150 kg ha-1 N was sufficient to promote the nutritional value in B. decumbens but above it the nitrogen use efficiency decline significantly. The highest dry matter yield (99.97 g/pot) was observed in autumn and the lowest was in winter (30.20 g/pot). While, as per nitrogen dose the average highest dry matter yield was at 150 kg ha-1 (79.98 g/pot). The highest crude protein was observed in winter (11.88%) and the lowest in autumn (7.78%). By the cutting heights; the 10 cm proved to have high CP (9.51%). In respect of fibrous contents, the highest acid detergent fiber was noted in summer (36.37%) and lowest in winter (30.88%). While the neutral detergent fiber was being highest in autumn and lowest in spring (79.60%). The highest in vitro dry matter and organic matter digestibilities were noted at 300 kg ha-1 N; being 68.06 and 60.57%; respectively; with the lowest observed in without N treatments (62.63% and 57.97), respectively. For determination of the classes, types and concentration of SM in B. decumbens, phytochemical tests, thin layer and liquid chromatography-mass spectrometry and nuclear magnetic resonance analysis were carried out. Height, nitrogen and seasons significantly (P <0.0001) affected the secondary metabolic profile. A new protodioscin isomer (protoneodioscin (25S-)) was identified for first time in B. decumbens and is supposed to be the probable toxicity reason. Its structure was verified by 1D and 2D NMR techniques (1H, 13C) and 1D (COSY-45, edited HSQC, HMBC, H2BC, HSQC -TOCSY, NOESY and 1 H, 1 H, J). All factors influence the metabolic profile significantly (P <0.0001). The lowest phenols were at 300 kg ha-1 while the lowest flavones were at 0 kg ha-1. Season wise the highest phenols occurred in autumn (19.65 mg/g d.wt.) and highest flavones (28.87 mg/g d.wt.) in spring. Seasons effect the saponin production significantly (P <0.0001) and the results showed significant differences in the protodioscin (17.63±4.3 - 22.57±2.2 mg/g d.wt.) and protoneodioscin (23.3±1.2 - 31.07±2.9 mg/g d.wt.) concentrations. The highest protodioscin isomers concentrations were observed in winter and spring and by N doses the highest were noted in 300 kg ha-1. Simply, all factors significantly played their role in varying concentrations of secondary metabolites.

Professor Sewall's Lectures on the Hebrew and Oriental Languages, Vol. 2d, 1767-1780

This volume contains lectures delivered by Sewall to Harvard students. The first lecture in the volume, Lecture XV, was read on March 9, 1767; October 8, 1770, August 22, 1774, and December 13, 1778. The last lecture in the volume, Lecture XXVII, was read on June 13, 1768; May 4, 1772; July 29, 1776; and June 5, 1780.

Tight-Binding Approximations in 1D and 2D Coupled-Cavity Photonic Crystal Structures

Light confinement and controlling an optical field has numerous applications in the field of telecommunications for optical signals processing. When the wavelength of the electromagnetic field is on the order of the period of a photonic microstructure, the field undergoes reflection, refraction, and coherent scattering. This produces photonic bandgaps, forbidden frequency regions or spectral stop bands where light cannot exist. Dielectric perturbations that break the perfect periodicity of these structures produce what is analogous to an impurity state in the bandgap of a semiconductor. The defect modes that exist at discrete frequencies within the photonic bandgap are spatially localized about the cavity-defects in the photonic crystal. In this thesis the properties of two tight-binding approximations (TBAs) are investigated in one-dimensional and two-dimensional coupled-cavity photonic crystal structures We require an efficient and simple approach that ensures the continuity of the electromagnetic field across dielectric interfaces in complex structures. In this thesis we develop \textrm{E} -- and \textrm{D} --TBAs to calculate the modes in finite 1D and 2D two-defect coupled-cavity photonic crystal structures. In the \textrm{E} -- and \textrm{D} --TBAs we expand the coupled-cavity \overrightarrow{E} --modes in terms of the individual \overrightarrow{E} -- and \overrightarrow{D} --modes, respectively. We investigate the dependence of the defect modes, their frequencies and quality factors on the relative placement of the defects in the photonic crystal structures. We then elucidate the differences between the two TBA formulations, and describe the conditions under which these formulations may be more robust when encountering a dielectric perturbation. Our 1D analysis showed that the 1D modes were sensitive to the structure geometry. The antisymmetric \textrm{D} mode amplitudes show that the \textrm{D} --TBA did not capture the correct (tangential \overrightarrow{E} --field) boundary conditions. However, the \textrm{D} --TBA did not yield significantly poorer results compared to the \textrm{E} --TBA. Our 2D analysis reveals that the \textrm{E} -- and \textrm{D} --TBAs produced nearly identical mode profiles for every structure. Plots of the relative difference between the \textrm{E} and \textrm{D} mode amplitudes show that the \textrm{D} --TBA did capture the correct (normal \overrightarrow{E} --field) boundary conditions. We found that the 2D TBA CC mode calculations were 125-150 times faster than an FDTD calculation for the same two-defect PCS. Notwithstanding this efficiency, the appropriateness of either TBA was found to depend on the geometry of the structure and the mode(s), i.e. whether or not the mode has a large normal or tangential component.