Graphical Model-Based Vertebra Identification from X-Ray Image(s)

Automated identification of vertebrae from X-ray image(s) is an important step for various medical image computing tasks such as 2D/3D rigid and non-rigid registration. In this chapter we present a graphical model-based solution for automated vertebra identification from X-ray image(s). Our solution does not ask for a training process using training data and has the capability to automatically determine the number of vertebrae visible in the image(s). This is achieved by combining a graphical model-based maximum a posterior probability (MAP) estimate with a mean-shift based clustering. Experiments conducted on simulated X-ray images as well as on a low-dose low quality X-ray spinal image of a scoliotic patient verified its performance.

Automatic X-ray landmark detection and shape segmentation via data-driven joint estimation of image displacements

In this paper, we propose a new method for fully-automatic landmark detection and shape segmentation in X-ray images. To detect landmarks, we estimate the displacements from some randomly sampled image patches to the (unknown) landmark positions, and then we integrate these predictions via a voting scheme. Our key contribution is a new algorithm for estimating these displacements. Different from other methods where each image patch independently predicts its displacement, we jointly estimate the displacements from all patches together in a data driven way, by considering not only the training data but also geometric constraints on the test image. The displacements estimation is formulated as a convex optimization problem that can be solved efficiently. Finally, we use the sparse shape composition model as the a priori information to regularize the landmark positions and thus generate the segmented shape contour. We validate our method on X-ray image datasets of three different anatomical structures: complete femur, proximal femur and pelvis. Experiments show that our method is accurate and robust in landmark detection, and, combined with the shape model, gives a better or comparable performance in shape segmentation compared to state-of-the art methods. Finally, a preliminary study using CT data shows the extensibility of our method to 3D data.

Morphological alterations in the liver of yellow perch (Perca flavescens) from a biological mercury hotspot

Mercury (Hg) contamination is a global issue due to its anthropogenic release, long-range transport, and deposition in remote areas. In Kejimkujik National Park and National Historic Site, Nova Scotia, Canada, high concentrations of total mercury (THg) were found in tissues of yellow perch (Perca flavescens). The aim of this study was to evaluate a possible relationship between THg concentrations and the morphology of perch liver as a main site of metal storage and toxicity. Yellow perch were sampled from five lakes known to contain fish representing a wide range in Hg concentrations in fall 2013. The ultrastructure of hepatocytes and the distribution of Hg within the liver parenchyma were analyzed by transmission electron microscopy (TEM) and electron energy loss spectrometry (EELS). The relative area of macrophage aggregates (MAs) in the liver was determined using image analysis software and fluorescence microscopy. No relation between general health indicators (Fulton's condition index) and THg was observed. In line with this, TEM examination of the liver ultrastructure revealed no prominent pathologies related to THg accumulation. However, a morphological parameter that appeared to increase with muscle THg was the relative area of MAs in the liver. The hepatic lysosomes appeared to be enlarged in samples with the highest THg concentrations. Interestingly, EELS analysis revealed that the MAs and hepatic lysosomes contained Hg.

Medical image computing in diagnosis and intervention of spinal diseases

Spinal image analysis and computer assisted intervention have emerged as new and independent research areas, due to the importance of treatment of spinal diseases, increasing availability of spinal imaging, and advances in analytics and navigation tools. Among others, multiple modality spinal image analysis and spinal navigation tools have emerged as two keys in this new area. We believe that further focused research in these two areas will lead to a much more efficient and accelerated research path, avoiding detours that exist in other applications, such as in brain and heart.

Inactivation and self -association of CaM kinase: Effects of ATP, substrate binding domains, and isozymic forms

Calcium/calmodulin-dependent protein kinase II (CaM kinase) is a multifunctional Ser/Thr protein kinase, that is highly enriched in brain and is involved in regulating many aspects of neuronal function. We observed that forebrain CaM kinase from crude homogenates, cytosolic fractions and purified preparations inactivates and translocates into the particulate fraction following autophosphorylation. Using purified forebrain CaM kinase as well as recombinant $\alpha$ isozyme, we determined that the formation of particulate enzyme was due to enzyme self-association. The conditions of autophosphorylation determine whether enzyme self-association and/or inactivation will occur. Self-association of CaM kinase is sensitive to pH, ATP concentration, and enzyme autophosphorylation. This process is prevented by saturating concentrations of ATP. However, in limiting ATP, pH is the dominant factor, and enzyme self-association occurs at pH values $\rm{<}7.0.$ Site-specific mutants were produced by substituting Ala for Thr286, Thr253, or Thr305,306 to determine whether these sites of autophosphorylation affect enzyme inactivation and self-association. The only mutation that influenced these processes was Ala286, which removed the protective effect afforded by autophosphorylation in saturating ATP. Enzyme inactivation occurs in the presence and absence of self-association and appears predominantly sensitive to nucleotide concentration, because saturating concentrations of $\rm Mg\sp{2+}/ADP$ or $\rm Mg\sp{2+}/ATP$ prevent this process. These data implicate the ATP binding pocket in both inactivation and self-association. We also observed that select peptide substrates and peptide inhibitors modeled after the autoregulatory domain of CaM kinase prevented these processes. The $\alpha$ and $\beta$ isozymes of CaM kinase were characterized independently, and were observed to exhibit differences in both enzyme inactivation and self-association. The $\beta$ isozyme was less sensitive to inactivation, and was never observed to self-associate. Biophysical characterization, and transmission electron microscopy coupled with image analysis indicated both isozymes were multimeric, however, the $\alpha$ and $\beta$ isozymes appeared structurally different. We hypothesize that the $\alpha$ subunit of CaM kinase plays both a structural and enzymatic role, and the $\beta$ subunit plays an enzymatic role. The ramifications for the functional differences observed for inactivation and self-association are discussed based on potential structural differences and autoregulation of the $\alpha$ and $\beta$ isozymes in both calcium-induced physiological and pathological processes. ^

Análisis de co-términos y de redes sociales para la generación de mapas temáticos

La mejora de las capacidades de búsqueda y de las interfaces de los opacs sigue siendo uno de los principales desafíos para las bibliotecas, especialmente en lo que respecta al acceso por materias. Las interfaces visuales pueden facilitar la recuperación. El objetivo del presente trabajo es explorar si la combinación de técnicas de análisis de co-términos y de redes sociales resulta ser una metodología válida para la generación de mapas temáticos de la colección. La principal conclusión es que el método es válido, y que los mapas obtenidos podrían servir como interfaz visual para el acceso por materias. También es útil para detectar problemas en los criterios de indización y contribuir a la mejora de la calidad de la descripción temática del conjunto documental

Análisis de co-términos y de redes sociales para la generación de mapas temáticos

La mejora de las capacidades de búsqueda y de las interfaces de los opacs sigue siendo uno de los principales desafíos para las bibliotecas, especialmente en lo que respecta al acceso por materias. Las interfaces visuales pueden facilitar la recuperación. El objetivo del presente trabajo es explorar si la combinación de técnicas de análisis de co-términos y de redes sociales resulta ser una metodología válida para la generación de mapas temáticos de la colección. La principal conclusión es que el método es válido, y que los mapas obtenidos podrían servir como interfaz visual para el acceso por materias. También es útil para detectar problemas en los criterios de indización y contribuir a la mejora de la calidad de la descripción temática del conjunto documental

Porosity contributions of radiolarians in ODP Site 110-671 and Hole 110-672A sediments

This study quantitatively addresses the significance of porosity within radiolarian tests in the décollement zone at the toe of the northern Barbados accretionary prism. Quantification was accomplished using scanning electron microscope images of core samples taken from Ocean Drilling Program (ODP) Sites 671 and 672, representing the décollement and proto-décollement, respectively. The décollement is localized to a radiolarian claystone, and its depth correlates with a low-density anomaly that has been attributed to high porosity at all relevant ODP drilling sites in the area (Moore, Klaus, et al., 1998, doi:10.2973/odp.proc.ir.171A.1998; Shipley, Ogawa, Blum, et al., 1995, doi:10.2973/odp.proc.ir.153.1995; Mascle, Moore, et al., 1988, doi:10.2973/odp.proc.ir.110.1988). Porosity in the décollement zone is presumably lost between Sites 672 and 671 because of shear enhanced consolidation (Moore et al., 1998, doi:10.1130/0091-7613(1998)026<0811:CPDIAE>2.3.CO;2).

Análisis de co-términos y de redes sociales para la generación de mapas temáticos

La mejora de las capacidades de búsqueda y de las interfaces de los opacs sigue siendo uno de los principales desafíos para las bibliotecas, especialmente en lo que respecta al acceso por materias. Las interfaces visuales pueden facilitar la recuperación. El objetivo del presente trabajo es explorar si la combinación de técnicas de análisis de co-términos y de redes sociales resulta ser una metodología válida para la generación de mapas temáticos de la colección. La principal conclusión es que el método es válido, y que los mapas obtenidos podrían servir como interfaz visual para el acceso por materias. También es útil para detectar problemas en los criterios de indización y contribuir a la mejora de la calidad de la descripción temática del conjunto documental

Comparisons of observed ice properties and Envisat Advanced Synthetic Aperture Radar (ASAR) data during Nathanial B. Palmer cruise NBP09-01 and Oden cruise OSO08/09

Envisat Advanced Synthetic Aperture Radar (ASAR) Wide Swath Mode (WSM) images are used to derive C-band HH-polarization normalized radar cross sections (NRCS). These are compared with ice-core analysis and visual ship-based observations of snow and ice properties observed according to the Antarctic Sea Ice Processes and Climate (ASPeCt) protocol during two International Polar Year summer cruises (Oden 2008 and Palmer 2009) in West Antarctica. Thick first-year (TFY) and multi-year (MY) ice were the dominant ice types. The NRCS value ranges between -16.3 ± 1.1 and -7.6 ± 1.0 dB for TFY ice, and is -12.6 ± 1.3 dB for MY ice; for TFY ice, NRCS values increase from ~-15 dB to -9 dB from December/January to mid-February. In situ and ASPeCt observations are not, however, detailed enough to interpret the observed NRCS change over time. Co-located Advanced Microwave Scanning Radiometer-Earth Observing System (AMSR-E) vertically polarized 37 GHz brightness temperatures (TB37V), 7 day and 1 day averages as well as the TB37V difference between ascending and descending AMSR-E overpasses suggest the low NRCS values (-15 dB) are associated with snowmelt being still in progress, while the change towards higher NRCS values (-9dB) is caused by commencement of melt-refreeze cycles after about mid-January.

Geotechnical properties of Lau Basin sediments

Distribution of pore space and degree of cementation appear to be the main factors controlling the permeability of sediments retrieved from the Lau Basin. The undisturbed microfabrics of two lithologies, nannofossil ooze and vitric sandy silt, commonly found at Holes 834A, 835A, 838A, and 839Aof Leg 135 were examined by scanning electron microscopy equipped with energy dispersive X-ray spectral analysis and image analysis systems. The results of these analyses were compared with laboratory determinations of porosity, grain-size distribution, and permeability on discrete samples from the same sediment depths. The permeability of the vitric sandy silt is 3-5 orders of magnitude higher than the nannofossil ooze samples. The porosity of nannofossil ooze ranges from 6% to 12% greater than the porosity of vitric sandy silt, which partially reflects the finer texture of nannofossil ooze. Although the correlation of higher porosity with lower permeability is not surprising, factors other than simply grain-size distribution must be invoked to explain the large differences in permeability found in these samples.

Growth increments of the recent brachiopod Magellania venosa mechanically marked in Paso Comau and Comau Fjord, Chile, 2011/2012

Magellania venosa, the largest recent brachiopod, occurs in clusters and banks in population densities of up to 416 ind/m**2 in Comau Fjord, Northern Chilean fjord region. Below 15 m, it co-occurs with the mytilid Aulacomya atra and it dominates the benthic community below 20 m. To determine the question of why M. venosa is a successful competitor, the in situ growth rate of the brachiopod was studied and its overall growth performance compared with that of other brachiopods and mussels. The growth in length was measured between February 2011 and March 2012 after mechanical tagging and calcein staining. Settlement and juvenile growth were determined from recruitment tiles installed in 2009 and from subsequent photocensus. Growth of M. venosa is best described by the general von Bertalanffy growth function, with a maximum shell length (Linf) of 71.53 mm and a Brody growth constant (K) of 0.336/year. The overall growth performance (OGP index = 5.1) is the highest recorded for a rynchonelliform brachiopod and in the range of that for Mytilus chilensis (4.8-5.27), but lower than that of A. atra (5.74). The maximal individual production (PInd) is 0.29 g AFDM/ind/year at 42 mm shell length and annual production ranges from 1.28 to 89.25 g AFDM/year/m**2 (1-57% of that of A. atra in the respective fjords). The high shell growth rate of M. venosa, together with its high overall growth performance may explain the locally high population density of this brachiopod in Comau Fjord. However, the production per biomass of the population (P/B-ratio) is low (0.535) and M. venosa may play only a minor role in the food chain. Settling dynamics indicates that M. venosa is a pioneer species with low juvenile mortality. The coexistence of the brachiopod and bivalve suggests that brachiopod survival is affected by neither the presence of potential brachiopod predators nor that of space competitors (i.e. mytilids).