Automatic classification of MR scans in Alzheimer's disease.

To be diagnostically useful, structural MRI must reliably distinguish Alzheimer's disease (AD) from normal aging in individual scans. Recent advances in statistical learning theory have led to the application of support vector machines to MRI for detection of a variety of disease states. The aims of this study were to assess how successfully support vector machines assigned individual diagnoses and to determine whether data-sets combined from multiple scanners and different centres could be used to obtain effective classification of scans. We used linear support vector machines to classify the grey matter segment of T1-weighted MR scans from pathologically proven AD patients and cognitively normal elderly individuals obtained from two centres with different scanning equipment. Because the clinical diagnosis of mild AD is difficult we also tested the ability of support vector machines to differentiate control scans from patients without post-mortem confirmation. Finally we sought to use these methods to differentiate scans between patients suffering from AD from those with frontotemporal lobar degeneration. Up to 96% of pathologically verified AD patients were correctly classified using whole brain images. Data from different centres were successfully combined achieving comparable results from the separate analyses. Importantly, data from one centre could be used to train a support vector machine to accurately differentiate AD and normal ageing scans obtained from another centre with different subjects and different scanner equipment. Patients with mild, clinically probable AD and age/sex matched controls were correctly separated in 89% of cases which is compatible with published diagnosis rates in the best clinical centres. This method correctly assigned 89% of patients with post-mortem confirmed diagnosis of either AD or frontotemporal lobar degeneration to their respective group. Our study leads to three conclusions: Firstly, support vector machines successfully separate patients with AD from healthy aging subjects. Secondly, they perform well in the differential diagnosis of two different forms of dementia. Thirdly, the method is robust and can be generalized across different centres. This suggests an important role for computer based diagnostic image analysis for clinical practice.

Caracterização Geológica e Geotécnica das Unidades Litológicas da Cidade da Praia (Santiago - Cabo Verde)

Este trabalho produz uma avaliação das características geológicas e geotécnicas de um território da ilha de Santiago, Cabo Verde, incidindo sobre a cidade da Praia e a área envolvente. Os objectivos principais do trabalho são a representação cartográfica das unidades litológicas, com uma proposta de coluna litológica sintética, a correlação com as unidades geológicas definidas por outros autores, bem como a realização de um conjunto de ensaios in situ e análises laboratoriais visando a caracterização dos parâmetros físicos e mecânicos das diferentes unidades litológicas definidas para a área em estudo. É efectuada uma compilação sobre as principais investigações geológicas realizadas em Cabo Verde, desde o séc. XIX até a actualidade, assim como a descrição das características geológicas da ilha de Santiago e dos principais processos de formação e evolução das formas de relevo e dos recursos naturais (hídricos e solos). A pesquisa incluiu uma revisão dos conceitos descritivos de caracterização dos vulcanitos e vulcanoclastitos presentes e compreendeu a redefinição das unidades litológicas da região, a respectiva representação cartográfica na escala 1: 10.000 (com maior detalhe do que a informação pré-existente) e o levantamento de campo dos principais alinhamentos estruturais. São igualmente apresentados os resultados do tratamento das bandas espectrais de imagens de satélite que suportam a definição das unidades litológicas, bem como dos principais alinhamentos tectónicos que afectam as unidades da área de estudo. Para a caracterização das diferentes unidades litológicas com base nas propriedades in situ, recorreu-se a perfis-tipo, estabelecendo uma descrição das características mineralógicas, petrográficas, texturais e estruturais das materiais presentes. Os materiais foram igualmente ensaiados in situ e amostrados para uma caracterização laboratorial. Os resultados dos ensaios geotécnicos, geomecânicos, mineralógicos e de radioactividade natural permitiram refinar a cartografia proposta e estabelecer parâmetros de comportamento para as 30 unidades litológicas consideradas, a partir de intervalos de valores não homogéneos, contudo representativos da variabilidade observada. Com base nestes resultados são apresentados valores indicativos de aptidão dos materiais, nomeadamente para fundações de edifícios, aterros, construção e potencial hidrogeológico.

Programa d'anàlisi d'imatges de provetes metal·logràfiques

L’objectiu del present TFM és explorar les possibilitats del programa matemàtic MATLAB i la seva eina Entorn de Disseny d’Interfícies Gràfiques d’Usuari (GUIDE), desenvolupant un programa d’anàlisi d’imatges de provetes metal·logràfiques que es pugui utilitzar per a realitzar pràctiques de laboratori de l’assignatura Tecnologia de Materials de la titulació de Grau en Enginyeria Mecatrònica que s’imparteix a la Universitat de Vic. Les àrees d’interès del treball són la Instrumentació Virtual, la programació MATLAB i les tècniques d’anàlisi d’imatges metal·logràfiques. En la memòria es posa un èmfasi especial en el disseny de la interfície i dels procediments per a efectuar les mesures. El resultat final és un programa que satisfà tots els requeriments que s’havien imposat en la proposta inicial. La interfície del programa és clara i neta, destinant molt espai a la imatge que s’analitza. L’estructura i disposició dels menús i dels comandaments ajuda a que la utilització del programa sigui fàcil i intuïtiva. El programa s’ha estructurat de manera que sigui fàcilment ampliable amb altres rutines de mesura, o amb l’automatització de les rutines existents. Al tractar-se d’un programa que funciona com un instrument de mesura, es dedica un capítol sencer de la memòria a mostrar el procediment de càlcul dels errors que s’ocasionen durant la seva utilització, amb la finalitat de conèixer el seu ordre de magnitud, i de saber-los calcular de nou en cas que variïn les condicions d’utilització. Pel que fa referència a la programació, malgrat que MATLAB no sigui un entorn de programació clàssic, sí que incorpora eines que permeten fer aplicacions no massa complexes, i orientades bàsicament a gràfics o a imatges. L’eina GUIDE simplifica la realització de la interfície d’usuari, malgrat que presenta problemes per tractar dissenys una mica complexos. Per altra banda, el codi generat per GUIDE no és accessible, cosa que no permet modificar manualment la interfície en aquells casos en els que GUIDE té problemes. Malgrat aquests petits problemes, la potència de càlcul de MATLAB compensa sobradament aquestes deficiències.

A rapid and effective vignetting correction for quantitative microscopy

Images acquired using optical microscopes are inherently subject to vignetting effects due to imperfect illumination and image acquisition. However, such vignetting effects hamper accurate extraction of quantitative information from biological images, leading to less effective image segmentation and increased noise in the measurements. Here, we describe a rapid and effective method for vignetting correction, which generates an estimate for a correction function from the background fluorescence without the need to acquire additional calibration images. We validate the usefulness of this algorithm using artificially distorted images as a gold standard for assessing the accuracy of the applied correction and then demonstrate that this correction method enables the reliable detection of biologically relevant variation in cell populations. A simple user interface called FlattifY was developed and integrated into the image analysis platform YeastQuant to facilitate easy application of vignetting correction to a wide range of images.

Soil structure transformations from ferralic to nitic horizons on a toposequence in southeastern Brazil

The soil structure transformation from ferralic to nitic horizons was studied in a toposequence on quaternary red clayey sediments and diabase in Piracicaba (SP), Brazil. Morphological and micromorphological studies, image analysis, soil water characteristic curves and monitoring of (total) soil water potential head were used. The presence of polyconcave vughs, clayskins and planar voids shows that the vertical and lateral transition and structural transformation from ferralic to nitic horizons is given by the coalescence of the microaggregates, probably due to tensions created in a drier period in the past. Changes to a more humid climate with a defined dry season and alternate drying and wetting cycles resulted in the fissuration of the previously coalesced material, forming polyhedral aggregates and microaggregates. Simultaneously, clay illuviation filled the voids and together with the compacting action of the biological activity of these soils contributed to the coalescence of microaggregates.

Quantification of the local heartwall motion by magnetic resonance myocardial tagging.

Sophisticated magnetic resonance tagging techniques provide powerful tools for the non-invasive assessment of the local heartwall motion towards a deeper fundamental understanding of local heart function. For the extraction of motion data from the time series of magnetic resonance tagged images and for the visualization of the local heartwall motion a new image analysis procedure has been developed. New parameters have been derived which allows quantification of the motion patterns and are highly sensitive to any changes in these patterns. The new procedure has been applied for heart motion analysis in healthy volunteers and in patient collectives with different heart diseases. The achieved results are summarized and discussed.

Soil functioning in a toposequence under rainforest in São Paulo, Brazil

Studies of soil-water dynamics using toposequences are essential to improve the understanding of soil-water-vegetation relationships. This study assessed the hydro-physical and morphological characteristics of soils of Atlantic Rainforest in the Parque Estadual de Carlos Botelho, state of São Paulo, Brazil. The study area of 10.24 ha (320 x 320 m) was covered by dense tropical rainforest (Atlantic Rainforest). Based on soil maps and topographic maps of the area, a representative transect of the soil in this plot was chosen and five soil trenches were opened to determine morphological properties. To evaluate the soil hydro-physical functioning, soil particle size distribution, bulk density (r), particle density (r s), soil water retention curves (SWRC), field saturated hydraulic conductivity (Ks), macroporosity (macro), and microporosity (micro) and total porosity (TP) were determined. Undisturbed samples were collected for micromorphometric image analysis, to determine pore size, shape, and connectivity. The soils in the study area were predominantly Inceptisols, and secondly Entisols and Epiaquic Haplustult. In the soil hydro-physical characterization of the selected transect, a change was observed in Ks between the surface and subsurface layers, from high/intermediate to intermediate/low permeability. This variation in soil-water dynamics was also observed in the SWRC, with higher water retention in the subsurface horizons. The soil hydro-physical behavior was influenced by the morphogenetic characteristics of the soils.

Variability of root traits in common bean genotypes at different levels of phosphorus supply and ontogenetic stages

Selection of common bean (Phaseolus vulgaris L.) cultivars with enhanced root growth would be a strategy for increasing P uptake and grain yield in tropical soils, but the strong plasticity of root traits may compromise their inclusion in breeding programs. The aim of this study was to evaluate the magnitude of the genotypic variability of root traits in common bean plants at two ontogenetic stages and two soil P levels. Twenty-four common bean genotypes, comprising the four growth habits that exist in the species and two wild genotypes, were grown in 4 kg pots at two levels of applied P (20 and 80 mg kg-1) and harvested at the stages of pod setting and early pod filling. Root area and root length were measured by digital image analysis. Significant genotype × P level and genotype × harvest interactions in analysis of variance indicate that the genotypic variation of root traits depended on soil nutrient availability and the stage at which evaluation was made. Genotypes differed for taproot mass, basal and lateral root mass, root area and root length at both P levels and growth stages; differences in specific root area and length were small. Genotypes with growth habits II (upright indeterminate) and III (prostrate indeterminate) showed better adaptation to limited P supply than genotypes of groups I (determinate) and IV (indeterminate climbing). Between the two harvests, genotypes of groups II and III increased the mass of basal and lateral roots by 40 and 50 %, respectively, whereas genotypes of groups I and IV by only 7 and 19 %. Values of the genotypic coefficient of determination, which estimates the proportion of phenotypic variance resulting from genetic effects, were higher at early pod filling than at pod setting. Correlations between shoot mass and root mass, which could indicate indirect selection of root systems via aboveground biomass, were higher at early pod filling than at pod setting. The results indicate that selection for root traits in common bean genotypes should preferentially be performed at the early pod-filling stage.

A post-processing pipeline to reconstruct the developing fetal brain using low-resolution MRI

Introduction. Development of the fetal brain surfacewith concomitant gyrification is one of the majormaturational processes of the human brain. Firstdelineated by postmortem studies or by ultrasound, MRIhas recently become a powerful tool for studying in vivothe structural correlates of brain maturation. However,the quantitative measurement of fetal brain developmentis a major challenge because of the movement of the fetusinside the amniotic cavity, the poor spatial resolution,the partial volume effect and the changing appearance ofthe developing brain. Today extensive efforts are made todeal with the âeurooepost-acquisitionâeuro reconstruction ofhigh-resolution 3D fetal volumes based on severalacquisitions with lower resolution (Rousseau, F., 2006;Jiang, S., 2007). We here propose a framework devoted tothe segmentation of the basal ganglia, the gray-whitetissue segmentation, and in turn the 3D corticalreconstruction of the fetal brain. Method. Prenatal MRimaging was performed with a 1-T system (GE MedicalSystems, Milwaukee) using single shot fast spin echo(ssFSE) sequences in fetuses aged from 29 to 32gestational weeks (slice thickness 5.4mm, in planespatial resolution 1.09mm). For each fetus, 6 axialvolumes shifted by 1 mm were acquired (about 1 min pervolume). First, each volume is manually segmented toextract fetal brain from surrounding fetal and maternaltissues. Inhomogeneity intensity correction and linearintensity normalization are then performed. A highspatial resolution image of isotropic voxel size of 1.09mm is created for each fetus as previously published byothers (Rousseau, F., 2006). B-splines are used for thescattered data interpolation (Lee, 1997). Then, basalganglia segmentation is performed on this superreconstructed volume using active contour framework witha Level Set implementation (Bach Cuadra, M., 2010). Oncebasal ganglia are removed from the image, brain tissuesegmentation is performed (Bach Cuadra, M., 2009). Theresulting white matter image is then binarized andfurther given as an input in the Freesurfer software(http://surfer.nmr.mgh.harvard.edu/) to provide accuratethree-dimensional reconstructions of the fetal brain.Results. High-resolution images of the cerebral fetalbrain, as obtained from the low-resolution acquired MRI,are presented for 4 subjects of age ranging from 29 to 32GA. An example is depicted in Figure 1. Accuracy in theautomated basal ganglia segmentation is compared withmanual segmentation using measurement of Dice similarity(DSI), with values above 0.7 considering to be a verygood agreement. In our sample we observed DSI valuesbetween 0.785 and 0.856. We further show the results ofgray-white matter segmentation overlaid on thehigh-resolution gray-scale images. The results arevisually checked for accuracy using the same principlesas commonly accepted in adult neuroimaging. Preliminary3D cortical reconstructions of the fetal brain are shownin Figure 2. Conclusion. We hereby present a completepipeline for the automated extraction of accuratethree-dimensional cortical surface of the fetal brain.These results are preliminary but promising, with theultimate goal to provide âeurooemovieâeuro of the normal gyraldevelopment. In turn, a precise knowledge of the normalfetal brain development will allow the quantification ofsubtle and early but clinically relevant deviations.Moreover, a precise understanding of the gyraldevelopment process may help to build hypotheses tounderstand the pathogenesis of several neurodevelopmentalconditions in which gyrification have been shown to bealtered (e.g. schizophrenia, autismâeuro¦). References.Rousseau, F. (2006), 'Registration-Based Approach forReconstruction of High-Resolution In Utero Fetal MR Brainimages', IEEE Transactions on Medical Imaging, vol. 13,no. 9, pp. 1072-1081. Jiang, S. (2007), 'MRI of MovingSubjects Using Multislice Snapshot Images With VolumeReconstruction (SVR): Application to Fetal, Neonatal, andAdult Brain Studies', IEEE Transactions on MedicalImaging, vol. 26, no. 7, pp. 967-980. Lee, S. (1997),'Scattered data interpolation with multilevel B-splines',IEEE Transactions on Visualization and Computer Graphics,vol. 3, no. 3, pp. 228-244. Bach Cuadra, M. (2010),'Central and Cortical Gray Mater Segmentation of MagneticResonance Images of the Fetal Brain', ISMRM Conference.Bach Cuadra, M. (2009), 'Brain tissue segmentation offetal MR images', MICCAI.

MORPHOLOGICAL AND MICROMORPHOLOGICAL CHANGES IN THE STRUCTURE OF A RHODIC HAPLUDOX AS A RESULT OF AGRICULTURAL MANAGEMENT

In evaluation of soil quality for agricultural use, soil structure is one of the most important properties, which is influenced not only by climate, biological activity, and management practices but also by mechanical and physico-chemical forces acting in the soil. The purpose of this study was to evaluate the influence of conventional agricultural management on the structure and microstructure of a Latossolo Vermelho distroférrico típico (Rhodic Hapludox) in an experimental area planted to maize. Soil morphology was described using the crop profile method by identifying the distinct structural volumes called Morphologically Homogeneous Units (MHUs). For comparison, we also described a profile in an adjacent area without agricultural use and under natural regrowth referred to as Memory. We took undisturbed samples from the main MHUs so as to form thin sections and blocks of soil for micromorphological and micromorphometrical analyses. Results from the application of the crop profile method showed the occurrence of the following structural types: loose (L), fragmented (F) and continuous (C) in both profiles analyzed. In the Memory soil profile, the fragmented structures were classified as Fptμ∆+tf and Fmt∆μ, whose micromorphology shows an enaulic-porphyric (porous) relative distribution with a great deal of biological activity as indicated by the presence of vughs and channels. Lower down, from 0.20 to 0.35 m, there was a continuous soil volume (sub-type C∆μ), with a subangular block microstructure and an enaulic-porphyric relative distribution, though in this case more compact and with aggregate coalescence and less biological activity. The micromorphometrical study of the soil of the Memory Plot showed the predominance of complex pores in NAM (15.03 %), Fmt∆μ (11.72 %), and Fptμ∆+tf (7.73 %), and rounded pores in C∆μ (8.21 %). In the soil under conventional agricultural management, we observed fragmented structures similar to the Memory Plot from 0.02 to 0.20 m, followed by a volume with a compact continuous structure (C∆μ), without visible porosity and with few roots. In the MHUs under conventional management, reduction in the packing pores (40 %) was observed, mainly in the continuous units (C). The microstructure had well-defined blocks, with the occurrence of planar pores and less evidence of biological activity. In conclusion, the morphological and micromorphological analyses of the soil profiles studied offered complementary information regarding soil structural quality, especially concerning the changes in pore types as result of mechanical stress undergone by the soil.

THREE DIMENSIONAL CHARACTERIZATION OF SOIL MACROPOROSITY BY X-RAY MICROTOMOGRAPHY

Analysis of the soil pore system represents an important way of characterizing soil structure. Properties such as the shape and number of pores can be determined through soil pore evaluations. This study presents a three-dimensional (3D) characterization of the shape and number of pores of a sub-tropical soil. To do so, a second generation X-ray microtomograph equipped with a plain type detector was employed. A voltage of 120 kV and current of 80 mA was applied to the X-ray tube. The soil samples analyzed were collected at three different depths (0-10, 10-20, and 20-30 cm). The results obtained allowed qualitative (images) and quantitative (3D) analyses of the soil structure, revealing the potential of the microtomographic technique, as well as the study of differences in soil macroporosity at different depths. Macroporosity was 5.14 % in the 0-10 cm layer, 5.10 % in the 10-20 cm layer, and 6.64 % in the 20-30 cm layer. The macroporosity of unclassified pores (UN) was 0.30 % (0-10 and 10-20 cm) and 0.40 % (20-30 cm), while equant pores (EQ) had values of 0.01 % at the three depths under analysis.

Evaluation of the RapidAir 457 Air Void Analyzer, March 2012

An adequate air void system is imperative to produce concrete with freeze-thaw durability in a wet freeze environment such as found in Iowa. Specifications rely on a percentage of air obtained in the plastic state by the pressure meter. Actual, in place air contents, of some concrete pavements in Iowa, have been found with reduced air content due to a number of factors such as excessive vibration and inadequate mixing. Determining hardened air void parameters is a time consuming process involving potential for human error. The RapidAir 457 air void analyzer is an automated device used to determine hardened air void parameters. The device is used in Europe and has been shown to quickly produce accurate and repeatable hardened air results. This research investigates how well the RapidAir 457 results correlate to plastic air content and the image analysis air technique. The repeatability and operator variation were also investigated, as well as, the impact of aggregate porosity and selection of threshold value on hardened air results.

Enhanced oligonucleotide delivery to mouse retinal cells using iontophoresis.

PURPOSE: To study the combination of oligodeoxynucleotides (ODNs) intravitreous injection and saline transpalpebral iontophoresis on the delivery of ODNs to photoreceptors in the newborn rd1/rd1 mice. METHODS: Cathodal or anodal transpalpebral iontophoresis (1.43 mA/cm(2) for 5 min) was applied to eyes of postnatal day 7 (PN7) rd1/rd1 mice immediately before the intravitreous injection of ODNs. The effect of cathodal iontophoresis after ODNs injection was also evaluated. The influence of current intensity (0.5, 1.5, and 2.5 mA) was assayed with cathodal iontophoresis performed prior to ODNs injection. The duration of current-induced facilitation of ODNs delivery to photoreceptors was evaluated for 6 h following iontophoresis. One group of control eyes received cathodal iontophoresis prior to the intravitreous injection of phosphate buffered saline (PBS) or hexachlorofluorescein (Hex). The second control group received ODN or Hex intravitreous injection without iontophoresis. The penetration of fluorescent ODNs in the outer nuclear layer (ONL) was quantified by image analysis of the ONL fluorescence intensity on cryosection microphotographs. Integrity of ODN was assessed using acrylamide gel migration after its extraction from the retina of treated mice. The integrity of retinal structure, 1 and 24 h after iontophoresis, was analyzed using light and electron microscopy. RESULTS: Transpalpebral anodal or cathodal saline iontophoresis enhanced the penetration of ODNs in all retinal layers. Cathodal iontophoresis was more efficient than anodal iontophoresis in enhancing the tissue penetration of the injected ODN. Photoreceptor delivery of ODN was significantly higher when cathodal saline transpalpebral iontophoresis was applied prior than after the injection. The extent of enhanced tissue penetration decreased in parallel to the increased interval between iontophoresis application and the intravitreous injection. Current of 1.5 mA was safe and optimal for the delivery of ODNs to the ONL. One hour after iontophoresis followed by injection, ODN extracted from the retina of treated eyes remained intact. Histology and electron microscopy observations demonstrated that iontophoresis using the optimal parameters did not induce any permanent tissue alterations or structure damage. CONCLUSIONS: Saline transpalpebral iontophoresis facilitates the penetration of injected ODNs in photoreceptors for at least 3 h. This method may be considered for photoreceptor targeted gene therapy.

The Escherichia coli RuvB branch migration protein forms double hexameric rings around DNA.

The RuvB protein is induced in Escherichia coli as part of the SOS response to DNA damage. It is required for genetic recombination and the postreplication repair of DNA. In vitro, the RuvB protein promotes the branch migration of Holliday junctions and has a DNA helicase activity in reactions that require ATP hydrolysis. We have used electron microscopy, image analysis, and three-dimensional reconstruction to show that the RuvB protein, in the presence of ATP, forms a dodecamer on double-stranded DNA in which two stacked hexameric rings encircle the DNA and are oriented in opposite directions with D6 symmetry. Although helicases are ubiquitous and essential for many aspects of DNA repair, replication, and transcription, three-dimensional reconstruction of a helicase has not yet been reported, to our knowledge. The structural arrangement that is seen may be common to other helicases, such as the simian virus 40 large tumor antigen.

Direct three-dimensional myocardial strain tensor quantification and tracking using zHARP.

Images of myocardial strain can be used to diagnose heart disease, plan and monitor treatment, and to learn about cardiac structure and function. Three-dimensional (3D) strain is typically quantified using many magnetic resonance (MR) images obtained in two or three orthogonal planes. Problems with this approach include long scan times, image misregistration, and through-plane motion. This article presents a novel method for calculating cardiac 3D strain using a stack of two or more images acquired in only one orientation. The zHARP pulse sequence encodes in-plane motion using MR tagging and out-of-plane motion using phase encoding, and has been previously shown to be capable of computing 3D displacement within a single image plane. Here, data from two adjacent image planes are combined to yield a 3D strain tensor at each pixel; stacks of zHARP images can be used to derive stacked arrays of 3D strain tensors without imaging multiple orientations and without numerical interpolation. The performance and accuracy of the method is demonstrated in vitro on a phantom and in vivo in four healthy adult human subjects.