Parallel imaging with phase scrambling.

PURPOSE: Most existing methods for accelerated parallel imaging in MRI require additional data, which are used to derive information about the sensitivity profile of each radiofrequency (RF) channel. In this work, a method is presented to avoid the acquisition of separate coil calibration data for accelerated Cartesian trajectories. METHODS: Quadratic phase is imparted to the image to spread the signals in k-space (aka phase scrambling). By rewriting the Fourier transform as a convolution operation, a window can be introduced to the convolved chirp function, allowing a low-resolution image to be reconstructed from phase-scrambled data without prominent aliasing. This image (for each RF channel) can be used to derive coil sensitivities to drive existing parallel imaging techniques. As a proof of concept, the quadratic phase was applied by introducing an offset to the x(2) - y(2) shim and the data were reconstructed using adapted versions of the image space-based sensitivity encoding and GeneRalized Autocalibrating Partially Parallel Acquisitions algorithms. RESULTS: The method is demonstrated in a phantom (1 × 2, 1 × 3, and 2 × 2 acceleration) and in vivo (2 × 2 acceleration) using a 3D gradient echo acquisition. CONCLUSION: Phase scrambling can be used to perform parallel imaging acceleration without acquisition of separate coil calibration data, demonstrated here for a 3D-Cartesian trajectory. Further research is required to prove the applicability to other 2D and 3D sampling schemes. Magn Reson Med, 2014. © 2014 Wiley Periodicals, Inc.

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.

Snapshot gradient-recalled echo-planar images of rat brains at long echo time at 9.4 T.

With improved B 0 homogeneity along with satisfactory gradient performance at high magnetic fields, snapshot gradient-recalled echo-planar imaging (GRE-EPI) would perform at long echo times (TEs) on the order of T2*, which intrinsically allows obtaining strongly T2*-weighted images with embedded substantial anatomical details in ultrashort time. The aim of this study was to investigate the feasibility and quality of long TE snapshot GRE-EPI images of rat brain at 9.4 T. When compensating for B 0 inhomogeneities, especially second-order shim terms, a 200 x 200 microm2 in-plane resolution image was reproducibly obtained at long TE (>25 ms). The resulting coronal images at 30 ms had diminished geometric distortions and, thus, embedded substantial anatomical details. Concurrently with the very consistent stability, such GRE-EPI images should permit to resolve functional data not only with high specificity but also with substantial anatomical details, therefore allowing coregistration of the acquired functional data on the same image data set.

The Energy metabolism of China and India between 1971-2010: studying the bifurcation

This paper presents a comparison of the changes in the energetic metabolic pattern of China and India, the two most populated countries in the world, with two economies undergoing an important economic transition. The comparison of the changes in the energetic metabolic pattern has the scope to characterize and explain a bifurcation in their evolutionary path in the recent years, using the Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism (MuSIASEM) approach. The analysis shows an impressive transformation of China’s energy metabolism determined by the joining of the WTO in 2001. Since then, China became the largest factory of the world with a generalized capitalization of all sectors ―especially the industrial sector― boosting economic labor productivity as well as total energy consumption. India, on the contrary, lags behind when considering these factors. Looking at changes in the household sector (energy metabolism associated with final consumption) in the case of China, the energetic metabolic rate (EMR) soared in the last decade, also thanks to a reduced growth of population, whereas in India it remained stagnant for the last 40 years. This analysis indicates a big challenge for India for the next decade. In the light of the data analyzed both countries will continue to require strong injections of technical capital requiring a continuous increase in their total energy consumption. When considering the size of these economies it is easy to guess that this may induce a dramatic increase in the price of energy, an event that at the moment will penalize much more the chance of a quick economic development of India.

Dense deformation field estimation for atlas-based segmentation of pathological MR brain images.

Atlas registration is a recognized paradigm for the automatic segmentation of normal MR brain images. Unfortunately, atlas-based segmentation has been of limited use in presence of large space-occupying lesions. In fact, brain deformations induced by such lesions are added to normal anatomical variability and they may dramatically shift and deform anatomically or functionally important brain structures. In this work, we chose to focus on the problem of inter-subject registration of MR images with large tumors, inducing a significant shift of surrounding anatomical structures. First, a brief survey of the existing methods that have been proposed to deal with this problem is presented. This introduces the discussion about the requirements and desirable properties that we consider necessary to be fulfilled by a registration method in this context: To have a dense and smooth deformation field and a model of lesion growth, to model different deformability for some structures, to introduce more prior knowledge, and to use voxel-based features with a similarity measure robust to intensity differences. In a second part of this work, we propose a new approach that overcomes some of the main limitations of the existing techniques while complying with most of the desired requirements above. Our algorithm combines the mathematical framework for computing a variational flow proposed by Hermosillo et al. [G. Hermosillo, C. Chefd'Hotel, O. Faugeras, A variational approach to multi-modal image matching, Tech. Rep., INRIA (February 2001).] with the radial lesion growth pattern presented by Bach et al. [M. Bach Cuadra, C. Pollo, A. Bardera, O. Cuisenaire, J.-G. Villemure, J.-Ph. Thiran, Atlas-based segmentation of pathological MR brain images using a model of lesion growth, IEEE Trans. Med. Imag. 23 (10) (2004) 1301-1314.]. Results on patients with a meningioma are visually assessed and compared to those obtained with the most similar method from the state-of-the-art.

10

This contribution introduces Data Envelopment Analysis (DEA), a performance measurement technique. DEA helps decision makers for the following reasons: (1) By calculating an efficiency score, it indicates if a firm is efficient or has capacity for improvement; (2) By setting target values for input and output, it calculates how much input must be decreased or output increased in order to become efficient; (3) By identifying the nature of returns to scale, it indicates if a firm has to decrease or increase its scale (or size) in order to minimise the average total cost; (4) By identifying a set of benchmarks, it specifies which other firms' processes need to be analysed in order to improve its own practices. This contribution presents the essentials about DEA, alongside a case study to intuitively understand its application. It also introduces Win4DEAP, a software package that conducts efficiency analysis based on DEA methodology. The methodical background of DEA is presented for more demanding readers. Finally, four advanced topics of DEA are treated: adjustment to the environment, preferences, sensitivity analysis and time series data.

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.

Bilateral olfactory sensory input enhances chemotaxis behavior.

Neural comparisons of bilateral sensory inputs are essential for visual depth perception and accurate localization of sounds in space. All animals, from single-cell prokaryotes to humans, orient themselves in response to environmental chemical stimuli, but the contribution of spatial integration of neural activity in olfaction remains unclear. We investigated this problem in Drosophila melanogaster larvae. Using high-resolution behavioral analysis, we studied the chemotaxis behavior of larvae with a single functional olfactory neuron on either the left or right side of the head, allowing us to examine unilateral or bilateral olfactory input. We developed new spectroscopic methods to create stable odorant gradients in which odor concentrations were experimentally measured. In these controlled environments, we observed that a single functional neuron provided sufficient information to permit larval chemotaxis. We found additional evidence that the overall accuracy of navigation is enhanced by the increase in the signal-to-noise ratio conferred by bilateral sensory input.

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.

Essays on the measurement of school efficiency

Measuring school efficiency is a challenging task. First, a performance measurement technique has to be selected. Within Data Envelopment Analysis (DEA), one such technique, alternative models have been developed in order to deal with environmental variables. The majority of these models lead to diverging results. Second, the choice of input and output variables to be included in the efficiency analysis is often dictated by data availability. The choice of the variables remains an issue even when data is available. As a result, the choice of technique, model and variables is probably, and ultimately, a political judgement. Multi-criteria decision analysis methods can help the decision makers to select the most suitable model. The number of selection criteria should remain parsimonious and not be oriented towards the results of the models in order to avoid opportunistic behaviour. The selection criteria should also be backed by the literature or by an expert group. Once the most suitable model is identified, the principle of permanence of methods should be applied in order to avoid a change of practices over time. Within DEA, the two-stage model developed by Ray (1991) is the most convincing model which allows for an environmental adjustment. In this model, an efficiency analysis is conducted with DEA followed by an econometric analysis to explain the efficiency scores. An environmental variable of particular interest, tested in this thesis, consists of the fact that operations are held, for certain schools, on multiple sites. Results show that the fact of being located on more than one site has a negative influence on efficiency. A likely way to solve this negative influence would consist of improving the use of ICT in school management and teaching. Planning new schools should also consider the advantages of being located on a unique site, which allows reaching a critical size in terms of pupils and teachers. The fact that underprivileged pupils perform worse than privileged pupils has been public knowledge since Coleman et al. (1966). As a result, underprivileged pupils have a negative influence on school efficiency. This is confirmed by this thesis for the first time in Switzerland. Several countries have developed priority education policies in order to compensate for the negative impact of disadvantaged socioeconomic status on school performance. These policies have failed. As a result, other actions need to be taken. In order to define these actions, one has to identify the social-class differences which explain why disadvantaged children underperform. Childrearing and literary practices, health characteristics, housing stability and economic security influence pupil achievement. Rather than allocating more resources to schools, policymakers should therefore focus on related social policies. For instance, they could define pre-school, family, health, housing and benefits policies in order to improve the conditions for disadvantaged children.

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.

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.