Compact Representations for Fast Nonrigid Registration of Medical Images

We develop efficient techniques for the non-rigid registration of medical images by using representations that adapt to the anatomy found in such images. Images of anatomical structures typically have uniform intensity interiors and smooth boundaries. We create methods to represent such regions compactly using tetrahedra. Unlike voxel-based representations, tetrahedra can accurately describe the expected smooth surfaces of medical objects. Furthermore, the interior of such objects can be represented using a small number of tetrahedra. Rather than describing a medical object using tens of thousands of voxels, our representations generally contain only a few thousand elements. Tetrahedra facilitate the creation of efficient non-rigid registration algorithms based on finite element methods (FEM). We create a fast, FEM-based method to non-rigidly register segmented anatomical structures from two subjects. Using our compact tetrahedral representations, this method generally requires less than one minute of processing time on a desktop PC. We also create a novel method for the non-rigid registration of gray scale images. To facilitate a fast method, we create a tetrahedral representation of a displacement field that automatically adapts to both the anatomy in an image and to the displacement field. The resulting algorithm has a computational cost that is dominated by the number of nodes in the mesh (about 10,000), rather than the number of voxels in an image (nearly 10,000,000). For many non-rigid registration problems, we can find a transformation from one image to another in five minutes. This speed is important as it allows use of the algorithm during surgery. We apply our algorithms to find correlations between the shape of anatomical structures and the presence of schizophrenia. We show that a study based on our representations outperforms studies based on other representations. We also use the results of our non-rigid registration algorithm as the basis of a segmentation algorithm. That algorithm also outperforms other methods in our tests, producing smoother segmentations and more accurately reproducing manual segmentations.

Face Detection in Still Gray Images

We present a trainable system for detecting frontal and near-frontal views of faces in still gray images using Support Vector Machines (SVMs). We first consider the problem of detecting the whole face pattern by a single SVM classifer. In this context we compare different types of image features, present and evaluate a new method for reducing the number of features and discuss practical issues concerning the parameterization of SVMs and the selection of training data. The second part of the paper describes a component-based method for face detection consisting of a two-level hierarchy of SVM classifers. On the first level, component classifers independently detect components of a face, such as the eyes, the nose, and the mouth. On the second level, a single classifer checks if the geometrical configuration of the detected components in the image matches a geometrical model of a face.

El uso de sangre fresca total en cardiopatías congénitas complejas

Objetivos: Describir si el uso de sangre fresca total (SFT) intraoperatoria en pacientes llevados a procedimientos RACHS 3 y 4 en la Fundación Cardioinfantil, disminuye el sangrado postoperatorio y el volumen de transfusión de elementos sanguíneos, en comparación a aquellos en quienes no se usa SFT. Materiales y métodos: Se realizó un estudio de cohorte histórica, tomando una población menor de 1 año expuesta a la sangre fresca total y comparándola con una población de similares características, llevadas a procedimientos de riesgo similar no expuesta. Los análisis se realizaron mediante pruebas estándar para variables continuas y discretas. Un valor de p menor a 0.05 fue aceptado como signficativo. Resultados: 46 pacientes expuestos a SFT y se compararon con 50 pacientes no expuestos. La principal diferencia entre los grupos fue la edad, siendo mayor en el grupo de no expuestos (3.8 años vs 0.9; p<0.001). El volumen de sangrado postoperatorio fue similar, sin embargo los pacientes expuestos a SFT recibieron mayor volumen de transfusiones, sin ser una diferencia estadísticamente significativa (155cc vs 203cc, P=0.9). No hubo diferencia significativa en complicaciones o mortalidad. Conclusiones: En nuestro estudio no se encontró una disminución en el volumen de sangrado postoperatorio en los pacientes menores de 1 año, sometidos a cirugías catalogadas como RACHS 3 y 4, expuestos a SFT, sin embargo se necesitan estudios clínicos controlados que respondan definitivamente a la pregunta.

Genotyping Klebsiella pneumoniae isolated from hepatic abscesses in three patients from Bogota, Colombia

Pyogenic liver abscess caused by Klebsiella pneumoniae represents an ever increasing entity which has mainly been described as occurring in Asia, even though, on a smaller scale, cases are being more frequently described from the USA and Europe, 13% overall mortality being reached worldwide. Affected patients are severely sick, suffering from fever, sweating, having increased acute phase reactants and risk factors such as Diabetes Mellitus, alcoholism and the inherent characteristics of the bacteria causing the disease. Objective: in this work we used a Multilocus Sequencing Typing (MLST), a nucleotide sequence-based method in order to characterize the genetic relationships among bacterial isolates. Materials and methods: the report is focused on three cases involving patients suffering from pyogenic liver abscess caused by Klebsiella pneumoniae in two hospitals in Bogota, Colombia, where phenotyping and hypermucoviscosity studies were carried out, as well as the genotyping of cultured Klebsiella isolates. Reults: it was found that the isolated microorganism in cases I and II corresponded to the same K. pneumoniae strain, having 100% sequence identity for the 5 genes being studied while the strain in Case III was genotypically different. Conclusion: it is important to carry out multidisciplinary studies allowing all pyogenic liver abscess cases reported in Colombia to be complied to ascertain the frequency of microorganisms causing this pathology in our country, as well as a genotyping study of different K. pneumoniae strains to compare them and confirm clonal and pathogenicity relationships through housekeeping gene analysis.

Estudio de las comunidades microbianas de embutidos fermentados ligeramente acidificados mediante técnicas moleculares. Estandarización, seguridad y mejora tecnológica.

Los embutidos fermentados ligeramente acidificados son un grupo de productos tradicionales mediterráneos, caracterizados por un pH superior a 5,3. Para un control eficiente de la seguridad microbiológica de los embutidos se necesitan técnicas rápidas para la identificación y recuento de los microorganismos patógenos a estudiar. En el presente trabajo, se desarrolló una técnica para la enumeración de L. monocytogenes que combinó el método del número más probable y la identificación mediante PCR específica. Para la detección de Salmonella spp. y L. monocytogenes se desarrolló un sistema de PCR-multiplex que permitió la identificación de ambos patógenos de forma simultánea en una sola reacción. El estudio de la calidad microbiológica de los embutidos fermentados ligeramente acidificados se completó con la caracterización de las comunidades microbianas más importantes en estos productos. Se identificaron a nivel de especie los aislados de bacterias del ácido láctico (BAL), de enterococos y de cocos gram-positivos catalasa-positivos (CGC+). Posteriormente se realizó una tipificación molecular de los mismos mediante RAPD y análisis del perfil plasmídico y se estudiaron las principales características de interés higiénico-sanitario y tecnológico de las cepas. Mediante PCR se identificó Lactobacillus sakei como la especie predominante (74%), seguida por Lactobacillus curvatus (21,2%). La actividad aminoácido-descarboxilasa se asoció a la especie L. curvatus (el 66% de los aislados presentaron esta actividad). La identificación de los enterococos se realizó mediante PCR-multiplex y por secuenciación del gen sodA. Enterococcus faecium fue la especie de enterococos predominante (51,9%) seguida por Enterococcus faecalis (14,2%). Todas las cepas de E. faecalis presentaron genes asociados a factores de virulencia. E. faecalis presentó mayor resistencia a antibióticos que el resto de las especies de enterococos estudiadas. Tan sólo una cepa de E. faecium presentó el genotipo vanA (que confiere resistencia de alto nivel a la vancomicina). La identificación de los aislados de CGC+ (mediante PCR específica y amplificación de la región intergénica 16S-23S ARNr) demostró que Staphylococcus xylosus es la especie predominante en los embutidos fermentados ligeramente acidificados (80,8%). La amina biógena más común en los CGC+ fue la feniletilamina, producida por un 10,8% de aislados. Un pequeño porcentaje de aislados fueron mecA+ (4,6%), presentando además resistencia a múltiples antibióticos. El potencial enterotoxigénico de las cepas de CGC+ fue muy reducido (3,3% de los aislados), detectándose únicamente el gen entC. El estudio pormenorizado de las comunidades bacterianas de interés permitió la selección de 2 cepas de L. sakei y 2 cepas de S. xylosus con características tecnológicas e higiénico-sanitarias óptimas. Para evaluar su efectividad como cultivos iniciadores se elaboraron dos tipos de embutidos ligeramente ácidos, chorizo y fuet, inoculados con microorganismos patógenos (Salmonella spp., L. monocytogenes y S. aureus). El uso de cultivos iniciadores permitió el control de L. monocytogenes, Enterobacteriaceae y Enterococcus así como del contenido en aminas biógenas. Los recuentos de Salmonella spp. disminuyeron de forma significante durante la maduración de los embutidos, independientemente del uso de cultivos iniciadores. El uso del tratamiento de alta presión (400 MPa) en los embutidos madurados consiguió la ausencia de Salmonella spp. en los lotes tratados.

Bryozoan populations reflect nutrient enrichment and productivity gradients in rivers

1. The hypothesis that nutrient enrichment will affect bryozoan abundance was tested using two complementary investigations; a field-based method determining bryozoan abundance in 20 rivers of different nutrient concentrations by deploying statoblast (dormant propagule) traps and an experimental laboratory microcosm study measuring bryozoan growth and mortality. These two methods confirmed independently that increased nutrient concentrations in water promote increases in the biomass of freshwater bryozoans. 2. Statoblasts of the genus Plumatella were recorded in all rivers, regardless of nutrient concentrations, demonstrating that freshwater bryozoans are widespread. Concentrations of Plumatella statoblasts were high in rivers with high nutrient concentrations relative to those with low to moderate nutrient concentrations. Regression analyses indicated that phosphorus concentrations, in particular, significantly influenced statoblast concentrations. 3. Concentrations of Lophopus crystallinus statoblasts were also higher in sites characterised by high nutrient concentrations. Logistic regression analysis revealed that the presence of L. crystallinus statoblasts was significantly associated with decreasing altitude and increasing phosphorus concentrations. This apparently rare species was found in nine rivers (out of 20), seven of which were new sites for L. crystallinus. 4. Growth rates of Fredericella sultana in laboratory microcosms increased with increasing nutrient concentration and high mortality rates were associated with low nutrient concentrations. 5. Our results indicate that bryozoans respond to increasing nutrient concentrations by increased growth, resulting in higher biomasses in enriched waters. We also found that an important component of bryozoan diets can derive from food items lacking chlorophyll a. Finally, bryozoans may be used as independent proxies for inferring trophic conditions, a feature that may be especially valuable in reconstructing historical environments by assessing the abundance of statoblasts in sediment cores.

Growth of the lava dome and extrusion rates at Soufrière Hills Volcano, Montserrat, West Indies: 2005–2008

The third episode of lava dome growth at Soufrière Hills Volcano began 1 August 2005 and ended 20 April 2007. Volumes of the dome and talus produced were measured using a photo-based method with a calibrated camera for increased accuracy. The total dense rock equivalent (DRE) volume of extruded andesite magma (306 ± 51 Mm3) was similar within error to that produced in the earlier episodes but the average extrusion rate was 5.6 ± 0.9 m3s−1 (DRE), higher than the previous episodes. Extrusion rates varied in a pulsatory manner from <0.5 m3s−1 to ∼20 m3s−1. On 18 May 2006, the lava dome had reached a volume of 85 Mm3 DRE and it was removed in its entirety during a massive dome collapse on 20 May 2006. Extrusion began again almost immediately and built a dome of 170 Mm3 DRE with a summit height 1047 m above sea level by 4 April 2007. There were few moderate-sized dome collapses (1–10 Mm3) during this extrusive episode in contrast to the first episode of dome growth in 1995–8 when they were numerous. The first and third episodes of dome growth showed a similar pattern of low (<0.5 m3s−1) but increasing magma flux during the early stages, with steady high flux after extrusion of ∼25 Mm3

Bryozoan populations reflect nutrient enrichment and productivity gradients in rivers

P>1. The hypothesis that nutrient enrichment will affect bryozoan abundance was tested using two complementary investigations; a field-based method determining bryozoan abundance in 20 rivers of different nutrient concentrations by deploying statoblast (dormant propagule) traps and an experimental laboratory microcosm study measuring bryozoan growth and mortality. These two methods confirmed independently that increased nutrient concentrations in water promote increases in the biomass of freshwater bryozoans. 2. Statoblasts of the genus Plumatella were recorded in all rivers, regardless of nutrient concentrations, demonstrating that freshwater bryozoans are widespread. Concentrations of Plumatella statoblasts were high in rivers with high nutrient concentrations relative to those with low to moderate nutrient concentrations. Regression analyses indicated that phosphorus concentrations, in particular, significantly influenced statoblast concentrations. 3. Concentrations of Lophopus crystallinus statoblasts were also higher in sites characterised by high nutrient concentrations. Logistic regression analysis revealed that the presence of L. crystallinus statoblasts was significantly associated with decreasing altitude and increasing phosphorus concentrations. This apparently rare species was found in nine rivers (out of 20), seven of which were new sites for L. crystallinus. 4. Growth rates of Fredericella sultana in laboratory microcosms increased with increasing nutrient concentration and high mortality rates were associated with low nutrient concentrations. 5. Our results indicate that bryozoans respond to increasing nutrient concentrations by increased growth, resulting in higher biomasses in enriched waters. We also found that an important component of bryozoan diets can derive from food items lacking chlorophyll a. Finally, bryozoans may be used as independent proxies for inferring trophic conditions, a feature that may be especially valuable in reconstructing historical environments by assessing the abundance of statoblasts in sediment cores.

Prediction of global and local model quality in CASP8 using the ModFOLD server

The development of effective methods for predicting the quality of three-dimensional (3D) models is fundamentally important for the success of tertiary structure (TS) prediction strategies. Since CASP7, the Quality Assessment (QA) category has existed to gauge the ability of various model quality assessment programs (MQAPs) at predicting the relative quality of individual 3D models. For the CASP8 experiment, automated predictions were submitted in the QA category using two methods from the ModFOLD server-ModFOLD version 1.1 and ModFOLDclust. ModFOLD version 1.1 is a single-model machine learning based method, which was used for automated predictions of global model quality (QMODE1). ModFOLDclust is a simple clustering based method, which was used for automated predictions of both global and local quality (QMODE2). In addition, manual predictions of model quality were made using ModFOLD version 2.0-an experimental method that combines the scores from ModFOLDclust and ModFOLD v1.1. Predictions from the ModFOLDclust method were the most successful of the three in terms of the global model quality, whilst the ModFOLD v1.1 method was comparable in performance to other single-model based methods. In addition, the ModFOLDclust method performed well at predicting the per-residue, or local, model quality scores. Predictions of the per-residue errors in our own 3D models, selected using the ModFOLD v2.0 method, were also the most accurate compared with those from other methods. All of the MQAPs described are publicly accessible via the ModFOLD server at: http://www.reading.ac.uk/bioinf/ModFOLD/. The methods are also freely available to download from: http://www.reading.ac.uk/bioinf/downloads/.

Genetic analysis of complex demographic scenarios: Spatially expanding populations of the cane toad, Bufo marinus

Inferring the spatial expansion dynamics of invading species from molecular data is notoriously difficult due to the complexity of the processes involved. For these demographic scenarios, genetic data obtained from highly variable markers may be profitably combined with specific sampling schemes and information from other sources using a Bayesian approach. The geographic range of the introduced toad Bufo marinus is still expanding in eastern and northern Australia, in each case from isolates established around 1960. A large amount of demographic and historical information is available on both expansion areas. In each area, samples were collected along a transect representing populations of different ages and genotyped at 10 microsatellite loci. Five demographic models of expansion, differing in the dispersal pattern for migrants and founders and in the number of founders, were considered. Because the demographic history is complex, we used an approximate Bayesian method, based on a rejection-regression algorithm. to formally test the relative likelihoods of the five models of expansion and to infer demographic parameters. A stepwise migration-foundation model with founder events was statistically better supported than other four models in both expansion areas. Posterior distributions supported different dynamics of expansion in the studied areas. Populations in the eastern expansion area have a lower stable effective population size and have been founded by a smaller number of individuals than those in the northern expansion area. Once demographically stabilized, populations exchange a substantial number of effective migrants per generation in both expansion areas, and such exchanges are larger in northern than in eastern Australia. The effective number of migrants appears to be considerably lower than that of founders in both expansion areas. We found our inferences to be relatively robust to various assumptions on marker. demographic, and historical features. The method presented here is the only robust, model-based method available so far, which allows inferring complex population dynamics over a short time scale. It also provides the basis for investigating the interplay between population dynamics, drift, and selection in invasive species.

Silica coated noble metal nanoparticle hydrosols as supported catalyst precursors

Synthesis of well-defined nanoparticles has been intensively pursued not only for their fundamental scientific interest, but also for many technological applications. One important development of the nanomaterial is in the area of chemical catalysis. We have now developed a new aqueous-based method for the synthesis of silica encapsulated noble metal nanoparticles in controlled dimensions. Thus, colloid stable silica encapsulated similar to 5 nm platinum nanoparticle is synthesized by a multi-step method. The thickness of the silica coating could be controlled using a different amount of silica precursor. These particles supported on a high surface area alumina are also demonstrated to display a superior hydrogenation activity and stability against metal sintering after thermal activation.

The business case development process in the delivery of NHS infrastructure

There is a lack of knowledge base in relation to experiences gained and lessons learnt from previously executed National Health Service (NHS) infrastructure projects in the UK. This is in part a feature of one-off construction projects, which typify healthcare infrastructure, and in part due to the absence of a suitable method for conveying such information. The complexity of infrastructure delivery process in the NHS makes the construction of healthcare buildings a formidable task. This is particularly the case for the NHS trusts who have little or no experience of construction projects. To facilitate understanding a most important aspect of the delivery process, which is the preparation of a capital investment proposal; steps taken in developing the business case for an NHS healthcare facility are examined. The context for such examination is provided by the planning process of a healthcare project, studied retrospectively. The process is analysed using a social science based method called ‘building stories’, developed at the University of California-Berkeley. By applying this method, stories or narratives are constructed around the data captured on the case study. The findings indicate that the business case process may be used to justify, rather than identify, trusts’ requirements. The study is useful for UK public sector clients as well as consultants and professionals who aim to participate in the delivery of healthcare infrastructure projects in the UK.

Unusually high differential attenuation at C band: Results from a two-year analysis of the French Trappes polarimetric radar data

The differential phase (ΦDP) measured by polarimetric radars is recognized to be a very good indicator of the path integrated by rain. Moreover, if a linear relationship is assumed between the specific differential phase (KDP) and the specific attenuation (AH) and specific differential attenuation (ADP), then attenuation can easily be corrected. The coefficients of proportionality, γH and γDP, are, however, known to be dependent in rain upon drop temperature, drop shapes, drop size distribution, and the presence of large drops causing Mie scattering. In this paper, the authors extensively apply a physically based method, often referred to as the “Smyth and Illingworth constraint,” which uses the constraint that the value of the differential reflectivity ZDR on the far side of the storm should be low to retrieve the γDP coefficient. More than 30 convective episodes observed by the French operational C-band polarimetric Trappes radar during two summers (2005 and 2006) are used to document the variability of γDP with respect to the intrinsic three-dimensional characteristics of the attenuating cells. The Smyth and Illingworth constraint could be applied to only 20% of all attenuated rays of the 2-yr dataset so it cannot be considered the unique solution for attenuation correction in an operational setting but is useful for characterizing the properties of the strongly attenuating cells. The range of variation of γDP is shown to be extremely large, with minimal, maximal, and mean values being, respectively, equal to 0.01, 0.11, and 0.025 dB °−1. Coefficient γDP appears to be almost linearly correlated with the horizontal reflectivity (ZH), differential reflectivity (ZDR), and specific differential phase (KDP) and correlation coefficient (ρHV) of the attenuating cells. The temperature effect is negligible with respect to that of the microphysical properties of the attenuating cells. Unusually large values of γDP, above 0.06 dB °−1, often referred to as “hot spots,” are reported for 15%—a nonnegligible figure—of the rays presenting a significant total differential phase shift (ΔϕDP > 30°). The corresponding strongly attenuating cells are shown to have extremely high ZDR (above 4 dB) and ZH (above 55 dBZ), very low ρHV (below 0.94), and high KDP (above 4° km−1). Analysis of 4 yr of observed raindrop spectra does not reproduce such low values of ρHV, suggesting that (wet) ice is likely to be present in the precipitation medium and responsible for the attenuation and high phase shifts. Furthermore, if melting ice is responsible for the high phase shifts, this suggests that KDP may not be uniquely related to rainfall rate but can result from the presence of wet ice. This hypothesis is supported by the analysis of the vertical profiles of horizontal reflectivity and the values of conventional probability of hail indexes.

Spatio-temporal surface soil heat flux estimates from satellite data: results for the AMMA experiment at the Fakara (Niger) supersite

This paper describes a method that employs Earth Observation (EO) data to calculate spatiotemporal estimates of soil heat flux, G, using a physically-based method (the Analytical Method). The method involves a harmonic analysis of land surface temperature (LST) data. It also requires an estimate of near-surface soil thermal inertia; this property depends on soil textural composition and varies as a function of soil moisture content. The EO data needed to drive the model equations, and the ground-based data required to provide verification of the method, were obtained over the Fakara domain within the African Monsoon Multidisciplinary Analysis (AMMA) program. LST estimates (3 km × 3 km, one image 15 min−1) were derived from MSG-SEVIRI data. Soil moisture estimates were obtained from ENVISAT-ASAR data, while estimates of leaf area index, LAI, (to calculate the effect of the canopy on G, largely due to radiation extinction) were obtained from SPOT-HRV images. The variation of these variables over the Fakara domain, and implications for values of G derived from them, were discussed. Results showed that this method provides reliable large-scale spatiotemporal estimates of G. Variations in G could largely be explained by the variability in the model input variables. Furthermore, it was shown that this method is relatively insensitive to model parameters related to the vegetation or soil texture. However, the strong sensitivity of thermal inertia to soil moisture content at low values of relative saturation (<0.2) means that in arid or semi-arid climates accurate estimates of surface soil moisture content are of utmost importance, if reliable estimates of G are to be obtained. This method has the potential to improve large-scale evaporation estimates, to aid land surface model prediction and to advance research that aims to explain failure in energy balance closure of meteorological field studies.

Ensemble data assimilation in the presence of cloud

In numerical weather prediction (NWP) data assimilation (DA) methods are used to combine available observations with numerical model estimates. This is done by minimising measures of error on both observations and model estimates with more weight given to data that can be more trusted. For any DA method an estimate of the initial forecast error covariance matrix is required. For convective scale data assimilation, however, the properties of the error covariances are not well understood. An effective way to investigate covariance properties in the presence of convection is to use an ensemble-based method for which an estimate of the error covariance is readily available at each time step. In this work, we investigate the performance of the ensemble square root filter (EnSRF) in the presence of cloud growth applied to an idealised 1D convective column model of the atmosphere. We show that the EnSRF performs well in capturing cloud growth, but the ensemble does not cope well with discontinuities introduced into the system by parameterised rain. The state estimates lose accuracy, and more importantly the ensemble is unable to capture the spread (variance) of the estimates correctly. We also find, counter-intuitively, that by reducing the spatial frequency of observations and/or the accuracy of the observations, the ensemble is able to capture the states and their variability successfully across all regimes.