Segmentació d'imatge de ressonància magnètica de pit utilitzant atlas probabilístic

La localització d'òrgans és un tòpic important en l'àmbit de la imatge mèdica per l'ajuda del tractament i diagnosi del càncer. Un exemple es pot trobar en la cal•libració de models farmacoquinètics. Aquesta pot ésser realitzada utilitzant un teixit de referència, on, per exemple en imatges de ressonància magnètica de pit, una correcta segmentació del múscul pectoral és necessària per a la detecció de signes de malignitat. Els mètodes de segmentació basat en atlas han estat altament avaluats en imatge de ressonància magnètica de cervell, obtenint resultats satisfactoris. En aquest projecte, en col•laboració amb el el Diagnostic Image Analysis Group de la Radboud University Nijmegen Medical Centre i la supervisió del Dr. N.Karssemeijer, es presenta la primera aproximació d'un mètode de segmentació basat en atlas per segmentar els diferents teixits visibles en imatges de ressonància magnètica (T1) del pit femení. L'atlas consisteix en 5 estructures (teixit greixòs, teixit dens, cor, pulmons i múscul pectoral) i ha estat utilitzat en un algorisme de segmentació Bayesià per tal de delinear les esmentades estructures. A més a més, s'ha dut a terme una comparació entre un mètode de registre global i un de local, utilitzats tant en la construcció de l'atlas com en la fase de segmentació, essent el primer el que ha presentat millors resultats en termes d'eficiència i precisió. Per a l'avaluació, s'ha dut a terme una comparació visual i numèrica entre les segmentacions obtingudes i les realitzades manualment pels experts col•laboradors. Pel que fa a la numèrica, s'ha emprat el coeficient de similitud de Dice ( mesura que dóna valors entre 0 i 1, on 0 significa no similitud i 1 similitud màxima) i s'ha obtingut una mitjana general de 0.8. Aquest resultat confirma la validesa del mètode presentat per a la segmentació d'imatges de ressonància magnètica del pit.

Phenotypic plasticity in adult worms of Schistosoma mansoni (Trematoda:Schistosomatidae) evidenced by brightfield and confocal laser scanning microscopies

A comparative morphometric study was performed to identify host-induced morphological alterations in Schistosoma mansoni adult worms. A wild parasite population was obtained from a naturally infected rodent (Nectomys squamipes)and then recovered from laboratory infected C3H/He mice. Furthermore, allopatric worm populations maintained for long-term under laboratory conditions in Swiss Webster mice were passed on to N. squamipes. Suckers and genital system (testicular lobes, uterine egg, and egg spine) were analyzed by a digital system for image analysis. Confocal laser scanning microscopy (CLSM) showed details of the genital system (testicular lobes, vitelline glands, and ovary) and the tegument just below the ventral sucker. Significant morphological changes (p < 0.05) were detected in male worms in all experimental conditions, with no significant variability as assessed by CLSM. Significant changes (p < 0.05) were evident in females from the wild population related to their ovaries and vitelline glands, whereas allopatric females presented differences only in this last character. We conclude that S. mansoni worms present the phenotypic plasticity induced by modifications in the parasite's microenvironment, mainly during the first passage under laboratory conditions.

Connectome alterations in schizophrenia

Introduction : DTI has proven to be an exquisite biomarker of tissue microstructure integrity. This technique has been successfully applied to schizophrenia in showing that fractional anisotropy (FA, a marker of white matter integrity) is diminished in several areas of the brain (Kyriakopoulos M et al (2008)). New ways of representing diffusion data emerged recently and achieved to create structural connectivity maps in healthy brains (Hagmann P et al. (2008)). These maps have the capacity to study alterations over the entire brain at the connection and network level. This is of high interest in complex disconnection diseases like schizophrenia. We report on the specific network alterations of schizophrenic patients. Methods : 13 patients with chronic schizophrenia were recruited from in-patient, day treatment, out-patient clinics. Comparison subjects were recruited and group-matched to patients on age, sex, handedness, and parental social economic-status. This study was approved by the local IRB and subjects had to give informed written consent. They were scanned with a 3T clinical MRI scanner. DTI and high-resolution anatomical T1w imaging were performed during the same session. The path from diffusion MRI to a multi-resolution structural connection matrices of the entire brain is a five steps process that was performed in a similar way as described in Hagmann P et al. (2008). (1) DTI and T1w MRI of the brain, (2) segmentation of white and gray matter, (3) white matter tractography, (4) segmentation of the cortex into 242 ROIs of equal surface area covering the entire cortex (Fig 1), (5) the connection network was constructed by measuring for each ROI to ROI connection the related average FA along the corresponding tract. Results : For every connection between 2 ROIs of the network we tested the hypothesis H0: "average FA along fiber pathway is larger or equal in patients than in controls". H0 was rejected for connections where average FA in a connection was significantly lower in patients than in controls. Threshold p-value was 0.01 corrected for multiple comparisons with false discovery rate. We identified consistently that temporal, occipito-temporal, precuneo-temporal as well as frontal inferior and precuneo-cingulate connections were altered (Fig 2: significant connections in yellow). This is in agreement with the known literature, which showed across several studies that FA is diminished in several areas of the brain. More precisely, abnormalities were reported in the prefrontal and temporal white matter and to some extent also in the parietal and occipital regions. The alterations reported in the literature specifically included the corpus callosum, the arcuate fasciculus and the cingulum bundle, which was the case here as well. In addition small world indexes are significantly reduced in patients (p<0.01) (Fig. 3). Conclusions : Using connectome mapping to characterize differences in structural connectivity between healthy and diseased subjects we were able to show widespread connectional alterations in schizophrenia patients and systematic small worldness decrease, which is a marker of network desorganization. More generally, we described a method that has the capacity to sensitively identify structure alterations in complex disconnection syndromes where lesions are widespread throughout the connectional network.

Development of Schistosoma mansoni worms in mice analyzed by bright field and confocal microscopy

The blood flukes of mammals (Digenea: Schistosomatidae) are among trematodes unique whose adult worms have separeted sexes which are dissimilar in appearance. The developmental features, growth and organogenesis of Schistosoma mansoni were studied in Swiss Webster mice by a digital system for image analysis and confocal microscopy. Data so far obtained showed two phases with significative morphological changes at 3-4 weeks post-infection, and a gradual similar development onwards in the reproductive system and tegument. Our male-dependent phase demonstrated that mating occurs before sexual maturing. At week three, the majority of male worms (59%) had formed the gynaecophoric canal although testicular lobes and tegumental tubercles were absent. By this time, 33% females had an incipient ovary (without cellular differentiation). At week four, 77.2% males presented testicular lobes with few germinative cells while 26% had developing tegumental tubercles. The immature ovary was observed in 69% females. Suckers followed different pattern of growth between male and females. The size of oral and ventral suckers from six-week-old male worms grew abruptly (3.0 fold) more than that of three-week-old. In female worms, maximum growth was attained at week four, reducing in size thereafter. From sixth week onwards, all specimens showed the fully developed reproductive system. Probably, these features are morphological traits which schistosome has experienced from hermaphrodite to dioecy.

Cluster kernels for semisupervised classification of VHR urban images

In this paper, we present and apply a semisupervised support vector machine based on cluster kernels for the problem of very high resolution image classification. In the proposed setting, a base kernel working with labeled samples only is deformed by a likelihood kernel encoding similarities between unlabeled examples. The resulting kernel is used to train a standard support vector machine (SVM) classifier. Experiments carried out on very high resolution (VHR) multispectral and hyperspectral images using very few labeled examples show the relevancy of the method in the context of urban image classification. Its simplicity and the small number of parameters involved make it versatile and workable by unexperimented users.

Estimating Gross Value Added (GVA) across multiple scales: theoretical approach and empirical validation

This paper presents an application of the Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism (MuSIASEM) approach to the estimation of quantities of Gross Value Added (GVA) referring to economic entities defined at different scales of study. The method first estimates benchmark values of the pace of GVA generation per hour of labour across economic sectors. These values are estimated as intensive variables –e.g. €/hour– by dividing the various sectorial GVA of the country (expressed in € per year) by the hours of paid work in that same sector per year. This assessment is obtained using data referring to national statistics (top down information referring to the national level). Then, the approach uses bottom-up information (the number of hours of paid work in the various economic sectors of an economic entity –e.g. a city or a province– operating within the country) to estimate the amount of GVA produced by that entity. This estimate is obtained by multiplying the number of hours of work in each sector in the economic entity by the benchmark value of GVA generation per hour of work of that particular sector (national average). This method is applied and tested on two different socio-economic systems: (i) Catalonia (considered level n) and Barcelona (considered level n-1); and (ii) the region of Lima (considered level n) and Lima Metropolitan Area (considered level n-1). In both cases, the GVA per year of the local economic entity –Barcelona and Lima Metropolitan Area – is estimated and the resulting value is compared with GVA data provided by statistical offices. The empirical analysis seems to validate the approach, even though the case of Lima Metropolitan Area indicates a need for additional care when dealing with the estimate of GVA in primary sectors (agriculture and mining).

3D Automated Lung Nodule Segmentation in HRCT

A fully-automated 3D image analysis method is proposed to segment lung nodules in HRCT. A specific gray-level mathematical morphology operator, the SMDC-connection cost, acting in the 3D space of the thorax volume is defined in order to discriminate lung nodules from other dense (vascular) structures. Applied to clinical data concerning patients with pulmonary carcinoma, the proposed method detects isolated, juxtavascular and peripheral nodules with sizes ranging from 2 to 20 mm diameter. The segmentation accuracy was objectively evaluated on real and simulated nodules. The method showed a sensitivity and a specificity ranging from 85% to 97% and from 90% to 98%, respectively.

Do we truly see what we think we see? The role of cognitive bias in pathological interpretation.

In the histomorphological grading of prostate carcinoma, pathologists have regularly assigned comparable scores for the architectural Gleason and the now-obsolete nuclear World Health Organization (WHO) grading systems. Although both systems demonstrate good correspondence between grade and survival, they are based on fundamentally different biological criteria. We tested the hypothesis that this apparent concurrence between the two grading systems originates from an interpretation bias in the minds of diagnostic pathologists, rather than reflecting a biological reality. Three pathologists graded 178 prostatectomy specimens, assigning Gleason and WHO scores on glass slides and on digital images of nuclei isolated out of their architectural context. The results were analysed with respect to interdependencies among the grading systems, to tumour recurrence (PSA relapse > 0.1 ng/ml at 48 months) and robust nuclear morphometry, as assessed by computer-assisted image analysis. WHO and Gleason grades were strongly correlated (r = 0.82) and demonstrated identical prognostic power. However, WHO grades correlated poorly with nuclear morphology (r = 0.19). Grading of nuclei isolated out of their architectural context significantly improved accuracy for nuclear morphology (r = 0.55), but the prognostic power was virtually lost. In conclusion, the architectural organization of a tumour, which the pathologist cannot avoid noticing during initial slide viewing at low magnification, unwittingly influences the subsequent nuclear grade assignment. In our study, the prognostic power of the WHO grading system was dependent on visual assessment of tumour growth pattern. We demonstrate for the first time the influence a cognitive bias can have in the generation of an error in diagnostic pathology and highlight a considerable problem in histopathological tumour grading.

A New Imaging Software To Evaluate The Centration Of Capsulorhexis And Intraocular Lens (IOL) After Cataract Surgery

Purpose: IOL centration and stability after cataract surgery is of high interest for cataract surgeons and IOL-producing companies. We present a new imaging software to evaluate the centration of the rhexis and the centration of the IOL after cataract surgery.Methods: We developed, in collaboration with the Biomedical Imaging Group (BIG), EPFL, Lausanne, a new working tool in order to assess precisely outcomes after IOL-implantation, such as ideal capsulorhexis and IOL-centration. The software is a plug-in of ImageJ, a general-purpose image processing and image-analysis package. The specifications of this software are: evaluation of the rhexis-centration and evaluation the position of the IOL in the posterior chamber. The end points are to analyze the quality of the centration of a rhexis after cataract surgery, the deformation of the rhexis with capsular bag retraction and the centration of the IOL after implantation.Results: This software delivers tools to interactively measure the distances between limbus, IOL and capsulorhexis and its changes over time. The user is invited to adjust nodes of three radial curves for the limbus, rhexis and the optic of the IOL. The radial distances of the curves are computed to evaluate the IOL implantation. The user is also able to define patterns for ideal capsulorhexis and optimal IOL-centration. We are going to present examples of calculations after cataract surgery.Conclusions: Evaluation of the centration of the rhexis and of the IOL after cataract surgery is an important end point for optimal IOL implantation after cataract surgery. Especially multifocal or accommodative lenses need a precise position in the bag with a good stability over time. This software is able to evaluate these parameters just after the surgery but also its changes over time. The results of these evaluations can lead to an optimizing of surgical procedures and materials.

Glucose and lactate are equally effective in energizing activity-dependent synaptic vesicle turnover in purified cortical neurons.

This study examines the role of glucose and lactate as energy substrates to sustain synaptic vesicle cycling. Synaptic vesicle turnover was assessed in a quantitative manner by fluorescence microscopy in primary cultures of mouse cortical neurons. An electrode-equipped perfusion chamber was used to stimulate cells both by electrical field and potassium depolarization during image acquisition. An image analysis procedure was elaborated to select in an unbiased manner synaptic boutons loaded with the fluorescent dye N-(3-triethylammoniumpropyl)-4-(4-(dibutylamino)styryl)pyridinium dibromide (FM1-43). Whereas a minority of the sites fully released their dye content following electrical stimulation, others needed subsequent K(+) depolarization to achieve full release. This functional heterogeneity was not significantly altered by the nature of metabolic substrates. Repetitive stimulation sequences of FM1-43 uptake and release were then performed in the absence of any metabolic substrate and showed that the number of active sites dramatically decreased after the first cycle of loading/unloading. The presence of 1 mM glucose or lactate was sufficient to sustain synaptic vesicle cycling under these conditions. Moreover, both substrates were equivalent for recovery of function after a phase of decreased metabolic substrate availability. Thus, lactate appears to be equivalent to glucose for sustaining synaptic vesicle turnover in cultured cortical neurons during activity.

From MuSIASEM theory to practice: report and reflections from field research in Kampot province, Cambodia

This document contains a report and summary of the field research activities in a rural community of rice farmers in Kampot province, Cambodia in 2011, which I conducted within the context of my PhD research at ICTA-UAB (Institute of Environmental Science and Technology, Autonomous University of Barcelona, Spain). The purpose of the field research was to gather data for a MuSIASEM analysis (Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism) at the village and household level, in order to analyze the multidimensional challenges that small farmers may face nowadays within the context of global rural change and declining access to land. While the literature on MuSIASEM offers a great variety of theoretical explanations and practical applications, there is little information available for students regarding the practical steps required for doing a MuSIASEM analysis at the local level. Within this context, this report offers not only a documentation of the field research design and data collection methods, but further provides a general overview on some organizational and preparative aspects, including some personal reflections, that one may face when preparing and conducting field research for MuSIASEM analysis. In summary, this document thus serves three objectives: (i) to assure methodological transparency for the future work, based on the collected data during field research, (ii) to share my personal experience on the preparative and practical steps required for field research and data collection for a MuSIASEM analysis at the local level, and (iii) to make available for the further interested reader some more detailed background information on the case study village.

Pacing redistributes glycogen within the developing myocardium.

Electrical pacing at physiological rate induces myocardial remodeling associated with regional changes in workload, blood flow and oxygen consumption. However, to what extent energy-producing pathways are also modified within the paced heart remains to be investigated. Pacing could particularly affect glycogen metabolism since hypertrophy stimulates glycolysis and increased workload favors glucose over fat oxidation. In order to test this hypothesis, we used the embryonic chick heart model in which ventricular pacing rapidly resulted in thinning of the ventricle wall and thickening of the atrial wall. Hearts of stage 22HH chick embryos were submitted in ovo to asynchronous and intermittent ventricular pacing delivered at physiological rate during 24 h. The resulting alterations of glycogen content were determined in atrium, ventricle and conotruncus of paced and sham-operated hearts. Hemodynamic parameters of the paced and spontaneously beating hearts were derived from computerized image analysis of video recordings. With respect to sham, paced hearts showed a significant decrease in glycogen content (nmoles glucose units/microg protein; mean+/-S.D.) only in atrium (1.48+/-0.40 v 0.84+/-0.34, n=8) and conotruncus (0.75+/-0.28 v 0.42+/-0.23, n=8). Pacing decreased the end diastolic and stroke volumes by 34 and 44%, respectively. Thus, the rapid glycogen depletion in regions remote from the stimulation site appears to be associated with regional changes in workload and remodeling. These findings underscore the importance of the coupling mechanisms between metabolic pathways and myocardial remodeling in the ectopically paced heart.

Cytotoxic effects of FGF2-saporin on bovine epithelial lens cells in vitro.

PURPOSE: To test the ability of two preparations of FGF2-saporin, either FGF2 chemically conjugated to saporin (FGF2-SAP) or genetically engineered FGF2-saporin (rFGF2-SAP) to inhibit the growth of bovine epithelial lens (BEL) cells in vitro when in solution and when immobilized on heparin surface-modified (HSM) polymethylmethacrylate (PMMA) intraocular lenses (IOLs). METHOD: Bovine epithelial lens cells were incubated with various concentrations FGF2-saporin for as long as 4 days. The number of surviving cells was determined by counting the number of nuclei. Because FGF2 binds to heparin, FGF2-saporin was incubated with HSM PMMA IOLs; excess toxin was washed off, and the BEL cells were grown on the FGF2-saporin-treated IOLs (HSM and non-HSM) for 4 days. Cell density was determined by image analysis. RESULTS: Both FGF2-SAP and rFGF2-SAP were highly cytotoxic (nM range), with rFGF2-SAP 10 times less active than FGF2-SAP. FGF2-saporin bound to the surface of HSM IOLs and eluted by 2M NaCl retained its activity. Toxin bound to HSM IOLs killed more than 90% of the BEL cells placed on the IOL surface within 4 days. The ability of FGF2-saporin to prevent the growth of cells on the IOL surface was strictly dependent on the presence of heparin on the IOL. CONCLUSIONS: FGF2-saporin is bound to HSM PMMA IOLs and prevents the growth of epithelial cells on the surface of the lens.

Quantitative distribution of parvalbumin, calretinin, and calbindin D-28k immunoreactive neurons in the visual cortex of normal and Alzheimer cases.

The distribution of parvalbumin (PV), calretinin (CR), and calbindin (CB) immunoreactive neurons was studied with the help of an image analysis system (Vidas/Zeiss) in the primary visual area 17 and associative area 18 (Brodmann) of Alzheimer and control brains. In neither of these areas was there a significant difference between Alzheimer and control groups in the mean number of PV, CR, or CB immunoreactive neuronal profiles, counted in a cortical column going from pia to white matter. Significant differences in the mean densities (numbers per square millimeter of cortex) of PV, CR, and CB immunoreactive neuronal profiles were not observed either between groups or areas, but only between superficial, middle, and deep layers within areas 17 and 18. The optical density of the immunoreactive neuropil was also similar in Alzheimer and controls, correlating with the numerical density of immunoreactive profiles in superficial, middle, and deep layers. The frequency distribution of neuronal areas indicated significant differences between PV, CR, and CB immunoreactive neuronal profiles in both areas 17 and 18, with more large PV than CR and CB positive profiles. There were also significantly more small and less large PV and CR immunoreactive neuronal profiles in Alzheimer than in controls. Our data show that, although the brain pathology is moderate to severe, there is no prominent decrease of PV, CR and CB positive neurons in the visual cortex of Alzheimer brains, but only selective changes in neuronal perikarya.

Comparative Study of Chemoembolization, Loadable Beads: In vitro Drug Release and Physical Properties of DC Bead and Hepasphere, Loaded with Doxorubicin and Irinotecan

Purpose To characterize in vitro the loadability, physical properties, and release of irinotecan and doxorubicin from two commercially available embolization microspheres. Materials and Methods DC Bead (500-700 μm) and Hepasphere (400-600 μm) microspheres were loaded with either doxorubicin or irinotecan solutions. Drug amount was quantified with spectrophotometry, bead elasticity was measured under compression, and bead size and loading homogeneity were assessed with microscopy image analysis. Drug release was measured over 1-week periods in saline by using a pharmacopeia flow-through method. Results Almost complete drug loading was obtained for both microsphere types and drugs. Doxorubicin-loaded DC Beads maintained their spherical shape throughout the release. In contrast, Hepaspheres showed less homogeneous doxorubicin loading and, after release, some fractured microspheres. Incomplete doxorubicin release was observed in saline over 1 week (27% ± 2 for DC beads and 18% ± 7 for Hepaspheres; P = .013). About 75% of this amount was released within 2.2 hours for both beads. For irinotecan, complete release was obtained for both types of beads, in a sustained manner over 2-3 hours for DC Beads, and in a significantly faster manner as a 7-minute burst for Hepaspheres. Conclusions The two drug-eluting microspheres could be efficiently loaded with both drugs. Incomplete doxorubicin release was attributed to strong drug-bead ionic interactions. Weaker interactions were observed with irinotecan, which led to faster drug release.