Steady-state equilibrium phase inversion recovery ON-resonant water suppression (IRON) MR angiography in conjunction with superparamagnetic nanoparticles. A robust technique for imaging within a wide range of contrast agent dosages.

PURPOSE: To investigate the ability of inversion recovery ON-resonant water suppression (IRON) in conjunction with P904 (superparamagnetic nanoparticles which consisting of a maghemite core coated with a low-molecular-weight amino-alcohol derivative of glucose) to perform steady-state equilibrium phase MR angiography (MRA) over a wide dose range. MATERIALS AND METHODS: Experiments were approved by the institutional animal care committee. Rabbits (n = 12) were imaged at baseline and serially after the administration of 10 incremental dosages of 0.57-5.7 mgFe/Kg P904. Conventional T1-weighted and IRON MRA were obtained on a clinical 1.5 Tesla (T) scanner to image the thoracic and abdominal aorta, and peripheral vessels. Contrast-to-noise ratios (CNR) and vessel sharpness were quantified. RESULTS: Using IRON MRA, CNR and vessel sharpness progressively increased with incremental dosages of the contrast agent P904, exhibiting constantly higher contrast values than T1 -weighted MRA over a very wide range of contrast agent doses (CNR of 18.8 ± 5.6 for IRON versus 11.1 ± 2.8 for T1 -weighted MRA at 1.71 mgFe/kg, P = 0.02 and 19.8 ± 5.9 for IRON versus -0.8 ± 1.4 for T1-weighted MRA at 3.99 mgFe/kg, P = 0.0002). Similar results were obtained for vessel sharpness in peripheral vessels, (Vessel sharpness of 46.76 ± 6.48% for IRON versus 33.20 ± 3.53% for T1-weighted MRA at 1.71 mgFe/Kg, P = 0.002, and of 48.66 ± 5.50% for IRON versus 19.00 ± 7.41% for T1-weighted MRA at 3.99 mgFe/Kg, P = 0.003). CONCLUSION: Our study suggests that quantitative CNR and vessel sharpness after the injection of P904 are consistently higher for IRON MRA when compared with conventional T1-weighted MRA. These findings apply for a wide range of contrast agent dosages.

Reduction in range of cervical motion on serial long-term follow-up in patients undergoing oblique corpectomy for cervical spondylotic myelopathy.

PURPOSE: To determine whether motion preservation following oblique cervical corpectomy (OCC) for cervical spondylotic myelopathy (CSM) persists with serial follow-up. METHODS: We included 28 patients with preoperative and at least two serial follow-up neutral and dynamic cervical spine radiographs who underwent OCC for CSM. Patients with an ossified posterior longitudinal ligament (OPLL) were excluded. Changes in sagittal curvature, segmental and whole spine range of motion (ROM) were measured. Nathan's system graded anterior osteophyte formation. Neurological function was measured by Nurick's grade and modified Japanese Orthopedic Association (JOA) scores. RESULTS: The majority (23 patients) had a single or 2-level corpectomy. The average duration of follow-up was 45 months. The Nurick's grade and the JOA scores showed statistically significant improvements after surgery (p < 0.001). 17% of patients with preoperative lordotic spines had a loss of lordosis at last follow-up, but with no clinical worsening. 77% of the whole spine ROM and 62% of segmental ROM was preserved at last follow-up. The whole spine and segmental ROM decreased by 11.2° and 10.9°, respectively (p ≤ 0.001). Patients with a greater range of segmental movement preoperatively had a statistically greater range of movement at follow-up. The analysis of serial radiographs indicated that the range of movement of the whole spine and the range of movement at the segmental spine levels significantly reduced during the follow-up period. Nathan's grade showed increase in osteophytosis in more than two-thirds of the patients (p ≤ 0.01). The whole spine range of movement at follow-up significantly correlated with Nathan's grade. CONCLUSIONS: Although the OCC preserves segmental and whole spine ROM, serial measurements show a progressive decrease in ROM albeit without clinical worsening. The reduction in this ROM is probably related to degenerative ossification of spinal ligaments.

Time-lapse and probabilistic inversion strategies for plane-wave electromagnetic data.

L'utilisation efficace des systèmes géothermaux, la séquestration du CO2 pour limiter le changement climatique et la prévention de l'intrusion d'eau salée dans les aquifères costaux ne sont que quelques exemples qui démontrent notre besoin en technologies nouvelles pour suivre l'évolution des processus souterrains à partir de la surface. Un défi majeur est d'assurer la caractérisation et l'optimisation des performances de ces technologies à différentes échelles spatiales et temporelles. Les méthodes électromagnétiques (EM) d'ondes planes sont sensibles à la conductivité électrique du sous-sol et, par conséquent, à la conductivité électrique des fluides saturant la roche, à la présence de fractures connectées, à la température et aux matériaux géologiques. Ces méthodes sont régies par des équations valides sur de larges gammes de fréquences, permettant détudier de manières analogues des processus allant de quelques mètres sous la surface jusqu'à plusieurs kilomètres de profondeur. Néanmoins, ces méthodes sont soumises à une perte de résolution avec la profondeur à cause des propriétés diffusives du champ électromagnétique. Pour cette raison, l'estimation des modèles du sous-sol par ces méthodes doit prendre en compte des informations a priori afin de contraindre les modèles autant que possible et de permettre la quantification des incertitudes de ces modèles de façon appropriée. Dans la présente thèse, je développe des approches permettant la caractérisation statique et dynamique du sous-sol à l'aide d'ondes EM planes. Dans une première partie, je présente une approche déterministe permettant de réaliser des inversions répétées dans le temps (time-lapse) de données d'ondes EM planes en deux dimensions. Cette stratégie est basée sur l'incorporation dans l'algorithme d'informations a priori en fonction des changements du modèle de conductivité électrique attendus. Ceci est réalisé en intégrant une régularisation stochastique et des contraintes flexibles par rapport à la gamme des changements attendus en utilisant les multiplicateurs de Lagrange. J'utilise des normes différentes de la norme l2 pour contraindre la structure du modèle et obtenir des transitions abruptes entre les régions du model qui subissent des changements dans le temps et celles qui n'en subissent pas. Aussi, j'incorpore une stratégie afin d'éliminer les erreurs systématiques de données time-lapse. Ce travail a mis en évidence l'amélioration de la caractérisation des changements temporels par rapport aux approches classiques qui réalisent des inversions indépendantes à chaque pas de temps et comparent les modèles. Dans la seconde partie de cette thèse, j'adopte un formalisme bayésien et je teste la possibilité de quantifier les incertitudes sur les paramètres du modèle dans l'inversion d'ondes EM planes. Pour ce faire, je présente une stratégie d'inversion probabiliste basée sur des pixels à deux dimensions pour des inversions de données d'ondes EM planes et de tomographies de résistivité électrique (ERT) séparées et jointes. Je compare les incertitudes des paramètres du modèle en considérant différents types d'information a priori sur la structure du modèle et différentes fonctions de vraisemblance pour décrire les erreurs sur les données. Les résultats indiquent que la régularisation du modèle est nécessaire lorsqu'on a à faire à un large nombre de paramètres car cela permet d'accélérer la convergence des chaînes et d'obtenir des modèles plus réalistes. Cependent, ces contraintes mènent à des incertitudes d'estimations plus faibles, ce qui implique des distributions a posteriori qui ne contiennent pas le vrai modèledans les régions ou` la méthode présente une sensibilité limitée. Cette situation peut être améliorée en combinant des méthodes d'ondes EM planes avec d'autres méthodes complémentaires telles que l'ERT. De plus, je montre que le poids de régularisation des paramètres et l'écart-type des erreurs sur les données peuvent être retrouvés par une inversion probabiliste. Finalement, j'évalue la possibilité de caractériser une distribution tridimensionnelle d'un panache de traceur salin injecté dans le sous-sol en réalisant une inversion probabiliste time-lapse tridimensionnelle d'ondes EM planes. Etant donné que les inversions probabilistes sont très coûteuses en temps de calcul lorsque l'espace des paramètres présente une grande dimension, je propose une stratégie de réduction du modèle ou` les coefficients de décomposition des moments de Legendre du panache de traceur injecté ainsi que sa position sont estimés. Pour ce faire, un modèle de résistivité de base est nécessaire. Il peut être obtenu avant l'expérience time-lapse. Un test synthétique montre que la méthodologie marche bien quand le modèle de résistivité de base est caractérisé correctement. Cette méthodologie est aussi appliquée à un test de trac¸age par injection d'une solution saline et d'acides réalisé dans un système géothermal en Australie, puis comparée à une inversion time-lapse tridimensionnelle réalisée selon une approche déterministe. L'inversion probabiliste permet de mieux contraindre le panache du traceur salin gr^ace à la grande quantité d'informations a priori incluse dans l'algorithme. Néanmoins, les changements de conductivités nécessaires pour expliquer les changements observés dans les données sont plus grands que ce qu'expliquent notre connaissance actuelle des phénomenès physiques. Ce problème peut être lié à la qualité limitée du modèle de résistivité de base utilisé, indiquant ainsi que des efforts plus grands devront être fournis dans le futur pour obtenir des modèles de base de bonne qualité avant de réaliser des expériences dynamiques. Les études décrites dans cette thèse montrent que les méthodes d'ondes EM planes sont très utiles pour caractériser et suivre les variations temporelles du sous-sol sur de larges échelles. Les présentes approches améliorent l'évaluation des modèles obtenus, autant en termes d'incorporation d'informations a priori, qu'en termes de quantification d'incertitudes a posteriori. De plus, les stratégies développées peuvent être appliquées à d'autres méthodes géophysiques, et offrent une grande flexibilité pour l'incorporation d'informations additionnelles lorsqu'elles sont disponibles. -- The efficient use of geothermal systems, the sequestration of CO2 to mitigate climate change, and the prevention of seawater intrusion in coastal aquifers are only some examples that demonstrate the need for novel technologies to monitor subsurface processes from the surface. A main challenge is to assure optimal performance of such technologies at different temporal and spatial scales. Plane-wave electromagnetic (EM) methods are sensitive to subsurface electrical conductivity and consequently to fluid conductivity, fracture connectivity, temperature, and rock mineralogy. These methods have governing equations that are the same over a large range of frequencies, thus allowing to study in an analogous manner processes on scales ranging from few meters close to the surface down to several hundreds of kilometers depth. Unfortunately, they suffer from a significant resolution loss with depth due to the diffusive nature of the electromagnetic fields. Therefore, estimations of subsurface models that use these methods should incorporate a priori information to better constrain the models, and provide appropriate measures of model uncertainty. During my thesis, I have developed approaches to improve the static and dynamic characterization of the subsurface with plane-wave EM methods. In the first part of this thesis, I present a two-dimensional deterministic approach to perform time-lapse inversion of plane-wave EM data. The strategy is based on the incorporation of prior information into the inversion algorithm regarding the expected temporal changes in electrical conductivity. This is done by incorporating a flexible stochastic regularization and constraints regarding the expected ranges of the changes by using Lagrange multipliers. I use non-l2 norms to penalize the model update in order to obtain sharp transitions between regions that experience temporal changes and regions that do not. I also incorporate a time-lapse differencing strategy to remove systematic errors in the time-lapse inversion. This work presents improvements in the characterization of temporal changes with respect to the classical approach of performing separate inversions and computing differences between the models. In the second part of this thesis, I adopt a Bayesian framework and use Markov chain Monte Carlo (MCMC) simulations to quantify model parameter uncertainty in plane-wave EM inversion. For this purpose, I present a two-dimensional pixel-based probabilistic inversion strategy for separate and joint inversions of plane-wave EM and electrical resistivity tomography (ERT) data. I compare the uncertainties of the model parameters when considering different types of prior information on the model structure and different likelihood functions to describe the data errors. The results indicate that model regularization is necessary when dealing with a large number of model parameters because it helps to accelerate the convergence of the chains and leads to more realistic models. These constraints also lead to smaller uncertainty estimates, which imply posterior distributions that do not include the true underlying model in regions where the method has limited sensitivity. This situation can be improved by combining planewave EM methods with complimentary geophysical methods such as ERT. In addition, I show that an appropriate regularization weight and the standard deviation of the data errors can be retrieved by the MCMC inversion. Finally, I evaluate the possibility of characterizing the three-dimensional distribution of an injected water plume by performing three-dimensional time-lapse MCMC inversion of planewave EM data. Since MCMC inversion involves a significant computational burden in high parameter dimensions, I propose a model reduction strategy where the coefficients of a Legendre moment decomposition of the injected water plume and its location are estimated. For this purpose, a base resistivity model is needed which is obtained prior to the time-lapse experiment. A synthetic test shows that the methodology works well when the base resistivity model is correctly characterized. The methodology is also applied to an injection experiment performed in a geothermal system in Australia, and compared to a three-dimensional time-lapse inversion performed within a deterministic framework. The MCMC inversion better constrains the water plumes due to the larger amount of prior information that is included in the algorithm. The conductivity changes needed to explain the time-lapse data are much larger than what is physically possible based on present day understandings. This issue may be related to the base resistivity model used, therefore indicating that more efforts should be given to obtain high-quality base models prior to dynamic experiments. The studies described herein give clear evidence that plane-wave EM methods are useful to characterize and monitor the subsurface at a wide range of scales. The presented approaches contribute to an improved appraisal of the obtained models, both in terms of the incorporation of prior information in the algorithms and the posterior uncertainty quantification. In addition, the developed strategies can be applied to other geophysical methods, and offer great flexibility to incorporate additional information when available.

CD34/QBEND10 immunostaining in bone marrow biopsies: an additional parameter for the diagnosis and classification of myelodysplastic syndromes.

CD34/QBEND10 immunostaining has been assessed in 150 bone marrow biopsies (BMB) including 91 myelodysplastic syndromes (MDS), 16 MDS-related AML, 25 reactive BMB, and 18 cases where RA could neither be established nor ruled out. All cases were reviewed and classified according to the clinical and morphological FAB criteria. The percentage of CD34-positive (CD34 +) hematopoietic cells and the number of clusters of CD34+ cells in 10 HPF were determined. In most cases the CD34+ cell count was similar to the blast percentage determined morphologically. In RA, however, not only typical blasts but also less immature hemopoietic cells lying morphologically between blasts and promyelocytes were stained with CD34. The CD34+ cell count and cluster values were significantly higher in RA than in BMB with reactive changes (p&lt;0.0001 for both), in RAEB than in RA (p=0.0006 and p=0.0189, respectively), in RAEBt than in RAEB (p=0.0001 and p=0.0038), and in MDS-AML than in RAEBt (p&lt;0.0001 and p=0.0007). Presence of CD34+ cell clusters in RA correlated with increased risk of progression of the disease. We conclude that CD34 immunostaining in BMB is a useful tool for distinguishing RA from other anemias, assessing blast percentage in MDS cases, classifying them according to FAB, and following their evolution.

Regional specificity of MRI contrast parameter changes in normal ageing revealed by voxel-based quantification (VBQ).

Normal ageing is associated with characteristic changes in brain microstructure. Although in vivo neuroimaging captures spatial and temporal patterns of age-related changes of anatomy at the macroscopic scale, our knowledge of the underlying (patho)physiological processes at cellular and molecular levels is still limited. The aim of this study is to explore brain tissue properties in normal ageing using quantitative magnetic resonance imaging (MRI) alongside conventional morphological assessment. Using a whole-brain approach in a cohort of 26 adults, aged 18-85years, we performed voxel-based morphometric (VBM) analysis and voxel-based quantification (VBQ) of diffusion tensor, magnetization transfer (MT), R1, and R2* relaxation parameters. We found age-related reductions in cortical and subcortical grey matter volume paralleled by changes in fractional anisotropy (FA), mean diffusivity (MD), MT and R2*. The latter were regionally specific depending on their differential sensitivity to microscopic tissue properties. VBQ of white matter revealed distinct anatomical patterns of age-related change in microstructure. Widespread and profound reduction in MT contrasted with local FA decreases paralleled by MD increases. R1 reductions and R2* increases were observed to a smaller extent in overlapping occipito-parietal white matter regions. We interpret our findings, based on current biophysical models, as a fingerprint of age-dependent brain atrophy and underlying microstructural changes in myelin, iron deposits and water. The VBQ approach we present allows for systematic unbiased exploration of the interaction between imaging parameters and extends current methods for detection of neurodegenerative processes in the brain. The demonstrated parameter-specific distribution patterns offer insights into age-related brain structure changes in vivo and provide essential baseline data for studying disease against a background of healthy ageing.

Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method.

Eukaryotic transcription is tightly regulated by transcriptional regulatory elements, even though these elements may be located far away from their target genes. It is now widely recognized that these regulatory elements can be brought in close proximity through the formation of chromatin loops, and that these loops are crucial for transcriptional regulation of their target genes. The chromosome conformation capture (3C) technique presents a snapshot of long-range interactions, by fixing physically interacting elements with formaldehyde, digestion of the DNA, and ligation to obtain a library of unique ligation products. Recently, several large-scale modifications to the 3C technique have been presented. Here, we describe chromosome conformation capture sequencing (4C-seq), a high-throughput version of the 3C technique that combines the 3C-on-chip (4C) protocol with next-generation Illumina sequencing. The method is presented for use in mammalian cell lines, but can be adapted to use in mammalian tissues and any other eukaryotic genome.

Systematic review of population pharmacokinetic analyses of imatinib and relationships with treatment outcomes

Several population pharmacokinetic (PPK) analyses of the anticancer drug imatinib have been performed to investigate different patient populations and covariate effects. The present analysis offers a systematic qualitative and quantitative summary and comparison of those. Its primary objective was to provide useful information for evaluating the expectedness of imatinib plasma concentration measurements in the frame of therapeutic drug monitoring. The secondary objective was to review clinically important concentration-effect relationships to provide help in evaluating the potential suitability of plasma concentration values. Nine PPK models describing total imatinib plasma concentration were identified. Parameter estimates were standardized to common covariate values whenever possible. Predicted median exposure (Cmin) was derived by simulations and ranged between models from 555 to 1388 ng/mL (grand median: 870 ng/mL and interquartile "reference" range: 520-1390 ng/mL). Covariates of potential clinical importance (up to 30% change in pharmacokinetic predicted by at least 1 model) included body weight, albumin, α1 acid glycoprotein, and white blood cell count. Various other covariates were included but were statistically not significant or seemed clinically less important or physiologically controversial. Concentration-response relationships had more importance below the average reference range and concentration-toxicity relationships above. Therapeutic drug monitoring-guided dosage adjustment seems justified for imatinib, but a formal predictive therapeutic range remains difficult to propose in the absence of prospective target concentration intervention trials. To evaluate the expectedness of a drug concentration measurement in practice, this review allows comparison of the measurement either to the average reference range or to a specific range accounting for individual patient characteristics. For future research, external PPK model validation or meta-model development should be considered.

Impact of free-range pigs on mountain pastures in the Swiss Jura

The consequences of foraging by free-range pigs on the vegetation of mountain pastures was investigated. 25 pigs (15 week-old, mean weight 50 kg) were enclosed from June to mid-September in a 2 ha-enclosure in Jura Mountains (Switzerland), fed with a mixture of lactoserum and cereals. The enclosure contained five different plant communities. Eutrophic pastures on deep soil were strongly overturned, but the recolonisation was quick and dominated by the original species. Mesotrophic pastures were less damaged on stony soil but completely destroyed on deep soil, and the recovery was slow, characterised by a shift of plant species in a more eutrophic direction. Four years were not sufficient for complete recovery. Oligotrophic calcareous pastures on shallow stony soil were not damaged. Extensive breeding of pigs in mountain pastures might be harmful to plant species and vegetation, and ought to be restricted to the less sensitive plant communities, with a rotation on two to three different sites.

Effect of a temperature increase in the non-noxious range on proton-evoked ASIC and TRPV1 activity.

Acid-sensing ion channels (ASICs) are neuronal H(+)-gated cation channels, and the transient receptor potential vanilloid 1 channel (TRPV1) is a multimodal cation channel activated by low pH, noxious heat, capsaicin, and voltage. ASICs and TRPV1 are present in sensory neurons. It has been shown that raising the temperature increases TRPV1 and decreases ASIC H(+)-gated current amplitudes. To understand the underlying mechanisms, we have analyzed ASIC and TRPV1 function in a recombinant expression system and in dorsal root ganglion (DRG) neurons at room and physiological temperature. We show that temperature in the range studied does not affect the pH dependence of ASIC and TRPV1 activation. A temperature increase induces, however, a small alkaline shift of the pH dependence of steady-state inactivation of ASIC1a, ASIC1b, and ASIC2a. The decrease in ASIC peak current amplitudes at higher temperatures is likely in part due to the observed accelerated open channel inactivation kinetics and for some ASIC types to the changed pH dependence of steady-state inactivation. The increase in H(+)-activated TRPV1 current at the higher temperature is at least in part due to a hyperpolarizing shift in its voltage dependence. The contribution of TRPV1 relative to ASICs to H(+)-gated currents in DRG neurons increases with higher temperature and acidity. Still, ASICs remain the principal pH sensors of DRG neurons at 35°C in the pH range ≥6.

Phylogeographic patterning of mtDNA in the widely distributed harvest mouse (Micromys minutus) suggests dramatic cycles of range contraction and expansion during the mid- to late Pleistocene

We examined sequence variation in the mitochondrial cytochrome b gene (1140 bp, n = 73) and control region (842-851 bp, n = 74) in the Eurasian harvest mouse (Micromys minutus (Pallas, 1771)), with samples drawn from across its range, from Western Europe to Japan. Phylogeographic analyses revealed region-specific haplotype groupings combined with overall low levels of inter-regional genetic divergence. Despite the enormous intervening distance, European and East Asian samples showed a net nucleotide divergence of only 0.36%. Based on an evolutionary rate for the cytochrome b gene of 2.4%(.)(site(.)lineage(.)million years)(-1), the initial divergence time of these populations is estimated at around 80 000 years before present. Our findings are consistent with available fossil evidence that has recorded repeated cycles of extinction and recolonization of Europe by M. minutus through the Quaternary. The molecular data further suggest that recolonization occurred from refugia in the Central to East Asian region. Japanese haplotypes of M. minutus, with the exception of those from Tsushima Is., show limited nucleotide diversity (0.15%) compared with those found on the adjacent Korean Peninsula. This finding suggests recent colonization of the Japanese Archipelago, probably around the last glacial period, followed by rapid population growth.

Natural selection in a postglacial range expansion: the case of the colour cline in the European barn owl.

Gradients of variation-or clines-have always intrigued biologists. Classically, they have been interpreted as the outcomes of antagonistic interactions between selection and gene flow. Alternatively, clines may also establish neutrally with isolation by distance (IBD) or secondary contact between previously isolated populations. The relative importance of natural selection and these two neutral processes in the establishment of clinal variation can be tested by comparing genetic differentiation at neutral genetic markers and at the studied trait. A third neutral process, surfing of a newly arisen mutation during the colonization of a new habitat, is more difficult to test. Here, we designed a spatially explicit approximate Bayesian computation (ABC) simulation framework to evaluate whether the strong cline in the genetically based reddish coloration observed in the European barn owl (Tyto alba) arose as a by-product of a range expansion or whether selection has to be invoked to explain this colour cline, for which we have previously ruled out the actions of IBD or secondary contact. Using ABC simulations and genetic data on 390 individuals from 20 locations genotyped at 22 microsatellites loci, we first determined how barn owls colonized Europe after the last glaciation. Using these results in new simulations on the evolution of the colour phenotype, and assuming various genetic architectures for the colour trait, we demonstrate that the observed colour cline cannot be due to the surfing of a neutral mutation. Taking advantage of spatially explicit ABC, which proved to be a powerful method to disentangle the respective roles of selection and drift in range expansions, we conclude that the formation of the colour cline observed in the barn owl must be due to natural selection.