A non-rigid registration approach for quantifying myocardial contraction in tagged MRI using generalized information measures.

International audienceWe address the problem of quantitatively assessing myocardial function from tagged MRI sequences. We develop a two-step method comprising (i) a motion estimation step using a novel variational non-rigid registration technique based on generalized information measures, and (ii) a measurement step, yielding local and segmental deformation parameters over the whole myocardium. Experiments on healthy and pathological data demonstrate that this method delivers, within a reasonable computation time and in a fully unsupervised way, reliable measurements for normal subjects and quantitative pathology-specific information. Beyond cardiac MRI, this work redefines the foundations of variational non-rigid registration for information-theoretic similarity criteria with potential interest in multimodal medical imaging

A new method of reconstructing the P-T conditions of fluid circulation in an accretionary prism (Shimanto, Japan) from microthermometry of methane-bearing aqueous inclusions

International audienceIn paleo-accretionary prisms and the shallow metamorphic domains of orogens, circulating fluids trapped in inclusions are commonly composed of a mixture of salt water and methane, producing two types of fluid inclusions: methane-bearing aqueous and methane-rich gaseous fluid inclusions. In such geological settings, where multiple stages of deformation, veining and fluid influx are prevalent, textural relationships between aqueous and gaseous inclusions are often ambiguous, preventing the microthermometric determination of fluid trapping pressure and temperature conditions. To assess the P-T conditions of deep circulating fluids from the Hyuga unit of the Shimanto paleo-accretionary prism on Kyushu, Japan, we have developed a new computational code, applicable to the H2O-CH4-NaCl system, which allows the characterization of CH4-bearing aqueous inclusions using only the temperatures of their phase transitions estimated by microthermometry: Tmi, the melting temperature of ice; Thyd, the melting temperature of gas hydrate and Th,aq, homogenization temperature. This thermodynamic modeling calculates the bulk density and composition of aqueous inclusions, as well as their P-T isochoric paths in a P-T diagram with an estimated precision of approximatively 10 %. We use this computational tool to reconstruct the entrapment P-T conditions of aqueous inclusions in the Hyuga unit, and we show that these aqueous inclusions cannot be cogenetic with methane gaseous inclusions present in the same rocks. As a result, we propose that pulses of a high-pressure, methane-rich fluid transiently percolated through a rock wetted by a lower-pressure aqueous fluid. By coupling microthermometric results with petrological data, we infer that the exhumation of the Hyuga unit from the peak metamorphic conditions was nearly isothermal and ended up under a very hot geothermal gradient. In subduction or collision zones, modeling aqueous fluid inclusions in the ternary H2O-CH4-NaCl system and not simply in the binary H2O-NaCl is necessary, as the addition of even a small amount of methane to the water raises significantly the isochores to higher pressures. Our new code provides therefore the possibility to estimate precisely the pressure conditions of fluids circulating at depth

Multiple melting stages and refertilization as indicators for ridge to subduction formation: The New Caledonia ophiolite

International audienceThe origin of the New Caledonia ophiolite (South West Pacific), one of the largest in the world, is controversial. This nappe of ultramafic rocks (300 km long, 50 km wide and 2 km thick) is thrust upon a smaller nappe (Poya terrane) composed of basalts from mid-ocean ridges (MORB), back arc basins (BABB) and ocean islands (OIB). This nappe was tectonically accreted from the subducting plate prior and during the obduction of the ultramafic nappe. The bulk of the ophiolite is composed of highly depleted harzburgites (± dunites) with characteristic U-shaped bulk-rock rare-earth element (REE) patterns that are attributed to their formation in a forearc environment. In contrast, the origin of spoon-shaped REE patterns of lherzolites in the northernmost klippes was unclear. Our new major element and REE data on whole rocks, spinel and clinopyroxene establish the abyssal affinity of these lherzolites. Significant LREE enrichment in the lherzolites is best explained by partial melting in a spreading ridge, followed by near in-situ refertilization from deeper mantle melts. Using equilibrium melting equations, we show that melts extracted from these lherzolites are compositionally similar to the MORB of the Poya terrane. This is used to infer that the ultramafic nappe and the mafic Poya terrane represent oceanic lithosphere of a single marginal basin that formed during the late Cretaceous. In contrast, our spinel data highlights the strong forearc affinities of the most depleted harzburgites whose compositions are best modeled by hydrous melting of a source that had previously experienced depletion in a spreading ridge. The New Caledonian boninites probably formed during this second stage of partial melting. The two melting events in the New Caledonia ophiolite record the rapid transition from oceanic accretion to convergence in the South Loyalty Basin during the Late Paleocene, with initiation of a new subduction zone at or near the ridge axis

Mesoscopic models for DNA stretching under force: new results and comparison to experiments

Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity. It has been proposed that the first transition, at forces of 60--80 pN, is a transition from B to S-DNA, viewed as a stretched duplex DNA, while the second one, at stronger forces, is a strand peeling resulting in single stranded DNAs (ssDNA), similar to thermal denaturation. But due to experimental conditions these two transitions can overlap, for instance for poly(dA-dT). We derive analytical formula using a coupled discrete worm like chain-Ising model. Our model takes into account bending rigidity, discreteness of the chain, linear and non-linear (for ssDNA) bond stretching. In the limit of zero force, this model simplifies into a coupled model already developed by us for studying thermal DNA melting, establishing a connexion with previous fitting parameter values for denaturation profiles. We find that: (i) ssDNA is fitted, using an analytical formula, over a nanoNewton range with only three free parameters, the contour length, the bending modulus and the monomer size; (ii) a surprisingly good fit on this force range is possible only by choosing a monomer size of 0.2 nm, almost 4 times smaller than the ssDNA nucleobase length; (iii) mesoscopic models are not able to fit B to ssDNA (or S to ss) transitions; (iv) an analytical formula for fitting B to S transitions is derived in the strong force approximation and for long DNAs, which is in excellent agreement with exact transfer matrix calculations; (v) this formula fits perfectly well poly(dG-dC) and $\lambda$-DNA force-extension curves with consistent parameter values; (vi) a coherent picture, where S to ssDNA transitions are much more sensitive to base-pair sequence than the B to S one, emerges.Comment: 14 pages, 9 figure

Cooperative Binding

Molecular binding is an interaction between molecules that results in a stable association between those molecules. Cooperative binding occurs if the number of binding sites of a macromolecule that are occupied by a specific type of ligand is a nonlinear function of this ligand’s concentration. This can be due, for instance, to an affinity for the ligand that depends on the amount of ligand bound. Cooperativity can be positive (supralinear) or negative (infralinear). Cooperative binding is most often observed in proteins, but nucleic acids can also exhibit cooperative binding, for instance of transcription factors. Cooperative binding has been shown to be the mechanism underlying a large range of biochemical and physiological processes

When and where did India and Asia collide?

Timing of the collision between India and Asia is the key boundary condition in all models for the evolution of the Himalaya-Tibetan orogenic system. Thus it profoundly affects the interpretation of the rates of a multitude of associated geological processes ranging from Tibetan Plateau uplift through continental extrusion across eastern Asia, as well as our understanding of global climate change during the Cenozoic. Although an abrupt slowdown in the rate of convergence between India and Asia around 55 Ma is widely regarded as indicating the beginning of the collision, most of the effects attributed to this major tectonic episode do not occur until more than 20 Ma later. Refined estimates of the relative positions of India and Asia indicate that they were not close enough to one another to have collided at 55 Ma. On the basis of new field evidence from Tibet and a reassessment of published data we suggest that continent-continent collision began around the Eocene/Oligocene boundary (∼34 Ma) and propose an alternative explanation for events at 55 Ma. Copyright 2007 by the American Geophysical Union.published_or_final_versio

Integrin Clustering Is Driven by Mechanical Resistance from the Glycocalyx and the Substrate

Integrins have emerged as key sensory molecules that translate chemical and physical cues from the extracellular matrix (ECM) into biochemical signals that regulate cell behavior. Integrins function by clustering into adhesion plaques, but the molecular mechanisms that drive integrin clustering in response to interaction with the ECM remain unclear. To explore how deformations in the cell-ECM interface influence integrin clustering, we developed a spatial-temporal simulation that integrates the micro-mechanics of the cell, glycocalyx, and ECM with a simple chemical model of integrin activation and ligand interaction. Due to mechanical coupling, we find that integrin-ligand interactions are highly cooperative, and this cooperativity is sufficient to drive integrin clustering even in the absence of cytoskeletal crosslinking or homotypic integrin-integrin interactions. The glycocalyx largely mediates this cooperativity and hence may be a key regulator of integrin function. Remarkably, integrin clustering in the model is naturally responsive to the chemical and physical properties of the ECM, including ligand density, matrix rigidity, and the chemical affinity of ligand for receptor. Consistent with experimental observations, we find that integrin clustering is robust on rigid substrates with high ligand density, but is impaired on substrates that are highly compliant or have low ligand density. We thus demonstrate how integrins themselves could function as sensory molecules that begin sensing matrix properties even before large multi-molecular adhesion complexes are assembled

Simulation expérimentale de l'ascension et de la vésiculation des magmas rhyolitiques

The purpose of this thesis was to characterize the kinetics of bubble nucleation in rhyolitic magmas. Isothermal decompression experiments (in externally heated pressure vessels fitted with a rapid quench) were carried out to better understand (i) the kinetics of heterogeneous bubble nucleation in hydrous rhyolitic melts, and (ii) the effect of carbon dioxide on homogeneous bubble nucleation in the rhyolite-H2O-CO2 system. The final objective of our research was to identify textural parameters which could constitute reliable markers of the dynamics of magma ascent. The kinetics of heterogeneous nucleation was studied in rhyolite-hematite-H2O and rhyolite-magnetite-H2O systems, using glasses saturated in water at 200 MPa and 775-825°C (≈ 6 wt% H2O), and comprising different number densities of crystals. We carried out several experiments at two decompression rates (⎪dP/dt⎪ = 27.8 and 1000 kPa/s). Our main results are as follows: (1) The degree of supersaturation ΔPN required for nucleation is strongly dependent on the mineral species present in the liquid (ΔPN is the difference between the water saturation pressure and the bubble nucleation pressure): in the presence of hematite, ΔPN is very large (≈ 135 MPa) like in the case of homogeneous nucleation, whereas it is reduced to 15-35 MPa in presence of magnetite crystals. (2) For a given system, ΔPN does not vary with the decompression rate. (3) During decompression, the bubble number density n3D first increases rapidly, and then stabilizes to a value strongly dependent on the decompression rate. The number of bubbles is not controlled by the number of crystals in the liquid but by the relative values of surface tension, water diffusivity and decompression rate, as predicted by Toramaru (1995, 2006). (4) Once the nucleation pressure is crossed, the degree water supersaturation rapidly decreases and the water content in the liquid approaches the equilibrium value, independently of the decompression rate. (5) A second event of nucleation was observed in the rhyolite-magnetite-H2O system, and was ascribed to a slight increase of the degree of water supersaturation at low pressure due to a decrease of water diffusivity. Homogeneous nucleation in the rhyolite-H2O-CO2 was studied at decompression rates of 27.8, 167 and 1000 kPa/s, using starting glasses saturated in volatiles at 250 MPa and 800°C and containing ≈ 5.2 wt% H2O and ≈ 590 ppm CO2. The main results are as follows: (i) the nucleation pressure is almost independent of the decompression rate; (ii) ΔPN is reduced at 115 MPa in the presence of CO2, compared to 150 MPa in the rhyolite-H2O system; and (iii) for a given decompression rate, bubble number densities are two orders of magnitude larger than those measured in the rhyolite-H2O system. The major outcome of this research is a very strong correlation between decompression rate and bubble number density: the larger ⎪dP/dt⎪, the larger n3D. The principal volcanological implication is that the textural study of natural pumices, and in particular the measurement of bubble number densities, could be used for velocimetric applications and to provide information on the dynamics of magma ascent in volcanic conduits.L'étude du processus de nucléation des bulles dans les magmas rhyolitiques a été abordée au cours de cette thèse. Des expériences de décompression isothermes en autoclave à chauffage externe et trempe rapide ont été réalisées afin de mieux comprendre : (1) les effets de différentes populations cristallines sur la cinétique de nucléation des bulles d'eau, et (2) les effets du CO2 sur la nucléation homogène des bulles. L'objectif ultime de nos travaux était d'identifier les paramètres texturaux qui pourraient constituer des marqueurs robustes de la dynamique d'ascension des magmas rhyolitiques. Le résultat majeur de cette étude est la démonstration que la relation très forte entre [dP/dt] et n3D tient aussi dans le cas de la nucléation hétérogène. La principale implication volcanologique est que l'étude texturale des ponces naturelles pourrait servir à des applications vélocimétriques et fournir des renseignements sur la dynamique d'ascension des magmas dans les conduits volcanique

U-Pb zircon dating of post-obduction volcanic-arc granitoids and a granulite-facies xenolith from New Caledonia. Inference on Southwest Pacific geodynamic models

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