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Additional file 5: Supplemental Table 1. Mean and standard deviation of SNR values (3 replicates) obtained for all spheres of the IEC phantoms visualized by both cameras (≥ 8-mm in diameter). Values are given for analog- and digital-PET images obtained with and without TOF (TOF and noTOF respectively) and with 1 to 10 OSEM iterations, as well as with NEMA-defined reconstruction parameters

Additional file 6: Supplemental Table 2. Mean and standard deviation of CRC values (3 replicates) obtained for all spheres of the IEC phantoms visualized by both cameras (≥ 8-mm in diameter). Values are given for analog- and digital-PET images obtained with and without TOF (TOF and noTOF respectively) and with 1 to 10 OSEM iterations, as well as with NEMA-defined reconstruction parameters

Objective: Treatment of infantile idiopathic scoliosis remains vague. Because implantation of temporary telescopic devices carries a high risk of complications, interest in the older technique of serial casting is growing as a temporising measure before invasive procedures. The goal of this review was to meta-analyse studies examining the effect and safety of casting in infantile idiopathic scoliosis.Methods: Two reviewers independently searched for relevant studies in PubMed and Embase databases through November 2018. The studies included were limited to infantile idiopathic scoliosis patients who underwent casting, had a mean Cobb angle of 20 or more and written in English. The methodological quality of the chosen studies was assessed. The primary outcome was the difference in Cobb angle means from before and after casting. The secondary outcome was adverse events of casting. Heterogeneity was explored and a funnel plot was drawn.Results: Of the 366 studies screened, 10 studies were included in the meta-analysis (243 subjects) and all were non-randomised. The casting was consistently associated with a reduction in the mean Cobb angle. The pooled mean difference was 24.85° (95% confidence interval: 19.25 to 30.46, p < 0.001). A number of reversible adverse events were reported, most commonly skin irritation and transient pulmonary symptoms. Heterogeneity between studies was high. In the meta-regression analysis, the starting Cobb angle did not influence Cobb angle change, but there was an inverse correlation between the mean difference in Cobb angle and mean age.Conclusion: Casting seems to be effective and safe in decreasing Cobb angle even in high curve magnitudes. In older patients, casting showed less Cobb angle correction.

In this paper, we address the problem of current-vortex sheets in ideal incompressible magnetohydrodynamics. More precisely, we prove a local-in-time existence and uniqueness result for analytic initial data using a Cauchy-Kowalevskaya theorem.

International audience; The forces exerted by growing crystals on the surrounding materials play a major role in many geological processes, from diagenetic replacement to rock weathering and uplifting of rocks and soils. Although crystallization is a nonequilibrium process, the available theoretical predictions for these forces are based on equilibrium thermodynamics. Here we show that nonequilibrium effects can lead to a drop of the crystallization force in large pores where the crystal surface dissociates from the surrounding walls during growth. The critical pore size above which such detachment can be observed depends only on the ratio of kinetic coefficients and cannot be predicted from thermodynamics. Our conclusions are based on a physical model which accounts for the nonequilibrium kinetics of mass transport, and disjoining pressure effects within the thin liquid film separating the crystal and the surrounding walls. Our results suggest that the maximum size of the pores that can sustain crystallization forces close to the equilibrium prediction ranges from micrometers for salts to a millimetre for low-solubility minerals such as calcite. These results are discussed in the light of recent experimental observations of the growth of confined salt crystals.

Under nitrogen-limiting conditions, legumes are able to interact symbiotically with bacteria of the Rhizobiaceae family. This interaction gives rise to a new organ, named a root nodule. Root nodules are characterized by an increased glutathione (GSH) and homoglutathione (hGSH) content compared to roots. These low molecular thiols are very important in the biological nitrogen fixation. In order to characterize the modification of nodule activity induced by the microsymbiont glutathione deficiency, physiological, biochemical, and gene expression modifications were analyzed in nodules after the inoculation of Medicago truncatula with the SmgshB mutant of Sinorhizobium meliloti which is deficient in GSH production. The decline in nitrogen fixation efficiency was correlated to the reduction in plant shoot biomass. Flow cytometry analysis showed that SmgshB bacteroids present a higher DNA content than free living bacteria. Live/dead microscopic analysis showed an early bacteroid degradation in SmgshB nodules compared to control nodules which is correlated to a lower bacteroid content at 20 dpi. Finally, the expression of two marker genes involved in nitrogen fixation metabolism, Leghemoglobin and Nodule Cysteine Rich Peptide 001, decreased significantly in mutant nodules at 20 dpi. In contrast, the expression of two marker genes involved in the nodule senescence, Cysteine Protease 6 and Purple Acid Protease, increased significantly in mutant nodules at 10 dpi strengthening the idea that an early senescence process occurs in SmgshB nodules. In conclusion, our results showed that bacterial GSH deficiency does not impair bacterial differentiation but induces an early nodule senescence.

Soil bacteria called rhizobia trigger the formation of root nodules on legume plants. The rhizobia infect these symbiotic organs and adopt an intracellular lifestyle within the nodule cells, where they differentiate into nitrogen-fixing bacteroids. Several legume lineages force their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this process in Bradyrhizobium sp. strain ORS285, a symbiont of Aeschynomene spp. In the absence of BclA, the bacteria proceed until the intracellular infection of nodule cells, but they cannot differentiate into enlarged polyploid and functional bacteroids. Thus, the bclA nodule bacteria constitute an intermediate stage between the free-living soil bacteria and the nitrogen-fixing bacteroids. Metabolomics on whole nodules of Aeschynomene afraspera and Aeschynomene indica infected with the wild type or the bclA mutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied by a first transcriptome switch involving several hundred upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving fewer genes but ones that are expressed to extremely elevated levels. The transcriptomes further suggested a dynamic role for oxygen and redox regulation of gene expression during nodule formation and a nonsymbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids. IMPORTANCE Legume-rhizobium symbiosis is a major ecological process, fueling the biogeochemical nitrogen cycle with reduced nitrogen. It also represents a promising strategy to reduce the use of chemical nitrogen fertilizers in agriculture, thereby improving its sustainability. This interaction leads to the intracellular accommodation of rhizobia within plant cells of symbiotic organs, where they differentiate into nitrogen-fixing bacteroids. In specific legume clades, this differentiation process requires the bacterial transporter BclA to counteract antimicrobial peptides produced by the host. Transcriptome analysis of Bradyrhizobium wild-type and bclA mutant bacteria in culture and in symbiosis with Aeschynomene host plants dissected the bacterial transcriptional response in distinct phases and highlighted functions of the transporter in the free-living stage of the bacterial life cycle.

International audience; Nanostructures on surfaces can be displaced by applying an electric eld or electric currents through a material. This induced mass transport is referred to as electromigration. In this article we show that the anisotropy of diusion may control the direction of motion of electromigrating nanostructures. For this purpose we study in situ and in real time, by Low Energy Electron Microscopy, the motion of 2D one-atom thick islands or one-atom deep holes on a highly anisotropic surface (reconstructed Si(100)). Based on experiments and Kinetic Monte Carlo simulations, we propose a simple analytical model that explains most of the observations. In particular, the direction of motion of the nanostructures depends on the diusion anisotropy and does not necessarily coincide with the electric eld direction. This work opens a way for the manipulation of 2D nanostructures by means of an electric eld on anisotropic surfaces.

Purpose This work presents our contribution to one of the data challenges organized by the French Radiology Society during the Journees Francophones de Radiologie. This challenge consisted in segmenting the kidney cortex from coronal computed tomography (CT) images, cropped around the cortex. Materials and methods We chose to train an ensemble of fully-convolutional networks and to aggregate their prediction at test time to perform the segmentation. An image database was made available in 3 batches. A first training batch of 250 images with segmentation masks was provided by the challenge organizers one month before the conference. An additional training batch of 247 pairs was shared when the conference began. Participants were ranked using a Dice score. Results The segmentation results of our algorithm match the renal cortex with a good precision. Our strategy yielded a Dice score of 0.867, ranking us first in the data challenge. Conclusion The proposed solution provides robust and accurate automatic segmentations of the renal cortex in CT images although the precision of the provided reference segmentations seemed to set a low upper bound on the numerical performance. However, this process should be applied in 3D to quantify the renal cortex volume, which would require a marked labelling effort to train the networks.

International audience; Recent experimental and theoretical investigations of crystal growth from solution in the vicinity of an impermeable wall have shown that: (i) growth can be maintained within the contact region when a liquid film is present between the crystal and the substrate; (ii) a cavity can form in the center of the contact region due to insufficient supply of mass through the liquid film. Here, we investigate the influence of surface kinetics on these phenomena using a thin film model. First, we determine the growth rate within the confined region in the absence of a cavity. Growth within the contact induces a drift of the crystal away from the substrate. Our results suggest novel strategies to measure surface kinetic coefficients based on the observation of this drift. For the specific case where growth is controlled by surface kinetics outside the contact, we show that the total displacement of the crystal due to the growth in the contact is finite. As a consequence, the growth shape approaches asymptotically the free growth shape truncated by a plane passing through the center of the crystal. Second, we investigate the conditions under which a cavity forms. The critical supersaturation above which the cavity forms is found to be larger for slower surface kinetics. In addition, the critical supersaturation decays as a power law of the contact size. The asymptotic value of the critical supersaturation and the exponent of the decay are found to be different for attractive and repulsive disjoining pressures. Finally, our previous representation of the transition within a morphology diagram appears to be uninformative in the limit of slow surface kinetics.

International audience; Interpretability of a neural network can be expressed as the identification of patterns or features to which the network can be either sensitive or indifferent. To this aim, a method inspired by DeepDream is proposed, where the activation of a neuron is maximized by performing gradient ascent on an input image. The method outputs curves that show the evolution of features during the maximization.A controlled experiment show how it enables assess the robustness to a given feature, or by contrast its sensitivity. The method is illustrated on the task of segmenting tumors in liver CT images.

Deep learning has proved to be a very efficient tool for organs automated segmentation in CT scans. However, variation of iodine contrast agent concentration within the vascular system or organs is a major source of variation in image contrast. This requires building large databases representative of the important differences in contrast enhancement across CT studies. Furthermore, creating a low- or non-enhanced annotated database is still a very laborious task as semi-automatic segmentation software and even expert eyes often fail to find structures’ edges on low contrast images.

International audience; Endoparasitoid wasps, which lay eggs inside the bodies of other insects, use various strategies to protect their offspring from the host immune response. The hymenopteran species of the genus Leptopilina, parasites of Drosophila, rely on the injection of a venom which contains proteins and peculiar vesicles (hereafter venosomes). We show here that the injection of purified L. boulardi venosomes is sufficient to impair the function of the Drosophila melanogaster lamellocytes, a hemocyte type specialized in the defense against wasp eggs, and thus the parasitic success of the wasp. These venosomes seem to have a unique extracellular biogenesis in the wasp venom apparatus where they acquire specific secreted proteins/virulence factors and act as a transport system to deliver these compounds into host lamellocytes. The level of venosomes entry into lamellocytes of different Drosophila species was correlated with the rate of parasitism success of the wasp, suggesting that this venosome-cell interaction may represent a new evolutionary level of host-parasitoid specificity.

International audience; Soil bacteria called rhizobia trigger the formation of root nodules on legume plants. The rhizobia infect these symbiotic organs and adopt an intracellular lifestyle within the nodule cells where they differentiate into nitrogen-fixing bacteroids. Several legume lineages enforce their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this process in Bradyrhizobium sp. ORS285, a symbiont of Aeschynomene spp.. In the absence of BclA, the bacteria proceed until the intracellular infection of nodule cells but they cannot differentiate into enlarged polyploid and functional bacteroids. The bclA nodule bacteria constitute thus an intermediate stage between the free-living soil bacteria and the nitrogen-fixing bacteroids. Metabolomics on whole nodules of Aeschynomene afraspera and Aeschynomene indica infected with the wild type or the bclA mutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied with a first transcriptome switch involving several hundreds of upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving less genes but ones that are expressed to extremely elevated levels. The transcriptomes further suggested a dynamic role for oxygen and redox regulation of gene expression during nodule formation and a non-symbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids.ImportanceThe legume-rhizobium symbiosis is a major ecological process fueling the biogeochemical nitrogen cycle with reduced nitrogen. It represents also a promising strategy to cut down the use of chemical nitrogen fertilizers in agriculture, thereby improving its sustainability. This interaction leads to the intracellular accommodation of rhizobia within plant cells of symbiotic organs where they differentiate into nitrogen-fixing bacteroids. In specific legume clades, this differentiation process requires the bacterial transporter BclA to counteract antimicrobial peptides produced by the host. Transcriptome analysis of Bradyrhizobium wild-type and bclA mutant bacteria in culture and in symbiosis with Aeschynomene host plants dissected the bacterial transcriptional response in distinct phases and highlighted functions of the transporter in the free-living stage of the bacterial life cycle.

The aim of this lecture is to provide an overview on solid-state wetting, starting from basic concepts, and introducing the useful mathematical paraphernalia. We review and discuss the similarities and the differences between liquid-state and solid-state wetting. Then, we show how wetting concepts provide tools to understand the morphology and stability of solid-state thin films and nano-islands.

We describe and analyze in detail the shapes of Fe islands encapsulated under the top graphene layers in graphite. Shapes are interrogated using scanning tunneling microscopy. The main outputs of the shape analysis are the slope of the graphene membrane around the perimeter of the island, and the aspect ratio of the central metal cluster. Modeling primarily uses a continuum elasticity (CE) model. As input to the CE model, we use density functional theory to calculate the surface energy of Fe, and the adhesion energies between Fe and graphene or graphite. We use the shaft-loaded blister test (SLBT) model to provide independent stretching and bending strain energies in the graphene membrane. We also introduce a model for the elastic strain in which stretching and bending are treated simultaneously. Measured side slopes agree very well with the CE model, both qualitatively and quantitatively. The fit is optimal for a graphene membrane consisting of 2–3 graphene monolayers, in agreement with experiment. Analysis of contributions to total energy shows that the side slope depends only on the properties of graphene/graphite. This reflects delamination of the graphene membrane from the underlying graphite, caused by upward pressure from the growing metal cluster. This insight leads us to evaluate the delamination geometry in the context of two related, classic models that give analytic results for the slope of a delaminated membrane. One of these, the point-loaded circular blister test model, reasonably predicts the delamination geometry at the edge of an Fe island. The aspect ratio also agrees well with the CE model in the limit of large island size, but not for small islands. Previously, we had speculated that this discrepancy was due to lack of coupling between bending and stretching in the SLBT model, but the new modeling shows that this explanation is not viable.

International audience; We report on the observation of thin salt shells that form at the periphery of evaporating pure water drops on salt. Shell shapes range from rings of inclined walls to hollow toroidal rims. We interpret this phenomenon as a consequence of a molecular coffee-stain effect by which the dissolved salt is advected toward the pinned contact line where an increased evaporation takes place. The subsequent salt supersaturation in the vicinity of the triple line drives the crystallization of the shell at the liquid-air interface. This interpretation is supported by a simple model for shell growth.

We report on the modeling of the dynamics of confined lipid membranes. We derive a thin film model in the lubrication limit which describes an inextensible liquid membrane with bending rigidity confined between two adhesive walls. The resulting equations share similarities with the Swift–Hohenberg model. However, inextensibility is enforced by a time-dependent nonlocal tension. Depending on the excess membrane area available in the system, three different dynamical regimes, denoted as A, B and C, are found from the numerical solution of the model. In regime A, membranes with small excess area form flat adhesion domains and freeze. Such freezing is interpreted by means of an effective model for curvature-driven domain wall motion. The nonlocal membrane tension tends to a negative value corresponding to the linear stability threshold of flat domain walls in the Swift–Hohenberg equation. In regime B, membranes with intermediate excess areas exhibit endless coarsening with coexistence of flat adhesion domains and wrinkle domains. The tension tends to the nonlinear stability threshold of flat domain walls in the Swift–Hohenberg equation. The fraction of the system covered by the wrinkle phase increases linearly with the excess area in regime B. In regime C, membranes with large excess area are completely covered by a frozen labyrinthine pattern of wrinkles. As the excess area is increased, the tension increases and the wavelength of the wrinkles decreases. For large membrane area, there is a crossover to a regime where the extrema of the wrinkles are in contact with the walls. In all regimes after an initial transient, robust localised structures form, leading to an exact conservation of the number of adhesion domains.

International audience; Phytoplankton primary production varies considerably with environmental parameters especially in dynamic ecosystems like estuaries. The aim of this study was to investigate short-term primary production along the salinity gradient of a temperate estuary over the course of 1 year. The combination of carbon incorporation and fluorescence methods enabled primary production estimation at short spatial and temporal scales. The electron requirement for carbon fixation was investigated in relation with physical-chemical parameters to accurately estimate primary production at high frequency. These results combined with the variability of the photic layer allowed the annual estimation of primary production along the estuary. Phytoplankton dynamics was closely related to salinity and turbidity gradients, which strongly influenced cells physiology and photoacclimatation. The number of electrons required to fix 1 mol of carbon (C) was ranged between 1.6 and 25 mol electron mol C−1 with a mean annual value of 8 ± 5 mol electron mol C−1. This optimum value suggests that in nutrient replete conditions like estuaries, alternative electron flows are low, while electrons transfer from photosystem II to carbon fixation is highly efficient. A statistical model was used to improve the estimation of primary production from electron transport rate as a function of significant environmental parameters. Based on this model, daily carbon production in the Seine estuary (France) was estimated by considering light and photic zone variability. A mean annual daily primary production of 0.12 ± 0.18 g C m−2 day−1 with a maximum of 1.18 g C m−2 day−1 in summer was estimated which lead to an annual mean of 64.75 g C m−2 year−1. This approach should be applied more frequently in dynamic ecosystems such as estuaries or coastal waters to accurately estimate primary production in those valuable ecosystems.

We provide a theoretical framework to analyze the properties of frontal collisions of two growing interfaces considering different short range interactions between them. Due to their roughness, the collision events spread in time and form rough domain boundaries, which defines collision interfaces in time and space. We show that statistical properties of such interfaces depend on the kinetics of the growing interfaces before collision, but are independent of the details of their interaction and of their fluctuations during the collision. Those properties exhibit dynamic scaling with exponents related to the growth kinetics, but their distributions may be non-universal. These results are supported by simulations of lattice models with irreversible dynamics and local interactions. Relations to first passage processes are discussed and a possible application to grain boundary formation in two-dimensional materials is suggested., Paper with 12 pages and 2 figures; supplemental material with 4 pages and 3 figures

International audience; We present a continuum model describing dissolution and growth of a crystal contact confined against a substrate. Diffusion and hydrodynamics in the liquid film separating the crystal and the substrate are modeled within the lubrication approximation. The model also accounts for the disjoining pressure and surface tension. Within this framework, we obtain evolution equations which govern the nonequilibrium dynamics of the crystal interface. Based on this model, we explore the problem of dissolution under an external load, known as pressure solution. We find that in steady state, diverging (power-law) crystal-surface repulsions lead to flat contacts with a monotonic increase of the dissolution rate as a function of the load. Forces induced by viscous dissipation then surpass those due to disjoining pressure at large enough loads. In contrast, finite repulsions (exponential) lead to sharp pointy contacts with a dissolution rate independent of the load and the liquid viscosity. Ultimately, in steady state, the crystal never touches the substrate when pressed against it. This result is independent from the nature of the crystal-surface interaction due to the combined effects of viscosity and surface tension.

International audience; Growing crystals form a cavity when placed against a wall. The birth of the cavity is observed both by optical microscopy of sodium chlorate crystals (NaClO3) growing in the vicinity of a glass surface, and in simulations with a thin film model. The cavity appears when growth cannot be maintained in the center of the contact region due to an insufficient supply of growth units through the liquid film between the crystal and the wall. We obtain a nonequilibrium morphology diagram characterizing the conditions under which a cavity appears. Cavity formation is a generic phenomenon at the origin of the formation of growth rims observed in many experiments, and is a source of complexity for the morphology of growing crystals in natural environments. Our results also provide restrictions for the conditions under which compact crystals can grow in confinement.