A level-set method for the evolution of cells and tissue during curvature-controlled growth

Most biological tissues grow by the synthesis of new material close to the tissue's interface, where spatial interactions can exert strong geometric influences on the local rate of growth. These geometric influences may be mechanistic, or cell behavioural in nature. The control of geometry on tissue growth has been evidenced in many in-vivo and in-vitro experiments, including bone remodelling, wound healing, and tissue engineering scaffolds. In this paper, we propose a generalisation of a mathematical model that captures the mechanistic influence of curvature on the joint evolution of cell density and tissue shape during tissue growth. This generalisation allows us to simulate abrupt topological changes such as tissue fragmentation and tissue fusion, as well as three dimensional cases, through a level-set-based method. The level-set method developed introduces another Eulerian field than the level-set function. This additional field represents the surface density of tissue synthesising cells, anticipated at future locations of the interface. Numerical tests performed with this level-set-based method show that numerical conservation of cells is a good indicator of simulation accuracy, particularly when cusps develop in the tissue's interface. We apply this new model to several situations of curvature-controlled tissue evolutions that include fragmentation and fusion.Comment: 15 pages, 10 figures, 3 supplementary figure

Coupling curvature-dependent and shear stress-stimulated neotissue growth in dynamic bioreactor cultures: a 3D computational model of a complete scaffold.

The main challenge in tissue engineering consists in understanding and controlling the growth process of in vitro cultured neotissues toward obtaining functional tissues. Computational models can provide crucial information on appropriate bioreactor and scaffold design but also on the bioprocess environment and culture conditions. In this study, the development of a 3D model using the level set method to capture the growth of a microporous neotissue domain in a dynamic culture environment (perfusion bioreactor) was pursued. In our model, neotissue growth velocity was influenced by scaffold geometry as well as by flow- induced shear stresses. The neotissue was modeled as a homogenous porous medium with a given permeability, and the Brinkman equation was used to calculate the flow profile in both neotissue and void space. Neotissue growth was modeled until the scaffold void volume was filled, thus capturing already established experimental observations, in particular the differences between scaffold filling under different flow regimes. This tool is envisaged as a scaffold shape and bioprocess optimization tool with predictive capacities. It will allow controlling fluid flow during long-term culture, whereby neotissue growth alters flow patterns, in order to provide shear stress profiles and magnitudes across the whole scaffold volume influencing, in turn, the neotissue growth

Solving the riddle of codon usage preferences: a test for translational selection

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model

Electron-Phonon Interacation in Quantum Dots: A Solvable Model

The relaxation of electrons in quantum dots via phonon emission is hindered by the discrete nature of the dot levels (phonon bottleneck). In order to clarify the issue theoretically we consider a system of $N$ discrete fermionic states (dot levels) coupled to an unlimited number of bosonic modes with the same energy (dispersionless phonons). In analogy to the Gram-Schmidt orthogonalization procedure, we perform a unitary transformation into new bosonic modes. Since only $N(N+1)/2$ of them couple to the fermions, a numerically exact treatment is possible. The formalism is applied to a GaAs quantum dot with only two electronic levels. If close to resonance with the phonon energy, the electronic transition shows a splitting due to quantum mechanical level repulsion. This is driven mainly by one bosonic mode, whereas the other two provide further polaronic renormalizations. The numerically exact results for the electron spectral function compare favourably with an analytic solution based on degenerate perturbation theory in the basis of shifted oscillator states. In contrast, the widely used selfconsistent first-order Born approximation proves insufficient in describing the rich spectral features.Comment: 8 pages, 4 figure

Multiexcitons confined within a sub-excitonic volume: Spectroscopic and dynamical signatures of neutral and charged biexcitons in ultrasmall semiconductor nanocrystals

The use of ultrafast gating techniques allows us to resolve both spectrally and temporally the emission from short-lived neutral and negatively charged biexcitons in ultrasmall (sub-10 nm) CdSe nanocrystals (nanocrystal quantum dots). Because of forced overlap of electronic wave functions and reduced dielectric screening, these states are characterized by giant interaction energies of tens (neutral biexcitons) to hundreds (charged biexcitons) of meV. Both types of biexcitons show extremely short lifetimes (from sub-100 picoseconds to sub-picosecond time scales) that rapidly shorten with decreasing nanocrystal size. These ultrafast relaxation dynamics are explained in terms of highly efficient nonradiative Auger recombination.Comment: 5 pages, 4 figures, to be published in Phys. Rev.

The Unique Origin of Colors of Armchair Carbon Nanotubes

The colors of suspended metallic colloidal particles are determined by their size-dependent plasma resonance, while those of semiconducting colloidal particles are determined by their size-dependent band gap. Here, we present a novel case for armchair carbon nanotubes, suspended in aqueous medium, for which the color depends on their size-dependent excitonic resonance, even though the individual particles are metallic. We observe distinct colors of a series of armchair-enriched nanotube suspensions, highlighting the unique coloration mechanism of these one-dimensional metals.Comment: 4 pages, 3 figure

Spectroscopic properties of Er3+-doped antimony oxide glass

International audienceSpectroscopic properties of Er3+ ions have been studied in the 60Sb2O3-20WO3-19Na2O-1Bi2O3 (SWNB) glasses doped with 0.25 and 0.50 mol% Er2O3 respectively. The Judd-Ofelt parameters measured from the absorption spectra have been used to calculate the radiative life-time (τr) and the stimulated emission cross section. The low phonon energy, a reduced quenching effect and a high quantum efficiency of 90% for the 1.53 μm expected laser emission into pumping at 980 nm are in favor of promising material laser application

PERC rule to exclude the diagnosis of pulmonary embolism in emergency low-risk patients: study protocol for the PROPER randomized controlled study.

BACKGROUND: The diagnosis of Pulmonary Embolism (PE) in the emergency department (ED) is crucial. As emergency physicians fear missing this potential life-threatening condition, PE tends to be over-investigated, exposing patients to unnecessary risks and uncertain benefit in terms of outcome. The Pulmonary Embolism Rule-out Criteria (PERC) is an eight-item block of clinical criteria that can identify patients who can safely be discharged from the ED without further investigation for PE. The endorsement of this rule could markedly reduce the number of irradiative imaging studies, ED length of stay, and rate of adverse events resulting from both diagnostic and therapeutic interventions. Several retrospective and prospective studies have shown the safety and benefits of the PERC rule for PE diagnosis in low-risk patients, but the validity of this rule is still controversial. We hypothesize that in European patients with a low gestalt clinical probability and who are PERC-negative, PE can be safely ruled out and the patient discharged without further testing. METHODS/DESIGN: This is a controlled, cluster randomized trial, in 15 centers in France. Each center will be randomized for the sequence of intervention periods: a 6-month intervention period (PERC-based strategy) followed by a 6-month control period (usual care), or in reverse order, with 2 months of "wash-out" between the 2 periods. Adult patients presenting to the ED with a suspicion of PE and a low pre test probability estimated by clinical gestalt will be eligible. The primary outcome is the percentage of failure resulting from the diagnostic strategy, defined as diagnosed venous thromboembolic events at 3-month follow-up, among patients for whom PE has been initially ruled out. DISCUSSION: The PERC rule has the potential to decrease the number of irradiative imaging studies in the ED, and is reported to be safe. However, no randomized study has ever validated the safety of PERC. Furthermore, some studies have challenged the safety of a PERC-based strategy to rule-out PE, especially in Europe where the prevalence of PE diagnosed in the ED is high. The PROPER study should provide high-quality evidence to settle this issue. If it confirms the safety of the PERC rule, physicians will be able to reduce the number of investigations, associated subsequent adverse events, costs, and ED length of stay for patients with a low clinical probability of PE. TRIAL REGISTRATION: NCT02375919

Surface Magnetization of Aperiodic Ising Systems: a Comparative Study of the Bond and Site Problems

We investigate the influence of aperiodic perturbations on the critical behaviour at a second order phase transition. The bond and site problems are compared for layered systems and aperiodic sequences generated through substitution. In the bond problem, the interactions between the layers are distributed according to an aperiodic sequence whereas in the site problem, the layers themselves follow the sequence. A relevance-irrelevance criterion introduced by Luck for the bond problem is extended to discuss the site problem. It involves a wandering exponent for pairs, which can be larger than the one considered before in the bond problem. The surface magnetization of the layered two-dimensional Ising model is obtained, in the extreme anisotropic limit, for the period-doubling and Thue-Morse sequences.Comment: 19 pages, Plain TeX, IOP macros + epsf, 6 postscript figures, minor correction