A fast solver for systems of reaction-diffusion equations

In this paper we present a fast algorithm for the numerical solution of systems of reaction-diffusion equations, $\partial_t u + a \cdot \nabla u = \Delta u + F (x, t, u)$, $x \in \Omega \subset \mathbf{R}^3$, $t > 0$. Here, $u$ is a vector-valued function, $u \equiv u(x, t) \in \mathbf{R}^m$, $m$ is large, and the corresponding system of ODEs, $\partial_t u = F(x, t, u)$, is stiff. Typical examples arise in air pollution studies, where $a$ is the given wind field and the nonlinear function $F$ models the atmospheric chemistry.Comment: 8 pages, 3 figures, to appear in Proc. 13th Domain Decomposition Conference, Lyon, October 200

Iron and bismuth bound human serum transferrin reveals a partially-opened conformation in the N-lobe

Human serum transferrin (hTF) binds Fe(III) tightly but reversibly, and delivers it to cells via a receptor-mediated endocytosis process. The metal-binding and release result in significant conformational changes of the protein. Here, we report the crystal structures of diferric-hTF (Fe N Fe C-hTF) and bismuth-bound hTF (Bi N Fe C-hTF) at 2.8 and 2.4 Å resolutions respectively. Notably, the N-lobes of both structures exhibit unique 'partially-opened' conformations between those of the apo-hTF and holo-hTF. Fe(III) and Bi(III) in the N-lobe coordinate to, besides anions, only two (Tyr95 and Tyr188) and one (Tyr188) tyrosine residues, respectively, in contrast to four residues in the holo-hTF. The C-lobe of both structures are fully closed with iron coordinating to four residues and a carbonate. The structures of hTF observed here represent key conformers captured in the dynamic nature of the transferrin family proteins and provide a structural basis for understanding the mechanism of metal uptake and release in transferrin families. © 2012 Macmillan Publishers Limited. All rights reserved.published_or_final_versio

Tracking team mental workload by multimodal measurements in the operating room

Mental workload and its effects on surgical performance are underexplored topics, despite their importance for operating room (OR) efficiency and patient safety. We developed a multimodal platform that can simultaneously collect data from EEG, heart rate and breathing rate, tool handle pressure, and eye tracker from mobile subjects. We performed experiments using the Fundamentals of Laparoscopic Surgery model, with 22 subjects of varying skill levels ranging from nonsurgeon to expert. The results indicated significant modulations of the measurements depending on pupil size, heart rate variability, P300 response, tool pressure, task difficulty, time-on-task, and skill level. These provide evidence that physiology based metrics can be used in automated classification of fine gradations of skill, the assessment and certification of surgery trainees, developing real-time flags and warnings for the OR, and validating new OR technology

Structural blueprint and ontogeny determine the adaptive value of the plastic response to competition in clonal plants: a modelling approach

International audienceLocal competitive interactions strongly influence plant community dynamics. To maintain their performance under competition, clonal plants may plastically modify their network architecture to grow in the direction of least interference. The adaptive value of this plastic avoidance response may depend, however, on traits linked with the plant's structural blueprint and ontogeny. We tested this hypothesis using virtual populations. We used an Individual Based Model to simulate competitive interactions among clones within a plant population. Clonal growth was studied under three competition intensities in plastic and non-plastic individuals. Plasticity buffered the negative impacts of competition at intermediate densities of competitors by promoting clone clumping. Success despite competition was promoted by traits linked with (1) the plant's structural blueprint (weak apical dominance and sympodial growth) and (2) ontogenetic processes, with an increasing or a decreasing dependence of the elongation process on the branch generation level or length along the competition intensity gradient respectively. The adaptive value of the plastic avoidance response depended on the same traits. This response only modulated their importance for clone success. Our results show that structural blueprint and ontogeny can be primary filters of plasticity and can have strong implications for evolutionary ecology, as they may explain why clonal plants have developed many species-specific plastic avoidance behaviours

Experimental Assessment of the Water Quality Influence on the Phosphorus Uptake of an Invasive Aquatic Plant: Biological Responses throughout Its Phenological Stage

International audienceUnderstanding how an invasive plant can colonize a large range of environments is still a great challenge in freshwater ecology. For the first time, we assessed the relative importance of four factors on the phosphorus uptake and growth of an invasive macrophyte Elodea nuttallii (Planch.) St. John. This study provided data on its phenotypic plasticity, which is frequently suggested as an important mechanism but remains poorly investigated. The phosphorus uptake of two Elodea nuttallii subpopulations was experimentally studied under contrasting environmental conditions. Plants were sampled in the Rhine floodplain and in the Northern Vosges mountains, and then maintained in aquaria in hard (Rhine) or soft (Vosges) water. Under these conditions, we tested the influence of two trophic states (eutrophic state, 100 mu g.l(-1) P-PO43- and hypertrophic state, 300 mu g.l(-1) P-PO43-) on the P metabolism of plant subpopulations collected at three seasons (winter, spring and summer). Elodea nuttallii was able to absorb high levels of phosphorus through its shoots and enhance its phosphorus uptake, continually, after an increase of the resource availability (hypertrophic > eutrophic). The lowest efficiency in nutrient use was observed in winter, whereas the highest was recorded in spring, what revealed thus a storage strategy which can be beneficial to new shoots. This experiment provided evidence that generally, the water trophic state is the main factor governing P uptake, and the mineral status (softwater > hardwater) of the stream water is the second main factor. The phenological stage appeared to be a confounding factor to P level in water. Nonetheless, phenology played a role in P turnover in the plant. Finally, phenotypic plasticity allows both subpopulations to adapt to a changing environment

Asymptotic Fourier Coefficients for a C ∞ Bell (Smoothed-“Top-Hat”) & the Fourier Extension Problem

In constructing local Fourier bases and in solving differential equations with nonperiodic solutions through Fourier spectral algorithms, it is necessary to solve the Fourier Extension Problem. This is the task of extending a nonperiodic function, defined on an interval , to a function which is periodic on the larger interval . We derive the asymptotic Fourier coefficients for an infinitely differentiable function which is one on an interval , identically zero for , and varies smoothly in between. Such smoothed “top-hat” functions are “bells” in wavelet theory. Our bell is (for x ≥ 0) where where . By applying steepest descents to approximate the coefficient integrals in the limit of large degree j , we show that when the width L is fixed, the Fourier cosine coefficients a j of on are proportional to where Λ( j ) is an oscillatory factor of degree given in the text. We also show that to minimize error in a Fourier series truncated after the N th term, the width should be chosen to increase with N as . We derive similar asymptotics for the function f ( x )= x as extended by a more sophisticated scheme with overlapping bells; this gives an even faster rate of Fourier convergencePeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43417/1/10915_2005_Article_9010.pd