Comparative Genomics of Eight Fusarium graminearum Strains with Contrasting Aggressiveness Reveals an Expanded Open Pangenome and Extended Effector Content Signatures

Fusarium graminearum, the primary cause of Fusarium head blight (FHB) in small-grain cereals, demonstrates remarkably variable levels of aggressiveness in its host, producing different infection dynamics and contrasted symptom severity. While the secreted proteins, including effectors, are thought to be one of the essential components of aggressiveness, our knowledge of the intra-species genomic diversity of F. graminearum is still limited. In this work, we sequenced eight European F. graminearum strains of contrasting aggressiveness to characterize their respective genome structure, their gene content and to delineate their specificities. By combining the available sequences of 12 other F. graminearum strains, we outlined a reference pangenome that expands the repertoire of the known genes in the reference PH-1 genome by 32%, including nearly 21,000 non-redundant sequences and gathering a common base of 9250 conserved core-genes. More than 1000 genes with high non-synonymous mutation rates may be under diverse selection, especially regarding the trichothecene biosynthesis gene cluster. About 900 secreted protein clusters (SPCs) have been described. Mostly localized in the fast sub-genome of F. graminearum supposed to evolve rapidly to promote adaptation and rapid responses to the host’s infection, these SPCs gather a range of putative proteinaceous effectors systematically found in the core secretome, with the chloroplast and the plant nucleus as the main predicted targets in the host cell. This work describes new knowledge on the intra-species diversity in F. graminearum and emphasizes putative determinants of aggressiveness, providing a wealth of new candidate genes potentially involved in the Fusarium head blight disease.     

A model-based approach to the analysis of patterns of length of stay in institutional long-term care.

Understanding the pattern of length of stay in institutional long-term care has important practical implications in the management of long-term care. Furthermore, residents' attributes are believed to have significant effects on these patterns. In this paper, we present a model-based approach to extract, from a routinely gathered administrative social care dataset, high-level length-of-stay patterns of residents in long-term care. This approach extends previous work by the authors to incorporate residents' features. Two applications using data provided by a local authority in England are presented to demonstrate the potential use of this approach.     

Polynomial chaos expansion for sensitivity analysis

In this paper, the computation of Sobol's sensitivity indices from the polynomial chaos expansion of a model output involving uncertain inputs is investigated. It is shown that when the model output is smooth with regards to the inputs, a spectral convergence of the computed sensitivity indices is achieved. However, even for smooth outputs the method is limited to a moderate number of inputs, say 10-20, as it becomes computationally too demanding to reach the convergence domain. Alternative methods (such as sampling strategies) are then more attractive. The method is also challenged when the output is non-smooth even when the number of inputs is limited.     

Spectral schemes as ringed lattices

We give a point-free definition of a Grothendieck scheme whose underlying topological space is spectral. Affine schemes aside, the prime examples are the projective spectrum of a graded ring and the space of valuations corresponding to an abstract nonsingular curve. With the appropriate notion of a morphism between spectral schemes, elementary proofs of the universal properties become possible. “What would have happened if topologies without points had been discovered before topologies with points, or if Grothendieck had known the theory of distributive lattices?” Gian-Carlo Rota, Indiscrete Thoughts. Birkhäuser (1997), p. 220     

A new SURE approach to image denoising: interscale orthonormal wavelet thresholding.

This paper introduces a new approach to orthonormal wavelet image denoising. Instead of postulating a statistical model for the wavelet coefficients, we directly parametrize the denoising process as a sum of elementary nonlinear processes with unknown weights. We then minimize an estimate of the mean square error between the clean image and the denoised one. The key point is that we have at our disposal a very accurate, statistically unbiased, MSE estimate--Stein's unbiased risk estimate--that depends on the noisy image alone, not on the clean one. Like the MSE, this estimate is quadratic in the unknown weights, and its minimization amounts to solving a linear system of equations. The existence of this a priori estimate makes it unnecessary to devise a specific statistical model for the wavelet coefficients. Instead, and contrary to the custom in the literature, these coefficients are not considered random anymore. We describe an interscale orthonormal wavelet thresholding algorithm based on this new approach and show its near-optimal performance--both regarding quality and CPU requirement--by comparing it with the results of three state-of-the-art nonredundant denoising algorithms on a large set of test images. An interesting fallout of this study is the development of a new, group-delay-based, parent-child prediction in a wavelet dyadic tree.     

Extension of the RBD-FAST method to the computation of global sensitivity indices

This paper deals with the sensitivity analysis method named Fourier amplitude sensitivity test (FAST). This method is known to be very robust for the computation of global sensitivity indices but their computational cost remains prohibitive for complex and large dimensional models. Recent developments in the implementation of FAST by use of the random balance designs (RBD) technique have allowed significant reduction of the computational cost. The method is now called RBD-FAST. The drawback of this improvement is that only individual first-order sensitivity indices can be computed. In this article, an extension of RBD is derived for the estimation of any global sensitivity indices of individual factor or group of factors. Several tests are proposed to compare the performances of classical FAST and RBD-FAST.     

Motion planning for cooperative unicycle-type mobile robots with limited sensing ranges: A distributed receding horizon approach

This paper presents a decentralized motion planner for a team of nonholonomic mobile robots subject to constraints imposed by sensors and the communication network. The motion planning scheme consists of decentralized receding horizon planners that reside on each vehicle to achieve coordination among flocking agents. The advantage of the proposed algorithm is that each vehicle only requires local knowledge of its neighboring vehicles. The main requirement for designing an optimal conflict-free trajectory in a decentralized way is that each robot does not deviate too far from its presumed trajectory designed without taking the coupling constraints into account. A comparative study between the proposed algorithm and other existing algorithms is provided in order to show the advantages, especially in terms of computing time. Finally, experiments are performed on a team of three mobile robots to demonstrate the validity of the proposed approach.     

Tailoring of elastomeric grafted coating via sol–gel chemistry of crosslinked polymethylhydrosiloxane

Thin coating of crosslinked polymethylhydrosiloxane are grafted on silica using sol–gel process that leads to polymer layers tailored in term of thickness and elasticity. The degree of crosslinking is tuned by sol–gel polycondensation of a mixture of methyldiethoxysilane(DH) HSi(CH₃)(OCH₂CH₃)₂ and triethoxysilane (TH) HSi(OCH₂CH₃)₃, yielding triethoxysilane‐based networks. Samples with well‐defined thicknesses from nanometer to micrometer range are prepared by sol–gel dip‐coating method on silicon surface. Homogeneous or gradient‐thickness coating can be produced in this way. It results in surface‐attached networks bearing Si? H functionalities covalently anchored to the substrate. Powdered gels of DH/TH composition from 50/50 to 95/5 (mol %) were also prepared for a comparison purpose. The structure of the gels was investigated by NMR and FTIR, showing that DH/TH mixtures react totally to yield homogeneous matrix. The surface‐attached polymer films are very stable and present high hydrophobicity as evidenced by contact angle measurements. Their surface and mechanical properties have been qualitatively studied using the atomic force microscopy. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 1504–1516, 2007     

Information Sharing as a Coordination Mechanism for Reducing the Bullwhip Effect in a Supply Chain

The bullwhip effect is an amplification of the variability of the orders placed by companies in a supply chain. This variability reduces the efficiency of supply chains, since it incurs costs due to higher inventory levels and supply chain agility reduction. Eliminating the bullwhip effect is surely simple; every company just has to order following the market demand, i.e., each company should use a lot-for-lot type of ordering policy. However, many reasons, such as inventory management, lot-sizing, and market, supply, or operation uncertainties, motivate companies not to use this strategy. Therefore, the bullwhip effect cannot be totally eliminated. However, it can be reduced by information sharing, which is the form of collaboration considered in this paper. More precisely, we study how to separate demand into original demand and adjustments. We describe two principles explaining how to use the shared information to reduce the amplification of order variability induced by lead times, which we propose as a cause of the effect. Simulations confirm the value of these two principles with regard to costs and customer service levels