Showing papers by "École Normale Supérieure published in 2004"

Supersonic shear imaging: a new technique for soft tissue elasticity mapping

Abstract: Supersonic shear imaging (SSI) is a new ultrasound-based technique for real-time visualization of soft tissue viscoelastic properties. Using ultrasonic focused beams, it is possible to remotely generate mechanical vibration sources radiating low-frequency, shear waves inside tissues. Relying on this concept, SSI proposes to create such a source and make it move at a supersonic speed. In analogy with the "sonic boom" created by a supersonic aircraft, the resulting shear waves will interfere constructively along a Mach cone, creating two intense plane shear waves. These waves propagate through the medium and are progressively distorted by tissue heterogeneities. An ultrafast scanner prototype is able to both generate this supersonic source and image (5000 frames/s) the propagation of the resulting shear waves. Using inversion algorithms, the shear elasticity of medium can be mapped quantitatively from this propagation movie. The SSI enables tissue elasticity mapping in less than 20 ms, even in strongly viscous medium like breast. Modalities such as shear compounding are implementable by tilting shear waves in different directions and improving the elasticity estimation. Results validating SSI in heterogeneous phantoms are presented. The first in vivo investigations made on healthy volunteers emphasize the potential clinical applicability of SSI for breast cancer detection.

The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism

Abstract: Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

Abstract: Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests ∼900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.

Plant functional markers capture ecosystem properties during secondary succession

Abstract: Although the structure and composition of plant communities is known to influence the functioning of ecosystems, there is as yet no agreement as to how these should be described from a functional perspective. We tested the biomass ratio hypothesis, which postulates that ecosystem properties should depend on species traits and on species contribution to the total biomass of the community, in a successional sere following vineyard abandonment in the Mediterranean region of France. Ecosystem-specific net primary productivity, litter decomposition rate, and total soil carbon and nitrogen varied significantly with field age, and correlated with community-aggregated (i.e., weighed according to the relative abundance of species) functional leaf traits. The three easily measurable traits tested, specific leaf area, leaf dry matter content, and nitrogen concentration, provide a simple means to scale up from organ to ecosystem functioning in complex plant communities. We propose that they be called ''functional markers,'' and be used to assess the impacts of community changes on ecosystem properties induced, in particular, by global change drivers.

Raptor codes

Abstract: This paper exhibits a class of universal Raptor codes: for a given integer k, and any real /spl epsiv/>0, Raptor codes in this class produce a potentially infinite stream of symbols such that any subset of symbols of size k(1 + /spl epsiv/) is sufficient to recover the original k symbols, with high probability. Each output symbol is generated using O(log(1//spl epsiv/)) operations, and the original symbols are recovered from the collected ones with O(klog(1//spl epsiv/)) operations.

Employee commitment and motivation: a conceptual analysis and integrative model.

Abstract: Theorists and researchers interested in employee commitment and motivation have not made optimal use of each other's work. Commitment researchers seldom address the motivational processes through which commitment affects behavior, and motivation researchers have not recognized important distinctions in the forms, foci, and bases of commitment. To encourage greater cross-fertilization, the authors present an integrative framework in which commitment is presented as one of several energizing forces for motivated behavior. E. A. Locke's (1997) model of the work motivation process and J. P. Meyer and L. Herscovitch's (2001) model of workplace commitments serve as the foundation for the development of this new framework. To facilitate the merger, a new concept, goal regulation, is derived from self-determination theory (E. L. Deci & R. M. Ryan, 1985) and regulatory focus theory (E. I. Higgins, 1997). By including goal regulation, it is acknowledged that motivated behavior can be accompanied by different mindsets that have particularly important implications for the explanation and prediction of discretionary work behavior.

The PARP superfamily.

Abstract: Poly(ADP-ribosyl)ation is an immediate DNA-damage-dependent post-translational modification of histones and other nuclear proteins that contributes to the survival of injured proliferating cells. Poly(ADP-ribose) polymerases (PARPs) now constitute a large family of 18 proteins, encoded by different genes and displaying a conserved catalytic domain in which PARP-1 (113 kDa), the founding member, and PARP-2 (62 kDa) are so far the sole enzymes whose catalytic activity has been shown to be immediately stimulated by DNA strand breaks. A large repertoire of sequences encoding novel PARPs now extends considerably the field of poly(ADP-ribosyl)ation reactions to various aspects of the cell biology including cell proliferation and cell death. Some of these new members interact with each other, share common partners and common subcellular localizations suggesting possible fine tuning in the regulation of this post-translational modification of proteins. This review summarizes our present knowledge of this emerging superfamily, which might ultimately improve pharmacological strategies to enhance both antitumor efficacy and the treatment of a number of inflammatory and neurodegenerative disorders. A provisional nomenclature is proposed.

Efficient waveform inversion and imaging: A strategy for selecting temporal frequencies

Abstract: Prestack migration and/or inversion may be implemented in either the time or the frequency domain. In the frequency domain, it is possible to discretize the frequencies with a much larger sampling interval than that dictated by the sampling theorem and still obtain an imaging result that does not suffer from aliasing (wrap around) in the depth domain. The selection of input frequencies can be reduced when a range of offsets is available; this creates a redundancy of information in the wavenumber coverage of the target. In order to optimize the use of this information, we define a new discretization strategy that depends on the maximum effective offset present in the surface seismic survey: the larger the range of offsets, the fewer frequencies are required. The strategy, exact in a homogeneous 1D earth, selects frequencies by making use of the well-known effect of image stretch in normal-moveout (NMO) correction and in migration (usually considered detrimental for the imaging). The strategy is also useful in more general earth models: we apply it to the 2D Marmousi model and recover a continuous range of wavenumbers using only three input frequencies. The Marmousi inversion result accurately predicts all other data frequencies, demonstrating the redundancy of the data.

Present‐day crustal deformation and plate kinematics in the Middle East constrained by GPS measurements in Iran and northern Oman

Abstract: SUMMARY A network of 27 GPS sites was implemented in Iran and northern Oman to measure displacements in this part of the Alpine‐Himalayan mountain belt. We present and interpret the results of two surveys performed in 1999 September and 2001 October. GPS sites in Oman show northward motion of the Arabian Plate relative to Eurasia slower than the NUVEL-1A estimates (e.g. 22 ± 2m m yr −1 at N8 ◦ ± 5 ◦ E instead of 30.5 mm yr −1 at N6 ◦ E at Bahrain longitude). We define a GPS Arabia‐Eurasia Euler vector of 27.9 ◦ ± 0.5 ◦ N, 19.5 ◦ ± 1.4 ◦ E, 0.41 ◦ ± 0.1 ◦ Myr −1 . The Arabia‐Eurasia convergence is accommodated differently in eastern and western Iran. East of 58 ◦ E, most of the shortening is accommodated by the Makran subduction zone (19.5 ± 2m m yr −1 ) and less by the Kopet-Dag (6.5 ± 2m m yr −1 ). West of 58 ◦ E, the deformation is distributed in separate fold and thrust belts. At the longitude of Tehran, the Zagros and the Alborz mountain ranges accommodate 6.5 ± 2m m yr −1 and 8 ± 2m m yr −1 respectively. The right-lateral displacement along the Main Recent Fault in the northern Zagros is about 3 ± 2m m yr −1 , smaller than what was generally expected. By contrast, large rightlateral displacement takes place in northwestern Iran (up to 8 ± mm yr −1 ). The Central Iranian Block is characterized by coherent plate motion (internal deformation < 2m m yr −1 ). Sites east of 61 ◦ E show very low displacements relative to Eurasia. The kinematic contrast between eastern and western Iran is accommodated by strike-slip motions along the Lut Block. To the south, the transition zone between Zagros and Makran is under transpression with right-lateral displacements of 11 ± 2m m yr −1 .

How to Talk About the Body? the Normative Dimension of Science Studies:

Abstract: Science studies has been often against the normative dimension of epistemology, which made a naturalistic study of science impossible. But this is not to say that a new type of normativity cannot be detected at work in science studies. This is especially true in the second wave of studies dealing with the body which has been aiming at criticizing the physicalisation of the body without falling nonetheless in the various traps of a phenomenology simply added to a physical substrate. This paper explores the work of Isabelle Stengers and Vinciane Despret in that respect and show how it can be used to rethink the articulation between the various levels that make up a body.

Dopamine depletion impairs precursor cell proliferation in Parkinson disease

Abstract: Cerebral dopamine depletion is the hallmark of Parkinson disease. Because dopamine modulates ontogenetic neurogenesis, depletion of dopamine might affect neural precursors in the subependymal zone and subgranular zone of the adult brain. Here we provide ultrastructural evidence showing that highly proliferative precursors in the adult subependymal zone express dopamine receptors and receive dopaminergic afferents. Experimental depletion of dopamine in rodents decreases precursor cell proliferation in both the subependymal zone and the subgranular zone. Proliferation is restored completely by a selective agonist of D2-like (D2L) receptors. Experiments with neural precursors from the adult subependymal zone grown as neurosphere cultures confirm that activation of D2L receptors directly increases the proliferation of these precursors. Consistently, the numbers of proliferating cells in the subependymal zone and neural precursor cells in the subgranular zone and olfactory bulb are reduced in postmortem brains of individuals with Parkinson disease. These observations suggest that the generation of neural precursor cells is impaired in Parkinson disease as a consequence of dopaminergic denervation.

Silver nanoparticle array structures that produce remarkably narrow plasmon lineshapes.

Abstract: Using electrodynamics calculations, we have discovered one dimensional array structures built from spherical silver nanoparticles that produce remarkably narrow (∼ meV or less) plasmon resonance spectra upon irradiation with light that is polarized perpendicular to the array axis. The narrow lines require a minimum particle radius of about 30 nm to achieve. Variations of the plasmon resonance wavelength, extinction efficiency and width with particle size, array structure, interparticle distance and polarization direction are examined, and conditions which lead to the smallest widths are demonstrated. A simple analytical expression valid for infinite lattices shows that the sharp resonance arises from cancellation between the single particle width and the imaginary part of the radiative dipolar interaction.

Classical/quantum integrability in AdS/CFT

Abstract: We discuss the AdS/CFT duality from the perspective of integrable systems and establish a direct relationship between the dimension of single trace local operators composed of two types of scalar fields in = 4 super Yang-Mills and the energy of their dual semiclassical string states in AdS5 × S5. The anomalous dimensions can be computed using a set of Bethe equations, which for ``long'' operators reduces to a Riemann-Hilbert problem. We develop a unified approach to the long wavelength Bethe equations, the classical ferromagnet and the classical string solutions in the SU(2) sector and present a general solution, governed by complex curves endowed with meromorphic differentials with integer periods. Using this solution we compute the anomalous dimensions of these long operators up to two loops and demonstrate that they agree with string-theory predictions.

Carbon input to soil may decrease soil carbon content

Abstract: It is commonly predicted that the intensity of primary production and soil carbon (C) content are positively linked. Paradoxically, many long-term field observations show that although plant litter is incorporated to soil in large quantities, soil C content does not necessarily increase. These results suggest that a negative relationship between C input and soil C conservation exists. Here, we demonstrate in controlled conditions that the supply of fresh C may accelerate the decomposition of soil C and induce a negative C balance. We show that soil C losses increase when soil microbes are nutrient limited. Results highlight the need for a better understanding of microbial mechanisms involved in the complex relationship between C input and soil C sequestration. We conclude that energy available to soil microbes and microbial competition are important determinants of soil C decomposition.

Motion-based background subtraction using adaptive kernel density estimation

Abstract: Background modeling is an important component of many vision systems. Existing work in the area has mostly addressed scenes that consist of static or quasi-static structures. When the scene exhibits a persistent dynamic behavior in time, such an assumption is violated and detection performance deteriorates. In this paper, we propose a new method for the modeling and subtraction of such scenes. Towards the modeling of the dynamic characteristics, optical flow is computed and utilized as a feature in a higher dimensional space. Inherent ambiguities in the computation of features are addressed by using a data-dependent bandwidth for density estimation using kernels. Extensive experiments demonstrate the utility and performance of the proposed approach.

Quantitative phase-field model of alloy solidification.

Abstract: We present a detailed derivation and thin interface analysis of a phase-field model that can accurately simulate microstructural pattern formation for low-speed directional solidification of a dilute binary alloy. This advance with respect to previous phase-field models is achieved by the addition of a phenomenological "antitrapping" solute current in the mass conservation relation [Phys. Rev. Lett. 87, 115701 (2001)]]. This antitrapping current counterbalances the physical, albeit artificially large, solute trapping effect generated when a mesoscopic interface thickness is used to simulate the interface evolution on experimental length and time scales. Furthermore, it provides additional freedom in the model to suppress other spurious effects that scale with this thickness when the diffusivity is unequal in solid and liquid [SIAM J. Appl. Math. 59, 2086 (1999)]], which include surface diffusion and a curvature correction to the Stefan condition. This freedom can also be exploited to make the kinetic undercooling of the interface arbitrarily small even for mesoscopic values of both the interface thickness and the phase-field relaxation time, as for the solidification of pure melts [Phys. Rev. E 53, R3017 (1996)]]. The performance of the model is demonstrated by calculating accurately within a phase-field approach the Mullins-Sekerka stability spectrum of a planar interface and nonlinear cellular shapes for realistic alloy parameters and growth conditions.

Recent Catalytic Advances in the Chemistry of Substituted Furans from Carbohydrates and in the Ensuing Polymers

Abstract: In this review, an overview is given on the last development of catalytic methods for the preparation of substituted furans from carbohydrates and ensuing polymers. The review starts with the recent aspects in the synthesis of some key furan monomers in the presence of solid catalysts. In the second part, selected examples are given of polymerization systems leading to furan-based materials with promising properties, thus constituting a serious alternative to petroleum-based counterparts. Finally, a short examination is given on what could be the future of furan chemistry with the recent development of ionic liquids as solvents.

Transduction peptides: from technology to physiology

Abstract: During the past fifteen years, a variety of peptides have been characterized for their ability to translocate into live cells. Most are efficient vectors that can internalize hydrophilic cargoes, and so provide a valuable biological (and potentially therapeutic) tool for targeting proteins into cells. Furthermore, translocation of cell-permeable peptides across the plasma membrane and their subsequent access to the cytosol, even when fused to large hydrophilic proteins, is challenging the perception of the plasma membrane as an impermeable barrier.

Biodiversity effects on soil processes explained by interspecific functional dissimilarity.

Abstract: The loss of biodiversity can have significant impacts on ecosystem functioning, but the mechanisms involved lack empirical confirmation. Using soil microcosms, we show experimentally that functional dissimilarity among detritivorous species, not species number, drives community compositional effects on leaf litter mass loss and soil respiration, two key soil ecosystem processes. These experiments confirm theoretical predictions that biodiversity effects on ecosystem functioning can be predicted by the degree of functional differences among species.

A Measure of Similarity between Graph Vertices: Applications to Synonym Extraction and Web Searching

Abstract: We introduce a concept of {similarity} between vertices of directed graphs. Let GA and GB be two directed graphs with, respectively, nA and nB vertices. We define an nB \times nA similarity matrix S whose real entry sij expresses how similar vertex j (in GA) is to vertex i (in GB): we say that sij is their similarity score. The similarity matrix can be obtained as the limit of the normalized even iterates of Sk+1 = BSkAT + BTSkA, where A and B are adjacency matrices of the graphs and S0 is a matrix whose entries are all equal to 1. In the special case where GA = GB = G, the matrix S is square and the score sij is the similarity score between the vertices i and j of G. We point out that Kleinberg's "hub and authority" method to identify web-pages relevant to a given query can be viewed as a special case of our definition in the case where one of the graphs has two vertices and a unique directed edge between them. In analogy to Kleinberg, we show that our similarity scores are given by the components of a dominant eigenvector of a nonnegative matrix. Potential applications of our similarity concept are numerous. We illustrate an application for the automatic extraction of synonyms in a monolingual dictionary.

Kleptocracy and divide-and-rule : a model of personal rule

Abstract: Many developing countries have suffered under the personal rule of kleptocrats, who implement highly inefe cient economic policies, expropriate the wealth of their citizens, and use the proceeds for their own glorie cation or consumption. We argue that the success of kleptocrats rests, in part, on their ability to use a divide-and-rule strategy, made possible by the weakness of institutions in these societies. Members of society need to cooperate in order to depose a kleptocrat, yet such cooperation may be defused by imposing punitive rates of taxation on any citizen who proposes such a move, and redistributing the benee ts to those who need to agree to it. Thus the collective action problem can be intensie ed by threats which remain off the equilibrium path. In equilibrium, all are exploited and no one challenges the kleptocrat. Kleptocratic policies are more likely when foreign aid and rents from natural resources provide rulers with substantial resources to buy off opponents; when opposition groups are shortsighted; when the average productivity in the economy is low; and when there is greater inequality between producer groups (because more productive groups are more dife cult to buy off). (JEL: O12, H00)

Manipulation of light signal transduction as a means of modifying fruit nutritional quality in tomato

Abstract: Fruit constitutes a major component of human diets, providing fiber, vitamins, and phytonutrients. Carotenoids are a major class of compounds found in many fruits, providing nutritional benefits as precursors to essential vitamins and as antioxidants. Although recent gene isolation efforts and metabolic engineering have primarily targeted genes involved in carotenoid biosynthesis, factors that regulate flux through the carotenoid pathway remain largely unknown. Characterization of the tomato high-pigment mutations (hp1 and hp2) suggests the manipulation of light signal transduction machinery may be an effective approach toward practical manipulation of plant carotenoids. We demonstrate here that hp1 alleles represent mutations in a tomato UV-DAMAGED DNA-BINDING PROTEIN 1 (DDB1) homolog. We further demonstrate that two tomato light signal transduction genes, LeHY5 and LeCOP1LIKE, are positive and negative regulators of fruit pigmentation, respectively. Down-regulated LeHY5 plants exhibit defects in light responses, including inhibited seedling photomorphogenesis, loss of thylakoid organization, and reduced carotenoid accumulation. In contrast, repression of LeCOP1LIKE expression results in plants with exaggerated photomorphogenesis, dark green leaves, and elevated fruit carotenoid levels. These results suggest genes encoding components of light signal transduction machinery also influence fruit pigmentation and represent genetic tools for manipulation of fruit quality and nutritional value.