Showing papers by "Centre national de la recherche scientifique published in 2004"
Stanford University1, Cleveland Clinic2, University of Toronto3, Centre national de la recherche scientifique4, Université Paris-Saclay5, University of Paris-Sud6, Rutgers University7, Avaya8, RAND Corporation9, IBM10, University of Pennsylvania11, University of Western Australia12, University of Minnesota13
TL;DR: A publicly available algorithm that requires only the same order of magnitude of computational effort as ordinary least squares applied to the full set of covariates is described.
Abstract: The purpose of model selection algorithms such as All Subsets, Forward Selection and Backward Elimination is to choose a linear model on the basis of the same set of data to which the model will be applied. Typically we have available a large collection of possible covariates from which we hope to select a parsimonious set for the efficient prediction of a response variable. Least Angle Regression (LARS), a new model selection algorithm, is a useful and less greedy version of traditional forward selection methods. Three main properties are derived: (1) A simple modification of the LARS algorithm implements the Lasso, an attractive version of ordinary least squares that constrains the sum of the absolute regression coefficients; the LARS modification calculates all possible Lasso estimates for a given problem, using an order of magnitude less computer time than previous methods. (2) A different LARS modification efficiently implements Forward Stagewise linear regression, another promising new model selection method; this connection explains the similar numerical results previously observed for the Lasso and Stagewise, and helps us understand the properties of both methods, which are seen as constrained versions of the simpler LARS algorithm. (3) A simple approximation for the degrees of freedom of a LARS estimate is available, from which we derive a Cp estimate of prediction error; this allows a principled choice among the range of possible LARS estimates. LARS and its variants are computationally efficient: the paper describes a publicly available algorithm that requires only the same order of magnitude of computational effort as ordinary least squares applied to the full set of covariates.
7,828 citations
Macquarie University1, University of Minnesota2, Stanford University3, Simón Bolívar University4, Wageningen University and Research Centre5, Smithsonian Environmental Research Center6, University of Alaska Fairbanks7, VU University Amsterdam8, University of Zurich9, Centre national de la recherche scientifique10, Curtin University11, Tohoku University12, University of Wisconsin–Eau Claire13, Landcare Research14, University of Concepción15, University of Cape Town16, University of Tartu17, Polish Academy of Sciences18, University of Tokyo19, Utrecht University20, University of Western Australia21, Charles Darwin University22, Ural State University23, University of Toronto24, Texas A&M University25, University of Córdoba (Spain)26
TL;DR: Reliable quantification of the leaf economics spectrum and its interaction with climate will prove valuable for modelling nutrient fluxes and vegetation boundaries under changing land-use and climate.
Abstract: Bringing together leaf trait data spanning 2,548 species and 175 sites we describe, for the first time at global scale, a universal spectrum of leaf economics consisting of key chemical, structural and physiological properties. The spectrum runs from quick to slow return on investments of nutrients and dry mass in leaves, and operates largely independently of growth form, plant functional type or biome. Categories along the spectrum would, in general, describe leaf economic variation at the global scale better than plant functional types, because functional types overlap substantially in their leaf traits. Overall, modulation of leaf traits and trait relationships by climate is surprisingly modest, although some striking and significant patterns can be seen. Reliable quantification of the leaf economics spectrum and its interaction with climate will prove valuable for modelling nutrient fluxes and vegetation boundaries under changing land-use and climate.
6,360 citations
TL;DR: The aim is to explicate a set of general concepts, of relevance across a wide range of situations and, therefore, helping communication and cooperation among a number of scientific and technical communities, including ones that are concentrating on particular types of system, of system failures, or of causes of systems failures.
Abstract: This paper gives the main definitions relating to dependability, a generic concept including a special case of such attributes as reliability, availability, safety, integrity, maintainability, etc. Security brings in concerns for confidentiality, in addition to availability and integrity. Basic definitions are given first. They are then commented upon, and supplemented by additional definitions, which address the threats to dependability and security (faults, errors, failures), their attributes, and the means for their achievement (fault prevention, fault tolerance, fault removal, fault forecasting). The aim is to explicate a set of general concepts, of relevance across a wide range of situations and, therefore, helping communication and cooperation among a number of scientific and technical communities, including ones that are concentrating on particular types of system, of system failures, or of causes of system failures.
4,695 citations
TL;DR: Before the 1960s, all anti-Stokes emissions, which were known to exist, involved emission energies in excess of excitation energies by only a few kT and were linked to thermal population of energy states above excitation states by such an energy amount.
Abstract: Before the 1960s, all anti-Stokes emissions, which were known to exist, involved emission energies in excess of excitation energies by only a few kT. They were linked to thermal population of energy states above excitation states by such an energy amount. It was the well-known case of anti-Stokes emission for the so-called thermal bands or in the Raman effect for the well-known anti-Stokes sidebands. Thermoluminescence, where traps are emptied by excitation energies of the order of kT, also constituted a field of anti-Stokes emission of its own. Superexcitation, i.e., raising an already excited electron to an even higher level by excited-state absorption (ESA), was also known but with very weak emissions. These types of well-known anti-Stokes processes have been reviewed in classical textbooks on luminescence.1 All fluorescence light emitters usually follow the well-known principle of the Stokes law which simply states that excitation photons are at a higher energy than emitted ones or, in other words, that output photon energy is weaker than input photon energy. This, in a sense, is an indirect statement that efficiency cannot be larger than 1. This principle is
4,279 citations
TL;DR: This work studies the scientific collaboration network and the world-wide air-transportation network, which are representative examples of social and large infrastructure systems, respectively, and defines appropriate metrics combining weighted and topological observables that enable it to characterize the complex statistical properties and heterogeneity of the actual strength of edges and vertices.
Abstract: Networked structures arise in a wide array of different contexts such as technological and transportation infrastructures, social phenomena, and biological systems. These highly interconnected systems have recently been the focus of a great deal of attention that has uncovered and characterized their topological complexity. Along with a complex topological structure, real networks display a large heterogeneity in the capacity and intensity of the connections. These features, however, have mainly not been considered in past studies where links are usually represented as binary states, i.e., either present or absent. Here, we study the scientific collaboration network and the world-wide air-transportation network, which are representative examples of social and large infrastructure systems, respectively. In both cases it is possible to assign to each edge of the graph a weight proportional to the intensity or capacity of the connections among the various elements of the network. We define appropriate metrics combining weighted and topological observables that enable us to characterize the complex statistical properties and heterogeneity of the actual strength of edges and vertices. This information allows us to investigate the correlations among weighted quantities and the underlying topological structure of the network. These results provide a better description of the hierarchies and organizational principles at the basis of the architecture of weighted networks.
3,650 citations
TL;DR: In this article, the authors present a comprehensive study of the physical properties of ∼ 10 5 galaxies with measurable star formation in the Sloan Digital Sky Survey (SDSS) by comparing physical information extracted from the emission lines with continuum properties, and build up a picture of the nature of star-forming galaxies at z < 0.2.
Abstract: We present a comprehensive study of the physical properties of ∼ 10 5 galaxies with measurable star formation in the Sloan Digital Sky Survey (SDSS). By comparing physical information extracted from the emission lines with continuum properties, we build up a picture of the nature of star-forming galaxies at z < 0.2. We develop a method for aperture correction using resolved imaging and show that our method takes out essentially all aperture bias in the star formation rate (SFR) estimates, allowing an accurate estimate of the total SFRs in galaxies. We determine the SFR density to be 1.915 +0.02 −0.01 (random) +0.14
3,262 citations
TL;DR: The therapeutic induction of MOMP may restore apoptosis in cancer cells in which it is disabled, and the general rules governing the pathophysiology and controversial issues regarding its regulation are discussed.
Abstract: In the mitochondrial pathway of apoptosis, caspase activation is closely linked to mitochondrial outer membrane permeabilization (MOMP). Numerous pro-apoptotic signal-transducing molecules and pathological stimuli converge on mitochondria to induce MOMP. The local regulation and execution of MOMP involve proteins from the Bcl-2 family, mitochondrial lipids, proteins that regulate bioenergetic metabolite flux, and putative components of the permeability transition pore. MOMP is lethal because it results in the release of caspase-activating molecules and caspase-independent death effectors, metabolic failure in the mitochondria, or both. Drugs designed to suppress excessive MOMP may avoid pathological cell death, and the therapeutic induction of MOMP may restore apoptosis in cancer cells in which it is disabled. The general rules governing the pathophysiology of MOMP and controversial issues regarding its regulation are discussed.
3,258 citations
TL;DR: In this article, a new solution for the astronomical computation of the insolation quantities on Earth spanning from −250 m to 250 m was presented, where the most regular components of the orbital solution could still be used over a much longer time span, which is why they provided here the solution over 250 m.
Abstract: We present here a new solution for the astronomical computation of the insolation quantities on Earth spanning from -250 Myr to 250 Myr. This solution has been improved with respect to La93 (Laskar et al. [CITE]) by using a direct integration of the gravitational equations for the orbital motion, and by improving the dissipative contributions, in particular in the evolution of the Earth–Moon System. The orbital solution has been used for the calibration of the Neogene period (Lourens et al. [CITE]), and is expected to be used for age calibrations of paleoclimatic data over 40 to 50 Myr, eventually over the full Palaeogene period (65 Myr) with caution. Beyond this time span, the chaotic evolution of the orbits prevents a precise determination of the Earth's motion. However, the most regular components of the orbital solution could still be used over a much longer time span, which is why we provide here the solution over 250 Myr. Over this time interval, the most striking feature of the obliquity solution, apart from a secular global increase due to tidal dissipation, is a strong decrease of about 0.38 degree in the next few millions of years, due to the crossing of the resonance (Laskar et al. [CITE]). For the calibration of the Mesozoic time scale (about 65 to 250 Myr), we propose to use the term of largest amplitude in the eccentricity, related to , with a fixed frequency of /yr, corresponding to a period of 405 000 yr. The uncertainty of this time scale over 100 Myr should be about , and over the full Mesozoic era.
2,992 citations
TL;DR: In this article, the authors reviewed existing knowledge with regard to organic aerosol (OA) of importance for global climate modelling and defined critical gaps needed to reduce the involved uncertainties, and synthesized the information to provide a continuous analysis of the flow from the emitted material to the atmosphere up to the point of the climate impact of the produced organic aerosols.
Abstract: The present paper reviews existing knowledge with regard to Organic Aerosol (OA) of importance for global climate modelling and defines critical gaps needed to reduce the involved uncertainties. All pieces required for the representation of OA in a global climate model are sketched out with special attention to Secondary Organic Aerosol (SOA): The emission estimates of primary carbonaceous particles and SOA precursor gases are summarized. The up-to-date understanding of the chemical formation and transformation of condensable organic material is outlined. Knowledge on the hygroscopicity of OA and measurements of optical properties of the organic aerosol constituents are summarized. The mechanisms of interactions of OA with clouds and dry and wet removal processes parameterisations in global models are outlined. This information is synthesized to provide a continuous analysis of the flow from the emitted material to the atmosphere up to the point of the climate impact of the produced organic aerosol. The sources of uncertainties at each step of this process are highlighted as areas that require further studies.
2,863 citations
TL;DR: The diverse examples show that in recent years organocatalysis has developed within organic chemistry into its own subdiscipline, whose "Golden Age" has already dawned.
Abstract: The term "organocatalysis" describes the acceleration of chemical reactions through the addition of a substoichiometric quantity of an organic compound. The interest in this field has increased spectacularly in the last few years as result of both the novelty of the concept and, more importantly, the fact that the efficiency and selectivity of many organocatalytic reactions meet the standards of established organic reactions. Organocatalytic reactions are becoming powerful tools in the construction of complex molecular skeletons. The diverse examples show that in recent years organocatalysis has developed within organic chemistry into its own subdiscipline, whose "Golden Age" has already dawned.
2,279 citations
TL;DR: It is shown that activation of the canonical Wnt pathway is sufficient to maintain self-renewal of both HESCs and MESCs, and the use of GSK-3-specific inhibitors such as BIO may have practical applications in regenerative medicine.
Abstract: Human and mouse embryonic stem cells (HESCs and MESCs, respectively) self-renew indefinitely while maintaining the ability to generate all three germ-layer derivatives. Despite the importance of ESCs in developmental biology and their potential impact on tissue replacement therapy, the molecular mechanism underlying ESC self-renewal is poorly understood. Here we show that activation of the canonical Wnt pathway is sufficient to maintain self-renewal of both HESCs and MESCs. Although Stat-3 signaling is involved in MESC self-renewal, stimulation of this pathway does not support self-renewal of HESCs. Instead we find that Wnt pathway activation by 6-bromoindirubin-3'-oxime (BIO), a specific pharmacological inhibitor of glycogen synthase kinase-3 (GSK-3), maintains the undifferentiated phenotype in both types of ESCs and sustains expression of the pluripotent state-specific transcription factors Oct-3/4, Rex-1 and Nanog. Wnt signaling is endogenously activated in undifferentiated MESCs and is downregulated upon differentiation. In addition, BIO-mediated Wnt activation is functionally reversible, as withdrawal of the compound leads to normal multidifferentiation programs in both HESCs and MESCs. These results suggest that the use of GSK-3-specific inhibitors such as BIO may have practical applications in regenerative medicine.
TL;DR: The recovery of a deep ice core from Dome C, Antarctica, that provides a climate record for the past 740,000 years is reported, suggesting that without human intervention, a climate similar to the present one would extend well into the future.
Abstract: The Antarctic Vostok ice core provided compelling evidence of the nature of climate, and of climate feedbacks, over the past 420,000 years. Marine records suggest that the amplitude of climate variability was smaller before that time, but such records are often poorly resolved. Moreover, it is not possible to infer the abundance of greenhouse gases in the atmosphere from marine records. Here we report the recovery of a deep ice core from Dome C, Antarctica, that provides a climate record for the past 740,000 years. For the four most recent glacial cycles, the data agree well with the record from Vostok. The earlier period, between 740,000 and 430,000 years ago, was characterized by less pronounced warmth in interglacial periods in Antarctica, but a higher proportion of each cycle was spent in the warm mode. The transition from glacial to interglacial conditions about 430,000 years ago ( Termination V) resembles the transition into the present interglacial period in terms of the magnitude of change in temperatures and greenhouse gases, but there are significant differences in the patterns of change. The interglacial stage following Termination V was exceptionally long - 28,000 years compared to, for example, the 12,000 years recorded so far in the present interglacial period. Given the similarities between this earlier warm period and today, our results may imply that without human intervention, a climate similar to the present one would extend well into the future.
TL;DR: Using the provided cassettes for N‐ and C‐terminal gene tagging or for deletion of any given gene, a set of only four primers is required, which makes this method very cost‐effective and reproducible.
Abstract: Tagging of genes by chromosomal integration of PCR amplified cassettes is a widely used and fast method to label proteins in vivo in the yeast Saccharomyces cerevisiae. This strategy directs the amplified tags to the desired chromosomal loci due to flanking homologous sequences provided by the PCR-primers, thus enabling the selective introduction of any sequence at any place of a gene, e.g. for the generation of C-terminal tagged genes or for the exchange of the promoter and N-terminal tagging of a gene. To make this method most powerful we constructed a series of 76 novel cassettes, containing a broad variety of C-terminal epitope tags as well as nine different promoter substitutions in combination with N-terminal tags. Furthermore, new selection markers have been introduced. The tags include the so far brightest and most yeast-optimized version of the red fluorescent protein, called RedStar2, as well as all other commonly used fluorescent proteins and tags used for the detection and purification of proteins and protein complexes. Using the provided cassettes for N- and C-terminal gene tagging or for deletion of any given gene, a set of only four primers is required, which makes this method very cost-effective and reproducible. This new toolbox should help to speed up the analysis of gene function in yeast, on the level of single genes, as well as in systematic approaches.
École Polytechnique Fédérale de Lausanne1, Centre national de la recherche scientifique2, Ghent University3, French Institute of Health and Medical Research4, Centre for Addiction and Mental Health5, Blaise Pascal University6, Vrije Universiteit Brussel7, University of California, Los Angeles8, Samsung Medical Center9, University of Massachusetts Medical School10, Memorial Sloan Kettering Cancer Center11, Delft University of Technology12, Claude Bernard University Lyon 113, Joseph Fourier University14, Forschungszentrum Jülich15, University of Santiago, Chile16, Curie Institute17
TL;DR: A detailed description of the design and development of GATE is given by the OpenGATE collaboration, whose continuing objective is to improve, document and validate GATE by simulating commercially available imaging systems for PET and SPECT.
Abstract: Monte Carlo simulation is an essential tool in emission tomography that can assist in the design of new medical imaging devices, the optimization of acquisition protocols and the development or assessment of image reconstruction algorithms and correction techniques. GATE, the Geant4 Application for Tomographic Emission, encapsulates the Geant4 libraries to achieve a modular, versatile, scripted simulation toolkit adapted to the field of nuclear medicine. In particular, GATE allows the description of time-dependent phenomena such as source or detector movement, and source decay kinetics. This feature makes it possible to simulate time curves under realistic acquisition conditions and to test dynamic reconstruction algorithms. This paper gives a detailed description of the design and development of GATE by the OpenGATE collaboration, whose continuing objective is to improve, document and validate GATE by simulating commercially available imaging systems for PET and SPECT. Large effort is also invested in the ability and the flexibility to model novel detection systems or systems still under design. A public release of GATE licensed under the GNU Lesser General Public License can be downloaded at http:/www-lphe.epfl.ch/GATE/. Two benchmarks developed for PET and SPECT to test the installation of GATE and to serve as a tutorial for the users are presented. Extensive validation of the GATE simulation platform has been started, comparing simulations and measurements on commercially available acquisition systems. References to those results are listed. The future prospects towards the gridification of GATE and its extension to other domains such as dosimetry are also discussed.
TL;DR: Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish, and reconstructs much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human 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.
TL;DR: It is found that the meridional overturning was nearly, or completely, eliminated during the coldest deglacial interval in the North Atlantic region, beginning with the catastrophic iceberg discharge Heinrich event H1, 17,500’yr ago, and declined sharply but briefly into the Younger Dryas cold event, about 12,700 yr ago.
Abstract: The Atlantic meridional overturning circulation is widely believed to affect climate. Changes in ocean circulation have been inferred from records of the deep water chemical composition derived from sedimentary nutrient proxies1, but their impact on climate is difficult to assess because such reconstructions provide insufficient constraints on the rate of overturning2. Here we report measurements of 231Pa/230Th, a kinematic proxy for the meridional overturning circulation, in a sediment core from the subtropical North Atlantic Ocean. We find that the meridional overturning was nearly, or completely, eliminated during the coldest deglacial interval in the North Atlantic region, beginning with the catastrophic iceberg discharge Heinrich event H1, 17,500 yr ago, and declined sharply but briefly into the Younger Dryas cold event, about 12,700 yr ago. Following these cold events, the 231Pa/230Th record indicates that rapid accelerations of the meridional overturning circulation were concurrent with the two strongest regional warming events during deglaciation. These results confirm the significance of variations in the rate of the Atlantic meridional overturning circulation for abrupt climate changes.
TL;DR: Analysis of the hydration process by solid-state NMR has clearly indicated that the trapped water molecules interact with the carboxylate groups through hydrogen bonds, but do not affect the hydroxyl species bridging the aluminum atoms.
Abstract: Aluminum 1,4-benzenedicarboxylate Al(OH)[O2CC6H4CO2]⋅ [HO2CC6H4CO2H]0.70 or MIL-53 as (Al) has been hydrothermally synthesized by heating a mixture of aluminum nitrate, 1,4-benzenedicarboxylic acid, and water, for three days at 220 °C. Its 3 D framework is built up of infinite trans chains of corner-sharing AlO4(OH)2 octahedra. The chains are interconnected by the 1,4-benzenedicarboxylate groups, creating 1 D rhombic-shaped tunnels. Disordered 1,4-benzenedicarboxylic acid molecules are trapped inside these tunnels. Their evacuation upon heating, between 275 and 420 °C, leads to a nanoporous open-framework (MIL-53 ht (Al) or Al(OH)[O2CC6H4CO2]) with empty pores of diameter 8.5 A. This solid exhibits a Langmuir surface area of 1590(1) m2 g−1 together with a remarkable thermal stability, since it starts to decompose only at 500 °C. At room temperature, the solid reversibly absorbs water in its tunnels, causing a very large breathing effect and shrinkage of the pores. Analysis of the hydration process by solid-state NMR (1H, 13C, 27Al) has clearly indicated that the trapped water molecules interact with the carboxylate groups through hydrogen bonds, but do not affect the hydroxyl species bridging the aluminum atoms. The hydrogen bonds between water and the oxygen atoms of the framework are responsible for the contraction of the rhombic channels. The structures of the three forms have been determined by means of powder X-ray diffraction analysis. Crystal data for MIL-53 as (Al) are as follows: orthorhombic system, Pnma (no. 62), a = 17.129(2), b = 6.628(1), c = 12.182(1) A; for MIL-53 ht (Al), orthorhombic system, Imma (no. 74), a = 6.608(1), b = 16.675(3), c = 12.813(2) A; for MIL-53 lt (Al), monoclinic system, Cc (no. 9), a = 19.513(2), b = 7.612(1), c = 6.576(1) A, β = 104.24(1)°.
Space Telescope Science Institute1, Johns Hopkins University2, Pennsylvania State University3, Centre national de la recherche scientifique4, European Southern Observatory5, Yale University6, California Institute of Technology7, Goddard Space Flight Center8, Max Planck Society9, University of California, Davis10, European Space Agency11, University of California, Santa Cruz12, University of Arizona13, University of Bonn14, University of California, Berkeley15, University of Oxford16
TL;DR: The GOODS survey as mentioned in this paper is based on multiband imaging data obtained with the Hubble Space Telescope and the Advanced Camera for Surveys (ACS) and covers roughly 320 arcmin2 in the ACS F435W, F606w, F814W, and F850LP bands, divided into two well-studied fields.
Abstract: This special issue of the Astrophysical Journal Letters is dedicated to presenting initial results from the Great Observatories Origins Deep Survey (GOODS) that are primarily, but not exclusively, based on multiband imaging data obtained with the Hubble Space Telescope and the Advanced Camera for Surveys (ACS). The survey covers roughly 320 arcmin2 in the ACS F435W, F606W, F814W, and F850LP bands, divided into two well-studied fields. Existing deep observations from the Chandra X-Ray Observatory and ground-based facilities are supplemented with new, deep imaging in the optical and near-infrared from the European Southern Observatory and from the Kitt Peak National Observatory. Deep observations with the Space Infrared Telescope Facility are scheduled. Reduced data from all facilities are being released worldwide within 3-6 months of acquisition. Together, this data set provides two deep reference fields for studies of distant normal and active galaxies, supernovae, and faint stars in our own Galaxy. This Letter serves to outline the survey strategy and describe the specific data that have been used in the accompanying letters, summarizing the reduction procedures and sensitivity limits.
TL;DR: A quantitative comparison between data coming from different experiments in the same geometry identifies the robust features in each case and a transverse analysis of the data across the different configurations allows to identify the relevant dimensionless parameters, the different flow regimes and to propose simple interpretations.
Abstract: The behaviour of dense assemblies of dry grains submitted to continuous shear deformation has been the subject of many experiments and discrete particle simulations. This paper is a collective work carried out among the French research group Groupement de Recherche Milieux Divises (GDR MiDi). It proceeds from the collection of results on steady uniform granular flows obtained by different groups in six different geometries both in experiments and numerical works. The goal is to achieve a coherent presentation of the relevant quantities to be measured i.e. flowing thresholds, kinematic profiles, effective friction, etc. First, a quantitative comparison between data coming from different experiments in the same geometry identifies the robust features in each case. Second, a transverse analysis of the data across the different configurations, allows us to identify the relevant dimensionless parameters, the different flow regimes and to propose simple interpretations. The present work, more than a simple juxtaposition of results, demonstrates the richness of granular flows and underlines the open problem of defining a single rheology.
TL;DR: Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.
Abstract: Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.
TL;DR: Changes in the subunits of tubulin as it switches from its straight conformation to a curved one correlate with the loss of lateral contacts and provide a rationale for the rapid microtubule depolymerization characteristic of dynamic instability.
Abstract: Microtubules are cytoskeletal polymers of tubulin involved in many cellular functions. Their dynamic instability is controlled by numerous compounds and proteins, including colchicine and stathmin family proteins. The way in which microtubule instability is regulated at the molecular level has remained elusive, mainly because of the lack of appropriate structural data. Here, we present the structure, at 3.5 A resolution, of tubulin in complex with colchicine and with the stathmin-like domain (SLD) of RB3. It shows the interaction of RB3-SLD with two tubulin heterodimers in a curved complex capped by the SLD amino-terminal domain, which prevents the incorporation of the complexed tubulin into microtubules. A comparison with the structure of tubulin in protofilaments shows changes in the subunits of tubulin as it switches from its straight conformation to a curved one. These changes correlate with the loss of lateral contacts and provide a rationale for the rapid microtubule depolymerization characteristic of dynamic instability. Moreover, the tubulin-colchicine complex sheds light on the mechanism of colchicine's activity: we show that colchicine binds at a location where it prevents curved tubulin from adopting a straight structure, which inhibits assembly.
TL;DR: This study demonstrates, for the first time, that adipocytes and endothelial cells have a common progenitor, and highlights the concept that adipose lineage cells represent a suitable new cell source for therapeutic angiogenesis in ischemic disease.
Abstract: Background— Adipose tissue development and remodeling are closely associated with the growth of vascular network. We hypothesized that adipose tissue may contain progenitor cells with angiogenic potential and that therapy based on adipose tissue-derived progenitor cells administration may constitute a promising cell therapy in patients with ischemic disease. Methods and Results— In mice, cultured stromal-vascular fraction (SVF) cells from adipose tissue have a great proangiogenic potential, comparable to that of bone marrow mononuclear cells in the mouse ischemic hindlimb model. Similarly, cultured human SVF cells differentiate into endothelial cells, incorporate into vessels, and promote both postischemic neovascularization in nude mice and vessel-like structure formation in Matrigel plug. In vitro, these cells represent a homogeneous population of CD34- and CD13-positive cells, which can spontaneously express the endothelial cell markers CD31 and von Willebrand factor when cultured in semisolid medium. ...
TL;DR: A large body of evidence suggests that human decision-making is strongly influenced by the behavior of others, which may then affect biological evolution.
Abstract: Psychologists, economists, and advertising moguls have long known that human decision-making is strongly influenced by the behavior of others A rapidly accumulating body of evidence suggests that the same is true in animals Individuals can use information arising from cues inadvertently produced by the behavior of other individuals with similar requirements Many of these cues provide public information about the quality of alternatives The use of public information is taxonomically widespread and can enhance fitness Public information can lead to cultural evolution, which we suggest may then affect biological evolution
TL;DR: Examining some of the main constituent processes of cognitive control as involved in dynamic decision making: goal-directed action selection, response activation and inhibition, performance monitoring, and reward-based learning finds medial frontal cortex is found to be involved in performance monitoring.
TL;DR: A detailed bioinformatic analysis of 441 members of the Arabidopsis PPR family plus genomic and genetic data on the expression, localization, and general function of many family members confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms.
Abstract: The complete sequence of the Arabidopsis thaliana genome revealed thousands of previously unsuspected genes, many of which cannot be ascribed even putative functions. One of the largest and most enigmatic gene families discovered in this way is characterized by tandem arrays of pentatricopeptide repeats (PPRs). We describe a detailed bioinformatic analysis of 441 members of the Arabidopsis PPR family plus genomic and genetic data on the expression (microarray data), localization (green fluorescent protein and red fluorescent protein fusions), and general function (insertion mutants and RNA binding assays) of many family members. The basic picture that arises from these studies is that PPR proteins play constitutive, often essential roles in mitochondria and chloroplasts, probably via binding to organellar transcripts. These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms.
TL;DR: It is shown that huntingtin specifically enhances vesicular transport of brain-derived neurotrophic factor (BDNF) along microtubules, indicating that a key role of huntingtin is to promote BDNF transport and suggesting that loss of this function might contribute to pathogenesis.
TL;DR: This work studied numerical cognition in speakers of Mundurukú, an Amazonian language with a very small lexicon of number words, and implies a distinction between a nonverbal system of number approximation and a language-based counting system for exact number and arithmetic.
Abstract: Is calculation possible without language ? Or is the human ability for arithmetic dependent on the language faculty ? To clarify the relation between language and arithmetic, we studied numerical cognition in speakers of munduruku, an Amazonian language with a very small lexicon of numbers words. Our results imply a distinction between a non-verbal system of number approximation and a language-based counting system for exact number and arithmetic.
TL;DR: Functional diversification of the surviving duplicated genes is a major feature of the long-term evolution of polyploidy, and the rate of protein sequence evolution has been significantly asymmetric in >20% of duplicate pairs.
Abstract: To study the evolutionary effects of polyploidy on plant gene functions, we analyzed functional genomics data for a large number of duplicated gene pairs formed by ancient polyploidy events in Arabidopsis thaliana. Genes retained in duplicate are not distributed evenly among Gene Ontology or Munich Information Center for Protein Sequences functional categories, which indicates a nonrandom process of gene loss. Genes involved in signal transduction and transcription have been preferentially retained, and those involved in DNA repair have been preferentially lost. Although the two members of each gene pair must originally have had identical transcription profiles, less than half of the pairs formed by the most recent polyploidy event still retain significantly correlated profiles. We identified several cases where groups of duplicated gene pairs have diverged in concert, forming two parallel networks, each containing one member of each gene pair. In these cases, the expression of each gene is strongly correlated with the other nonhomologous genes in its network but poorly correlated with its paralog in the other network. We also find that the rate of protein sequence evolution has been significantly asymmetric in >20% of duplicate pairs. Together, these results suggest that functional diversification of the surviving duplicated genes is a major feature of the long-term evolution of polyploids.
TL;DR: Transmission electron microscopy analysis was performed at the microscopy facility of the Institute of Biomedical Problems and was cofinanced by CNRS, R=gion Alsace, Louis Pasteur University, and the Association de la Recherche pour le Cancer.
Abstract: [*] Dipl.-Chem. D. Pantarotto, Prof. M. Prato Dipartimento di Scienze Farmaceutiche Universit di Trieste 34127 Trieste (Italy) Fax: (+39)040-5272 E-mail: prato@univ.trieste.it Dipl.-Chem. R. Singh, Dipl.-Chem. D. McCarthy, Dr. K. Kostarelos Centre for Drug Delivery Research and Electron Microscopy Unit The School of Pharmacy University of London London WC1N 1AX (United Kingdom) Fax: (+39)207-7535942 E-mail: kostas.kostarelos@ulsop.ac.uk Dipl.-Chem. D. Pantarotto, Dr. J.-P. Briand, Dr. A. Bianco Institut de Biologie Mol=culaire et Cellulaire UPR9021 CNRS Immunologie et Chimie Th=rapeutiques 67084 Strasbourg (France) Fax: (+33)388-610-680 E-mail: A.Bianco@ibmc.u-strasbg.fr Dr. M. Erhardt Institut de Biologie Mol=culaire des Plantes 67084 Strasbourg (France) [**] This work was supported by the Centre National de la Recherche Scientifique (CNRS), Universit di Trieste, and Ministero dell’Istruzione, dell’ Universit e della Ricerca (MIUR; cofin 2002, prot. 2002032171). Transmission electron microscopy (TEM) analysis was performed at the microscopy facility of the Institute of Biomedical Problems and was cofinanced by CNRS, R=gion Alsace, Louis Pasteur University, and the Association de la Recherche pour le Cancer. The authors wish to acknowledge C. D. Partidos for helpful and stimulating discussions. We thank Mr. Claudio Gamboz (Centro Servizi Polivalenti di Ateneo (CSPA), Universit di Trieste) for his great help with the TEM measurements. Supporting information for this article is available on the WWW under http://www.angewandte.org or from the author. Communications