Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes

An ordered draft sequence of the 17-gigabase hexaploid bread wheat ( Triticum aestivum ) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

The increasing integration of technology into our lives has created unprecedented volumes of data on society’s everyday behaviour. Such data opens up exciting new opportunities to work towards a quantitative understanding of our complex social systems, within the realms of a new discipline known as Computational Social Science. Against a background of financial crises, riots and international epidemics, the urgent need for a greater comprehension of the complexity of our interconnected global society and an ability to apply such insights in policy decisions is clear. This manifesto outlines the objectives of this new scientific direction, considering the challenges involved in it, and the extensive impact on science, technology and society that the success of this endeavour is likely to bring about.

Mammalian spermatozoa are unique cells in many ways, and the acquisition of their main function, i.e. fertilization capacity, is a multistep process starting in the male gonad and ending near the female egg for the few cells reaching this point. Owing to the unique character of this cell, the molecular pathways necessary to achieve its maturation also show some specific characteristics. One of the most striking specificities of the spermatozoon is that its DNA is highly compacted after the replacement of histones by protamines, making the classical processes of transcription and translation impossible. The sperm cells are thus totally dependent on their extracellular environment for their protection against oxidative stress, for example, or for the molecular changes occurring during the transit of the epididymis; the first organ in which post-testicular maturation takes place. The molecular mechanisms underlying sperm maturation are still largely unknown, but it has been shown in the past three decades that extracellular vesicles secreted by the male reproductive tract are involved in this process. This review will examine the roles played by two types of naturally occurring extracellular vesicles, epididymosomes and prostasomes, secreted by the epididymis and the prostate respectively. We will also describe how the use of artificial vesicles, liposomes, contributed to the study of male reproductive physiology.

The ALICE measurement of ${K}_{S}^{0}$ and $\ensuremath{\Lambda}$ production at midrapidity in Pb-Pb collisions at $\sqrt{{s}_{NN}}=2.76\text{ }\text{ }\mathrm{TeV}$ is presented. The transverse momentum (${p}_{T}$) spectra are shown for several collision centrality intervals and in the ${p}_{T}$ range from $0.4\text{ }\text{ }\mathrm{GeV}/c$ ($0.6\text{ }\text{ }\mathrm{GeV}/c$ for $\ensuremath{\Lambda}$) to $12\text{ }\text{ }\mathrm{GeV}/c$. The ${p}_{T}$ dependence of the $\ensuremath{\Lambda}/{K}_{S}^{0}$ ratios exhibits maxima in the vicinity of $3\text{ }\text{ }\mathrm{GeV}/c$, and the positions of the maxima shift towards higher ${p}_{T}$ with increasing collision centrality. The magnitude of these maxima increases by almost a factor of three between most peripheral and most central Pb-Pb collisions. This baryon excess at intermediate ${p}_{T}$ is not observed in $pp$ interactions at $\sqrt{s}=0.9\text{ }\text{ }\mathrm{TeV}$ and at $\sqrt{s}=7\text{ }\text{ }\mathrm{TeV}$. Qualitatively, the baryon enhancement in heavy-ion collisions is expected from radial flow. However, the measured ${p}_{T}$ spectra above $2\text{ }\text{ }\mathrm{GeV}/c$ progressively decouple from hydrodynamical-model calculations. For higher values of ${p}_{T}$, models that incorporate the influence of the medium on the fragmentation and hadronization processes describe qualitatively the ${p}_{T}$ dependence of the $\ensuremath{\Lambda}/{K}_{S}^{0}$ ratio.

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article Free Access Share on Mining frequent patterns with counting inference Authors: Yves Bastide LIMOS, université Blaise Pascal, complexe scientifique des, C6zeanx, 24 av. des Landais, 63177 Aubière Cedex, France LIMOS, université Blaise Pascal, complexe scientifique des, C6zeanx, 24 av. des Landais, 63177 Aubière Cedex, FranceView Profile , Rafik Taouil INRIA Lorraine, 54506 Vandoeuvre-lès-Nancy Cedex, France INRIA Lorraine, 54506 Vandoeuvre-lès-Nancy Cedex, FranceView Profile , Nicolas Pasquier I3S (CNRS UPRESA 6070) - uuiversité de Nice, 06903, Sophia Antipolis, France I3S (CNRS UPRESA 6070) - uuiversité de Nice, 06903, Sophia Antipolis, FranceView Profile , Gerd Stumme Institut für Angewandte Informatik und Formale Beschreibungsverfahren, Universität Karlsruhe (TH), D-76128 Karlsruhe, Germany Institut für Angewandte Informatik und Formale Beschreibungsverfahren, Universität Karlsruhe (TH), D-76128 Karlsruhe, GermanyView Profile , Lotfi Lakhal LIM (CNRS FRE 2246) - université de la Méditerranée, 13288 Marseille Cedex 09, France LIM (CNRS FRE 2246) - université de la Méditerranée, 13288 Marseille Cedex 09, FranceView Profile Authors Info & Claims ACM SIGKDD Explorations NewsletterVolume 2Issue 2Dec. 2000 pp 66–75https://doi.org/10.1145/380995.381017Published:01 December 2000Publication History 205citation795DownloadsMetricsTotal Citations205Total Downloads795Last 12 Months63Last 6 weeks6 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF

We present measurements of the ratio of the proton elastic electromagnetic form factors, ${\ensuremath{\mu}}_{p}{G}_{\mathrm{Ep}}{/G}_{\mathrm{Mp}}.$ The Jefferson Lab Hall A Focal Plane Polarimeter was used to determine the longitudinal and transverse components of the recoil proton polarization in $\mathrm{ep}$ elastic scattering; the ratio of these polarization components is proportional to the ratio of the two form factors. These data reproduce the observation of Jones et al. [Phys. Rev. Lett. 84, 1398 (2000)], that the form factor ratio decreases significantly from unity above ${Q}^{2}=1 {\mathrm{GeV}}^{2}.$

Previously published and as vet unpublished QCD results obtained with the ALEPH detector at LEP1 are presented. The unprecedented statistics allows detailed studies of both perturbative and non-perturbative aspects of strong interactions to be carried out using hadronic Z and tau decays. The studies presented include precise determinations of the strong coupling constant. tests of its flavour independence, tests of the SU(3) gauge structure of QCD, study of coherence effects, and measurements of single-particle inclusive distributions and two-particle correlations for many identified baryons and mesons. (C) 1998 Elsevier Science B.V.

Production of charged pions, kaons and protons at large transverse momenta

The flexible job shop scheduling problem (FJSP) is an NP-hard combinatorial optimization problem, which has wide applications in the real world. The complexity and relevance of the FJSP have led to numerous research works on its modeling and resolution. This paper reviews some of the research of the past 30 years on the problem, by presenting and classifying the different criteria, constraints, configurations and solution approaches that have been considered. Recent emerging topics on complex shop scheduling, multi-criteria optimization and uncertain and dynamic environments are discussed. Finally, future research opportunities are proposed.

We study shapes of facial surfaces for the purpose of face recognition. The main idea is to 1) represent surfaces by unions of level curves, called facial curves, of the depth function and 2) compare shapes of surfaces implicitly using shapes of facial curves. The latter is performed using a differential geometric approach that computes geodesic lengths between closed curves on a shape manifold. These ideas are demonstrated using a nearest-neighbor classifier on two 3D face databases: Florida State University and Notre Dame, highlighting a good recognition performance.

We report a new, high-precision measurement of the proton elastic form factor ratio μpGE/GM for the four-momentum transfer squared Q2=0.3–0.7(GeV/c)2. The measurement was performed at Jefferson Lab (JLab) in Hall A using recoil polarimetry. With a total uncertainty of approximately 1%, the new data clearly show that the deviation of the ratio μpGE/GM from unity observed in previous polarization measurements at high Q2 continues down to the lowest Q2 value of this measurement. The updated global fit that includes the new results yields an electric (magnetic) form factor roughly 2% smaller (1% larger) than the previous global fit in this Q2 range. We obtain new extractions of the proton electric and magnetic radii, which are 〈rE2〉1/2=0.875±0.010 fm and 〈rM2〉1/2=0.867±0.020 fm. The charge radius is consistent with other recent extractions based on the electron–proton interaction, including the atomic hydrogen Lamb shift measurements, which suggests a missing correction in the comparison of measurements of the proton charge radius using electron probes and the recent extraction from the muonic hydrogen Lamb shift.

We report on measurements of the neutron spin asymmetries ${A}_{1,2}^{n}$ and polarized structure functions ${g}_{1,2}^{n}$ at three kinematics in the deep inelastic region, with $x=0.33$, 0.47, and 0.60 and ${Q}^{2}=2.7$, 3.5, and $4.8\phantom{\rule{0.3em}{0ex}}{(\mathrm{GeV}∕c)}^{2}$, respectively. These measurements were performed using a $5.7\phantom{\rule{0.3em}{0ex}}\mathrm{GeV}$ longitudinally polarized electron beam and a polarized $^{3}\mathrm{He}$ target. The results for ${A}_{1}^{n}$ and ${g}_{1}^{n}$ at $x=0.33$ are consistent with previous world data and, at the two higher-$x$ points, have improved the precision of the world data by about an order of magnitude. The new ${A}_{1}^{n}$ data show a zero crossing around $x=0.47$ and the value at $x=0.60$ is significantly positive. These results agree with a next-to-leading-order QCD analysis of previous world data. The trend of data at high $x$ agrees with constituent quark model predictions but disagrees with that from leading-order perturbative QCD (PQCD) assuming hadron helicity conservation. Results for ${A}_{2}^{n}$ and ${g}_{2}^{n}$ have a precision comparable to the best world data in this kinematic region. Combined with previous world data, the moment ${d}_{2}^{n}$ was evaluated and the new result has improved the precision of this quantity by about a factor of 2. When combined with the world proton data, polarized quark distribution functions were extracted from the new ${g}_{1}^{n}∕{F}_{1}^{n}$ values based on the quark-parton model. While results for $\ensuremath{\Delta}u∕u$ agree well with predictions from various models, results for $\ensuremath{\Delta}d∕d$ disagree with the leading-order PQCD prediction when hadron helicity conservation is imposed.

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Search for pair-produced third-generation squarks decaying via charm quarks or in compressed supersymmetric scenarios in pp collisions at ffiffi s p 8 TeV with the ATLAS detector

The Tile hadronic calorimeter of the ATLAS detector has undergone extensive testing in the experimental hall since its installation in late 2005. The readout, control and calibration systems have been fully operational since 2007 and the detector has successfully collected data from the LHC single beams in 2008 and first collisions in 2009. This paper gives an overview of the Tile Calorimeter performance as measured using random triggers, calibration data, data from cosmic ray muons and single beam data. The detector operation status, noise characteristics and performance of the calibration systems are presented, as well as the validation of the timing and energy calibration carried out with minimum ionising cosmic ray muons data. The calibration systems' precision is well below the design value of 1%. The determination of the global energy scale was performed with an uncertainty of 4%. © 2010 CERN for the benefit of the ATLAS collaboration.

Segmentation and classification of urban range data into different object classes have several challenges due to certain properties of the data, such as density variation, inconsistencies due to missing data and the large data size that require heavy computation and large memory. A method to classify urban scenes based on a super-voxel segmentation of sparse 3D data obtained from LiDAR sensors is presented. The 3D point cloud is first segmented into voxels, which are then characterized by several attributes transforming them into super-voxels. These are joined together by using a link-chain method rather than the usual region growing algorithm to create objects. These objects are then classified using geometrical models and local descriptors. In order to evaluate the results, a new metric that combines both segmentation and classification results simultaneously is presented. The effects of voxel size and incorporation of RGB color and laser reflectance intensity on the classification results are also discussed. The method is evaluated on standard data sets using different metrics to demonstrate its efficacy.

ABSTRACT To identify the mechanisms underlying muscle aging, we have undertaken a high‐resolution differential proteomic analysis of gastrocnemius muscle in young adults, mature adults, and old LOU/c/jall rats. Two‐dimensional gel electrophoresis and subsequent MALDI‐ToF mass spectrometry analyses led to the identification of 40 differentially expressed proteins. Strikingly, most differences characterized old (30‐month) animals, whereas young (7‐month) and mature (18‐month) adults exhibited similar patterns of expression. Important modifications in contractile (actin, myosin light‐chains, troponins‐T) and cytoskeletal (desmin, tubulin) proteins, and in essential regulatory proteins (gelsolin, myosin binding proteins, CapZ‐β, P23), likely account for dysfunctions in old muscle force generation and speed of contraction. Other features support decreases in cytosolic (triose‐phosphate isomerase, enolase, glycerol‐3‐P dehydrogenase, creatine kinase) and mitochondrial (isocitrate dehydrogenase, cytochrome‐c oxidase) energy metabolisms. Muscle aging is often associated with increased oxidative stress. Accordingly, we observed differential regulation of molecular chaperones (hsp20, hsp27, reticuloplasmin ER60) and of proteins implicated in reactive aldehyde detoxification (aldehyde dehydrogenase, glutathione transferase, glyoxalase). We further noticed up‐regulation of proteins involved in transcriptional elongation (RNA capping protein) and RNA‐editing (Apobec2). Most of these proteins were previously unrecognized as differentially expressed in old muscles, and they represent novel starting points for elucidating the mechanisms of muscle aging.

The transverse momentum ( pT ) spectrum and nuclear modification factor ( RAA ) of reconstructed jets in 0–10% and 10–30% central Pb–Pb collisions at sNN=2.76 TeV were measured. Jets were reconstructed using the anti- kT jet algorithm with a resolution parameter of R=0.2 from charged and neutral particles, utilizing the ALICE tracking detectors and Electromagnetic Calorimeter (EMCal). The jet pT spectra are reported in the pseudorapidity interval of |ηjet|<0.5 for 405 GeV/c to suppress jets constructed from the combinatorial background in Pb–Pb collisions. The leading charged particle requirement applied to jet spectra both in pp and Pb–Pb collisions had a negligible effect on the RAA . The nuclear modification factor RAA was found to be 0.28±0.04 in 0–10% and 0.35±0.04 in 10–30% collisions, independent of pT,jet within the uncertainties of the measurement. The observed suppression is in fair agreement with expectations from two model calculations with different approaches to jet quenching.

The first measurements from proton–proton collisions recorded with the ATLAS detector at the LHC are presented. Data were collected in December 2009 using a minimum-bias trigger during collisions at a centre-of-mass energy of 900 GeV. The charged-particle multiplicity, its dependence on transverse momentum and pseudorapidity, and the relationship between mean transverse momentum and charged-particle multiplicity are measured for events with at least one charged particle in the kinematic range |η|<2.5 and pT>500 MeV. The measurements are compared to Monte Carlo models of proton–proton collisions and to results from other experiments at the same centre-of-mass energy. The charged-particle multiplicity per event and unit of pseudorapidity at η=0 is measured to be 1.333±0.003(stat.)±0.040(syst.), which is 5–15% higher than the Monte Carlo models predict.