Centrale Méditerranée

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

Abstract: SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

Optical wireless communication (OWC) refers to transmission in unguided propagation media through the use of optical carriers, i.e., visible, infrared (IR), and ultraviolet (UV) bands. In this survey, we focus on outdoor terrestrial OWC links which operate in near IR band. These are widely referred to as free space optical (FSO) communication in the literature. FSO systems are used for high rate communication between two fixed points over distances up to several kilometers. In comparison to radio-frequency (RF) counterparts, FSO links have a very high optical bandwidth available, allowing much higher data rates. They are appealing for a wide range of applications such as metropolitan area network (MAN) extension, local area network (LAN)-to-LAN connectivity, fiber back-up, backhaul for wireless cellular networks, disaster recovery, high definition TV and medical image/video transmission, wireless video surveillance/monitoring, and quantum key distribution among others. Despite the major advantages of FSO technology and variety of its application areas, its widespread use has been hampered by its rather disappointing link reliability particularly in long ranges due to atmospheric turbulence-induced fading and sensitivity to weather conditions. In the last five years or so, there has been a surge of interest in FSO research to address these major technical challenges. Several innovative physical layer concepts, originally introduced in the context of RF systems, such as multiple-input multiple-output communication, cooperative diversity, and adaptive transmission have been recently explored for the design of next generation FSO systems. In this paper, we present an up-to-date survey on FSO communication systems. The first part describes FSO channel models and transmitter/receiver structures. In the second part, we provide details on information theoretical limits of FSO channels and algorithmic-level system design research activities to approach these limits. Specific topics include advances in modulation, channel coding, spatial/cooperative diversity techniques, adaptive transmission, and hybrid RF/FSO systems.

The complexity of many biological, social and technological systems stems from the richness of the interactions among their units. Over the past decades, a variety of complex systems has been successfully described as networks whose interacting pairs of nodes are connected by links. Yet, from human communications to chemical reactions and ecological systems, interactions can often occur in groups of three or more nodes and cannot be described simply in terms of dyads. Until recently little attention has been devoted to the higher-order architecture of real complex systems. However, a mounting body of evidence is showing that taking the higher-order structure of these systems into account can enhance our modeling capacities and help us understand and predict their dynamical behavior. Here we present a complete overview of the emerging field of networks beyond pairwise interactions. We discuss how to represent higher-order interactions and introduce the different frameworks used to describe higher-order systems, highlighting the links between the existing concepts and representations. We review the measures designed to characterize the structure of these systems and the models proposed to generate synthetic structures, such as random and growing bipartite graphs, hypergraphs and simplicial complexes. We introduce the rapidly growing research on higher-order dynamical systems and dynamical topology, discussing the relations between higher-order interactions and collective behavior. We focus in particular on new emergent phenomena characterizing dynamical processes, such as diffusion, synchronization, spreading, social dynamics and games, when extended beyond pairwise interactions. We conclude with a summary of empirical applications, and an outlook on current modeling and conceptual frontiers.

The complexity of many biological, social and technological systems stems from the richness of the interactions among their units. Over the past decades, a variety of complex systems has been successfully described as networks whose interacting pairs of nodes are connected by links. Yet, from human communications to chemical reactions and ecological systems, interactions can often occur in groups of three or more nodes and cannot be described simply in terms of dyads. Until recently little attention has been devoted to the higher-order architecture of real complex systems. However, a mounting body of evidence is showing that taking the higher-order structure of these systems into account can enhance our modeling capacities and help us understand and predict their dynamical behavior. Here we present a complete overview of the emerging field of networks beyond pairwise interactions. We discuss how to represent higher-order interactions and introduce the different frameworks used to describe higher-order systems, highlighting the links between the existing concepts and representations. We review the measures designed to characterize the structure of these systems and the models proposed to generate synthetic structures, such as random and growing bipartite graphs, hypergraphs and simplicial complexes. We introduce the rapidly growing research on higher-order dynamical systems and dynamical topology, discussing the relations between higher-order interactions and collective behavior. We focus in particular on new emergent phenomena characterizing dynamical processes, such as diffusion, synchronization, spreading, social dynamics and games, when extended beyond pairwise interactions. We conclude with a summary of empirical applications, and an outlook on current modeling and conceptual frontiers.

We describe the legacy Planck cosmic microwave background (CMB) likelihoods derived from the 2018 data release. The overall approach is similar in spirit to the one retained for the 2013 and 2015 data release, with a hybrid method using different approximations at low ( ℓ < 30) and high ( ℓ ≥ 30) multipoles, implementing several methodological and data-analysis refinements compared to previous releases. With more realistic simulations, and better correction and modelling of systematic effects, we can now make full use of the CMB polarization observed in the High Frequency Instrument (HFI) channels. The low-multipole EE cross-spectra from the 100 GHz and 143 GHz data give a constraint on the ΛCDM reionization optical-depth parameter τ to better than 15% (in combination with the TT low- ℓ data and the high- ℓ temperature and polarization data), tightening constraints on all parameters with posterior distributions correlated with τ . We also update the weaker constraint on τ from the joint TEB likelihood using the Low Frequency Instrument (LFI) channels, which was used in 2015 as part of our baseline analysis. At higher multipoles, the CMB temperature spectrum and likelihood are very similar to previous releases. A better model of the temperature-to-polarization leakage and corrections for the effective calibrations of the polarization channels (i.e., the polarization efficiencies) allow us to make full use of polarization spectra, improving the ΛCDM constraints on the parameters θ MC , ω c , ω b , and H 0 by more than 30%, and n s by more than 20% compared to TT-only constraints. Extensive tests on the robustness of the modelling of the polarization data demonstrate good consistency, with some residual modelling uncertainties. At high multipoles, we are now limited mainly by the accuracy of the polarization efficiency modelling. Using our various tests, simulations, and comparison between different high-multipole likelihood implementations, we estimate the consistency of the results to be better than the 0.5 σ level on the ΛCDM parameters, as well as classical single-parameter extensions for the joint likelihood (to be compared to the 0.3 σ levels we achieved in 2015 for the temperature data alone on ΛCDM only). Minor curiosities already present in the previous releases remain, such as the differences between the best-fit ΛCDM parameters for the ℓ < 800 and ℓ > 800 ranges of the power spectrum, or the preference for more smoothing of the power-spectrum peaks than predicted in ΛCDM fits. These are shown to be driven by the temperature power spectrum and are not significantly modified by the inclusion of the polarization data. Overall, the legacy Planck CMB likelihoods provide a robust tool for constraining the cosmological model and represent a reference for future CMB observations.

Abstract Chemotherapy-resistant human acute myeloid leukemia (AML) cells are thought to be enriched in quiescent immature leukemic stem cells (LSC). To validate this hypothesis in vivo, we developed a clinically relevant chemotherapeutic approach treating patient-derived xenografts (PDX) with cytarabine (AraC). AraC residual AML cells are enriched in neither immature, quiescent cells nor LSCs. Strikingly, AraC-resistant preexisting and persisting cells displayed high levels of reactive oxygen species, showed increased mitochondrial mass, and retained active polarized mitochondria, consistent with a high oxidative phosphorylation (OXPHOS) status. AraC residual cells exhibited increased fatty-acid oxidation, upregulated CD36 expression, and a high OXPHOS gene signature predictive for treatment response in PDX and patients with AML. High OXPHOS but not low OXPHOS human AML cell lines were chemoresistant in vivo. Targeting mitochondrial protein synthesis, electron transfer, or fatty-acid oxidation induced an energetic shift toward low OXPHOS and markedly enhanced antileukemic effects of AraC. Together, this study demonstrates that essential mitochondrial functions contribute to AraC resistance in AML and are a robust hallmark of AraC sensitivity and a promising therapeutic avenue to treat AML residual disease. Significance: AraC-resistant AML cells exhibit metabolic features and gene signatures consistent with a high OXPHOS status. In these cells, targeting mitochondrial metabolism through the CD36–FAO–OXPHOS axis induces an energetic shift toward low OXPHOS and strongly enhanced antileukemic effects of AraC, offering a promising avenue to design new therapeutic strategies and fight AraC resistance in AML. Cancer Discov; 7(7); 716–35. ©2017 AACR. See related commentary by Schimmer, p. 670. This article is highlighted in the In This Issue feature, p. 653

Noble metal nanoparticles supporting plasmonic resonances behave as efficient nanosources of light, heat and energetic electrons. Owing to these properties, they offer a unique playground to trigger chemical reactions on the nanoscale. In this tutorial review, we discuss how nanoplasmonics can benefit chemistry and review the most recent developments in this new and fast growing field of research.

Materials engineered at the micro- and nanometer scales have had a tremendous and lasting impact in photonics and phononics. At much larger scales, natural soils civil engineered at decimeter to meter scales may interact with seismic waves when the global properties of the medium are modified, or alternatively thanks to a seismic metamaterial constituted of a mesh of vertical empty inclusions bored in the initial soil. Here, we show the experimental results of a seismic test carried out using seismic waves generated by a monochromatic vibrocompaction probe. Measurements of the particles' velocities show a modification of the seismic energy distribution in the presence of the metamaterial in agreement with numerical simulations using an approximate plate model. For complex natural materials such as soils, this large-scale experiment was needed to show the practical feasibility of seismic metamaterials and to stress their importance for applications in civil engineering. We anticipate this experiment to be a starting point for smart devices for anthropic and natural vibrations.

Magnetodielectric small spheres present unusual electromagnetic scattering features, theoretically predicted a few decades ago. However, achieving such behaviour has remained elusive, due to the non-magnetic character of natural optical materials or the difficulty in obtaining low-loss highly permeable magnetic materials in the gigahertz regime. Here we present unambiguous experimental evidence that a single low-loss dielectric subwavelength sphere of moderate refractive index (n=4 like some semiconductors at near-infrared) radiates fields identical to those from equal amplitude crossed electric and magnetic dipoles, and indistinguishable from those of ideal magnetodielectric spheres. The measured scattering radiation patterns and degree of linear polarization (3–9 GHz/33–100 mm range) show that, by appropriately tuning the a/λ ratio, zero-backward (‘Huygens’ source) or almost zero-forward (‘Huygens’ reflector) radiated power can be obtained. These Kerker scattering conditions only depend on a/λ. Our results open new technological challenges from nano- and micro-photonics to science and engineering of antennas, metamaterials and electromagnetic devices. The absence of forward or backward scattered radiation by magnetodielectric spheres was predicted decades ago, yet direct measurements have remained elusive. Geffrin et al. present unambiguous evidence of such scattering effects in the gigahertz range for a sub-wavelength dielectric sphere.

Phase imaging with a high-resolution wavefront sensor is considered. This is based on a quadriwave lateral shearing interferometer mounted on a non-modified transmission white-light microscope. The measurement technology is explained both in the scope of wave optics and geometrical optics in order to discuss its implementation on a conventional microscope. In particular we consider the effect of a non spatially coherent source on the phase-image signal-to-noise ratio. Precise measurements of the phase-shift introduced by microscopic beads or giant unilamellar vesicles validate the principle and show the accuracy of the methods. Diffraction limited images of living COS-7 cells are then presented, with a particular focus on the membrane and organelle dynamics.

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTMetal-Free Multicomponent Syntheses of PyridinesChristophe Allais, Jean-Marie Grassot, Jean Rodriguez*, and Thierry Constantieux*View Author Information Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397 MARSEILLE, France*E-mail: [email protected]*E-mail: [email protected]Cite this: Chem. Rev. 2014, 114, 21, 10829–10868Publication Date (Web):October 10, 2014Publication History Received19 February 2014Published online10 October 2014Published inissue 12 November 2014https://pubs.acs.org/doi/10.1021/cr500099bhttps://doi.org/10.1021/cr500099breview-articleACS PublicationsCopyright © 2014 American Chemical SocietyRequest reuse permissionsArticle Views9483Altmetric-Citations417LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Aldehydes,Aromatic compounds,Cations,Pyridines,Reaction products Get e-Alerts

We consider channel characterization for underwater wireless optical communication (UWOC) systems. We focus on the channel impulse response and, in particular, quantify the channel time dispersion for different water types, link distances, and transmitter/receiver characteristics, taking into account realistic parameters. We use the Monte Carlo approach to simulate the trajectories of emitted photons propagating in water from the transmitter towards the receiver. During their propagation, photons are absorbed or scattered as a result of their interaction with different particles present in water. To model angle scattering, we use the two-term Henyey–Greenstein model in our channel simulator. We show that this model is more accurate than the commonly used Henyey–Greenstein model, especially in pure sea waters. Through the numerical results that we present, we show that, except for highly turbid waters, the channel time dispersion can be neglected when working over moderate distances. In other words, under such conditions, we do not suffer from any inter-symbol interference in the received signal. Lastly, we study the performance of a typical UWOC system in terms of bit-error-rate using the simple on–off-keying modulation. The presented results give insight into the design of UWOC systems.

The temperature distribution throughout arrays of illuminated metal nanoparticles is investigated numerically and experimentally. The two cases of continuous and femtosecond-pulsed illumination are addressed. In the case of continuous illumination, two distinct regimes are evidenced: a temperature confinement regime, where the temperature increase remains confined at the vicinity of each nanosource of heat, and a temperature delocalization regime, where the temperature is uniform throughout the whole nanoparticle assembly despite the heat sources' nanometric size. We show that the occurrence of one regime or another simply depends on the geometry of the nanoparticle distribution. In particular, we derived (i) simple expressions of dimensionless parameters aimed at predicting the degree of temperature confinement and (ii) analytical expressions aimed at estimating the actual temperature increase at the center of an assembly of nanoparticles under illumination, preventing heavy numerical simulations. All these theoretical results are supported by experimental measurements of the temperature distribution on regular arrays of gold nanoparticles under illumination. In the case of femtosecond-pulsed illumination, we explain the two conditions that must be fulfilled to observe a further enhanced temperature spatial confinement.

Aims. The Euclid space telescope will measure the shapes and redshifts of galaxies to reconstruct the expansion history of the Universe and the growth of cosmic structures. The estimation of the expected performance of the experiment, in terms of predicted constraints on cosmological parameters, has so far relied on various individual methodologies and numerical implementations, which were developed for different observational probes and for the combination thereof. In this paper we present validated forecasts, which combine both theoretical and observational ingredients for different cosmological probes. This work is presented to provide the community with reliable numerical codes and methods for Euclid cosmological forecasts. Methods. We describe in detail the methods adopted for Fisher matrix forecasts, which were applied to galaxy clustering, weak lensing, and the combination thereof. We estimated the required accuracy for Euclid forecasts and outline a methodology for their development. We then compare and improve different numerical implementations, reaching uncertainties on the errors of cosmological parameters that are less than the required precision in all cases. Furthermore, we provide details on the validated implementations, some of which are made publicly available, in different programming languages, together with a reference training-set of input and output matrices for a set of specific models. These can be used by the reader to validate their own implementations if required. Results. We present new cosmological forecasts for Euclid . We find that results depend on the specific cosmological model and remaining freedom in each setting, for example flat or non-flat spatial cosmologies, or different cuts at non-linear scales. The numerical implementations are now reliable for these settings. We present the results for an optimistic and a pessimistic choice for these types of settings. We demonstrate that the impact of cross-correlations is particularly relevant for models beyond a cosmological constant and may allow us to increase the dark energy figure of merit by at least a factor of three.

With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root of the teleost lineage about 350 million years ago (Mya) and more recent WGD events in salmonids, carps, suckers and others. In plants and animals, WGD events are associated with adaptive radiations and evolutionary innovations. WGD-spurred innovation may be especially relevant in the case of teleost fish, which colonized a wide diversity of habitats on earth, including many extreme environments. Fish biodiversity, the use of fish models for human medicine and ecological studies, and the importance of fish in human nutrition, fuel an important need for the characterization of gene expression repertoires and corresponding evolutionary histories of ray-finned fish genes. To this aim, we performed transcriptome analyses and developed the PhyloFish database to provide (i) de novo assembled gene repertoires in 23 different ray-finned fish species including two holosteans (i.e. a group that diverged from teleosts before TGD) and 21 teleosts (including six salmonids), and (ii) gene expression levels in ten different tissues and organs (and embryos for many) in the same species. This resource was generated using a common deep RNA sequencing protocol to obtain the most exhaustive gene repertoire possible in each species that allows between-species comparisons to study the evolution of gene expression in different lineages. The PhyloFish database described here can be accessed and searched using RNAbrowse, a simple and efficient solution to give access to RNA-seq de novo assembled transcripts.

Abstract The Square Kilometre Array (SKA) is a planned large radio interferometer designed to operate over a wide range of frequencies, and with an order of magnitude greater sensitivity and survey speed than any current radio telescope. The SKA will address many important topics in astronomy, ranging from planet formation to distant galaxies. However, in this work, we consider the perspective of the SKA as a facility for studying physics. We review four areas in which the SKA is expected to make major contributions to our understanding of fundamental physics: cosmic dawn and reionisation; gravity and gravitational radiation; cosmology and dark energy; and dark matter and astroparticle physics. These discussions demonstrate that the SKA will be a spectacular physics machine, which will provide many new breakthroughs and novel insights on matter, energy, and spacetime.

Motivation: Recent years have witnessed an exponential growth in the number of identified interactions between biological molecules. These interactions are usually represented as large and complex networks, calling for the development of appropriated tools to exploit the functional information they contain. Random walk with restart (RWR) is the state-of-the-art guilt-by-association approach. It explores the network vicinity of gene/protein seeds to study their functions, based on the premise that nodes related to similar functions tend to lie close to each other in the networks. Results: In this study, we extended the RWR algorithm to multiplex and heterogeneous networks. The walk can now explore different layers of physical and functional interactions between genes and proteins, such as protein-protein interactions and co-expression associations. In addition, the walk can also jump to a network containing different sets of edges and nodes, such as phenotype similarities between diseases. We devised a leave-one-out cross-validation strategy to evaluate the algorithms abilities to predict disease-associated genes. We demonstrate the increased performances of the multiplex-heterogeneous RWR as compared to several random walks on monoplex or heterogeneous networks. Overall, our framework is able to leverage the different interaction sources to outperform current approaches. Finally, we applied the algorithm to predict candidate genes for the Wiedemann-Rautenstrauch syndrome, and to explore the network vicinity of the SHORT syndrome. Availability and implementation: The source code is available on GitHub at: https://github.com/alberto-valdeolivas/RWR-MH. In addition, an R package is freely available through Bioconductor at: http://bioconductor.org/packages/RandomWalkRestartMH/. Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract We identify the impact of intermediate goods markets imperfections on productivity downstream. Our empirical specification is based on a model of multifactor productivity (MFP) growth in which the effects of upstream competition can vary with distance to frontier. This model is estimated on a panel of fifteen OECD countries and twenty industries over 1985 to 2007. Competitive pressures are proxied with industry product market regulation data. We find evidence that anticompetitive upstream regulations have significantly curbed MFP growth over the past fifteen years, and more strongly so for observations that are close to the productivity frontier.

Light absorption and scattering of plasmonic metal nanoparticles can lead to non-equilibrium charge carriers, intense electromagnetic near-fields, and heat generation, with promising applications in a vast range of fields, from chemical and physical sensing to nanomedicine and photocatalysis for the sustainable production of fuels and chemicals. Disentangling the relative contribution of thermal and non-thermal contributions in plasmon-driven processes is, however, difficult. Nanoscale temperature measurements are technically challenging, and macroscale experiments are often characterized by collective heating effects, which tend to make the actual temperature increase unpredictable. This work is intended to help the reader experimentally detect and quantify photothermal effects in plasmon-driven chemical reactions, to discriminate their contribution from that due to photochemical processes and to cast a critical eye on the current literature. To this aim, we review, and in some cases propose, seven simple experimental procedures that do not require the use of complex or expensive thermal microscopy techniques. These proposed procedures are adaptable to a wide range of experiments and fields of research where photothermal effects need to be assessed, such as plasmonic-assisted chemistry, heterogeneous catalysis, photovoltaics, biosensing, and enhanced molecular spectroscopy.