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Identifying the footprints of selection in coding sequences can inform about the importance and function of individual sites. Analyses of the ratio of non-synonymous to synonymous sub-stitutions (dN/dS) have been widely used to pinpoint changes in the intensity of selection, but cannot distinguish them from changes in the direction of selection, i.e., changes in the fitness of specific amino acids at a given position. A few methods that rely on amino acid profiles to detect changes in directional selection have been designed, but their performance have not been well characterized. In this paper, we investigate the performance of 6 of these methods. We evaluate them on simulations along empirical phylogenies in which transition events have been annotated, and compare their ability to detect sites that have undergone changes in the direction or intensity of selection to that of a widely used dN/dS approach, codeml’s branch-site model A. We show that all methods have reduced performance in the presence of biased gene conversion but not CpG hypermutability. The best profile method, Pelican, a new implementation of [Tamuri et al., 2009], performs as well as codeml in a range of conditions except for detecting relaxations of selection, and performs better when tree length increases, or in the presence of persistent positive selection. It is fast, enabling genome-scale searches for site-wise changes in the direction of selection associated with phenotypic changes.

Iron phosphate materials have attracted a lot of attention due to their potential as cathode materials for lithium-ion rechargeable batteries. It has been shown that lithium insertion or extraction depends on the Fe mixed valence and reduction or oxidation of the Fe ions' valences. In this paper, we report a new synthesis method for the Fe

While the genomic positions and the patterns of activity of enhancer elements can now be efficiently determined, predicting their target genes remains a difficult task. Although chromatin conformation capture data has revealed numerous long-range regulatory interactions between genes and enhancers, enhancer target genes are still traditionally inferred based on genomic proximity. This approach is at the basis of GREAT, a widely used tool for analyzing the functional significance of sets of cis-regulatory elements. Here, we propose a new tool, named GOntact, which infers regulatory relationships using promoter-capture Hi-C (PCHi-C) data and uses these predictions to derive Gene Ontology enrichments for sets of cis-regulatory elements. We apply GOntact on enhancer and PCHi-C data from human and mouse and show that it generates functional annotations that are coherent with the patterns of activity of enhancers. We find that there is substantial overlap between functional predictions obtained with GREAT and GOntact but that each method can yield unique testable hypotheses, reflecting the underlying differences in target gene assignment. With the increasing availability of high-resolution chromatin contact data, we believe that GOntact can provide better-informed functional predictions for cis-regulatory elements.

In this paper, we revisit the high-pressure behavior of BaZrO3 by a combination of first-principle calculations, Raman spectroscopy, and x-ray diffraction under high pressure. We confirm experimentally the cubic-to-tetragonal transition at 10 GPa and find no evidence for any other phase transition up to 45 GPa, the highest pressures investigated, at variance with past reports. We re-investigate phase stability with density functional theory considering not only the known tetragonal (I4/mcm) phase but also other potential antiferrodistortive candidates. This shows that the tetragonal phase becomes progressively more stable upon increasing pressure as compared to phases with more complex tilt systems. The possibility for a second transition to another tilted phase at higher pressures, and in particular to the very common orthorhombic Pnma structure, is therefore ruled out.

Interspecific hybridization is often seen as a genomic stress that may lead to new gene expression patterns and deregulation of transposable elements (TEs). The understanding of expression changes in hybrids compared with parental species is essential to disentangle their putative role in speciation processes. However, to date we ignore the detailed mechanisms involved in genomic deregulation in hybrids. We studied the ovarian transcriptome and epigenome of the Drosophila buzzatii and Drosophila koepferae species together with their F1 hybrid females. We found a trend toward underexpression of genes and TE families in hybrids. The epigenome in hybrids was highly similar to the parental epigenomes and showed intermediate histone enrichments between parental species in most cases. Differential gene expression in hybrids was often associated only with changes in H3K4me3 enrichments, whereas differential TE family expression in hybrids may be associated with changes in H3K4me3, H3K9me3, or H3K27me3 enrichments. We identified specific genes and TE families, which their differential expression in comparison with the parental species was explained by their differential chromatin mark combination enrichment. Finally, cis–trans compensatory regulation could also contribute in some way to the hybrid deregulation. This work provides the first study of histone content in Drosophila interspecific hybrids and their effect on gene and TE expression deregulation.

International audience; Artificial light at night (ALAN) affects numerous physiological and behavioural mechanisms in various species by po- tentially disturbing circadian timekeeping systems and modifying melatonin levels. However, given the multiple direct and indirect effects of ALAN on organisms, large-scale transcriptomic approaches are essential to assess the global ef- fect of ALAN on biological processes. Moreover, although studies have focused mainly on variations in gene expression during the night in the presence of ALAN, it is necessary to investigate the effect of ALAN on gene expression during the day. In this study, we combined de novo transcriptome sequencing and assembly, and a controlled laboratory experi- ment to evaluate the transcriptome-wide gene expression response using high-throughput (RNA-seq) in Bufo bufo tad- poles exposed to ecologically relevant light levels. Here, we demonstrated for the first time that ALAN affected gene expression at night (3.5% and 11% of differentially expressed genes when exposed to 0.1 and 5 lx compared to con- trols, respectively), but also during the day (11.2% of differentially expressed genes when exposed to 5 lx compared to controls) with a dose-dependent effect. ALAN globally induced a downregulation of genes (during the night, 58% and 62% of the genes were downregulated when exposed to 0.1 and 5 lx compared to controls, respectively, and dur- ing the day, 61.2% of the genes were downregulated when exposed to 5 lx compared to controls). ALAN effects were detected at very low levels of illuminance (0.1 lx) and affected mainly genes related to the innate immune system and, to a lesser extend to lipid metabolism. These results provide new insights into understanding the effects of ALAN on organism. ALAN impacted the expression of genes linked to a broad range of physiological pathways at very low levels of ALAN during night-time and during daytime, potentially resulting in reduced immune capacity under environmen- tal immune challenges.

Materials 15(22), 8059 (2022). doi:10.3390/ma15228059, Iron phosphate materials have attracted a lot of attention due to their potential as cathode materials for lithium-ion rechargeable batteries. It has been shown that lithium insertion or extraction depends on the Fe mixed valence and reduction or oxidation of the Fe ions’ valences. In this paper, we report a new synthesis method for the Fe$_3$(PO$_3$OH)$_4$(H$_2$O)$_4$ mixed valence iron phosphate. In addition, we perform temperature-dependent measurements of structural and physical properties in order to obtain an understanding of electronic–structural interplay in this compound. Scanning electron microscope images show needle-like single crystals of 50 μm to 200 μm length which are stable up to approximately 200 °C, as revealed by thermogravimetric analysis. The crystal structure of Fe$_3$(PO$_3$OH)$_4$(H$_2$O)$_4$ single crystals has been determined in the temperature range of 90 K to 470 K. A monoclinic isostructural phase transition was found at ~213 K, with unit cell volume doubling in the low temperature phase. While the local environment of the Fe$^{2+}$ ions does not change significantly across the structural phase transition, small antiphase rotations occur for the Fe$^{3+}$ octahedra, implying some kind of electronic order. These results are corroborated by first principle calculations within density functional theory, which also point to ordering of the electronic degrees of freedom across the transition. The structural phase transition is confirmed by specific heat measurements. Moreover, hints of 3D antiferromagnetic ordering appear below ~11 K in the magnetic susceptibility measurements. Room temperature visible light absorption is consistent with the Fe$^{2+}$/Fe$^ {3+}$ mixed valence., Published by MDPI, Basel

In this study, we report an experimental investigation of (Gd1−xYbx)2O3 under high pressure by means of Raman scattering measurements complemented with ab initio calculations in pure Gd2O3. Raman spectroscopy of compressed (Gd1−xYbx)2O3 (x = 0.11) revealed a first phase transition from the cubic Ia 3 phase (C-type) to the monoclinic C2/m phase (B-type) at 6.2 GPa followed by a second phase transition towards the trigonal P 3 m1 phase (A-type) at 9.8 GPa. This sequence of phase transitions is different to that previously reported for pure Gd2O3. A phase transition from the trigonal to the monoclinic phase is observed on downstroke, so the B-type phase remains metastable at room pressure, as observed in all C-type rare earth sesquioxides. Theoretical calculations have helped to identify the different polymorphs and to assign the symmetry of the observed first-order Raman-active modes in the three phases. The pressure coefficients of the Raman-active modes of the three phases followed under pressure have been reported and compared to those of pure Gd2O3 and other rare-earth sesquioxides.

Artificial light at night (ALAN) affects numerous physiological and behavioural mechanisms in various species by potentially disturbing circadian timekeeping systems. Although gene-specific approaches have already shown the deleterious effect of ALAN on the circadian clock, immunity and reproduction, large-scale transcriptomic approaches with ecologically relevant light levels are still lacking to assess the global impact of ALAN on biological processes. Moreover, studies have focused mainly on variations in gene expression during the night in the presence of ALAN but never during the day. In a controlled laboratory experiment, transcriptome sequencing of Bufo bufo tadpoles revealed that ALAN affected gene expression at both night and daytime with a dose-dependent effect and globally induced a downregulation of genes. ALAN effects were detected at very low levels of illuminance (0.1 lux) and affected mainly genes related to the innate immune system and, to a lesser extend to lipid metabolism. These results indicate that a broad range of physiological pathways is impacted at the molecular level by very low levels of ALAN potentially resulting in reduced survival under environmental immune challenges.

International audience; BaTiO3-based crystal fibres with mm-sized grains were grown by the micro-pulling down technique from the BaTiO3–CaTiO3–BaZrO3 solid solution with pulling velocities of about 6, 9 and 15 mm h−1. The natural growth direction was identified as (001)pc. For the pulling velocities of about 15 mm h−1 and 9 mm h−1, effective partition coefficients have been calculated from Castaing micro-probe measurements, and gave, respectively, 1.3 and 2 for Zr, and 0.95 and 0.9 for Ca. Laser-induced breakdown spectroscopy measurements reveal a strong inhomogeneity and variations of Zr contents while Ca contents show an opposite variation trend with a more steady distribution. Coexistence of two crystallized perovskite solid solutions is suggested. Most efficient polycrystals with mm-sized grains and 0.5 mol% Zr and 11 mol% Ca as average contents exhibit Curie temperatures higher than 113 °C, electromechanical coupling factors kt up to 41% and piezoelectric charge coefficients d33 up to 242 pC N−1 at room temperature. These values are similar to piezoelectric coefficients reported in the literature for oriented flux-grown single crystals with close compositions. Both chemical and physical results obtained in the BCTZ system make the μ-PD technique a promising way to improve the piezoelectric response of lead-free solid solution-based single crystals.

The SARS-CoV-2 epidemic in France has focused a lot of attention as it has had one of the largest death tolls in Europe. It provides an opportunity to examine the effect of the lockdown and of other events on the dynamics of the epidemic. In particular, it has been suggested that municipal elections held just before lockdown was ordered may have helped spread the virus. In this manuscript we use Bayesian models of the number of deaths through time to study the epidemic in 13 regions of France. We found that the models accurately predict the number of deaths 2 to 3 weeks in advance, and recover estimates that are in agreement with recent models that rely on a different structure and different input data. In particular, the lockdown reduced the viral reproduction number by ≈ 80%. However, using a mixture model, we found that the lockdown had had different effectiveness depending on the region, and that it had been slightly more effective in decreasing the reproduction number in denser regions. The mixture model predicts that 2.08 (95% CI: 1.85-2.47) million people had been infected by May 11, and that there were 2567 (95% CI: 1781-5182) new infections on May 10. We found no evidence that the reproduction numbers differ between week-ends and week days, and no evidence that the reproduction numbers increased on the election day. Finally, we evaluated counterfactual scenarios showing that ordering the lockdown 1 to 7 days sooner would have resulted in 19% to 76% fewer deaths, but that ordering it 1 to 7 days later would have resulted in 21% to 266% more deaths. Overall, the predictions of the model indicate that holding the elections on March 15 did not have a detectable impact on the total number of deaths, unless it motivated a delay in imposing the lockdown.

The search for new biomarkers and drug targets for hepatocellular carcinoma (HCC) has spurred an interest in long non-coding RNAs (lncRNAs), often proposed as oncogenes or tumor suppressors. Furthermore, lncRNA expression patterns can bring insights into the global de-regulation of cellular machineries in tumors. Here, we examine lncRNAs in a large HCC cohort, comprising RNA-seq data from paired tumor and adjacent tissue biopsies from 114 patients. We find that numerous lncRNAs are differentially expressed between tumors and adjacent tissues and between tumor progression stages. Although we find strong differential expression for most lncRNAs previously associated with HCC, the expression patterns of several prominent HCC-associated lncRNAs disagree with their previously proposed roles. We examine the genomic characteristics of HCC-expressed lncRNAs and reveal an enrichment for repetitive elements among the lncRNAs with the strongest expression increases in advanced-stage tumors. This enrichment is particularly striking for lncRNAs that overlap with satellite repeats, a major component of centromeres. Consistently, we find increased non-coding RNA transcription from centromeres in tumors, in the majority of patients, suggesting that aberrant centromere activation takes place in HCC.

International audience; Highly textured cm-sized (Ba1−xCax)TiO3 (x = 0.05) polycrystals at off-eutectic composition were grown by the micro-pulling down freezing technique from a BaTiO3–CaTiO3 system at a high pulling velocity of about 48 mm h−1. Textured polycrystals exhibiting submillimetre-sized dendrites along the (110)pc growth direction and geometrical grains along the (100)pc direction were revealed by a complementary analysis performed by Laue diffraction and EBSD techniques. An average Ca content of about x = 0.0435 was measured throughout the whole volume of the boule and led to an effective partition coefficient of Ca of about 0.87. LIBS measurements highlighted the local segregation of Ca and major impurity contents within dendrites, grains and at the grain boundaries. Dielectric and piezoelectric measurements performed on oriented polycrystalline textured samples led to Curie temperatures up to 116 °C and d33 up to 214 pC N−1, in very good agreement with literature values. Both chemical and physical results obtained in the BCT system make the μ-PD technique a promising and alternative way to improve the piezoelectric response of lead-free solid solution-based crystals through their texturing along preferential crystallographic directions.

We report a joint experimental and theoretical investigation of the high pressure structural and vibrational properties of terbium sesquioxide (Tb2O3). Powder X-ray diffraction and Raman scattering measurements show that cubic Ia3̅ (C-type) Tb2O3 undergoes two phase transitions up to 25 GPa. We observe a first irreversible reconstructive transition to the monoclinic C2/m (B-type) phase at ∼7 GPa and a subsequent reversible displacive transition from the monoclinic to the trigonal P3̅m1 (A-type) phase at ∼12 GPa. Thus, Tb2O3 is found to follow the well-known C → B → A phase transition sequence found in other cubic rare earth sesquioxides with cations of larger atomic mass than Tb. Our ab initio theoretical calculations predict phase transition pressures and bulk moduli for the three phases in rather good agreement with experimental results. Moreover, Raman-active modes of the three phases have been monitored as a function of pressure, while lattice-dynamics calculations have allowed us to confirm the assignment of the experimental phonon modes in the C- and A-type phases as well as to make a tentative assignment of the symmetry of most vibrational modes in the B-type phase. Finally, we extract the bulk moduli and the Raman-active mode frequencies together with their pressure coefficients for the three phases of Tb2O3. These results are thoroughly compared and discussed in relation to those reported for rare earth and other related sesquioxides as well as with new calculations for selected sesquioxides. It is concluded that the evolution of the volume and bulk modulus of all the three phases of these technologically relevant compounds exhibit a nearly linear trend with respect to the third power of the ionic radii of the cations and that the values of the bulk moduli for the three phases depend on the filling of the f orbitals., High pressure powder X-ray diffraction and Raman scattering measurements show that cubic Tb2O3 undergoes a phase transition to a monoclinic phase at ∼7 GPa and to a trigonal phase above ∼12 GPa. The measured bulk modulus and the pressure dependence of the phonon modes for the 3 phases are supported by density functional theory calculations. The obtained results are compared to those reported for other rare earth and related sesquioxides.

International audience; Piezoelectric single crystals based on the perovskite ferroelectric system (K,Na)NbO3 have been widely investigated over the past 20 years due to large piezoelectric coefficients, high transition temperatures, low density, and the nontoxic chemical composition. Various crystal growth methods were examined, including high-temperature solution growth, solid-state crystal growth, Bridgman–Stockbarger method, and the floating zone method. Increased understanding of the crystal growth process and post-growth treatments resulted in improved crystal quality and larger sizes. Recently, crystals with high piezoelectric and electromechanical coupling coefficients exceeding 1000 pC/N and 0.90, respectively, were reported. Moreover, their large potential for high-frequency ultrasonic medical imaging was demonstrated. This work provides a review of the development of piezoelectric (K,Na)NbO3-based single crystals, including their growth, defect chemistry, domain structures, electromechanical properties, and applications. Approaches for reducing growth defects, controlling point defects, and domain engineering are discussed. The remaining open issues are presented and an outlook on the future is provided.

International audience; A new technology for the mass production of lithium molybdate (Li2MoO4) crystals needed for the realization of the cryogenic neutrinoless double-beta decay detectors is under development within the framework of the CLYMENE project. Crystals with 4 and 5 cm in diameter were grown in two different Czochralski configurations. The first configuration, based on inductive heating of a RF coil coupled with a platinum crucible, was used to grow crystals of 4 cm in diameter. Bolometric tests performed with two samples cut from a 230 g crystal have shown less performances of the large sample (158 g), which had a cleavage, as compared to the small non-cracked sample (13.5 g). Numerical 2 modeling was applied to investigate the temperature field in the furnace, the melt convection and thermo-elastic stresses in the crystal. Numerical results reveal 30% higher thermal stress at the bottom part of the ingot in the case of a concave shape of the crystal tail (experimental case) as compared to the case of a convex shaped tail. This could explain why the fracture started at the bottom part of the 230 g crystal boule, and highlights the importance of the crystal shape in the last stage of growth process. The furnace configuration used to grow 5 cm-diameter crystals was numerically optimized in order to reduce the thermal stress in the crystals. The first kg-mass Li2MoO4 ingot grown in the optimized configuration exhibit regular shape and good structural quality.

International audience; The aqueous solution growth of mm-sized, pure, 17O- or D-enriched herbertsmithite ZnxCu4-x(OH)6Cl2 single crystals is presented. A relationship between x values, antisite disorder amounts and the growth temperature is established. The crystal chemical composition and stability, structural phase and antisite disorder amounts have been characterized by powder X-ray diffraction (XRD), X-ray Photoelectron Spectroscopy (XPS), Electron Probe Micro Analysis/Wavelength Dispersive Spectroscopy (EPMA/WDS), Inductively Coupled Plasma/Atomic Emission Spectroscopy analysis (ICP/AES), coupled Thermo Gravimetric Analysis-Mass Spectrometry (TGA/MS) and magnetic susceptibility measurements. An unambiguous relationship between the c lattice parameter and the x value has been found.

We report a joint experimental and theoretical investigation of the high pressure structural and vibrational properties of terbium sesquioxide (Tb2O3). Powder X-ray diffraction and Raman scattering measurements show that cubic Ia3̅ (C-type) Tb2O3 undergoes two phase transitions up to 25 GPa. We observe a first irreversible reconstructive transition to the monoclinic C2/m (B-type) phase at ∼7 GPa and a subsequent reversible displacive transition from the monoclinic to the trigonal P3̅m1 (A-type) phase at ∼12 GPa. Thus, Tb2O3 is found to follow the well-known C → B → A phase transition sequence found in other cubic rare earth sesquioxides with cations of larger atomic mass than Tb. Our ab initio theoretical calculations predict phase transition pressures and bulk moduli for the three phases in rather good agreement with experimental results. Moreover, Raman-active modes of the three phases have been monitored as a function of pressure, while lattice-dynamics calculations have allowed us to confirm the assignment of the experimental phonon modes in the C- and A-type phases as well as to make a tentative assignment of the symmetry of most vibrational modes in the B-type phase. Finally, we extract the bulk moduli and the Raman-active mode frequencies together with their pressure coefficients for the three phases of Tb2O3. These results are thoroughly compared and discussed in relation to those reported for rare earth and other related sesquioxides as well as with new calculations for selected sesquioxides. It is concluded that the evolution of the volume and bulk modulus of all the three phases of these technologically relevant compounds exhibit a nearly linear trend with respect to the third power of the ionic radii of the cations and that the values of the bulk moduli for the three phases depend on the filling of the f orbitals., The authors are thankful for the financial support of Generalitat Valenciana under Project PROMETEO 2018/ 123-EFIMAT and of the Spanish Ministerio de Economiá y Competitividad under Projects MAT2015-71035-R, MAT2016-75586-C4-2/3/4-P, and FIS2017-2017-83295-P as well as MALTA Consolider Team research network under project RED2018-102612-T. J.A.S. also acknowledges the Ramón y Cajal program for funding support through RYC- 2015-17482. A.M. and P.R.-H. acknowledge computing time provided by Red Española de Supercomputación (RES) and the MALTA Consolider Team cluster. HP-XRD experiments were performed at MPSD beamline of Alba Synchrotron (experiment no. 2016071772).

Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. Here, we describe an efficient pipeline to accurately recover TE insertion (TEI) sites and sequences from long reads obtained by Oxford Nanopore Technology (ONT) sequencing. With this pipeline, we could precisely describe the landscapes of the most recent TEIs in wild-type strains of Drosophila melanogaster and Drosophila simulans. Their comparison suggests that this subset of TE sequences is more similar than previously thought in these two species. The chromosome assemblies obtained using this pipeline also allowed recovering piRNA cluster sequences, which was impossible using short-read sequencing. Finally, we used our pipeline to analyze ONT sequencing data from a D. melanogaster unstable line in which LTR transposition was derepressed for 73 successive generations. We could rely on single reads to identify new insertions with intact target site duplications. Moreover, the detailed analysis of TEIs in the wild-type strains and the unstable line did not support the trap model claiming that piRNA clusters are hotspots of TE insertions., This research was funded by the Fondation pour la Recherche Médicale, grant number “DEQ20180339167” to S.C, by the ANR Exhyb to C.V., by the CNRS.

Mechanistic modeling approaches, such as the toxicokinetic-toxicodynamic (TKTD) framework, are promoted by international institutions such as the European Food Safety Authority and the Organization for Economic Cooperation and Development to assess the environmental risk of chemical products generated by human activities. TKTD models can encompass a large set of mechanisms describing the kinetics of compounds inside organisms (e.g., uptake and elimination) and their effect at the level of individuals (e.g., damage accrual, recovery, and death mechanism). Compared to classical dose-response models, TKTD approaches have many advantages, including accounting for temporal aspects of exposure and toxicity, considering data points all along the experiment and not only at the end, and making predictions for untested situations as realistic exposure scenarios. Among TKTD models, the general unified threshold model of survival (GUTS) is within the most recent and innovative framework but is still underused in practice, especially by risk assessors, because specialist programming and statistical skills are necessary to run it. Making GUTS models easier to use through a new module freely available from the web platform MOSAIC (standing for MOdeling and StAtistical tools for ecotoxIClogy) should promote GUTS operability in support of the daily work of environmental risk assessors. This paper presents the main features of MOSAIC_GUTS: uploading of the experimental data, GUTS fitting analysis, and LCx estimates with their uncertainty. These features will be exemplified from literature data. Integr Environ Assess Manag 2018;14:625-630. © 2018 SETAC.

International audience; Lithium molybdate Li2MoO4 (LMO) crystals of mass ranging between 350 and 500 g are excellent candidates to build heat-scintillation cryogenic bolometers likely to be used for the detection of rare events in astroparticle physics. In this work, numerical modeling is applied in order to investigate the Czochralski growth of Li2MoO4 crystals in an inductive furnace. The numerical model was validated by comparing the numerical predictions of the crystal-melt interface shape to experimental visualization of the growth interface. Modeling was performed for two different Czochralski furnaces that use inductive heating. The simulation of the first furnace, which was used to grow Li2MoO4 crystals of 3–4 cm in diameter, reveals non-optimal heat transfer conditions for obtaining good quality crystals. The second furnace, which will be used to grow crystals of 5 cm in diameter, was numerically optimized in order to reduce the temperature gradients in the crystal and to avoid fast crystallization of the bath at the later stages of the growth process.

A new R&D on lithium molybdate scintillators has begun within a project CLYMENE (Czochralski growth of Li 2 MoO 4 crYstals for the scintillating boloMeters used in the rare EveNts sEarches). One of the main goals of the CLYMENE is a realization of a Li 2 MoO 4 crystal growth line to be complementary to the one recently developed by LUMINEU in view of a mass production capacity for CUPID, a next-generation tonne-scale bolometric experiment to search for neutrinoless double-beta decay. In the present paper we report the investigation of performance and radiopurity of 158-g and 13.5-g scintillating bolometers based on a first large-mass (230 g) Li 2 MoO 4 crystal scintillator developed within the CLYMENE project. In particular, a good energy resolution (2–7 keV FWHM in the energy range of 0.2–5 MeV), one of the highest light yield (0.97 keV/MeV) amongst Li 2 MoO 4 scintillating bolometers, an efficient alpha particles discrimination (10 σ ) and potentially low internal radioactive contamination (below 0.2–0.3 mBq/kg of U/Th, but 1.4 mBq/kg of 210Po) demonstrate prospects of the CLYMENE in the development of high quality and radiopure Li 2 MoO 4 scintillators for CUPID.

${\mathrm{BaZrO}}_{3}$ is a perovskite that remains in the simple cubic phase at all temperatures, hence with no first-order Raman-active phonon mode allowed by symmetry. Yet, it exhibits an intense Raman spectrum with sharp and well-defined features. Here, we report the evolution of the Raman spectrum of ${\mathrm{BaZrO}}_{3}$ single crystals in a broad temperature range (4--1200 K) and discuss its origin with the support of detailed first-principle calculations of the lattice dynamics. Phonon calculations are performed not only for the cubic phase of ${\mathrm{BaZrO}}_{3}$, but also for the low-symmetry phases with octahedra tilts that have been suspected to exist at the nanoscale. We show that the Raman spectrum shows no direct evidence for these nanodomains, but can instead be explained by classical second-order Raman scattering. We provide an assignment of the dominant features to phonon mode combinations. In particular, we show that the high frequency range of the spectrum is dominated by overtones and shows an image of the phonon density of states corresponding to the stretching modes of the oxygen octahedra.

In evolutionary genomics, researchers have taken an interest in identifying substitutions that subtend convergent phenotypic adaptations. This is a difficult question that requires distinguishing foreground convergent substitutions that are involved in the convergent phenotype from background convergent substitutions. Those may be linked to other adaptations, may be neutral or may be the consequence of mutational biases. Furthermore, there is no generally accepted definition of convergent substitutions. Various methods that use different definitions have been proposed in the literature, resulting in different sets of candidate foreground convergent substitutions. In this article, we first describe the processes that can generate foreground convergent substitutions in coding sequences, separating adaptive from non-adaptive processes. Second, we review methods that have been proposed to detect foreground convergent substitutions in coding sequences and expose the assumptions that underlie them. Finally, we examine their power on simulations of convergent changes—including in the presence of a change in the efficacy of selection—and on empirical alignments. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions'.

The availability of bacterial pangenome data grows exponentially, requiring efficient new methods of analysis. Currently popular approaches for the fast comparison of genomes have the drawback of not being based on explicit evolutionary models of diversification. Making sense of bacterial genome evolution, and notably in the accessory genome, requires however to take into account the complex processes by which the genomes evolve. Here we present the Pantagruel bioinformatic software pipeline, which enables the construction of a complete bacterial pangenome database geared towards the inference of gene evolution scenarios using gene tree/species tree reconciliation. Pantagruel is a modular pipeline that combines state-of-the-art external software with unique new methods. It can be executed with no supervision to perform a standard pangenome analysis, or be configured by advanced users to integrate methods of choice. A relational database underlies its data structure, allowing efficient retrieval of the large-scale data generated by integrative analyses of pangenome evolutionary history. From the reconstructed gene evolution scenarios, two main outputs are derived: firstly the gene tree-aware assignation of orthology, allowing the fine analysis of gene gain and loss history over the species phylogeny, and secondly a network of gene-to-gene association based on correlated events in scenarios of gene evolution, leading to the definition of co-evolved gene modules. Pantagruel is available as an open source software package at https://github.com/flass/pantagruel.

In evolutionary genomics, researchers have taken an interest in identifying in the genomes substitutions that subtend convergent phenotypic adaptations. This is a difficult question to address, because genomes contain billions of sites, many of which have substituted in the lineages where the adaptations took place, and yet are not linked to them. Those extra substitutions may be linked to other adaptations, may be neutral, or may be linked to mutational biases. Furthermore, one can think of various ways of defining substitutions of interest, and various methods that match those definitions have been used, resulting in different sets of candidate substitutions. In this manuscript we first clarify how adaptation to convergent phenotypic evolution can manifest itself in coding sequences. Second, we review methods that have been proposed to detect convergent adaptive evolution in coding sequences and expose the assumptions that underlie them. Finally, we examine their power on simulations of convergent changes, including in the presence of a confounding factor.

International audience; We report the growth of BaZrO3 single crystals by the optical floating zone technique and the investigation on its flux growth using BaB2O4 as a solvent. 6 mm long colorless and transparent single crystals were obtained with a mirror furnace without the need for post-treatment annealing. Its properties are determined and compared with those of two commercial crystals grown by the tri-arc Czochralski method. The chemical composition was investigated using glow discharge mass spectrometry (GDMS) and secondary ion mass spectrometry (SIMS), which indicate minor impurities of Sr, Hf, Ca and Ti, with maximal concentrations for Sr and Hf in the range of 0.3–0.5% at. The optical band gap determined by UV-visible spectroscopy is found to be ∼4.8 eV and indicates the high quality of the BaZrO3 crystals grown by the optical floating zone technique. Raman spectroscopy at ambient conditions and at low temperatures down to 4.2 K reveals a relatively sharp second-order spectrum and does not reveal any structural phase transition. Prospective high-temperature solution growth using BaB2O4 self-flux was investigated and led to 150–200 μm BaZrO3 crystals. This solvent opens the way to grow BaZrO3 at half its melting point by the flux method.

International audience; La2NiO4+δ is a mixed ionic–electronic conducting material with the 2D K2NiF4-type structure garnering much interest as a potential intermediate-temperature solid-oxide fuel cell (IT-SOFC) cathode. The oxygen diffusion along the ab-plane exhibiting the highest oxygen ionic conductivity governs the behavior of the bulk materials in this family of oxides. The oxygen surface exchange processes, however, are not well-understood and large differences in the surface exchange coefficient (k*) values can be found in the literature for this and other cathode materials. The isotopic exchange depth profiling (IEDP) technique was used in combination with low energy ion scattering (LEIS) measurements on two sets of La2NiO4+δ single crystals with precisely cut crystal faces but different thermal histories. For each set of single crystals, the oxygen diffusion and surface exchange coefficient were evaluated for two different orientations in the temperature range of 450–600 °C. The differences in k* have been correlated with differences in surface chemistry: surface termination, near-surface rearrangement, and the presence of extrinsic impurities. Finally, the predominant La termination at the immediate outer surface is evidenced, confirming recent results for other Ruddlesden–Popper phases with mixed ionic–electronic conducting properties.