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688,151 results on '"Centre National de la Recherche Scientifique (CNRS)"'

1. Parametrized uncertainties in the spectral function model of neutrino charged-current quasielastic interactions for oscillation analyses

Author: Universidad de Sevilla. Departamento de Física Atómica, Molecular y Nuclear, Agence Nationale de la Recherche. France, Ministry of Science and Higher Education. Poland, National Science Centre, Poland, Centre national de la recherche scientifique (CNRS). France, international inter universityresearch ICRR, Tokyo, Japan, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Junta de Andalucía, España, Chakrani, J., Dolan, S., Avanzini, M. Buizza, Ershova, A., Koch, L., McFarland, K., Megías Vázquez, Guillermo Daniel, Wret, C., Universidad de Sevilla. Departamento de Física Atómica, Molecular y Nuclear, Agence Nationale de la Recherche. France, Ministry of Science and Higher Education. Poland, National Science Centre, Poland, Centre national de la recherche scientifique (CNRS). France, international inter universityresearch ICRR, Tokyo, Japan, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Junta de Andalucía, España, Chakrani, J., Dolan, S., Avanzini, M. Buizza, Ershova, A., Koch, L., McFarland, K., Megías Vázquez, Guillermo Daniel, and Wret, C.
Abstract: A substantial fraction of systematic uncertainties in neutrino oscillation experiments stem from the lack of precision in modeling the nuclear target in neutrino-nucleus interactions. Whilst this has driven significant progress in the development of improved nuclear models for neutrino scattering, it is crucial that the models used in neutrino data analyses be accompanied by parameters and associated uncertainties that allow the coverage of plausible nuclear physics. Based on constraints from electron scattering data, we propose such a set of parameters, which can be applied to nuclear shell models, and test their application to the Benhar et al. [Nucl. Phys. A579, 493 (1994)] spectral function model. The parametrization is validated through a series of maximum likelihood fits to cross section measurements made by the T2K and MINERvA experiments, which also permit an exploration of the power of near-detector data to provide constraints on the parameters in neutrino oscillation analyses.
Published: 2024

2. Transcription-driven DNA supercoiling counteracts H-NS-mediated gene silencing in bacterial chromatin.

Author: Universidad de Sevilla. Departamento de Microbiología y Parasitología, Universidad de Sevilla. Departamento de Genética, Centre national de la recherche scientifique (CNRS). France, Agence Nationale de la Recherche. France, Ministerio de Ciencia e Innovación (MICIN). España, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Figueroa Bossi, Nara, Fernández Fernández, Rocío, Kerboriou, Patricia, Bouloc, Philippe, Casadesús Pursals, Josep, Sánchez Romero, María Antonia, Bossi, Lionello, Universidad de Sevilla. Departamento de Microbiología y Parasitología, Universidad de Sevilla. Departamento de Genética, Centre national de la recherche scientifique (CNRS). France, Agence Nationale de la Recherche. France, Ministerio de Ciencia e Innovación (MICIN). España, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Figueroa Bossi, Nara, Fernández Fernández, Rocío, Kerboriou, Patricia, Bouloc, Philippe, Casadesús Pursals, Josep, Sánchez Romero, María Antonia, and Bossi, Lionello
Abstract: In all living cells, genomic DNA is compacted through interactions with dedicated proteins and/or the formation of plectonemic coils. In bacteria, DNA compaction is achieved dynamically, coordinated with dense and constantly changing transcriptional activity. H-NS, a major bacterial nucleoid structuring protein, is of special interest due to its interplay with RNA polymerase. H-NS:DNA nucleoprotein filaments inhibit transcription initiation by RNA polymerase. However, the discovery that genes silenced by H-NS can be activated by transcription originating from neighboring regions has suggested that elongating RNA polymerases can disassemble H-NS:DNA filaments. In this study, we present evidence that transcription-induced counter-silencing does not require transcription to reach the silenced gene; rather, it exerts its effect at a distance. Counter-silencing is suppressed by introducing a DNA gyrase binding site within the intervening segment, suggesting that the long-range effect results from transcription-driven positive DNA supercoils diffusing toward the silenced gene. We propose a model wherein H-NS:DNA complexes form in vivo on negatively supercoiled DNA, with H-NS bridging the two arms of the plectoneme. Rotational diffusion of positive supercoils generated by neighboring transcription will cause the H-NS-bound negativelysupercoiled plectoneme to “unroll” disrupting the H-NS bridges and releasing H-NS.
Published: 2024

3. First measurement of muon neutrino charged-current interactions on hydrocarbon without pions in the final state using multiple detectors with correlated energy spectra at T2K

Author: Universidad de Sevilla. Departamento de Física Atómica, Molecular y Nuclear, Ministerio de Ciencia, Innovación y Universidades (MICINN). España, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Centre national de la recherche scientifique (CNRS). France, German Research Foundation (DFG), Istituto Nazionale di Fisica Nucleare (INFN) Italia, T2K Collaboration, Abe, K., Akhlaq, N., Akutsu, R., Alarakia-Charles, H., Ali, A., Alj Hakim, Y. I., Caballero Carretero, Juan Antonio, Franco Patiño, Juan Manuel, González Rosa, Jesús, Megías Vázquez, Guillermo Daniel, Universidad de Sevilla. Departamento de Física Atómica, Molecular y Nuclear, Ministerio de Ciencia, Innovación y Universidades (MICINN). España, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Centre national de la recherche scientifique (CNRS). France, German Research Foundation (DFG), Istituto Nazionale di Fisica Nucleare (INFN) Italia, T2K Collaboration, Abe, K., Akhlaq, N., Akutsu, R., Alarakia-Charles, H., Ali, A., Alj Hakim, Y. I., Caballero Carretero, Juan Antonio, Franco Patiño, Juan Manuel, González Rosa, Jesús, and Megías Vázquez, Guillermo Daniel
Abstract: This paper reports the first measurement of muon neutrino charged-current interactions without pions in the final state using multiple detectors with correlated energy spectra at T2K. The data was collected on hydrocarbon targets using the off-axis T2K near detector (ND280) and the on-axis T2K near detector (INGRID) with neutrino energy spectra peaked at 0.6 GeV and 1.1 GeV, respectively. The correlated neutrino flux presents an opportunity to reduce the impact of the flux uncertainty and to study the energy dependence of neutrino interactions. The extracted double-differential cross sections are compared to several Monte Carlo neutrino-nucleus interaction event generators showing the agreement between both detectors individually and with the correlated result.
Published: 2023

4. Multilayer models for hydrostatic Herschel-Bulkley viscoplastic flows

Author: Universidad de Sevilla. Departamento de Matemática Aplicada I (ETSII), Universidad de Sevilla. FQM120: Modelado Matemático y Simulación de Sistemas Medioambientales, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Gobierno de España, French National Research Agency (ANR), Centre national de la recherche scientifique (CNRS). France, Fernández Nieto, Enrique Domingo, Garres-Díaz, José, Vigneaux, Paul, Universidad de Sevilla. Departamento de Matemática Aplicada I (ETSII), Universidad de Sevilla. FQM120: Modelado Matemático y Simulación de Sistemas Medioambientales, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Gobierno de España, French National Research Agency (ANR), Centre national de la recherche scientifique (CNRS). France, Fernández Nieto, Enrique Domingo, Garres-Díaz, José, and Vigneaux, Paul
Abstract: Starting from Navier-Stokes’ equation we derive two shallow water multilayer models for yield stress fluids, depending on the asymptotic analysis. One of them takes into account the normal stress contributions, making possible to recover a pseudoplug layer instead of a purely plug zone. A specific numerical scheme is designed to solve this model thanks to a finite volume discretization. It involves well-balancing techniques to be able to compute accurately the transitions between yielded and unyielded (or pseudoplug) zones, an important feature of the original partial differential equations’ model. We perform numerical simulations on various test cases relevant to these physics: analytical solution of a uniform flow, steady solutions for arrested state, and a viscoplastic dam break. Simulations agree well when we perform comparisons with physical experiments of the group of Christophe Ancey (EPFL) and we make a comparative study including shallow water models and lubrication models that they present in Ancey et al. (2012) [3]. Thanks to the multilayer structure of our model, we can go further on the description of the vertical structure associated to the (bottom) sheared layer and the top (pseudo-)plug layer.
Published: 2023

5. Increasing the Scalability of Toxin-Intein Orthogonal Combinations

Author: Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular, Centre national de la recherche scientifique (CNRS). France, French Government, Fondation pour la Recherche Medicale, Ministerio de Ciencia e Innovación (MICIN). España, López Igual, Rocío, Dorado Morales, Pedro, Mazel, Didier, Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular, Centre national de la recherche scientifique (CNRS). France, French Government, Fondation pour la Recherche Medicale, Ministerio de Ciencia e Innovación (MICIN). España, López Igual, Rocío, Dorado Morales, Pedro, and Mazel, Didier
Abstract: Inteins are proteins embedded into host proteins from which they are excised in an autocatalytic reaction. Specifically, split inteins are separated into two independent fragments that reconstitute the host protein during the catalytic process. We recently developed a novel strategy for the specific killing of pathogenic and antibiotic resistant bacteria based on toxin-intein combinations. Bacterial type II toxin-antitoxin systems are protein modules in which the toxin can provoke cell death whereas the antitoxin inhibits toxin activity. Although our previous system was based on a split intein (iDnaE) and the CcdB toxin, we demonstrated that iDnaE is able to reconstitute four different toxins. To expand the applicability of our system by widening the repertoire of toxin-intein combinations for complex set-ups, we introduced a second intein, iDnaX, which was artificially split. We demonstrate that iDnaX is able to reconstitute the four toxins, and we manage to reduce its scar size to facilitate their use. In addition, we prove the orthogonality of both inteins (iDnaE and iDnaX) through a toxin reconstitution assay, thus opening the possibility for complex set-ups based on these toxin-intein modules. This could be used to develop specific antimicrobial and other biotechnological applications.
Published: 2023

6. Chemo-selective Stille-type coupling of acyl-chlorides upon phosphine-borane Au(i) catalysis

Author: Universidad de Sevilla. Departamento de Química Inorgánica, Centre national de la recherche scientifique (CNRS). France, Université Paul Sabatier (UPS), Agence Nationale de la Recherche. France, Hidalgo Reinoso, Nereida, Le Gac, Arnaud, Mallet-Ladeira, Sonia, Bouhadir, Ghenwa, Bourissou, Didier, Universidad de Sevilla. Departamento de Química Inorgánica, Centre national de la recherche scientifique (CNRS). France, Université Paul Sabatier (UPS), Agence Nationale de la Recherche. France, Hidalgo Reinoso, Nereida, Le Gac, Arnaud, Mallet-Ladeira, Sonia, Bouhadir, Ghenwa, and Bourissou, Didier
Abstract: Phosphine-boranes do not promote oxidative addition of acyl chlorides to gold, but the phosphine-borane gold triflimide complex [i Pr2P(o-C6H4)BCy2]AuNTf2 was found to catalyze the coupling of acyl chlorides and aryl stannanes. The reaction involves aryl/chloride-bridged dinuclear gold(I) complexes as key intermediates, as substantiated by spectroscopic and crystallographic analyses. Similar to Pd(0)/Pd(II)- catalyzed Stille coupling with phosphine-borane ligands, the gold-catalyzed variant shows complete chemoselectivity for acyl chlorides over aryl iodides and bromides, enabling straightforward access to halogenated aryl ketones.
Published: 2023

7. Marguerite Duras/Claude Régy: L’Amante Anglaise, genèse d’une écriture, gésine d’un théâtre

Author: Almuth Grésillon and Marie-Madeleine Mervant-Roux (Centre National de la Recherche Scientifique, CNRS – Paris, França)
Subjects: Genèse, Texte, Scène, Production, Inachèvement, Drama, PN1600-3307, Dramatic representation. The theater, PN2000-3307
Abstract: L’article prend pour objet la genèse de la première mise en scène de L’Amante Anglaise de Marguerite Duras due à Claude Régy, une genèse heureuse, du fait de l’influence réciproque entre l’écriture et la scène. Il affronte, sans la résoudre, une question théorique majeure de la critique génétique appliquée au théâtre: l’œuvre à étudier est-elle le texte dramatique, ou bien le spectacle? Selon que l’on privilégie la première réponse ou la seconde, l’axe organisateur du dossier génétique est le travail scriptural de l’auteur, toutes les mises en scène de L’Amante anglaise formant alors un ensemble théoriquement unifié, ou bien celui du metteur en scène, l’ensemble cohérent étant constitué par toutes les créations de ce dernier. L’étude explore une troisième voie en stipulant un nécessaire croisement des deux hypothèses.
Published: 2013

8. Pour une Génétique Théâtrale: prémisses et enjeux

Author: Almuth Grésillon, Marie-Madeleine Mervant-Roux (Centre National de la Recherche Scientifique, CNRS - Paris, França), and Dominique Budor (Université Paris III Sorbonne Nouvelle – França)
Subjects: Génétique Théâtrale, Théâtre, Texte, Performance, Inachèvement, Drama, PN1600-3307, Dramatic representation. The theater, PN2000-3307
Abstract: Est-il possible d’ap- pliquer au théâtre la méthode génétique, connue pour avoir fait ses preuves en littérature? L’œuvre théâtrale est un ensemble hétérogène de données textuelles et scéniques, une entité éphémère et fugitive, puisque toute mise en scène, mais aussi chaque représentation en- gendre nécessairement de nouvelles modifications: coupures dans le texte, variantes dans les mouvements des corps, les timbres des voix, les lumières, le rythme de l’événement, etc. Comment, dans ces conditions, retracer la genèse de l’œuvre, entre objets de diverses sortes et multiples achèvements?
Published: 2013

9. sp2-Iminosugar Glycolipids as Inhibitors of Lipopolysaccharide-mediated Human Dendritic Cell Activation in Vitro and of Acute Inflammation in Mice in Vivo

Author: Universidad de Sevilla. Departamento de Química orgánica, Centre national de la recherche scientifique (CNRS). France, Ministerio de Economía y Competitividad (MINECO). España, Schaeffer, Evelyne, Sánchez Fernández, Elena Matilde, Gonçalves-Pereira, Rita, Flacher, Vincent, Lamon, Delphine, Duval, Monique, Fauny, Jean Daniel, García Fernández, José Manuel, Mueller, Christopher G., Ortiz Mellet, Carmen, Universidad de Sevilla. Departamento de Química orgánica, Centre national de la recherche scientifique (CNRS). France, Ministerio de Economía y Competitividad (MINECO). España, Schaeffer, Evelyne, Sánchez Fernández, Elena Matilde, Gonçalves-Pereira, Rita, Flacher, Vincent, Lamon, Delphine, Duval, Monique, Fauny, Jean Daniel, García Fernández, José Manuel, Mueller, Christopher G., and Ortiz Mellet, Carmen
Published: 2019

10. Engineered toxin–intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations

Author: Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla. Departamento de Genética, Centre national de la recherche scientifique (CNRS). France, French Government Investissement d'Avenir. France, Agencia Estatal de Investigación. España, Comunidad Autónoma de Madrid, Fondation pour la Recherche Médicale. France, López Igual, Rocío, Bernal Bayard, Joaquín, Rodríguez Patón, Alfonso, Ghigo, Jean Marc, Mazel, Didier, Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla. Departamento de Genética, Centre national de la recherche scientifique (CNRS). France, French Government Investissement d'Avenir. France, Agencia Estatal de Investigación. España, Comunidad Autónoma de Madrid, Fondation pour la Recherche Médicale. France, López Igual, Rocío, Bernal Bayard, Joaquín, Rodríguez Patón, Alfonso, Ghigo, Jean Marc, and Mazel, Didier
Abstract: Targeted killing of pathogenic bacteria without harming beneficial members of host microbiota holds promise as a strategy to cure disease and limit both antimicrobial-related dysbiosis and development of antimicrobial resistance. We engineer toxins that are split by inteins and deliver them by conjugation into a mixed population of bacteria. Our toxin–intein antimicrobial is only activated in bacteria that harbor specific transcription factors. We apply our antimicrobial to specifically target and kill antibiotic-resistant Vibrio cholerae present in mixed populations. We find that 100% of antibiotic-resistant V. cholerae receiving the plasmid are killed. Escape mutants were extremely rare (10−6–10−8). We show that conjugation and specific killing of targeted bacteria occurs in the microbiota of zebrafish and crustacean larvae, which are natural hosts for Vibrio spp. Toxins split with inteins could form the basis of precision antimicrobials to target pathogens that are antibiotic resistant.
Published: 2019

11. For a Theatrical Genetics: assumptions and challenges

Author: Grésillon, Almuth, Mervant-Roux (Centre National de la Recherche Scientifique, CNRS - Paris, França), Marie-Madeleine, and Budor (Université Paris III Sorbonne Nouvelle – França), Dominique
Subjects: Théâtre, Génétique Théâtrale, Teatro, Texto, lcsh:PN1600-3307, Performance, lcsh:Drama, Genética Teatral, Text, Texte, Theatrical Genetics, Inachèvement, Inacabamento, Theatre, Unfinishedness, lcsh:PN2000-3307, lcsh:Dramatic representation. The theater
Abstract: Is it possible to apply to theatre the genetic method, known and used in the field of literature? A theatrical work is a heterogeneous set of textual and scenic data, an ephemeral and fleeting entity, because every staging – but also every presentation – necessarily produces new modifications: text cuts; variations in body movements; different voice timbres; lighting; the pace of the event, etc. In these conditions, how is it possible to retrace the genesis of the work, among objects of several kinds and with multiple finishes?, Est-il possible d’ap- pliquer au théâtre la méthode génétique, connue pour avoir fait ses preuves en littérature? L’œuvre théâtrale est un ensemble hétérogène de données textuelles et scéniques, une entité éphémère et fugitive, puisque toute mise en scène, mais aussi chaque représentation en- gendre nécessairement de nouvelles modifications: coupures dans le texte, variantes dans les mouvements des corps, les timbres des voix, les lumières, le rythme de l’événement, etc. Comment, dans ces conditions, retracer la genèse de l’œuvre, entre objets de diverses sortes et multiples achèvements?, É possível aplicar ao teatro o método genético, conhecido e utilizado no domínio da literatura? A obra teatral é um conjunto heterogêneo de dados textuais e cênicos, uma entidade efêmera e fugidia, pois toda encenação, mas também cada apresentação, engendra necessariamente novas modificações: cortes no texto; variações nos movimentos dos corpos; os timbres das vozes; as luzes; o ritmo do acontecimento, etc. Como, nessas condições, retraçar a gênese da obra, entre objetos de diversos tipos e de múltiplos acabamentos?
Published: 2013

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Author: Universidad de Sevilla. Departamento de Química orgánica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Argentina, Centre national de la recherche scientifique (CNRS). France, Ministerio de Economía y Competitividad (MINECO). España, Junta de Andalucía, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Cano, María Emilia, Varela, Oscar, García Moreno, M. Isabel, García Fernández, José Manuel, Kovensky, José, Uhrig, María Laura, Universidad de Sevilla. Departamento de Química orgánica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Argentina, Centre national de la recherche scientifique (CNRS). France, Ministerio de Economía y Competitividad (MINECO). España, Junta de Andalucía, European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER), Cano, María Emilia, Varela, Oscar, García Moreno, M. Isabel, García Fernández, José Manuel, Kovensky, José, and Uhrig, María Laura
Published: 2017

13. On the numerical controllability of the two-dimensional heat, Stokes and Navier-Stokes equations

Author: Universidad de Sevilla. Departamento de Ecuaciones Diferenciales y Análisis Numérico, Universidad de Sevilla. FQM131: Ec.diferenciales,Simulación Num.y Desarrollo Software, Ministerio de Economía y Competitividad (MINECO). España, Centre national de la recherche scientifique (CNRS). France, Fernández Cara, Enrique, Münch, Arnaud, Araujo de Souza, Diego, Universidad de Sevilla. Departamento de Ecuaciones Diferenciales y Análisis Numérico, Universidad de Sevilla. FQM131: Ec.diferenciales,Simulación Num.y Desarrollo Software, Ministerio de Economía y Competitividad (MINECO). España, Centre national de la recherche scientifique (CNRS). France, Fernández Cara, Enrique, Münch, Arnaud, and Araujo de Souza, Diego
Abstract: The aim of this work is to present some strategies to solve numerically controllability problems for the two-dimensional heat equation, the Stokes equations and the Navier-Stokes equations with Dirichlet boundary conditions. The main idea is to adapt the Fursikov-Imanuvilov formulation, see [A.V. Fursikov, O.Yu. Imanuvilov: Controllability of Evolutions Equations, Lectures Notes Series, Vol. 34, Seoul National University, 1996]; this approach has been followed recently for the onedimensional heat equation by the first two authors. More precisely, we minimize over the class of admissible null controls a functional that involves weighted integrals of the state and the control, with weights that blow up near the final time. The associated optimality conditions can be viewed as a differential system in the three variables x1, x2 and t that is second–order in time and fourth–order in space, completed with appropriate boundary conditions. We present several mixed formulations of the problems and, then, associated mixed finite element Lagrangian approximations that are easy to handle. Finally, we exhibit some numerical experiments.
Published: 2016

14. Processamento do verbo francês através da decomposição lexical

Author: Centre National de la Recherche Scientifique - CNRS, França, Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq, Brasil, Estivalet, Gustavo Lopez, Meunier, Fanny Elise, Centre National de la Recherche Scientifique - CNRS, França, Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq, Brasil, Estivalet, Gustavo Lopez, and Meunier, Fanny Elise
Abstract: O presente trabalho realizou uma investigação psicolinguística da decomposição morfológica verbal no acesso lexical em francês. Aplicou-se um experimento de decisão lexical visual com diferentes tipos de estruturas verbais como estímulos, a fim de identificar os processos de decomposição lexical, a estrutura hierárquica do verbo francês e o processamento dos diferentes morfemas para o acesso lexical no reconhecimento visual de verbos. Testaram-se diferentes tipos de verbos e pseudoverbos com as seguintes estruturas: a. morfologicamente ilegais (*abrou), b. contendo somente base existente (*[aim]ou), c. contendo somente sufixo flexional existente (*abr[ons]), d. inexistentes mas morfologicamente legais (*[aim][ir]) e e. existentes e morfologicamente legais ([[aim][ons]]). Ainda, testaram-se verbos com: a. um (aim[ons]) ou b. dois (aim[i][ons]) sufixos flexionais, e a mesma testagem foi feita com pseudoverbos (*abr[ons], *abr[i][ons]), para identificar diferenças no processamento morfossintático. As análises estatísticas apresentaram diferenças significativas entre pseudoverbos contendo apenas base existente e verbos existentes, e entre pseudoverbos contendo apenas sufixo flexional existente e verbos inexistentes mas morfologicamente legais. Houve diferenças significativas em relação ao número de sufixos flexionais nos pseudoverbos contendo somente sufixo flexional existente, assim como nos verbos existentes e morfologicamente legais. Assim, esse estudo estabeleceu a hierarquia do processamento dos diferentes morfemas que constituem o verbo francês. Os resultados mostram que todos os verbos do francês são passíveis de decomposição, sendo primeiramente decompostos em base e sufixos flexionais e posteriormente possuem seu morfema lexical da base ativado para o acesso semântico. A presente investigação sugere um modelo de decomposição morfológica completa em unidades mínimas para o acesso lexical e reconhecimento visual do verbo francês.This study conducted a psycholingu
Published: 2016

15. Chloroplast acetyl-CoA carboxylase activity is 2-oxoglutarate–regulated by interaction of PII with the biotin carboxyl carrier subunit

Author: Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Fundación Alfonso Martín Escudero. España, Centre national de la recherche scientifique (CNRS). France, Université de Paris, Feria Bourrellier, Ana Belén, Valot, Benoit, Guillot, Alain, Ambard-Bretteville, Françoise, Vidal, Jean, Hodges, Michael, Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Fundación Alfonso Martín Escudero. España, Centre national de la recherche scientifique (CNRS). France, Université de Paris, Feria Bourrellier, Ana Belén, Valot, Benoit, Guillot, Alain, Ambard-Bretteville, Françoise, Vidal, Jean, and Hodges, Michael
Abstract: The PII protein is a signal integrator involved in the regulation of nitrogen metabolism in bacteria and plants. Upon sensing of cellular carbon and energy availability, PII conveys the signal by interacting with target proteins, thereby modulating their biological activity. Plant PII is located to plastids; therefore, to identify new PII target proteins, PII-affinity chromatography of soluble extracts from Arabidopsis leaf chloroplasts was performed. Several proteins were retained only when Mg-ATP was present in the binding medium and they were specifically released from the resin by application of a 2-oxoglutarate-containing elution buffer. Mass spectroscopy of SDS/PAGE-resolved protein bands identified the biotin carboxyl carrier protein subunits of the plastidial acetyl-CoA carboxylase (ACCase) and three other proteins containing a similar biotin/lipoyl-binding motif as putative PII targets. ACCase is a key enzyme initiating the synthesis of fatty acids in plastids. In in vitro reconstituted assays supplemented with exogenous ATP, recombinant Arabidopsis PII inhibited chloroplastic ACCase activity, and this was completely reversed in the presence of 2-oxoglutarate, pyruvate, or oxaloacetate. The inhibitory effect was PII-dosedependent and appeared to be PII-specific because ACCase activity was not altered in the presence of other tested proteins. PII decreased the Vmax of the ACCase reaction without altering the Km for acetyl-CoA. These data show that PII function has evolved between bacterial and plant systems to control the carbon metabolism pathway of fatty acid synthesis in plastids.
Published: 2010

16. Les évêques d'Afrique parlent (1969-1991) - Documents pour le synode africain

Author: UCL - TECO - Faculté de théologie, Institut catholique de Paris - chercheur en sociologie de la religion au Centre national de la recherche scientifique (CNRS), Cheza, Maurice, Derroitte, Henri, Luneau, René, UCL - TECO - Faculté de théologie, Institut catholique de Paris - chercheur en sociologie de la religion au Centre national de la recherche scientifique (CNRS), Cheza, Maurice, Derroitte, Henri, and Luneau, René
Published: 1993

17. Complexity, algorithmic, and computational aspects of a dial-a-ride type problem

Author: Mourad Baïou, Rafael Colares, Hervé Kerivin, Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Department of Mathematical Sciences [Clemson], Clemson University, and COLARES, RAFAEL
Subjects: [INFO.INFO-CC]Computer Science [cs]/Computational Complexity [cs.CC], Combinatorial optimization, computational complexity, Information Systems and Management, [INFO.INFO-RO] Computer Science [cs]/Operations Research [cs.RO], General Computer Science, polyhedral study, [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], Management Science and Operations Research, Industrial and Manufacturing Engineering, [MATH.MATH-CO] Mathematics [math]/Combinatorics [math.CO], Computer Science::Robotics, Modeling and Simulation, [MATH.MATH-CO]Mathematics [math]/Combinatorics [math.CO], [INFO.INFO-CC] Computer Science [cs]/Computational Complexity [cs.CC], autonomous vehicles, dial-a-ride
Abstract: In dial-a-ride systems involving autonomous vehicles circulating along a circuit, a fleet of vehicles must serve clients who request rides between stations of the circuit such that the total number of pickup and drop-off operations is minimized. In this paper, we focus on a unitary variant where each client requests a single place in the vehicles and all the clients must be served within a single tour of the circuit. Such unitary variant induces a combinatorial optimization problem for which we introduce a nontrivial special case that is polynomially solvable when the capacity of each vehicle is at most 2 but it is NP-Hard otherwise. We also study the polytope associated with the solutions to this problem. We introduce new families of valid inequalities and give necessary and sufficient conditions under which they are facet-defining. Based on these inequalities, we devise an efficient branch-and-cut algorithm that outperforms the state-of-the-art commercial solvers.
Published: 2023

18. Neighbour sum distinguishing edge-weightings with local constraints

Author: Antoine Dailly, Elżbieta Sidorowicz, Instituto de Matematicas (UNAM), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Optimisation Combinatoire (G-SCOP_OC), Laboratoire des sciences pour la conception, l'optimisation et la production (G-SCOP), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), and University of Zielona Góra
Subjects: FOS: Computer and information sciences, Discrete Mathematics (cs.DM), Applied Mathematics, [MATH.MATH-CO]Mathematics [math]/Combinatorics [math.CO], FOS: Mathematics, Mathematics - Combinatorics, Discrete Mathematics and Combinatorics, Combinatorics (math.CO), [INFO.INFO-DM]Computer Science [cs]/Discrete Mathematics [cs.DM], Computer Science - Discrete Mathematics
Abstract: A $k$-edge-weighting of $G$ is a mapping $\omega:E(G)\longrightarrow \{1,\ldots,k\}$. The edge-weighting of $G$ naturally induces a vertex-colouring $\sigma_{\omega}:V(G)\longrightarrow \mathbb{N}$ given by$\sigma_{\omega}(v)=\sum_{u\in N_G(v)}\omega(vu)$ for every $v\in V(G)$. The edge-weighting $\omega$ is neighbour sum distinguishing if it yields a proper vertex-colouring $\sigma_{\omega}$, \emph{i.e.}, $\sigma_{\omega}(u)\neq \sigma_{\omega}(v)$ for every edge $uv$ of $G$.We investigate a neighbour sum distinguishing edge-weighting with local constraints, namely, we assume that the set of edges incident to a vertex of large degree is not monochromatic. A graph is nice if it has no components isomorphic to $K_2$. We prove that every nice graph with maximum degree at most~5 admits a neighbour sum distinguishing $(\Delta(G)+2)$-edge-weighting such that all the vertices of degree at least~2 are incident with at least two edges of different weights. Furthermore, we prove that every nice graph admits a neighbour sum distinguishing $7$-edge-weighting such that all the vertices of degree at least~6 are incident with at least two edges of different weights. Finally, we show that nice bipartite graphs admit a neighbour sum distinguishing $6$-edge-weighting such that all the vertices of degree at least~2 are incident with at least two edges of different weights.
Published: 2023

19. Deactivation of Pd/C catalysts by irreversible loss of hydrogen spillover ability of the carbon support

Author: Laurent Vanoye, Boris Guicheret, Camila Rivera-Cárcamo, Jérémy Audevard, Javier Navarro-Ruiz, Iker del Rosal, Iann C. Gerber, Cristian H. Campos, Bruno Fernandes Machado, Jérôme Volkman, Régis Philippe, Philippe Serp, Alain Favre-Réguillon, Catalyse, Polymérisation, Procédés et Matériaux (CP2M), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Supérieure de Chimie Physique Électronique de Lyon (CPE)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie de coordination (LCC), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physique et chimie des nano-objets (LPCNO), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut de Chimie de Toulouse (ICT), Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Fédération de recherche « Matière et interactions » (FeRMI), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Universidad de Concepción - University of Concepcion [Chile], Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials (LSRE-LCM), Faculdade de Engenharia (LSRE-LCM), Universidade do Porto = University of Porto, Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), and ANR-19-CE07-0030,COMET,Catalyse Coopérative Entre Atomes Et Nanoparticules Métalliques(2019)
Subjects: [CHIM]Chemical Sciences, [CHIM.CATA]Chemical Sciences/Catalysis, Physical and Theoretical Chemistry, Catalysis
Abstract: International audience; General interest in solvent-free catalytic processes is driven by the development of environmentally and economically acceptable procedures. Such processes require the use of highly active and stable catalysts. This study reports on the synthesis, characterization, and kinetic evaluation of two highly active Pd catalysts supported on different carbons support, i.e., multi-walled carbon nanotubes (CNT) and few-layer graphene (FLG). These catalysts, with similar Pd loading (∼2 wt%) and containing both Pd single atoms (PdSA) and nanoparticles (PdNP), were systematically tested for solvent-free total hydrogenation of squalene (SQE) to obtain high-purity squalane (SQA). Thanks to the unique cooperative catalysis between PdSA and PdNP involving H-spillover, the activities of both catalysts were high compared to catalysts described in the literature. Solvent-free total hydrogenation of SQE could be performed under mild conditions (120 °C, 20 bar H2, 4 h) using ultralow Pd loading (60 ppm). However, since this reduction reaction is highly exothermic (ΔHR= − 765 kJ.mol−1), heat management during the reactor operation with these highly active catalysts is crucial to avoid deactivation and thermal runaway. Under these conditions, Pd/FLG was highly active but deactivated, unlike Pd/CNT, which still has high activity, but does not deactivate. Characterizations (ICP, XPS, Raman, TPD-MS, HAADF-STEM) of the Pd/FLG catalyst before and after reaction, supported by calculations based on density functional theory, allowed us to propose a new mechanism of catalyst deactivation involving the chemical reduction of specific surface oxygen groups of the carbon support induced by H-spillover.
Published: 2023

20. WSDesc: Weakly Supervised 3D Local Descriptor Learning for Point Cloud Registration

Author: Lei Li, Hongbo Fu, Maks Ovsjanikov, La Géometrie au Service du Numérique (GEOMERIX), Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Institut Polytechnique de Paris (IP Paris), City University of Hong Kong [Hong Kong] (CUHK), the ANR AI Chair AIGRETTE, and European Project: 758800,ERC,ERC-2017-StG-758800,EXPROTEA(2018)
Subjects: FOS: Computer and information sciences, Computer Vision and Pattern Recognition (cs.CV), Computer Science - Computer Vision and Pattern Recognition, ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, [INFO.INFO-CV]Computer Science [cs]/Computer Vision and Pattern Recognition [cs.CV], Computer Graphics and Computer-Aided Design, Graphics (cs.GR), [INFO.INFO-GR]Computer Science [cs]/Graphics [cs.GR], weak supervision, Point cloud, 3D CNN, Computer Science - Graphics, differentiable voxelization, Signal Processing, geometric registration, Computer Vision and Pattern Recognition, 3D local descriptor, Software
Abstract: In this work, we present a novel method called WSDesc to learn 3D local descriptors in a weakly supervised manner for robust point cloud registration. Our work builds upon recent 3D CNN-based descriptor extractors, which leverage a voxel-based representation to parameterize local geometry of 3D points. Instead of using a predefined fixed-size local support in voxelization, we propose to learn the optimal support in a data-driven manner. To this end, we design a novel differentiable voxelization layer that can back-propagate the gradient to the support size optimization. To train the extracted descriptors, we propose a novel registration loss based on the deviation from rigidity of 3D transformations, and the loss is weakly supervised by the prior knowledge that the input point clouds have partial overlap, without requiring ground-truth alignment information. Through extensive experiments, we show that our learned descriptors yield superior performance on existing geometric registration benchmarks., Comment: To appear in IEEE TVCG
Published: 2023

21. A silicone-based slippery polymer coating with humidity–dependent nanoscale topography

Author: Callau, M., Fajolles, C., Leroy, J., Verneuil, E., Guenoun, P., Laboratoire Interdisciplinaire sur l'Organisation Nanométrique et Supramoléculaire (LIONS), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Innovation en Chimie des Surfaces et NanoSciences (LICSEN UMR 3685), Sciences et Ingénierie de la Matière Molle (UMR 7615) (SIMM), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Biomaterials, Colloid and Surface Chemistry, [CHIM]Chemical Sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials
Abstract: International audience; Hypothesis: Slippery Omniphobic Covalently Attached Liquids (SOCAL) have been proposed for making omnirepellent thin films of self-assembled dimethylsiloxane polymerbrushes grafted from silica surfaces. Smooth and flat at very small scale, these fluid surfaces could exhibit a more complex multiscale structure though showing very weak contact angle hysteresis (less than 5°).Experiment: In this work, coatings were deposited on glass surfaces from an acidic dimethoxydimethylsilane solution under carefully controlled relative humidity. Ellipsometry mapping was used to analyze the surface structuration with nanometric thickness sensitivity. The sliding properties were determined using a drop shape analyzer with a tilting device, and chemical analyses of the coatings were performed using on-surface techniques (XPS, ATR-FTIR spectroscopy).Findings: Coated materials possessed an unexpected surface structure with multiscale semispherical-like features, which surprisingly, did not increase the contact angle hysteresis. A careful study of some parameters of the coating process and the related evolution of the surface properties allowed us to propose a new model of the chemical organization of the polymer to support this remarkable liquid-like behavior. These structures are made of endgrafted strongly adsorbed Guiselin brushes with humidity-dependent thickness: the higher the humidity, the thinner and the more slippery the coating.
Published: 2023

22. Acute tubulointerstitial nephritis with or without uveitis: a novel form of post-acute COVID-19 syndrome in children

Author: Marina Avramescu, Pierre Isnard, Sarah Temmam, Agnès Chevalier, Paul Bastard, Mikael Attia, Romain Berthaud, Marc Fila, Claire Dossier, Julien Hogan, Tim Ulinski, Damia Leguevaques, Férielle Louillet, Edouard Martinez Casado, Jean-Michel Halimi, Sylvie Cloarec, Ariane Zaloszyc, Camille Faudeux, Caroline Rousset-Rouvière, Stéphanie Clavé, Jérôme Harambat, Edouard Rollot, Thomas Simon, Megan Nallet-Amate, Bruno Ranchin, Justine Bacchetta, Florence Porcheret, Josselin Bernard, Amélie Ryckewaert, Anne Jamet, Jacques Fourgeaud, Nicolas Da Rocha, Philippe Pérot, Nicolas Kuperwasser, Naïm Bouazza, Marion Rabant, Jean-Paul Duong Van Huyen, Matthieu P Robert, Julien Zuber, Jean-Laurent Casanova, Marc Eloit, Isabelle Sermet-Gaudelus, Olivia Boyer, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte [CHU-Necker] (MARHEA), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Découverte de pathogènes – Pathogen discovery, Institut Pasteur [Paris] (IP), Hôpital Arnaud de Villeneuve [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Human genetics of infectious diseases : Mendelian predisposition (Equipe Inserm U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Rockefeller University [New York], Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), AP-HP Hôpital universitaire Robert-Debré [Paris], CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), CHU Rouen, Normandie Université (NU), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), CHU Strasbourg, Centre Hospitalier Universitaire de Nice (CHU Nice), Assistance Publique - Hôpitaux de Marseille (APHM), CHU Bordeaux [Bordeaux], Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), CHU Dijon, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Hospices Civils de Lyon (HCL), Centre hospitalier universitaire de Nantes (CHU Nantes), CHU Pontchaillou [Rennes], Pharmacologie et évaluations thérapeutiques chez l'enfant et la femme enceinte (URP_7323), Université Paris Cité (UPCité), Site Tarnier (hôpital Cochin) - APHP, CIC - Mère Enfant Necker Cochin Paris Centre (CIC 1419), Hôpital Cochin [AP-HP], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)
Subjects: pediatric, SARS-CoV, Nephrology, [SDV]Life Sciences [q-bio], 2 TINUs, tubule-interstitial nephritis, uveitis, COVID-19
Abstract: BackgroundCOVID-19 is a complex multisystem disease, frequently associated with kidney injury. Since the beginning of the COVID-19 pandemic, we observed a striking increase in the incidence of acute tubulointerstitial nephritis (aTIN) without or with uveitis (TINUs) among children. This prompted us to examine whether SARS-CoV-2 might be the underlying trigger.MethodsWe conducted a French nationwide retrospective cohort study. We included all consecutive children diagnosed with aTIN or TINUs of undetermined cause between April-2020 and March-2021. SARS-CoV-2 antibody responses were tested by a luciferase immunoprecipitation system and compared to age-matched controls. Immunohistochemistry, immunofluorescence and molecular microbiology analyses were performed on kidney biopsies.ResultsForty-eight children were included with a median age at diagnosis of 14.7 years (9.4-17.6). aTIN and TINUs incidence rates increased 3-fold and 12-fold, respectively, compared to pre-pandemic years. All patients had impaired kidney function with a median eGFR of 31.9 ml/min/1.73m² at diagnosis. Kidney biopsies showed lesions of acute tubulointerstitial nephritis and 25% of patients had fibrosis. No patient had concomitant acute COVID-19. All 16 children tested had high anti-N IgG titers and one had anti-S IgGs. Next-generation sequencing failed to detect any infectious agents in kidney biopsies. However, SARS-CoV-2 RNA was detected by PCR in two kidney samples supporting a potential direct link between SARS-CoV-2 and aTIN/TINUs.ConclusionsWe describe a novel form of post-acute COVID-19 syndrome in children, unique in its exclusive kidney and eye involvement, and its distinctive anti-SARS-CoV-2 N+/S-serological profile. Our results support a causal association linking SARS-CoV-2 infection to this newly-reported burst of renal/eye inflammation.
Published: 2023

23. Bus network decomposition for fault detection and isolation through power line communication

Author: Abdel Karim Abdel Karim, M. Amine Atoui, Virginie Degardin, Pierre Laly, Vincent Cocquempot, Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Télécommunication, Interférences et Compatibilité Electromagnétique - IEMN (TELICE - IEMN), Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Plateforme de Caractérisation Multi-Physiques - IEMN (PCMP - IEMN), This research work is done in the framework of the ELSAT2020 project which is co-financed by the European Union with the European Regional Development Fund, the French state and the Hauts-de-France Region Council, and PCMP C2EM
Subjects: Network decomposition, Applied Mathematics, Fault isolation, [SPI.TRON]Engineering Sciences [physics]/Electronics, Computer Science Applications, [INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI], Power line communication, Control and Systems Engineering, Residual, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, Electrical and Electronic Engineering, Fault detection, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Instrumentation
Abstract: International audience; This paper deals with fault detection and isolation (FDI) in complex embedded wired communication networks. The considered faults are soft faults which do not prevent the communication, but may evolve into hard faults, i.e. short or open circuit. A novel FDI method based on power line communication (PLC) transmission systems is proposed. In these PLC systems, the transmission coefficients between the source and each receiver are estimated for communication purposes using orthogonal frequency division multiplexing (OFDM). Health indicators and residuals are computed by comparing the online estimated transmission coefficients with the reference coefficients. A methodology for dealing with complex networks, such as bus networks, is proposed. It is based on the decomposition of the network into several Y-shaped sub-networks. Each of these sub-networks is monitored to detect the presence of a fault. The FDI method is first validated using real data extracted from a Y-shaped network test bench. Then, the proposed approach is validated on a more complex network using realistic simulated data.
Published: 2023

24. Drift Estimation of the Threshold Ornstein-Uhlenbeck Process From Continuous and Discrete Observations

Author: Mazzonetto, Sara, Pigato, Paolo, Institut Élie Cartan de Lorraine (IECL), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Processus aléatoires spatio-temporels et leurs applications (PASTA), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Élie Cartan de Lorraine (IECL), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Roma Tor Vergata [Roma], and Department of Economics and Finance, University of Rome Tor Vergata
Subjects: Statistics and Probability, Probability (math.PR), Mathematics - Statistics Theory, Statistics Theory (math.ST), interest rates, threshold Vasicek model, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], MCS 2010 primary: 62M05, secondary: 62F12, 60J60.JEL Classification primary: C58, secondary: C22, G12, Threshold diffusion, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], 62M05 (Primary) 62F12, 60J60 (Secondary), FOS: Mathematics, multi-threshold, threshold Vasicek, maximum likelihood, Statistics, Probability and Uncertainty, Settore SECS-S/01, self-exciting process, regime-switching, Mathematics - Probability
Abstract: We refer by threshold Ornstein-Uhlenbeck to a continuous-time threshold autoregressive process. It follows the Ornstein-Uhlenbeck dynamics when above or below a fixed level, yet at this level (threshold) its coefficients can be discontinuous. We discuss (quasi)-maximum likelihood estimation of the drift parameters, both assuming continuous and discrete time observations. In the ergodic case, we derive consistency and speed of convergence of these estimators in long time and high frequency. Based on these results, we develop a test for the presence of a threshold in the dynamics. Finally, we apply these statistical tools to short-term US interest rates modeling.
Published: 2024

25. Fotografía y fetiche

Author: Metz, Christian; Centre National de la Recherche Scientifique, CNRS and Metz, Christian; Centre National de la Recherche Scientifique, CNRS

26. Fotografía y fetiche

Author: Metz, Christian; Centre National de la Recherche Scientifique, CNRS and Metz, Christian; Centre National de la Recherche Scientifique, CNRS
Abstract: Este artículo tema de un aseminario del Profesor Metz en la EHESS en Paría, fue publicado en la revista OCTOBRE (New York) en el No. 34, 1985. Fue remitido al Profesor Germán Muñoz G., para utilizarlo en Jornadas sobre Semiótica y Psicoanálisis que debían realizarase en su presencia en marzo de 1987. La traducción es de Marianne Ponsford, alumna de VII semestre de la Facultad de Comunicación Social.

27. Modifications of the endosomal compartment in fibroblasts from sporadic Alzheimer’s disease patients are associated with cognitive impairment

Author: Laura Xicota, Julien Lagarde, Fanny Eysert, Benjamin Grenier-Boley, Isabelle Rivals, Alexandra Botté, Sylvie Forlani, Sophie Landron, Clément Gautier, Cecilia Gabriel, Michel Bottlaender, Jean-Charles Lambert, Mounia Chami, Marie Sarazin, Marie-Claude Potier, Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), GHU Paris Psychiatrie et Neurosciences, Université Paris Cité (UPCité), Université Paris-Saclay, Centre Hospitalier Sainte Anne [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), LaBoratoire d'Imagerie biOmédicale MultimodAle Paris-Saclay (BIOMAPS), Service Hospitalier Frédéric Joliot (SHFJ), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA), Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Université de Lille, CHU Lille, Facteurs de Risque et Déterminants Moléculaires des Maladies liées au Vieillissement - U 1167 (RID-AGE), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL), Neurophysiologie Respiratoire Expérimentale et Clinique (UMRS 1158), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institut de Recherches SERVIER (IRS), Service NEUROSPIN (NEUROSPIN), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Xicota, Laura
Subjects: [SDV] Life Sciences [q-bio], Cellular and Molecular Neuroscience, Psychiatry and Mental health, [SDV]Life Sciences [q-bio], Biological Psychiatry
Abstract: Morphological alterations of the endosomal compartment have been widely described in post-mortem brains from Alzheimer’s disease (AD) patients and subjects with Down syndrome (DS) who are at high risk for AD. Immunostaining with antibodies against endosomal markers such as Early Endosome Antigen 1 (EEA1) revealed increased size of EEA1-positive puncta. In DS, peripheral cells such as peripheral blood mononuclear cells (PBMCs) and fibroblasts, share similar phenotype even in the absence of AD. We previously found that PBMCs from AD patients have larger EEA1-positive puncta, correlating with brain amyloid load. Here we analysed the endosomal compartment of fibroblasts from a very well characterised cohort of AD patients (IMABio3) who underwent thorough clinical, imaging and biomarkers assessments. Twenty-one subjects were included (7 AD with mild cognitive impairment (AD-MCI), 7 AD with dementia (AD-D) and 7 controls) who had amyloid-PET at baseline (PiB) and neuropsychological tests at baseline and close to skin biopsy. Fibroblasts isolated from skin biopsies were immunostained with anti-EEA1 antibody and imaged using a spinning disk microscope. Endosomal compartment ultrastructure was also analysed by electron microscopy. All fibroblast lines were genotyped and their AD risk factors identified. Our results show a trend to an increased EEA1-positive puncta volume in fibroblasts from AD-D as compared to controls (p.adj = 0.12) and reveal enhanced endosome area in fibroblasts from AD-MCI and AD-AD versus controls. Larger puncta size correlated with PiB retention in different brain areas and with worse cognitive scores at the time of biopsy as well as faster decline from baseline to the time of biopsy. Finally, we identified three genetic risk factors for AD (ABCA1, COX7C and MYO15A) that were associated with larger EEA1 puncta volume. In conclusion, the endosomal compartment in fibroblasts could be used as cellular peripheral biomarker for both amyloid deposition and cognitive decline in AD patients.
Published: 2023

28. Pacpaint: a histology-based deep learning model uncovers the extensive intratumor molecular heterogeneity of pancreatic adenocarcinoma

Author: Saillard, Charlie, Delecourt, Flore, Schmauch, Benoit, Moindrot, Olivier, Svrcek, Magali, Bardier-Dupas, Armelle, Emile, Jean Francois, Ayadi, Mira, Rebours, Vinciane, de Mestier, Louis, Hammel, Pascal, Neuzillet, Cindy, Bachet, Jean Baptiste, Iovanna, Juan, Dusetti, Nelson, Blum, Yuna, Richard, Magali, Kermezli, Yasmina, Paradis, Valerie, Zaslavskiy, Mikhail, Courtiol, Pierre, Kamoun, Aurelie, Nicolle, Remy, Cros, Jerome, Owkin France, Centre de recherche sur l'Inflammation (CRI (UMR_S_1149 / ERL_8252 / U1149)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut Curie [Paris], Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC ), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), and This work was granted access to the HPC resources of IDRIS under the allocation AD011012519 made by GENCI.
Subjects: MESH: Deep Learning, MESH: Humans, MESH: Aggression, MESH: Adenocarcinoma, [SDV.CAN]Life Sciences [q-bio]/Cancer, MESH: Pancreatic Neoplasms
Abstract: Two tumor (Classical/Basal) and stroma (Inactive/active) subtypes of Pancreatic adenocarcinoma (PDAC) with prognostic and theragnostic implications have been described. These molecular subtypes were defined by RNAseq, a costly technique sensitive to sample quality and cellularity, not used in routine practice. To allow rapid PDAC molecular subtyping and study PDAC heterogeneity, we develop PACpAInt, a multi-step deep learning model. PACpAInt is trained on a multicentric cohort ( n = 202) and validated on 4 independent cohorts including biopsies (surgical cohorts n = 148; 97; 126 / biopsy cohort n = 25), all with transcriptomic data ( n = 598) to predict tumor tissue, tumor cells from stroma, and their transcriptomic molecular subtypes, either at the whole slide or tile level (112 µm squares). PACpAInt correctly predicts tumor subtypes at the whole slide level on surgical and biopsies specimens and independently predicts survival. PACpAInt highlights the presence of a minor aggressive Basal contingent that negatively impacts survival in 39% of RNA-defined classical cases. Tile-level analysis ( > 6 millions) redefines PDAC microheterogeneity showing codependencies in the distribution of tumor and stroma subtypes, and demonstrates that, in addition to the Classical and Basal tumors, there are Hybrid tumors that combine the latter subtypes, and Intermediate tumors that may represent a transition state during PDAC evolution.
Published: 2023

29. FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards

Author: Gaignard, Alban, Rosnet, Thomas, de Lamotte, Frédéric, Lefort, Vincent, Devignes, Marie-Dominique, Nantes Université (Nantes Univ), Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Français de Bioinformatique (IFB-CORE), Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Nantes Université - UFR de Médecine et des Techniques Médicales (Nantes Univ - UFR MEDECINE), Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Santé, and Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)
Subjects: [INFO.INFO-IR]Computer Science [cs]/Information Retrieval [cs.IR], [INFO.INFO-WB]Computer Science [cs]/Web, Bioschemas, [INFO]Computer Science [cs], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], SPARQL, SHACL, FAIR, Schema.org
Abstract: International audience; The current rise of Open Science and Reproducibility in the Life Sciences requires the creation of rich, machine-actionable metadata in order to better share and reuse biological digital resources such as datasets, bioinformatics tools, training materials, etc. For this purpose, FAIR principles have been defined for both data and metadata and adopted by large communities, leading to the definition of specific metrics. However, automatic FAIRness assessment is still difficult because computational evaluations frequently require technical expertise and can be time-consuming. As a first step to address these issues, we propose FAIR-Checker , a web-based tool to assess the FAIRness of metadata presented by digital resources. FAIR-Checker offers two main facets: a “Check” module providing a thorough metadata evaluation and recommendations, and an “Inspect” module which assists users in improving metadata quality and therefore the FAIRness of their resource. FAIR-Checker leverages Semantic Web standards and technologies such as SPARQL queries and SHACL constraints to automatically assess FAIR metrics. Users are notified of missing, necessary, or recommended metadata for various resource categories. We evaluate FAIR-Checker in the context of improving the FAIRification of individual resources, through better metadata, as well as analyzing the FAIRness of more than 25 thousand bioinformatics software descriptions.
Published: 2023

30. Seasonal and habitat-based variations in vertical export of biogenic sea-ice proxies in Hudson Bay

Author: Tiia Luostarinen, Kaarina Weckström, Jens Ehn, Michelle Kamula, Amanda Burson, Aura Diaz, Guillaume Massé, Suzanne McGowan, Zou Zou Kuzyk, Maija Heikkilä, Helsinki Institute of Sustainability Science (HELSUS), Faculty of Biological and Environmental Sciences [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Geological Survey of Denmark and Greenland (GEUS), Centre for Earth Observation Science [Winnipeg], University of Manitoba [Winnipeg], British Antarctic Survey (BAS), Natural Environment Research Council (NERC), University of Nottingham, UK (UON), Variabilité de l'Océan et de la Glace de mer (VOG), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Netherlands Institute of Ecology (NIOO-KNAW), Ecosystems and Environment Research Programme, Environmental Change Research Unit (ECRU), and Aquatic Ecology (AqE)
Subjects: Diatoms, Canada, Dinoflagellate cysts, Quebec, Fresh-water, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Biomarker, North-atlantic, 1181 Ecology, evolutionary biology, General Earth and Planetary Sciences, Variability, Manitounuk sound, Late quaternary, General Environmental Science
Abstract: Despite their wide use in past sea-ice reconstructions, the seasonal, habitat and species-based sources of sedimentary sea-ice proxies are poorly understood. Here, we conduct direct observations of the community composition of diatoms, dinoflagellate cysts and highly branched isoprenoid lipids within the sea ice, water column, sediment traps and sediment surface in the Belcher Islands Archipelago, Hudson Bay throughout spring 2019. We find that Arctic diatom and dinoflagellate cysts species commonly used as sea-ice proxies appear to be only indirectly linked to sea-ice conditions, and that the sediment assemblages of these groups overrepresent summertime pelagic blooms. Species contributing to the diverse sea-ice diatom communities are rare in the sediment. Dinoflagellate cysts form a typical Arctic assemblage in the sediment, although they are virtually absent in the sea ice and water column in spring. We also find that certain highly branched isoprenoid lipids that were previously considered indicators of open water, can be produced in sea-ice. We conclude that contextual knowledge and a multiproxy approach are necessary in reconstruction, encouraging further studies on the sources and controls of sea-ice proxy production in different geographic areas. Sedimentary assemblages of biogenic sea-ice proxies incorporate limited representation of the diverse sea-ice connected communities, according to direct springtime observations in the Belcher Islands Archipelago, Hudson Bay, Canada.Despite their wide use in past sea-ice reconstructions, the seasonal, habitat and species-based sources of sedimentary sea-ice proxies are poorly understood. Here, we conduct direct observations of the community composition of diatoms, dinoflagellate cysts and highly branched isoprenoid lipids within the sea ice, water column, sediment traps and sediment surface in the Belcher Islands Archipelago, Hudson Bay throughout spring 2019. We find that Arctic diatom and dinoflagellate cysts species commonly used as sea-ice proxies appear to be only indirectly linked to sea-ice conditions, and that the sediment assemblages of these groups overrepresent summertime pelagic blooms. Species contributing to the diverse sea-ice diatom communities are rare in the sediment. Dinoflagellate cysts form a typical Arctic assemblage in the sediment, although they are virtually absent in the sea ice and water column in spring. We also find that certain highly branched isoprenoid lipids that were previously considered indicators of open water, can be produced in sea-ice. We conclude that contextual knowledge and a multiproxy approach are necessary in reconstruction, encouraging further studies on the sources and controls of sea-ice proxy production in different geographic areas.
Published: 2023

31. Widening the landscape of transcriptional regulation of green algal photoprotection

Author: Marius Arend, Yizhong Yuan, M. Águila Ruiz-Sola, Nooshin Omranian, Zoran Nikoloski, Dimitris Petroutsos, Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Systems Biology and Mathematical Modeling Group, Max-Planck-Institute of Molecular Plant Physiology, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), The Human Frontiers Science Program (project RGP0046/2018), The Prestige Marie-Curie co-financing grant PRESTIGE-2017-1-0028, The International Max Planck Research School ‘Primary Metabolism and Plant Growth at the Max Planck Institute of Molecular Plant Physiology, ANR-18-CE20-0006,MetaboLIGHT,Regulation de la photosynthèse par la Lumière et le métabolisme chez les algues(2018), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), and Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular
Subjects: MESH: Chlamydomonas reinhardtii, Multidisciplinary, [SDV]Life Sciences [q-bio], General Physics and Astronomy, MESH: Carbon, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, General Chemistry, MESH: Carbon Dioxide, MESH: Chlamydomonas, MESH: Gene Expression Regulation, General Biochemistry, Genetics and Molecular Biology, MESH: Photosynthesis
Abstract: Availability of light and CO2, substrates of microalgae photosynthesis, is frequently far from optimal. Microalgae activate photoprotection under strong light, to prevent oxidative damage, and the CO2 Concentrating Mechanism (CCM) under low CO2, to raise intracellular CO2 levels. The two processes are interconnected; yet, the underlying transcriptional regulators remain largely unknown. Employing a large transcriptomic data compendium of Chlamydomonas reinhardtii’s responses to different light and carbon supply, we reconstruct a consensus genome-scale gene regulatory network from complementary inference approaches and use it to elucidate transcriptional regulators of photoprotection. We show that the CCM regulator LCR1 also controls photoprotection, and that QER7, a Squamosa Binding Protein, suppresses photoprotection- and CCM-gene expression under the control of the blue light photoreceptor Phototropin. By demonstrating the existence of regulatory hubs that channel light- and CO2-mediated signals into a common response, our study provides an accessible resource to dissect gene expression regulation in this microalga.
Published: 2023

32. Core genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing

Author: Linda Grillova, Thomas Cokelaer, Jean-François Mariet, Juliana Pipoli da Fonseca, Mathieu Picardeau, Biologie des Spirochètes / Biology of Spirochetes, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence de la Leptospirose - National Reference Center Leptospirosis (CNR), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Biomics (plateforme technologique), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, This work was supported by the Institut Pasteur through grant PTR 30-2017 and Santé Publique France to MP. TC and JP (Biomics Platform, C2RT, Institut Pasteur, Paris, France), supported by France Génomique (ANR-10-INBS-09) and IBISA., and ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)
Subjects: Leptospira, MESH: Genotype, Genotyping, MESH: Leptospira interrogans, Infectious Diseases, MESH: Humans, [SDV]Life Sciences [q-bio], Leptospirosis, MESH: Animals, Genomics, MESH: Leptospirosis, MESH: Zoonoses, MESH: Leptospira
Abstract: Background The life-threatening pathogen Leptospira interrogans is the most common agent of leptospirosis, an emerging zoonotic disease. However, little is known about the strains that are currently circulating worldwide due to the fastidious nature of the bacteria and the difficulty to isolate cultures. In addition, the paucity of bacteria in blood and other clinical samples has proven to be a considerable challenge for directly genotyping the agent of leptospirosis directly from patient material. Our understanding of the genetic diversity of strains during human infection is therefore limited. Methods Here, we carried out hybridization capture followed by Illumina sequencing of the core genome directly from 20 clinical samples that were PCR positive for pathogenic Leptospira to elucidate the genetic diversity of currently circulating Leptospira strains in mainland France. Results Capture with RNA probes covering the L. interrogans core genome resulted in a 72 to 13,000-fold increase in pathogen reads relative to standard sequencing without capture. Variant analysis of the genomes sequenced from the biological samples using 273 Leptospira reference genomes was then carried out to determine the genotype of the infecting strain. For samples with sufficient coverage (19/20 samples with coverage > 8×), we could unambiguously identify L. interrogans serovars Icterohaemorrhagiae and Copenhageni (14 samples), L. kirschneri serovar Grippotyphosa (4 samples), and L. interrogans serovar Pyrogenes (1 sample) as the infecting strains. Conclusions We obtained high-quality genomic data with suitable coverage for confident core genome genotyping of the agent of leptospirosis for most of our clinical samples. The recovery of the genome of the serovars Icterohaemorrhagiae and Copenhageni directly from multiple clinical samples revealed low adaptive diversification of the core genes during human infection. The ability to generate culture-free genomic data opens new opportunities for better understanding of the epidemiology of this fastidious pathogen and pathogenesis of this neglected disease.
Published: 2023

33. Structural basis of Ty1 integrase tethering to RNA polymerase III for targeted retrotransposon integration

Author: Phong Quoc Nguyen, Sonia Huecas, Amna Asif-Laidin, Adrián Plaza-Pegueroles, Beatrice Capuzzi, Noé Palmic, Christine Conesa, Joël Acker, Juan Reguera, Pascale Lesage, Carlos Fernández-Tornero, Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institut de Recherche Saint-Louis - Hématologie Immunologie Oncologie (Département de recherche de l’UFR de médecine, ex- Institut Universitaire Hématologie-IUH) (IRSL), Université Paris Cité (UPCité), Génomes, biologie cellulaire et thérapeutiques (GenCellDi (U944 / UMR7212)), Collège de France (CdF (institution))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), the Spanish Ministry of Science / Agencia Estatal de Investigación (BFU2017-87397-P, RED2018-102467-T and PID2020-116722GB-I00 to C. F.-T., PRE2018-087012 to A. P.-P.), intramural funding from CSIC (2020AEP152 and PIE-202120E047-Conexiones-Life to C. F.-T.), Fondation pour la Recherche Médicale (FRM-EQU202203014635 to P. L., FRM-SPF20170938755 to A. A.-L., FRM-ECO202206015504 to B. C.), and intramural funding from CNRS, Université de Paris and INSERM (to P. L.), ANR-17-CE11-0025,INstruc,Etude structurale du mécanisme d'intégration des rétrotransposons de levure dans les gènes transcrits par l'ARN Polymérase III(2017), Agence Nationale de la Recherche (France), Agencia Estatal de Investigación (España), Consejo Superior de Investigaciones Científicas (España), Fondation pour la Recherche Médicale, Centre National de la Recherche Scientifique (France), Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (France), Nguyen, Phong Quoc, Huecas, Sonia, Asif-Laidin, Amna, Plaza-Pegueroles, Adrián, Capuzzi, Beatrice, Palmic, Noé, Acker, Joël, Reguera, Juan, Lesage, Pascale, and Fernández-Tornero, Carlos
Subjects: Multidisciplinary, Cryoelectron microscopy, DNA recombination, [SDV]Life Sciences [q-bio], General Physics and Astronomy, General Chemistry, Transcription, General Biochemistry, Genetics and Molecular Biology
Abstract: 13 p.-6 fig., The yeast Ty1 retrotransposon integrates upstream of genes transcribed by RNA polymerase III (Pol III). Specificity of integration is mediated by an interaction between the Ty1 integrase (IN1) and Pol III, currently uncharacterized at the atomic level. We report cryo-EM structures of Pol III in complex with IN1, revealing a 16-residue segment at the IN1 C-terminus that contacts Pol III subunits AC40 and AC19, an interaction that we validate by in vivo mutational analysis. Binding to IN1 associates with allosteric changes in Pol III that may affect its transcriptional activity. The C-terminal domain of subunit C11, involved in RNA cleavage, inserts into the Pol III funnel pore, providing evidence for a two-metal mechanism during RNA cleavage. Additionally, ordering next to C11 of an N-terminal portion from subunit C53 may explain the connection between these subunits during termination and reinitiation. Deletion of the C53 N-terminal region leads to reduced chromatin association of Pol III and IN1, and a major fall in Ty1 integration events. Our data support a model in which IN1 binding induces a Pol III configuration that may favor its retention on chromatin, thereby improving the likelihood of Ty1 integration., This work was supported by the Agence Nationale de la Recherche (ANR-17-CE11-0025 to P.L., J.A., J.R. and C.F.-T.), the Spanish Ministry of Science/Agencia Estatal de Investigación (BFU2017-87397-P, RED2018-102467-T and PID2020-116722GB-I00 to C.F.-T.; PRE2018-087012 to A.P.-P.), intramural funding from CSIC (2020AEP152 and PIE-202120E047-Conexiones-Life to C. F.-T.), Fondation pour la Recherche Médicale (FRM-EQU202203014635 to P.L.; FRM-SPF20170938755 to A.A.-L.; FRM-ECO202206015504 to B.C.), and intramural funding from CNRS, Université Paris Cité and INSERM (to P.L.).
Published: 2023

34. Rapid protection induced by a single-shot Lassa vaccine in male cynomolgus monkeys

Author: Mathieu Mateo, Stéphanie Reynard, Natalia Pietrosemoli, Emeline Perthame, Alexandra Journeaux, Kodie Noy, Clara Germain, Xavier Carnec, Caroline Picard, Virginie Borges-Cardoso, Jimmy Hortion, Hélène Lopez-Maestre, Pierrick Regnard, Lyne Fellmann, Audrey Vallve, Stéphane Barron, Ophélie Jourjon, Orianne Lacroix, Aurélie Duthey, Manon Dirheimer, Maïlys Daniau, Catherine Legras-Lachuer, Caroline Carbonnelle, Hervé Raoul, Frédéric Tangy, Sylvain Baize, Biologie des Infections Virales Émergentes - Biology of Emerging Viral Infections (UBIVE), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Université de Strasbourg (UNISTRA), Simian Laboratory Europe (SILABE), Laboratoire P4 Jean Mérieux-Inserm [Lyon] (Unité de service 3), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Européen de Recherche en Virologie et Immunologie [Lyon] (Tour Inserm CERVI), Délégation régionale Auvergne Rhône-Alpes [Bron, France], Institut National de la Santé et de la Recherche Médicale (INSERM), ViroScan3D SAS [Trévoux, France], Laboratoire d’innovation : vaccins – Innovation lab : vaccines, This study was funded by a grant from the Coalition for Epidemic Preparedness and Innovations (CEPI-CfP-001) to S. Baize and by a grant from the Agence Nationale de la Recherche (ANR-21-CE18-0004-01) to M. Mateo., and ANR-21-CE18-0004,EXPUNGER,Vaccins post exposition contre les virus emergents(2021)
Subjects: Multidisciplinary, [SDV]Life Sciences [q-bio], General Physics and Astronomy, General Chemistry, General Biochemistry, Genetics and Molecular Biology
Abstract: Lassa fever hits West African countries annually in the absence of licensed vaccine to limit the burden of this viral hemorrhagic fever. We previously developed MeV-NP, a single-shot vaccine protecting cynomolgus monkeys against divergent strains one month or more than a year before Lassa virus infection. Given the limited dissemination area during outbreaks and the risk of nosocomial transmission, a vaccine inducing rapid protection could be useful to protect exposed people during outbreaks in the absence of preventive vaccination. Here, we test whether the time to protection can be reduced after immunization by challenging measles virus pre-immune male cynomolgus monkeys sixteen or eight days after a single shot of MeV-NP. None of the immunized monkeys develop disease and they rapidly control viral replication. Animals immunized eight days before the challenge are the best controllers, producing a strong CD8 T-cell response against the viral glycoprotein. A group of animals was also vaccinated one hour after the challenge, but was not protected and succumbed to the disease as the control animals. This study demonstrates that MeV-NP can induce a rapid protective immune response against Lassa fever in the presence of MeV pre-existing immunity but can likely not be used as therapeutic vaccine.
Published: 2023

35. Gravity complexes as a focus of seafloor fluid seepage: the Rio Grande Cone, SE Brazil

Author: Ketzer, M., Praeg, Daniel, Augustin, A., Rodrigues, L., Steiger, A., Rahmati-Abkenar, M., Viana, A., Miller, D., Malinverno, A., Dickens, G., Cupertino, J., Linneaus University, Géoazur (GEOAZUR 7329), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut des Sciences de la Terre de Paris (iSTeP), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Pontifical Catholic University of Rio Grande do Sul (PUC-RS), Universidade Federal do Rio Grande (FURG), Petrobras [Rio de Janeiro], Lamont-Doherty Earth Observatory (LDEO), Columbia University [New York], Trinity College Dublin, and European Project: 656821,H2020,H2020-MSCA-IF-2014,SEAGAS(2016)
Subjects: Multidisciplinary, Geochemistry, Solid Earth sciences, [SDU]Sciences of the Universe [physics], [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Geology, Sedimentology
Abstract: Seafloor methane emissions can affect Earth’s climate and ocean chemistry. Vast quantities of methane formed by microbial decomposition of organic matter are locked within gas hydrate and free gas on continental slopes, particularly in large areas with high sediment accumulations such as deep-sea fans. The release of methane in slope environments has frequently been associated with dissociation of gas hydrates near the edge of the gas hydrate stability zone on the upper slope, with discharges in greater water depths less understood. Here we show, using data from the Rio Grande Cone (western South Atlantic), that the intrinsic, gravity-induced downslope collapse of thick slope sediment accumulations creates structures that serve as pathways for gas migration, unlocking methane and causing seafloor emissions via giant gas flares in the water column. The observed emissions in the study region (up to 310 Mg year−1) are three times greater than estimates for the entire US North Atlantic margin and reveal the importance of collapsing sediment accumulations for ocean carbon cycling. Similar outgassing systems on the Amazon and Niger fans suggest that gravity tectonics on passive margins is a common yet overlooked mechanism driving massive seafloor methane emissions in sediment-laden continental slopes.
Published: 2023

36. Small grains from Ryugu: handling and analysis pipeline for infrared synchrotron microspectroscopy

Author: Stefano Rubino, Zélia Dionnet, Alice Aléon-Toppani, Rosario Brunetto, Tomoki Nakamura, Donia Baklouti, Zahia Djouadi, Cateline Lantz, Obadias Mivumbi, Ferenc Borondics, Stephane Lefrançois, Christophe Sandt, Francesco Capitani, Eva Héripré, David Troadec, Megumi Matsumoto, Kana Amano, Tomoyo Morita, Hisayoshi Yurimoto, Takaaki Noguchi, Ryuji Okazaki, Hikaru Yabuta, Hiroshi Naraoka, Kanako Sakamoto, Shogo Tachibana, Seiichiro Watanabe, Yuichi Tsuda, Institut d'astrophysique spatiale (IAS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Tohoku University [Sendai], Université Paris-Sud - Paris 11 (UP11)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), DISCO beamline, Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de mécanique des sols, structures et matériaux (MSSMat), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Centrale de Micro Nano Fabrication - IEMN (CMNF - IEMN), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), Hokkaido University [Sapporo, Japan], Kyushu University, Hiroshima University, Japan Aerospace Exploration Agency [Sagamihara] (JAXA), Tokyo National University of Fine Arts and Music (Tokyo Geijutsu Daigaku) (GEIDAI), Nagoya University, This work has been funded by the CNES-France (Hayabusa2 mission) and by the ANR project CLASSY (Grant ANR-17-CE31-0004-02). The micro-spectroscopy measurements were supported by grants from Region Ile-de-France (DIM-ACAV) and SOLEIL., Renatech Network, CMNF, and ANR-17-CE31-0004,CLASSY,Composition des surfaces du Système Solaire de bas albédo(2017)
Subjects: [SPI]Engineering Sciences [physics]
Abstract: preprint: https://doi.org/10.21203/rs.3.rs-1622610/v2; International audience; Sample-return missions allow the study of materials collected directly from celestial bodies, unbiased by atmospheric entry effects and/or terrestrial alteration and contamination phenomena, using state-of-the-art techniques which are available only in a laboratory environment—but only if the collected material stays pristine. The scarcity of outer-space unaltered material recovered until now makes this material extremely precious for the potential scientific insight it can bring. To maximize the scientific output of current and future sample-return missions, the scientific community needs to plan for ways of storing, handling, and measuring this precious material while preserving their pristine state for as long as the ‘invasiveness’ of measurements allows. In July 2021, as part of the Hayabusa2 (JAXA) “Stone” preliminary examination team, we received several microscopic particles from the asteroid Ryugu, with the goal of performing IR hyper-spectral imaging and IR micro-tomography studies. Here, we describe the sample transfer, handling methods and analytical pipeline we implemented to study this very precious material while minimizing and surveilling their alteration history on Earth.
Published: 2023

37. Brucella effectors NyxA and NyxB target SENP3 to modulate the subcellular localisation of nucleolar proteins

Author: Arthur Louche, Amandine Blanco, Thais Lourdes Santos Lacerda, Lison Cancade-Veyre, Claire Lionnet, Célia Bergé, Monica Rolando, Frédérique Lembo, Jean-Paul Borg, Carmen Buchrieser, Masami Nagahama, Francine C. A. Gérard, Jean-Pierre Gorvel, Virginie Gueguen-Chaignon, Laurent Terradot, Suzana P. Salcedo, Microbiologie moléculaire et biochimie structurale / Molecular Microbiology and Structural Biochemistry (MMSB), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Meiji Pharmaceutical University, Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), SFR Biosciences, Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CB lab was funded by the Institut Pasteur and ANR-10-LABX-62-IBEID for the Legionella experiments. These effectors were discovered under the ERA-Net Pathogenomics grant and the remaining work funded by ANR-15-CE15-0011-01 attributed to Suzana Salcedo. The work was completed with the ANR SNAPshot ANR-21-CE15-0024 attributed to Suzana Salcedo., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-15-CE15-0011,NucPath,Caractérisation du rôle cellulaire de nouveaux effecteurs bactériens ciblant les noyaux des cellules hôtes(2015), ANR-21-CE15-0024,SNAPshot,Détournement du stress nucléaire par les bactéries pathogènes(2021), Laurent, Terradot, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Caractérisation du rôle cellulaire de nouveaux effecteurs bactériens ciblant les noyaux des cellules hôtes - - NucPath2015 - ANR-15-CE15-0011 - AAPG2015 - VALID, Détournement du stress nucléaire par les bactéries pathogènes - - SNAPshot2021 - ANR-21-CE15-0024 - AAPG2021 - VALID, and École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: [SDV] Life Sciences [q-bio], Multidisciplinary, [SDV]Life Sciences [q-bio], General Physics and Astronomy, General Chemistry, General Biochemistry, Genetics and Molecular Biology
Abstract: The cell nucleus is a primary target for intracellular bacterial pathogens to counteract immune responses and hijack host signalling pathways to cause disease. Here we identify two Brucella abortus effectors, NyxA and NyxB, that interfere with host protease SENP3, and this facilitates intracellular replication of the pathogen. The translocated Nyx effectors directly interact with SENP3 via a defined acidic patch (identified from the crystal structure of NyxB), preventing nucleolar localisation of SENP3 at late stages of infection. By sequestering SENP3, the effectors promote cytoplasmic accumulation of nucleolar AAA-ATPase NVL and ribosomal protein L5 (RPL5) in effector-enriched structures in the vicinity of replicating bacteria. The shuttling of ribosomal biogenesis-associated nucleolar proteins is inhibited by SENP3 and requires the autophagy-initiation protein Beclin1 and the SUMO-E3 ligase PIAS3. Our results highlight a nucleomodulatory function of two Brucella effectors and reveal that SENP3 is a crucial regulator of the subcellular localisation of nucleolar proteins during Brucella infection, promoting intracellular replication of the pathogen.
Published: 2023

38. Migration of surface-associated microbial communities in spaceflight habitats

Author: Daniele Marra, Thodoris Karapantsios, Sergio Caserta, Eleonora Secchi, Malgorzata Holynska, Simon Labarthe, Bastien Polizzi, Sandra Ortega, Margaritis Kostoglou, Christophe Lasseur, Ioannis Karapanagiotis, Sigolene Lecuyer, Arnaud Bridier, Marie-Françoise Noirot-Gros, Romain Briandet, 'Federico II' University of Naples Medical School, Aristotle University of Thessaloniki, Department of Civil, Environmental and Geomatic Engineering [ETH Zürich] (D-BAUG), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), ESA - ESTEC (Netherlands), Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mathématiques de Besançon (UMR 6623) (LMB), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut Pascal (IP), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Laboratoire de Fougères - ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Elsevier
Subjects: Space flight, Biofilm, Microgravity, Transcriptomic, Adaptation, Evolution, Control, [SDV]Life Sciences [q-bio], Cell Biology, Molecular Biology, Applied Microbiology and Biotechnology, Microbiology
Abstract: Astronauts are spending longer periods locked up in ships or stations for scientific and exploration spatial missions. The International Space Station (ISS) has been inhabited continuously for more than 20 years and the duration of space stays by crews could lengthen with the objectives of human presence on the moon and Mars. If the environment of these space habitats is designed for the comfort of astronauts, it is also conducive to other forms of life such as embarked microorganisms. The latter, most often associated with surfaces in the form of biofilm, have been implicated in significant degradation of the functionality of pieces of equipment in space habitats. The most recent research suggests that microgravity could increase the persistence, resistance and virulence of pathogenic microorganisms detected in these communities, endangering the health of astronauts and potentially jeopardizing long-duration manned missions. In this review, we describe the mechanisms and dynamics of installation and propagation of these microbial communities associated with surfaces (spatial migration), as well as long-term processes of adaptation and evolution in these extreme environments (phenotypic and genetic migration), with special reference to human health. We also discuss the means of control envisaged to allow a lasting cohabitation between these vibrant microscopic passengers and the astronauts., Biofilm, 5, ISSN:2590-2075
Published: 2023

39. Dynamical diagnostic of extreme events in Venice lagoon and their mitigation with the MoSE

Author: Alberti, Tommaso, Anzidei, Marco, Faranda, Davide, Vecchio, Antonio, Favaro, Marco, Papa, Alvise, Istituto Nazionale di Geofisica e Vulcanologia - Sezione di Roma (INGV), Istituto Nazionale di Geofisica e Vulcanologia, Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), London Mathematical Laboratory, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Extrèmes : Statistiques, Impacts et Régionalisation (ESTIMR), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Radboud University [Nijmegen], Laboratoire d'études spatiales et d'instrumentation en astrophysique = Laboratory of Space Studies and Instrumentation in Astrophysics (LESIA), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and Istituzione Centro Previsioni e Segnalazioni Maree &ndash
Subjects: [SDU]Sciences of the Universe [physics], [SDE]Environmental Sciences
Abstract: International audience; Extreme events are becoming more frequent due to anthropogenic climate change, posing serious concerns on societal and economic impacts and asking for mitigating strategies, as for Venice. Here, tidal gauge data from 4 stations of the Venice lagoon are used to characterize Extreme Sea Level (ESL) events by means of two dynamical indicators: the instantaneous dimension and the inverse persistence. A close connection is found between the occurrence of ESLs and the inverse persistence, while the instantaneous dimension informs us on the number of interfering factors contributing to the increase of sea level. We further examined the capability of the MoSE (Experimental Electromechanical Module), a safeguarding system recently put into operation, in mitigating extreme flooding events and its operational performances in relation with the values of the two dynamical indicators. We show that the two metrics can provide a valuable support to evaluate and inform operational lagoon forecasts.
Published: 2023

40. Light-independent regulation of algal photoprotection by CO2 availability

Author: M. Águila Ruiz-Sola, Serena Flori, Yizhong Yuan, Gaelle Villain, Emanuel Sanz-Luque, Petra Redekop, Ryutaro Tokutsu, Anika Küken, Angeliki Tsichla, Georgios Kepesidis, Guillaume Allorent, Marius Arend, Fabrizio Iacono, Giovanni Finazzi, Michael Hippler, Zoran Nikoloski, Jun Minagawa, Arthur R. Grossman, Dimitris Petroutsos, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Light Photosynthesis & Metabolism (Photosynthesis), Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science, Universidad de Córdoba = University of Córdoba [Córdoba], National Institute for Basic Biology [Okazaki] (NIBB), Graduate University for Advanced Studies [Hayama] (SOKENDAI), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, University of Potsdam = Universität Potsdam, The Human Frontiers Science Program through the funding of the project RGP0046/2018, Prestige Marie-Curie co-financing grant PRESTIGE-2017-1-0028, The International Max Planck Research School 'Primary Metabolism and Plant Growth' at the Max Planck Institute of Molecular Plant Physiology, The program ‘Plan Propio UCO’ from University of Cordoba, The Carnegie Institution for Science and the Department of Energy, DE-SC0019417, The Marie Curie Initial Training Network Accliphot FP7-PEPOPLE-2012-ITN, The Japan Society for the Promotion of Science, JSPS, for the grants-in-Aid for Scientific Research, KAKENHI, 21H04778 and 21H05040, The German Research Foundation DFG HI 739/9.2, ANR-18-CE20-0006,MetaboLIGHT,Regulation de la photosynthèse par la Lumière et le métabolisme chez les algues(2018), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), and European Project: 751039,UNREDE
Subjects: MESH: Chlamydomonas reinhardtii, Multidisciplinary, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Photosystem II Protein Complex, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], General Physics and Astronomy, MESH: Proteins, General Chemistry, MESH: Carbon Dioxide, General Biochemistry, Genetics and Molecular Biology, MESH: Photosynthesis
Abstract: Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO2 conditions. When light energy exceeds CO2 fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the CO2 Concentrating Mechanism (CCM). How light and CO2 signals converge to regulate these processes remains unclear. Here, we show that excess light activates photoprotection- and CCM-related genes by altering intracellular CO2 concentrations and that depletion of CO2 drives these responses, even in total darkness. High CO2 levels, derived from respiration or impaired photosynthetic fixation, repress LHCSR3/CCM genes while stabilizing the LHCSR1 protein. Finally, we show that the CCM regulator CIA5 also regulates photoprotection, controlling LHCSR3 and PSBS transcript accumulation while inhibiting LHCSR1 protein accumulation. This work has allowed us to dissect the effect of CO2 and light on CCM and photoprotection, demonstrating that light often indirectly affects these processes by impacting intracellular CO2 levels.
Published: 2023

41. FT-GPI, a highly sensitive and accurate predictor of GPI-anchored proteins, reveals the composition and evolution of the GPI proteome in Plasmodium species

Author: Lena M. Sauer, Rodrigo Canovas, Daniel Roche, Hosam Shams-Eldin, Patrice Ravel, Jacques Colinge, Ralph T. Schwarz, Choukri Ben Mamoun, Eric Rivals, Emmanuel Cornillot, Institut de Biologie Computationnelle (IBC), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Institute for Virology [Marburg], Philipps Universität Marburg = Philipps University of Marburg, Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), and Yale School of Medicine [New Haven, Connecticut] (YSM)
Subjects: GPI-proteome, GPI-anchored protein, Infectious Diseases, FT-GPI, [SDV]Life Sciences [q-bio], Plasmodium falciparum, P. vivax, Parasitology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology
Abstract: Background Protozoan parasites are known to attach specific and diverse group of proteins to their plasma membrane via a GPI anchor. In malaria parasites, GPI-anchored proteins (GPI-APs) have been shown to play an important role in host–pathogen interactions and a key function in host cell invasion and immune evasion. Because of their immunogenic properties, some of these proteins have been considered as malaria vaccine candidates. However, identification of all possible GPI-APs encoded by these parasites remains challenging due to their sequence diversity and limitations of the tools used for their characterization. Methods The FT-GPI software was developed to detect GPI-APs based on the presence of a hydrophobic helix at both ends of the premature peptide. FT-GPI was implemented in C ++and applied to study the GPI-proteome of 46 isolates of the order Haemosporida. Using the GPI proteome of Plasmodium falciparum strain 3D7 and Plasmodium vivax strain Sal-1, a heuristic method was defined to select the most sensitive and specific FT-GPI software parameters. Results FT-GPI enabled revision of the GPI-proteome of P. falciparum and P. vivax, including the identification of novel GPI-APs. Orthology- and synteny-based analyses showed that 19 of the 37 GPI-APs found in the order Haemosporida are conserved among Plasmodium species. Our analyses suggest that gene duplication and deletion events may have contributed significantly to the evolution of the GPI proteome, and its composition correlates with speciation. Conclusion FT-GPI-based prediction is a useful tool for mining GPI-APs and gaining further insights into their evolution and sequence diversity. This resource may also help identify new protein candidates for the development of vaccines for malaria and other parasitic diseases.
Published: 2023

42. Faceting the post-disaster built heritage reconstruction process within the digital twin framework for Notre-Dame de Paris

Author: Gros, Antoine, Guillem, Anaïs, De Luca, Livio, Baillieul, Élise, Duvocelle, Benoit, Malavergne, Olivier, Leroux, Lise, Zimmer, Thierry, Modèles et simulations pour l'Architecture et le Patrimoine (MAP), Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherches Historiques du Septentrion (IRHiS) - UMR 8529 (IRHiS), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire de recherche des monuments historiques (LRMH), Centre de Recherche sur la Conservation (CRC ), and Muséum national d'Histoire naturelle (MNHN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: reverse engineering, [SHS.ARCHI]Humanities and Social Sciences/Architecture, space management, Multidisciplinary, Notre-Dame de Paris, reconstruction, digital twin, operational research, anastylosis, [SHS.MUSEO]Humanities and Social Sciences/Cultural heritage and museology, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SHS]Humanities and Social Sciences
Abstract: April 15th, 2019: Notre-Dame Cathedral in Paris was burning, the spire collapsed on the nave, vaults crumbled and most of the timber roof was gone. In the post-disaster context, the authenticity and the monitoring of the archaeological remains are crucial for their potential reuse during reconstruction. This paper analyzes the collapsed transverse arch from the nave of Notre-Dame as a case study of reconstruction, using the digital twin framework. We propose four facets for the digital twin experiment—physical anastylosis, reverse engineering, spatio-temporal tracking of assets, and operational research—that are described in detail, while being assembled to support a hybrid reconstruction hypothesis. The digital twin can realize the parallel unfolding of physical-native and digital-native processes, while acquiring and storing heterogeneous information as semantically structured data. The results demonstrate that the proposed modeling method facilitates the formalization and validation of the reconstruction problem and increases solutions performances. As result, we present a digital twin framework application ranging from acquisition to data processing that informs a successful hybrid reconstruction hypothesis.
Published: 2023

43. A non-inferiority randomized phase III trial of standard immunotherapy by checkpoint inhibitors vs. reduced dose intensity in responding patients with metastatic cancer: the MOIO protocol study

Author: Gravis, Gwenaelle, Marino, Patricia, Olive, Daniel, Penault-Llorca, Frederique, Delord, Jean-Pierre, Simon, Clotilde, Lamrani-Ghaouti, Assia, Sabatier, Renaud, Ciccolini, Joseph, Boher, Jean-Marie, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des sciences de la santé publique [Marseille] (ISSPAM), Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA), Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER, Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Claudius Regaud, Méthodes computationnelles pour la prise en charge thérapeutique en oncologie : Optimisation des stratégies par modélisation mécaniste et statistique (COMPO), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Cancérologie de Marseille (CRCM), and Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut Paoli-Calmettes
Subjects: Cancer Research, Oncology, Genetics, [SDV.CAN]Life Sciences [q-bio]/Cancer
Abstract: Background Immunotherapy (IO) has become a standard of care for treating various types of metastatic cancers and has significantly improved clinical outcome. With the exception of metastatic melanoma in complete response for which treatment can be stopped at 6 months, these treatments are currently administered until either disease progression for some IO, 2 years for others, or unacceptable toxicity. However, a growing number of studies are reporting maintenance of response despite discontinuation of therapy. There is currently no evidence of a dose effect of IO in pharmacokinetic studies. Maintaining efficacy despite a reduction in treatment intensity by decreasing the frequency of administration in patients with highly selected metastatic cancer, is the hypothesis evaluated in the MOIO study. Method/design This non-inferiority, randomized phase III study aims to compare the standard regimen to a 3 monthly regimen of variousIO drugs in adult patients with metastatic cancer in partial (PR) or complete response (CR) after 6 months of standard IO dosing (except melanoma in CR). This is a French national study conducted in 36 centers. The main objective is to demonstrate that the efficacy of a three-monthly administration is not unacceptably less efficacious than a standard administration. Secondary objectives are cost-effectiveness, quality of life (QOL), anxiety, fear of relapse, response rate, overall survival and toxicity. After 6 months of standard IO, patients with partial or complete response will be randomized 1:1 between standard IO or a reduced intensity dose of IO, administered every 3 months. The randomization will be stratified on therapy line,, tumor type, IO type and response status. The primary endpoint is the hazard ratio of progression-free survival. With a planned study duration of 6 years, including 36 months enrolment time, 646 patients are planned to demonstrate with a statistical level of evidence of 5% that the reduced IO regimen is non-inferior to the standard IO regimen, with a relative non-inferiority margin set at 1.3. Discussion Should the hypothesis of non-inferiority with an IO reduced dose intensity be validated, alternate scheduling could preserve efficacy while being cost-effective and allowing a reduction of the toxicity, with an increase in patient’s QOL. Trial registration NCT05078047.
Published: 2023

44. Survey of ticks and tick-borne pathogens in wild chimpanzee habitat in Western Uganda

Author: Lacroux, Camille, Bonnet, Sarah, Pouydebat, Emmanuelle, Buysse, Marie, Rahola, Nil, Rakotobe, Sabine, Okimat, John-Paul, Duron, Olivier, Koual, Rachid, Asalu, Edward, Krief, Sabrina, Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Kibale National Park, Mécanismes Adaptatifs et Evolution (MECADEV), La Phocéenne de Cosmétique, Écologie et Émergence des Pathogènes Transmis par les Arthropodes / Ecology and Emergence of Arthropod-borne Pathogens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Département Santé Animale (DEPT SA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Uganda Wildlife Authority (UWA), The Great Ape Conservation Project, the Fondation Ensemble, the Fondation pour la Nature et l’Homme, the Fondation Prince Albert II and the Fonds Français pour l’Environnement Mondial provided financial support for the research conducted at Sebitoli. La Phocéenne de Cosmétique and the Association Nationale de la Recherche et de la Technologie provided funds for the PhD scholarship of Camille Lacroux. This work has benefited from ‘Investissements d’Avenir’ managed by the French Agence Nationale de la Recherche (ANR, Laboratoire d’Excellence CEBA, ref. ANR-10-LABX-25-01)., and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)
Subjects: Vector-borne pathogens, Borrelia, Cryptoplasma, Ehrlichia, MESH: Rickettsia, MESH: Ixodidae, Piroplasmids, MESH: Ixodes, MESH: Tick-Borne Diseases, Infectious Diseases, Ticks, Amblyomma, [SDE]Environmental Sciences, Apes, Kibale, Parasitology, MESH: Tick Infestations, Rickettsia, MESH: Uganda
Abstract: Background Ticks and tick-borne pathogens significantly impact both human and animal health and therefore are of major concern to the scientific community. Knowledge of tick-borne pathogens is crucial for prescription of mitigation measures. In Africa, much research on ticks has focused on domestic animals. Little is known about ticks and their pathogens in wild habitats and wild animals like the endangered chimpanzee, our closest relative. Methods In this study, we collected ticks in the forested habitat of a community of 100 chimpanzees living in Kibale National Park, Western Uganda, and assessed how their presence and abundance are influenced by environmental factors. We used non-invasive methods of flagging the vegetation and visual search of ticks both on human team members and in chimpanzee nests. We identified adult and nymph ticks through morphological features. Molecular techniques were used to detect and identify tick-borne piroplasmids and bacterial pathogens. Results A total of 470 ticks were collected, which led to the identification of seven tick species: Haemaphysalis parmata (68.77%), Amblyomma tholloni (20.70%), Ixodes rasus sensu lato (7.37%), Rhipicephalus dux (1.40%), Haemaphysalis punctaleachi (0.70%), Ixodes muniensis (0.70%) and Amblyomma paulopunctatum (0.35%). The presence of ticks, irrespective of species, was influenced by temperature and type of vegetation but not by relative humidity. Molecular detection revealed the presence of at least six genera of tick-borne pathogens (Babesia, Theileria, Borrelia, Cryptoplasma, Ehrlichia and Rickettsia). The Afrotopical tick Amblyomma tholloni found in one chimpanzee nest was infected by Rickettsia sp. Conclusions In conclusion, this study presented ticks and tick-borne pathogens in a Ugandan wildlife habitat whose potential effects on animal health remain to be elucidated. Graphical Abstract
Published: 2023

45. Ultraviolet exposure regulates skin metabolome based on the microbiome

Author: Vijaykumar Patra, Natalie Bordag, Yohann Clement, Harald Köfeler, Jean-Francois Nicolas, Marc Vocanson, Sophie Ayciriex, Peter Wolf, Medical University Graz, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Medical University of Graz, CheMod, Institut des Sciences Analytiques (ISA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), ANABIO-MS - Analyse biomoléculaire par spectrométrie de masse - Biological Analysis by Mass Spectrometry, BioTechMed-Graz, Graz University of Technology [Graz] (TU Graz)-Karl-Franzens-Universität Graz-Medical University Graz, and Austrian Science Fund (FWF, W1241)
Subjects: [STAT]Statistics [stat], Multidisciplinary, [SDV]Life Sciences [q-bio]
Abstract: Skin metabolites (
Published: 2023

46. Increased precipitation over land due to climate feedback of large-scale bioenergy cultivation

Author: Li, Zhao, Ciais, Philippe, Wright, Jonathon, Wang, Yong, Liu, Shu, Wang, Jingmeng, Li, Laurent, Lu, Hui, Huang, Xiaomeng, Zhu, Lei, Goll, Daniel, Li, Wei, Tsinghua University [Beijing] (THU), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Modélisation des Surfaces et Interfaces Continentales (MOSAIC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Ministry of Education Ecological Field Station for East Asian Migratory Birds
Subjects: [SDU]Sciences of the Universe [physics]
Abstract: Bioenergy with carbon capture and storage (BECCS) is considered to be a key technology for removing carbon dioxide from the atmosphere. However, large-scale bioenergy crop cultivation results in land cover changes and activates biophysical effects on climate, with earth’s water recycling altered and energy budget re-adjusted. Here, we use a coupled atmosphere-land model with explicit representations of high-transpiration woody (i.e., eucalypt) and low-transpiration herbaceous (i.e., switchgrass) bioenergy crops to investigate the range of impact of large-scale rainfed bioenergy crop cultivation on the global water cycle and atmospheric water recycling. We find that global land precipitation increases under BECCS scenarios, due to enhanced evapotranspiration and inland moisture advection. Despite enhanced evapotranspiration, soil moisture decreases only slightly, due to increased precipitation and reduced runoff. Our results indicate that, at the global scale, the water consumption by bioenergy crop growth would be partially compensated by atmospheric feedbacks. Thus, to support more effective climate mitigation policies, a more comprehensive assessment, including the biophysical effects of bioenergy cultivation, is highly recommended.
Published: 2023

47. On the spectral theory of groups of automorphisms of S-adic nilmanifolds

Author: Bekka, Bachir, Guivarc'h, Yves, Institut de Recherche Mathématique de Rennes (IRMAR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-11-LABX-0020,LEBESGUE,Centre de Mathématiques Henri Lebesgue : fondements, interactions, applications et Formation(2011), Bekka, Bachir, AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)
Subjects: Applied Mathematics, General Mathematics, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], FOS: Mathematics, [MATH.MATH-DS] Mathematics [math]/Dynamical Systems [math.DS], Dynamical Systems (math.DS), Group Theory (math.GR), Mathematics - Dynamical Systems, 37A05, 22F30, 60B15, 60G50, Mathematics - Group Theory
Abstract: Let $S=\{p_1, \dots, p_r,\infty\}$ for prime integers $p_1, \dots, p_r.$ Let $X$ be an $S$-adic compact nilmanifold, equipped with the unique translation invariant probability measure $\mu.$ We characterize the countable groups $\Gamma$ of automorphisms of $X$ for which the Koopman representation $\kappa$ on $L^2(X,\mu)$ has a spectral gap. More specifically, we show that $\kappa$ does not have a spectral gap if and only if there exists a non-trivial $\Gamma$-invariant quotient solenoid (that is, a finite-dimensional, connected, compact abelian group) on which $\Gamma$ acts as a virtually abelian group., Comment: 25 pages
Published: 2023

48. Halogen chemistry in volcanic plumes: a 1D framework based on MOCAGE 1D (version R1.18.1) preparing 3D global chemistry modelling

Author: Virginie Marécal, Ronan Voisin-Plessis, Tjarda Jane Roberts, Alessandro Aiuppa, Herizo Narivelo, Paul David Hamer, Béatrice Josse, Jonathan Guth, Luke Surl, Lisa Grellier, Centre national de recherches météorologiques (CNRM), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Centre National d’Études Spatiales [Paris] (CNES), Dipartimento di Scienze della Terra e del Mare [Palermo] (DiSTeM), Università degli studi di Palermo - University of Palermo, Norwegian Institute for Air Research (NILU), Department of Chemistry [Aberdeen], School of Natural and Computing Sciences, University of Aberdeen-University of Aberdeen, STRATO - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre Interprofessionnel Technique d'Etude des Pollutions Atmosphériques (CITEPA), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Norsk Institutt for Luftforskning (NILU), VOLC-HAL-CLIM: ANR-18-CE1-0018, and ANR-18-CE01-0018,VOLC-HAL-CLIM,Halogènes volcaniques : de la Terre profonde aux impacts atmosphériques(2018)
Subjects: [PHYS.PHYS.PHYS-AO-PH]Physics [physics]/Physics [physics]/Atmospheric and Oceanic Physics [physics.ao-ph], [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Halogen chemistry, [SDE]Environmental Sciences, Volcanic emissions, [SDU.STU.VO]Sciences of the Universe [physics]/Earth Sciences/Volcanology, General Medicine
Abstract: HBr emissions from volcanoes lead rapidly to the formation of BrO within volcanic plumes and have an impact on tropospheric chemistry, at least at the local and regional scales. The motivation of this paper is to prepare a framework for further 3D modelling of volcanic halogen emissions in order to determine their fate within the volcanic plume and then in the atmosphere at the regional and global scales. The main aim is to evaluate the ability of the model to produce a realistic partitioning of bromine species within a grid box size typical of MOCAGE (Model Of atmospheric Chemistry At larGE scale) 3D (0.5∘ × 0.5∘). This work is based on a 1D single-column configuration of the global chemistry-transport model MOCAGE that has low enough computational cost to allow us to perform a large set of sensitivity simulations. This paper uses the emissions from the Mount Etna eruption on 10 May 2008. Several reactions are added to MOCAGE to represent the volcanic plume halogen chemistry. A simple plume parameterisation is also implemented and tested. The use of this parameterisation tends to only slightly limit the efficiency of BrO net production. Both simulations with and without the parameterisation give results for the partitioning of the bromine species, of ozone depletion and of the BrO/SO2 ratio that are consistent with previous studies. A series of test experiments were performed to evaluate the sensitivity of the results to the composition of the emissions (primary sulfate aerosols, Br radical and NO) and to the effective radius assumed for the volcanic sulfate aerosols. Simulations show that the plume chemistry is sensitive to all these parameters. We also find that the maximum altitude of the eruption changes the BrO production, which is linked to the vertical variability of the concentrations of oxidants in the background air. These sensitivity tests display changes in the bromine chemistry cycles that are generally at least as important as the plume parameterisation. Overall, the version of the MOCAGE chemistry developed for this study is suitable to produce the expected halogen chemistry in volcanic plumes during daytime and night-time.
Published: 2023

49. Asymptotic stability of scalar multi-D inviscid shock waves

Author: Serre, Denis, Unité de Mathématiques Pures et Appliquées (UMPA-ENSL), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS), and École normale supérieure de Lyon (ENS de Lyon)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Mathematics - Analysis of PDEs, Algebra and Number Theory, contraction semigroup, 35B40, asymptotic stability. MSC2010: 35L65, FOS: Mathematics, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], shock waves, Geometry and Topology, Scalar conservation laws, Burgers equation, Analysis of PDEs (math.AP)
Abstract: In several space dimensions, scalar shock waves between two constant states u $\pm$ are not necessarily planar. We describe them in detail. Then we prove their asymptotic stability, assuming that they are uniformly non-characteristic. Our result is conditional for a general flux, while unconditional for the multi-D Burgers equation.
Published: 2023

50. Tropical Linear Regression and Mean Payoff Games: Or, How to Measure the Distance to Equilibria

Author: Marianne Akian, Stéphane Gaubert, Yang Qi, Omar Saadi, TROPICAL (TROPICAL), Centre de Mathématiques Appliquées - Ecole Polytechnique (CMAP), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: FOS: Computer and information sciences, Computer Science::Computer Science and Game Theory, Optimization and Control (math.OC), Computer Science - Computer Science and Game Theory, General Mathematics, FOS: Mathematics, Mathematics - Combinatorics, Combinatorics (math.CO), [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], MSC Primary 06F20, 14T10, 15A80, 16Y20, 16Y60, Secondary 20N20, 15A24, Mathematics - Optimization and Control, Physics::Atmospheric and Oceanic Physics, Computer Science and Game Theory (cs.GT)
Abstract: We study a tropical linear regression problem consisting in finding the best approximation of a set of points by a tropical hyperplane. We establish a strong duality theorem, showing that the value of this problem coincides with the maximal radius of a Hilbert's ball included in a tropical polyhedron. We also show that this regression problem is polynomial-time equivalent to mean payoff games. We illustrate our results by solving an inverse problem from auction theory. In this setting, a tropical hyperplane represents the set of equilibrium prices. Tropical linear regression allows us to quantify the distance of a market to the set of equilibria, and infer secret preferences of a decision maker.
Published: 2023

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