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2. Multidisciplinary team meetings in treatment of spinal muscular atrophy adult patients: a real-life observatory for innovative treatments

Author

Salort-Campana, Emmanuelle, Solé, Guilhem, Magot, Armelle, Tard, Céline, Noury, Jean-Baptiste, Behin, Anthony, De La Cruz, Elisa, Boyer, François, Lefeuvre, Claire, Masingue, Marion, Debergé, Louise, Finet, Armelle, Brison, Mélanie, Spinazzi, Marco, Pegat, Antoine, Sacconi, Sabrina, Malfatti, Edoardo, Choumert, Ariane, Bellance, Rémi, Bedat-Millet, Anne-Laure, Feasson, Léonard, Vuillerot, Carole, Jacquin-Piques, Agnès, Michaud, Maud, Pereon, Yann, Stojkovic, Tanya, Laforêt, Pascal, Attarian, Shahram, and Cintas, Pascal

Published
2024
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3. Modulation of fungal phosphate homeostasis by the plant hormone strigolactone

Author

Bradley, James M., Bunsick, Michael, Ly, George, Aquino, Bruno, Wang, Flora Zhiqi, Holbrook-Smith, Duncan, Suginoo, Shingo, Bradizza, Dylan, Kato, Naoki, As’sadiq, Omar, Marsh, Nina, Osada, Hiroyuki, Boyer, François-Didier, McErlean, Christopher S.P., Tsuchiya, Yuichiro, Subramaniam, Rajagopal, Bonetta, Dario, McCourt, Peter, and Lumba, Shelley

Published
2024
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5. Structural and functional analyses explain Pea KAI2 receptor diversity and reveal stereoselective catalysis during signal perception

Author

Guercio, Angelica M, Torabi, Salar, Cornu, David, Dalmais, Marion, Bendahmane, Abdelhafid, Le Signor, Christine, Pillot, Jean-Paul, Le Bris, Philippe, Boyer, François-Didier, Rameau, Catherine, Gutjahr, Caroline, de Saint Germain, Alexandre, and Shabek, Nitzan

Subjects
Biochemistry and Cell Biology, Biological Sciences, Arabidopsis, Arabidopsis Proteins, Catalysis, Pisum sativum, Perception, Plant Growth Regulators, Biological sciences, Biomedical and clinical sciences
Abstract

KAI2 proteins are plant α/β hydrolase receptors which perceive smoke-derived butenolide signals and endogenous, yet unidentified KAI2-ligands (KLs). The number of functional KAI2 receptors varies among species and KAI2 gene duplication and sub-functionalization likely plays an adaptative role by altering specificity towards different KLs. Legumes represent one of the largest families of flowering plants and contain many agronomic crops. Prior to their diversification, KAI2 underwent duplication resulting in KAI2A and KAI2B. Here we demonstrate that Pisum sativum KAI2A and KAI2B are active receptors and enzymes with divergent ligand stereoselectivity. KAI2B has a higher affinity for and hydrolyses a broader range of substrates including strigolactone-like stereoisomers. We determine the crystal structures of PsKAI2B in apo and butenolide-bound states. The biochemical, structural, and mass spectra analyses of KAI2s reveal a transient intermediate on the catalytic serine and a stable adduct on the catalytic histidine, confirming its role as a bona fide enzyme. Our work uncovers the stereoselectivity of ligand perception and catalysis by diverged KAI2 receptors and proposes adaptive sensitivity to KAR/KL and strigolactones by KAI2B.

Published
2022

6. Module-per-Object: a Human-Driven Methodology for C++-based High-Level Synthesis Design

Author

da Silva, Jeferson Santiago, Boyer, François-Raymond, and Langlois, J. M. Pierre

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing
Abstract

High-Level Synthesis (HLS) brings FPGAs to audiences previously unfamiliar to hardware design. However, achieving the highest Quality-of-Results (QoR) with HLS is still unattainable for most programmers. This requires detailed knowledge of FPGA architecture and hardware design in order to produce FPGA-friendly codes. Moreover, these codes are normally in conflict with best coding practices, which favor code reuse, modularity, and conciseness. To overcome these limitations, we propose Module-per-Object (MpO), a human-driven HLS design methodology intended for both hardware designers and software developers with limited FPGA expertise. MpO exploits modern C++ to raise the abstraction level while improving QoR, code readability and modularity. To guide HLS designers, we present the five characteristics of MpO classes. Each characteristic exploits the power of HLS-supported modern C++ features to build C++-based hardware modules. These characteristics lead to high-quality software descriptions and efficient hardware generation. We also present a use case of MpO, where we use C++ as the intermediate language for FPGA-targeted code generation from P4, a packet processing domain specific language. The MpO methodology is evaluated using three design experiments: a packet parser, a flow-based traffic manager, and a digital up-converter. Based on experiments, we show that MpO can be comparable to hand-written VHDL code while keeping a high abstraction level, human-readable coding style and modularity. Compared to traditional C-based HLS design, MpO leads to more efficient circuit generation, both in terms of performance and resource utilization. Also, the MpO approach notably improves software quality, augmenting parametrization while eliminating the incidence of code duplication., Comment: 9 pages. Paper accepted for publication at The 27th IEEE International Symposium on Field-Programmable Custom Computing Machines, San Diego CA, April 28 - May 1, 2019

Published
2019

7. Three mutations repurpose a plant karrikin receptor to a strigolactone receptor

Author

Arellano-Saab, Amir, Bunsick, Michael, Galib, Hasan Al, Zhao, Wenda, Schuetz, Stefan, Bradley, James Michael, Xu, Zhenhua, Adityani, Claresta, Subha, Asrinus, McKay, Hayley, de Saint Germain, Alexandre, Boyer, François-Didier, McErlean, Christopher S. P., Toh, Shigeo, McCourt, Peter, Stogios, Peter J., and Lumba, Shelley

Published
2021

9. P4-compatible High-level Synthesis of Low Latency 100 Gb/s Streaming Packet Parsers in FPGAs

Author

da Silva, Jeferson Santiago, Boyer, François-Raymond, and Langlois, J. M. Pierre

Subjects
Computer Science - Hardware Architecture
Abstract

Packet parsing is a key step in SDN-aware devices. Packet parsers in SDN networks need to be both reconfigurable and fast, to support the evolving network protocols and the increasing multi-gigabit data rates. The combination of packet processing languages with FPGAs seems to be the perfect match for these requirements. In this work, we develop an open-source FPGA-based configurable architecture for arbitrary packet parsing to be used in SDN networks. We generate low latency and high-speed streaming packet parsers directly from a packet processing program. Our architecture is pipelined and entirely modeled using templated C++ classes. The pipeline layout is derived from a parser graph that corresponds a P4 code after a series of graph transformation rounds. The RTL code is generated from the C++ description using Xilinx Vivado HLS and synthesized with Xilinx Vivado. Our architecture achieves 100 Gb/s data rate in a Xilinx Virtex-7 FPGA while reducing the latency by 45% and the LUT usage by 40% compared to the state-of-the-art., Comment: Accepted for publication at the 26th ACM/SIGDA International Symposium on Field-Programmable Gate Arrays February 25 - 27, 2018 Monterey Marriott Hotel, Monterey, California, 7 pages, 7 figures, 1 table

Published
2017
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11. Convergence of patient- and physician-reported outcomes in the French National Registry of Facioscapulohumeral Dystrophy

Author

Sanson, Benoît, Stalens, Caroline, Guien, Céline, Villa, Luisa, Eng, Catherine, Rabarimeriarijaona, Sitraka, Bernard, Rafaëlle, Cintas, Pascal, Solé, Guilhem, Tiffreau, Vincent, Echaniz-Laguna, Andoni, Magot, Armelle, Juntas Morales, Raul, Boyer, François Constant, Nadaj-Pakleza, Aleksandra, Jacquin-Piques, Agnès, Béroud, Christophe, and Sacconi, Sabrina

Published
2022
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12. Extern Objects in P4: an ROHC Header Compression Scheme Case Study

Author

da Silva, Jeferson Santiago, Boyer, François-Raymond, Chiquette, Laurent-Olivier, and Langlois, J. M. Pierre

Subjects
Computer Science - Networking and Internet Architecture
Abstract

P4 is an emergent packet-processing language with which the user can describe how the packets are to be processed in a switching element. This paper presents a way to implement complex operations that are not natively supported in P4. In this work, we explored two different methods to add extensions to P4: i) using new native primitives and ii) using extern instances. As a case study, an ROHC entity was implemented and invoked in a P4 program. The tests showed similar relative performance in both methods in terms of normalized packet latency. However, extern instances appear to be more suitable for target-specific switching applications, where the manufacturer/vendor can specify its own specific operations without changes in the P4 syntax and semantics. Extern instances only require changes in the target-specific backend compiler while keeping the P4 frontend compiler unchanged. The use of externs also results in a more elegant code solution since they are implemented outside the switch-core, thus reducing side effects risks that can be caused by a modification in a switch pipeline implementation., Comment: 6 pages, 4 figures, 3 listings

Published
2016

15. HTL/KAI2 signalling substitutes for light to control plant germination.

Author

Hountalas, Jenna E., Bunsick, Michael, Xu, Zhenhua, Taylor, Andrea A., Pescetto, Gianni, Ly, George, Boyer, François-Didier, McErlean, Christopher S. P., and Lumba, Shelley

Subjects
GENE expression profiling, CELLULAR signal transduction, ARABIDOPSIS thaliana, CONVERGENT evolution, PARASITIC plants
Abstract

Plants monitor multiple environmental cues, such as light and temperature, to ensure they germinate at the right time and place. Some specialist plants, like ephemeral fire-following weeds and root parasitic plants, germinate primarily in response to small molecules found in specific environments. Although these species come from distinct clades, they use the same HYPOSENSITIVE TO LIGHT/KARRIKIN INSENSITIVE 2 (HTL/KAI2) signalling pathway, to perceive different small molecules suggesting convergent evolution on this pathway. Here, we show that HTL/KAI2 signalling in Arabidopsis thaliana bypasses the light requirement for germination. The HTL/KAI2 downstream component, SUPPRESSOR OF MAX2 1 (SMAX1) accumulates in the dark and is necessary for PHYTOCHROME INTERACTING FACTOR 1/PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIF1/PIL5) to regulate hormone response pathways conducive to germination. The interaction of HTL/KAI2 and light signalling may help to explain how specialist plants like ephemeral and parasitic weeds evolved their germination behaviour in response to specific environments. Author summary: Specialist plants have convergently evolved to use the same family of receptors to perceive different small molecules in lieu of necessary germination cues, like light. Although light is necessary for the germination of many generalist plants such as the model organism Arabidopsis thaliana, we show that activating the conserved receptor in Arabidopsis promotes germination in the absence of light. We show that the downstream component of the AtKAI2 signalling pathway is stable in the dark which explains its ability to negatively regulate germination. Additionally, we show that activating the receptor in the dark can modulate the gene expression profile by regulating key components of the light signalling pathway. Our study highlights how specialist plants may recycle components of conserved signaling pathways to thrive in new environments. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Immunoglobulin light-chain toxicity in a mouse model of monoclonal immunoglobulin light-chain deposition disease

Author

Bender, Sébastien, Ayala, Maria Victoria, Bonaud, Amélie, Javaugue, Vincent, Carrion, Claire, Oblet, Christelle, Rinsant, Alexia, Kaaki, Sihem, Oruc, Zeliha, Boyer, François, Paquet, Agnès, Pons, Nicolas, Hervé, Bastien, Ashi, Mohamad Omar, Jaccard, Arnaud, Delpy, Laurent, Touchard, Guy, Cogné, Michel, Bridoux, Frank, and Sirac, Christophe

Published
2020
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17. Réponses rapides dans le cadre du COVID-19 – Mesures et précautions essentielles pour le masseur-kinésithérapeute auprès des patients à domicile

Author

Despeyroux, Sophie, Lascols, Sylvie, Billet, Didier, Contal, Olivier, Freynet, Anne, Médrinal, Clément, Reffiena, Matthieu, Wild, Pauline, Bonnevie, Tristan, Boyer, François-Constant, Houze, Marie-Hélène, Kubicki, Alexandre, Lebret, Marius, Mathieu, Pascale, Mourey, France, Olivon, Damien, Poncin, William, Portero, Pierre, Rambaud, Alexandre, Roren, Alexandra, Sancho, Pierre-Olivier, Sarhan, François-Régis, Tourjansky, Yvan, Prieur, Guillaume, Wiart, Laurent, and Gedda, Michel

Published
2020
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20. Drop impact of shear thickening liquids

Author

Boyer, Francois, Snoeijer, Jacco H., Dijksman, J. Frits, and Lohse, Detlef

Subjects
Physics - Fluid Dynamics, Condensed Matter - Soft Condensed Matter
Abstract

The impact of drops of concentrated non-Brownian suspensions (cornstarch and polystyrene spheres) onto a solid surface is investigated experimentally. The spreading dynamics and maxi- mal deformation of the droplet of such shear thickening liquids are found to be markedly different from the impact of Newtonian drops. A particularly striking observation is that the maximal de- formation is independent of the drop velocity and that the deformation suddenly stops during the impact phase. Both observations are due to the shear-thickening rheology of the suspensions, as is theoretically explained from a balance between the kinetic energy and the viscously-dissipated en- ergy, from which we establish a scaling relation between drop maximal deformation and rheological parameters of concentrated suspensions., Comment: 5 pages, submitted to Phys. Rev. Lett

Published
2013
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23. Two-Dimensional Melting of a Crystal of Ferrofluid Spikes

Author

Boyer, François and Falcon, Eric

Subjects
Condensed Matter - Soft Condensed Matter, Condensed Matter - Other Condensed Matter, Condensed Matter - Statistical Mechanics, Nonlinear Sciences - Chaotic Dynamics
Abstract

We report the observation of the transition from an ordered solid-like phase to a disordered liquid-like phase of a lattice of spikes on a ferrofluid surface submitted to horizontal sinusoidal vibrations. The melting transition occurs for a critical spike displacement which is experimentally found to follow the Lindemann criterion, for two different lattice topologies (hexagonal and square) and over a wide range of lattice wavelengths. An intermediate hexatic-like phase between the solid and isotropic liquid phases is also observed and characterized by standard correlation functions. This dissipative out-of-equilibrium system exhibits strong similarities with 2D melting in solid-state physics., Comment: to be published in Phys. Rev. Lett

Published
2009
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24. SUPPRESSOR OF MAX2 1-LIKE (SMXL) homologs are MAX2-dependent repressors of Physcomitrium patens growth

Author

Guillory, Ambre, primary, Lopez-Obando, Mauricio, additional, Bouchenine, Khalissa, additional, Le Bris, Philippe, additional, Lécureuil, Alain, additional, Pillot, Jean-Paul, additional, Steinmetz, Vincent, additional, Boyer, François-Didier, additional, Rameau, Catherine, additional, de Saint Germain, Alexandre, additional, and Bonhomme, Sandrine, additional

Published
2024
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27. Wave turbulence on the surface of a ferrofluid submitted to a magnetic field

Author

Boyer, François and Falcon, Eric

Subjects
Physics - Classical Physics, Condensed Matter - Statistical Mechanics, Nonlinear Sciences - Chaotic Dynamics, Physics - Fluid Dynamics
Abstract

We report the observation of wave turbulence on the surface of a ferrofluid mechanically forced and submitted to a static normal magnetic field. We show that magnetic surface waves arise only above a critical field. The power spectrum of their amplitudes displays a frequency-power law leading to the observation of a magnetic wave turbulence regime which is experimentally shown to involve a 4-wave interaction process. The existence of the regimes of gravity, magnetic and capillary wave turbulence is reported in the phase space parameters as well as a triple point of coexistence of these three regimes. Most of these features are understood using dimensional analysis or the dispersion relation of the ferrohydrodynamics surface waves.

Published
2008
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41. Les strigolactones : hormones végétales et médiateurs chimiques dans le sol, une opportunité pour la croissance des plantes

Author

Boyer, François-Didier, Keita, Antoinette, de Saint Germain, Alexandre, and Boyer, François-Didier

Subjects
agroecology, allelochemicals, récepteurs α/β hydrolases, α/β hydrolase receptors, allélochimiques, [CHIM.OTHE] Chemical Sciences/Other, agroécologie, hormones végétales, plant hormones, Chémobiologie, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, strigolactones, Chemical biology
Abstract

At the beginning of the 21 st century, agriculture must change its paradigm. It is reasonable that it limits, or even in the longer term, abandons the use of artificial pesticides but also that it adapts to global warming. These pesticides have made it possible to produce food products efficiently and in quantity, but at the cost of impacts on health and the environment Agroecology, among others, by promoting favorable natural interactions in the rhizosphere, offers interesting perspectives for changing the type of agriculture. Strigolactones, the latest class of phytohormones to be discovered, are also chemical mediators in the rhizosphere. They are particularly interesting molecules to study in this context. Striga, Phelipanche and Orobanche parasitic plants cause significant yield losses in Africa and in the Mediterranean basin. SLs activate the seed germination mechanisms of these parasitic plants. Targeting their receptors is therefore essential to control these parasites., Dans ce début de XXIe siècle, l’agriculture doit changer de paradigme. Il est raisonnable qu’elle limite, voire à plus long terme, abandonne l’usage des pesticides artificiels mais aussi qu’elle s’adapte au réchauffement climatique. Ces pesticides ont permis de produire efficacement et en quantité les produits alimentaires mais au prix d’impacts sur la santé et l’environnement. L’agroécologie, entre autres, en favorisant les interactions naturelles favorables dans la rhizosphère, offre des perspectives intéressantes pour changer de type d’agriculture. Les strigolactones (SL), dernière classe d’hormone végétale à avoir été découverte, sont aussi des médiateurs chimiques dans la rhizosphère. Ce sont des molécules particulièrement intéressantes à étudier dans ce contexte. Les plantes parasites de type Striga, Phelipanche et Orobanche provoquent des pertes importantes de rendement en Afrique et dans le bassin méditerranéen. Les SL activent les mécanismes de germination des graines de ces plantes parasites. Le ciblage de leurs récepteurs est donc primordial pour lutter contre ces parasites.

Published
2023

43. Impact des variations climatiques sur l’émission des biocides organiques résiduels dans les collections d’histoire naturelle

Author

Edoumba, Elise, Minchin, Sébastien, Marcotte, Stéphane, Boyer, François, Colson, Isabelle, Leboucher, Sandra, and Kermanach, Thierry

Subjects
organic materials, climat, matériaux organiques, naturalia, pollutants, polluants, climate
Abstract

La présence de biocides dans les différentes collections formées de matériaux organiques est un facteur de dégradation des spécimens et des objets qui peut avoir des conséquences en matière de santé publique. L’ampleur du phénomène d’émission de ces polluants dépend des variations climatiques dans les espaces d’exposition et dans les réserves. Le département Conservation préventive du C2RMF, le Muséum d’histoire naturelle de Rouen et l’Institut national des sciences appliquées de Rouen présentent les résultats d’une étude menée sur différents matériaux organiques visant à caractériser le mécanisme d’émission d’un certain nombre de biocides en fonction des conditions climatiques. The presence of biocides in different collections containing organic materials is one of the reasons for the deterioration of specimens and objects that may have consequences for public health. The extent of these pollutant emissions depends on variations in temperature in the exhibition rooms and storage areas. The C2RMF’s Preventive Conservation Department, the Muséum d’Histoire Naturelle, Rouen, and the Institut National des Sciences Appliquées, Rouen, present the results of a study carried out on different organic materials, with the aim of characterizing the emission mechanism of a certain number of biocides according to climatic conditions.

Published
2023

44. Physcomitrium patensSMXL homologs are PpMAX2-dependent negative regulators of growth

Author

Guillory, Ambre, primary, Lopez-Obando, Mauricio, additional, Bouchenine, Khalissa, additional, Bris, Philippe Le, additional, Lécureuil, Alain, additional, Pillot, Jean-Paul, additional, Steinmetz, Vincent, additional, Boyer, François-Didier, additional, Rameau, Catherine, additional, de Saint Germain, Alexandre, additional, and Bonhomme, Sandrine, additional

Published
2023
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45. Effects of Whole-Body Vibration Exercise on Athletes with Ankle Instability: A Systematic Review

Author

Coelho-Oliveira, Ana Carolina, primary, Taiar, Redha, additional, Pessanha-Freitas, Juliana, additional, Reis-Silva, Aline, additional, Ferreira-Souza, Luiz Felipe, additional, Jaques-Albuquerque, Luelia Teles, additional, Lennertz, Aline, additional, Moura-Fernandes, Márcia Cristina, additional, Rodrigues Lacerda, Ana Cristina, additional, Mendonça, Vanessa A., additional, Sañudo, Borja, additional, Seixas, Adérito, additional, Boyer, François Constant, additional, Bernardo-Filho, Mario, additional, Rapin, Amandine, additional, and Sá-Caputo, Danúbia, additional

Published
2023
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48. Annexe 3. Meules et mortiers

Author

Boyer, François

Abstract

Le nombre total de fragments de pièces de mouture assurées recueillies lors de la fouille du site du Lycée militaire est de 44, dont 5 mortiers. Le collage de deux fragments ramène à 38 le nombre des meules ; le plus souvent fragmentaires, elles se répartissent entre : 20 meules fixes (meta), dont 4 entières, et 18 mobiles (catillus), dont 4 sont également entières. Les contextes Sept meules peuvent être associées à un contexte artisanal (tabl. I). Une meta complète a été trouvée dans l’ateli...

Published
2023

49. Un quartier antique d’artisanat métallurgique à Autun

Author

Alfonso, Guy, Allag, Claudine, Boyer, François, Chardron‑Picault, Pascale, Creuzenet, Fabienne, Ducreux, Franck, Grapin, Claude, Groetembril, Sabine, Haut, Philippe, Mangin, Michel, Olmer, Fabienne, Pernot, Michel, Ploquin, Alain, Popovitch, Laurent, Renel, François, RodeT‑Belarbi, Isabelle, Serneels, Vincent, Solari, Maria‑Eugenia, Vaxelaire, Laurent, Chardron-Picault, Pascale, and Pernot, Michel

Subjects
HD, rempart, urbanisme, archéométallurgie, 1er-Ille s. ap. J.-C, peinture murale, artisanat céramique, fer, bronze, travail de l’os, période galloromaine, îlot, Archaeology, Bourgogne, SOC003000
Abstract

C’est à l’occasion de travaux au Lycée militaire d’Autun qu’ont été mis au jour les vestiges d’ateliers gallo-romains ayant fonctionné entre le Ier et le IIIe s. de n.è., au sein de la cité d’Augustodunum. Après une description précise des bâtiments, replacés dans leur contexte urbain, les différents artisanats sont étudiés en détail : travail des alliages cuivreux et du fer, céramique, tabletterie. Grâce à ces travaux, c’est notamment la chaîne de production de l’artisanat métallurgique qui est désormais mieux connue. L’analyse des nombreux fragments de moules, des vestiges de fours et des déchets de forge a fourni des données inédites pour la fabrication d’objets usuels tels que fibules en laiton et clochettes en tôle de fer bronzé. L’artisanat apparaît enfin, selon des processus déjà connus à Bibracte, comme une forte composante économique de la cité éduenne. La richesse de sa documentation fait de cet ouvrage une importante contribution aux recherches sur l’artisanat antique. Vestiges of Gallo-Roman workshops that were in activity between the 1st and 3rd centuries AD in the city of Augustodunum were found in the course of work carried out at the Lycée militaire in Autun. The workshop buildings are described in detail and situated in their urban setting. The different crafts activities are studied closely: metalworking with copper and iron alloys, ceramics, crafts of bone. This work has enhanced our knowledge of the chain of production in metallurgical crafts in particular. Fresh data on the manufacture of common objects such as brass fibulae and bells of bronze coated iron sheet is obtained from the analysis of mould fragments, of furnace remains and of forge slag and waste. Crafts emerge as a major feature of the economy in the city of the Aedui, according to processes already identified at Bibracte. The rich documentation of this work constitutes a significant contribution to research on crafts in ancient times.

Published
2023

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