1,128 results on '"Oger P"'
Search Results
2. Sensitivity Analysis for Active Sampling, with Applications to the Simulation of Analog Circuits
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Chhaibi, Reda, Gamboa, Fabrice, Oger, Christophe, Oliveira, Vinicius, Pellegrini, Clément, and Remot, Damien
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Statistics - Machine Learning ,Computer Science - Machine Learning ,Statistics - Applications ,Statistics - Methodology - Abstract
We propose an active sampling flow, with the use-case of simulating the impact of combined variations on analog circuits. In such a context, given the large number of parameters, it is difficult to fit a surrogate model and to efficiently explore the space of design features. By combining a drastic dimension reduction using sensitivity analysis and Bayesian surrogate modeling, we obtain a flexible active sampling flow. On synthetic and real datasets, this flow outperforms the usual Monte-Carlo sampling which often forms the foundation of design space exploration., Comment: 7 pages
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- 2024
3. Linear isometries of Hol(D)
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Chalendar, I., Oger, L., and Partington, J. R.
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Mathematics - Complex Variables ,47B33, 30H05, 47A10 - Abstract
A complete characterisation is given of all the linear isometries of the Fr\'echet space of all holomorphic functions on the unit disc, when it is given one of the two standard metrics: these turn out to be weighted composition operators of a particular form. Operators similar to an isometry are also classified. Further, the larger class of operators isometric when restricted to one of the defining seminorms is identified. Finally, the spectra of such operators are studied., Comment: 19 pages
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- 2024
4. Lineage-dependent partitioning of activities in chemoclines defines Woesearchaeota ecotypes in an extreme aquatic ecosystem
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Lilian A. Cloarec, Thomas Bacchetta, Maxime Bruto, Christophe Leboulanger, Vincent Grossi, Céline Brochier-Armanet, Jean-Pierre Flandrois, Adrian Zurmely, Cécile Bernard, Marc Troussellier, Hélène Agogué, Magali Ader, Christine Oger-Desfeux, Philippe M. Oger, Adrien Vigneron, and Mylène Hugoni
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Archaeal genomic diversity ,Woesearchaeales ,Ecotypes ,Metagenomics ,Metatranscriptomics ,Extreme lake ,Microbial ecology ,QR100-130 - Abstract
Abstract Background DPANN archaea, including Woesearchaeota, encompass a large fraction of the archaeal diversity, yet their genomic diversity, lifestyle, and role in natural microbiomes remain elusive. With an archaeal assemblage naturally enriched in Woesearchaeota and steep vertical geochemical gradients, Lake Dziani Dzaha (Mayotte) provides an ideal model to decipher their in-situ activity and ecology. Results Using genome-resolved metagenomics and phylogenomics, we identified highly diversified Woesearchaeota populations and defined novel halophilic clades. Depth distribution of these populations in the water column showed an unusual double peak of abundance, located at two distinct chemoclines that are hotspots of microbial diversity in the water column. Genome-centric metatranscriptomics confirmed this vertical distribution and revealed a fermentative activity, with acetate and lactate as end products, and active cell-to-cell processes, supporting strong interactions with other community members at chemoclines. Our results also revealed distinct Woesearchaeota ecotypes, with different transcriptional patterns, contrasted lifestyles, and ecological strategies, depending on environmental/host conditions. Conclusions This work provides novel insights into Woesearchaeota in situ activity and metabolism, revealing invariant, bimodal, and adaptative lifestyles among halophilic Woesearchaeota. This challenges our precepts of an invariable host-dependent metabolism for all the members of this taxa and revises our understanding of their contributions to ecosystem functioning and microbiome assemblage. Video Abstract
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- 2024
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5. Coverings of the plane by self-avoiding curves which satisfy the local isomorphism property
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Oger, Francis
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Mathematics - Combinatorics ,05B45 (Primary) 52C20, 52C23 (Secondary) - Abstract
A self-avoiding plane-filling curve cannot be periodic, but we show that it can satisfy the local isomorphism property. We investigate three families of coverings of the plane by finite sets of nonoverlapping self-avoiding curves which satisfy that property in a strong form. These curves are respectively inductive limits of: 1) $n$-folding square curves such as the dragon curve, obtained by folding $n$ times a strip of paper in $2$ and unfolding it with $\pi /2$ angles; 2) $n$-folding triangular curves such as the terdragon curve, obtained by folding $n$ times a strip of paper in $3$ and unfolding it with $\pi /3$ angles; 3) generalizations of Peano-Gosper curves. In each family, the coverings consist of a small number of curves (at most $6$), and in many examples only $1$ curve. We do not know presently if similar examples exist in spaces of dimension $\geq 3$., Comment: 30 pages, 8 figures. arXiv admin note: substantial text overlap with arXiv:1712.09545, arXiv:1705.00787
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- 2023
6. Efficacy of a pharmacist care protocol to manage uncomplicated female cystitis in community pharmacies: an open-label, multicenter, randomized, controlled, cluster study: the PharmaCyst’ protocol
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Piraux, Arthur, Parot-Schinkel, Elsa, Hamel, Jean-François, Naber, Kurt, Oger, Anne-Claire, Guilleminot, Alain, Ramond-Roquin, Aline, and Faure, Sébastien
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- 2024
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7. Seismic events as potential drivers of the microbial community structure and evolution in a paleo-ocean analog
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Vigneron, Adrien, Cloarec, Lilian A., Agogué, Hélène, Bernard, Cécile, Duperron, Sébastien, Leboulanger, Christophe, Carré, Claire, Got, Patrice, Roques, Cécile, Troussellier, Marc, Jézéquel, Didier, Groleau, Alexis, Ader, Magali, Oger, Philipe M., and Hugoni, Mylène
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- 2024
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8. Calcium-rich dairy matrix protects better than mineral calcium against colonic luminal haem-induced alterations in male rats
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Olier, Maïwenn, Naud, Nathalie, Fouché, Edwin, Tondereau, Valérie, Ahn, Ingrid, Leconte, Nadine, Blas-Y-Estrada, Florence, Garric, Gilles, Heliès-Toussaint, Cécile, Harel-Oger, Marielle, Marmonier, Corinne, Théodorou, Vassilia, Guéraud, Françoise, Jan, Gwénaël, and Pierre, Fabrice
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- 2024
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9. Activation of hTREK-1 by polyunsaturated fatty acids involves direct interaction
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Bechard, Emilie, Arel, Elodie, Bride, Jamie, Louradour, Julien, Bussy, Xavier, Elloumi, Anis, Vigor, Claire, Soule, Pierre, Oger, Camille, Galano, Jean-Marie, Durand, Thierry, Le Guennec, Jean-Yves, Moha-Ou-Maati, Hamid, and Demion, Marie
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- 2024
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10. Adverse effects of excessive dietary arachidonic acid on survival, PUFA-derived enzymatic and non-enzymatic oxylipins, stress response in rainbow trout fry
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Cardona, Emilie, Segret, Emilien, Heraud, Cécile, Roy, Jerome, Vigor, Claire, Gros, Valérie, Reversat, Guillaume, Sancho-Zubeldia, Battitte, Oger, Camille, Durbec, Anaelle, Bertrand-Michel, Justine, Surget, Anne, Galano, Jean-Marie, Corraze, Geneviève, Cachelou, Yoann, Marchand, Yann, Durand, Thierry, Cachelou, Frederic, and Skiba-Cassy, Sandrine
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- 2024
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11. From MS/MS library implementation to molecular networks: Exploring oxylipin diversity with NEO-MSMS
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Elloumi, Anis, Mas-Normand, Lindsay, Bride, Jamie, Reversat, Guillaume, Bultel-Poncé, Valérie, Guy, Alexandre, Oger, Camille, Demion, Marie, Le Guennec, Jean-Yves, Durand, Thierry, Vigor, Claire, Sánchez-Illana, Ángel, and Galano, Jean-Marie
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- 2024
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12. Senolytics: from pharmacological inhibitors to immunotherapies, a promising future for patients’ treatment
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Lelarge, V., Capelle, R., Oger, F., Mathieu, T., and Le Calvé, B.
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- 2024
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13. Linear Dynamics of Multiplication and Composition Operators on Hol(D)
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Oger, L.
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- 2024
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14. Decoupling of δ18O from surface temperature in Antarctica in an ensemble of historical simulations
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S. Goursaud Oger, L. C. Sime, and M. Holloway
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Environmental pollution ,TD172-193.5 ,Environmental protection ,TD169-171.8 ,Environmental sciences ,GE1-350 - Abstract
Stable water isotopes recorded in Antarctic ice cores have traditionally been used to infer past surface air temperatures (SATs). During the historical period (1850 onward), observational data and good-quality ice core records overlap, yielding an opportunity to investigate key relationships between ice core stable water isotope (δ18O) measurements and the Antarctic climate. We present a new ensemble of climate model simulations covering 1851–2004 using the UK Met Office HadCM3 general circulation model equipped with stable water isotopes. Our ensemble captures observed historical SAT and precipitation trends and weak δ18O trends. The weak δ18O trends mean there is no significant relationship between SAT and δ18O over one-third of Antarctica, and also half of our considered ice core sites, though relationships are stronger when using regional averages. The strongest regional relationships occur in the West Antarctic Ice Sheet (WAIS) region. This decoupling between SAT and δ18O occurs primarily because of the impact of autumnal sea ice loss during the simulated warming. The warming and sea ice loss are associated with (i) changes in near-coastal air mass intrusions (synoptic effects) induced by changes in the large-scale circulation and/or sea ice; (ii) direct sea-ice-driven changes in moisture pathways (especially lengths) to Antarctica; and (iii) precipitation seasonality changes, again mostly driven by sea ice changes. Consequently, when reconstructing temperatures over these timescales, changes in sea ice need to be considered, both to determine the most appropriate SAT and δ18O relationship and to understand how uncertainties affect the inference of past temperature from ice core δ18O measurements.
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- 2024
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15. Efficacy of a pharmacist care protocol to manage uncomplicated female cystitis in community pharmacies: an open-label, multicenter, randomized, controlled, cluster study: the PharmaCyst’ protocol
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Arthur Piraux, Elsa Parot-Schinkel, Jean-François Hamel, Kurt Naber, Anne-Claire Oger, Alain Guilleminot, Aline Ramond-Roquin, and Sébastien Faure
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Urinary tract infections ,Uncomplicated cystitis ,Dispensing under protocol ,Community pharmacist ,Primary care ,Study protocol ,Medicine (General) ,R5-920 - Abstract
Abstract Background Urinary tract infections are common affections, especially for women. Difficult access to a general practitioner to obtain a prescription has led France to offer dispensing under protocol by community pharmacists. The primary objective of this study is to evaluate the effectiveness of a pharmacist care protocol provided to manage women with urinary tract infection symptoms. This objective will be assessed using the Acute Cystitis Symptom Score. Methods PharmaCyst’ is an open-label, multicenter, controlled, cluster-randomized study conducted in the Loire region, France. Women aged between 18 and 65 years presenting to a pharmacy complaining of at least one symptom of an uncomplicated urinary tract infection present over the last 3 days (including burning pain during micturition, dysuria, pollakiuria, urgent urination) will be considered for inclusion. All patients will be contacted on day 3, 10, and month 3. A total of 480 patients need to be recruited for the 24 clusters participating in the research. The quantitative data will be described using means and standard deviations and compared using Student’s t-test. The qualitative data will be described using numbers and percentages and compared using chi2 test (or Fisher’s exact test if necessary). The primary and secondary outcomes analyses will consider the intention-to-treat population. Discussion PharmaCyst’ is the first clinical trial conducted in France only by community pharmacists. Its results could lead to an extension of the protocol. Trial registration The protocol has been approved by the French ethics committee on 2022/12/02 and is registered under the number 49RC22_0240 on ClinicalTrials.gov.
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- 2024
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16. Cellular diagonals of permutahedra
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Delcroix-Oger, Bérénice, Laplante-Anfossi, Guillaume, Pilaud, Vincent, and Stoeckl, Kurt
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Mathematics - Combinatorics ,Mathematics - Algebraic Topology ,05A15, 05C05, 18M70, 52B11, 52C35 - Abstract
We provide a systematic enumerative and combinatorial study of geometric cellular diagonals on the permutahedra. In the first part of the paper, we study the combinatorics of certain hyperplane arrangements obtained as the union of $\ell$ generically translated copies of the classical braid arrangement. Based on Zaslavsky's theory, we derive enumerative results on the faces of these arrangements involving combinatorial objects named partition forests and rainbow forests. This yields in particular nice formulas for the number of regions and bounded regions in terms of exponentials of generating functions of Fuss-Catalan numbers. By duality, the specialization of these results to the case $\ell = 2$ gives the enumeration of any geometric diagonal of the permutahedron. In the second part of the paper, we study diagonals which respect the operadic structure on the family of permutahedra. We show that there are exactly two such diagonals, which are moreover isomorphic. We describe their facets by a simple rule on paths in partition trees, and their vertices as pattern-avoiding pairs of permutations. We show that one of these diagonals is a topological enhancement of the Sanbeblidze-Umble diagonal, and unravel a natural lattice structure on their sets of facets. In the third part of the paper, we use the preceding results to show that there are precisely two isomorphic topological cellular operadic structures on the families of operahedra and multiplihedra, and exactly two infinity-isomorphic geometric universal tensor products of homotopy operads and A-infinity morphisms., Comment: 71 pages, 28 figures, 8 tables
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- 2023
17. Indonesian Health Question Multi-Class Classification Based on Deep Learning
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Wayan Oger Vihikan and I Nyoman Prayana Trisna
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health question ,text classification ,deep learning ,indobert ,Mathematics ,QA1-939 ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
The health online forum is commonly used by Indonesian to ask questions related to diseases. A well-known example, Alodokter, has hundreds of thousands of health questions which are assigned to certain topics. Building a model to classify questions into a topic is important for better organization and faster response by relevant health professionals. This research experimented on 20 deep learning methods from RNN, CNN, and IndoBERT with different configurations to see the performance of each model when classifying questions into six different most common diseases that cause death in Indonesia. The results show the majority of the model can outperform the SVM as baseline. Bidirectional RNN such BiLSTM and BiGRU combined with CNN show a good metric score even though a certain version of the IndoBERT model generally outperforms all the other models.
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- 2024
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18. Sentiment Analysis of Indonesian Citizens on Electric Vehicle Using FastText and BERT Method
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Darryl Rayhan Wijaya, Gusti Made Arya Sasmitha, and Wayan Oger Vihikan
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sentiment analysis ,electric vehicle ,indobert ,fasttext ,Mathematics ,QA1-939 ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
Electric vehicles have become one of the most important innovations in the automotive industry in recent years. This is not only related to technological developments, but also to its significant impact on the environment and lifestyle of global society. Lot of people do not know about the benefit of using electric vehicles for our environment. The transition from conventional vehicles to electric vehicles can really make our environment healthier and also reducing the pollution. At the same time, debates and feelings about electric vehicles continue to grow around the world. This study aims to understand the dynamics of people's feelings and opinions about electric vehicles through sentiment analysis using the FastText and IndoBERT methods. FastText is an efficient text classification and representation learning method developed by Facebook's AI Research (FAIR) lab. IndoBERT is a pre-trained language model specifically designed for the Indonesian language, leveraging the Bidirectional Encoder Representations from Transformers (BERT) architecture. By analyzing a total of 119,310 data from January 2020 to June 2023, the tweets data were categorized into negative, neutral, and positive classes. Model yielded the highest accuracy of 82.5% using IndoBERT method. The results outcomes positive perceptions of electric vehicles among Indonesian citizen with a percentage of 58%. By carrying out this research, it is hoped that it can produce quality information for producers, the community and the government in developing and advancing public interest in purchasing electric vehicles considering the very positive impact they have on the surrounding environment.
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- 2024
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19. Seismic events as potential drivers of the microbial community structure and evolution in a paleo-ocean analog
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Adrien Vigneron, Lilian A. Cloarec, Hélène Agogué, Cécile Bernard, Sébastien Duperron, Christophe Leboulanger, Claire Carré, Patrice Got, Cécile Roques, Marc Troussellier, Didier Jézéquel, Alexis Groleau, Magali Ader, Philipe M. Oger, and Mylène Hugoni
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Geology ,QE1-996.5 ,Environmental sciences ,GE1-350 - Abstract
Abstract Anthropogenic perturbations profoundly affect aquatic ecosystem microbiomes and associated ecological functions. Comparatively, the effects of geological stresses on microbiome composition and stability remain poorly explored. Here, we monitored the archaeal, bacterial and microeukaryotes community structure over an 8-years period in Lake Dziani Dzaha (Comoros archipelago), that experienced a major earthquake swarm mid-survey, providing a rare opportunity to investigate the aftermaths of seismo-volcanic events on microbiome. Our results revealed the sensitivity of the aquatic microbial community towards seismicity and associated environmental changes, that triggered a major shift in microbiome composition and abundance with persisting consequences on structure and richness of the microbial ecosystem. Our findings suggest that seismological perturbations could be major drivers of the microbial community structure in aquatic environments through cascading effects on environmental conditions. Over geological time scales, such events may have been significant yet underestimated forces driving diversification and evolution of microbial communities.
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- 2024
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20. Activation of hTREK-1 by polyunsaturated fatty acids involves direct interaction
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Emilie Bechard, Elodie Arel, Jamie Bride, Julien Louradour, Xavier Bussy, Anis Elloumi, Claire Vigor, Pierre Soule, Camille Oger, Jean-Marie Galano, Thierry Durand, Jean-Yves Le Guennec, Hamid Moha-Ou-Maati, and Marie Demion
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Medicine ,Science - Abstract
Abstract TREK-1 is a mechanosensitive channel activated by polyunsaturated fatty acids (PUFAs). Its activation is supposed to be linked to changes in membrane tension following PUFAs insertion. Here, we compared the effect of 11 fatty acids and ML402 on TREK-1 channel activation using the whole cell and the inside-out configurations of the patch-clamp technique. Firstly, TREK-1 activation by PUFAs is variable and related to the variable constitutive activity of TREK-1. We observed no correlation between TREK-1 activation and acyl chain length or number of double bonds suggesting that the bilayer-couple hypothesis cannot explain by itself the activation of TREK-1 by PUFAs. The membrane fluidity measurement is not modified by PUFAs at 10 µM. The spectral shift analysis in TREK-1-enriched microsomes indicates a KD,TREK1 at 44 µM of C22:6 n-3. PUFAs display the same activation and reversible kinetics than the direct activator ML402 and activate TREK-1 in both whole-cell and inside-out configurations of patch-clamp suggesting that the binding site of PUFAs is accessible from both sides of the membrane, as for ML402. Finally, we proposed a two steps mechanism: first, insertion into the membrane, with no fluidity or curvature modifications at 10 µM, and then interaction with TREK-1 channel to open it.
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- 2024
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21. Calcium-rich dairy matrix protects better than mineral calcium against colonic luminal haem-induced alterations in male rats
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Maïwenn Olier, Nathalie Naud, Edwin Fouché, Valérie Tondereau, Ingrid Ahn, Nadine Leconte, Florence Blas-Y-Estrada, Gilles Garric, Cécile Heliès-Toussaint, Marielle Harel-Oger, Corinne Marmonier, Vassilia Théodorou, Françoise Guéraud, Gwénaël Jan, and Fabrice Pierre
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Nutrition. Foods and food supply ,TX341-641 ,Food processing and manufacture ,TP368-456 - Abstract
Abstract The haemoglobin content in meat is consistently associated with an increased risk of colorectal cancer, whereas calcium may play a role as a chemopreventive agent. Using rodent models, calcium salts have been shown to prevent the promotion of haem-induced and red meat-induced colorectal carcinogenesis by limiting the bioavailability of the gut luminal haem iron. Therefore, this study aimed to compare impacts of dietary calcium provided as calcium salts or dairy matrix on gut homoeostasis perturbations by high haeminic or non-haeminic iron intakes. A 3-week intervention study was conducted using Fischer 344 rats. Compared to the ferric citrate-enriched diet, the haemoglobin-enriched diet led to increased faecal, mucosal, and urinary lipoperoxidation-related biomarkers, resulting from higher gut luminal haem iron bioavailability. This redox imbalance was associated to a dysbiosis of faecal microbiota. The addition of calcium to haemoglobin-enriched diets limited haem iron bioavailability and counteracted redox imbalance, with improved preventive efficacy when calcium was provided in dairy matrix. Data integration revealed correlations between haem-induced lipoperoxidation products and bacterial communities belonging to Peptococcaceae, Eubacterium coprostanoligenes group, and Bifidobacteriaceae. This integrated approach provides evidence of the benefits of dairy matrix as a dietary calcium vehicle to counteract the deleterious side-effects of meat consumption.
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- 2024
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22. Ventilation effect on the fire behavior in a vehicle engine compartment
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Junjunan, Soleh F., Robinet, Antonin, Chetehouna, Khaled, Cablé, Axel, Oger, Antoine, Gascoin, Nicolas, and Bura, Romie O.
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- 2024
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23. Sentiment Analysis of X (Twitter) Comments on The Influence of South Korean Culture in Indonesia
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Putu Rheya Ananda Savitri, I Made Agus Dwi Suarjaya, and Wayan Oger Vihikan
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korean wave ,convolutional neural network ,x (twitter) ,sentiment ,Mathematics ,QA1-939 ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
Hallyu or Korean wave refers to the phenomenon of South Korean values and culture spreading to other countries, ultimately influencing global culture. South Korean culture, such as K-pop music, dramas, films, fashion, food, and lifestyle, has gained popularity in Indonesia since 2002. Because South Korean culture influences many aspects of life in Indonesia, responses to this Korean wave are widely discussed in social media, especially through X (Twitter) ranging from positive sentiment to negative sentiment. To gain a more in-depth and detailed understanding of public opinion, a classification process was conducted on the social media platform X (Twitter) using a deep learning algorithm based on the CNN method. The results of this classification provide more accurate and informative insight into the attitudes, opinions, and reactions of the Indonesian people towards the influence of South Korean culture in this country. The research was conducted using 717,998 tweet data resulting in an accuracy of 79%.
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- 2024
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24. Study of weighted elliptic composition operators on the unit ball of ℂN
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Oger Lucas
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weighted composition operator ,spectrum ,holomorphic functions in several variables ,fréchet space ,47b33 ,32a10 ,47a10 ,Mathematics ,QA1-939 - Abstract
We study the general properties, point spectrum and spectrum of a weighted composition operator Wm,φ{W}_{m,\varphi } with elliptic symbol φ\varphi on the unit ball BN{{\mathbb{B}}}_{N} of CN{{\mathbb{C}}}^{N}, and general weight m∈Hol(BN)m\in {\rm{Hol}}\left({{\mathbb{B}}}_{N}). We give a complete description of the spectra in the majority of cases, and we provide inclusions in general.
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- 2024
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25. Adverse effects of excessive dietary arachidonic acid on survival, PUFA-derived enzymatic and non-enzymatic oxylipins, stress response in rainbow trout fry
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Emilie Cardona, Emilien Segret, Cécile Heraud, Jerome Roy, Claire Vigor, Valérie Gros, Guillaume Reversat, Battitte Sancho-Zubeldia, Camille Oger, Anaelle Durbec, Justine Bertrand-Michel, Anne Surget, Jean-Marie Galano, Geneviève Corraze, Yoann Cachelou, Yann Marchand, Thierry Durand, Frederic Cachelou, and Sandrine Skiba-Cassy
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Trout ,Arachidonic acid ,Oxylipin ,Confinement stress ,Serotonin ,Dopamine ,Medicine ,Science - Abstract
Abstract Arachidonic acid (C20: 4n-6, AA) plays a fundamental role in fish physiology, influencing growth, survival and stress resistance. However, imbalances in dietary AA can have detrimental effects on fish health and performance. Optimal AA requirements for rainbow trout have not been established. This study aimed to elucidate the effects of varying dietary AA levels on survival, growth, long-chain polyunsaturated fatty acid (LC-PUFA) biosynthetic capacity, oxylipin profiles, lipid peroxidation, and stress resistance of rainbow trout fry. Over a period of eight weeks, 4000 female rainbow trout fry at the resorptive stage (0.12 g) from their first feeding were fed diets with varying levels of AA (0.6%, 1.1% or 2.5% of total fatty acids) while survival and growth metrics were closely monitored. The dietary trial was followed by an acute confinement stress test. Notably, while the fatty acid profiles of the fish reflected dietary intake, those fed an AA-0.6% diet showed increased expression of elongase5, highlighting their inherent ability to produce LC-PUFAs from C18 PUFAs and suggesting potential AA or docosapentaenoic acidn-6 (DPAn-6) biosynthesis. However, even with this biosynthetic capacity, the trout fed reduced dietary AA had higher mortality rates. The diet had no effect on final weight (3.38 g on average for the three diets). Conversely, increased dietary AA enhanced eicosanoid production from AA, suggesting potential inflammatory and oxidative consequences. This was further evidenced by an increase in non-enzymatic lipid oxidation metabolites, particularly in the AA-2.5% diet group, which had higher levels of phytoprostanes and isoprostanes, markers of cellular oxidative damage. Importantly, the AA-1.1% diet proved to be particularly beneficial for stress resilience. This was evidenced by higher post-stress turnover rates of serotonin and dopamine, neurotransmitters central to the fish's stress response. In conclusion, a dietary AA intake of 1.1% of total fatty acids appears to promote overall resilience in rainbow trout fry.
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- 2024
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26. Editorial: Insights in extreme microbiology: 2023
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Andreas Teske and Philippe M. Oger
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editorial ,extremophiles ,Research Topic ,Deinococcus ,diversity ,Microbiology ,QR1-502 - Published
- 2024
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27. How to better estimate bunch number at field level?
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Baptiste Oger, Cécile Laurent, Philippe Vismara, and Bruno Tisseyre
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Agriculture (General) ,S1-972 ,Plant culture ,SB1-1110 - Abstract
In viticulture, early-season estimation of average number of grape bunches per vine is crucial for vineyard planning, investments and marketing (Laurent et al., 2021). Although sampling is widely carried out to estimate grape bunches per vine, there is no clearly established sampling protocol that can be used as a reference when performing these estimations. Each practitioner therefore has their own sampling protocol. In this work, the effect of differences between sampling protocols in terms of estimation errors were investigated to give some recommendations on the best possible sampling practices.
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- 2024
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28. From MS/MS library implementation to molecular networks: Exploring oxylipin diversity with NEO-MSMS
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Anis Elloumi, Lindsay Mas-Normand, Jamie Bride, Guillaume Reversat, Valérie Bultel-Poncé, Alexandre Guy, Camille Oger, Marie Demion, Jean-Yves Le Guennec, Thierry Durand, Claire Vigor, Ángel Sánchez-Illana, and Jean-Marie Galano
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Science - Abstract
Abstract Oxylipins, small polar molecules derived from the peroxidation of polyunsaturated fatty acids (PUFAs), serve as biomarkers for many diseases and play crucial roles in human physiology and inflammation. Despite their significance, many non-enzymatic oxygenated metabolites of PUFAs (NEO-PUFAs) remain poorly reported, resulting in a lack of public datasets of experimental data and limiting their dereplication in further studies. To overcome this limitation, we constructed a high-resolution tandem mass spectrometry (MS/MS) dataset comprising pure NEO-PUFAs (both commercial and self-synthesized) and in vitro free radical-induced oxidation of diverse PUFAs. By employing molecular networking techniques with this dataset and the existent ones in public repositories, we successfully mapped a wide range of NEO-PUFAs, expanding the strategies for annotating oxylipins, and NEO-PUFAs and offering a novel workflow for profiling these molecules in biological samples.
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- 2024
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29. Tridendriform algebras on hypergraph polytopes
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Curien, Pierre-Louis, Delcroix-Oger, Bérénice, and Obradović, Jovana
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Mathematics - Combinatorics ,18M60, 52B05 - Abstract
We extend the works of Loday-Ronco and Burgunder-Ronco on the tridendriform decomposition of the shuffle product on the faces of associahedra and permutohedra, to other families of hypergraph polytopes (or nestohedra), including simplices, hypercubes and some new families. We also extend the shuffle product to take more than two arguments, and define accordingly a new algebraic structure, that we call polydendriform, from which the original tridendriform equations can be crisply synthesized., Comment: 30 pages
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- 2022
30. Transcriptomic insights into the dominance of two phototrophs throughout the water column of a tropical hypersaline-alkaline crater lake (Dziani Dzaha, Mayotte)
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Sébastien Duperron, Sébastien Halary, Jean-Pierre Bouly, Théotime Roussel, Myléne Hugoni, Maxime Bruto, Philippe M. Oger, Charlotte Duval, Anthony Woo, Didier Jézéquel, Magali Ader, Christophe Leboulanger, Hélène Agogué, Vincent Grossi, Marc Troussellier, and Cécile Bernard
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Limnospira platensis ,Picocystis salinarum ,metatranscriptomics ,photosynthesis ,fermentation ,transcriptomics ,Microbiology ,QR1-502 - Abstract
Saline-alkaline lakes often shelter high biomasses despite challenging conditions, owing to the occurrence of highly adapted phototrophs. Dziani Dzaha (Mayotte) is one such lake characterized by the stable co-dominance of the cyanobacterium Limnospira platensis and the picoeukaryote Picocystis salinarum throughout its water column. Despite light penetrating only into the uppermost meter, the prevailing co-dominance of these species persists even in light- and oxygen-deprived zones. Here, a depth profile of phototrophs metatranscriptomes, annotated using genomic data from isolated strains, is employed to identify expression patterns of genes related to carbon processing pathways including photosynthesis, transporters and fermentation. The findings indicate a prominence of gene expression associated with photosynthesis, with a peak of expression around 1 m below the surface, although the light intensity is very low and only red and dark red wavelengths can reach it, given the very high turbidity linked to the high biomass of L. platensis. Experiments on strains confirmed that both species do grow under these wavelengths, at rates comparable to those obtained under white light. A decrease in the expression of photosynthesis-related genes was observed in L. platensis with increasing depth, whereas P. salinarum maintained a very high pool of psbA transcripts down to the deepest point as a possible adaptation against photodamage, in the absence and/or very low levels of expression of genes involved in protection. In the aphotic/anoxic zone, expression of genes involved in fermentation pathways suggests active metabolism of reserve or available dissolved carbon compounds. Overall, L. platensis seems to be adapted to the uppermost water layer, where it is probably maintained thanks to gas vesicles, as evidenced by high expression of the gvpA gene. In contrast, P. salinarum occurs at similar densities throughout the water column, with a peak in abundance and gene expression levels which suggests a better adaptation to lower light intensities. These slight differences may contribute to limited inter-specific competition, favoring stable co-dominance of these two phototrophs.
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- 2024
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31. Identification of novel F2-isoprostane metabolites by specific UDP-glucuronosyltransferases
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Ginger L. Milne, Marina S. Nogueira, Benlian Gao, Stephanie C. Sanchez, Warda Amin, Sarah Thomas, Camille Oger, Jean-Marie Galano, Harvey J. Murff, Gong Yang, and Thierry Durand
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Isoprostanes ,Metabolism ,Mass spectrometry ,Glucuronidation ,Fish oil ,Medicine (General) ,R5-920 ,Biology (General) ,QH301-705.5 - Abstract
UDP-glucuronosyltransferases (UGTs) catalyze the conjugation of glucuronic acid with endogenous and exogenous lipophilic small molecules to facilitate their inactivation and excretion from the body. This represents approximately 35 % of all phase II metabolic transformations. Fatty acids and their oxidized eicosanoid derivatives can be metabolized by UGTs. F2-isoprostanes (F2-IsoPs) are eicosanoids formed from the free radical oxidation of arachidonic acid. These molecules are potent vasoconstrictors and are widely used as biomarkers of endogenous oxidative damage. An increasing body of evidence demonstrates the efficacy of measuring the β-oxidation metabolites of F2-IsoPs rather than the unmetabolized F2-IsoPs to quantify oxidative damage in certain settings. Yet, the metabolism of F2-IsoPs is incompletely understood. This study sought to identify and characterize novel phase II metabolites of 15-F2t-IsoP and 5-epi-5-F2t-IsoP, two abundantly produced F2-IsoPs, in human liver microsomes (HLM). Utilizing liquid chromatography-mass spectrometry, we demonstrated that glucuronide conjugates are the major metabolites of these F2-IsoPs in HLM. Further, we showed that these molecules are metabolized by specific UGT isoforms. 15-F2t-IsoP is metabolized by UGT1A3, 1A9, and 2B7, while 5-epi-5-F2t-IsoP is metabolized by UGT1A7, 1A9, and 2B7. We identified, for the first time, the formation of intact glucuronide F2-IsoPs in human urine and showed that F2-IsoP glucuronidation is reduced in people supplemented with eicosapentaenoic and docosahexaenoic acids for 12 weeks. These studies demonstrate that endogenous F2-IsoP levels can be modified by factors other than redox mechanisms.
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- 2024
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32. French dermatologists' opinions and practices with regard to adjuvant therapy in stage III melanoma
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Marion Rolland, Emmanuel Oger, Monica Dinulescu, Thierry Lesimple, David Russo, Marc Pracht, Marc Porneuf, Sophie Dalac, Damien Giacchero, Thomas Jouary, Celeste Lebbé, Marie-Thérèse Leccia, Eve Maubec, Nicolas Meyer, Laurent Mortier, and Alain Dupuy
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adjuvant therapy ,melanoma ,stage III ,survey ,Dermatology ,RL1-803 ,Diseases of the genitourinary system. Urology ,RC870-923 - Abstract
Abstract Background In 2018, the European Medicines Agency authorized adjuvant therapy for patients with resected stage III melanoma. Objectives The objective of the present study (performed in France) was to assess dermatologists' and oncologists' opinions and prescribing habits in this context. Methods From 28 May to 8 June 2021, we performed an online survey of members of the French Groupe de Cancérologie Cutanée (GCC) skin cancer interest group. Results Thirty‐eight practitioners replied to the survey. For BRAF‐mutant melanoma, 58% of the practitioners favoured immunotherapy (IT). If they themselves were to suffer from melanoma with a BRAFV600 mutation, 65% would choose IT for stage IIIB disease, and 72% would choose IT for stage IIID disease. For stage IIIA melanoma with a positive sentinel lymphatic node (SLN) biopsy
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- 2023
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33. Atmospheric Sciences Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science
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Blanken, P. D, Brunet, D., Dominguez, C., Goursaud Oger, S., Hussain, S., Jain, M., Koren, G., Mu, Y., Ray, P., Saxena, P., Sonwani, S., and Sur, D.
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- 2022
34. Some properties of the parking function poset
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Delcroix-Oger, Bérénice, Josuat-Vergès, Matthieu, and Randazzo, Lucas
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Computer Science - Discrete Mathematics ,Mathematics - Combinatorics - Abstract
In 1980, Edelman defined a poset on objects called the noncrossing 2-partitions. They are closely related with noncrossing partitions and parking functions. To some extent, his definition is a precursor of the parking space theory, in the framework of finite reflection groups. We present some enumerative and topological properties of this poset. In particular, we get a formula counting certain chains, that encompasses formulas for Whitney numbers (of both kinds). We prove shellability of the poset, and compute its homology as a representation of the symmetric group. We moreover link it with two well-known polytopes : the associahedron and the permutohedron.
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- 2021
35. Non-ambiguous trees: new results and generalisation (Full version)
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Delcroix-Oger, Bérénice, Hivert, Florent, Laborde-Zubieta, Patxi, Aval, Jean-Christophe, and Boussicault, Adrien
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Computer Science - Discrete Mathematics ,Mathematics - Combinatorics - Abstract
We present a new definition of non-ambiguous trees (NATs) as labelled binary trees. We thus get a differential equation whose solution can be described combinatorially. This yields a new formula for the number of NATs. We also obtain q-versions of our formula. We finally generalise NATs to higher dimension., Comment: full version of arXiv:2103.07294. European Journal of Combinatorics, Elsevier
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- 2021
36. Stress-Induced Production of Bioactive Oxylipins in Marine Microalgae
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Amandyne Linares-Maurizi, Rana Awad, Anaelle Durbec, Guillaume Reversat, Valérie Gros, Jean-Marie Galano, Justine Bertrand-Michel, Thierry Durand, Rémi Pradelles, Camille Oger, and Claire Vigor
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microalgae ,oxidative stress ,osmotic stress ,oxylipins ,LC-MS/MS ,Biology (General) ,QH301-705.5 - Abstract
Microalgae, stemming from a complex evolutionary lineage, possess a metabolic composition influenced by their evolutionary journey. They have the capacity to generate diverse polyunsaturated fatty acids (PUFAs), akin to those found in terrestrial plants and oily fish. Also, because of their numerous double bonds, these metabolic compounds are prone to oxidation processes, leading to the creation of valuable bioactive molecules called oxylipins. Moreover, owing to their adaptability across various environments, microalgae offer an intriguing avenue for biosynthesizing these compounds. Thus, modifying the culture conditions could potentially impact the profiles of oxylipins. Indeed, the accumulation of oxylipins in microalgae is subject to the influence of growth conditions, nutrient availability, and stressors, and adjusting these factors can enhance their production in microalgae culture. Consequently, the present study scrutinized the LC-MS/MS profiles of oxylipins from three marine microalgae species (two Haptagophytes and one Chlorophyte) cultivated in 1 L of photobioreactors under varying stress-inducing conditions, such as the introduction of H2O2, EtOAc, and NaCl, during their exponential growth phase. Approximately 50 oxylipins were identified, exhibiting different concentrations depending on the species and growth circumstances. This research suggests that microalgae metabolisms can be steered toward the production of bioactive oxylipins through modifications in the culture conditions. In this instance, the application of a low dose of hydrogen peroxide to Mi 124 appears to stimulate the production of nonenzymatic oxylipins. For Mi136, it is the application of salt stress that seems to increase the overall production of oxylipins. In the case of Mi 168, either a low concentration of H2O2 or a high concentration of AcOEt appears to have this effect.
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- 2024
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37. Haloarchaea as Promising Chassis to Green Chemistry
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Emma Bonnaud, Philippe M. Oger, Avigaël Ohayon, and Yoann Louis
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haloarchaea ,cellular chassis ,green chemistry ,extremozymes ,genetic tools ,genetic modifications ,Biology (General) ,QH301-705.5 - Abstract
Climate change and the scarcity of primary resources are driving the development of new, more renewable and environmentally friendly industrial processes. As part of this green chemistry approach, extremozymes (extreme microbial enzymes) can be used to replace all or part of the chemical synthesis stages of traditional industrial processes. At present, the production of these enzymes is limited by the cellular chassis available. The production of a large number of extremozymes requires extremophilic cellular chassis, which are not available. This is particularly true of halophilic extremozymes. The aim of this review is to present the current potential and challenges associated with the development of a haloarchaea-based cellular chassis. By overcoming the major obstacle of the limited number of genetic tools, it will be possible to propose a robust cellular chassis for the production of functional halophilic enzymes that can participate in the industrial transition of many sectors.
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- 2024
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38. Quality of Life at School: Between Vulnerability and Robustness of Students
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Oger, Marie, Martin-Krumm, Charles, Fenouillet, Fabien, Müller, Anita, Le Roux, Fleur, Tarquinio, Cyril, and Broc, Guillaume
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The quality of life of students at school is an increasingly topical issue in relation both to public health issues, made more acute by the pandemic and successive confinements, and to the technical nature of future jobs which means training has become an economic issue. There are therefore two issues, one linked to health and the other to school performance. A cross-sectional design was adopted. Questionnaires were administered to 470 volunteer student's seventh grade US to the first year of the Senior Technician Curriculum aged from 12 to 23 years (139 girls and 331 boys, mage = 15.7 years). Latent profiles analysis and the Games-Howell post hoc test were used. Analyses carried out with MPlus reveal three possible profiles. They also show that these profiles have a strong predictive power on motivation and perceived health.
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- 2022
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39. Validity, sensitivity and resolution limit of the PCR-RFLP analysis of the rrs (16S rRNA gene) as a tool to identify soil-borne and plant-associated bacterial populations
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Chomel Cécil, Manceau Charles, Gardan Louis, Petit Annick, Dessaux Yves, Oger Phil, and Nesme Xavier
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Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Published
- 1998
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40. Spirometry practice by French general practitioners between 2010 and 2018 in adults aged 40 to 75 years
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A. Chapron, T. Lemée, G. Pau, S. Jouneau, S. Kerbrat, F. Balusson, and E. Oger
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Diseases of the respiratory system ,RC705-779 - Abstract
Abstract In France, most spirometries are performed by pneumologists. Spirometry is difficult to access due to the distance to medical office and long delays for appointments. This lack of accessibility contributes to the underdiagnosis of chronic obstructive pulmonary disease (COPD) among patients aged between 40 and 75 years. In recent years, general practitioners (GPs) have been performing spirometry in private practice. However, the extent of this practice is unknown. A French retrospective, repetitive transversal study analysed data from the “Système National des Données de Santé” (SNDS) database. The targeted population was GPs in primary care that performed spirometries between 2010 and 2018, in patients aged between 40 and 75 years. Between 2010 and 2018, 302,674 (7.2%) spirometries were performed in France by GPs in private practices, in patients 40 to 75 years old. 5.4% by “expert GPs” (>60 spirometries/year) and 1.8% by “non-expert GPs”. In “non-expert GPs” (2.8% of French GPs in 2018), the annual number of spirometries increased by 701 each year (p
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- 2023
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41. Heterogeneity of right ventricular echocardiographic parameters in systemic lupus erythematosus among four clinical subgroups, as stratified by clinical organ involvement in observational cohort
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Elizabeth Curtis, Erwan Donal, Charlotte Lee, Emmanuel Oger, Corentin Bourg, Erwan Le Tallec, Guillaume Bouzille, and Alain Lescort
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Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Background Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Cardiac involvement in SLE is rare but plays an important prognostic role. The degree of cardiac involvement according to SLE subsets defined by non-cardiac manifestations is unknown. The objective of this study was to identify differences in transthoracic echocardiography (TTE) parameters associated with different SLE subgroups.Methods One hundred eighty-one patients who fulfilled the 2019 American College of Rheumatology/EULAR classification criteria for SLE and underwent baseline TTE were included in this cross-sectional study. We defined four subsets of SLE based on the predominant clinical manifestations. A multivariate multinomial regression analysis was performed to determine whether TTE parameters differed between groups.Results Four clinical subsets were defined according to non-cardiac clinical manifestations: group A (n=37 patients) showed features of mixed connective tissue disease, group B (n=76 patients) had primarily cutaneous involvement, group C (n=18) exhibited prominent serositis and group D (n=50) had severe, multi-organ involvement, including notable renal disease. Forty TTE parameters were assessed between groups. Per multivariate multinomial regression analysis, there were statistically significant differences in early diastolic tricuspid annular velocity (RV-Ea, p
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- 2024
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42. Spirometry practice by French general practitioners between 2010 and 2018 in adults aged 40 to 75 years
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Chapron, A., Lemée, T., Pau, G., Jouneau, S., Kerbrat, S., Balusson, F., and Oger, E.
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- 2023
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43. Long‐term outcomes in heart failure with preserved ejection fraction: Predictors of cardiac and non‐cardiac mortality
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Angiza Shahim, Marion Hourqueig, Lars H. Lund, Gianluigi Savarese, Emmanuel Oger, Ashwin Venkateshvaran, Lina Benson, Jean‐Claude Daubert, Cecilia Linde, Erwan Donal, and Camilla Hage
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Heart failure with preserved ejection fraction ,Diastolic heart failure ,Prognosis ,Outcome ,Cardiovascular mortality ,Non‐cardiovascular mortality ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Abstract Aims Heart failure (HF) with preserved ejection fraction (HFpEF) is associated with cardiovascular (CV) and non‐CV events, but long‐term risk is poorly studied. We assessed incidence and predictors of the long‐term CV and non‐CV events. Methods and results Patients presenting with acute HF, EF ≥ 45%, and N‐terminal pro‐brain natriuretic peptide > 300 ng/L were enrolled in the Karolinska‐Rennes study in 2007–11 and were reassessed after 4–8 weeks in a stable state. Long‐term follow‐up was conducted in 2018. The Fine–Gray sub‐distribution hazard regression was used to detect predictors of CV and non‐CV deaths, investigated separately from baseline acute presentation (demographic data only) and from the 4–8 week outpatient visit (including echocardiographic data). Of 539 patients enrolled [median age 78 (interquartile range: 72–84) years; 52% female], 397 patients were available for the long‐term follow‐up. Over a median follow‐up time from acute presentation of 5.4 (2.1–7.9) years, 269 (68%) patients died, 128 (47%) from CV and 120 (45%) from non‐CV causes. Incidence rates per 1000 patient‐years were 62 [95% confidence interval (CI) 52–74] for CV and 58 (95% CI 48–69) for non‐CV death. Higher age and coronary artery disease (CAD) were independent predictors of CV death, and anaemia, stroke, kidney disease, and lower body mass index (BMI) and sodium concentrations of non‐CV death. From the stable 4–8 week visit, anaemia, CAD, and tricuspid regurgitation (>3.1 m/s) were independent predictors of CV death, and higher age of non‐CV death. Conclusions In patients with acute decompensated HFpEF, over 5 years of follow‐up, nearly two‐thirds of patients died, half from CV and the other half from non‐CV causes. CAD and tricuspid regurgitation were associated with CV death. Stroke, kidney disease, lower BMI, and lower sodium were associated with non‐CV death. Anaemia and higher age were associated with both outcomes. [Correction added on 24 March 2023, after first online publication: In the first sentence of the Conclusions, ‘two‐thirds’ has been inserted before ‘of patients died...’ in this version.]
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- 2023
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44. Isolated functional tricuspid regurgitation: how to define patients at risk for event?
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Guillaume L'Official, Mathilde Vely, Wojciech Kosmala, Elena Galli, Anne Guerin, Elisabeth Chen, Catherine Sportouch, Julien Dreyfus, Emmanuel Oger, and Erwan Donal
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Functional tricuspid regurgitation ,Echocardiography ,Prognosis ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Abstract Aims Functional tricuspid regurgitation (TR) is a turning point in cardiac diseases. Symptoms typically appear late. The optimal timing for proposing a valve repair remains a challenge. We sought to analyse the characteristics of right heart remodelling in patients with significant functional TR to identify the parameters that could be used in a simple prognostic model predicting clinical events. Methods and results We designed a prospective observational French multicentre study including 160 patients with significant functional TR (effective regurgitant orifice area > 30 mm2) and left ventricular ejection fraction > 40%. Clinical, echocardiographic, and electrocardiogram data were collected at baseline and at the 1 and 2 year follow‐up. The primary outcome was all‐cause death or hospitalization for heart failure. At 2 years, 56 patients (35%) achieved the primary outcome. The subset with events showed more advanced right heart remodelling at baseline, but similar TR severity. Right atrial volume index (RAVI) and the tricuspid annular plane systolic excursion to systolic pulmonary arterial pressure (TAPSE/sPAP) ratio, reflecting right ventricular–pulmonary arterial coupling, were 73 mL/m2 and 0.40 vs. 64.7 mL/m2 and 0.50 in the event vs. event‐free groups, respectively (both P 0.4 (odds ratio = 0.41, 95% confidence limit 0.2 to 0.82) and RAVI > 60 mL/m2 (odds ratio = 2.13, 95% confidence limit 0.96 to 4.75), providing a clinically valid prognostic evaluation. Conclusions RAVI and TAPSE/sPAP are relevant for predicting the risk for event at 2 year follow‐up in patients with an isolated functional TR.
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- 2023
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45. Chemical Compositional Changes in Over-oxidized Fish Oils.
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Bannenberg, Gerard, Phung, Austin, Vigor, Claire, Reversat, Guillaume, Oger, Camille, Roumain, Martin, Galano, Jean-Marie, Durand, Thierry, Muccioli, Giulio, Ismail, Adam, and Wang, Selina
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Chemical Engineering ,Nutrition & Dietetics ,Food sciences - Abstract
A recent study has reported that the administration during gestation of a highly rancid hoki liver oil, obtained by oxidation through sustained exposure to oxygen gas and incident light for 30 days, causes newborn mortality in rats. This effect was attributed to lipid hydroperoxides formed in the omega-3 long-chain polyunsaturated fatty acid-rich oil, while other chemical changes in the damaged oil were overlooked. In the present study, the oxidation condition employed to damage the hoki liver oil was replicated, and the extreme rancidity was confirmed. A detailed analysis of temporal chemical changes resulting from the sustained oxidative challenge involved measures of eicosapentaenoic acid/docosahexaenoic acid (EPA/DHA) omega-3 oil oxidative quality (peroxide value, para-anisidine value, total oxidation number, acid value, oligomers, antioxidant content, and induction time) as well as changes in fatty acid content, volatiles, isoprostanoids, and oxysterols. The chemical description was extended to refined anchovy oil, which is a more representative ingredient oil used in omega-3 finished products. The present study also analyzed the effects of a different oxidation method involving thermal exposure in the dark in contact with air, which is an oxidation condition that is more relevant to retail products. The two oils had different susceptibility to the oxidation conditions, resulting in distinct chemical oxidation signatures that were determined primarily by antioxidant protection as well as specific methodological aspects of the applied oxidative conditions. Unique isoprostanoids and oxysterols were formed in the over-oxidized fish oils, which are discussed in light of their potential biological activities.
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- 2021
46. High spatial resolution dataset of grapevine yield components at the within-field level
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Baptiste Oger, Yulin Zhang, Jean-Philippe Gras, Yoann Valloo, Pauline Faure, Guilhem Brunel, and Bruno Tisseyre
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Grapes ,Missing vines ,Dead vines ,Spatial data ,Vegetation index, Soil resistivity ,Computer applications to medicine. Medical informatics ,R858-859.7 ,Science (General) ,Q1-390 - Abstract
In order to enhance the understanding of vine yield development and facilitate the design of innovative agricultural practices in viticulture (i.e., new estimation methods), it is essential to have accurate and detailed data on vine yield components, including unproductive vines, number of bunches, and bunch weight. However, obtaining accurate and high spatial resolution yield data at the vine scale is costly and difficult to have for the main yield components (number of bunches, weight of bunch, missing plants, etc.). As a result, existing vine yield data are frequently estimated or measured at the field level. Unfortunately, the accuracy of these vine yield data is insufficient to study the intricate relationships between different yield components and their spatial distribution within vineyards. In this context, this article proposes a complete vine yield dataset that was specifically collected to develop and to test new sampling protocols in precision viticulture.This dataset comprises a comprehensive mapping of vine yield at the plant scale over two vine fields located in the southern region of France. Both vine fields were planted with the Vitis vinifera: cv. Syrah. The first field (Field 1) occupies 0.8 ha and data were collected in 2022, while the second field (Field 2) has an area of 0.5 ha and data were collected in 2008. Throughout the growing season, information regarding unproductive vines, inflorescence number, and bunch weight was collected for both vine fields. For both fields, at the flowering stage, the location of each productive and unproductive vines (dead and missing vines) was georeferenced, and the number of inflorescences was manually counted for all productive vines. For Field 1, at harvest, all bunches of the field were manually weighed with an accuracy of ±1 gram and georeferenced precisely (one point per vine). For each vine, total yield (grams per vine) was then computed as as the sum of the weight of its bunches. For Field 2, at harvest, the total yield per vine was estimated based on the weighing of representative bunches obtained from several regularly spaced set of 5 vines. In addition to the yield data, two ancillary data, including soil apparent resistivity measurements and common vegetative index derived from remote sensed imagery, are provided for both vine fields. Overall, the dataset consists of 3644 vines, with 2151 being productive, along with a total count of 33354 inflorescences and 19635 manually weighed bunches at harvest.This dataset is of interest as it contains information on grape yield organization at the within-field level. This dataset could be used to assess the impact of unproductive vines on neighbouring vines yield, as well as the correlations between available ancillary data and all yield components.
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- 2023
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47. Epidemiological evidence for a hereditary contribution to myasthenia gravis: a retrospective cohort study of patients from North America
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Green, Joshua D, Barohn, Richard J, Bartoccion, Emanuela, Benatar, Michael, Blackmore, Derrick, Chaudhry, Vinay, Chopra, Manisha, Corse, Andrea, Dimachkie, Mazen M, Evoli, Amelia, Florence, Julaine, Freimer, Miriam, Howard, James F, Jiwa, Theresa, Kaminski, Henry J, Kissel, John T, Koopman, Wilma J, Lipscomb, Bernadette, Maestri, Michelanglo, Marino, Mariapaola, Massey, Janice M, McVey, April, Mezei, Michelle M, Muppidi, Srikanth, Nicolle, Michael W, Oger, Joel, Pascuzzi, Robert M, Pasnoor, Mamatha, Pestronk, Alan, Provenzano, Carlo, Ricciardi, Roberta, Richman, David P, Rowin, Julie, Sanders, Donald B, Siddiqi, Zaeem, Soloway, Aimee, Wolfe, Gil I, Wulf, Charlie, Drachman, Daniel B, and Traynor, Bryan J
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Genetics ,Neurodegenerative ,Clinical Research ,Myasthenia Gravis ,Autoimmune Disease ,Rare Diseases ,Neurosciences ,2.1 Biological and endogenous factors ,Aetiology ,Autoantibodies ,Humans ,North America ,Receptors ,Cholinergic ,Retrospective Studies ,epidemiology ,neuromuscular disease ,genetics ,neurology ,neurogenetics ,Clinical Sciences ,Public Health and Health Services ,Other Medical and Health Sciences - Abstract
ObjectivesTo approximate the rate of familial myasthenia gravis and the coexistence of other autoimmune disorders in the patients and their families.DesignRetrospective cohort study.SettingClinics across North America.ParticipantsThe study included 1032 patients diagnosed with acetylcholine receptor antibody (AChR)-positive myasthenia gravis.MethodsPhenotype information of 1032 patients diagnosed with AChR-positive myasthenia gravis was obtained from clinics at 14 centres across North America between January 2010 and January 2011. A critical review of the epidemiological literature on the familial rate of myasthenia gravis was also performed.ResultsAmong 1032 patients, 58 (5.6%) reported a family history of myasthenia gravis. A history of autoimmune diseases was present in 26.6% of patients and in 28.4% of their family members.DiscussionThe familial rate of myasthenia gravis was higher than would be expected for a sporadic disease. Furthermore, a high proportion of patients had a personal or family history of autoimmune disease. Taken together, these findings suggest a genetic contribution to the pathogenesis of myasthenia gravis.
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- 2020
48. Minimal manifestation status and prednisone withdrawal in the MGTX trial.
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Lee, Ikjae, Kuo, Hui-Chien, Aban, Inmaculada B, Cutter, Gary R, McPherson, Tarrant, Kaminski, Henry J, Sussman, Jon, Ströbel, Philipp, Oger, Joel, Cea, Gabriel, Heckmann, Jeannine M, Evoli, Amelia, Nix, Wilfred, Ciafaloni, Emma, Antonini, Giovanni, Witoonpanich, Rawiphan, King, John O, Beydoun, Said R, Chalk, Colin H, Barboi, Alexandru C, Amato, Anthony A, Shaibani, Aziz I, Katirji, Bashar, Lecky, Bryan RF, Buckley, Camilla, Vincent, Angela, Dias-Tosta, Elza, Yoshikawa, Hiroaki, Waddington-Cruz, Marcia, Pulley, Michael T, Rivner, Michael H, Kostera-Pruszczyk, Anna, Pascuzzi, Robert M, Jackson, Carlayne E, Verschuuren, Jan JG, Massey, Janice M, Kissel, John T, Werneck, Lineu C, Benatar, Michael, Barohn, Richard J, Tandan, Rup, Mozaffar, Tahseen, Conwit, Robin, Minisman, Greg, Sonett, Joshua R, and Wolfe, Gil I
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Biomedical and Clinical Sciences ,Clinical Sciences ,Clinical Research ,Clinical Trials and Supportive Activities ,Myasthenia Gravis ,Autoimmune Disease ,Neurosciences ,Rare Diseases ,Evaluation of treatments and therapeutic interventions ,6.1 Pharmaceuticals ,Adolescent ,Adult ,Animals ,Combined Modality Therapy ,Female ,Humans ,Immunosuppressive Agents ,Male ,Middle Aged ,Prednisone ,Rats ,Single-Blind Method ,Substance Withdrawal Syndrome ,Thymectomy ,Thymoma ,Thymus Neoplasms ,Young Adult ,MGTX study group ,Cognitive Sciences ,Neurology & Neurosurgery ,Clinical sciences - Abstract
ObjectiveTo examine whether sustained minimal manifestation status (MMS) with complete withdrawal of prednisone is better achieved in thymectomized patients with myasthenia gravis (MG).MethodsThis study is a post hoc analysis of data from a randomized trial of thymectomy in MG (Thymectomy Trial in Non-Thymomatous Myasthenia Gravis Patients Receiving Prednisone Therapy [MGTX]). MGTX was a multicenter, randomized, rater-blinded 3-year trial that was followed by a voluntary 2-year extension for patients with acetylcholine receptor (AChR) antibody-positive MG without thymoma. Patients were randomized 1:1 to thymectomy plus prednisone vs prednisone alone. Participants were age 18-65 years at enrollment with disease duration less than 5 years. All patients received oral prednisone titrated up to 100 mg on alternate days until they achieved MMS, which prompted a standardized prednisone taper as long as MMS was maintained. The achievement rate of sustained MMS (no symptoms of MG for 6 months) with complete withdrawal of prednisone was compared between the thymectomy plus prednisone and prednisone alone groups.ResultsPatients with MG in the thymectomy plus prednisone group achieved sustained MMS with complete withdrawal of prednisone more frequently (64% vs 38%) and quickly compared to the prednisone alone group (median time 30 months vs no median time achieved, p < 0.001) over the 5-year study period. Prednisone-associated adverse symptoms were more frequent in the prednisone alone group and distress level increased with higher doses of prednisone.ConclusionsThymectomy benefits patients with MG by increasing the likelihood of achieving sustained MMS with complete withdrawal of prednisone.Clinicaltrialsgov identifierNCT00294658.Classification of evidenceThis study provides Class II evidence that for patients with generalized MG with AChR antibody, those receiving thymectomy plus prednisone are more likely to attain sustained MMS and complete prednisone withdrawal than those on prednisone alone.
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- 2020
49. R(refracted)-PIV measurements of water film flow: application to flow under a rolling tire
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Ben Khodja, Arbia, Simoëns, Serge, Michard, Marc, Le Touzé, David, Hermange, Corentin, Poncet, Clément, and Oger, Guillaume
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- 2022
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50. Structural insight into Tn3 family transposition mechanism
- Author
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Alexander V. Shkumatov, Nicolas Aryanpour, Cédric A. Oger, Gérôme Goossens, Bernard F. Hallet, and Rouslan G. Efremov
- Subjects
Science - Abstract
Here the structure of transposase from Tn3 family is reported in apo form and bound to the transposon ends. The activation of the transposase induces metamorphic refolding of the catalytic domain suggesting the family-specific regulation mechanism.
- Published
- 2022
- Full Text
- View/download PDF
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