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4. Comprehensive Catalog of Variants Potentially Associated with Hidradenitis Suppurativa, Including Newly Identified Variants from a Cohort of 100 Patients.

Author

Muret, Kévin, Le Goff, Vincent, Dandine-Roulland, Claire, Hotz, Claire, Jean-Louis, Francette, Boisson, Bertrand, Mesrob, Lilia, Sandron, Florian, Daian, Delphine, Olaso, Robert, Le Floch, Edith, Meyer, Vincent, Wolkenstein, Pierre, Casanova, Jean-Laurent, Lévy, Yves, Bonnet, Eric, Deleuze, Jean-François, and Hüe, Sophie

Subjects
NOTCH signaling pathway, INFLAMMATORY bowel diseases, NOTCH genes, SKIN diseases, CELLULAR control mechanisms, HIDRADENITIS suppurativa
Abstract

Hidradenitis suppurativa (HS) is a chronic skin disease characterized by painful, recurrent abscesses, nodules, and scarring, primarily in skin folds. The exact causes of HS are multifactorial, involving genetic, hormonal, and environmental factors. It is associated with systemic diseases such as metabolic syndrome and inflammatory bowel disease. Genetic studies have identified mutations in the γ-secretase complex that affect Notch signaling pathways critical for skin cell regulation. Despite its high heritability, most reported HS cases do not follow a simple genetic pattern. In this article, we performed whole-exome sequencing (WES) on a cohort of 100 individuals with HS, and we provide a comprehensive review of the variants known to be described or associated with HS. 91 variants were associated with the γ-secretase complex, and 78 variants were associated with other genes involved in the Notch pathway, keratinization, or immune response. Through this new genetic analysis, we have added ten new variants to the existing catalogs. All variants are available in a.vcf file and are provided as a resource for future studies. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Microbiological Profile of Instrumented Spinal Infections: 10-Year Study at a French Spine Center.

Author

Reissier, Sophie, Couzigou, Carine, Courseau, Romain, Aubert, Elise, Le Monnier, Alban, Bonnet, Eric, Upex, Peter, Moreau, Pierre-Emmanuel, Riouallon, Guillaume, and Lourtet-Hascoët, Julie

Subjects
SURGICAL site infections, CUTIBACTERIUM acnes, SPINAL surgery, GRAM-negative bacteria, STAPHYLOCOCCUS aureus
Abstract

Objective: The objective was to compare the microbiological characteristics and treatment of early and late surgical site infections (SSIs) in instrumented spinal surgery. Methods: Those patients admitted for SSIs in a single center between January 2010 and December 2022 were included. The subjects were divided into early (eSSIs) and late (lSSIs) SSIs, and demographic, microbiological, treatment, and follow-up data were collected. Results: Instrumented spinal surgery was performed in 2136 patients. Ninety-six cases of infections were identified (prevalence = 4.5%), with 47.9% eSSIs and 52.1% lSSIs. In 58.7% of the cases, the eSSIs were monomicrobial: Staphylococcus aureus (37%) and Enterobacterales (33.3%) were the main bacteria involved. In 66% of the cases, the lSSIs, were monomicrobial: Cutibacterium acnes (30.3%) and staphylococci were predominant. Enterobacterales were isolated in more than 70% of the polymicrobial samples in both the eSSIs and lSSIs. The treatment of the eSSIs mostly consisted of lavage-debridement surgery associated with antibiotic treatment, while the treatment of the lSSIs combined hardware removal or replacement and long-duration antibiotic treatment. A negative outcome was observed in 17.1% of the eSSIs and 5.7% of the lSSIs. Enterobacterales were associated with negative outcomes of eSSIs. Conclusions: Enterobacterales were found in most of the polymicrobial infections regardless of the time of infection onset. Further large studies should be conducted to precisely determine the management and prevention regarding the increasing Gram-negative bacteria SSIs. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Osteosynthesis-associated infection of the lower limbs by multidrug-resistant and extensively drug-resistant Gram-negative bacteria: a multicentre cohort study

Author

Giannitsioti, Efthymia, Salles, Mauro José, Mavrogenis, Andreas, Rodriguez-Pardo, Dolors, Los-Arcos, Ibai, Ribera, Alba, Ariza, Javier, Toro, María Dolores, Nguyen, Sophie, Senneville, Eric, Bonnet, Eric, Chan, Monica, Pasticci, Maria Bruna, Petersdorf, Sabine, Benito, Natividad, Connell, Nuala, Blanco García, Antonio, Skaliczki, Gábor, Tattevin, Pierre, Kocak Tufan, Zeliha, Pantazis, Nikolaos, Megaloikonomos, Panayiotis D., Papagelopoulos, Panayiotis, Soriano, Alejandro, Papadopoulos, Antonios, the ESGIAI collaborators study group, National and Kapodistrian University of Athens (NKUA), CHU Pontchaillou [Rennes], ARN régulateurs bactériens et médecine (BRM), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Salles, Mauro José, Pasticci, Maria Bruna, Benito, Natividad, O' Connell, Nuala, Skaliczki, Gábor, Pantazis, Nikolaos, Megaloikonomos, Panayiotis D ., and Soriano, Alejandro

Subjects
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, Original Full-Length Article, Orthopedics and Sports Medicine, Surgery
Abstract

[Purpose] The purpose of this study was the clinical and therapeutic assessment of lower-limb osteosynthesis-associated infection (OAI) by multidrug-resistant (MDR) and extensively drug-resistant (XDR) Gram-negative bacteria (GNB), which have been poorly studied to date., [Methods] A prospective multicentre observational study was conducted on behalf of ESGIAI (the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group on Implant-Associated Infections). Factors associated with remission of the infection were evaluated by multivariate and Cox regression analysis for a 24-month follow-up period., [Results] Patients ( n=57 ) had a history of trauma (87.7 %), tumour resection (7 %) and other bone lesions (5.3 %). Pathogens included Escherichia coli ( n=16 ), Pseudomonas aeruginosa ( n=14 ; XDR 50 %), Klebsiella spp. ( n=7 ), Enterobacter spp. ( n=9 ), Acinetobacter spp. ( n=5 ), Proteus mirabilis ( n=3 ), Serratia marcescens ( n=2 ) and Stenotrophomonas maltophilia ( n=1 ). The prevalence of ESBL (extended-spectrum β -lactamase), fluoroquinolone and carbapenem resistance were 71.9 %, 59.6 % and 17.5 % respectively. Most patients ( n=37 ; 64.9 %) were treated with a combination including carbapenems ( n=32 ) and colistin ( n=11 ) for a mean of 63.3 d. Implant retention with debridement occurred in early OAI (66.7 %), whereas the infected device was removed in late OAI (70.4 %) ( p=0.008 ). OAI remission was achieved in 29 cases (50.9 %). The type of surgery, antimicrobial resistance and duration of treatment did not significantly influence the outcome. Independent predictors of the failure to eradicate OAI were age >60 years (hazard ratio, HR, of 3.875; 95 % confidence interval, CI95 %, of 1.540-9.752; p=0.004 ) and multiple surgeries for OAI (HR of 2.822; CI95 % of 1.144-6.963; p=0.024 )., [Conclusions] Only half of the MDR/XDR GNB OAI cases treated by antimicrobials and surgery had a successful outcome. Advanced age and multiple surgeries hampered the eradication of OAI. Optimal therapeutic options remain a challenge.

Published
2022

17. Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Author

Waltemath, Dagmar, Bergmann, Frank T., Chaouiya, Claudine, Czauderna, Tobias, Gleeson, Padraig, Goble, Carole, Golebiewski, Martin, Hucka, Michael, Juty, Nick, Krebs, Olga, Le Novère, Nicolas, Mi, Huaiyu, Moraru, Ion I., Myers, Chris J., Nickerson, David, Olivier, Brett G., Rodriguez, Nicolas, Schreiber, Falk, Smith, Lucian, Zhang, Fengkai, and Bonnet, Eric

Published
2018
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18. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Author

Waltemath, Dagmar, Bergmann, Frank T., Chaouiya, Claudine, Czauderna, Tobias, Gleeson, Padraig, Goble, Carole, Golebiewski, Martin, Hucka, Michael, Juty, Nick, Krebs, Olga, Le Novère, Nicolas, Mi, Huaiyu, Moraru, Ion I., Myers, Chris J., Nickerson, David, Olivier, Brett G., Rodriguez, Nicolas, Schreiber, Falk, Smith, Lucian, Zhang, Fengkai, and Bonnet, Eric

Published
2014
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19. Using convolutional neural networks for the classification of breast cancer images

Author

Bonnet, Eric

Subjects
FOS: Biological sciences, Image and Video Processing (eess.IV), FOS: Electrical engineering, electronic engineering, information engineering, Electrical Engineering and Systems Science - Image and Video Processing, Quantitative Biology - Quantitative Methods, Quantitative Methods (q-bio.QM)
Abstract

In this study I compare different architectures of convolutional neural networks and different hardware acceleration devices for the detection of breast cancer from microscopic images of sentinel lymph nodes tissue. Convolutional models with increasing depth are trained and tested on a public data set of more than 300,000 images of lymph node tissue, on four different hardware acceleration cards, using an off-the-shelf deep learning framework. The impact of transfer learning, data augmentation and hyperparameters fine-tuning are also tested. Hardware acceleration device performance can improve training time by a factor of five to twelve, depending on the model used. On the other hand, increasing convolutional depth will augment the training time by a factor of four to six times, depending on the acceleration device used. Increasing the depth of the model, as could be expected, clearly improves performance, while data augmentation and transfer learning do not. Fine-tuning the hyperparameters of the model notably improves the results, with the best model showing a performance comparable to state-of-the-art models., 9 pages, 2 figures, 4 tables; corrected typos; added one more (recent) GPU card

Published
2021

23. A new low-density nuclear matter equation of state from an experimental data analysis including in-medium effects

Author

Pais, Helena, Bougault, Rémi, Gulminelli, Francesca, Providência, Constança, Bonnet, Eric, Borderie, Bernard, Chbihi, Abdelouahad, Frankland, John D., Galichet, Emmanuelle, Gruyer, Diégo, Henri, Maxime, Le Neindre, Nicolas, Lopez, Olivier, Manduci, Loredana, Parlôg, Marian, Verde, Giuseppe, Laboratoire de physique corpusculaire de Caen (LPCC), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physique subatomique et des technologies associées (SUBATECH), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut de Physique Nucléaire d'Orsay (IPNO), Université Paris-Sud - Paris 11 (UP11)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Grand Accélérateur National d'Ions Lourds (GANIL), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Conservatoire National des Arts et Métiers [CNAM] (CNAM), Ecole des Applications Militaires de l'Energie Atomique (EAMEA), Ecole des Applications Militaires de l'Energie Atomique, and Université de Nantes (UN)-Université de Nantes (UN)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique)

Subjects
[PHYS.NUCL]Physics [physics]/Nuclear Theory [nucl-th], Nuclear Experiment, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph]
Abstract

The modification of the ground state properties of light atomic nuclei in the nuclear and stellar medium is addressed, using chemical equilibrium constants evaluated from a new analysis of the intermediate energy heavy-ion (Xe+Sn) collision data measured by the INDRA collaboration. Three different reactions are considered, mainly differing by the isotopic content of the emission source. The thermodynamic conditions of the data samples are extracted from the measured multiplicities allowing for an in-medium correction, with the single hypothesis that the different nuclear species in a given sample correspond to a unique common value for the density of the expanding source. We show that this new correction, which was not considered in previous analyses of chemical constants from heavy ion collisions, is necessary, since the observables of the analysed systems show strong deviations from the expected results for an ideal gas of clusters. This experimental data set is further compared to a relativistic mean-field model, and seen to be reasonably compatible with a universal correction of the attractive $\sigma$5 pages,-meson coupling.

Published
2020

26. The genome of Tetranychus urticae reveals herbivorous pest adaptations

Author

Grbić, Miodrag, Van Leeuwen, Thomas, Clark, Richard M., Rombauts, Stephane, Rouzé, Pierre, Grbić, Vojislava, Osborne, Edward J., Dermauw, Wannes, Thi Ngoc, Phuong Cao, Ortego, Félix, Hernández-Crespo, Pedro, Diaz, Isabel, Martinez, Manuel, Navajas, Maria, Sucena, Élio, Magalhães, Sara, Nagy, Lisa, Pace, Ryan M., Djuranović, Sergej, Smagghe, Guy, Iga, Masatoshi, Christiaens, Olivier, Veenstra, Jan A., Ewer, John, Villalobos, Rodrigo Mancilla, Hutter, Jeffrey L., Hudson, Stephen D., Velez, Marisela, Yi, Soojin V., Zeng, Jia, Pires-daSilva, Andre, Roch, Fernando, Cazaux, Marc, Navarro, Marie, Zhurov, Vladimir, Acevedo, Gustavo, Bjelica, Anica, Fawcett, Jeffrey A., Bonnet, Eric, Martens, Cindy, Baele, Guy, Wissler, Lothar, Sanchez-Rodriguez, Aminael, Tirry, Luc, Blais, Catherine, Demeestere, Kristof, Henz, Stefan R., Gregory, Ryan T., Mathieu, Johannes, Verdon, Lou, Farinelli, Laurent, Schmutz, Jeremy, Lindquist, Erika, Feyereisen, René, and Van de Peer, Yves

Published
2011
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29. The Ectocarpus genome and the independent evolution of multicellularity in brown algae

Author

Cock, Mark J., Sterck, Lieven, Rouzé, Pierre, Scornet, Delphine, Allen, Andrew E., Amoutzias, Grigoris, Anthouard, Veronique, Artiguenave, François, Aury, Jean-Marc, Badger, Jonathan H., Beszteri, Bank, Billiau, Kenny, Bonnet, Eric, Bothwell, John H., Bowler, Chris, Boyen, Catherine, Brownlee, Colin, Carrano, Carl J., Charrier, Bénédicte, Cho, Ga Youn, Coelho, Susana M., Collén, Jonas, Corre, Erwan, Da Silva, Corinne, Delage, Ludovic, Delaroque, Nicolas, Dittami, Simon M., Doulbeau, Sylvie, Elias, Marek, Farnham, Garry, Gachon, Claire M. M., Gschloessl, Bernhard, Heesch, Svenja, Jabbari, Kamel, Jubin, Claire, Kawai, Hiroshi, Kimura, Kei, Kloareg, Bernard, Küpper, Frithjof C., Lang, Daniel, Le Bail, Aude, Leblanc, Catherine, Lerouge, Patrice, Lohr, Martin, Lopez, Pascal J., Martens, Cindy, Maumus, Florian, Michel, Gurvan, Miranda-Saavedra, Diego, Morales, Julia, Moreau, Hervé, Motomura, Taizo, Nagasato, Chikako, Napoli, Carolyn A., Nelson, David R., Nyvall-Collén, Pi, Peters, Akira F., Pommier, Cyril, Potin, Philippe, Poulain, Julie, Quesneville, Hadi, Read, Betsy, Rensing, Stefan A., Ritter, Andrés, Rousvoal, Sylvie, Samanta, Manoj, Samson, Gaelle, Schroeder, Declan C., Ségurens, Béatrice, Strittmatter, Martina, Tonon, Thierry, Tregear, James W., Valentin, Klaus, von Dassow, Peter, Yamagishi, Takahiro, Van de Peer, Yves, and Wincker, Patrick

Published
2010
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30. Charged particle identification using time of flight with FAZIA

Author

Valdré, S., Barlini, S., Bini, M., Boiano, A., Bonnet, Eric, Borderie, B., Bougault, R., Bruno, M., Buccola, A., Camaiani, A., Casini, G., Chbihi, A., Ciampi, C., Cicerchia, M., Cinausero, M., Dueñas, J. A., Fabris, D., Frankland, J. D., Frosin, C., Galichet, Emmanuelle, Gramegna, F., Gruyer, D., Henri, M., Kordyasz, A., Kozik, T., Lemarié, J., Neindre, N. Le, Lombardo, I., Lopez, O., Mantovani, G., Marchi, T., Morelli, L., Nam, S., Olmi, A., Ordine, A., Ottanelli, P., Pârlog, M., Pasquali, G., Pastore, G., Piantelli, S., Poggi, G., Quicray, J., Stefanini, A. A., Tortone, G., Upadhyaya, S., Verde, G., Vient, E., Vigilante, M., Istituto Nazionale di Fisica Nucleare, Sezione di Firenze (INFN, Sezione di Firenze), Istituto Nazionale di Fisica Nucleare (INFN), Istituto Nazionale di Fisica Nucleare, Sezione di Napoli (INFN, Sezione di Napoli), Laboratoire de physique subatomique et des technologies associées (SUBATECH), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut de Physique Nucléaire d'Orsay (IPNO), Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris-Sud - Paris 11 (UP11), Laboratoire de physique corpusculaire de Caen (LPCC), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), Dipartimento di Fisica [Bologna], Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Grand Accélérateur National d'Ions Lourds (GANIL), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), Dipartimento di Fisica [Padova], Universita degli Studi di Padova, Universidad de Huelva, Istituto Nazionale di Fisica Nucleare, Sezione di Padova (INFN, Sezione di Padova), Conservatoire National des Arts et Métiers [CNAM] (CNAM), University of Warsaw (UW), Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ), Istituto Nazionale di Fisica Nucleare, Sezione di Catania (INFN), Università degli studi di Catania [Catania], Korea University [Seoul], Valdre, S., Barlini, S., Bini, M., Boiano, A., Bonnet, E., Borderie, B., Bougault, R., Bruno, M., Buccola, A., Camaiani, A., Casini, G., Chbihi, A., Ciampi, C., Cicerchia, M., Cinausero, M., Duenas, J. A., Fabris, D., Frankland, J. D., Frosin, C., Galichet, E., Gramegna, F., Gruyer, D., Henri, M., Kordyasz, A., Kozik, T., Lemarie, J., Le Neindre, N., Lombardo, I., Lopez, O., Mantovani, G., Marchi, T., Morelli, L., Nam, S., Olmi, A., Ordine, A., Ottanelli, P., Parlog, M., Pasquali, G., Pastore, G., Piantelli, S., Poggi, G., Quicray, J., Stefanini, A. A., Tortone, G., Upadhyaya, S., Verde, G., Vient, E., Vigilante, M., Université de Nantes (UN)-Université de Nantes (UN)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Université Paris-Sud - Paris 11 (UP11)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Padova = University of Padua (Unipd), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), and Università degli studi di Catania = University of Catania (Unict)

Subjects
[PHYS.NEXP]Physics [physics]/Nuclear Experiment [nucl-ex], ComputingMilieux_MISCELLANEOUS
Abstract

This contribution reports on the time of flight implementation in the FAZIA Si-Si-CsI(Tl) telescopes, focusing on the basic ideas of the method and on some results from recent experiments at LNS.

Published
2019

31. Multidrug (MDR) and extensively drug resistant (XDR) Gram negative prosthetic joint infections (PJI): Role of surgery and impact of colistin administration

Author

Papadopoulos, Antonios, Ribera, A., Mavrogenis, Andreas F., Rodríguez-Pardo, Dolors, Bonnet, Eric, Salles, Mauro José, Toro, María Dolores del, Nguyen, Sophie, Blanco-García, Antonio, Skaliczki, Gábor, Soriano, Álex, Benito, Natividad, Petersdorf, Sabine, Pasticci, Maria Bruna, Tattevin, Pierre, Kocak Tufan, Z., Chan, Monica, O'Connell, Nuala, Pantazis, Nikos, Kyprianou, Aikaterini, Pigrau, Carlos, Megaloikonomos, Panayiotis D., Senneville, Eric, Ariza, Javier, Papagelopoulos, Panayiotis J., Giannitsioti, Efthymia, and Hellenic Institute for the Study of Sepsis

Subjects
Prosthetic joint infection, Multidrug resistant, Bones, Gram-negative bacteria, multidrug-resistant, bone and joint infections, extensively drug-resistant, prosthetic joint infection, Extensively drug resistant, Gram negative bacteria, Joint infection
Abstract

Factors influencing treatment outcome of patients with Gram-negative bacterial (GNB) multidrug-resistant (MDR) and extensively drug-resistant (XDR) prosthetic joint infection (PJIs) were analysed. Data were collected (2000–2015) by 18 centres. Treatment success was analysed by surgery type for PJI, resistance (MDR/XDR) and antimicrobials (colistin/non-colistin) using logistic regression and survival analyses. A total of 131 patients (mean age 73.0 years, 35.9% male, 58.8% with co-morbidities) with MDR (n = 108) or XDR (n = 23) GNB PJI were assessed. The most common pathogens were Escherichia coli (33.6%), Pseudomonas aeruginosa (25.2%), Klebsiella pneumoniae (21.4%) and Enterobacter cloacae (17.6%). Pseudomonas aeruginosa predominated in XDR cases. Isolates were carbapenem-resistant (n = 12), fluoroquinolone-resistant (n = 63) and ESBL-producers (n = 94). Treatment outcome was worse in XDR versus MDR cases (P = 0.018). Success rates did not differ for colistin versus non-colistin in XDR cases (P = 0.657), but colistin was less successful in MDR cases (P = 0.018). Debridement, antibiotics and implant retention (DAIR) (n = 67) was associated with higher failure rates versus non-DAIR (n = 64) (OR = 3.57, 95% CI 1.68–7.58; P < 0.001). Superiority of non-DAIR was confirmed by Kaplan–Meir analysis (HR = 0.36, 95% CI 0.20–0.67) and remained unchangeable by time of infection (early/late), antimicrobial resistance (MDR/XDR) and antimicrobials (colistin/non-colistin) (Breslow–Day, P = 0.737). DAIR is associated with higher failure rates even in early MDR/XDR GNB PJIs versus implant removal. Colistin should be preserved for XDR cases as it is detrimental in MDR infections., Statistical analysis of the study was performed with the financial support of the Hellenic Institute for the Study of Sepsis.

Published
2019

40. Risk factors for serotype 19A carriage after introduction of 7-valent pneumococcal vaccination

Author

Derkx Véronique, Fritzell Bernard, Boucherat Michel, Thollot Franck, Bonnet Eric, Levy Corinne, Cohen Robert, Bingen Edouard, and Varon Emmanuelle

Subjects
Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background After the implementation of 7-valent pneumococcal conjugate vaccine (PCV7), in several countries, serotype 19A is now the serotype most frequently involved in pneumococcal diseases and carriage. To determine factors potentially related to 19A nasopharyngeal (NP) carriage we analyzed data from an ongoing prospective French national surveillance study of pneumococcal NP carriage in young children. Methods NP swabs were obtained from children aged 6 to 24 months, either during routine check-ups with normal findings, or when they presented with acute otitis media (AOM). The swabs were sent for analysis to the French National Reference Centre for Pneumococci. Factors influencing pneumococcal carriage and carriage of penicillin non-susceptible (PNSP), 19A and PNS-19A were investigated by multivariate logistic regression. Results From 2006 to 2009, 66 practitioners enrolled 3507 children (mean age 13.6 months), of whom, 98.3% of children had been vaccinated with PCV7 and 33.4% of children attended daycare centres (DCC). Serotype 19A was found in 10.4% of the overall population, 20.5% of S. pneumoniae carriers (n = 1780) and 40.8% of PNSP carriers (n = 799). Among 19A strains, 10.7% were penicillin-susceptible, 80% intermediate and 9.3% fully resistant. Logistic regression analysis showed that the main factors associated with PNSP carriage were AOM (OR = 3.09, 95% CI [2.39;3.98]), DCC (OR = 1.70, 95% CI [1.42;2.03]), and recent antibiotic use (OR = 1.24, 95% CI [1.05;1.47]. The main factors predictive of 19A carriage were recent antibiotic use (OR = 1.81, 95% CI [1.42;2.30]), AOM (OR = 1.67, 95% CI [1.11;2.49]), DCC (OR = 1.56, 95% CI [1.21;2.2] and young age, Conclusion In a population of children aged from 6 to 24 months with a high rate of PCV7 vaccination coverage, we found that antibiotic exposure, DCC attendance and AOM were linked to 19A carriage.

Published
2011
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41. Sequential fission of highly excited compound nuclei in a 4D Langevin approach

Author

Gruyer, Diego, Mazurek, K., Frankland, J.D., Bonnet, Eric, Nadtochy, P. N., Chbihi, A., Wieleczko, J-P., Laboratoire de physique corpusculaire de Caen (LPCC), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), Grand Accélérateur National d'Ions Lourds (GANIL), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), Laboratoire de physique subatomique et des technologies associées (SUBATECH), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Polish National Science Centre under Contract No. 2013/08/M/ST2/00257 (LEA COPIGAL) (Project No. 18) and IN2P3-COPIN (Project No. 12-145, 09-146), and by the Russian Foundation for Basic Research (Project No. 13-02-00168)., Normandie Université (NU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), and Université de Nantes (UN)-Université de Nantes (UN)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique)

Subjects
Nuclear Theory (nucl-th), [PHYS.NUCL]Physics [physics]/Nuclear Theory [nucl-th], Nuclear Theory, FOS: Physical sciences, Nuclear Experiment (nucl-ex), [PHYS.NEXP]Physics [physics]/Nuclear Experiment [nucl-ex], Nuclear Experiment
Abstract

In highly dissipative collisions between heavy ions, the optimal conditions to investigate different de-excitation channels of hot nuclei such as evaporation, fission or multifragmentation are well known. One crucial issue remains the excitation energy region where fission gives way to multi-fragmentation. In this paper, the onset of multi-fragment exit channels is investigated in terms of sequential fission. For the first time, the dynamical approach based on solving Langevin transport equations in multidimensional collective coordinate space is used to follow the de-excitation of highly excited (up to E =223–656 MeV) 248 Rf compound nuclei. The sequential fission model we propose contains two steps: (1) time evolution of the compound nucleus up to either scission or residue formation, followed by (2) dynamical calculations of each primary fragment separately. This procedure allows to obtain from one to four cold fragments correlated with the light particles emitted during the de-excitation process. Experimental data measured with the INDRA detector for the 129 Xe+ nat Sn reaction at beam energies 8, 12 and 15 MeV/nucleon provide strong constraints for this sequential fission scenario.

Published
2017

42. Learning differential module networks across multiple experimental conditions

Author

Erola, Pau, Bonnet, Eric, and Michoel, Tom

Subjects
ComputingMethodologies_PATTERNRECOGNITION, q-bio.QM, q-bio.GN, q-bio.MN, ComputingMethodologies_GENERAL
Abstract

Module network inference is a statistical method to reconstruct gene regulatory networks, which uses probabilistic graphical models to learn modules of coregulated genes and their upstream regulatory programs from genome-wide gene expression and other omics data. Here we review the basic theory of module network inference, present protocols for common gene regulatory network reconstruction scenarios based on the Lemon-Tree software, and show, using human gene expression data, how the software can also be applied to learn differential module networks across multiple experimental conditions.

Published
2017

45. article publié dans actes de colloque

Author

Bonnet, Eric, Arts des Images et Art Contemporain (AIAC), Université Paris 8 Vincennes-Saint-Denis (UP8), and Shtalbi, Haki

Subjects
[SHS.ART] Humanities and Social Sciences/Art and art history, [SHS] Humanities and Social Sciences, [SHS.ART]Humanities and Social Sciences/Art and art history, ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract

International audience

Published
2017

46. Improved method for the experimental determination of in-medium effects from heavy-ion collisions.

Author

Pais, Helena, Bougault, Rémi, Gulminelli, Francesca, Providęncia, Constança, Bonnet, Eric, Borderie, Bernard, Chbihi, Abdelouahad, Frankland, John D, Galichet, Emmanuelle, Gruyer, Diégo, Henri, Maxime, Neindre, Nicolas Le, Lopez, Olivier, Manduci, Loredana, Parlôg, Marian, and Verde, Giuseppe

Subjects
THERMODYNAMICS, CHEMICAL equilibrium, THERMODYNAMIC equilibrium, BINDING energy, CLUSTER theory (Nuclear physics), NUCLEAR matter, EQUATIONS of state, MESONS
Abstract

The equation of state with light clusters for nuclear and stellar matter is determined using chemical equilibrium constants evaluated from the analysis of the recently published (Xe + Sn) heavy ion data, corresponding to three reactions with different isotopic contents of the emission source. The measured multiplicities are used to extract the thermodynamic properties, and an in-medium correction to the ideal gas internal partition function of the clusters is included in the analysis. This in-medium correction and its respective uncertainty are calculated via a Bayesian analysis, with the unique hypothesis that the different nuclear species in a given sample must correspond to a unique common value for the density of the expanding source. Different parameter sets for the correction are tested, and the effect of the radius of the clusters on the thermodynamics and on the chemical equilibrium constants is also addressed. It is shown that the equilibrium constants obtained are almost independent of the isospin content of the analysed systems. Finally, a comparison with a relativistic mean field model proves that data are consistent with a universal in-medium correction of the scalar σ-meson coupling for nucleons bound in clusters. The obtained value, , is larger than that obtained in a previous study not including in-medium effects in the data analysis. This result implies a smaller effect on the binding energy of the clusters and, as a consequence, larger melting densities, and an increased cluster contribution in supernova matter. [ABSTRACT FROM AUTHOR]

Published
2020
Full Text
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47. RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis.

Author

Singh, Vidisha, Kalliolias, George D, Ostaszewski, Marek, Veyssiere, Maëva, Pilalis, Eleftherios, Gawron, Piotr, Mazein, Alexander, Bonnet, Eric, Petit-Teixeira, Elisabeth, and Niarakis, Anna

Subjects
RHEUMATOID arthritis, GENE mapping, SYSTEMS biology, CELLULAR signal transduction, AUTOIMMUNE diseases
Abstract

Rheumatoid arthritis (RA) is a progressive, inflammatory autoimmune disease of unknown aetiology. The complex mechanism of aetiopathogenesis, progress and chronicity of the disease involves genetic, epigenetic and environmental factors. To understand the molecular mechanisms underlying disease phenotypes, one has to place implicated factors in their functional context. However, integration and organization of such data in a systematic manner remains a challenging task. Molecular maps are widely used in biology to provide a useful and intuitive way of depicting a variety of biological processes and disease mechanisms. Recent large-scale collaborative efforts such as the Disease Maps Project demonstrate the utility of such maps as versatile tools to organize and formalize disease-specific knowledge in a comprehensive way, both human and machine-readable. We present a systematic effort to construct a fully annotated, expert validated, state-of-the-art knowledge base for RA in the form of a molecular map. The RA map illustrates molecular and signalling pathways implicated in the disease. Signal transduction is depicted from receptors to the nucleus using the Systems Biology Graphical Notation (SBGN) standard representation. High-quality manual curation, use of only human-specific studies and focus on small-scale experiments aim to limit false positives in the map. The state-of-the-art molecular map for RA, using information from 353 peer-reviewed scientific publications, comprises 506 species, 446 reactions and 8 phenotypes. The species in the map are classified to 303 proteins, 61 complexes, 106 genes, 106 RNA entities, 2 ions and 7 simple molecules. The RA map is available online at ramap.elixir-luxembourg.org as an open-access knowledge base allowing for easy navigation and search of molecular pathways implicated in the disease. Furthermore, the RA map can serve as a template for omics data visualization. [ABSTRACT FROM AUTHOR]

Published
2020
Full Text
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48. Vaporization events in HIC

Author

Bonnet, Eric, Grand Accélérateur National d'Ions Lourds (GANIL), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), Lion, Michel, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.NEXP] Physics [physics]/Nuclear Experiment [nucl-ex], [PHYS.NEXP]Physics [physics]/Nuclear Experiment [nucl-ex], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

49. Reaction mechanisms leading to 3-body exit channels in central collisions of 129Xe+ natSn at 12 MeV/u

Author

D. Frankland, J., Gruyer, D., Bonnet, Eric, Chbihi, A., Grand Accélérateur National d'Ions Lourds (GANIL), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), INDRA, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.NEXP]Physics [physics]/Nuclear Experiment [nucl-ex], Nuclear Experiment
Abstract

International audience; We attempt to ascertain whether well-known sub-Fermi energy reaction mechanisms (fusion-fission, quasifission, deep-inelastic reactions) can explain the cross-sections and other characteristics recently observed for 3-fragment exit channels of central 129Xe + natSn collisions from 8 to 25 MeV/u measured with INDRA. In a first step, we have simulated deep-inelastic and capture (fusion-fission and/or quasifission) reactions at 12 MeV/u using the Deep Inelastic Transfers model coupled with GEMINI++, which we compare with data using a detailed software simulation of the INDRA array. Although minimum-bias measured and simulated reaction cross-sections are in good agreement, the cross-sections for 3-fragment exit channels are largely underestimated by the simulation. Moreover, 90% of simulated 3-body events are associated with mid-peripheral deep-inelastic collisions, whereas the measured coincident light charged-particle yields are consistent with central collisions leading to fusion or quasifission. However the observed 3-body yield seems beyond the reach of standard statistical decay of the primary (quasi)fission fragments.

Published
2016

50. Progresses in FAZIA detection system and preliminary results from the ISO-FAZIA experiment

Author

Pastore, G., Piantelli, S., Gruyer, D., Augey, L., Barlini, S., Bougault, R., Bini, M., Boiano, A., Bonnet, Eric, Borderie, B., Bruno, M., Casini, G., Chbihi, A., Cinausero, M., Dell'Aquila, D., A. Dueñas, J., Fable, Q., Fabris, D., Francalanza, L., D. Frankland, J., Gramegna, F., Henri, M., Kordyasz, A., Kozik, T., La Torre, R., Le Neindre, N., Lombardo, I., Lopez, O., Mabiala, J., Marchi, T., Morelli, L., Olmi, A., Pârlog, M., Pasquali, G., Poggi, G., Salomon, F., A. Stefanini, A., Valdrè, S., Tortone, G., Vient, E., Verde, G., Vigilante, M., Alba, R., Maiolino, C., Santonocito, D., Laboratoire de physique corpusculaire de Caen (LPCC), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), Grand Accélérateur National d'Ions Lourds (GANIL), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), Institut de Physique Nucléaire d'Orsay (IPNO), Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris-Sud - Paris 11 (UP11), Normandie Université (NU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Pastore, G., Piantelli, S., Gruyer, D., Augey, L., Barlini, S., Bougault, R., Bini, M., Boiano, A., Bonnet, E., Borderie, B., Bruno, M., Casini, G., Chbibi, A., Cinausero, M., Dell'Aquila, D., Dueñas, J. A., Fable, Q., Fabris, D., Francalanza, L., Frankland, J. D., Gramegna, F., Henri, M., Kordyasz, A., Kozik, T., La Torre, R., Le Neindre, N., Lombardo, I., Lopez, L. O., Mabiala, J., Marchi, T., Morelli, L., Olmi, A., Pârlog, M., Pasquali, G., Poggi, G., Salomon, F., Stefanini, A. A., Valdrè, S., Tortone, G., Vient, E., Verde, G., Vigilante, M., Alba, R., Maiolino, C., and Santonocito, D.

Subjects
Physics and Astronomy (miscellaneous), [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Astronomy and Astrophysic, [PHYS.NEXP]Physics [physics]/Nuclear Experiment [nucl-ex]
Abstract

International audience; In this contribution the status of the FAZIA project is presented, with a particular focus on the first experiment (identified as ISO-FAZIA) after the R&D phase. In this experiment four complete FAZIA blocks in a fully operating configuration were used. They were mounted in a planar “belt” geometry, symmetrically positioned with respect to the beam axis, covering the polar angles between 2.5◦ and 17.4◦ degrees. The investigated systems were 84Kr + 48,40Ca at 35 AMeV. The main goal of the experiment was the study of the isospin transport phenomena, extending a previous analysis. This contribution will report on the isotopic identi- fication capability of the FAZIA detector as well as preliminary results concerning the average isospin of the quasi-projectile produced in semiperipheral collisions as a function of the isospin of the target.

Published
2016

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