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6,513 results on '"A Devaux"'

1. Edges' Riemannian energy analysis for synchronization of multi-agent nonlinear systems over undirected weighted graphs

Author

Andrieu, Vincent, Astolfi, Daniele, and Cellier-Devaux, Alexandre

Subjects
Mathematics - Optimization and Control
Abstract

In this note we investigate the problem of global exponential synchronization of multi-agent systems described by nonlinear input affine dynamics. We consider the case of networks described by undirected connected graphs possibly without leader. We present a set of sufficient conditions based on a Riemannian metric approach in order to design a state-feedback distributed control law. Then, we study the convergence properties of the overall network. By exploiting the properties of the edge Laplacian we construct a Lyapunov function that allows to conclude global exponential synchronization of the overall network., Comment: Automatica, In press

Published
2024
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2. Detecting single photons is not always necessary to evidence interference of photon probability amplitudes

Author

Lantz, Eric, Devaux, Fabrice, and Massar, Serge

Subjects
Quantum Physics
Abstract

Subtracting accidental coincidences is a common practice quantum optics experiments. For zero mean Gaussian states, such as squeezed vacuum, we show that if one removes accidental coincidences the measurement results are quantitatively the same, both for photon coincidences at very low flux and for intensity covariances. Consequently, pure quantum effects at the photon level, like interference of photon wave functions or photon bunching, are reproduced in the correlation of fluctuations of macroscopic beams issued from spontaneous down conversion. This is true both in experiment if the detection resolution is smaller than the coherence cell (size of the mode), and in stochastic simulations based on sampling the Wigner function. We discuss the limitations of this correspondence, such as Bell inequalities (for which one cannot substract accidental coincidences), highly multimode situations such as quantum imaging, and higher order correlations., Comment: 10 pages, 2 figures

Published
2024
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3. Leveraging edge detection and neural networks for better UAV localization

Author

Di Piazza, Theo, Meinhardt-Llopis, Enric, Facciolo, Gabriele, Bascle, Benedicte, Abgrall, Corentin, and Devaux, Jean-Clement

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

We propose a novel method for geolocalizing Unmanned Aerial Vehicles (UAVs) in environments lacking Global Navigation Satellite Systems (GNSS). Current state-of-the-art techniques employ an offline-trained encoder to generate a vector representation (embedding) of the UAV's current view, which is then compared with pre-computed embeddings of geo-referenced images to determine the UAV's position. Here, we demonstrate that the performance of these methods can be significantly enhanced by preprocessing the images to extract their edges, which exhibit robustness to seasonal and illumination variations. Furthermore, we establish that utilizing edges enhances resilience to orientation and altitude inaccuracies. Additionally, we introduce a confidence criterion for localization. Our findings are substantiated through synthetic experiments., Comment: Accepted for publication in IGARSS2024. 4 pages, 3 figures, 3 tables

Published
2024

7. Increased [18F]FDG uptake in the infarcted myocardial area displayed by combined PET/CMR correlates with snRNA-seq-detected inflammatory cell invasion

Author

Lukovic, Dominika, Gyöngyösi, Mariann, Pavo, Imre J., Mester-Tonczar, Julia, Einzinger, Patrick, Zlabinger, Katrin, Kastner, Nina, Spannbauer, Andreas, Traxler, Denise, Pavo, Noemi, Goliasch, Georg, Pils, Dietmar, Jakab, Andras, Szankai, Zsuzsanna, Michel-Behnke, Ina, Zhang, Lu, Devaux, Yvan, Graf, Senta, Beitzke, Dietrich, and Winkler, Johannes

Published
2024
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11. Workshop summary -- Kaons@CERN 2023

Author

Anzivino, G., Cuendis, S. Arguedas, Bernard, V., Bijnens, J., Bloch-Devaux, B., Bordone, M., Brizioli, F., Brod, J., Camalich, J. M., Ceccucci, A., Cenci, P., Christ, N. H., Colangelo, G., Cornella, C., Crivellin, A., D'Ambrosio, G., Deppisch, F. F., Dery, A., Dettori, F., Di Carlo, M., Döbrich, B., Engelfried, J., Fantechi, R., González-Alonso, M., Gorbahn, M., Goudzovski, E., Grossman, Y., Hermansson-Truedsson, N., Hives, Z., Hoferichter, M., Hoid, B. -L., Husek, T., Isidori, G., Jüttner, A., Kampf, K., Kholodenko, S., Knecht, M., Kolesár, M., Koval, M., Lazzeroni, C., Ligeti, Z., Mahmoudi, F., Marchevski, R., Santos, D. Martínez, Massri, K., Mombächer, T., Nanjo, H., Neshatpour, S., Nomura, T., Passemar, E., Peruzzo, L., Piccini, M., Pich, A., Sachrajda, C. T., Schacht, S., Shiomi, K., Stangl, P., Stoffer, P., Swallow, J., Tsang, J. T., Valencia, G., Wanke, R., and Zupan, J.

Subjects
High Energy Physics - Phenomenology, High Energy Physics - Experiment, High Energy Physics - Lattice
Abstract

Kaon physics is at a turning point -- while the rare-kaon experiments NA62 and KOTO are in full swing, the end of their lifetime is approaching and the future experimental landscape needs to be defined. With HIKE, KOTO-II and LHCb-Phase-II on the table and under scrutiny, it is a very good moment in time to take stock and contemplate about the opportunities these experiments and theoretical developments provide for particle physics in the coming decade and beyond. This paper provides a compact summary of talks and discussions from the Kaons@CERN 2023 workshop., Comment: 55 pages, Summary of Kaons@CERN 23 workshop, references updated, typos fixed, version as published in EPJC

Published
2023

12. First observation and study of the $K^{\pm} \rightarrow \pi^{0} \pi^{0} \mu^{\pm} \nu$ decay

Author

Collaboration, NA48/2, Batley, J. R., Kalmus, G., Lazzeroni, C., Munday, D. J., Slater, M. W., Wotton, S. A., Arcidiacono, R., Ceccucci, A., Bocquet, G., Cabibbo, N., Cundy, D., Falaleev, V., Gatignon, L., Fidecaro, M., Gonidec, A., Kubischta, W., Maier, A., Norton, A., Patel, M., Peters, A., Balev, S., Frabetti, P. L., Gersabeck, E., Goudzovski, E., Hristov, P., Kekelidze, V., Madigozhin, D., Molokanova, N., Polenkevich, I., Potrebenikov, Yu., Korotkova, A., Stoynev, S., Zinchenko, A., Kozhuharov, V., Litov, L., Monnier, E., Swallow, E., Winston, R., Rubin, P., Walker, A., Baldini, W., Ramusino, A. Cotta, Dalpiaz, P., Damiani, C., Fiorini, M., Gianoli, A., Martini, M., Petrucci, F., Savrié, M., Scarpa, M., Wahl, H., Bizzeti, A., Veltri, M., Calvetti, M., Celeghini, E., Iacopini, E., Lenti, M., Ruggiero, G., Behler, M., Eppard, K., Hita-Hochgesand, M., Kleinknecht, K., Marouelli, P., Masetti, L., Moosbrugger, U., Morales, C. Morales, Renk, B., Wache, M., Winhart, A., Wanke, R., Coward, D., Dabrowski, A., Martin, T. Fonseca, Shieh, M., Szleper, M., Velasco, M., Wood, M. D., Cenci, P., Pepe, M., Petrucci, M. C., Anzivino, G., Imbergamo, E., Nappi, A., Piccini, M., Raggi, M., Valdata-Nappi, M., Cerri, C., Fantechi, R., Collazuol, G., Di Lella, L., Lamanna, G., Mannelli, I., Michetti, A., Costantini, F., Doble, N., Fiorini, L., Giudici, S., Pierazzini, G., Sozzi, M., Venditti, S., Bloch-Devaux, B., Peyaud, B., Cheshkov, C., Chèze, J. B., De Beer, M., Derré, J., Marel, G., Mazzucato, E., Vallage, B., Holder, M., Ziolkowski, M., Biino, C., Cartiglia, N., Marchetto, F., Bifani, S., Clemencic, M., Lopez, S. Goy, Dibon, H., Jeitler, M., Markytan, M., Mikulec, I., Neuhofer, G., and Widhalm, L.

Subjects
High Energy Physics - Experiment
Abstract

The NA48/2 experiment at CERN reports the first observation of the $K^{\pm} \rightarrow \pi^{0} \pi^{0} \mu^{\pm} \nu$ decay based on a sample of 2437 candidates with 15% background contamination collected in 2003--2004. The decay branching ratio in the kinematic region of the squared dilepton mass above $0.03$~GeV$^2/c^4$ is measured to be $(0.65 \pm 0.03) \times 10^{-6}$. The extrapolation to the full kinematic space, using a specific model, is found to be $(3.45 \pm 0.16) \times 10^{-6}$, in agreement with chiral perturbation theory predictions., Comment: 16 pages, 9 figures

Published
2023
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17. Development of a long noncoding RNA-based machine learning model to predict COVID-19 in-hospital mortality

Author

Devaux, Yvan, Zhang, Lu, Lumley, Andrew I., Karaduzovic-Hadziabdic, Kanita, Mooser, Vincent, Rousseau, Simon, Shoaib, Muhammad, Satagopam, Venkata, Adilovic, Muhamed, Srivastava, Prashant Kumar, Emanueli, Costanza, Martelli, Fabio, Greco, Simona, Badimon, Lina, Padro, Teresa, Lustrek, Mitja, Scholz, Markus, Rosolowski, Maciej, Jordan, Marko, Brandenburger, Timo, Benczik, Bettina, Agg, Bence, Ferdinandy, Peter, Vehreschild, Jörg Janne, Lorenz-Depiereux, Bettina, Dörr, Marcus, Witzke, Oliver, Sanchez, Gabriel, Kul, Seval, Baker, Andy H., Fagherazzi, Guy, Ollert, Markus, Wereski, Ryan, Mills, Nicholas L., and Firat, Hüseyin

Published
2024
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18. Increased levels of GM-CSF and CXCL10 and low CD8+ memory stem T Cell count are markers of immunosenescence and severe COVID-19 in older people

Author

Poisson, Johanne, El-Sissy, Carine, Serret-Larmande, Arnaud, Smith, Nikaïa, Lebraud, Morgane, Augy, Jean-Loup, Conti, Catherine, Gonnin, Cécile, Planquette, Benjamin, Arlet, Jean-Benoît, Hermann, Bertrand, Charbit, Bruno, Pastre, Jean, Devaux, Floriane, Ladavière, Cyrielle, Lim, Lydie, Ober, Pauline, Cannovas, Johanna, Biard, Lucie, Gulczynski, Marie-Christelle, Blumenthal, Noémie, Péré, Hélène, Knosp, Camille, Gey, Alain, Benhamouda, Nadine, Murris, Juliette, Veyer, David, Tartour, Eric, Diehl, Jean-Luc, Duffy, Darragh, Paillaud, Elena, and Granier, Clémence

Published
2024
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19. Association between acute exacerbation of chronic obstructive pulmonary disease and short-term exposure to ambient air pollutants in France

Author

Damien Basille, Lola Soriot, Florence Weppe, Peggy Desmettres, Paulo Henriques, Nicolas Benoit, Stéphanie Devaux, Momar Diouf, Vincent Jounieaux, and Claire Andrejak

Subjects
Nitrogen dioxide, Ozone, Particulate matter, Chronic obstructive pulmonary disease, Morbidity, Industrial medicine. Industrial hygiene, RC963-969, Public aspects of medicine, RA1-1270
Abstract

Abstract Background Ambient air pollution is recognized as a major risk factor for chronic obstructive pulmonary disease (COPD) which is the third leading cause of death worldwide. We examined whether variations in daily outdoor air pollutants levels were associated with excess hospital emergency room visits (ERV) for acute exacerbation of COPD (AECOPD). Methods This two-center ecological cohort study was conducted in Amiens, France. We collected all consecutive ERV for AECOPD throughout 2017 and developed single pollutant models to assess the association between AECOPD and nitrogen dioxide (NO2), ozone (O3), or particulate matter (PM2.5 and PM10) levels, while adjusting for temperature, hygrometry, influenza circulation and pollen allergy risk. For a subgroup of patients, we also applied geographical modeling to analyze annual exposure to outdoor air pollutants. Results We recorded 240 ERV among 168 COPD patients in 2017 and identified 9 peaks of ERV. There was a statistically significant positive correlation between the daily ERV for AECOPD and the daily average concentrations of PM2.5 (RR = 1.06 (95%CI = [1.00–1.11]), p = 0.049), but no correlation with NO2, O3 or PM10 (p = 0.073, p = 0.114 and p = 0.119, respectively). Our geographical modeling study revealed that long-term exposure to any of the four outdoor air pollutants was not associated with more frequent AECOPD. Conclusion Even though the pollution levels measured generally remained below or near the 2021 short-term air quality guidelines issued by the World Health Organization, significant aggregate-level associations were found between severe AECOPD leading to ERV and daily concentrations of PM2.5. Clinical trial registration NCT03079661.

Published
2024
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20. Selective haematological cancer eradication with preserved haematopoiesis

Author

Garaudé, Simon, Marone, Romina, Lepore, Rosalba, Devaux, Anna, Beerlage, Astrid, Seyres, Denis, Dell’ Aglio, Alessandro, Juskevicius, Darius, Zuin, Jessica, Burgold, Thomas, Wang, Sisi, Katta, Varun, Manquen, Garret, Li, Yichao, Larrue, Clément, Camus, Anna, Durzynska, Izabela, Wellinger, Lisa C., Kirby, Ian, Van Berkel, Patrick H., Kunz, Christian, Tamburini, Jérôme, Bertoni, Francesco, Widmer, Corinne C., Tsai, Shengdar Q., Simonetta, Federico, Urlinger, Stefanie, and Jeker, Lukas T.

Published
2024
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23. The challenges of research data management in cardiovascular science: a DGK and DZHK position paper—executive summary

Author

Steffens, Sabine, Schröder, Katrin, Krüger, Martina, Maack, Christoph, Streckfuss-Bömeke, Katrin, Backs, Johannes, Backofen, Rolf, Baeßler, Bettina, Devaux, Yvan, Gilsbach, Ralf, Heijman, Jordi, Knaus, Jochen, Kramann, Rafael, Linz, Dominik, Lister, Allyson L., Maatz, Henrike, Maegdefessel, Lars, Mayr, Manuel, Meder, Benjamin, Nussbeck, Sara Y., Rog-Zielinska, Eva A., Schulz, Marcel H., Sickmann, Albert, Yigit, Gökhan, and Kohl, Peter

Published
2024
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24. Submolecular-scale control of phototautomerization

Author

Rosławska, Anna, Kaiser, Katharina, Romeo, Michelangelo, Devaux, Eloïse, Scheurer, Fabrice, Berciaud, Stéphane, Neuman, Tomáš, and Schull, Guillaume

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Chemical Physics
Abstract

Many natural and artificial reactions including photosynthesis or photopolymerization are initiated by stimulating organic molecules into an excited state, which enables new reaction paths. Controlling light-matter interaction can influence this key concept of photochemistry, however, it remained a challenge to apply this strategy to control photochemical reactions at the atomic scale. Here, we profit from the extreme confinement of the electromagnetic field at the apex of a scanning tunneling microscope (STM) tip to drive and control the rate of a free-base phthalocyanine phototautomerization with submolecular precision. By tuning the laser excitation wavelength and choosing the STM tip position, we control the phototautomerization rate and the relative tautomer population. This sub-molecular optical control can be used to study any other photochemical processes.

Published
2023

25. Multiomic biomarkers after cardiac arrest

Author

Victoria Stopa, Gabriele Lileikyte, Anahita Bakochi, Prasoon Agarwal, Rasmus Beske, Pascal Stammet, Christian Hassager, Filip Årman, Niklas Nielsen, and Yvan Devaux

Subjects
Cardiac arrest, Biomarkers, Clinical outcomes, Prognosis, Multiomics, Artificial intelligence, Medical emergencies. Critical care. Intensive care. First aid, RC86-88.9
Abstract

Abstract Cardiac arrest is a sudden cessation of heart function, leading to an abrupt loss of blood flow and oxygen to vital organs. This life-threatening emergency requires immediate medical intervention and can lead to severe neurological injury or death. Methods and biomarkers to predict neurological outcome are available but lack accuracy. Such methods would allow personalizing healthcare and help clinical decisions. Extensive research has been conducted to identify prognostic omic biomarkers of cardiac arrest. With the emergence of technologies allowing to combine different levels of omics data, and with the help of artificial intelligence and machine learning, there is a potential to use multiomic signatures as prognostic biomarkers after cardiac arrest. This review article delves into the current knowledge of cardiac arrest biomarkers across various omic fields and suggests directions for future research aiming to integrate multiple omics data layers to improve outcome prediction and cardiac arrest patient’s care.

Published
2024
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26. Pembrolizumab with platinum-based chemotherapy with or without epacadostat as first-line treatment for metastatic non-small cell lung cancer: a randomized, partially double-blind, placebo-controlled phase II study

Author

Michael Boyer, Rina Hui, Damien Urban, Philip Clingan, Wu-Chou Su, Celine Devaux, Shirish Gadgeel, Marina Garassino, Lance Leopold, Jeannie Daniel, Mihaela C. Munteanu, Ayman Samkari, Yiwen Luo, and Delvys Rodriguez Abreu

Subjects
Epacadostat, Combination immunotherapy, Non-small cell lung cancer, Pembrolizumab, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background The combination of the checkpoint inhibitor (CPI) pembrolizumab and platinum-based chemotherapy is effective frontline therapy for advanced non-small cell lung cancer (NSCLC) lacking targetable mutations. Indoleamine 2,3- dioxygenase 1 (IDO1), an enzyme involved in kynurenine production, inhibits immune responses. Inhibition of IDO1 may restore antitumor immunity and augment CPI activity. This trial evaluated addition of epacadostat, a potent and highly selective IDO1 inhibitor, to pembrolizumab and chemotherapy for metastatic NSCLC. Methods ECHO-306/KEYNOTE-715 was a partial double-blind, randomized phase II study of adults with treatment-naïve stage IV NSCLC not indicated for EGFR-, ALK-, or ROS1-directed therapy. Patients were randomized to one of three treatment arms: epacadostat-pembrolizumab-chemotherapy (E + P + C; blinded), epacadostat-pembrolizumab (E + P; open-label) or placebo-pembrolizumab-chemotherapy (PBO + P + C; blinded). Stratification was by PD-L1 tumor proportion score (

Published
2024
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27. Cardiovascular history and risk of idiopathic Parkinson’s disease: a cross-sectional observational study

Author

Shubhra Acharya, Andrew I. Lumley, Yvan Devaux, and NCER-PD Consortium

Subjects
Parkinson’s disease, Cardiovascular health, Comorbidities, Sex-differences, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Neurophysiology and neuropsychology, QP351-495
Abstract

Abstract Background Parkinson's disease (PD), while often associated with its distinctive motor symptoms, can also exert a notable impact on the cardiovascular system due to the development of severe autonomic dysfunction. One of the initial indicators of PD is the appearance of cardiovascular dysautonomia. As such, it is vital to monitor and manage cardiovascular health of individuals with PD, as it may have clinical implications in the development of commonly recognized motor and non-motor aspects of the disease. To study the association of history of cardiovascular disease (CVD) with occurrence and severity of PD, here, we lend data on the association of CVD history with the frequency and the occurrence of idiopathic PD (iPD) using data from the Luxembourg Parkinson’s study (iPD n = 676 patients and non-PD n = 874 controls). Results We report that patients with a history of CVD are at high risk of developing iPD (odds ratio; OR = 1.56, 95% confidence interval; CI 1.09–2.08). This risk is stronger in males and remains significant after adjustment with confounders (OR 1.55, 95% CI 1.05–2.30). This increased susceptibility to iPD is linked to the severity of iPD symptoms mainly the non-motor symptoms of daily living (MDS-UPDRS I) and motor complications (MDS-UPDRS IV) in the affected individuals. Conclusion Individuals with history of CVD have a high risk of developing severe forms of iPD. This observation suggests that careful monitoring and management of patients with a history of cardiac problems may reduce the burden of iPD.

Published
2024
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28. Dissecting the genetic basis of resistance to Soil-borne cereal mosaic virus (SBCMV) in durum wheat by bi-parental mapping and GWAS

Author

Bruschi, Martina, Bozzoli, Matteo, Ratti, Claudio, Sciara, Giuseppe, Goudemand, Ellen, Devaux, Pierre, Ormanbekova, Danara, Forestan, Cristian, Corneti, Simona, Stefanelli, Sandra, Castelletti, Sara, Fusari, Elena, Novi, Jad B, Frascaroli, Elisabetta, Salvi, Silvio, Perovic, Dragan, Gadaleta, Agata, Rubies-Autonell, Concepcion, Sanguineti, Maria Corinna, Tuberosa, Roberto, and Maccaferri, Marco

Published
2024
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29. Pembrolizumab with platinum-based chemotherapy with or without epacadostat as first-line treatment for metastatic non-small cell lung cancer: a randomized, partially double-blind, placebo-controlled phase II study

Author

Boyer, Michael, Hui, Rina, Urban, Damien, Clingan, Philip, Su, Wu-Chou, Devaux, Celine, Gadgeel, Shirish, Garassino, Marina, Leopold, Lance, Daniel, Jeannie, Munteanu, Mihaela C., Samkari, Ayman, Luo, Yiwen, and Abreu, Delvys Rodriguez

Published
2024
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30. Inotuzumab Ozogamicin and Low-Intensity Chemotherapy in Older Patients With Newly Diagnosed CD22+ Philadelphia Chromosome–Negative B-Cell Precursor Acute Lymphoblastic Leukemia

Author

Chevallier, Patrice, Leguay, Thibaut, Delord, Marc, Salek, Cyril, Kim, Rathana, Huguet, Françoise, Hicheri, Yosr, Wartiovaara-Kautto, Ulla, Raffoux, Emmanuel, Cluzeau, Thomas, Balsat, Marie, Roth-Guepin, Gabrielle, Tavernier, Emmanuelle, Lepretre, Stephane, Bilger, Karin, Bergugnat, Hugo, Berceanu, Ana, Alexis, Magda, Doubek, Michael, Brissot, Eolia, Hunault-Berger, Mathilde, Lebon, Delphine, Turlure, Pascal, Chantepie, Sylvain, Belhabri, Amine, Wickenhauser, Stefan, Bastie, Jean-Noel, Cacheux, Victoria, Himberlin, Chantal, Banos, Anne, Gardin, Claude, Bonnet, Sarah, Plantier, Isabelle, Pica, Gian Matteo, Escoffre-Barbe, Martine, Boissel, Nicolas, Dombret, Herve, Clappier, Emmanuelle, Rousselot, Philippe, Lebon, Delphine, Charbonnier, Amandine, Assouan, Deborah, Hubert, Amandine, Quint, Marine, Kossi, Fulvia Guenbem, Deruche, Elodie, Hunault, Mathilde, Marie, Céline, Banos, Anne, Robin, Jean-Baptiste, Gay, Julie, Capdupuy, Claudie, Labarrere, Sévérine, Vincent, Edith, Simonet-Boissard, Marion, BeRceanu, Ana, Larosa, Fabrice, Desbrosses, Yohan, Boiteux, Guillaume, Dufour, Vinciane, Tissot, Elise, Braun, Thorsten, Gardin, Pr Claude, Vidal, Valérie, Edouart, Geoffrey, Chantepie, Sylvain, Vilque, Jean-Pierre, Johnson Ansah, Hyacinthe, Lebouvier, Angélique, Zapalovicz, Marie Charlotte, Renault, Léa, Gian Matteo, Pica, Courouau, Alix, Prieur, Fabienne, Dupre, Charlene, Cacheux, Victoria, De Renzis, Benoit, Chaleteix, Carine, Fayard, Amandine, Roy, Gwendoline, Bastie, Jean-Noël, Caillot, Denis, Devaux, Laetitia, Chevallier, Patrice, Lebourgeois, Amandine, Bonnet, Antoine, Peterlin, Pierre, Lok, Anne, Guilllaume, Thierry, Fontaine, Alexis Morice, Turlure, Pascal, Touati, Mohamed, Kennel, Céline, Dmytruck, Natalya, Abraham, Julie, Jaccard, Arnaud, Remenieras, Liliane, Girault, Stéphane, Gourin, Marie Pierre, Penot, Amélie, Moreau, Stéphane, Philipon, Céline, Roche, Delphine, Belhabri, Amine, Gilis, Lila, Virelizier, Nicolas, Michalet, Anne-Sophie, Monfray, Jérémy, Balsat, Marie, Thomas, Xavier, Praire, Aline, Guepin, Gabrielle Roth, Bonmati, Caroline, Moulin, Charline, Jacquet, Caroline, Carpodomi, Anne, Bouillet, Hélène, Carpentier, Odile, Montero, Mélanie, Pires, Aude, Gastaud, Lauris, Gama, Anastasia, Coelle, Céline, Karmout, Sonia, Cluzeau, Thomas, Loschi, Michael, Lechardeur, Jessica, Chokri, Hatroubi, Broussot, Loic, Wickenhauser, Stefan, Waulthier, Agathe, Jourdan, Eric, Scherman, Elodie, Umuhire, Diane, Damiano, Maria Alessandra, Hicheri, Yors, Saillard, Colombe, DʼIncan, Evelyne, Hospital, Marie-Anne, LʼAttention, Jean Laurent, Rabah, Mme Nassima, Cesari, Laura Castillo, Gehlkopf, Eve, Vincent, Laure, Navarro, Robert, Quittet, Philippe, Fegueux, Nathalie, Ceballos, Patrice, Marin, Fanny Baguet, Sabadash, Véra, Alexis, Magda, Ochmann, Marlène, Laboure, Nina Akakelyan, Bembrahmi, Omar, Michel, Olivier, Ouahrawi, Brahim, Brissot, Eolia, Legrand, Olivier, Vekhoff, Anne, Isnard, Françoise, Sa, Sara E., Dombret, Hervé, Raffoux, Emmanuel, Lenguine, Etienne, Rabian, Florence, Lebras, Karine Celli, Fauvaux, Catherine, Leguay, Thibaut, Gros, François-Xavier, Debus, Cazaubiel, Titouan, Melot, Cyril, Dematteis, Valentin, Messina, Antonella, Himberlin, Chantal, Le, Quoc-Hung, Maggi, Lucia, Barre, Martine Escoffre, Moignet, Aline, De Guibert, Sophie, Bernard, Marc, Decaux, Olivier, de la Chapelle, Thierry Lamy, Nimubona, Stanislas, Kadende, Mme Erica, Flavigny, Aloyse, Plantier, Isabelle, Detourmignies, Laurence, Wemeau, Mathieu, Dervite, Isabelle, Dernivoix, Kathy, Camille, Mme, Denizart, Ingrid, Lepretre, Stéphane, Stamatoullas-Bastard, Aspasia, Fontoura, Marie-Laure, Jardin, Fabrice, Menard, Anne-Lise, Camus, Vincent, Lanic, Helene, Contentin, Nathalie, Cardinael, Nathalie, Lemasle-Hue, Emilie, Alani, Mustafa, Lebreton, Pierre, Atia, Youcef, Bilger, Karin, Ledoux, Marie-Pierre, Sonntag, Cécile, Collin, Camille, Tavernier, Emmanuelle, Guyotat, Denis, Soglu, Gilbert, Le Jeune, Caroline, Cornillon, Jérôme, Durieux, Coralie, Lavoué, Céline, Miler, Dorante, Huguet, Françoise, Tavitian, Suzanne, Soldan, Justine, Rousselot, Philippe, Rigaudeau, Sophie, Philippe, Laure, Lambert, Juliette, Besson, Caroline, Cabannes, Aurélie, Longval, Thomas, Taksin, Anne-Laure, Bah, Mariama, BeulayGue, Anaïs, Doubek, Michael, Folber, Frantisek, Hrabovsky, Stepan, Brzonova, Jana, Vejsadova, Hana, Salek, Cyril, Novotova, Elena, Mertova, Jolana, Brzonova, Jana, Vejsadova, Hana, Wartiovaara-Kautto, Ulla, Salonen, Minna, and Vaalas, Saara

Published
2024
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31. Random Forests for time-fixed and time-dependent predictors: The DynForest R package

Author

Devaux, Anthony, Proust-Lima, Cécile, and Genuer, Robin

Subjects
Statistics - Machine Learning, Computer Science - Machine Learning
Abstract

The R package DynForest implements random forests for predicting a continuous, a categorical or a (multiple causes) time-to-event outcome based on time-fixed and time-dependent predictors. The main originality of DynForest is that it handles time-dependent predictors that can be endogeneous (i.e., impacted by the outcome process), measured with error and measured at subject-specific times. At each recursive step of the tree building process, the time-dependent predictors are internally summarized into individual features on which the split can be done. This is achieved using flexible linear mixed models (thanks to the R package lcmm) which specification is pre-specified by the user. DynForest returns the mean for continuous outcome, the category with a majority vote for categorical outcome or the cumulative incidence function over time for survival outcome. DynForest also computes variable importance and minimal depth to inform on the most predictive variables or groups of variables. This paper aims to guide the user with step-by-step examples for fitting random forests using DynForest.

Published
2023

32. First search for K+ → π0πμe decays

Author

M.U. Ashraf, E. Cortina Gil, E. Minucci, S. Padolski, P. Petrov, A. Shaikhiev, R. Volpe, T. Numao, Y. Petrov, B. Velghe, V.W.S. Wong, D. Bryman, J. Fu, Z. Hives, T. Husek, J. Jerhot, K. Kampf, M. Kolesar, M. Zamkovsky, B. De Martino, M. Perrin-Terrin, B. Döbrich, S. Lezki, J. Schubert, A.T. Akmete, R. Aliberti, G. Khoriauli, J. Kunze, D. Lomidze, L. Peruzzo, M. Vormstein, R. Wanke, P. Dalpiaz, M. Fiorini, I. Neri, A. Norton, F. Petrucci, M. Soldani, H. Wahl, L. Bandiera, A. Cotta Ramusino, A. Gianoli, M. Romagnoni, A. Sytov, E. Iacopini, G. Latino, M. Lenti, P. Lo Chiatto, I. Panichi, A. Parenti, A. Bizzeti, F. Bucci, A. Antonelli, G. Georgiev, V. Kozhuharov, G. Lanfranchi, S. Martellotti, M. Moulson, T. Spadaro, G. Tinti, F. Ambrosino, T. Capussela, M. Corvino, M. D'Errico, D. Di Filippo, R. Fiorenza, M. Francesconi, R. Giordano, P. Massarotti, M. Mirra, M. Napolitano, I. Rosa, G. Saracino, G. Anzivino, F. Brizioli, E. Imbergamo, R. Lollini, R. Piandani, C. Santoni, M. Barbanera, P. Cenci, B. Checcucci, P. Lubrano, M. Lupi, M. Pepe, M. Piccini, F. Costantini, L. Di Lella, N. Doble, M. Giorgi, S. Giudici, G. Lamanna, E. Lari, E. Pedreschi, M. Sozzi, C. Cerri, R. Fantechi, L. Pontisso, F. Spinella, I. Mannelli, G. D'Agostini, M. Raggi, A. Biagioni, P. Cretaro, O. Frezza, E. Leonardi, A. Lonardo, M. Turisini, P. Valente, P. Vicini, R. Ammendola, V. Bonaiuto, A. Fucci, A. Salamon, F. Sargeni, R. Arcidiacono, B. Bloch-Devaux, M. Boretto, E. Menichetti, E. Migliore, D. Soldi, C. Biino, A. Filippi, F. Marchetto, A. Briano Olvera, J. Engelfried, N. Estrada-Tristan, M.A. Reyes Santos, K.A. Rodriguez Rivera, P. Boboc, A.M. Bragadireanu, S.A. Ghinescu, O.E. Hutanu, L. Bician, T. Blazek, V. Cerny, Z. Kucerova, T. Velas, J. Bernhard, A. Ceccucci, M. Ceoletta, H. Danielsson, N. De Simone, F. Duval, L. Federici, E. Gamberini, L. Gatignon, R. Guida, F. Hahn, E.B. Holzer, B. Jenninger, M. Koval, P. Laycock, G. Lehmann Miotto, P. Lichard, A. Mapelli, K. Massri, M. Noy, V. Palladino, J. Pinzino, V. Ryjov, S. Schuchmann, S. Venditti, X. Chang, A. Kleimenova, R. Marchevski, T. Bache, M.B. Brunetti, V. Duk, V. Fascianelli, J.R. Fry, F. Gonnella, E. Goudzovski, J. Henshaw, L. Iacobuzio, C. Kenworthy, C. Lazzeroni, N. Lurkin, F. Newson, C. Parkinson, A. Romano, J. Sanders, A. Sergi, A. Sturgess, J. Swallow, A. Tomczak, H. Heath, R. Page, S. Trilov, B. Angelucci, D. Britton, C. Graham, D. Protopopescu, J. Carmignani, J.B. Dainton, R.W.L. Jones, G. Ruggiero, L. Fulton, D. Hutchcroft, E. Maurice, B. Wrona, A. Conovaloff, P. Cooper, D. Coward, P. Rubin, A. Baeva, D. Baigarashev, V. Bautin, D. Emelyanov, T. Enik, V. Falaleev, S. Fedotov, K. Gorshanov, E. Gushchin, V. Kekelidze, D. Kereibay, S. Kholodenko, A. Khotyantsev, A. Korotkova, Y. Kudenko, V. Kurochka, V. Kurshetsov, L. Litov, D. Madigozhin, M. Medvedeva, A. Mefodev, M. Misheva, N. Molokanova, S. Movchan, V. Obraztsov, A. Okhotnikov, A. Ostankov, I. Polenkevich, Yu. Potrebenikov, A. Sadovskiy, K. Salamatin, V. Semenov, S. Shkarovskiy, V. Sugonyaev, O. Yushchenko, and A. Zinchenko

Subjects
Physics, QC1-999
Abstract

The first search for the lepton number violating decay K+→π0π−μ+e+ and lepton flavour violating decays K+→π0π+μ−e+, K+→π0π+μ+e− has been performed using a dataset collected by the NA62 experiment at CERN in 2016–2018. Upper limits of 2.9×10−10, 3.1×10−10 and 5.0×10−10, respectively, are obtained at 90% CL for the branching ratios of the three decays on the assumption of uniform phase-space distributions.

Published
2024
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33. 'Outlaw' mutations in quasispecies of SARS-CoV-2 inhibit replication

Author

Philippe Colson, Jacques Fantini, Jeremy Delerce, Wahiba Bader, Anthony Levasseur, Pierre Pontarotti, Christian Devaux, and Didier Raoult

Subjects
SARS-CoV-2, genomics, mutations, quasispecies, evolution, next-generation sequencing, Infectious and parasitic diseases, RC109-216, Microbiology, QR1-502
Abstract

The evolution of SARS-CoV-2, the agent of COVID-19, has been remarkable for its high mutation potential, leading to the appearance of variants. Some mutations have never appeared in the published genomes, which represent consensus, or bona fide genomes. Here we tested the hypothesis that mutations that did not appear in consensus genomes were, in fact, as frequent as the mutations that appeared during the various epidemic episodes, but were not expressed because lethal. To identify these mutations, we analysed the genomes of 90 nasopharyngeal samples and the quasispecies determined by next-generation sequencing. Mutations observed in the quasispecies and not in the consensus genomes were considered to be lethal, what we called “outlaw” mutations. Among these mutations, we analysed the 21 most frequent. Eight of these “outlaws” were in the RNA polymerase and we were able to use a structural biology model and molecular dynamics simulations to demonstrate the functional incapacity of these mutated RNA polymerases. Three other mutations affected the spike, a major protein involved in the pathogenesis of COVID-19. Overall, by analysing the SARS-CoV-2 quasispecies obtained during sequencing, this method made it possible to identify “outlaws,” showing areas that could potentially become the target of treatments.

Published
2024
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34. Prediction of COVID‐19 severity using machine learning

Author

Kanita Karaduzovic‐Hadziabdic, Muhamed Adilovic, Lu Zhang, Andrew I Lumley, Pranay Shah, Muhammad Shoaib, Venkata Satagopam, Prashant Kumar Srivastava, Costanza Emanueli, Simona Greco, Alisia Madè, Teresa Padro, Pedro Domingo, Mitja Lustrek, Markus Scholz, Maciej Rosolowski, Marko Jordan, Bettina Benczik, Bence Ágg, Péter Ferdinandy, Andrew H Baker, Guy Fagherazzi, Markus Ollert, Joanna Michel, Gabriel Sanchez, Hüseyin Firat, Timo Brandenburger, Fabio Martelli, Lina Badimon, Yvan Devaux, and COVIRNA consortium (www.covirna.eu)

Subjects
Medicine (General), R5-920
Published
2024
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36. Epitaxial Au/Fe4N/MgO thin films on GaAs (001) substrates.

Author

Dainone, Pambiang Abel, Stoffel, Mathieu, Chen, Tongxin, Pasquier, Ludovic, Bouché, Alexandre, Devaux, Xavier, Vergnat, Michel, Boulet, Pascal, and Lu, Yuan

Subjects
MOLECULAR beam epitaxy, ANALYTICAL chemistry, SUBSTRATES (Materials science), THIN films, EPITAXY
Abstract

We investigate the growth of Au/FexNy/MgO trilayers on GaAs(001) substrates by plasma-assisted molecular beam epitaxy. The optimization of the growth conditions made it possible to obtain the compound of stoichiometric Fe4N. Microstructural studies show that Fe4N forms 3D islands at the initial stages of growth. As the Fe4N thickness increases, a columnar growth sets in leading to a strong texturing and to the formation of grains having the same crystallographic orientation. The growth is epitaxial with the relationship GaAs (001) [110]//MgO (001) [110]//Fe4N (001) [110]//Au (012) [0–32]. A chemical analysis at the nanoscale reveals that the interfaces are rather sharp with a limited interdiffusion. Magnetic characterizations show that a trilayer containing a 1-nm-thick Fe4N layer is already ferromagnetic. The easy magnetization axis is in-plane independent of the Fe4N layer thickness (from 1 to 6 nm). This study shows the potential to use Fe4N as a spin injector for spin-optoelectronic applications. [ABSTRACT FROM AUTHOR]

Published
2024
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37. HIKE, High Intensity Kaon Experiments at the CERN SPS

Author

Gil, E. Cortina, Jerhot, J., Lurkin, N., Numao, T., Velghe, B., Wong, V. W. S., Bryman, D., Bician, L., Hives, Z., Husek, T., Kampf, K., Koval, M., Akmete, A. T., Aliberti, R., Büscher, V., Di Lella, L., Doble, N., Peruzzo, L., Schott, M., Wahl, H., Wanke, R., Döbrich, B., Montalto, L., Rinaldi, D., Dettori, F., Cardini, A., Lai, A., Bomben, L., Carsi, S., Prest, M., Selmi, A., Lezzani, G., Monti-Guarnieri, P., Perna, L., Dalpiaz, P., Guidi, V., Mazzolari, A., Neri, I., Petrucci, F., Soldani, M., Bandiera, L., Ramusino, A. Cotta, Gianoli, A., Romagnoni, M., Sytov, A., Lenti, M., Panichi, I., Ruggiero, G., Bizzeti, A., Bucci, F., Antonelli, A., Di Meco, E., Lanfranchi, G., Martellotti, S., Martini, M., Moulson, M., Paesani, D., Sarra, I., Spadaro, T., Tinti, G., Vallazza, E., Ambrosino, F., Giordano, R., Massarotti, P., Napolitano, M., Saracino, G., Di Donato, C., D'Ambrosio, G., D'Errico, M., Mirra, M., Neshatpour, S., Fiorenza, R., Rosa, I., De Salvador, D., Sgarbossa, F., Anzivino, G., Germani, S., Volpe, R., Cenci, P., Cutini, S., Duk, V., Lubrano, P., Pepe, M., Piccini, M., Costantini, F., Donati, S., Giorgi, M., Giudici, S., Lamanna, G., Pedreschi, E., Pinzino, J., Sozzi, M., Fantechi, R., Giusti, V., Spinella, F., Mannelli, I., Raggi, M., Biagioni, A., Cretaro, P., Frezza, O., Cicero, F. Lo, Lonardo, A., Turisini, M., Vicini, P., Ammendola, R., Bonaiuto, V., Fucci, A., Salamon, A., Sargeni, F., Arcidiacono, R., Bloch-Devaux, B., Menichetti, E., Migliore, E., Biino, C., Marchetto, F., Baigarashev, D., Kambar, Y., Kereibay, D., Mukhamejanov, Y., Sakhiyev, S., Olvera, A. Briano, Engelfried, J., Estrada-Tristan, N., Piandani, R., Santos, M. A. Reyes, Rivera, K. A. Rodriguez, Boboc, P. C., Bragadireanu, A. M., Ghinescu, S. A., Hutanu, O. E., Blazek, T., Cerny, V., Kleimenova, A., Kucerova, Z., Santos, D. Martinez, Prouve, C., Boretto, M., Brizioli, F., Ceccucci, A., Corvino, M., Danielsson, H., Duval, F., Gamberini, E., Guida, R., Holzer, E. B., Jenninger, B., Miotto, G. Lehmann, Lichard, P., Massri, K., Minucci, E., Perrin-Terrin, M., Ryjov, V., Swallow, J., Van Dijk, M., Zamkovsky, M., Marchevski, R., Gerbershagen, A., Fry, J. R., Gonnella, F., Goudzovski, E., Henshaw, J., Kenworthy, C., Lazzeroni, C., Parkinson, C., Romano, A., Sanders, J., Shaikhiev, A., Tomczak, A., Heath, H., Britton, D., Norton, A., Protopopescu, D., Dainton, J. B., Jones, R. W. L., De Santo, A., Salvatore, F., Cooper, P., Coward, D., and Rubin, P.

Subjects
High Energy Physics - Experiment, Physics - Instrumentation and Detectors
Abstract

A timely and long-term programme of kaon decay measurements at a new level of precision is presented, leveraging the capabilities of the CERN Super Proton Synchrotron (SPS). The proposed programme is firmly anchored on the experience built up studying kaon decays at the SPS over the past four decades, and includes rare processes, CP violation, dark sectors, symmetry tests and other tests of the Standard Model. The experimental programme is based on a staged approach involving experiments with charged and neutral kaon beams, as well as operation in beam-dump mode. The various phases will rely on a common infrastructure and set of detectors., Comment: Letter of Intent submitted to CERN SPSC. Address all correspondence to hike-eb@cern.ch

Published
2022

38. Multiphoton Correlations between Quantum Images

Author

Massar, Serge, Devaux, Fabrice, and Lantz, Eric

Subjects
Quantum Physics
Abstract

Experimental demonstrations of entangled quantum images produced through parametric downconversion have so far been confined to studying two photon correlations. Here we show that multiphoton correlations between quantum images are accessible experimentally and exhibit many new features including being sensitive to the phase of the bi-photon wavefunction. As a concrete example, we consider a modification of existing quantum imaging experiments in which the CCD cameras are moved out of focus, provide detailed analytical predictions for the resulting 4 photon intereferences, and support these by numerical simulations. The proposed experiment can also be interpreted as entanglement swapping: Bob's photons are initially unentangled, but the joint detection of Alice's photons projects Bob's photons onto an entangled state. The general approach proposed here can be extended to other quantum optics experiments involving high dimensional entanglement., Comment: 13 pages, 3 figures

Published
2022
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39. Controlling the helicity of light by electrical magnetization switching

Author

Dainone, Pambiang Abel, Prestes, Nicholas Figueiredo, Renucci, Pierre, Bouché, Alexandre, Morassi, Martina, Devaux, Xavier, Lindemann, Markus, George, Jean-Marie, Jaffrès, Henri, Lemaitre, Aristide, Xu, Bo, Stoffel, Mathieu, Chen, Tongxin, Lombez, Laurent, Lagarde, Delphine, Cong, Guangwei, Ma, Tianyi, Pigeat, Philippe, Vergnat, Michel, Rinnert, Hervé, Marie, Xavier, Han, Xiufeng, Mangin, Stephane, Rojas-Sánchez, Juan-Carlos, Wang, Jian-Ping, Beard, Matthew C., Gerhardt, Nils C., Žutić, Igor, and Lu, Yuan

Published
2024
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41. Abstract 4117883: Long noncoding RNAs and machine learning to improve cardiovascular outcomes of COVID-19

Author

Karaduzovic-Hadziabdic, Kanita, Adilović, Muhamed, Zhang, Lu, Lumley, Andrew, Shah, Pranay, Shoaib, Muhammad, Satagopam, Venkata, Srivastava, Prashant, Emanueli, Costanza, Greco, Simona, Padro, Teresa, Domingo, Pedro, Lustrek, Mitja, Scholz, Markus, Rosolowski, Maciej, Jordan, Marko, Benczik, Bettina, Agg, Bence, Ferdinandy, Peter, Baker, Andrew, Fagherazzi, Guy, Ollert, Markus, Michel, Joanna, Sanchez, Gabriel, Firat, Hueseyin, Brandenburger, Timo, Martelli, Fabio, Badimon, Lina, and Devaux, Yvan

Published
2024
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43. How effective is the BNT162b2 mRNA vaccine against SARS-CoV-2 transmission and infection? A national programme analysis in Monaco, July 2021 to September 2022

Author

Thomas Althaus, Christopher E. Overton, Isabelle Devaux, Thomas House, Arnaud Lapouze, Alexa Troel, Bertrand Vanzo, Margaux Laroche, Alexandre Bordero, Pernille Jorgensen, Richard Pebody, and Eric J. Voiglio

Subjects
SARS-CoV-2, COVID-19, Vaccine effectiveness, Transmission, Medicine
Abstract

Abstract Background We quantified SARS-CoV-2 dynamics in different community settings and the direct and indirect effect of the BNT162b2 mRNA vaccine in Monaco for different variants of concern (VOC). Methods Between July 2021 and September 2022, we prospectively investigated 20,443 contacts from 6320 index cases using data from the Monaco COVID-19 Public Health Programme. We calculated secondary attack rates (SARs) in households (n = 13,877), schools (n = 2508) and occupational (n = 6499) settings. We used binomial regression with a complementary log–log link function to measure adjusted hazard ratios (aHR) and vaccine effectiveness (aVE) for index cases to infect contacts and contacts to be infected in households. Results In households, the SAR was 55% (95% CI 54–57) and 50% (48–51) among unvaccinated and vaccinated contacts, respectively. The SAR was 32% (28–36) and 12% (10–13) in workplaces, and 7% (6–9) and 6% (3–10) in schools, among unvaccinated and vaccinated contacts respectively. In household, the aHR was lower in contacts than in index cases (aHR 0.68 [0.55–0.83] and 0.93 [0.74–1.1] for delta; aHR 0.73 [0.66–0.81] and 0.89 [0.80–0.99] for omicron BA.1&2, respectively). Vaccination had no significant effect on either direct or indirect aVE for omicron BA.4&5. The direct aVE in contacts was 32% (17, 45) and 27% (19, 34), and for index cases the indirect aVE was 7% (− 17, 26) and 11% (1, 20) for delta and omicron BA.1&2, respectively. The greatest aVE was in contacts with a previous SARS-CoV-2 infection and a single vaccine dose during the omicron BA.1&2 period (45% [27, 59]), while the lowest were found in contacts with either three vaccine doses (aVE − 24% [− 63, 6]) or one single dose and a previous SARS-CoV-2 infection (aVE − 36% [− 198, 38]) during the omicron BA.4&5 period. Conclusions Protection conferred by the BNT162b2 mRNA vaccine against transmission and infection was low for delta and omicron BA.1&2, regardless of the number of vaccine doses and previous SARS-CoV-2 infection. There was no significant vaccine effect for omicron BA.4&5. Health authorities carrying out vaccination campaigns should bear in mind that the current generation of COVID-19 vaccines may not represent an effective tool in protecting individuals from either transmitting or acquiring SARS-CoV-2 infection.

Published
2024
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44. Development of a long noncoding RNA-based machine learning model to predict COVID-19 in-hospital mortality

Author

Yvan Devaux, Lu Zhang, Andrew I. Lumley, Kanita Karaduzovic-Hadziabdic, Vincent Mooser, Simon Rousseau, Muhammad Shoaib, Venkata Satagopam, Muhamed Adilovic, Prashant Kumar Srivastava, Costanza Emanueli, Fabio Martelli, Simona Greco, Lina Badimon, Teresa Padro, Mitja Lustrek, Markus Scholz, Maciej Rosolowski, Marko Jordan, Timo Brandenburger, Bettina Benczik, Bence Agg, Peter Ferdinandy, Jörg Janne Vehreschild, Bettina Lorenz-Depiereux, Marcus Dörr, Oliver Witzke, Gabriel Sanchez, Seval Kul, Andy H. Baker, Guy Fagherazzi, Markus Ollert, Ryan Wereski, Nicholas L. Mills, and Hüseyin Firat

Subjects
Science
Abstract

Abstract Tools for predicting COVID-19 outcomes enable personalized healthcare, potentially easing the disease burden. This collaborative study by 15 institutions across Europe aimed to develop a machine learning model for predicting the risk of in-hospital mortality post-SARS-CoV-2 infection. Blood samples and clinical data from 1286 COVID-19 patients collected from 2020 to 2023 across four cohorts in Europe and Canada were analyzed, with 2906 long non-coding RNAs profiled using targeted sequencing. From a discovery cohort combining three European cohorts and 804 patients, age and the long non-coding RNA LEF1-AS1 were identified as predictive features, yielding an AUC of 0.83 (95% CI 0.82–0.84) and a balanced accuracy of 0.78 (95% CI 0.77–0.79) with a feedforward neural network classifier. Validation in an independent Canadian cohort of 482 patients showed consistent performance. Cox regression analysis indicated that higher levels of LEF1-AS1 correlated with reduced mortality risk (age-adjusted hazard ratio 0.54, 95% CI 0.40–0.74). Quantitative PCR validated LEF1-AS1’s adaptability to be measured in hospital settings. Here, we demonstrate a promising predictive model for enhancing COVID-19 patient management.

Published
2024
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45. Increased levels of GM-CSF and CXCL10 and low CD8+ memory stem T Cell count are markers of immunosenescence and severe COVID-19 in older people

Author

Johanne Poisson, Carine El-Sissy, Arnaud Serret-Larmande, Nikaïa Smith, Morgane Lebraud, Jean-Loup Augy, Catherine Conti, Cécile Gonnin, Benjamin Planquette, Jean-Benoît Arlet, Bertrand Hermann, Bruno Charbit, Jean Pastre, Floriane Devaux, Cyrielle Ladavière, Lydie Lim, Pauline Ober, Johanna Cannovas, Lucie Biard, Marie-Christelle Gulczynski, Noémie Blumenthal, Hélène Péré, Camille Knosp, Alain Gey, Nadine Benhamouda, Juliette Murris, David Veyer, Eric Tartour, Jean-Luc Diehl, Darragh Duffy, Elena Paillaud, and Clémence Granier

Subjects
Immunosenescence, Inflammaging, Immune-ageing, COVID-19, Geriatrics, Infections, Immunologic diseases. Allergy, RC581-607, RC952-954.6
Abstract

Abstract Background Ageing leads to altered immune responses, resulting in higher susceptibility to certain infections in the elderly. Immune ageing is a heterogeneous process also associated with inflammaging, a low-grade chronic inflammation. Altered cytotoxic T cell responses and cytokine storm have previously been described in severe COVID-19 cases, however the parameters responsible for such immune response failures are not well known. The aim of our study was to characterize CD8+ T cells and cytokines associated with ageing, in a cohort of patients aged over 70 years stratified by COVID-19 severity. Results One hundred and four patients were included in the study. We found that, in older people, COVID-19 severity was associated with (i) higher level of GM-CSF, CXCL10 (IP-10), VEGF, IL-1β, CCL2 (MCP-1) and the neutrophil to lymphocyte ratio (NLR), (ii) increased terminally differentiated CD8+T cells, and (ii) decreased early precursors CD8+ T stem cell-like memory cells (TSCM) and CD27+CD28+. The cytokines mentioned above were found at higher concentrations in the COVID-19+ older cohort compared to a younger cohort in which they were not associated with disease severity. Conclusions Our results highlight the particular importance of the myeloid lineage in COVID-19 severity among older people. As GM-CSF and CXCL10 were not associated with COVID-19 severity in younger patients, they may represent disease severity specific markers of ageing and should be considered in older people care.

Published
2024
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46. Workshop summary: Kaons@CERN 2023

Author

G. Anzivino, Sergio Arguedas Cuendis, V. Bernard, J. Bijnens, B. Bloch-Devaux, M. Bordone, F. Brizioli, J. Brod, J. M. Camalich, A. Ceccucci, P. Cenci, N. H. Christ, G. Colangelo, C. Cornella, A. Crivellin, G. D’Ambrosio, F. F. Deppisch, A. Dery, F. Dettori, M. Di Carlo, B. Döbrich, J. Engelfried, R. Fantechi, M. González-Alonso, M. Gorbahn, E. Goudzovski, Y. Grossman, N. Hermansson-Truedsson, Z. Hives, M. Hoferichter, B.-L. Hoid, T. Husek, G. Isidori, A. Jüttner, K. Kampf, S. Kholodenko, M. Knecht, M. Kolesár, M. Koval, C. Lazzeroni, Z. Ligeti, F. Mahmoudi, R. Marchevski, Diego Martínez Santos, K. Massri, T. Mombächer, H. Nanjo, S. Neshatpour, T. Nomura, E. Passemar, L. Peruzzo, M. Piccini, A. Pich, C. T. Sachrajda, S. Schacht, K. Shiomi, P. Stangl, P. Stoffer, J. Swallow, J. T. Tsang, G. Valencia, R. Wanke, and J. Zupan

Subjects
Astrophysics, QB460-466, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract

Abstract Kaon physics is at a turning point – while the rare-kaon experiments NA62 and KOTO are in full swing, the end of their lifetime is approaching and the future experimental landscape needs to be defined. With HIKE, KOTO-II and LHCb-Phase-II on the table and under scrutiny, it is a very good moment in time to take stock and contemplate about the opportunities these experiments and theoretical developments provide for particle physics in the coming decade and beyond. This paper provides a compact summary of talks and discussions from the Kaons@CERN 2023 workshop, held in September 2023 at CERN.

Published
2024
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47. Random survival forests with multivariate longitudinal endogenous covariates

Author

Devaux, Anthony, Helmer, Catherine, Genuer, Robin, and Proust-Lima, Cécile

Subjects
Statistics - Machine Learning
Abstract

Predicting the individual risk of a clinical event using the complete patient history is still a major challenge for personalized medicine. Among the methods developed to compute individual dynamic predictions, the joint models have the assets of using all the available information while accounting for dropout. However, they are restricted to a very small number of longitudinal predictors. Our objective was to propose an innovative alternative solution to predict an event probability using a possibly large number of longitudinal predictors. We developed DynForest, an extension of competing-risk random survival forests that handles endogenous longitudinal predictors. At each node of the tree, the time-dependent predictors are translated into time-fixed features (using mixed models) to be used as candidates for splitting the subjects into two subgroups. The individual event probability is estimated in each tree by the Aalen-Johansen estimator of the leaf in which the subject is classified according to his/her history of predictors. The final individual prediction is given by the average of the tree-specific individual event probabilities. We carried out a simulation study to demonstrate the performances of DynForest both in a small dimensional context (in comparison with joint models) and in a large dimensional context (in comparison with a regression calibration method that ignores informative dropout). We also applied DynForest to (i) predict the individual probability of dementia in the elderly according to repeated measures of cognitive, functional, vascular and neuro-degeneration markers, and (ii) quantify the importance of each type of markers for the prediction of dementia. Implemented in the R package DynForest, our methodology provides a novel and appropriate solution for the prediction of events from any number of longitudinal endogenous predictors.

Published
2022
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48. Unveiling Unconventional Ferroelectric Switching in Multiferroic Ga0.6 Fe1.4O3 Thin Films Through Multiscale Electron Microscopy Investigations

Author

Demchenko, Anna, Homkar, Suvidyakumar, Bouillet, Corinne, Lefèvre, Christophe, Roulland, François, Preziosi, Daniele, Versini, Gilles, Leuvrey, Cédric, Boullay, Philippe, Devaux, Xavier, and Viart, Nathalie

Subjects
Condensed Matter - Materials Science
Abstract

Understanding the polarization switching mechanisms at play in ferroelectric materials is crucial for their exploitation in electronic devices. The conventional centrosymmetric reference structure-based mechanism which accounts for ferroelectricity in most of the usual displacive ferroelectric materials is too energy-demanding for some newly diagnosed ferroelectric materials such as the Ga2-xFexO3 (0.8 < x < 1.4) compounds. Some alternative theoretical propositions have been made and need experimental confirmation. A dual-scale electron microscopy study is performed on thin films of the Ga0.6Fe1.4O3 multiferroic compound. A wide scale precession-assisted electron diffraction tomography study first allows the determination of the structure the compound adopts in thin films, and even permits the refinement of the atomic positions within this structure. Cationic mobility is suggested for two of the atomic positions through the existence of extra electronic density. A local in situ high resolution scanning transmission electron microscopy study then allows confirming these mobilities by directly spotting the cationic displacements on successively acquired images. The whole study confirms an unconventional switching mechanism via local domain wall motion in this compound.

Published
2022

49. Workshop summary: Kaons@CERN 2023

Author

Anzivino, G., Cuendis, Sergio Arguedas, Bernard, V., Bijnens, J., Bloch-Devaux, B., Bordone, M., Brizioli, F., Brod, J., Camalich, J. M., Ceccucci, A., Cenci, P., Christ, N. H., Colangelo, G., Cornella, C., Crivellin, A., D’Ambrosio, G., Deppisch, F. F., Dery, A., Dettori, F., Di Carlo, M., Döbrich, B., Engelfried, J., Fantechi, R., González-Alonso, M., Gorbahn, M., Goudzovski, E., Grossman, Y., Hermansson-Truedsson, N., Hives, Z., Hoferichter, M., Hoid, B.-L., Husek, T., Isidori, G., Jüttner, A., Kampf, K., Kholodenko, S., Knecht, M., Kolesár, M., Koval, M., Lazzeroni, C., Ligeti, Z., Mahmoudi, F., Marchevski, R., Santos, Diego Martínez, Massri, K., Mombächer, T., Nanjo, H., Neshatpour, S., Nomura, T., Passemar, E., Peruzzo, L., Piccini, M., Pich, A., Sachrajda, C. T., Schacht, S., Shiomi, K., Stangl, P., Stoffer, P., Swallow, J., Tsang, J. T., Valencia, G., Wanke, R., and Zupan, J.

Published
2024
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50. Decreasing ganglioside synthesis delays motor and cognitive symptom onset in Spg11 knockout mice

Author

Manon Fortier, Margaux Cauhapé, Suzie Buono, Julien Becker, Alexia Menuet, Julien Branchu, Ivana Ricca, Serena Mero, Karim Dorgham, Khalid-Hamid El Hachimi, Kostantin Dobrenis, Benoit Colsch, Dominic Samaroo, Morgan Devaux, Alexandra Durr, Giovanni Stevanin, Filippo M. Santorelli, Sophie Colombo, Belinda Cowling, and Frédéric Darios

Subjects
Hereditary spastic paraplegia, Motor neuron disease, Neurodegeneration, Therapy, Small molecule, Lysosome, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract

Biallelic variants in the SPG11 gene account for the most common form of autosomal recessive hereditary spastic paraplegia characterized by motor and cognitive impairment, with currently no therapeutic option. We previously observed in a Spg11 knockout mouse that neurodegeneration is associated with accumulation of gangliosides in lysosomes. To test whether a substrate reduction therapy could be a therapeutic option, we downregulated the key enzyme involved in ganglioside biosynthesis using an AAV-PHP.eB viral vector expressing a miRNA targeting St3gal5. Downregulation of St3gal5 in Spg11 knockout mice prevented the accumulation of gangliosides, delayed the onset of motor and cognitive symptoms, and prevented the upregulation of serum levels of neurofilament light chain, a biomarker widely used in neurodegenerative diseases. Importantly, similar results were observed when Spg11 knockout mice were administrated venglustat, a pharmacological inhibitor of glucosylceramide synthase expected to decrease ganglioside synthesis. Downregulation of St3gal5 or venglustat administration in Spg11 knockout mice strongly decreased the formation of axonal spheroids, previously associated with impaired trafficking. Venglustat had similar effect on cultured human SPG11 neurons. In conclusion, this work identifies the first disease-modifying therapeutic strategy in SPG11, and provides data supporting its relevance for therapeutic testing in SPG11 patients.

Published
2024
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