7,275 results on '"P. Joly"'
Search Results
152. High-quality genome of the basidiomycete yeast Dioszegia hungarica PDD-24b-2 isolated from cloud water
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Jarrige, Domitille, Haridas, Sajeet, Bleykasten-Grosshans, Claudine, Joly, Muriel, Nadalig, Thierry, Sancelme, Martine, Vuilleumier, Stéphane, Grigoriev, Igor V, Amato, Pierre, and Bringel, Françoise
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Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Saccharomyces cerevisiae ,Water ,Basidiomycota ,Sequence Analysis ,DNA ,Tremellaceae ,mitochondrial genome ,de novo sequencing ,fungi ,airborne microorganisms ,transposable elements ,Dioszegia hungarica strain PDD-24b-2 ,aeromicrobiology ,fungal spore ,cold environment ,Dioszegia hungarica strain PDD-24b-2 ,Tremellaceae ,Biochemistry and cell biology ,Statistics - Abstract
The genome of the basidiomycete yeast Dioszegia hungarica strain PDD-24b-2 isolated from cloud water at the summit of puy de Dôme (France) was sequenced using a hybrid PacBio and Illumina sequencing strategy. The obtained assembled genome of 20.98 Mb and a GC content of 57% is structured in 16 large-scale contigs ranging from 90 kb to 5.56 Mb, and another 27.2 kb contig representing the complete circular mitochondrial genome. In total, 8,234 proteins were predicted from the genome sequence. The mitochondrial genome shows 16.2% cgu codon usage for arginine but has no canonical cognate tRNA to translate this codon. Detected transposable element (TE)-related sequences account for about 0.63% of the assembled genome. A dataset of 2,068 hand-picked public environmental metagenomes, representing over 20 Tbp of raw reads, was probed for D. hungarica related ITS sequences, and revealed worldwide distribution of this species, particularly in aerial habitats. Growth experiments suggested a psychrophilic phenotype and the ability to disperse by producing ballistospores. The high-quality assembled genome obtained for this D. hungarica strain will help investigate the behavior and ecological functions of this species in the environment.
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- 2022
153. The influence of genetic architecture on responses to selection under drought in rice
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Ćalić, Irina, Groen, Simon C, Choi, Jae Young, Joly‐Lopez, Zoé, Hamann, Elena, Natividad, Mignon A, Dorph, Katherine, Cabral, Carlo Leo U, Torres, Rolando O, Vergara, Georgina V, Henry, Amelia, Purugganan, Michael D, and Franks, Steven J
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Biological Sciences ,Ecology ,Evolutionary Biology ,Genetics ,drought resistance ,genetic architecture ,G-matrix ,natural selection ,Oryza sativa ,pleiotropy ,G‐matrix ,Medicinal and Biomolecular Chemistry ,Evolutionary biology - Abstract
Accurately predicting responses to selection is a major goal in biology and important for successful crop breeding in changing environments. However, evolutionary responses to selection can be constrained by such factors as genetic and cross-environment correlations, linkage, and pleiotropy, and our understanding of the extent and impact of such constraints is still developing. Here, we conducted a field experiment to investigate potential constraints to selection for drought resistance in rice (Oryza sativa) using phenotypic selection analysis and quantitative genetics. We found that traits related to drought response were heritable, and some were under selection, including selection for earlier flowering, which could allow drought escape. However, patterns of selection generally were not opposite under wet and dry conditions, and we did not find individual or closely linked genes that influenced multiple traits, indicating a lack of evidence that antagonistic pleiotropy, linkage, or cross-environment correlations would constrain selection for drought resistance. In most cases, genetic correlations had little influence on responses to selection, with direct and indirect selection largely congruent. The exception to this was seed mass under drought, which was predicted to evolve in the opposite direction of direct selection due to correlations. Because of this indirect effect on selection on seed mass, selection for drought resistance was not accompanied by a decrease in seed mass, and yield increased with fecundity. Furthermore, breeding lines with high fitness and yield under drought also had high fitness and yield under wet conditions, indicating that there was no evidence for a yield penalty on drought resistance. We found multiple genes in which expression influenced both water use efficiency (WUE) and days to first flowering, supporting a genetic basis for the trade-off between drought escape and avoidance strategies. Together, these results can provide helpful guidance for understanding and managing evolutionary constraints and breeding stress-resistant crops.
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- 2022
154. The state of plant conservation in Canada: a survey of practitioners
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J.L. McCune, Sarah J. Baldwin, Joseph R. Bennett, Brian C. Husband, Simon Joly, Daniel Kraus, Eric G. Lamb, Jana C. Vamosi, Alyson C. Van Natto, and Jeannette Whitton
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conservation translocation ,endangered species ,habitat protection ,rare plants ,species at risk ,recovery strategies ,Education ,Science - Abstract
Plants make up more than one quarter of all species listed under Canada’s Species at Risk Act, but very few have improved in status over time. Ineffective legal protections, lack of public awareness, difficulties in prioritizing species, and a scarcity of research relevant to the recovery of plant species at risk are some of the many challenges facing effective plant conservation in Canada. We used an online survey to ask 243 people who work in plant conservation or who do research in plant ecology or evolution to assess the state of plant conservation in Canada and to identify the actions needed to improve it. Most respondents agreed that Canada is underperforming or merely average when it comes to conserving plants. Based on their responses, we outline a set of recommendations that could form the basis of a national strategy for plant conservation in Canada. These include greater advocacy for habitat protection, connecting researchers with funding opportunities, supporting graduate students working on research related to plant conservation, increasing public awareness of plants, collaborating with and respecting Indigenous knowledge holders, promoting collaboration between researchers and local conservation groups, and increasing capacity to assess the status of species that are potentially at risk.
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- 2024
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155. Microscopic origins of the viscosity of a Lennard-Jones liquid
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Rizk, Farid, Gelin, Simon, Biance, Anne-Laure, and Joly, Laurent
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Condensed Matter - Soft Condensed Matter ,Condensed Matter - Statistical Mechanics ,Physics - Chemical Physics - Abstract
Unlike crystalline solids or ideal gases, transport properties remain difficult to describe from a microscopic point of view in liquids, whose dynamics result from complex energetic and entropic contributions at the atomic scale. Two scenarios are generally proposed: one represents the dynamics in a fluid as a series of energy barrier crossings, leading to Arrhenius-like laws, while the other assumes that atoms rearrange themselves by collisions, as exemplified by the free volume model. To assess the validity of these two views, we computed, using molecular dynamics simulations, the transport properties of the Lennard-Jones fluid and tested to what extent the Arrhenius equation and the free volume model describe the temperature dependence of the viscosity and of the diffusion coefficient at fixed pressure. Although both models reproduce the simulation results over a wide range of pressure and temperature covering the liquid and supercritical states of the Lennard-Jones fluid, we found that the parameters of the free volume model can be estimated directly from local structural parameters, also obtained in the simulations. This consistency of the results gives more credibility to the free volume description of transport properties in liquids., Comment: 6 pages, 4 figures
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- 2022
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156. Control of the Schr\'odinger equation by slow deformations of the domain
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Duca, Alessandro, Joly, Romain, and Turaev, Dmitry
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Mathematics - Analysis of PDEs ,Mathematics - Optimization and Control - Abstract
The aim of this work is to study the controllability of the Schr\"odinger equation \begin{equation}\label{eq_abstract} i\partial_t u(t)=-\Delta u(t)~~~~~\text{ on }\Omega(t) \tag{$\ast$} \end{equation} with Dirichlet boundary conditions, where $\Omega(t)\subset\mathbb{R}^N$ is a time-varying domain. We prove the global approximate controllability of \eqref{eq_abstract} in $L^2(\Omega)$, via an adiabatic deformation $\Omega(t)\subset\mathbb{R}$ ($t\in[0,T]$) such that $\Omega(0)=\Omega(T)=\Omega$. This control is strongly based on the Hamiltonian structure of \eqref{eq_abstract} provided by [18], which enables the use of adiabatic motions. We also discuss several explicit interesting controls that we perform in the specific framework of rectangular domains.
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- 2022
157. Distribution augmentation for low-resource expressive text-to-speech
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Lajszczak, Mateusz, Prasad, Animesh, van Korlaar, Arent, Bollepalli, Bajibabu, Bonafonte, Antonio, Joly, Arnaud, Nicolis, Marco, Moinet, Alexis, Drugman, Thomas, Wood, Trevor, and Sokolova, Elena
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Electrical Engineering and Systems Science - Audio and Speech Processing ,Computer Science - Computation and Language ,Computer Science - Machine Learning - Abstract
This paper presents a novel data augmentation technique for text-to-speech (TTS), that allows to generate new (text, audio) training examples without requiring any additional data. Our goal is to increase diversity of text conditionings available during training. This helps to reduce overfitting, especially in low-resource settings. Our method relies on substituting text and audio fragments in a way that preserves syntactical correctness. We take additional measures to ensure that synthesized speech does not contain artifacts caused by combining inconsistent audio samples. The perceptual evaluations show that our method improves speech quality over a number of datasets, speakers, and TTS architectures. We also demonstrate that it greatly improves robustness of attention-based TTS models., Comment: ICASSP 2022: camera-ready
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- 2022
158. Stochastic smoothing of the top-K calibrated hinge loss for deep imbalanced classification
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Garcin, Camille, Servajean, Maximilien, Joly, Alexis, and Salmon, Joseph
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Statistics - Machine Learning ,Computer Science - Machine Learning - Abstract
In modern classification tasks, the number of labels is getting larger and larger, as is the size of the datasets encountered in practice. As the number of classes increases, class ambiguity and class imbalance become more and more problematic to achieve high top-1 accuracy. Meanwhile, Top-K metrics (metrics allowing K guesses) have become popular, especially for performance reporting. Yet, proposing top-K losses tailored for deep learning remains a challenge, both theoretically and practically. In this paper we introduce a stochastic top-K hinge loss inspired by recent developments on top-K calibrated losses. Our proposal is based on the smoothing of the top-K operator building on the flexible "perturbed optimizer" framework. We show that our loss function performs very well in the case of balanced datasets, while benefiting from a significantly lower computational time than the state-of-the-art top-K loss function. In addition, we propose a simple variant of our loss for the imbalanced case. Experiments on a heavy-tailed dataset show that our loss function significantly outperforms other baseline loss functions.
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- 2022
159. Analogue quantum simulation of the Hawking effect in a polariton superfluid
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Jacquet, Maxime J., Joly, Malo, Giacomelli, Luca, Claude, Ferdinand, Glorieux, Quentin, Bramati, Alberto, Carusotto, Iacopo, and Giacobino, Elisabeth
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Quantum Physics ,Condensed Matter - Quantum Gases ,General Relativity and Quantum Cosmology - Abstract
Quantum effects of fields on curved spacetimes may be studied in the laboratory thanks to quantum fluids. Here we use a polariton fluid to study the Hawking effect, the correlated emission from the quantum vacuum at the acoustic horizon. We show how out-of-equilibrium physics affects the dispersion relation, and hence the emission and propagation of correlated waves: the fluid properties on either side of the horizon are critical to observing the Hawking effect. We find that emission may be optimised by supporting the phase and density of the fluid upstream of the horizon in a regime of optical bistability. This opens new avenues for the observation of the Hawking effect in out-of-equilibrium systems as well as for the study of new phenomenology of fields on curved spacetimes., Comment: 16 pages + appendix, 6 figures, comments are welcome. arXiv admin note: substantial text overlap with arXiv:2110.14452
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- 2022
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160. Integrated global assessment of the natural forest carbon potential
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Mo, Lidong, Zohner, Constantin M., Reich, Peter B., Liang, Jingjing, de Miguel, Sergio, Nabuurs, Gert-Jan, Renner, Susanne S., van den Hoogen, Johan, Araza, Arnan, Herold, Martin, Mirzagholi, Leila, Ma, Haozhi, Averill, Colin, Phillips, Oliver L., Gamarra, Javier G. P., Hordijk, Iris, Routh, Devin, Abegg, Meinrad, Adou Yao, Yves C., Alberti, Giorgio, Almeyda Zambrano, Angelica M., Alvarado, Braulio Vilchez, Alvarez-Dávila, Esteban, Alvarez-Loayza, Patricia, Alves, Luciana F., Amaral, Iêda, Ammer, Christian, Antón-Fernández, Clara, Araujo-Murakami, Alejandro, Arroyo, Luzmila, Avitabile, Valerio, Aymard, Gerardo A., Baker, Timothy R., Bałazy, Radomir, Banki, Olaf, Barroso, Jorcely G., Bastian, Meredith L., Bastin, Jean-Francois, Birigazzi, Luca, Birnbaum, Philippe, Bitariho, Robert, Boeckx, Pascal, Bongers, Frans, Bouriaud, Olivier, Brancalion, Pedro H. S., Brandl, Susanne, Brearley, Francis Q., Brienen, Roel, Broadbent, Eben N., Bruelheide, Helge, Bussotti, Filippo, Cazzolla Gatti, Roberto, César, Ricardo G., Cesljar, Goran, Chazdon, Robin L., Chen, Han Y. H., Chisholm, Chelsea, Cho, Hyunkook, Cienciala, Emil, Clark, Connie, Clark, David, Colletta, Gabriel D., Coomes, David A., Cornejo Valverde, Fernando, Corral-Rivas, José J., Crim, Philip M., Cumming, Jonathan R., Dayanandan, Selvadurai, de Gasper, André L., Decuyper, Mathieu, Derroire, Géraldine, DeVries, Ben, Djordjevic, Ilija, Dolezal, Jiri, Dourdain, Aurélie, Engone Obiang, Nestor Laurier, Enquist, Brian J., Eyre, Teresa J., Fandohan, Adandé Belarmain, Fayle, Tom M., Feldpausch, Ted R., Ferreira, Leandro V., Finér, Leena, Fischer, Markus, Fletcher, Christine, Frizzera, Lorenzo, Gianelle, Damiano, Glick, Henry B., Harris, David J., Hector, Andrew, Hemp, Andreas, Hengeveld, Geerten, Hérault, Bruno, Herbohn, John L., Hillers, Annika, Honorio Coronado, Eurídice N., Hui, Cang, Ibanez, Thomas, Imai, Nobuo, Jagodziński, Andrzej M., Jaroszewicz, Bogdan, Johannsen, Vivian Kvist, Joly, Carlos A., Jucker, Tommaso, Jung, Ilbin, Karminov, Viktor, Kartawinata, Kuswata, Kearsley, Elizabeth, Kenfack, David, Kennard, Deborah K., Kepfer-Rojas, Sebastian, Keppel, Gunnar, Khan, Mohammed Latif, Killeen, Timothy J., Kim, Hyun Seok, Kitayama, Kanehiro, Köhl, Michael, Korjus, Henn, Kraxner, Florian, Kucher, Dmitry, Laarmann, Diana, Lang, Mait, Lu, Huicui, Lukina, Natalia V., Maitner, Brian S., Malhi, Yadvinder, Marcon, Eric, Marimon, Beatriz Schwantes, Marimon-Junior, Ben Hur, Marshall, Andrew R., Martin, Emanuel H., Meave, Jorge A., Melo-Cruz, Omar, Mendoza, Casimiro, Mendoza-Polo, Irina, Miscicki, Stanislaw, Merow, Cory, Monteagudo Mendoza, Abel, Moreno, Vanessa S., Mukul, Sharif A., Mundhenk, Philip, Nava-Miranda, María Guadalupe, Neill, David, Neldner, Victor J., Nevenic, Radovan V., Ngugi, Michael R., Niklaus, Pascal A., Oleksyn, Jacek, Ontikov, Petr, Ortiz-Malavasi, Edgar, Pan, Yude, Paquette, Alain, Parada-Gutierrez, Alexander, Parfenova, Elena I., Park, Minjee, Parren, Marc, Parthasarathy, Narayanaswamy, Peri, Pablo L., Pfautsch, Sebastian, Picard, Nicolas, Piedade, Maria Teresa F., Piotto, Daniel, Pitman, Nigel C. A., Poulsen, Axel Dalberg, Poulsen, John R., Pretzsch, Hans, Ramirez Arevalo, Freddy, Restrepo-Correa, Zorayda, Rodeghiero, Mirco, Rolim, Samir G., Roopsind, Anand, Rovero, Francesco, Rutishauser, Ervan, Saikia, Purabi, Salas-Eljatib, Christian, Saner, Philippe, Schall, Peter, Schelhaas, Mart-Jan, Schepaschenko, Dmitry, Scherer-Lorenzen, Michael, Schmid, Bernhard, Schöngart, Jochen, Searle, Eric B., Seben, Vladimír, Serra-Diaz, Josep M., Sheil, Douglas, Shvidenko, Anatoly Z., Silva-Espejo, Javier E., Silveira, Marcos, Singh, James, Sist, Plinio, Slik, Ferry, Sonké, Bonaventure, Souza, Alexandre F., Stereńczak, Krzysztof J., Svenning, Jens-Christian, Svoboda, Miroslav, Swanepoel, Ben, Targhetta, Natalia, Tchebakova, Nadja, ter Steege, Hans, Thomas, Raquel, Tikhonova, Elena, Umunay, Peter M., Usoltsev, Vladimir A., Valencia, Renato, Valladares, Fernando, van der Plas, Fons, Van Do, Tran, van Nuland, Michael E., Vasquez, Rodolfo M., Verbeeck, Hans, Viana, Helder, Vibrans, Alexander C., Vieira, Simone, von Gadow, Klaus, Wang, Hua-Feng, Watson, James V., Werner, Gijsbert D. A., Wiser, Susan K., Wittmann, Florian, Woell, Hannsjoerg, Wortel, Verginia, Zagt, Roderik, Zawiła-Niedźwiecki, Tomasz, Zhang, Chunyu, Zhao, Xiuhai, Zhou, Mo, Zhu, Zhi-Xin, Zo-Bi, Irie C., Gann, George D., and Crowther, Thomas W.
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- 2023
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161. Use of Leukocyte- and Platelet-Rich Fibrin to Prevent Osteonecrosis of the Jaws Associated with the Use of Bisphosphonate Therapy: A Case Series
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Stresser, Fernanda Aparecida, Parise, Guilherme Klein, Macedo, Fernanda Joly, Sassi, Laurindo Moacir, and Schussel, Juliana Lucena
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- 2023
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162. The global biogeography of tree leaf form and habit
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Ma, Haozhi, Crowther, Thomas W., Mo, Lidong, Maynard, Daniel S., Renner, Susanne S., van den Hoogen, Johan, Zou, Yibiao, Liang, Jingjing, de-Miguel, Sergio, Nabuurs, Gert-Jan, Reich, Peter B., Niinemets, Ülo, Abegg, Meinrad, Adou Yao, Yves C., Alberti, Giorgio, Almeyda Zambrano, Angelica M., Alvarado, Braulio Vilchez, Alvarez-Dávila, Esteban, Alvarez-Loayza, Patricia, Alves, Luciana F., Ammer, Christian, Antón-Fernández, Clara, Araujo-Murakami, Alejandro, Arroyo, Luzmila, Avitabile, Valerio, Aymard, Gerardo A., Baker, Timothy R., Bałazy, Radomir, Banki, Olaf, Barroso, Jorcely G., Bastian, Meredith L., Bastin, Jean-Francois, Birigazzi, Luca, Birnbaum, Philippe, Bitariho, Robert, Boeckx, Pascal, Bongers, Frans, Bouriaud, Olivier, Brancalion, Pedro H. S., Brandl, Susanne, Brearley, Francis Q., Brienen, Roel, Broadbent, Eben N., Bruelheide, Helge, Bussotti, Filippo, Cazzolla Gatti, Roberto, César, Ricardo G., Cesljar, Goran, Chazdon, Robin, Chen, Han Y. H., Chisholm, Chelsea, Cho, Hyunkook, Cienciala, Emil, Clark, Connie, Clark, David, Colletta, Gabriel D., Coomes, David A., Valverde, Fernando Cornejo, Corral-Rivas, José J., Crim, Philip M., Cumming, Jonathan R., Dayanandan, Selvadurai, de Gasper, André L., Decuyper, Mathieu, Derroire, Géraldine, DeVries, Ben, Djordjevic, Ilija, Dolezal, Jiri, Dourdain, Aurélie, Engone Obiang, Nestor Laurier, Enquist, Brian J., Eyre, Teresa J., Fandohan, Adandé Belarmain, Fayle, Tom M., Feldpausch, Ted R., Ferreira, Leandro V., Finér, Leena, Fischer, Markus, Fletcher, Christine, Fridman, Jonas, Frizzera, Lorenzo, Gamarra, Javier G. P., Gianelle, Damiano, Glick, Henry B., Harris, David J., Hector, Andrew, Hemp, Andreas, Hengeveld, Geerten, Hérault, Bruno, Herbohn, John L., Herold, Martin, Hillers, Annika, Honorio Coronado, Eurídice N., Hui, Cang, Ibanez, Thomas T., Amaral, Iêda, Imai, Nobuo, Jagodziński, Andrzej M., Jaroszewicz, Bogdan, Johannsen, Vivian Kvist, Joly, Carlos A., Jucker, Tommaso, Jung, Ilbin, Karminov, Viktor, Kartawinata, Kuswata, Kearsley, Elizabeth, Kenfack, David, Kennard, Deborah K., Kepfer-Rojas, Sebastian, Keppel, Gunnar, Khan, Mohammed Latif, Killeen, Timothy J., Kim, Hyun Seok, Kitayama, Kanehiro, Köhl, Michael, Korjus, Henn, Kraxner, Florian, Kucher, Dmitry, Laarmann, Diana, Lang, Mait, Lewis, Simon L., Lu, Huicui, Lukina, Natalia V., Maitner, Brian S., Malhi, Yadvinder, Marcon, Eric, Marimon, Beatriz Schwantes, Marimon-Junior, Ben Hur, Marshall, Andrew R., Martin, Emanuel H., Meave, Jorge A., Melo-Cruz, Omar, Mendoza, Casimiro, Merow, Cory, Monteagudo Mendoza, Abel, Moreno, Vanessa S., Mukul, Sharif A., Mundhenk, Philip, Nava-Miranda, María Guadalupe, Neill, David, Neldner, Victor J., Nevenic, Radovan V., Ngugi, Michael R., Niklaus, Pascal A., Oleksyn, Jacek, Ontikov, Petr, Ortiz-Malavasi, Edgar, Pan, Yude, Paquette, Alain, Parada-Gutierrez, Alexander, Parfenova, Elena I., Park, Minjee, Parren, Marc, Parthasarathy, Narayanaswamy, Peri, Pablo L., Pfautsch, Sebastian, Phillips, Oliver L., Picard, Nicolas, Piedade, Maria Teresa F., Piotto, Daniel, Pitman, Nigel C. A., Mendoza-Polo, Irina, Poulsen, Axel D., Poulsen, John R., Pretzsch, Hans, Ramirez Arevalo, Freddy, Restrepo-Correa, Zorayda, Rodeghiero, Mirco, Rolim, Samir G., Roopsind, Anand, Rovero, Francesco, Rutishauser, Ervan, Saikia, Purabi, Salas-Eljatib, Christian, Saner, Philippe, Schall, Peter, Schelhaas, Mart-Jan, Schepaschenko, Dmitry, Scherer-Lorenzen, Michael, Schmid, Bernhard, Schöngart, Jochen, Searle, Eric B., Seben, Vladimír, Serra-Diaz, Josep M., Sheil, Douglas, Shvidenko, Anatoly Z., Silva-Espejo, Javier E., Silveira, Marcos, Singh, James, Sist, Plinio, Slik, Ferry, Sonké, Bonaventure, Souza, Alexandre F., Miścicki, Stanislaw, Stereńczak, Krzysztof J., Svenning, Jens-Christian, Svoboda, Miroslav, Swanepoel, Ben, Targhetta, Natalia, Tchebakova, Nadja, ter Steege, Hans, Thomas, Raquel, Tikhonova, Elena, Umunay, Peter M., Usoltsev, Vladimir A., Valencia, Renato, Valladares, Fernando, van der Plas, Fons, Van Do, Tran, van Nuland, Michael E., Vasquez, Rodolfo M., Verbeeck, Hans, Viana, Helder, Vibrans, Alexander C., Vieira, Simone, von Gadow, Klaus, Wang, Hua-Feng, Watson, James V., Werner, Gijsbert D. A., Westerlund, Bertil, Wiser, Susan K., Wittmann, Florian, Woell, Hannsjoerg, Wortel, Verginia, Zagt, Roderick, Zawiła-Niedźwiecki, Tomasz, Zhang, Chunyu, Zhao, Xiuhai, Zhou, Mo, Zhu, Zhi-Xin, Zo-Bi, Irie C., and Zohner, Constantin M.
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- 2023
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163. Magnesium sulphate in patients with thrombotic thrombocytopenic purpura (MAGMAT): a randomised, double-blind, superiority trial
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Zafrani, Lara, Canet, Emmanuel, Walter-Petrich, Anouk, Joly-Laffargue, Bérangère, Veyradier, Agnès, Faguer, Stanislas, Bigé, Naïke, Calvet, Laure, Mayaux, Julien, Grangé, Steven, Rafat, Cédric, Poulain, Coralie, Klouche, Kada, Perez, Pierre, Pène, Frédéric, Pichereau, Claire, Duceau, Baptiste, Mariotte, Eric, Chevret, Sylvie, and Azoulay, Elie
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- 2023
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164. Monitoring of Ammonium and Nitrate Ions in Soil Using Ion-Sensitive Potentiometric Microsensors
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Matthieu Joly, Maurane Marlet, David Barreau, Arnaud Jourdan, Céline Durieu, Jérôme Launay, and Pierre Temple-Boyer
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ion-sensitive field-effect transistor ,ISFET ,potentiometric sensor ,ion-sensitive layers ,ammonium NH4+ ion ,nitrate NO3− ion ,Chemical technology ,TP1-1185 - Abstract
Focusing on the ChemFET (chemical field-effect transistor) technology, the development of a multi-microsensor platform for soil analysis is described in this work. Thus, different FET-based microdevices (i.e., pH-ChemFET pNH4-ISFET and pNO3-ISFET sensors) were realized with the aim of monitoring nitrogen-based ionic species in soil, evidencing quasi-Nernstian detection properties (>50 mV/decade) in appropriate concentration ranges for agricultural applications. Using a specific test bench adapted to important earth samples (mass: ~50 kg), first experiments were done in a lab, mimicking rainy periods as well as nitrogen-based fertilizer inputs. By monitoring pH, pNH4, and pNO3 in an acidic (pH ≈ 4.7) clay-silt soil matrix, different processes associated to the nitrogen cycle were characterized over a fortnight, demonstrating comprehensive results for ammonium nitrate NH4NO3 inputs at different concentrations, water additions, nitrification phenomena, and ammonium NH4+ ion trapping. Even if the ChemFET-based measurement system should be improved according to the soil(electrolyte)/sensor contact, such realizations and results show the ChemFET technology potentials for long-term analysis in soil, paving the way for future “in situ” approaches in the frame of modern farming.
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- 2024
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165. Dynamics of Long-Term Patient-Reported Quality of Life and Health Behaviors After Adjuvant Breast Cancer Chemotherapy
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Di Meglio, Antonio, Havas, Julie, Gbenou, Arnauld S, Martin, Elise, El-Mouhebb, Mayssam, Pistilli, Barbara, Menvielle, Gwenn, Dumas, Agnes, Everhard, Sibille, Martin, Anne-Laure, Cottu, Paul H, Lerebours, Florence, Coutant, Charles, Lesur, Anne, Tredan, Olivier, Soulie, Patrick, Vanlemmens, Laurence, Joly, Florence, Delaloge, Suzette, Ganz, Patricia A, André, Fabrice, Partridge, Ann H, Jones, Lee W, Michiels, Stefan, and Vaz-Luis, Ines
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Breast Cancer ,Prevention ,Clinical Research ,Behavioral and Social Science ,Cancer ,Good Health and Well Being ,Breast Neoplasms ,Chemotherapy ,Adjuvant ,Female ,Health Behavior ,Humans ,Patient Reported Outcome Measures ,Quality of Life ,Clinical Sciences ,Oncology and Carcinogenesis ,Oncology & Carcinogenesis - Abstract
PurposeWe aimed to characterize long-term quality of life (QOL) trajectories among patients with breast cancer treated with adjuvant chemotherapy and to identify related patterns of health behaviors.MethodsFemale stage I-III breast cancer patients receiving chemotherapy in CANTO (CANcer TOxicity; ClinicalTrials.gov identifier: NCT01993498) were included. Trajectories of QOL (European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire-C30 Summary Score) and associations with trajectory group membership were identified by iterative estimations of group-based trajectory models and multivariable multinomial logistic regression, respectively.ResultsFour trajectory groups were identified (N = 4,131): excellent (51.7%), very good (31.7%), deteriorating (10.0%), and poor (6.6%) QOL. The deteriorating trajectory group reported fairly good baseline QOL (mean [95% CI], 78.3/100 [76.2 to 80.5]), which significantly worsened at year-1 (58.1/100 [56.4 to 59.9]) and never recovered to pretreatment values through year-4 (61.1/100 [59.0 to 63.3]) postdiagnosis. Healthy behaviors were associated with better performing trajectory groups. Obesity (adjusted odds ratio [aOR] v lean, 1.51 [95% CI, 1.28 to 1.79]; P < .0001) and current smoking (aOR v never, 1.52 [95% CI, 1.27 to 1.82]; P < .0001) at diagnosis were associated with membership to the deteriorating group, which was also characterized by a higher prevalence of patients with excess body weight and insufficient physical activity through year-4 and by frequent exposure to tobacco smoking during chemotherapy. Additional factors associated with membership to the deteriorating group included younger age (aOR, 1-year decrement 1.01 [95% CI, 1.01 to 1.02]; P = .043), comorbidities (aOR v no, 1.22 [95% CI, 1.06 to 1.40]; P = .005), lower income (aOR v wealthier households, 1.21 [95% CI, 1.07 to 1.37]; P = .002), and endocrine therapy (aOR v no, 1.14 [95% CI, 1.01 to 1.30]; P = .047).ConclusionThis latent-class analysis identified some patients with upfront poor QOL and a high-risk cluster with severe, persistent postchemotherapy QOL deterioration. Screening relevant patient-level characteristics may inform tailored interventions to mitigate the detrimental impact of chemotherapy and preserve QOL, including early addressal of behavioral concerns and provision of healthy lifestyle support programs.
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- 2022
166. Classification Under Ambiguity: When Is Average-K Better Than Top-K?
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Lorieul, Titouan, Joly, Alexis, and Shasha, Dennis
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Statistics - Machine Learning ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
When many labels are possible, choosing a single one can lead to low precision. A common alternative, referred to as top-$K$ classification, is to choose some number $K$ (commonly around 5) and to return the $K$ labels with the highest scores. Unfortunately, for unambiguous cases, $K>1$ is too many and, for very ambiguous cases, $K \leq 5$ (for example) can be too small. An alternative sensible strategy is to use an adaptive approach in which the number of labels returned varies as a function of the computed ambiguity, but must average to some particular $K$ over all the samples. We denote this alternative average-$K$ classification. This paper formally characterizes the ambiguity profile when average-$K$ classification can achieve a lower error rate than a fixed top-$K$ classification. Moreover, it provides natural estimation procedures for both the fixed-size and the adaptive classifier and proves their consistency. Finally, it reports experiments on real-world image data sets revealing the benefit of average-$K$ classification over top-$K$ in practice. Overall, when the ambiguity is known precisely, average-$K$ is never worse than top-$K$, and, in our experiments, when it is estimated, this also holds., Comment: 53 pages, 21 figures
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- 2021
167. Connection between water's dynamical and structural properties: insights from ab initio simulations
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Herrero, Cecilia, Pauletti, Michela, Tocci, Gabriele, Iannuzzi, Marcella, and Joly, Laurent
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Physics - Chemical Physics ,Physics - Fluid Dynamics - Abstract
Among all fluids, water has always been of special concern for scientists from a broad variety of research fields due to its rich behavior. In particular, some questions remain unanswered nowadays concerning the temperature dependence of bulk and interfacial transport properties of supercooled and liquid water, e.g. regarding the fundamentals of the violation of the Stokes-Einstein relation in the supercooled regime or the subtle relation between structure and dynamical properties. Here we investigated the temperature dependence of the bulk transport properties from ab initio molecular dynamics based on density functional theory, down to the supercooled regime. We determined from a selection of functionals, that SCAN better describes the experimental viscosity and self-diffusion coefficient, although we found disagreements at the lowest temperatures. For a limited set of temperatures, we also explored the role of nuclear quantum effects on water dynamics using ab initio molecular dynamics that has been accelerated via a recently introduced machine learning approach. We then investigated the molecular mechanisms underlying the different functionals performance and assessed the validity of the Stokes-Einstein relation. We also explored the connection between structural properties and the transport coefficients, verifying the validity of the excess entropy scaling relations for all the functionals. These results pave the way to predict the transport coefficients from the radial distribution function, helping to develop better functionals. On this line, they indicate the importance of describing the long-range features of the radial distribution function., Comment: 10 pages, 5 figures
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- 2021
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168. Barcodes for Hamiltonian homeomorphisms of surfaces
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Joly, Benoît
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Mathematics - Symplectic Geometry ,Mathematics - Dynamical Systems - Abstract
In this article, the main goal is to give a dynamical point of view of Floer homology barcodes for Hamiltonian homeomorphisms of surfaces. More specifically, we describe a way to construct barcodes for Hamiltonian homeomorphisms of surfaces from graphs. We will define graphes associated to maximal isotopies of a Hamiltonian homeomorphism using Le Calvez's positively transverse foliation theory and to those graphs we will associate barcodes. In particular, we will prove that for the simplest cases, our constructions coincide with the Floer Homology barcodes.
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- 2021
169. Electro-osmosis at surfactant-laden liquid-gas interfaces: beyond standard models
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de Lima, Alexia Barbosa and Joly, Laurent
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Condensed Matter - Soft Condensed Matter ,Physics - Fluid Dynamics - Abstract
Electro-osmosis (EO) is a powerful tool to manipulate liquids in micro and nanofluidic systems. While EO has been studied extensively at liquid-solid interfaces, the case of liquid-vapor interfaces, found e.g. in foam films and bubbles, remains to be explored. Here we perform molecular dynamics (MD) simulations of EO in a film of aqueous electrolyte covered with fluid layers of ionic surfactants and surrounded by gas. Following the experimental procedure, we compute the zeta potential from the EO velocity, defined as the velocity difference between the middle of the liquid film and the surrounding gas. We show that the zeta potential can be smaller or larger than existing predictions depending on the surfactant coverage. We explain the failure of previous descriptions by the fact that surfactants and bound ions move as rigid bodies and do not transmit the electric driving force to the liquid locally. Considering the reciprocal streaming current effect, we then develop an extended model, which can be used to predict the experimental zeta potential of surfactant-laden liquid-gas interfaces., Comment: 11 pages, 10 figures; accepted version
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- 2021
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170. Quantum vacuum excitation of a quasi-normal mode in an analog model of black hole spacetime
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Jacquet, Maxime J, Giacomelli, Luca, Valnais, Quentin, Joly, Malo, Claude, Ferdinand, Giacobino, Elisabeth, Glorieux, Quentin, Carusotto, Iacopo, and Bramati, Alberto
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General Relativity and Quantum Cosmology ,Quantum Physics - Abstract
Vacuum quantum fluctuations near horizons are known to yield correlated emission by the Hawking effect. We use a driven-dissipative quantum fluid of microcavity polaritons as an analog model of a quantum field theory on a black-hole spacetime and numerically calculate correlated emission. We show that, in addition to the Hawking effect at the sonic horizon, quantum fluctuations may result in a sizeable stationary excitation of a quasi-normal mode of the field theory. Observable signatures of the excitation of the quasi-normal mode are found in the spatial density fluctuations as well as in the spectrum of Hawking emission. This suggests an intrinsic fluctuation-driven mechanism leading to the quantum excitation of quasi-normal modes on black hole spacetimes., Comment: Version accepted for publication
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- 2021
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171. Regression with Missing Data, a Comparison Study of TechniquesBased on Random Forests
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Gómez-Méndez, Irving and Joly, Emilien
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Mathematics - Statistics Theory ,Statistics - Machine Learning - Abstract
In this paper we present the practical benefits of a new random forest algorithm to deal withmissing values in the sample. The purpose of this work is to compare the different solutionsto deal with missing values with random forests and describe our new algorithm performanceas well as its algorithmic complexity. A variety of missing value mechanisms (such as MCAR,MAR, MNAR) are considered and simulated. We study the quadratic errors and the bias ofour algorithm and compare it to the most popular missing values random forests algorithms inthe literature. In particular, we compare those techniques for both a regression and predictionpurpose. This work follows a first paper Gomez-Mendez and Joly (2020) on the consistency ofthis new algorithm.
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- 2021
172. Spectral theory for Maxwell's equations at the interface of a metamaterial. Part II: Limiting absorption, limiting amplitude principles and interface resonance
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Cassier, Maxence, Hazard, Christophe, and Joly, Patrick
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Mathematics - Analysis of PDEs ,Mathematical Physics ,Mathematics - Numerical Analysis ,Mathematics - Spectral Theory ,35P10, 35Q60, 47A70, 78A25 - Abstract
This paper is concerned with the time-dependent Maxwell's equations for a plane interface between a negative material described by the Drude model and the vacuum, which fill, respectively, two complementary half-spaces. In a first paper, we have constructed a generalized Fourier transform which diagonalizes the Hamiltonian that represents the propagation of transverse electric waves. In this second paper, we use this transform to prove the limiting absorption and limiting amplitude principles, which concern, respectively, the behavior of the resolvent near the continuous spectrum and the long time response of the medium to a time-harmonic source of prescribed frequency. This paper also underlines the existence of an interface resonance which occurs when there exists a particular frequency characterized by a ratio of permittivities and permeabilities equal to $-1$ across the interface. At this frequency, the response of the system to a harmonic forcing term blows up linearly in time. Such a resonance is unusual for wave problem in unbounded domains and corresponds to a non-zero embedded eigenvalue of infinite multiplicity of the underlying operator. This is the time counterpart of the ill-posdness of the corresponding harmonic problem., Comment: 64 pages, 4 figures
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- 2021
173. Probing the energy conversion pathways between light, carriers and lattice in real time with attosecond core-level spectroscopy
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Sidiropoulos, T. P. H., Di Palo, N., Rivas, D. E., Severino, S., Reduzzi, M., Nandy, B., Bauerhenne, B., Krylow, S., Vasileiadis, T., Danz, T., Elliott, P., Sharma, S., Dewhurst, K., Ropers, C., Joly, Y., Garcia, K. M. E., Wolf, M., Ernstorfer, R., and Biegert, J.
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Condensed Matter - Materials Science ,Physics - Applied Physics ,Physics - Instrumentation and Detectors ,Physics - Optics - Abstract
Detection of the energy conversion pathways, between photons, charge carriers, and the lattice is of fundamental importance to understand fundamental physics and to advance materials and devices. Yet, such insight remains incomplete due to experimental challenges in disentangling the various signatures on overlapping time scales. Here, we show that attosecond core-level X-ray spectroscopy can identify these interactions with attosecond precision and across a picosecond range. We demonstrate this methodology on graphite since its investigation is complicated by a variety of mechanisms occurring across a wide range of temporal scales. Our methodology reveals, through the simultaneous real-time detection of electrons and holes, the different dephasing mechanisms for each carrier type dependent on excitation with few-cycle-duration light fields. These results demonstrate the general ability of our methodology to detect and distinguish the various dynamic contributions to the flow of energy inside materials on their native time scales.
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- 2021
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174. High-rate tests on resistive plate chambers operated with eco-friendly gas mixtures
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Abbrescia, M., Aielli, G., Aly, R., Arena, M. C., Barroso, M., Benussi, L., Bianco, S., Bordon, F., Boscherini, D., Bruni, A., Buontempo, S., Busato, M., Camarri, P., Cardarelli, R., Congedo, L., De Jesus Damiao, D., De Serio, M., Di Ciaccio, A., Di Stante, L., Dupieux, P., Eysermans, J., Ferretti, A., Galati, G., Gagliardi, M., Guida, R., Iaselli, G., Joly, B., Lee, K. S., Liberti, B., Lucero Ramirez, D., Mandelli, B., Manen, S. P., Massa, L., Pastore, A., Pastori, E., Piccolo, D., Pizzimento, L., Polini, A., Proto, G., Pugliese, G., Quaglia, L., Ramos, D., Rigoletti, G., Rocchi, A., Romano, M., Samalan, A., Salvini, P., Santonico, R., Saviano, G., Simone, S., Terlizzi, L., Tytgat, M., Vercellin, E., Verzeroli, M., and Zaganidis, N.
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- 2024
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175. Investigation of nanoparticle dispersibility and stability based on TiO2 analysis by SMLS, DLS, and SEM
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Sentis, Matthias. P. L., Feltin, Nicolas, Lambeng, Nora, Lemahieu, Guillaume, Brambilla, Giovanni, Meunier, Gérard, and Chivas-Joly, Carine
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- 2024
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176. Influence of a Succinimide Dispersant on the Tribological Performance of MoS2 Nanoparticles
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Benmansour, Marina, Afanasiev, Pavel, Galipaud, Jules, Vacher, Beatrice, Trillaud, Victor, Joly-Pottuz, Lucile, and Dassenoy, Fabrice
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- 2024
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177. Inferring gene regulation dynamics from static snapshots of gene expression variability
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Joly-Smith, Euan, Wang, Zitong Jerry, and Hilfinger, Andreas
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Quantitative Biology - Molecular Networks ,Quantitative Biology - Quantitative Methods - Abstract
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data obtained from single-cell sequencing or flow-cytometry experiments into regulatory dynamics. We show how static population snapshots of co-variability can be exploited to rigorously infer properties of gene expression dynamics when gene expression reporters probe their upstream dynamics on separate time-scales. This can be experimentally exploited in dual-reporter experiments with fluorescent proteins of unequal maturation times, thus turning an experimental bug into an analysis feature. We derive correlation conditions that detect the presence of closed-loop feedback regulation in gene regulatory networks. Furthermore, we show how genes with cell-cycle dependent transcription rates can be identified from the variability of co-regulated fluorescent proteins. Similar correlation constraints might prove useful in other areas of science in which static correlation snapshots are used to infer causal connections between dynamically interacting components.
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- 2021
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178. Osmotic transport at the aqueous graphene and hBN interfaces: scaling laws from a unified, first principles description
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Joly, Laurent, Meißner, Robert H., Iannuzzi, Marcella, and Tocci, Gabriele
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Physics - Chemical Physics - Abstract
Osmotic transport in nanoconfined aqueous electrolytes provides new venues for water desalination and "blue energy" harvesting; the osmotic response of nanofluidic systems is controlled by the interfacial structure of water and electrolyte solutions in the so-called electrical double layer (EDL), but a molecular-level picture of the EDL is to a large extent still lacking. Particularly, the role of the electronic structure has not been considered in the description of electrolyte/surface interactions. Here, we report enhanced sampling simulations based on ab initio molecular dynamics, aiming at unravelling the free energy of prototypical ions adsorbed at the aqueous graphene and hBN interfaces, and its consequences on nanofluidic osmotic transport. Specifically, we predicted the zeta potential, the diffusio-osmotic mobility and the diffusio-osmotic conductivity for a wide range of salt concentrations from the ab initio water and ion spatial distributions through an analytical framework based on Stokes equation and a modified Poisson-Boltzmann equation. We observed concentration-dependent scaling laws, together with dramatic differences in osmotic transport between the two interfaces, including diffusio-osmotic flow and current reversal on hBN, but not on graphene. We could rationalize the results for the three osmotic responses with a simple model based on characteristic length scales for ion and water adsorption at the surface, which are quite different on graphene and on hBN. Our work provides first principles insights into the structure and osmotic transport of aqueous electrolytes on two-dimensional materials and explores new pathways for efficient water desalination and osmotic energy conversion., Comment: 19 pages, 3 figures
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- 2021
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179. Optical signatures of the coupled spin-mechanics of a levitated magnetic microparticle
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Wachter, Vanessa, Bittencourt, Victor A. S. V., Xie, Shangran, Sharma, Sanchar, Joly, Nicolas, Russell, Philip, Marquardt, Florian, and Kusminskiy, Silvia Viola
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Condensed Matter - Mesoscale and Nanoscale Physics ,Physics - Optics - Abstract
We propose a platform that combines the fields of cavity optomagnonics and levitated optomechanics in order to control and probe the coupled spin-mechanics of magnetic dielectric particles. We theoretically study the dynamics of a levitated Faraday-active dielectric microsphere serving as an optomagnonic cavity, placed in an external magnetic field and driven by an external laser. We find that the optically driven magnetization dynamics induces angular oscillations of the particle with low associated damping. Further, we show that the magnetization and angular motion dynamics can be probed via the power spectrum of the outgoing light. Namely, the characteristic frequencies attributed to the angular oscillations and the spin dynamics are imprinted in the light spectrum by two main resonance peaks. Additionally, we demonstrate that a ferromagnetic resonance setup with an oscillatory perpendicular magnetic field can enhance the resonance peak corresponding to the spin oscillations and induce fast rotations of the particle around its anisotropy axis., Comment: 22 pages, 13 figures
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- 2021
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180. Reproducible Performance Optimization of Complex Applications on the Edge-to-Cloud Continuum
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Rosendo, Daniel, Costan, Alexandru, Antoniu, Gabriel, Simonin, Matthieu, Lombardo, Jean-Christophe, Joly, Alexis, and Valduriez, Patrick
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Computer Science - Distributed, Parallel, and Cluster Computing ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning ,Computer Science - Performance - Abstract
In more and more application areas, we are witnessing the emergence of complex workflows that combine computing, analytics and learning. They often require a hybrid execution infrastructure with IoT devices interconnected to cloud/HPC systems (aka Computing Continuum). Such workflows are subject to complex constraints and requirements in terms of performance, resource usage, energy consumption and financial costs. This makes it challenging to optimize their configuration and deployment. We propose a methodology to support the optimization of real-life applications on the Edge-to-Cloud Continuum. We implement it as an extension of E2Clab, a previously proposed framework supporting the complete experimental cycle across the Edge-to-Cloud Continuum. Our approach relies on a rigorous analysis of possible configurations in a controlled testbed environment to understand their behaviour and related performance trade-offs. We illustrate our methodology by optimizing Pl@ntNet, a world-wide plant identification application. Our methodology can be generalized to other applications in the Edge-to-Cloud Continuum.
- Published
- 2021
181. Enhanced local viscosity around colloidal nanoparticles probed by Equilibrium Molecular Dynamics Simulations
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Rabani, Reza, Saidi, Mohammad Hassan, Joly, Laurent, Merabia, Samy, and Rajabpour, Ali
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Condensed Matter - Soft Condensed Matter ,Condensed Matter - Materials Science - Abstract
Nanofluids; dispersions of nanometer-sized particles in a liquid medium; have been proposed for a wide variety of thermal management applications. It is known that a solid-like nanolayer of liquid of typical thickness 0.5-1 nm surrounding the colloidal nanoparticles can act as a thermal bridge between the nanoparticle and the bulk liquid. Yet, its effect on the nanofluid viscosity has not been elucidated so far. In this article, we compute the local viscosity of the nanolayer using equilibrium molecular dynamics based on the Green-Kubo formula. We first assess the validity of the method to predict the viscosity locally. We apply this methodology to the calculation of the local viscosity in the immediate vicinity of a metallic nanoparticle for a wide range of solid-liquid interaction strength, where a nanolayer of thickness 1 nm is observed as a result of the interaction with the nanoparticle. The viscosity of the nanolayer, which is found to be higher than its corresponding bulk value, is directly dependent on the solid-liquid interaction strength. We discuss the origin of this viscosity enhancement and show that the liquid density increment alone cannot explain the values of the viscosity observed. Rather, we suggest that the solid-like structure of the distribution of the liquid atoms in the vicinity of the nanoparticle contributes to the nanolayer viscosity enhancement. Finally, we observe a failure of the Stokes-Einstein relation between viscosity and diffusion close to the wall, depending on the liquid-solid interaction strength, which we rationalize in terms of hydrodynamic slip.
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- 2021
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182. Theoretical framework for the atomistic modeling of frequency-dependent liquid-solid friction
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Oga, Haruki, Omori, Takeshi, Herrero, Cecilia, Merabia, Samy, Joly, Laurent, and Yamaguchi, Yasutaka
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Condensed Matter - Soft Condensed Matter ,Physics - Chemical Physics ,Physics - Fluid Dynamics - Abstract
Nanofluidics shows great promise for energy conversion and desalination applications. The performance of nanofluidic devices is controlled by liquid-solid friction, quantified by the Navier friction coefficient (FC). Despite decades of research, there is no well-established generic framework to determine the frequency dependent Navier FC from atomistic simulations. Here, we have derived analytical expressions to connect the Navier FC to the random force autocorrelation on the confining wall, from the observation that the random force autocorrelation can be related to the hydrodynamic boundary condition, where the Navier FC appears. The analytical framework is generic in the sense that it explicitly includes the system size dependence and also the frequency dependence of the FC, which enabled us to address (i) the long-standing plateau issue in the evaluation of the FC and (ii) the non-Markovian behavior of liquid-solid friction of a Lennard-Jones liquid and of water on various walls and at various temperatures, including the supercooled regime. This new framework opens the way to explore the frequency dependent FC for a wide range of complex liquids., Comment: 5 pages, 3 figures
- Published
- 2021
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183. Deep-UV-enhanced supercontinuum generated in tapered gas-filled photonic crystal fiber
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Suresh, Mallika Irene, Hammer, Jonas, Joly, Nicolas Y., Russell, Philip St. J., and Tani, Francesco
- Subjects
Physics - Optics - Abstract
We present the use of linearly down-tapered gas-filled hollow-core photonic crystal fiber in a single-stage, pumped with pulses from a compact infrared laser source, to generate a supercontinuum carrying significant spectral power in the deep ultraviolet (200 - 300 nm). The generated supercontinuum extends from the near infrared down to around 213 nm with up to 0.83 mW/nm in the deep ultraviolet., Comment: 4 pages (+1 page for full reference list), 3 figures
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- 2021
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184. Native diversity buffers against severity of non-native tree invasions
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Delavaux, Camille S., Crowther, Thomas W., Zohner, Constantin M., Robmann, Niamh M., Lauber, Thomas, van den Hoogen, Johan, Kuebbing, Sara, Liang, Jingjing, de-Miguel, Sergio, Nabuurs, Gert-Jan, Reich, Peter B., Abegg, Meinrad, Adou Yao, Yves C., Alberti, Giorgio, Almeyda Zambrano, Angelica M., Alvarado, Braulio Vilchez, Alvarez-Dávila, Esteban, Alvarez-Loayza, Patricia, Alves, Luciana F., Ammer, Christian, Antón-Fernández, Clara, Araujo-Murakami, Alejandro, Arroyo, Luzmila, Avitabile, Valerio, Aymard, Gerardo A., Baker, Timothy R., Bałazy, Radomir, Banki, Olaf, Barroso, Jorcely G., Bastian, Meredith L., Bastin, Jean-Francois, Birigazzi, Luca, Birnbaum, Philippe, Bitariho, Robert, Boeckx, Pascal, Bongers, Frans, Bouriaud, Olivier, Brancalion, Pedro H. S., Brandl, Susanne, Brienen, Roel, Broadbent, Eben N., Bruelheide, Helge, Bussotti, Filippo, Gatti, Roberto Cazzolla, César, Ricardo G., Cesljar, Goran, Chazdon, Robin, Chen, Han Y. H., Chisholm, Chelsea, Cho, Hyunkook, Cienciala, Emil, Clark, Connie, Clark, David, Colletta, Gabriel D., Coomes, David A., Cornejo Valverde, Fernando, Corral-Rivas, José J., Crim, Philip M., Cumming, Jonathan R., Dayanandan, Selvadurai, de Gasper, André L., Decuyper, Mathieu, Derroire, Géraldine, DeVries, Ben, Djordjevic, Ilija, Dolezal, Jiri, Dourdain, Aurélie, Engone Obiang, Nestor Laurier, Enquist, Brian J., Eyre, Teresa J., Fandohan, Adandé Belarmain, Fayle, Tom M., Feldpausch, Ted R., Ferreira, Leandro V., Fischer, Markus, Fletcher, Christine, Frizzera, Lorenzo, Gamarra, Javier G. P., Gianelle, Damiano, Glick, Henry B., Harris, David J., Hector, Andrew, Hemp, Andreas, Hengeveld, Geerten, Hérault, Bruno, Herbohn, John L., Herold, Martin, Hillers, Annika, Honorio Coronado, Eurídice N., Hui, Cang, Ibanez, Thomas T., Amaral, Iêda, Imai, Nobuo, Jagodziński, Andrzej M., Jaroszewicz, Bogdan, Johannsen, Vivian Kvist, Joly, Carlos A., Jucker, Tommaso, Jung, Ilbin, Karminov, Viktor, Kartawinata, Kuswata, Kearsley, Elizabeth, Kenfack, David, Kennard, Deborah K., Kepfer-Rojas, Sebastian, Keppel, Gunnar, Khan, Mohammed Latif, Killeen, Timothy J., Kim, Hyun Seok, Kitayama, Kanehiro, Köhl, Michael, Korjus, Henn, Kraxner, Florian, Laarmann, Diana, Lang, Mait, Lewis, Simon L., Lu, Huicui, Lukina, Natalia V., Maitner, Brian S., Malhi, Yadvinder, Marcon, Eric, Marimon, Beatriz Schwantes, Marimon-Junior, Ben Hur, Marshall, Andrew R., Martin, Emanuel H., Martynenko, Olga, Meave, Jorge A., Melo-Cruz, Omar, Mendoza, Casimiro, Merow, Cory, Mendoza, Abel Monteagudo, Moreno, Vanessa S., Mukul, Sharif A., Mundhenk, Philip, Nava-Miranda, María Guadalupe, Neill, David, Neldner, Victor J., Nevenic, Radovan V., Ngugi, Michael R., Niklaus, Pascal A., Oleksyn, Jacek, Ontikov, Petr, Ortiz-Malavasi, Edgar, Pan, Yude, Paquette, Alain, Parada-Gutierrez, Alexander, Parfenova, Elena I., Park, Minjee, Parren, Marc, Parthasarathy, Narayanaswamy, Peri, Pablo L., Pfautsch, Sebastian, Phillips, Oliver L., Picard, Nicolas, Piedade, Maria Teresa T. F., Piotto, Daniel, Pitman, Nigel C. A., Polo, Irina, Poorter, Lourens, Poulsen, Axel D., Pretzsch, Hans, Ramirez Arevalo, Freddy, Restrepo-Correa, Zorayda, Rodeghiero, Mirco, Rolim, Samir G., Roopsind, Anand, Rovero, Francesco, Rutishauser, Ervan, Saikia, Purabi, Salas-Eljatib, Christian, Saner, Philippe, Schall, Peter, Schepaschenko, Dmitry, Scherer-Lorenzen, Michael, Schmid, Bernhard, Schöngart, Jochen, Searle, Eric B., Seben, Vladimír, Serra-Diaz, Josep M., Sheil, Douglas, Shvidenko, Anatoly Z., Silva-Espejo, Javier E., Silveira, Marcos, Singh, James, Sist, Plinio, Slik, Ferry, Sonké, Bonaventure, Souza, Alexandre F., Miscicki, Stanislaw, Stereńczak, Krzysztof J., Svenning, Jens-Christian, Svoboda, Miroslav, Swanepoel, Ben, Targhetta, Natalia, Tchebakova, Nadja, ter Steege, Hans, Thomas, Raquel, Tikhonova, Elena, Umunay, Peter M., Usoltsev, Vladimir A., Valencia, Renato, Valladares, Fernando, van der Plas, Fons, Do, Tran Van, van Nuland, Michael E., Vasquez, Rodolfo M., Verbeeck, Hans, Viana, Helder, Vibrans, Alexander C., Vieira, Simone, von Gadow, Klaus, Wang, Hua-Feng, Watson, James V., Werner, Gijsbert D. A., Wiser, Susan K., Wittmann, Florian, Woell, Hannsjoerg, Wortel, Verginia, Zagt, Roderik, Zawiła-Niedźwiecki, Tomasz, Zhang, Chunyu, Zhao, Xiuhai, Zhou, Mo, Zhu, Zhi-Xin, Zo-Bi, Irie C., and Maynard, Daniel S.
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- 2023
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185. Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk
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Wilcox, Naomi, Dumont, Martine, González-Neira, Anna, Carvalho, Sara, Joly Beauparlant, Charles, Crotti, Marco, Luccarini, Craig, Soucy, Penny, Dubois, Stéphane, Nuñez-Torres, Rocio, Pita, Guillermo, Gardner, Eugene J., Dennis, Joe, Alonso, M. Rosario, Álvarez, Nuria, Baynes, Caroline, Collin-Deschesnes, Annie Claude, Desjardins, Sylvie, Becher, Heiko, Behrens, Sabine, Bolla, Manjeet K., Castelao, Jose E., Chang-Claude, Jenny, Cornelissen, Sten, Dörk, Thilo, Engel, Christoph, Gago-Dominguez, Manuela, Guénel, Pascal, Hadjisavvas, Andreas, Hahnen, Eric, Hartman, Mikael, Herráez, Belén, Jung, Audrey, Keeman, Renske, Kiechle, Marion, Li, Jingmei, Loizidou, Maria A., Lush, Michael, Michailidou, Kyriaki, Panayiotidis, Mihalis I., Sim, Xueling, Teo, Soo Hwang, Tyrer, Jonathan P., van der Kolk, Lizet E., Wahlström, Cecilia, Wang, Qin, Perry, John R. B., Benitez, Javier, Schmidt, Marjanka K., Schmutzler, Rita K., Pharoah, Paul D. P., Droit, Arnaud, Dunning, Alison M., Kvist, Anders, Devilee, Peter, Easton, Douglas F., and Simard, Jacques
- Published
- 2023
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186. Climate, Temporal Abundance of Key Food Sources and Home Ranges of Crested Macaques (Macaca nigra) in Sulawesi, Indonesia: A Longitudinal Phenological Study
- Author
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Joly, Marine, Tamengge, Meldy, Pfeiffer, Jan-Boje, Price, Megan, Agil, Muhammad, and Engelhardt, Antje
- Published
- 2023
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187. Insights into the expanding intestinal phenotypic spectrum of SOCS1 haploinsufficiency and therapeutic options
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Rodari, Marco M., Cazals-Hatem, Dominique, Uzzan, Mathieu, Martin Silva, Nicolas, Khiat, Anis, Ta, Minh Chau, Lhermitte, Ludovic, Touzart, Aurore, Hanein, Sylvain, Rouillon, Cléa, Joly, Francisca, Elmorjani, Adrienne, Steffann, Julie, Cerf-Bensussan, Nadine, Parlato, Marianna, and Charbit-Henrion, Fabienne
- Published
- 2023
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188. Glutamine-dependent signaling controls pluripotent stem cell fate
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Lu, Vivian, Roy, Irena J, Torres, Alejandro, Joly, James H, Ahsan, Fasih M, Graham, Nicholas A, and Teitell, Michael A
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Biochemistry and Cell Biology ,Biological Sciences ,Stem Cell Research - Induced Pluripotent Stem Cell ,Stem Cell Research - Embryonic - Human ,Stem Cell Research - Induced Pluripotent Stem Cell - Human ,Stem Cell Research ,Regenerative Medicine ,Underpinning research ,1.1 Normal biological development and functioning ,Cell Differentiation ,Cell Lineage ,Endoderm ,Germ Layers ,Glutamine ,Humans ,Mesoderm ,Pluripotent Stem Cells ,auxotroph ,cell fate ,development ,glutamine ,nutrient ,pluripotent stem cell ,prototroph ,Medical and Health Sciences ,Developmental Biology ,Biochemistry and cell biology - Abstract
Human pluripotent stem cells (hPSCs) can self-renew indefinitely or can be induced to differentiate. We previously showed that exogenous glutamine (Gln) withdrawal biased hPSC differentiation toward ectoderm and away from mesoderm. We revealed that, although all three germ lineages are capable of de novo Gln synthesis, only ectoderm generates sufficient Gln to sustain cell viability and differentiation, and this finding clarifies lineage fate restrictions under Gln withdrawal. Furthermore, we found that Gln acts as a signaling molecule for ectoderm that supersedes lineage-specifying cytokine induction. In contrast, Gln in mesoderm and endoderm is the preferred precursor of α-ketoglutarate without a direct signaling role. Our work raises a question about whether the nutrient environment functions directly in cell differentiation during development. Interestingly, transcriptome analysis of a gastrulation-stage human embryo shows that unique Gln enzyme-encoding gene expression patterns may also distinguish germ lineages in vivo. Together, our study suggests that intracellular Gln may help coordinate differentiation of the three germ layers.
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- 2022
189. Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems.
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Groen, Simon C, Joly-Lopez, Zoé, Platts, Adrian E, Natividad, Mignon, Fresquez, Zoë, Mauck, William M, Quintana, Marinell R, Cabral, Carlo Leo U, Torres, Rolando O, Satija, Rahul, Purugganan, Michael D, and Henry, Amelia
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Clean Water and Sanitation ,Adaptation ,Physiological ,Crops ,Agricultural ,Domestication ,Droughts ,Gene Expression Regulation ,Plant ,Gene Regulatory Networks ,Genetic Variation ,Mycorrhizae ,Oryza ,Photosynthesis ,Plant Proteins ,Plant Roots ,Plant Shoots ,Selection ,Genetic ,Systems Biology ,Biochemistry and Cell Biology ,Genetics ,Plant Biology ,Plant Biology & Botany - Abstract
Rice (Oryza sativa) was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.
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- 2022
190. Wildlife in Cameroon harbor diverse coronaviruses, including many closely related to human coronavirus 229E.
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Ntumvi, Nkom, Ndze, Valantine, Gillis, Amethyst, Le Doux Diffo, Joseph, Tamoufe, Ubald, Takuo, Jean-Michel, Mouiche, Moctar, Nwobegahay, Julius, LeBreton, Matthew, Rimoin, Anne, Schneider, Bradley, Monagin, Corina, McIver, David, Roy, Sanjit, Ayukekbong, James, Saylors, Karen, Joly, Damien, Wolfe, Nathan, Rubin, Edward, and Lange, Christian
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Coronavirus ,HCoV-229E ,bats ,cameroon ,seasonality ,wildlife - Abstract
Zoonotic spillover of animal viruses into human populations is a continuous and increasing public health risk. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the global impact of emergence. Considering the history and diversity of coronaviruses (CoVs), especially in bats, SARS-CoV-2 will likely not be the last to spillover from animals into human populations. We sampled and tested wildlife in the Central African country Cameroon to determine which CoVs are circulating and how they relate to previously detected human and animal CoVs. We collected animal and ecological data at sampling locations and used family-level consensus PCR combined with amplicon sequencing for virus detection. Between 2003 and 2018, samples were collected from 6,580 animals of several different orders. CoV RNA was detected in 175 bats, a civet, and a shrew. The CoV RNAs detected in the bats represented 17 different genetic clusters, coinciding with alpha (n = 8) and beta (n = 9) CoVs. Sequences resembling human CoV-229E (HCoV-229E) were found in 40 Hipposideridae bats. Phylogenetic analyses place the human-derived HCoV-229E isolates closest to those from camels in terms of the S and N genes but closest to isolates from bats for the envelope, membrane, and RNA-dependent RNA polymerase genes. The CoV RNA positivity rate in bats varied significantly (P
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- 2022
191. Predicting the potential for zoonotic transmission and host associations for novel viruses
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Pandit, Pranav S, Anthony, Simon J, Goldstein, Tracey, Olival, Kevin J, Doyle, Megan M, Gardner, Nicole R, Bird, Brian, Smith, Woutrina, Wolking, David, Gilardi, Kirsten, Monagin, Corina, Kelly, Terra, Uhart, Marcela M, Epstein, Jonathan H, Machalaba, Catherine, Rostal, Melinda K, Dawson, Patrick, Hagan, Emily, Sullivan, Ava, Li, Hongying, Chmura, Aleksei A, Latinne, Alice, Lange, Christian, O’Rourke, Tammie, Olson, Sarah, Keatts, Lucy, Mendoza, A Patricia, Perez, Alberto, de Paula, Cátia Dejuste, Zimmerman, Dawn, Valitutto, Marc, LeBreton, Matthew, McIver, David, Islam, Ariful, Duong, Veasna, Mouiche, Moctar, Shi, Zhengli, Mulembakani, Prime, Kumakamba, Charles, Ali, Mohamed, Kebede, Nigatu, Tamoufe, Ubald, Bel-Nono, Samuel, Camara, Alpha, Pamungkas, Joko, Coulibaly, Kalpy J, Abu-Basha, Ehab, Kamau, Joseph, Silithammavong, Soubanh, Desmond, James, Hughes, Tom, Shiilegdamba, Enkhtuvshin, Aung, Ohnmar, Karmacharya, Dibesh, Nziza, Julius, Ndiaye, Daouda, Gbakima, Aiah, Sajali, Zikankuba, Wacharapluesadee, Supaporn, Robles, Erika Alandia, Ssebide, Benard, Suzán, Gerardo, Aguirre, Luis F, Solorio, Monica R, Dhole, Tapan N, Nga, Nguyen TT, Hitchens, Peta L, Joly, Damien O, Saylors, Karen, Fine, Amanda, Murray, Suzan, Karesh, William B, Daszak, Peter, Mazet, Jonna AK, and Johnson, Christine K
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Biological Sciences ,Biomedical and Clinical Sciences ,Infectious Diseases ,2.2 Factors relating to the physical environment ,2.1 Biological and endogenous factors ,Infection ,Africa ,Animals ,Animals ,Wild ,Host Specificity ,Humans ,Viruses ,Zoonoses ,PREDICT Consortium ,Biological sciences ,Biomedical and clinical sciences - Abstract
Host-virus associations have co-evolved under ecological and evolutionary selection pressures that shape cross-species transmission and spillover to humans. Observed virus-host associations provide relevant context for newly discovered wildlife viruses to assess knowledge gaps in host-range and estimate pathways for potential human infection. Using models to predict virus-host networks, we predicted the likelihood of humans as hosts for 513 newly discovered viruses detected by large-scale wildlife surveillance at high-risk animal-human interfaces in Africa, Asia, and Latin America. Predictions indicated that novel coronaviruses are likely to infect a greater number of host species than viruses from other families. Our models further characterize novel viruses through prioritization scores and directly inform surveillance targets to identify host ranges for newly discovered viruses.
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- 2022
192. Multi-Scale Spectrogram Modelling for Neural Text-to-Speech
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Abbas, Ammar, Bollepalli, Bajibabu, Moinet, Alexis, Joly, Arnaud, Karanasou, Penny, Makarov, Peter, Slangens, Simon, Karlapati, Sri, and Drugman, Thomas
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Electrical Engineering and Systems Science - Audio and Speech Processing ,Computer Science - Machine Learning ,Computer Science - Sound - Abstract
We propose a novel Multi-Scale Spectrogram (MSS) modelling approach to synthesise speech with an improved coarse and fine-grained prosody. We present a generic multi-scale spectrogram prediction mechanism where the system first predicts coarser scale mel-spectrograms that capture the suprasegmental information in speech, and later uses these coarser scale mel-spectrograms to predict finer scale mel-spectrograms capturing fine-grained prosody. We present details for two specific versions of MSS called Word-level MSS and Sentence-level MSS where the scales in our system are motivated by the linguistic units. The Word-level MSS models word, phoneme, and frame-level spectrograms while Sentence-level MSS models sentence-level spectrogram in addition. Subjective evaluations show that Word-level MSS performs statistically significantly better compared to the baseline on two voices., Comment: Accepted for the 11th ISCA Speech Synthesis Workshop (SSW11)
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- 2021
193. Fiber-based biphoton source with ultrabroad frequency tunability
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Lopez-Huidobro, Santiago, Lippl, Markus, Joly, Nicolas Y., and Chekhova, Maria V.
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Physics - Optics - Abstract
Tunable biphotons are highly important for a wide range of quantum applications. For some applications, especially interesting are cases where two photons of a pair are far apart in frequency. Here, we report a tunable biphoton source based on a xenon-filled hollow-core photonic crystal fiber. Tunability is achieved by adjusting the pressure of the gas inside the fiber. This allows us to tailor the dispersion landscape of the fiber, overcoming the principal limitations of solid-core fiber-based biphoton sources. We report a maximum tunability of 120 THz for a pressure range of 4 bar with a continuous shift of 30 THz/bar. At 21 bar, the photons of a pair are separated by more than one octave. Despite the large separation, both photons have large bandwidths. At 17 bar, they form a very broad (110 THz) band around the frequency of the pump., Comment: 5 pages, 4 figures
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- 2021
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194. A learned conditional prior for the VAE acoustic space of a TTS system
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Karanasou, Penny, Karlapati, Sri, Moinet, Alexis, Joly, Arnaud, Abbas, Ammar, Slangen, Simon, Trueba, Jaime Lorenzo, and Drugman, Thomas
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Electrical Engineering and Systems Science - Audio and Speech Processing ,Computer Science - Machine Learning ,Computer Science - Sound - Abstract
Many factors influence speech yielding different renditions of a given sentence. Generative models, such as variational autoencoders (VAEs), capture this variability and allow multiple renditions of the same sentence via sampling. The degree of prosodic variability depends heavily on the prior that is used when sampling. In this paper, we propose a novel method to compute an informative prior for the VAE latent space of a neural text-to-speech (TTS) system. By doing so, we aim to sample with more prosodic variability, while gaining controllability over the latent space's structure. By using as prior the posterior distribution of a secondary VAE, which we condition on a speaker vector, we can sample from the primary VAE taking explicitly the conditioning into account and resulting in samples from a specific region of the latent space for each condition (i.e. speaker). A formal preference test demonstrates significant preference of the proposed approach over standard Conditional VAE. We also provide visualisations of the latent space where well-separated condition-specific clusters appear, as well as ablation studies to better understand the behaviour of the system., Comment: in Proceedings of Interspeech 2021
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- 2021
195. Poisson-Boltzmann formulary: Third edition
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Herrero, Cecilia and Joly, Laurent
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Condensed Matter - Soft Condensed Matter - Abstract
The Poisson-Boltzmann (PB) equation provides a mean-field theory of electrolyte solutions at interfaces and in confinement, describing how ions reorganize close to charged surfaces to form the so-called electrical double layer (EDL), with numerous applications ranging from colloid science to biology. This formulary focuses on situations of interest for micro and nanofluidics, and gathers important formulas for the PB description of a Z:Z electrolyte solution inside slit and cylindrical channels. Different approximated solutions (thin EDLs, no co-ion, Debye-H\"uckel, and homogeneous/parabolic potential limits) and their range of validity are discussed, together with the full solution for the slit channel. Common boundary conditions are presented, the thermodynamics of the EDL is introduced, and an overview of the application of the PB framework to the description of electrokinetic effects is given. Finally, the limits of the PB framework are briefly discussed, and Python scripts to solve the PB equation numerically are provided., Comment: 24 pages, 6 figures
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- 2021
196. The Calabi invariant for Hamiltonian diffeomorphisms of the unit disk
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Joly, Benoît
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Mathematics - Symplectic Geometry ,Mathematics - Dynamical Systems - Abstract
In this article, we study the Calabi invariant on the unit disk usually defined on compactly supported Hamiltonian diffeomorphisms of the open disk. In particular we extend the Calabi invariant to the group of $C^1$ diffeomorphisms of the closed disk which preserves the standard symplectic form. We also compute the Calabi invariant for some diffeomorphisms of the disk which satisfies some rigidity hypothesis., Comment: 30 pages. Comments are welcome
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- 2021
197. Hyperspherical embedding for novel class classification
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Pereira, Rafael S., Joly, Alexis, Valduriez, Patrick, and Porto, Fabio
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence ,cs.LG, cs.AI, cs:CV - Abstract
Deep learning models have become increasingly useful in many different industries. On the domain of image classification, convolutional neural networks proved the ability to learn robust features for the closed set problem, as shown in many different datasets, such as MNIST FASHIONMNIST, CIFAR10, CIFAR100, and IMAGENET. These approaches use deep neural networks with dense layers with softmax activation functions in order to learn features that can separate classes in a latent space. However, this traditional approach is not useful for identifying classes unseen on the training set, known as the open set problem. A similar problem occurs in scenarios involving learning on small data. To tackle both problems, few-shot learning has been proposed. In particular, metric learning learns features that obey constraints of a metric distance in the latent space in order to perform classification. However, while this approach proves to be useful for the open set problem, current implementation requires pair-wise training, where both positive and negative examples of similar images are presented during the training phase, which limits the applicability of these approaches in large data or large class scenarios given the combinatorial nature of the possible inputs.In this paper, we present a constraint-based approach applied to the representations in the latent space under the normalized softmax loss, proposed by[18]. We experimentally validate the proposed approach for the classification of unseen classes on different datasets using both metric learning and the normalized softmax loss, on disjoint and joint scenarios. Our results show that not only our proposed strategy can be efficiently trained on larger set of classes, as it does not require pairwise learning, but also present better classification results than the metric learning strategies surpassing its accuracy by a significant margin., Comment: 9 pages with 10 figures and 6 tables. Not currently published
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- 2021
198. GA4GH: International policies and standards for data sharing across genomic research and healthcare
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Rehm, Heidi L, Page, Angela JH, Smith, Lindsay, Adams, Jeremy B, Alterovitz, Gil, Babb, Lawrence J, Barkley, Maxmillian P, Baudis, Michael, Beauvais, Michael JS, Beck, Tim, Beckmann, Jacques S, Beltran, Sergi, Bernick, David, Bernier, Alexander, Bonfield, James K, Boughtwood, Tiffany F, Bourque, Guillaume, Bowers, Sarion R, Brookes, Anthony J, Brudno, Michael, Brush, Matthew H, Bujold, David, Burdett, Tony, Buske, Orion J, Cabili, Moran N, Cameron, Daniel L, Carroll, Robert J, Casas-Silva, Esmeralda, Chakravarty, Debyani, Chaudhari, Bimal P, Chen, Shu Hui, Cherry, J Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L, Cook-Deegan, Robert M, Courtot, Mélanie, Cunningham, Fiona, Cupak, Miro, Davies, Robert M, Denisko, Danielle, Doerr, Megan J, Dolman, Lena I, Dove, Edward S, Dursi, L Jonathan, Dyke, Stephanie OM, Eddy, James A, Eilbeck, Karen, Ellrott, Kyle P, Fairley, Susan, Fakhro, Khalid A, Firth, Helen V, Fitzsimons, Michael S, Fiume, Marc, Flicek, Paul, Fore, Ian M, Freeberg, Mallory A, Freimuth, Robert R, Fromont, Lauren A, Fuerth, Jonathan, Gaff, Clara L, Gan, Weiniu, Ghanaim, Elena M, Glazer, David, Green, Robert C, Griffith, Malachi, Griffith, Obi L, Grossman, Robert L, Groza, Tudor, Auvil, Jaime M Guidry, Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A, Hamosh, Ada, Hansen, David P, Hart, Reece K, Hartley, Dean Mitchell, Haussler, David, Hendricks-Sturrup, Rachele M, Ho, Calvin WL, Hobb, Ashley E, Hoffman, Michael M, Hofmann, Oliver M, Holub, Petr, Hsu, Jacob Shujui, Hubaux, Jean-Pierre, Hunt, Sarah E, Husami, Ammar, Jacobsen, Julius O, Jamuar, Saumya S, Janes, Elizabeth L, Jeanson, Francis, Jené, Aina, Johns, Amber L, Joly, Yann, Jones, Steven JM, Kanitz, Alexander, Kato, Kazuto, Keane, Thomas M, and Kekesi-Lafrance, Kristina
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Biological Sciences ,Genetics ,Human Genome ,Clinical Research ,Health Services ,Generic health relevance ,Good Health and Well Being - Abstract
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
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- 2021
199. Regulating cancer risk prediction: legal considerations and stakeholder perspectives on the Canadian context
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Moreno, Palmira Granados, Knoppers, Terese, Zawati, Ma’n H., Lang, Michael, Knoppers, Bartha M., Wolfson, Michael, Nabi, Hermann, Dorval, Michel, Simard, Jacques, and Joly, Yann
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- 2023
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200. Applicability of the Edinburgh CT Criteria for Lobar Intracerebral Hemorrhage Associated with Cerebral Amyloid Angiopathy
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Grangeon, Lou, Roussel, Melanie, Gillibert, Andre, Verdalle-Cazes, Mikael, Dolores, Mickael, Ozkul-Wermester, Ozlem, Gilard, Vianney, Derrey, Stephane, Maltête, David, Gerardin, Emmanuel, Joly, Luc-Marie, Wallon, David, and Magne, Nicolas
- Published
- 2023
- Full Text
- View/download PDF
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