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1. Fermionic quantum walkers coupled to a bosonic reservoir

Author

Bourget, Olivier, Joye, Alain, and Spehner, Dominique

Subjects
Mathematical Physics
Abstract

We analyze the discrete-time dynamics of a model of non-interacting fermions on a finite graph coupled to an infinite reservoir formed by a bosonic quantum walk on Z. This dynamics consists of consecutive applications of free evolutions of the fermions and bosons followed by a local coupling between them. The unitary operator implementing this coupling generates fermionic transitions between two fixed vertices induced by absorption and emission of bosons at a single lattice site. The free fermion evolution is given by a second-quantized single-particle unitary operator satisfying some genericity assumptions, in particular it produces hopping of fermions between all vertices. The free boson evolution is given by the second-quantized shift operator on Z. We derive explicitly the Heisenberg dynamics of fermionic observables and obtain a systematic expansion in the large-coupling regime, which we control by using spectral methods. We also prove that the reduced state of the fermions converges in the large-time limit to an infinite-temperature Gibbs

Published
2024

2. Unitary and Open Scattering Quantum Walks on Graphs

Author

Joye, Alain

Subjects
Mathematical Physics, Quantum Physics, 81Q12
Abstract

We study a class of Unitary Quantum Walks on arbitrary graphs, parameterized by a family of scattering matrices. These Scattering Quantum Walks model the discrete dynamics of a system on the edges of the graph, with a scattering process at each vertex governed by the scattering matrix assigned to it. We show that Scattering Quantum Walks encompass several known Quantum Walks. Additionally, we introduce two classes of Open Scattering Quantum Walks on arbitrary graphs, also parameterized by scattering matrices: one class defined on the edges and the other on the vertices of the graph. We show that these walks give rise to proper Quantum Channels and describe their main spectral and dynamical properties, relating them to naturally associated classical Markov chains.

Published
2024

3. Two-Time Measurement of Entropy Transfer in Markovian Quantum Dynamics

Author

Joye, A. and Pillet, C. -A.

Subjects
Mathematical Physics, Quantum Physics, 81P15, 81P17
Abstract

We consider a protocol for the two-time measurement of entropic observables in quantum open systems driven out of thermal equilibrium by coupling to several heat baths. We concentrate on the Markovian approximation of the time-evolution and relate the expected value of the so defined entropy variations with the well-known expression of entropy production due to Lebowitz and Spohn. We do so under the detailed balance condition and, as a byproduct, we show that the probabilities of outcomes of two-time measurements are given by a continuous time Markov process determined by the Lindblad generator of the Markovian quantum dynamics., Comment: Published version

Published
2024
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4. Exponential tail estimates for quantum lattice dynamics

Author

Cedzich, Christopher, Joye, Alain, Werner, Albert H., and Werner, Reinhard F.

Subjects
Quantum Physics, Mathematical Physics
Abstract

We consider the quantum dynamics of a particle on a lattice for large times. Assuming translation invariance, and either discrete or continuous time parameter, the distribution of the ballistically scaled position $Q(t)/t$ converges weakly to a distribution that is compactly supported in velocity space, essentially the distribution of group velocity in the initial state. We show that the total probability of velocities strictly outside the support of the asymptotic measure goes to zero exponentially with $t$, and we provide a simple method to estimate the exponential rate uniformly in the initial state. Near the boundary of the allowed region the rate function goes to zero like the power 3/2 of the distance to the boundary. The method is illustrated in several examples., Comment: 20 pages, 6 figures

Published
2024

5. Multimodal Imaging of Posterior Corneal Opacities in Multicentric Osteolysis Nodulosis and Arthropathy (MONA).

Author

Eppley, Sarah E, Pasricha, Neel D, Seitzman, Gerami D, Joye, Ashlin, Arboleda, Alejandro, and Qureshi, Azam

Subjects
Biomedical and Clinical Sciences, Ophthalmology and Optometry, Clinical Research, Rare Diseases, Biomedical Imaging, Clinical Trials and Supportive Activities, Eye Disease and Disorders of Vision, 2.1 Biological and endogenous factors, Eye, collagenase, corneal opacity, gelatinase, matrix metalloproteinase 2, multicentric osteolysis nodulosis and arthropathy
Abstract

PurposeMulticentric osteolysis nodulosis and arthropathy (MONA) syndrome is a rare autosomal recessive skeletal dysplasia. Caused by mutations in the matrix metalloproteinase 2 gene (MMP2) on chromosome 16q12, this syndrome has infrequently been associated with ophthalmic manifestations. Corneal opacities have been reported but not described or documented in detail.MethodsComplete ophthalmologic examination and multimodal anterior segment imaging were used to characterize the corneal findings in a patient with MONA syndrome.ResultsA 19-year-old with MONA syndrome was referred for an eye exam based upon MONA screening recommendations. Visually insignificant peripheral corneal opacities were noted. Anterior segment optical coherence tomography (AS-OCT) demonstrated posterior stromal and endothelial hyperreflectivity. Confocal microscopy demonstrated an acellular peripheral endothelium with a normal central endothelium.ConclusionsCorneal opacities can occur with MONA syndrome, which is caused by mutations in the MMP2 gene. In the patient presented here, the corneal opacities are peripheral, deep stromal, with sparing of the anterior stroma and epithelium.

Published
2024

6. Metatranscriptomic response of deep ocean microbial populations to infusions of oil and/or synthetic chemical dispersant.

Author

Peña-Montenegro, Tito, Kleindienst, Sara, Allen, Andrew, Eren, A, McCrow, John, Arnold, Jonathan, and Joye, Samantha

Subjects
Colwellia, Corexit, Marinobacter, deepwater horizon oil spill, giant virus, metatranscriptome, mobilome, Petroleum, Microbiota, Seawater, Petroleum Pollution, Surface-Active Agents, Bacteria, Transcriptome, Hydrocarbons, Water Pollutants, Chemical
Abstract

Oil spills are a frequent perturbation to the marine environment that has rapid and significant impacts on the local microbiome. Previous studies have shown that exposure to synthetic dispersant alone did not enhance heterotrophic microbial activity or oxidation rates of specific hydrocarbon components but increased the abundance of some taxa (e.g., Colwellia). In contrast, exposure to oil, but not dispersants, increased the abundance of other taxa (e.g., Marinobacter) and stimulated hydrocarbon oxidation rates. Here, we advance these findings by interpreting metatranscriptomic data from this experiment to explore how and why specific components of the microbial community responded to distinct organic carbon exposure regimes. Dispersant alone was selected for a unique community and for dominant organisms that reflected treatment- and time-dependent responses. Dispersant amendment also led to diverging functional profiles among the different treatments. Similarly, oil alone was selected for a community that was distinct from treatments amended with dispersants. The presence of oil and dispersants with added nutrients led to substantial differences in microbial responses, likely suggesting increased fitness driven by the presence of additional inorganic nutrients. The oil-only additions led to a marked increase in the expression of phages, prophages, transposable elements, and plasmids (PPTEPs), suggesting that aspects of microbial community response to oil are driven by the mobilome, potentially through viral-associated regulation of metabolic pathways in ciliates and flagellates that would otherwise throttle the microbial community through grazing.IMPORTANCEMicrocosm experiments simulated the April 2010 Deepwater Horizon oil spill by applying oil and synthetic dispersants (Corexit EC9500A and EC9527A) to deep ocean water samples. The exposure regime revealed severe negative alterations in the treatments heterotrophic microbial activity and hydrocarbon oxidation rates. We expanded these findings by exploring metatranscriptomic signatures of the microbial communities during the chemical amendments in the microcosm experiments. Here we report how dominant organisms were uniquely associated with treatment- and time-dependent trajectories during the exposure regimes; nutrient availability was a significant factor in driving changes in metatranscriptomic responses. Remarkable signals associated with PPTEPs showed the potential role of mobilome and viral-associated survival responses. These insights underscore the time-dependent environmental perturbations of fragile marine environments under oil and anthropogenic stress.

Published
2024

10. Entropy Production of Quantum Reset Models

Author

Haack, Géraldine and Joye, Alain

Subjects
Mathematical Physics, Quantum Physics
Abstract

We analyze the entropy production of Quantum Reset Models (QRMs) corresponding to quantum dynamical semigroups driven by Lindbladians motivated by a probabilistic description of dissipation in an external environment. We investigate the strict positivity of entropy production for Lindbladians given as sums of QRMs, when the Hamiltonian of the total Lindbladian is split as an affine combination of Hamiltonians of the individual QRMs. In this setup, we derive conditions on the coefficients of the combination and on the reset states ensuring either positive or zero entropy production. Second, we deal with a tri-partite system subject at its ends to two independent QRMs and a weak coupling Hamiltonian. The latter is split as an affine combination of individual Hamiltonians, and we provide necessary and sufficient conditions ensuring strict positivity of the entropy production to leading order, with the possible exception of one affine combination. We apply these results to a physically motivated model and exhibit explicit expressions for the leading orders steady-state solution, entropy production and entropy fluxes. Moreover, these approximations are numerically shown to hold beyond the expected regimes., Comment: 35 pages, 5 figures, comments are welcome

Published
2024

11. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M., Formenti, Giulio, Mouton, Alice, De Panis, Diego, Marins, Luísa S., Leitão, Henrique G., Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, De Pooter, Tim, Joris, Geert, Strazisar, Mojca, Wood, Jonathan M. D., Herron, Katie E., Seehausen, Ole, Watts, Phillip C., Shaw, Felix, Davey, Robert P., Minotto, Alice, Fernández, José M., Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C., Amorim, Isabel R., Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, BedHom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo A. V., Dias, Guilherme Borges, Bosse, Mirte, Brown, Tom, Bruggmann, Rémy, Buena-Atienza, Elena, Burgin, Josephine, Buzan, Elena, Cariani, Alessia, Casadei, Nicolas, Chiara, Matteo, Chozas, Sergio, Čiampor, Jr., Fedor, Crottini, Angelica, Cruaud, Corinne, Cruz, Fernando, Dalen, Love, De Biase, Alessio, del Campo, Javier, Delic, Teo, Dennis, Alice B., Derks, Martijn F. L., Diroma, Maria Angela, Djan, Mihajla, Duprat, Simone, Eleftheriadi, Klara, Feulner, Philine G. D., Flot, Jean-François, Forni, Giobbe, Fosso, Bruno, Fournier, Pascal, Fournier-Chambrillon, Christine, Gabaldon, Toni, Garg, Shilpa, Gissi, Carmela, Giupponi, Luca, Gomez-Garrido, Jessica, González, Josefa, Grilo, Miguel L., Grüning, Björn, Guerin, Thomas, Guiglielmoni, Nadege, Gut, Marta, Haesler, Marcel P., Hahn, Christoph, Halpern, Balint, Harrison, Peter W., Heintz, Julia, Hindrikson, Maris, Höglund, Jacob, Howe, Kerstin, Hughes, Graham M., Istace, Benjamin, Cock, Mark J., Janžekovič, Franc, Jonsson, Zophonias O., Joye-Dind, Sagane, Koskimäki, Janne J., Krystufek, Boris, Kubacka, Justyna, Kuhl, Heiner, Kusza, Szilvia, Labadie, Karine, Lähteenaro, Meri, Lantz, Henrik, Lavrinienko, Anton, Leclère, Lucas, Lopes, Ricardo Jorge, Madsen, Ole, Magdelenat, Ghislaine, Magoga, Giulia, Manousaki, Tereza, Mappes, Tapio, Marques, Joao Pedro, Redondo, Gemma I. Martinez, Maumus, Florian, McCarthy, Shane A., Megens, Hendrik-Jan, Melo-Ferreira, Jose, Mendes, Sofia L., Montagna, Matteo, Moreno, Joao, Mosbech, Mai-Britt, Moura, Mónica, Musilova, Zuzana, Myers, Eugene, Nash, Will J., Nater, Alexander, Nicholson, Pamela, Niell, Manuel, Nijland, Reindert, Noel, Benjamin, Noren, Karin, Oliveira, Pedro H., Olsen, Remi-Andre, Ometto, Lino, Oomen, Rebekah A., Ossowski, Stephan, Palinauskas, Vaidas, Palsson, Snaebjorn, Panibe, Jerome P., Pauperio, Joana, Pavlek, Martina, Payen, Emilie, Pawlowska, Julia, Pellicer, Jaume, Pesole, Graziano, Pimenta, Joao, Pippel, Martin, Pirttilä, Anna Maria, Poulakakis, Nikos, Rajan, Jeena, M.C. Rego, Rúben, Resendes, Roberto, Resl, Philipp, Riesgo, Ana, Rodin-Morch, Patrik, Soares, Andre E. R., Fernandes, Carlos Rodriguez, Romeiras, Maria M., Roxo, Guilherme, Rüber, Lukas, Ruiz-Lopez, Maria Jose, Saarma, Urmas, da Silva, Luis P., Sim-Sim, Manuela, Soler, Lucile, Sousa, Vitor C., Santos, Carla Sousa, Spada, Alberto, Stefanovic, Milomir, Steger, Viktor, Stiller, Josefin, Stöck, Matthias, Struck, Torsten H., Sudasinghe, Hiranya, Tapanainen, Riikka, Tellgren-Roth, Christian, Trindade, Helena, Tukalenko, Yevhen, Urso, Ilenia, Vacherie, Benoit, Van Belleghem, Steven M., Van Oers, Kees, Vargas-Chavez, Carlos, Velickovic, Nevena, Vella, Noel, Vella, Adriana, Vernesi, Cristiano, Vicente, Sara, Villa, Sara, Pettersson, Olga Vinnere, Volckaert, Filip A. M., Voros, Judit, Wincker, Patrick, Winkler, Sylke, Ciofi, Claudio, Waterhouse, Robert M., and Mazzoni, Camila J.

Published
2024
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12. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M., Formenti, Giulio, Mouton, Alice, De Panis, Diego, Marins, Luísa S., Leitão, Henrique G., Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, De Pooter, Tim, Joris, Geert, Strazisar, Mojca, Wood, Jonathan M. D., Herron, Katie E., Seehausen, Ole, Watts, Phillip C., Shaw, Felix, Davey, Robert P., Minotto, Alice, Fernández, José M., Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C., Amorim, Isabel R., Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, BedHom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo A. V., Dias, Guilherme Borges, Bosse, Mirte, Brown, Tom, Bruggmann, Rémy, Buena-Atienza, Elena, Burgin, Josephine, Buzan, Elena, Cariani, Alessia, Casadei, Nicolas, Chiara, Matteo, Chozas, Sergio, Čiampor, Jr., Fedor, Crottini, Angelica, Cruaud, Corinne, Cruz, Fernando, Dalen, Love, De Biase, Alessio, del Campo, Javier, Delic, Teo, Dennis, Alice B., Derks, Martijn F. L., Diroma, Maria Angela, Djan, Mihajla, Duprat, Simone, Eleftheriadi, Klara, Feulner, Philine G. D., Flot, Jean-François, Forni, Giobbe, Fosso, Bruno, Fournier, Pascal, Fournier-Chambrillon, Christine, Gabaldon, Toni, Garg, Shilpa, Gissi, Carmela, Giupponi, Luca, Gomez-Garrido, Jessica, González, Josefa, Grilo, Miguel L., Grüning, Björn, Guerin, Thomas, Guiglielmoni, Nadege, Gut, Marta, Haesler, Marcel P., Hahn, Christoph, Halpern, Balint, Harrison, Peter W., Heintz, Julia, Hindrikson, Maris, Höglund, Jacob, Howe, Kerstin, Hughes, Graham M., Istace, Benjamin, Cock, Mark J., Janžekovič, Franc, Jonsson, Zophonias O., Joye-Dind, Sagane, Koskimäki, Janne J., Krystufek, Boris, Kubacka, Justyna, Kuhl, Heiner, Kusza, Szilvia, Labadie, Karine, Lähteenaro, Meri, Lantz, Henrik, Lavrinienko, Anton, Leclère, Lucas, Lopes, Ricardo Jorge, Madsen, Ole, Magdelenat, Ghislaine, Magoga, Giulia, Manousaki, Tereza, Mappes, Tapio, Marques, Joao Pedro, Redondo, Gemma I. Martinez, Maumus, Florian, McCarthy, Shane A., Megens, Hendrik-Jan, Melo-Ferreira, Jose, Mendes, Sofia L., Montagna, Matteo, Moreno, Joao, Mosbech, Mai-Britt, Moura, Mónica, Musilova, Zuzana, Myers, Eugene, Nash, Will J., Nater, Alexander, Nicholson, Pamela, Niell, Manuel, Nijland, Reindert, Noel, Benjamin, Noren, Karin, Oliveira, Pedro H., Olsen, Remi-Andre, Ometto, Lino, Oomen, Rebekah A., Ossowski, Stephan, Palinauskas, Vaidas, Palsson, Snaebjorn, Panibe, Jerome P., Pauperio, Joana, Pavlek, Martina, Payen, Emilie, Pawlowska, Julia, Pellicer, Jaume, Pesole, Graziano, Pimenta, Joao, Pippel, Martin, Pirttilä, Anna Maria, Poulakakis, Nikos, Rajan, Jeena, M.C. Rego, Rúben, Resendes, Roberto, Resl, Philipp, Riesgo, Ana, Rodin-Morch, Patrik, Soares, Andre E. R., Fernandes, Carlos Rodriguez, Romeiras, Maria M., Roxo, Guilherme, Rüber, Lukas, Ruiz-Lopez, Maria Jose, Saarma, Urmas, da Silva, Luis P., Sim-Sim, Manuela, Soler, Lucile, Sousa, Vitor C., Santos, Carla Sousa, Spada, Alberto, Stefanovic, Milomir, Steger, Viktor, Stiller, Josefin, Stöck, Matthias, Struck, Torsten H., Sudasinghe, Hiranya, Tapanainen, Riikka, Tellgren-Roth, Christian, Trindade, Helena, Tukalenko, Yevhen, Urso, Ilenia, Vacherie, Benoit, Van Belleghem, Steven M., Van Oers, Kees, Vargas-Chavez, Carlos, Velickovic, Nevena, Vella, Noel, Vella, Adriana, Vernesi, Cristiano, Vicente, Sara, Villa, Sara, Pettersson, Olga Vinnere, Volckaert, Filip A. M., Voros, Judit, Wincker, Patrick, Winkler, Sylke, Ciofi, Claudio, Waterhouse, Robert M., and Mazzoni, Camila J.

Published
2024
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14. IL-15-secreting CAR natural killer cells directed toward the pan-cancer target CD70 eliminate both cancer cells and cancer-associated fibroblasts

Author

Van den Eynde, Astrid, Gehrcken, Laura, Verhezen, Tias, Lau, Ho Wa, Hermans, Christophe, Lambrechts, Hilde, Flieswasser, Tal, Quatannens, Delphine, Roex, Gils, Zwaenepoel, Karen, Marcq, Elly, Joye, Philippe, Cardenas De La Hoz, Edgar, Deben, Christophe, Gasparini, Alessia, Montay-Gruel, Pierre, Le Compte, Maxim, Lion, Eva, Lardon, Filip, Van Laere, Steven, Siozopoulou, Vasiliki, Campillo-Davo, Diana, De Waele, Jorrit, Pauwels, Patrick, Jacobs, Julie, Smits, Evelien, and Van Audenaerde, Jonas R. M.

Published
2024
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15. Physicochemical perturbation increases nitrous oxide production from denitrification in soils and sediments

Author

N. B. Weston, C. Troy, P. J. Kearns, J. L. Bowen, W. Porubsky, C. Hyacinthe, C. Meile, P. Van Cappellen, and S. B. Joye

Subjects
Ecology, QH540-549.5, Life, QH501-531, Geology, QE1-996.5
Abstract

Atmospheric concentrations of nitrous oxide (N2O), a potent greenhouse gas that is also responsible for significant stratospheric ozone depletion, have increased in response to the intensified use of agricultural fertilizers and other human activities that have accelerated nitrogen cycling processes. Microbial denitrification in soils and sediments is a major source of N2O, produced as an intermediate during the reduction of oxidized forms of nitrogen to dinitrogen gas (N2). Substrate availability (nitrate and organic matter) and environmental factors such as oxygen levels, temperature, moisture, and pH influence rates of denitrification and N2O production. Here we describe the role of physicochemical perturbation (defined here as a change from the ambient environmental conditions) in influencing rates of denitrification and N2O production. Changes in salinity, temperature, moisture, pH, and zinc in agricultural soils induced a short-term perturbation response characterized by lower rates of total denitrification and higher rates of net N2O production. The ratio of N2O to total denitrification (N2O : DNF) increased strongly with physicochemical perturbation. A salinity press experiment on tidal freshwater marsh soils revealed that increased N2O production was likely driven by transcriptional inhibition of the nitrous oxide reductase (nos) gene and that the microbial community adapted to altered salinity over a relatively short time frame (within 1 month). Perturbation appeared to confer resilience to subsequent disturbance, and denitrifiers from an environment without salinity fluctuations (tidal freshwater estuarine sediments) demonstrated a stronger N2O perturbation response than denitrifiers from environments with more variable salinity (oligohaline and mesohaline estuarine sediments), suggesting that the denitrifying community from physicochemically stable environments may have a stronger perturbation response. These findings provide a framework for improving our understanding of the dynamic nature of N2O production in soils and sediments, in which changes in physical and/or chemical conditions initiate a short-term perturbation response that promotes N2O production that moderates over time and with subsequent physicochemical perturbation.

Published
2024
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16. Hyperbolicity of Alternating Links in Thickened Surfaces with Boundary

Author

Adams, Colin and Chen, Joye

Subjects
Mathematics - Geometric Topology, 57K32
Abstract

Let $F$ be a compact orientable surface with nonempty boundary other than a disk. Let $L$ be a link in $F \times I$ with a connected weakly prime cellular alternating projection to $F$. We provide simple conditions that determine exactly when $(F \times I) \setminus N(L)$ is hyperbolic. We also consider suitable embeddings of $F \times I$ in an ambient manifold $Y$ with boundary and provide conditions on links $L \subset F \times I$ which guarantee tg-hyperbolicity of $Y \setminus N(L)$. These results provide many examples of hyperbolic links in handlebodies and fiber bundles. It also provides many examples of staked links that are hyperbolic., Comment: 37 pages, 20 figures

Published
2023

17. Prior traumatic brain injury is a risk factor for in-hospital mortality in moderate to severe traumatic brain injury: a TRACK-TBI cohort study.

Author

Yue, John, Etemad, Leila, Elguindy, Mahmoud, van Essen, Thomas, Belton, Patrick, Nelson, Lindsay, McCrea, Michael, Vreeburg, Rick, Gotthardt, Christine, Tracey, Joye, Coskun, Bukre, Krishnan, Nishanth, Halabi, Cathra, Eagle, Shawn, Korley, Frederick, Robertson, Claudia, Duhaime, Ann-Christine, Satris, Gabriela, Tarapore, Phiroz, Huang, Michael, Madhok, Debbie, Giacino, Joseph, Mukherjee, Pratik, Yuh, Esther, Valadka, Alex, Puccio, Ava, Okonkwo, David, Sun, Xiaoying, Jain, Sonia, Manley, Geoffrey, DiGiorgio, Anthony, Badjatia, Neeraj, Barber, Jason, Bodien, Yelena, Fabian, Brian, Ferguson, Adam, Foreman, Brandon, Gardner, Raquel, Gopinath, Shankar, Grandhi, Ramesh, Russell Huie, J, Dirk Keene, C, Lingsma, Hester, MacDonald, Christine, Markowitz, Amy, Merchant, Randall, Ngwenya, Laura, Rodgers, Richard, Schneider, Andrea, Schnyer, David, Taylor, Sabrina, Temkin, Nancy, Torres-Espin, Abel, Vassar, Mary, Wang, Kevin, Wong, Justin, and Zafonte, Ross

Subjects
mortality, patient outcome assessment, risk factor, traumatic brain injury
Abstract

OBJECTIVES: An estimated 14-23% of patients with traumatic brain injury (TBI) incur multiple lifetime TBIs. The relationship between prior TBI and outcomes in patients with moderate to severe TBI (msTBI) is not well delineated. We examined the associations between prior TBI, in-hospital mortality, and outcomes up to 12 months after injury in a prospective US msTBI cohort. METHODS: Data from hospitalized subjects with Glasgow Coma Scale score of 3-12 were extracted from the Transforming Research and Clinical Knowledge in Traumatic Brain Injury Study (enrollment period: 2014-2019). Prior TBI with amnesia or alteration of consciousness was assessed using the Ohio State University TBI Identification Method. Competing risk regressions adjusting for age, sex, psychiatric history, cranial injury and extracranial injury severity examined the associations between prior TBI and in-hospital mortality, with hospital discharged alive as the competing risk. Adjusted HRs (aHR (95% CI)) were reported. Multivariable logistic regressions assessed the associations between prior TBI, mortality, and unfavorable outcome (Glasgow Outcome Scale-Extended score 1-3 (vs. 4-8)) at 3, 6, and 12 months after injury. RESULTS: Of 405 acute msTBI subjects, 21.5% had prior TBI, which was associated with male sex (87.4% vs. 77.0%, p=0.037) and psychiatric history (34.5% vs. 20.7%, p=0.010). In-hospital mortality was 10.1% (prior TBI: 17.2%, no prior TBI: 8.2%, p=0.025). Competing risk regressions indicated that prior TBI was associated with likelihood of in-hospital mortality (aHR=2.06 (1.01-4.22)), but not with hospital discharged alive. Prior TBI was not associated with mortality or unfavorable outcomes at 3, 6, and 12 months. CONCLUSIONS: After acute msTBI, prior TBI history is independently associated with in-hospital mortality but not with mortality or unfavorable outcomes within 12 months after injury. This selective association underscores the importance of collecting standardized prior TBI history data early after acute hospitalization to inform risk stratification. Prospective validation studies are needed. LEVEL OF EVIDENCE: IV. TRIAL REGISTRATION NUMBER: NCT02119182.

Published
2024

18. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, and Camila J. Mazzoni

Subjects
General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

Abstract A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.

Published
2024
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19. Hyperbolic knotoids

Author

Adams, Colin, Bonat, Alexandra, Chande, Maya, Chen, Joye, Jiang, Maxwell, Romrell, Zachary, Santiago, Daniel, Shapiro, Benjamin, and Woodruff, Dora

Published
2024
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20. Species-specific responses of marine bacteria to environmental perturbation.

Author

Peña-Montenegro, Tito, Kleindienst, Sara, Allen, Andrew, Eren, A, McCrow, John, Sánchez-Calderón, Juan, Arnold, Jonathan, and Joye, Samantha

Abstract

Environmental perturbations shape the structure and function of microbial communities. Oil spills are a major perturbation and resolving spills often requires active measures like dispersant application that can exacerbate the initial disturbance. Species-specific responses of microorganisms to oil and dispersant exposure during such perturbations remain largely unknown. We merged metatranscriptomic libraries with pangenomes to generate Core-Accessory Metatranscriptomes (CA-Metatranscriptomes) for two microbial hydrocarbon degraders that played important roles in the aftermath of the Deepwater Horizon oil spill. The Colwellia CA-Metatranscriptome illustrated pronounced dispersant-driven acceleration of core (~41%) and accessory gene (~59%) transcription, suggesting an opportunistic strategy. Marinobacter responded to oil exposure by expressing mainly accessory genes (~93%), suggesting an effective hydrocarbon-degrading lifestyle. The CA-Metatranscriptome approach offers a robust way to identify the underlying mechanisms of key microbial functions and highlights differences of specialist-vs-opportunistic responses to environmental disturbance.

Published
2023

21. Radiomics on slice-reduced versus full-chest computed tomography for diagnosis and staging of interstitial lung disease in systemic sclerosis: A comparative analysis

Author

Anja A. Joye, Marta Bogowicz, Janine Gote-Schniering, Thomas Frauenfelder, Matthias Guckenberger, Britta Maurer, Stephanie Tanadini-Lang, and Hubert S. Gabryś

Subjects
Systemic sclerosis, Interstitial lung disease, Slice-reduced computed tomography, Radiomics, Machine learning, Medical image analysis, Medical physics. Medical radiology. Nuclear medicine, R895-920
Abstract

Purpose: The purpose of this study was to evaluate the efficacy of radiomics derived from slice-reduced CT (srCT) scans versus full-chest CT (fcCT) for diagnosing and staging of interstitial lung disease (ILD) in systemic sclerosis (SSc), considering the potential to reduce radiation exposure. Material and methods: The fcCT corresponded to a standard high-resolution full-chest CT whereas the srCT consisted of nine axial slices. 1451 radiomic features in two dimensions from srCT and 1375 features in three dimensions from fcCT scans were extracted from 166 SSc patients. The study included first- and second-order features from original and wavelet-transformed images. We assessed the predictive performance of quantitative CT (qCT)-based logistic regression (LR) models relying on preselected features and machine learning workflows involving LR and extra-trees classifiers with data-driven feature selection. The area under the receiver operating characteristic curve (AUC) was used to estimate model performance. Results: The best models for diagnosis and staging ILD achieved AUC=0.85±0.08 and AUC=0.82±0.08 with srCT, and AUC=0.83±0.06 and AUC=0.76±0.08 with fcCT, respectively. srCT-based models showed slightly superior performance over fcCT-based models, particularly in 2D-radiomic analyses when interpolation resolution closely matched the original in-plane resolution. For diagnosis, the LR outperformed qCT-models, whereas for staging, the best results were obtained with a qCT-based model. Conclusions: Radiomics from srCT is an effective and preferable alternative to fcCT for diagnosing and staging SSc-ILD. This approach not only enhances predictive accuracy but also minimizes radiation exposure risks, offering a promising avenue for improved treatment decision support in SSc-ILD management.

Published
2024
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22. Clinical profile of patients with acute traumatic brain injury undergoing cranial surgery in the United States: report from the 18-centre TRACK-TBI cohort studyResearch in context

Author

John K. Yue, John H. Kanter, Jason K. Barber, Michael C. Huang, Thomas A. van Essen, Mahmoud M. Elguindy, Brandon Foreman, Frederick K. Korley, Patrick J. Belton, Dana Pisică, Young M. Lee, Ryan S. Kitagawa, Mary J. Vassar, Xiaoying Sun, Gabriela G. Satris, Justin C. Wong, Adam R. Ferguson, J. Russell Huie, Kevin K.W. Wang, Hansen Deng, Vincent Y. Wang, Yelena G. Bodien, Sabrina R. Taylor, Debbie Y. Madhok, Michael A. McCrea, Laura B. Ngwenya, Anthony M. DiGiorgio, Phiroz E. Tarapore, Murray B. Stein, Ava M. Puccio, Joseph T. Giacino, Ramon Diaz-Arrastia, Hester F. Lingsma, Pratik Mukherjee, Esther L. Yuh, Claudia S. Robertson, David K. Menon, Andrew I.R. Maas, Amy J. Markowitz, Sonia Jain, David O. Okonkwo, Nancy R. Temkin, Geoffrey T. Manley, Jason E. Chung, Bukre Coskun, Shawn R. Eagle, Leila L. Etemad, Brian Fabian, Feeser V. Ramana, Shankar Gopinath, Christine J. Gotthardt, Ramesh Grandhi, Sabah Hamidi, Ruchira M. Jha, Christopher Madden, Randall Merchant, Lindsay D. Nelson, Richard B. Rodgers, Andrea L.C. Schneider, David M. Schnyer, Abel Torres-Espin, Joye X. Tracey, Alex B. Valadka, and Ross D. Zafonte

Subjects
Decompressive craniectomy, Craniotomy, Glasgow outcome scale, Medical decisionmaking, Neuroimaging, Triage, Public aspects of medicine, RA1-1270
Abstract

Summary: Background: Contemporary surgical practices for traumatic brain injury (TBI) remain unclear. We describe the clinical profile of an 18-centre US TBI cohort with cranial surgery. Methods: The prospective, observational Transforming Research and Clinical Knowledge in Traumatic Brain Injury Study (2014–2018; ClinicalTrials.gov #NCT02119182) enrolled subjects who presented to trauma centre and received head computed tomography within 24-h (h) post-TBI. We performed a secondary data analysis in subjects aged ≥17-years with hospitalisation. Clinical characteristics, surgery type/timing, hospital and six-month outcomes were reported. Findings: Of 2032 subjects (age: mean = 41.4-years, range = 17–89-years; male = 71% female = 29%), 260 underwent cranial surgery, comprising 65% decompressive craniectomy, 23% craniotomy, 12% other surgery. Subjects with surgery (vs. without surgery) presented with worse neurological injury (median Glasgow Coma Scale = 6 vs. 15; midline shift ≥5 mm: 48% vs. 2%; cisternal effacement: 61% vs. 4%; p

Published
2024
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25. Exploring How Children with Reading Difficulties Respond to Instructional Supports in Literacy Games and the Role of Prior Knowledge

Author

Benton, Laura, Joye, Nelly, Sumner, Emma, Gauthier, Andrea, Ibrahim, Seray, and Vasalou, Asimina

Abstract

Digital literacy games can be beneficial for children with reading difficulties as a supplement to classroom instruction and an important feature of these games are the instructional supports, such as feedback. To be effective, feedback needs to build on prior instruction and match a learner's level of prior knowledge. However, there is limited research around the relationship between prior knowledge, instruction and feedback in the context of learning games. This paper presents an empirical study exploring the influence of prior knowledge on response to feedback, in two conditions: with or without instruction. Thirty-six primary children (age 8-11) with reading difficulties participated: each child was assessed for their prior knowledge of two suffix types--noun and adjective suffixes. They subsequently received additional instruction for one suffix type and then played two rounds of a literacy game--one round for each suffix type. Our analysis shows that prior knowledge predicted initial success rates and performance after a verbal hint differently, depending on whether instruction was provided. These results are discussed with regards to learning game feedback design and the impact on different types of knowledge involved in gameplay, as well as other game design elements that might support knowledge building during gameplay.

Published
2023
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26. The Adiabatic Wigner-Weisskopf Model

Author

Joye, Alain and Merkli, Marco

Subjects
Mathematical Physics, Quantum Physics, 81Q05
Abstract

We consider a slowly varying time dependent d-level atom interacting with a photon field. Restricted to the single excitation atom-field sector, the model is a time-dependent generalization of the Wigner-Weisskopf model describing spontaneous emission of an atomic excitation into the radiation field. We analyze the dynamics of the atom and of the radiation field in the adiabatic and small coupling approximations, in various regimes. In particular, starting with an excited atomic state, we provide a description of both the radiative decay of the atom and of the buildup of the photon excitation in the field.

Published
2022
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27. Hyperbolic Knotoids

Author

Adams, Colin, Bonat, Alexandra, Chande, Maya, Chen, Joye, Jiang, Maxwell, Romrell, Zachary, Santiago, Daniel, Shapiro, Benjamin, and Woodruff, Dora

Subjects
Mathematics - Geometric Topology, 57K12, 57K32
Abstract

In 2010, Turaev introduced knotoids as a variation on knots that replaces the embedding of a circle with the embedding of a closed interval with two endpoints. A variety of knot invariants have been extended to knotoids. Here we provide definitions of hyperbolicity for both spherical and planar knotoids. We prove that the product of hyperbolic spherical knotoids is hyperbolic and the volumes add. We also determine the least volume of a rational spherical knotoid and provide various classes of hyperbolic knotoids. We also include tables of hyperbolic volumes for both spherical and planar knotoids., Comment: 36 pages, 30 figures

Published
2022

28. Generalizations of Knotoids and Spatial Graphs

Author

Adams, Colin, Bonat, Alexandra, Chande, Maya, Chen, Joye, Jiang, Maxwell, Romrell, Zachary, Santiago, Daniel, Shapiro, Benjamin, and Woodruff, Dora

Subjects
Mathematics - Geometric Topology, 57K12, 57K32
Abstract

In 2010, Turaev introduced knotoids as a variation on knots that replaces the embedding of a circle with the embedding of a closed interval with two endpoints which here we call poles. We define generalized knotoids to allow arbitrarily many poles, intervals, and circles, each pole corresponding to any number of interval endpoints, including zero. This theory subsumes a variety of other related topological objects and introduces some particularly interesting new cases. We explore various analogs of knotoid invariants, including height, index polynomials, bracket polynomials and hyperbolicity. We further generalize to knotoidal graphs, which are a natural extension of spatial graphs that allow both poles and vertices., Comment: 43 pages, 22 figures

Published
2022

31. The effect of sprouted wheat wholemeal inclusion in bread recipes on postprandial blood glucose and satiety responses in healthy adults: a randomized trial

Author

Wei Cao, Amy Tucker, Allison Hoang, Reihaneh Abdi, Amanda Wright, and Iris J. Joye

Subjects
Sprouted wheat, Bread, Blood glucose response, Satiety response, Sensory quality, Nutrition. Foods and food supply, TX341-641
Abstract

Sprouted wheat wholemeal was reported to enhance the nutritional and sensory properties of cereal products, but few human studies exist. The effect of blending 50 % sprouted wheat wholemeal in a bread recipe on the postprandial glycemic and satiety responses, and sensory-related sensations was investigated in this randomized crossover human study with 12 healthy participants. Capillary blood samples were collected and glycemic response was determined at 0, 15, 30, 45, 60, 90, 120 min. Satiety visual analogue scales were given every 30 min. While substituting bread wheat flour with sprouted wheat wholemeal significantly increased the α-amylase activity in the dough (p 0.05). Likewise, participant overall acceptability was not adversely affected. Sprouted wheat wholemeal can be used as a functional ingredient in breadmaking, although it did not, in this study, significantly affect digestibility parameters.

Published
2024
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36. Clinical profile of patients with acute traumatic brain injury undergoing cranial surgery in the United States: report from the 18-centre TRACK-TBI cohort study

Author

Chung, Jason E., Coskun, Bukre, Eagle, Shawn R., Etemad, Leila L., Fabian, Brian, Ramana, Feeser V., Gopinath, Shankar, Gotthardt, Christine J., Grandhi, Ramesh, Hamidi, Sabah, Jha, Ruchira M., Madden, Christopher, Merchant, Randall, Nelson, Lindsay D., Rodgers, Richard B., Schneider, Andrea L.C., Schnyer, David M., Torres-Espin, Abel, Tracey, Joye X., Valadka, Alex B., Zafonte, Ross D., Yue, John K., Kanter, John H., Barber, Jason K., Huang, Michael C., van Essen, Thomas A., Elguindy, Mahmoud M., Foreman, Brandon, Korley, Frederick K., Belton, Patrick J., Pisică, Dana, Lee, Young M., Kitagawa, Ryan S., Vassar, Mary J., Sun, Xiaoying, Satris, Gabriela G., Wong, Justin C., Ferguson, Adam R., Huie, J. Russell, Wang, Kevin K.W., Deng, Hansen, Wang, Vincent Y., Bodien, Yelena G., Taylor, Sabrina R., Madhok, Debbie Y., McCrea, Michael A., Ngwenya, Laura B., DiGiorgio, Anthony M., Tarapore, Phiroz E., Stein, Murray B., Puccio, Ava M., Giacino, Joseph T., Diaz-Arrastia, Ramon, Lingsma, Hester F., Mukherjee, Pratik, Yuh, Esther L., Robertson, Claudia S., Menon, David K., Maas, Andrew I.R., Markowitz, Amy J., Jain, Sonia, Okonkwo, David O., Temkin, Nancy R., and Manley, Geoffrey T.

Published
2024
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41. SGD-OD: investigating the potential oxygen demand of submarine groundwater discharge in coastal systems

Author

Willard S. Moore, Claudia Benitez-Nelson, Charles Schutte, Amy Moody, Alan Shiller, Ryan J. Sibert, and Samantha Joye

Subjects
Medicine, Science
Abstract

Abstract Submarine groundwater discharge (SGD) supplies nutrients, carbon, metals, and radionuclide tracers to estuarine and coastal waters. One aspect of SGD that is poorly recognized is its direct effect on dissolved oxygen (DO) demand in receiving waters, denoted here as SGD-OD. Sulfate-mediated oxidation of organic matter in salty coastal aquifers produces numerous reduced byproducts including sulfide, ammonia, dissolved organic carbon and nitrogen, methane, and reduced metals. When these byproducts are introduced to estuarine and coastal systems by SGD and are oxidized, they may substantially reduce the DO concentration in receiving waters and impact organisms living there. We consider six estuarine and coastal sites where SGD derived fluxes of reduced byproducts are well documented. Using data from these sites we present a semiquantitative model to estimate the effect of these byproducts on DO in the receiving waters. Without continued aeration with atmospheric oxygen, the study sites would have experienced periodic hypoxic conditions due to SGD-OD. The presence of H2S supplied by SGD could also impact organisms. This process is likely prevalent in other systems worldwide.

Published
2024
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42. IL-15-secreting CAR natural killer cells directed toward the pan-cancer target CD70 eliminate both cancer cells and cancer-associated fibroblasts

Author

Astrid Van den Eynde, Laura Gehrcken, Tias Verhezen, Ho Wa Lau, Christophe Hermans, Hilde Lambrechts, Tal Flieswasser, Delphine Quatannens, Gils Roex, Karen Zwaenepoel, Elly Marcq, Philippe Joye, Edgar Cardenas De La Hoz, Christophe Deben, Alessia Gasparini, Pierre Montay-Gruel, Maxim Le Compte, Eva Lion, Filip Lardon, Steven Van Laere, Vasiliki Siozopoulou, Diana Campillo-Davo, Jorrit De Waele, Patrick Pauwels, Julie Jacobs, Evelien Smits, and Jonas R. M. Van Audenaerde

Subjects
Diseases of the blood and blood-forming organs, RC633-647.5, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background It remains challenging to obtain positive outcomes with chimeric antigen receptor (CAR)-engineered cell therapies in solid malignancies, like colorectal cancer (CRC) and pancreatic ductal adenocarcinoma (PDAC). A major obstacle is the lack of targetable surface antigens that are not shared by healthy tissues. CD70 emerges as interesting target, due to its stringent expression pattern in healthy tissue and its apparent role in tumor progression in a considerable amount of malignancies. Moreover, CD70 is also expressed on cancer-associated fibroblasts (CAFs), another roadblock for treatment efficacy in CRC and PDAC. We explored the therapeutic potential of CD70 as target for CAR natural killer (NK) cell therapy in CRC, PDAC, focusing on tumor cells and CAFs, and lymphoma. Methods RNA-seq data and immunohistochemical analysis of patient samples were used to explore CD70 expression in CRC and PDAC patients. In addition, CD70-targeting CAR NK cells were developed to assess cytotoxic activity against CD70+ tumor cells and CAFs, and the effect of cytokine stimulation on their efficacy was evaluated. The in vitro functionality of CD70-CAR NK cells was investigated against a panel of tumor and CAF cell lines with varying CD70 expression. Lymphoma-bearing mice were used to validate in vivo potency of CD70-CAR NK cells. Lastly, to consider patient variability, CD70-CAR NK cells were tested on patient-derived organoids containing CAFs. Results In this study, we identified CD70 as a target for tumor cells and CAFs in CRC and PDAC patients. Functional evaluation of CD70-directed CAR NK cells indicated that IL-15 stimulation is essential to obtain effective elimination of CD70+ tumor cells and CAFs, and to improve tumor burden and survival of mice bearing CD70+ tumors. Mechanistically, IL-15 stimulation resulted in improved potency of CD70-CAR NK cells by upregulating CAR expression and increasing secretion of pro-inflammatory cytokines, in a mainly autocrine or intracellular manner. Conclusions We disclose CD70 as an attractive target both in hematological and solid tumors. IL-15 armored CAR NK cells act as potent effectors to eliminate these CD70+ cells. They can target both tumor cells and CAFs in patients with CRC and PDAC, and potentially other desmoplastic solid tumors.

Published
2024
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43. Administering Nitric Oxide (NO) with High Flow Nasal Cannulas: A Simple Method

Author

Vladimir L. Cousin, Raphael Joye, and Angelo Polito

Subjects
nitric oxide, pediatric intensive care unit, pulmonary hypertension, high-flow nasal cannula, Diseases of the respiratory system, RC705-779, Medicine (General), R5-920
Abstract

Inhaled nitric oxide (iNO) is a pulmonary vasodilator that plays an important clinical ICU role. The administration of iNO is usually performed through an endotracheal tube, but spontaneously breathing patients might also benefit from iNO administration. The use of the non-invasive administration of iNO through high-flow nasal cannula (HFNC) allows for NO delivery in spontaneously breathing patients who still need supplemental oxygen and positive airway pressure. A simple method to administer NO through HFNC is described here using standard commercially available NO administration and HFNC.

Published
2024
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44. Markovian Repeated Interaction Quantum Systems

Author

Bougron, Jean-François, Joye, Alain, and Pillet, Claude-Alain

Subjects
Mathematical Physics, Condensed Matter - Statistical Mechanics, Quantum Physics
Abstract

We study a class of dynamical semigroups $(\mathbb{L}^n)_{n\in\mathbb{N}}$ that emerge, by a Feynman--Kac type formalism, from a random quantum dynamical system $(\mathcal{L}_{\omega_n}\circ\cdots\circ\mathcal{L}_{\omega_1}(\rho_{\omega_0}))_{n\in\mathbb{N}}$ driven by a Markov chain $(\omega_n)_{n\in\mathbb{N}}$. We show that the almost sure large time behavior of the system can be extracted from the large $n$ asymptotics of the semigroup, which is in turn directly related to the spectral properties of the generator $\mathbb{L}$. As a physical application, we consider the case where the $\mathcal{L}_\omega$'s are the reduced dynamical maps describing the repeated interactions of a system $\mathcal{S}$ with thermal probes $\mathcal{C}_\omega$. We study the full statistics of the entropy in this system and derive a fluctuation theorem for the heat exchanges and the associated linear response formulas.

Published
2022
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48. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, and Camila J. Mazzoni

Subjects
General. Including nature conservation, geographical distribution, QH1-199.5
Published
2024
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50. Prior traumatic brain injury is a risk factor for in-hospital mortality in moderate to severe traumatic brain injury: a TRACK-TBI cohort study

Author

Hester F Lingsma, Ramesh Grandhi, Amy J Markowitz, Debbie Y Madhok, Geoffrey T Manley, Jason Barber, Xiaoying Sun, Michael A McCrea, Kevin K W Wang, Lindsay D Nelson, Pratik Mukherjee, Neeraj Badjatia, Ava M Puccio, David O Okonkwo, Patrick J Belton, Sonia Jain, Nancy R Temkin, Cathra Halabi, Richard B Rodgers, Andrea L C Schneider, Shawn R Eagle, Shankar Gopinath, Randall Merchant, Ross D Zafonte, Raquel C Gardner, John K Yue, Leila L Etemad, Mahmoud M Elguindy, Thomas A van Essen, Rick J G Vreeburg, Christine J Gotthardt, Joye X Tracey, Bukre C Coskun, Nishanth Krishnan, Frederick K Korley, Claudia S Robertson, Ann-Christine Duhaime, Gabriela G Satris, Phiroz E Tarapore, Michael C Huang, Joseph T Giacino, Esther L Yuh, Alex B Valadka, Anthony M DiGiorgio, Yelena G Bodien, Brian Fabian, Adam R Ferguson, Brandon Foreman, J Russell Huie, C Dirk Keene, Christine L MacDonald, Laura B Ngwenya, David M Schnyer, Sabrina R Taylor, Abel Torres-Espin, Mary J Vassar, and Justin C Wong

Subjects
Surgery, RD1-811, Medical emergencies. Critical care. Intensive care. First aid, RC86-88.9
Abstract

Objectives An estimated 14–23% of patients with traumatic brain injury (TBI) incur multiple lifetime TBIs. The relationship between prior TBI and outcomes in patients with moderate to severe TBI (msTBI) is not well delineated. We examined the associations between prior TBI, in-hospital mortality, and outcomes up to 12 months after injury in a prospective US msTBI cohort.Methods Data from hospitalized subjects with Glasgow Coma Scale score of 3–12 were extracted from the Transforming Research and Clinical Knowledge in Traumatic Brain Injury Study (enrollment period: 2014–2019). Prior TBI with amnesia or alteration of consciousness was assessed using the Ohio State University TBI Identification Method. Competing risk regressions adjusting for age, sex, psychiatric history, cranial injury and extracranial injury severity examined the associations between prior TBI and in-hospital mortality, with hospital discharged alive as the competing risk. Adjusted HRs (aHR (95% CI)) were reported. Multivariable logistic regressions assessed the associations between prior TBI, mortality, and unfavorable outcome (Glasgow Outcome Scale-Extended score 1–3 (vs. 4–8)) at 3, 6, and 12 months after injury.Results Of 405 acute msTBI subjects, 21.5% had prior TBI, which was associated with male sex (87.4% vs. 77.0%, p=0.037) and psychiatric history (34.5% vs. 20.7%, p=0.010). In-hospital mortality was 10.1% (prior TBI: 17.2%, no prior TBI: 8.2%, p=0.025). Competing risk regressions indicated that prior TBI was associated with likelihood of in-hospital mortality (aHR=2.06 (1.01–4.22)), but not with hospital discharged alive. Prior TBI was not associated with mortality or unfavorable outcomes at 3, 6, and 12 months.Conclusions After acute msTBI, prior TBI history is independently associated with in-hospital mortality but not with mortality or unfavorable outcomes within 12 months after injury. This selective association underscores the importance of collecting standardized prior TBI history data early after acute hospitalization to inform risk stratification. Prospective validation studies are needed.Level of evidence IV.Trial registration number NCT02119182.

Published
2024
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