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19,034 results on '"A, Bron"'

1. The Explabox: Model-Agnostic Machine Learning Transparency & Analysis

Author

Robeer, Marcel, Bron, Michiel, Herrewijnen, Elize, Hoeseni, Riwish, and Bex, Floris

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Computer Science - Software Engineering, I.2, D.2.5
Abstract

We present the Explabox: an open-source toolkit for transparent and responsible machine learning (ML) model development and usage. Explabox aids in achieving explainable, fair and robust models by employing a four-step strategy: explore, examine, explain and expose. These steps offer model-agnostic analyses that transform complex 'ingestibles' (models and data) into interpretable 'digestibles'. The toolkit encompasses digestibles for descriptive statistics, performance metrics, model behavior explanations (local and global), and robustness, security, and fairness assessments. Implemented in Python, Explabox supports multiple interaction modes and builds on open-source packages. It empowers model developers and testers to operationalize explainability, fairness, auditability, and security. The initial release focuses on text data and models, with plans for expansion. Explabox's code and documentation are available open-source at https://explabox.readthedocs.io/., Comment: 5 pages, 3 figures

Published
2024

2. Examining the Effect of Problem-Based Learning Approach on Learners' Mathematical Creativity: A Meta-Analysis

Author

Joseph F. Bron and Maricar S. Prudente

Abstract

Problem-based learning (PBL) is linked to developing learners' creative thinking in mathematics. This process-oriented approach capitalizes on using problems to stimulate learning through independent and collaborative investigations. This meta-analysis looked at the effectiveness of using PBL to influence mathematical creativity. Fifteen results from 13 studies were analyzed in which a medium effect (g=0.580) was computed using the random effects model. Further, the analysis of heterogeneity statistics suggests conducting a subgroup analysis in which only the strategy used in the comparison group and educational level, among the identified characteristics, moderates the effect of PBL on mathematical creativity. Future research should expand geographically to encompass a more diverse educational landscape and include a broader demographic to validate the efficacy of PBL across different age groups and cultural contexts.

Published
2024

3. Toward a robust physical and chemical characterization of heterogeneous lines of sight: The case of the Horsehead nebula

Author

Ségal, Léontine, Roueff, Antoine, Pety, Jérôme, Gerin, Maryvonne, Roueff, Evelyne, Goicoechea, R. Javier, Bešlic, Ivana, Coud'e, Simon, Einig, Lucas, Mazurek, Helena, Orkisz, H. Jan, Palud, Pierre, Santa-Maria, G. Miriam, Zakardjian, Antoine, Bardeau, S'ebastien, Bron, Emeric, Chainais, Pierre, Demyk, Karine, Magalhaes, Victor de Souza, Gratier, Pierre, Guzman, V. Viviana, Hughes, Annie, Languignon, David, Levrier, François, Bourlot, Jacques Le, Petit, Franck Le, Lis, C. Dariusz, Liszt, S. Harvey, Peretto, Nicolas, Sievers, Albrecht, and Thouvenin, Pierre-Antoine

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

Dense cold molecular cores/filaments are surrounded by an envelope of translucent gas. Some of the low-J emission lines of CO and HCO$^+$ isotopologues are more sensitive to the conditions either in the translucent environment or in the dense cold one. We propose a cloud model composed of three homogeneous slabs of gas along each line of sight (LoS), representing an envelope and a shielded inner layer. IRAM-30m data from the ORION-B large program toward the Horsehead nebula are used to demonstrate the method's capability. We use the non-LTE radiative transfer code RADEX to model the line profiles from the kinetic temperature $T_{kin}$, the volume density $n_{H_2}$, kinematics and chemical properties of the different layers. We then use a maximum likelihood estimator to simultaneously fit the lines of the CO and HCO$^+$ isotopologues. We constrain column density ratios to limit the variance on the estimates. This simple heterogeneous model provides good fits of the fitted lines over a large part of the cloud. The decomposition of the intensity into three layers allows to discuss the distribution of the estimated physical/chemical properties along the LoS. About 80$\%$ the CO integrated intensity comes from the envelope, while $\sim55\%$ of that of the (1-0) and (2-1) lines of C$^{18}$O comes from the inner layer. The $N(^{13}CO)/N(C^{18}O)$ in the envelope increases with decreasing $A_v$, and reaches $25$ in the pillar outskirts. The envelope $T_{kin}$ varies from 25 to 40 K, that of the inner layer drops to $\sim 15$ K in the western dense core. The inner layer $n_{H_2}$ is $\sim 3\times10^4\,\text{cm}^{-3}$ toward the filament and it increases by a factor $10$ toward dense cores. The proposed method correctly retrieves the physical/chemical properties of the Horsehead nebula and offers promising prospects for less supervised model fits of wider-field datasets.

Published
2024

4. MRI-based and metabolomics-based age scores act synergetically for mortality prediction shown by multi-cohort federated learning

Author

Mateus, Pedro, Garst, Swier, Yu, Jing, Cats, Davy, Harms, Alexander G. J., Birhanu, Mahlet, Beekman, Marian, Slagboom, P. Eline, Reinders, Marcel, van der Grond, Jeroen, Dekker, Andre, Jansen, Jacobus F. A., Beran, Magdalena, Schram, Miranda T., Visser, Pieter Jelle, Moonen, Justine, Ghanbari, Mohsen, Roshchupkin, Gennady, Vojinovic, Dina, Bermejo, Inigo, Mei, Hailiang, and Bron, Esther E.

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Machine Learning, I.2.1
Abstract

Biological age scores are an emerging tool to characterize aging by estimating chronological age based on physiological biomarkers. Various scores have shown associations with aging-related outcomes. This study assessed the relation between an age score based on brain MRI images (BrainAge) and an age score based on metabolomic biomarkers (MetaboAge). We trained a federated deep learning model to estimate BrainAge in three cohorts. The federated BrainAge model yielded significantly lower error for age prediction across the cohorts than locally trained models. Harmonizing the age interval between cohorts further improved BrainAge accuracy. Subsequently, we compared BrainAge with MetaboAge using federated association and survival analyses. The results showed a small association between BrainAge and MetaboAge as well as a higher predictive value for the time to mortality of both scores combined than for the individual scores. Hence, our study suggests that both aging scores capture different aspects of the aging process.

Published
2024

5. Quantifying the informativity of emission lines to infer physical conditions in giant molecular clouds. I. Application to model predictions

Author

Einig, Lucas, Palud, Pierre, Roueff, Antoine, Pety, Jérôme, Bron, Emeric, Petit, Franck Le, Gerin, Maryvonne, Chanussot, Jocelyn, Chainais, Pierre, Thouvenin, Pierre-Antoine, Languignon, David, Bešlić, Ivana, Coudé, Simon, Mazurek, Helena, Orkisz, Jan H., Santa-Maria, Miriam G., Ségal, Léontine, Zakardjian, Antoine, Bardeau, Sébastien, Demyk, Karine, Magalhães, Victor de Souza, Goicoechea, Javier R., Gratier, Pierre, Guzmán, Viviana V., Hughes, Annie, Levrier, François, Bourlot, Jacques Le, Lis, Dariusz C., Liszt, Harvey S., Peretto, Nicolas, Roueff, Evelyne, and Sievers, Albrecht

Subjects
Astrophysics - Astrophysics of Galaxies, Statistics - Applications
Abstract

Observations of ionic, atomic, or molecular lines are performed to improve our understanding of the interstellar medium (ISM). However, the potential of a line to constrain the physical conditions of the ISM is difficult to assess quantitatively, because of the complexity of the ISM physics. The situation is even more complex when trying to assess which combinations of lines are the most useful. Therefore, observation campaigns usually try to observe as many lines as possible for as much time as possible. We search for a quantitative statistical criterion to evaluate the constraining power of a (or combination of) tracer(s) with respect to physical conditions in order to improve our understanding of the statistical relationships between ISM tracers and physical conditions and helps observers to motivate their observation proposals. The best tracers are obtained by comparing the mutual information between a physical parameter and different sets of lines. We apply this method to simulations of radio molecular lines emitted by a photodissociation region similar to the Horsehead Nebula that would be observed at the IRAM 30m telescope. We search for the best lines to constrain the visual extinction $A_v^{tot}$ or the far UV illumination $G_0$. The most informative lines change with the physical regime (e.g., cloud extinction). Short integration time of the CO isotopologue $J=1-0$ lines already yields much information on the total column density most regimes. The best set of lines to constrain the visual extinction does not necessarily combine the most informative individual lines. Precise constraints on $G_0$ are more difficult to achieve with molecular lines. They require spectral lines emitted at the cloud surface (e.g., [CII] and [CI] lines). This approach allows one to better explore the knowledge provided by ISM codes, and to guide future observation campaigns.

Published
2024
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6. PDRs4All. X. ALMA and JWST detection of neutral carbon in the externally irradiated disk d203-506: Undepleted gas-phase carbon

Author

Goicoechea, Javier R., Bourlot, J. Le, Black, J. H., Alarcón, F., Bergin, E. A., Berné, O., Bron, E., Canin, A., Chapillon, E., Chown, R., Dartois, E., Gerin, M., Habart, E., Haworth, T. J., Joblin, C., Kannavou, O., Petit, F. Le, Onaka, T., Peeters, E., Pety, J., Roueff, E., Sidhu, A., Schroetter, I., Tabone, B., Tielens, A. G. G. M., Trahin, B., Van De Putte, D., Vicente, S., and Zannese, M.

Subjects
Astrophysics - Astrophysics of Galaxies, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics
Abstract

The gas-phase abundance of carbon, x_C = C/H, and its depletion factors are essential parameters for understanding the gas and solid compositions that are ultimately incorporated into planets. The majority of protoplanetary disks are born in clusters and, as a result, are exposed to external FUV radiation. These FUV photons potentially affect the disk's evolution, chemical composition, and line excitation. We present the first detection of the [CI]609um fine-structure line of neutral carbon (CI), achieved with ALMA, toward one of these disks, d203-506, in the Orion Nebula Cluster. We also report the detection of CI forbidden and permitted lines (from electronically excited states up to 10 eV) observed with JWST in the IR. These lines trace the irradiated outer disk and photo-evaporative wind. Contrary to the common belief that these IR lines are C+ recombination lines, we find that they are dominated by FUV-pumping of CI followed by fluorescence cascades. They trace the transition from atomic to molecular gas, and their intensities scale with G0. The lack of outstanding IR OI fluorescent emission, however, implies a sharper attenuation of external FUV radiation with E > 12 eV (~Lyman-beta). This is related to a lower effective FUV dust absorption cross section compared to that of interstellar grains, implying a more prominent role for FUV shielding by the CI photoionization continuum. The [CI]609um intensity is proportional to N(CI) and can be used to infer x_C. We derive x_C ~ 1.4E-4. This implies that there is no major depletion of volatile carbon compared to x_C measured in the natal cloud, hinting at a young disk. We also show that external FUV radiation impacts the outer disk and wind by vertically shifting the water freeze-out depth, which results in less efficient grain growth and settling. This shift leads to nearly solar gas-phase C/O abundance ratios in these irradiated layers., Comment: Accepted for publication in A&A Letters. 14 pages including Appendices

Published
2024
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7. Evaluating the Fairness of Neural Collapse in Medical Image Classification

Author

Mouheb, Kaouther, Elbatel, Marawan, Klein, Stefan, and Bron, Esther E.

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Deep learning has achieved impressive performance across various medical imaging tasks. However, its inherent bias against specific groups hinders its clinical applicability in equitable healthcare systems. A recently discovered phenomenon, Neural Collapse (NC), has shown potential in improving the generalization of state-of-the-art deep learning models. Nonetheless, its implications on bias in medical imaging remain unexplored. Our study investigates deep learning fairness through the lens of NC. We analyze the training dynamics of models as they approach NC when training using biased datasets, and examine the subsequent impact on test performance, specifically focusing on label bias. We find that biased training initially results in different NC configurations across subgroups, before converging to a final NC solution by memorizing all data samples. Through extensive experiments on three medical imaging datasets -- PAPILA, HAM10000, and CheXpert -- we find that in biased settings, NC can lead to a significant drop in F1 score across all subgroups. Our code is available at https://gitlab.com/radiology/neuro/neural-collapse-fairness

Published
2024
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8. PDRs4All IX. Sulfur elemental abundance in the Orion Bar

Author

Fuente, Asunción, Roueff, Evelyne, Petit, Franck Le, Bourlot, Jacques Le, Bron, Emeric, Wolfire, Mark G., Babb, James F., Yan, Pei-Gen, Onaka, Takashi, Black, John H., Schroetter, Ilane, Van De Putte, Dries, Sidhu, Ameek, Canin, Amélie, Trahin, Boris, Alarcón, Felipe, Chown, Ryan, Kannavou, Olga, Berné, Olivier, Habart, Emilie, Peeters, Els, Goicoechea, Javier R., Zannese, Marion, Meshaka, Raphael, Okada, Yoko, Röllig, Markus, Gal, Romane Le, Sales, Dinalva A., Palumbo, Maria Elisabetta, Baratta, Giuseppe Antonio, Madden, Suzanne C., Neelamkodan, Naslim, Zhang, Ziwei E., and Stancil, P. C.

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

One of the main problems in astrochemistry is determining the amount of sulfur in volatiles and refractories in the interstellar medium. The detection of the main sulfur reservoirs (icy H$_2$S and atomic gas) has been challenging, and estimates are based on the reliability of models to account for the abundances of species containing less than 1% of the total sulfur. The high sensitivity of the James Webb Space Telescope provides an unprecedented opportunity to estimate the sulfur abundance through the observation of the [S I] 25.249 $\mu$m line. We used the [S III] 18.7 $\mu$m, [S IV] 10.5 $\mu$m, and [S l] 25.249 $\mu$m lines to estimate the amount of sulfur in the ionized and molecular gas along the Orion Bar. For the theoretical part, we used an upgraded version of the Meudon photodissociation region (PDR) code to model the observations. New inelastic collision rates of neutral atomic sulfur with ortho- and para- molecular hydrogen were calculated to predict the line intensities. The [S III] 18.7 $\mu$m and [S IV] 10.5 $\mu$m lines are detected over the imaged region with a shallow increase (by a factor of 4) toward the HII region. We estimate a moderate sulfur depletion, by a factor of $\sim$2, in the ionized gas. The corrugated interface between the molecular and atomic phases gives rise to several edge-on dissociation fronts we refer to as DF1, DF2, and DF3. The [S l] 25.249 $\mu$m line is only detected toward DF2 and DF3, the dissociation fronts located farthest from the HII region. The detailed modeling of DF3 using the Meudon PDR code shows that the emission of the [S l] 25.249 $\mu$m line is coming from warm ($>$ 40 K) molecular gas located at A$_{\rm V}$ $\sim$ 1$-$5 mag from the ionization front. Moreover, the intensity of the [S l] 25.249 $\mu$m line is only accounted for if we assume the presence of undepleted sulfur., Comment: 16 pages, 6 figures. Accepted for publication in Astronomy and Astrophysics

Published
2024

9. PDRs4All VIII: Mid-IR emission line inventory of the Orion Bar

Author

Van De Putte, Dries, Meshaka, Raphael, Trahin, Boris, Habart, Emilie, Peeters, Els, Berné, Olivier, Alarcón, Felipe, Canin, Amélie, Chown, Ryan, Schroetter, Ilane, Sidhu, Ameek, Boersma, Christiaan, Bron, Emeric, Dartois, Emmanuel, Goicoechea, Javier R., Gordon, Karl D., Onaka, Takashi, Tielens, Alexander G. G. M., Verstraete, Laurent, Wolfire, Mark G., Abergel, Alain, Bergin, Edwin A., Bernard-Salas, Jeronimo, Cami, Jan, Cuadrado, Sara, Dicken, Daniel, Elyajouri, Meriem, Fuente, Asunción, Joblin, Christine, Khan, Baria, Lacinbala, Ozan, Languignon, David, Gal, Romane Le, Maragkoudakis, Alexandros, Okada, Yoko, Pasquini, Sofia, Pound, Marc W., Robberto, Massimo, Röllig, Markus, Schefter, Bethany, Schirmer, Thiébaut, Tabone, Benoit, Vicente, Sílvia, Zannese, Marion, Colgan, Sean W. J., He, Jinhua, Rouillé, Gaël, Togi, Aditya, Aleman, Isabel, Auchettl, Rebecca, Baratta, Giuseppe Antonio, Bejaoui, Salma, Bera, Partha P., Black, John H., Boulanger, Francois, Bouwman, Jordy, Brandl, Bernhard, Brechignac, Philippe, Brünken, Sandra, Buragohain, Mridusmita, Burkhardt, Andrew, Candian, Alessandra, Cazaux, Stéphanie, Cernicharo, Jose, Chabot, Marin, Chakraborty, Shubhadip, Champion, Jason, Cooke, Ilsa R., Coutens, Audrey, Cox, Nick L. J., Demyk, Karine, Meyer, Jennifer Donovan, Foschino, Sacha, García-Lario, Pedro, Gerin, Maryvonne, Gottlieb, Carl A., Guillard, Pierre, Gusdorf, Antoine, Hartigan, Patrick, Herbst, Eric, Hornekaer, Liv, Issa, Lina, Jäger, Cornelia, Janot-Pacheco, Eduardo, Kannavou, Olga, Kaufman, Michael, Kemper, Francisca, Kendrew, Sarah, Kirsanova, Maria S., Klaassen, Pamela, Kwok, Sun, Labiano, Álvaro, Lai, Thomas S. -Y., Floch, Bertrand Le, Petit, Franck Le, Li, Aigen, Linz, Hendrik, Mackie, Cameron J., Madden, Suzanne C., Mascetti, Joëlle, McGuire, Brett A., Merino, Pablo, Micelotta, Elisabetta R., Morse, Jon A., Mulas, Giacomo, Neelamkodan, Naslim, Ohsawa, Ryou, Omont, Alain, Paladini, Roberta, Palumbo, Maria Elisabetta, Pathak, Amit, Pendleton, Yvonne J., Petrignani, Annemieke, Pino, Thomas, Puga, Elena, Rangwala, Naseem, Rapacioli, Mathias, Rho, Jeonghee, Ricca, Alessandra, Roman-Duval, Julia, Roser, Joseph, Roueff, Evelyne, Salama, Farid, Sales, Dinalva A., Sandstrom, Karin, Sarre, Peter, Sciamma-O'Brien, Ella, Sellgren, Kris, Shenoy, Sachindev S., Teyssier, David, Thomas, Richard D., Witt, Adolf N., Wootten, Alwyn, Ysard, Nathalie, Zettergren, Henning, Zhang, Yong, Zhang, Ziwei E., and Zhen, Junfeng

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

Mid-infrared emission features probe the properties of ionized gas, and hot or warm molecular gas. The Orion Bar is a frequently studied photodissociation region (PDR) containing large amounts of gas under these conditions, and was observed with the MIRI IFU aboard JWST as part of the "PDRs4All" program. The resulting IR spectroscopic images of high angular resolution (0.2") reveal a rich observational inventory of mid-IR emission lines, and spatially resolve the substructure of the PDR, with a mosaic cutting perpendicularly across the ionization front and three dissociation fronts. We extracted five spectra that represent the ionized, atomic, and molecular gas layers, and measured the most prominent gas emission lines. An initial analysis summarizes the physical conditions of the gas and the potential of these data. We identified around 100 lines, report an additional 18 lines that remain unidentified, and measured the line intensities and central wavelengths. The H I recombination lines originating from the ionized gas layer bordering the PDR, have intensity ratios that are well matched by emissivity coefficients from H recombination theory, but deviate up to 10% due contamination by He I lines. We report the observed emission lines of various ionization stages of Ne, P, S, Cl, Ar, Fe, and Ni, and show how certain line ratios vary between the five regions. We observe the pure-rotational H$_2$ lines in the vibrational ground state from 0-0 S(1) to 0-0 S(8), and in the first vibrationally excited state from 1-1 S(5) to 1-1 S(9). We derive H$_2$ excitation diagrams, and approximate the excitation with one thermal (~700 K) component representative of an average gas temperature, and one non-thermal component (~2700 K) probing the effect of UV pumping. We compare these results to an existing model for the Orion Bar PDR and highlight the differences with the observations., Comment: 26 pages, 12 figures, 3 tables. Submitted to A&A, under review (1st revision)

Published
2024
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10. Using Chao's Estimator as a Stopping Criterion for Technology-Assisted Review

Author

Bron, Michiel P., van der Heijden, Peter G. M., Feelders, Ad J., and Siebes, Arno P. J. M.

Subjects
Computer Science - Information Retrieval
Abstract

Technology-Assisted Review (TAR) aims to reduce the human effort required for screening processes such as abstract screening for systematic literature reviews. Human reviewers label documents as relevant or irrelevant during this process, while the system incrementally updates a prediction model based on the reviewers' previous decisions. After each model update, the system proposes new documents it deems relevant, to prioritize relevant documentsover irrelevant ones. A stopping criterion is necessary to guide users in stopping the review process to minimize the number of missed relevant documents and the number of read irrelevant documents. In this paper, we propose and evaluate a new ensemble-based Active Learning strategy and a stopping criterion based on Chao's Population Size Estimator that estimates the prevalence of relevant documents in the dataset. Our simulation study demonstrates that this criterion performs well on several datasets and is compared to other methods presented in the literature.

Published
2024

11. Bias versus variance when fitting multi-species molecular lines with a non-LTE radiative transfer model

Author

Roueff, Antoine, Pety, Jérôme, Gerin, Maryvonne, Ségal, Léontine, Goicoechea, Javier, Liszt, Harvey, Gratier, Pierre, Bešlić, Ivana, Einig, Lucas, Gaudel, M., Orkisz, Jan, Palud, Pierre, Santa-Maria, Miriam, Magalhaes, Victor de Souza, Zakardjian, Antoine, Bardeau, Sebastien, Bron, Emeric E., Chainais, Pierre, Coudé, Simon, Demyk, Karine, Veloso, Viviana Guzman, Hughes, Annie, Languignon, David, Levrier, François, Lis, Dariusz C, Bourlot, Jacques Le, Petit, Franck Le, Peretto, Nicolas, Roueff, Evelyne, Sievers, Albrecht, and Thouvenin, Pierre-Antoine

Subjects
Astrophysics - Astrophysics of Galaxies, Statistics - Applications
Abstract

Robust radiative transfer techniques are requisite for efficiently extracting the physical and chemical information from molecular rotational lines.We study several hypotheses that enable robust estimations of the column densities and physical conditions when fitting one or two transitions per molecular species. We study the extent to which simplifying assumptions aimed at reducing the complexity of the problem introduce estimation biases and how to detect them.We focus on the CO and HCO+ isotopologues and analyze maps of a 50 square arcminutes field. We used the RADEX escape probability model to solve the statistical equilibrium equations and compute the emerging line profiles, assuming that all species coexist. Depending on the considered set of species, we also fixed the abundance ratio between some species and explored different values. We proposed a maximum likelihood estimator to infer the physical conditions and considered the effect of both the thermal noise and calibration uncertainty. We analyzed any potential biases induced by model misspecifications by comparing the results on the actual data for several sets of species and confirmed with Monte Carlo simulations. The variance of the estimations and the efficiency of the estimator were studied based on the Cram{\'e}r-Rao lower bound.Column densities can be estimated with 30% accuracy, while the best estimations of the volume density are found to be within a factor of two. Under the chosen model framework, the peak 12CO(1--0) is useful for constraining the kinetic temperature. The thermal pressure is better and more robustly estimated than the volume density and kinetic temperature separately. Analyzing CO and HCO+ isotopologues and fitting the full line profile are recommended practices with respect to detecting possible biases.Combining a non-local thermodynamic equilibrium model with a rigorous analysis of the accuracy allows us to obtain an efficient estimator and identify where the model is misspecified. We note that other combinations of molecular lines could be studied in the future., Comment: Astronomy and Astrophysics - A\&A, In press

Published
2024

12. A far-ultraviolet-driven photoevaporation flow observed in a protoplanetary disk

Author

Berné, Olivier, Habart, Emilie, Peeters, Els, Schroetter, Ilane, Canin, Amélie, Sidhu, Ameek, Chown, Ryan, Bron, Emeric, Haworth, Thomas J., Klaassen, Pamela, Trahin, Boris, Van De Putte, Dries, Alarcón, Felipe, Zannese, Marion, Abergel, Alain, Bergin, Edwin A., Bernard-Salas, Jeronimo, Boersma, Christiaan, Cami, Jan, Cuadrado, Sara, Dartois, Emmanuel, Dicken, Daniel, Elyajouri, Meriem, Fuente, Asunción, Goicoechea, Javier R., Gordon, Karl D., Issa, Lina, Joblin, Christine, Kannavou, Olga, Khan, Baria, Lacinbala, Ozan, Languignon, David, Gal, Romane Le, Maragkoudakis, Alexandros, Meshaka, Raphael, Okada, Yoko, Onaka, Takashi, Pasquini, Sofia, Pound, Marc W., Robberto, Massimo, Röllig, Markus, Schefter, Bethany, Schirmer, Thiébaut, Simmer, Thomas, Tabone, Benoit, Tielens, Alexander G. G. M., Vicente, Sílvia, Wolfire, Mark G., Aleman, Isabel, Allamandola, Louis, Auchettl, Rebecca, Baratta, Giuseppe Antonio, Baruteau, Clément, Bejaoui, Salma, Bera, Partha P., Black, John H., Boulanger, Francois, Bouwman, Jordy, Brandl, Bernhard, Brechignac, Philippe, Brünken, Sandra, Buragohain, Mridusmita, Burkhardt, Andrew, Candian, Alessandra, Cazaux, Stéphanie, Cernicharo, Jose, Chabot, Marin, Chakraborty, Shubhadip, Champion, Jason, Colgan, Sean W. J., Cooke, Ilsa R., Coutens, Audrey, Cox, Nick L. J., Demyk, Karine, Meyer, Jennifer Donovan, Engrand, Cécile, Foschino, Sacha, García-Lario, Pedro, Gavilan, Lisseth, Gerin, Maryvonne, Godard, Marie, Gottlieb, Carl A., Guillard, Pierre, Gusdorf, Antoine, Hartigan, Patrick, He, Jinhua, Herbst, Eric, Hornekaer, Liv, Jäger, Cornelia, Janot-Pacheco, Eduardo, Kaufman, Michael, Kemper, Francisca, Kendrew, Sarah, Kirsanova, Maria S., Knight, Collin, Kwok, Sun, Labiano, Álvaro, Lai, Thomas S. -Y., Lee, Timothy J., Lefloch, Bertrand, Petit, Franck Le, Li, Aigen, Linz, Hendrik, Mackie, Cameron J., Madden, Suzanne C., Mascetti, Joëlle, McGuire, Brett A., Merino, Pablo, Micelotta, Elisabetta R., Morse, Jon A., Mulas, Giacomo, Neelamkodan, Naslim, Ohsawa, Ryou, Paladini, Roberta, Palumbo, Maria Elisabetta, Pathak, Amit, Pendleton, Yvonne J., Petrignani, Annemieke, Pino, Thomas, Puga, Elena, Rangwala, Naseem, Rapacioli, Mathias, Ricca, Alessandra, Roman-Duval, Julia, Roueff, Evelyne, Rouillé, Gaël, Salama, Farid, Sales, Dinalva A., Sandstrom, Karin, Sarre, Peter, Sciamma-O'Brien, Ella, Sellgren, Kris, Shannon, Matthew J., Simonnin, Adrien, Shenoy, Sachindev S., Teyssier, David, Thomas, Richard D., Togi, Aditya, Verstraete, Laurent, Witt, Adolf N., Wootten, Alwyn, Ysard, Nathalie, Zettergren, Henning, Zhang, Yong, Zhang, Ziwei E., and Zhen, Junfeng

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

Most low-mass stars form in stellar clusters that also contain massive stars, which are sources of far-ultraviolet (FUV) radiation. Theoretical models predict that this FUV radiation produces photo-dissociation regions (PDRs) on the surfaces of protoplanetary disks around low-mass stars, impacting planet formation within the disks. We report JWST and Atacama Large Millimetere Array observations of a FUV-irradiated protoplanetary disk in the Orion Nebula. Emission lines are detected from the PDR; modelling their kinematics and excitation allows us to constrain the physical conditions within the gas. We quantify the mass-loss rate induced by the FUV irradiation, finding it is sufficient to remove gas from the disk in less than a million years. This is rapid enough to affect giant planet formation in the disk.

Published
2024

13. Psychoeducation for Suicidal Behavior (PEPSUI)

Author

CHU Marius Lacroix, Lille, FRANCE, CHU Gabriel Montpied, Clermont Ferrand, FRANCE, CHU Pasteur, Nice, FRANCE, Centre Psychothérapique de Nancy, FRANCE, CHU Le Vinatier, Bron, FRANCE, CHU Albert Michallon, La Tronche, FRANCE, and CHU Tarnier, Paris, FRANCE

Published
2024

14. Formation of the Methyl Cation by Photochemistry in a Protoplanetary Disk

Author

Berné, Olivier, Martin-Drumel, Marie-Aline, Schroetter, Ilane, Goicoechea, Javier R., Jacovella, Ugo, Gans, Bérenger, Dartois, Emmanuel, Coudert, Laurent, Bergin, Edwin, Alarcon, Felipe, Cami, Jan, Roueff, Evelyne, Black, John H., Asvany, Oskar, Habart, Emilie, Peeters, Els, Canin, Amelie, Trahin, Boris, Joblin, Christine, Schlemmer, Stephan, Thorwirth, Sven, Cernicharo, Jose, Gerin, Maryvonne, Tielens, Alexander, Zannese, Marion, Abergel, Alain, Bernard-Salas, Jeronimo, Boersma, Christiaan, Bron, Emeric, Chown, Ryan, Cuadrado, Sara, Dicken, Daniel, Elyajouri, Meriem, Fuente, Asunción, Gordon, Karl D., Issa, Lina, Kannavou, Olga, Khan, Baria, Lacinbala, Ozan, Languignon, David, Gal, Romane Le, Maragkoudakis, Alexandros, Meshaka, Raphael, Okada, Yoko, Onaka, Takashi, Pasquini, Sofia, Pound, Marc W., Robberto, Massimo, Röllig, Markus, Schefter, Bethany, Schirmer, Thiébaut, Sidhu, Ameek, Tabone, Benoit, Van De Putte, Dries, Vicente, Sílvia, and Wolfire, Mark G.

Subjects
Astrophysics - Astrophysics of Galaxies, Physics - Chemical Physics
Abstract

Forty years ago it was proposed that gas phase organic chemistry in the interstellar medium was initiated by the methyl cation CH3+, but hitherto it has not been observed outside the Solar System. Alternative routes involving processes on grain surfaces have been invoked. Here we report JWST observations of CH3+ in a protoplanetary disk in the Orion star forming region. We find that gas-phase organic chemistry is activated by UV irradiation., Comment: Published in Nature

Published
2024
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15. OH as a probe of the warm water cycle in planet-forming disks

Author

Zannese, Marion, Tabone, Benoît, Habart, Emilie, Goicoechea, Javier R., Zanchet, Alexandre, van Dishoeck, Ewine F., van Hemert, Marc C., Black, John H., Tielens, Alexander G. G. M., Veselinova, A., Jambrina, P. G., Menendez, M., Verdasco, E., Aoiz, F. J., Gonzalez-Sanchez, L., Trahin, Boris, Dartois, Emmanuel, Berné, Olivier, Peeters, Els, He, Jinhua, Sidhu, Ameek, Chown, Ryan, Schroetter, Ilane, Van De Putte, Dries, Canin, Amélie, Alarcón, Felipe, Abergel, Alain, Bergin, Edwin A., Bernard-Salas, Jeronimo, Boersma, Christiaan, Bron, Emeric, Cami, Jan, Dicken, Daniel, Elyajouri, Meriem, Fuente, Asunción, Gordon, Karl D., Issa, Lina, Joblin, Christine, Kannavou, Olga, Khan, Baria, Lacinbala, Ozan, Languignon, David, Gal, Romane Le, Maragkoudakis, Alexandros, Meshaka, Raphael, Okada, Yoko, Onaka, Takashi, Pasquini, Sofia, Pound, Marc W., Robberto, Massimo, Röllig, Markus, Schefter, Bethany, Schirmer, Thiébaut, Vicente, Sílvia, and Wolfire, Mark G.

Subjects
Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Astrophysics of Galaxies, Astrophysics - Solar and Stellar Astrophysics
Abstract

Water is a key ingredient for the emergence of life as we know it. Yet, its destruction and reformation in space remains unprobed in warm gas. Here, we detect the hydroxyl radical (OH) emission from a planet-forming disk exposed to external far-ultraviolet (FUV) radiation with the James Webb Space Telescope. The observations are confronted with the results of quantum dynamical calculations. The highly excited OH infrared rotational lines are the tell-tale signs of H2O destruction by FUV. The OH infrared ro-vibrational lines are attributed to chemical excitation via the key reaction O+H=OH+H which seeds the formation of water in the gas-phase. We infer that the equivalent of the Earth ocean's worth of water is destroyed per month and replenished. These results show that under warm and irradiated conditions water is destroyed and efficiently reformed via gas-phase reactions. This process, assisted by diffusive transport, could reduce the HDO/H2O ratio in the warm regions of planet-forming disks., Comment: Version submitted to Nature Astronomy

Published
2023

16. Density Field Reconstruction of an Overexpanded Supersonic Jet using Tomographic Background-Oriented Schlieren

Author

Bron, Joachim A., Baars, Woutijn J., and Schrijer, Ferdinand F. J.

Subjects
Physics - Fluid Dynamics
Abstract

A Tomographic Background-Oriented Schlieren (TBOS) technique is developed to aid in the visualization of compressible flows. An experimental setup was devised around a sub-scale rocket nozzle, in which four cameras were set up in a circular configuration with 30{\deg} angular spacing in azimuth. Measurements were taken of the overexpanded supersonic jet plume at various nozzle pressure ratios (NPR), corresponding to different flow regimes during the start-up and shut-down of rocket nozzles. Measurements were also performed for different camera parameters using different exposure times and f-stops in order to study the effect of measurement accuracy. Density gradients and subsequently two-dimensional line-of-sight integrated density fields for each of the camera projections are recovered from the index of refraction field by solving a Poisson equation. The results of this stage are then used to reconstruct two-dimensional slices of the (time-averaged) density field using a tomographic reconstruction algorithm employing the filtered back-projection and the simultaneous algebraic reconstruction technique. By stacking these two-dimensional slices, the (quasi-) three-dimensional density field is obtained. The accuracy of the implemented method with a relatively low number of sparse cameras is briefly assessed and basic flow features are extracted such as the shock spacing in the overexpanded jet plume.

Published
2023

17. PDRs4All III: JWST's NIR spectroscopic view of the Orion Bar

Author

Peeters, Els, Habart, Emilie, Berne, Olivier, Sidhu, Ameek, Chown, Ryan, Van De Putte, Dries, Trahin, Boris, Schroetter, Ilane, Canin, Amelie, Alarcon, Felipe, Schefter, Bethany, Khan, Baria, Pasquini, Sofia, Tielens, Alexander G. G. M., Wolfire, Mark G., Dartois, Emmanuel, Goicoechea, Javier R., Maragkoudakis, Alexandros, Onaka, Takashi, Pound, Marc W., Vicente, Silvia, Abergel, Alain, Bergin, Edwin A., Bernard-Salas, Jeronimo, Boersma, Christiaan, Bron, Emeric, Cami, Jan, Cuadrado, Sara, Dicken, Daniel, Elyajour, Meriem, Fuente, Asuncion, Gordon, Karl D., Issa, Lina, Joblin, Christine, Kannavou, Olga, Lacinbala, Ozan, Languignon, David, Gal, Romane Le, Meshaka, Raphael, Okada, Yoko, Robberto, Massimo, Roellig, Markus, Schirmer, Thiebaut, Tabone, Benoit, Zannese, Marion, Aleman, Isabel, Allamandola, Louis, Auchettl, Rebecca, Baratta, Giuseppe Antonio, Bejaoui, Salma, Bera, Partha P., Black, John H., Boulanger, Francois, Bouwman, Jordy, Brandl, Bernhard, Brechignac, Philippe, Brunken, Sandra, Buragohain, Mridusmita, Burkhardt, Andrew, Candian, Alessandra, Cazaux, Stephanie, Cernicharo, Jose, Chabot, Marin, Chakraborty, Shubhadip, Champion, Jason, Colgan, Sean W. J., Cooke, Ilsa R., Coutens, Audrey, Cox, Nick L. J., Demyk, Karine, Meyer, Jennifer Donovan, Foschino, Sacha, Garcia-Lario, Pedro, Gerin, Maryvonne, Gottlieb, Carl A., Guillard, Pierre, Gusdorf, Antoine, Hartigan, Patrick, He, Jinhua, Herbst, Eric, Hornekaer, Liv, Jager, Cornelia, Janot-Pacheco, Eduardo, Kaufman, Michael, Kendrew, Sarah, Kirsanova, Maria S., Klaassen, Pamela, Kwok, Sun, Labiano, Alvaro, Lai, Thomas S. -Y., Lee, Timothy J., Lefloch, Bertrand, Petit, Franck Le, Li, Aigen, Linz, Hendrik, Mackie, Cameron J., Madden, Suzanne C., Mascetti, Joelle, McGuire, Brett A., Merino, Pablo, Micelotta, Elisabetta R., Misselt, Karl, Morse, Jon A., Mulas, Giacomo, Neelamkodan, Naslim, Ohsawa, Ryou, Paladini, Roberta, Palumbo, Maria Elisabetta, Pathak, Amit, Pendleton, Yvonne J., Petrignani, Annemieke, Pino, Thomas, Puga, Elena, Rangwala, Naseem, Rapacioli, Mathias, Ricca, Alessandra, Roman-Duval, Julia, Roser, Joseph, Roueff, Evelyne, Rouille, Gael, Salama, Farid, Sales, Dinalva A., Sandstrom, Karin, Sarre, Peter, Sciamma-O'Brien, Ella, Sellgren, Kris, Shenoy, Sachindev S., Teyssier, David, Thomas, Richard D., Togi, Aditya, Verstraete, Laurent, Witt, Adolf N., Wootten, Alwyn, Ysard, Nathalie, Zettergren, Henning, Zhang, Yong, Zhang, Ziwei E., and Zhen, Junfeng

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

(Abridged) We investigate the impact of radiative feedback from massive stars on their natal cloud and focus on the transition from the HII region to the atomic PDR (crossing the ionisation front (IF)), and the subsequent transition to the molecular PDR (crossing the dissociation front (DF)). We use high-resolution near-IR integral field spectroscopic data from NIRSpec on JWST to observe the Orion Bar PDR as part of the PDRs4All JWST Early Release Science Program. The NIRSpec data reveal a forest of lines including, but not limited to, HeI, HI, and CI recombination lines, ionic lines, OI and NI fluorescence lines, Aromatic Infrared Bands (AIBs including aromatic CH, aliphatic CH, and their CD counterparts), CO2 ice, pure rotational and ro-vibrational lines from H2, and ro-vibrational lines HD, CO, and CH+, most of them detected for the first time towards a PDR. Their spatial distribution resolves the H and He ionisation structure in the Huygens region, gives insight into the geometry of the Bar, and confirms the large-scale stratification of PDRs. We observe numerous smaller scale structures whose typical size decreases with distance from Ori C and IR lines from CI, if solely arising from radiative recombination and cascade, reveal very high gas temperatures consistent with the hot irradiated surface of small-scale dense clumps deep inside the PDR. The H2 lines reveal multiple, prominent filaments which exhibit different characteristics. This leaves the impression of a "terraced" transition from the predominantly atomic surface region to the CO-rich molecular zone deeper in. This study showcases the discovery space created by JWST to further our understanding of the impact radiation from young stars has on their natal molecular cloud and proto-planetary disk, which touches on star- and planet formation as well as galaxy evolution., Comment: 52 pages, 30 figures, submitted to A&A

Published
2023
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18. AI-based association analysis for medical imaging using latent-space geometric confounder correction

Author

Liu, Xianjing, Li, Bo, Vernooij, Meike W., Wolvius, Eppo B., Roshchupkin, Gennady V., and Bron, Esther E.

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence, Computer Science - Machine Learning
Abstract

AI has greatly enhanced medical image analysis, yet its use in epidemiological population imaging studies remains limited due to visualization challenges in non-linear models and lack of confounder control. Addressing this, we introduce an AI method emphasizing semantic feature interpretation and resilience against multiple confounders. Our approach's merits are tested in three scenarios: extracting confounder-free features from a 2D synthetic dataset; examining the association between prenatal alcohol exposure and children's facial shapes using 3D mesh data; exploring the relationship between global cognition and brain images with a 3D MRI dataset. Results confirm our method effectively reduces confounder influences, establishing less confounded associations. Additionally, it provides a unique visual representation, highlighting specific image alterations due to identified correlations., Comment: 18 pages; 7 figures

Published
2023

26. Distribution of C30 carotenoid biosynthesis genes suggests habitat adaptation function in insect-adapted and nomadic Lactobacillaceae

Author

Tom Eilers, Marie Legein, Jari Temmermans, Jelle Dillen, Ine Vandendriessche, Koen Sandra, Peter A. Bron, Stijn Wittouck, and Sarah Lebeer

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Carotenoids are membrane-bound pigments that are essential for photosynthesizing plants and algae, widely applied in food, feed and cosmetics due to their antioxidant and anti-inflammatory properties. The production of carotenoids, particularly C30 forms, has been documented in some non-photosynthetic prokaryotes. However, their function, distribution and ecology beyond photosynthesizing organisms remains understudied. In this study, we performed an eco-evolutionary analysis of terpenoid biosynthetic gene clusters in the Lactobacillaceae family, screening 4203 dereplicated genomes for terpenoid biosynthesis genes, and detected crtMN genes in 28/361 (7.7%) species across 14/34 (41.2%) genera. These genes encode key enzymes for producing the C30 carotenoid 4,4′-diaponeurosporene. crtMN genes appeared to be convergently gained within Fructilactobacillus and horizontally transferred across species and genera, including Lactiplantibacillus to Levilactobacillus. The phenotype was confirmed in 87% of the predicted crtMN gene carriers (27/31). Nomadic and insect-adapted species, particularly those isolated from vegetable fermentations, e.g., Lactiplantibacillus, and floral habitats, e.g., Fructilactobacillus, contained crtMN genes, while vertebrate-associated species, including vaginal associated species, lacked this trait. This habitat association aligned with the observations that C30 carotenoid-producing strains were more resistant to UV-stress. In summary, C30 carotenoid biosynthesis plays a role in habitat adaptation and is scattered across Lactobacillaceae in line with this habitat adaptation.

Published
2024
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27. Serotype independent protection induced by a vaccine based on the IgM protease of Streptococcus suis and proposal for a new immunity-based classification system

Author

A. A. C. Jacobs, A. W. F. Grommen, S. Badbanchi, A. J. van Hout, T. J. van Kasteren-Westerneng, L. Garcia Morales, R. Bron, and R. P. A. M. Segers

Subjects
Animal culture, SF1-1100, Veterinary medicine, SF600-1100
Abstract

Abstract The IgM protease (Ide Ssuis gene; Gene ID 8153996) of Streptococcus suis is a putative virulence factor that has been shown to be a protective vaccine antigen for pigs (Seele et al. Vaccine 33:2207–12, 2015). To assess its potential as a cross-protective antigen, the amino acid variability among prevalent clinical isolates in various regions and among various serotypes was investigated. Multi-sequence alignment of full-length amino acid sequences of S. suis IgM protease, available in the public domain (status Jan-2022) supplemented with in-house sequences, i.e. a total of 1999 sequences, revealed that the IgM protease of S. suis clusters into three main evolutionary distinct branches: groups A, B and C. Group A, 82% of the sequences in the database, was associated with clinical isolates of various serotypes. Group B, 6% of the strains in the database, was associated with clinical isolates mainly in the EU and mainly belonging to serotype (st) 9. Group C, 12% of the strains in the database, was largely associated with healthy carrier isolates, i.e. nose or tonsil isolates of various serotypes but in particular with st9 and un-typable strains. Within the groups A, B and C, high levels of amino acid identity were observed (> 75%), whereas between groups A and B, the percentage amino acid identity was approximately 30% and between groups A and C approximately 55%. Experimental Escherichia coli expressed recombinant subunit vaccines based on the IgM protease group A sequence of st1 strain B10-99, st2 strain 10 or st7 strain 14009-1, induced serotype independent protection in pigs against challenge with all group A strains tested, i.e. strains of different parts of the phylogenetic tree and of different serotypes including st1, 2, 9 and 14. Protection was observed after vaccination of piglets at 3 and 5 weeks of age and subsequent challenge at 7 weeks but also after vaccination of gilts at 6 and 2 weeks before anticipated parturition and challenge of the offspring up to at least 8 weeks of age. No protection was observed against challenge with st9 strain SZ2000-6264 having group B IgM protease. A recombinant subunit vaccine based on the group B IgM protease sequence, also did not protect against challenge with the homologous group B st9 challenge strain. The results indicate that a vaccine based on a group A IgM protease induces protection against all S. suis strains that express the group A IgM protease. Depending on the geographical region such a vaccine is expected to protect against 60–100% of the virulent S. suis strains. Since the novel proposed IgM protease classification is highly relevant, a PCR was developed and validated, to be able to classify clinical isolates into IgM protease groups A, B and C and predict the cross-protection that can be expected from a group A based IgM protease vaccine.

Published
2024
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28. Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species

Author

Lize Delanghe, Ilke De Boeck, Joke Van Malderen, Camille Nina Allonsius, Tim Van Rillaer, Peter A. Bron, Ingmar Claes, Margo Hagendorens, Sarah Lebeer, and Julie Leysen

Subjects
Medicine, Science
Abstract

Abstract Atopic dermatitis is the most common inflammatory skin condition with a severe negative impact on patients’ quality of life. The etiology of AD is complex and depends on age, genetics, the immune system, environmental factors, and the skin microbiome, with a key role for pathogenic Staphylococcus aureus in the development of severe AD. However, the composition of the skin microbiome in mild AD is understudied. Here, using metagenomic shallow shotgun sequencing, we showed that mild AD lesions did not show a significant difference in the diversity of the skin microbiome compared to samples from non-AD patients and that the relative abundance of S. aureus did not differ in these mild AD lesions. However, when we assessed other taxa, Mycobacterium ostraviense, Pedobacter panaciterrae_A and four Streptomyces species were identified with higher abundances in mild AD lesions and species of 15 genera were decreased in abundance. The highest fold decreases were observed for Paracoccus marcusii, Microbacterium lacticum, Micrococcus luteus, and Moraxella sp002478835. These microbiome compositional insights are a first step towards novel microbiome-based diagnostics and therapeutics for early intervention at the stage of mild AD and provide a path forward for the functional study of species involved in this often-overlooked patient population.

Published
2024
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29. HCN emission from translucent gas and UV-illuminated cloud edges revealed by wide-field IRAM 30m maps of Orion B GMC: Revisiting its role as tracer of the dense gas reservoir for star formation

Author

Santa-Maria, M. G., Goicoechea, J. R., Pety, J., Gerin, M., Orkisz, J. H., Petit, F. Le, Einig, L., Palud, P., Magalhaes, V. de Souza, Bešlić, I., Segal, L., Bardeau, S., Bron, E., Chainais, P., Chanussot, J., Gratier, P., Guzmán, V. V., Hughes, A., Languignon, D., Levrier, F., Lis, D. C., Liszt, H. S., Bourlot, J. Le, Oya, Y., Öberg, K., Peretto, N., Roueff, E., Roueff, A., Sievers, A., Thouvenin, P. -A., and Yamamoto, S.

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

We present 5 deg^2 (~250 pc^2) HCN, HNC, HCO+, and CO J=1-0 maps of the Orion B GMC, complemented with existing wide-field [CI] 492 GHz maps, as well as new pointed observations of rotationally excited HCN, HNC, H13CN, and HN13C lines. We detect anomalous HCN J=1-0 hyperfine structure line emission almost everywhere in the cloud. About 70% of the total HCN J=1-0 luminosity arises from gas at A_V < 8 mag. The HCN/CO J=1-0 line intensity ratio shows a bimodal behavior with an inflection point at A_V < 3 mag typical of translucent gas and UV-illuminated cloud edges. We find that most of the HCN J=1-0 emission arises from extended gas with n(H2) ~< 10^4 cm^-3, even lower density gas if the ionization fraction is > 10^-5 and electron excitation dominates. This result explains the low-A_V branch of the HCN/CO J=1-0 intensity ratio distribution. Indeed, the highest HCN/CO ratios (~0.1) at A_V < 3 mag correspond to regions of high [CI] 492 GHz/CO J=1-0 intensity ratios (>1) characteristic of low-density PDRs. Enhanced FUV radiation favors the formation and excitation of HCN on large scales, not only in dense star-forming clumps. The low surface brightness HCN and HCO+ J=1-0 emission scale with I_FIR (a proxy of the stellar FUV radiation field) in a similar way. Together with CO J=1-0, these lines respond to increasing I_FIR up to G0~20. On the other hand, the bright HCN J=1-0 emission from dense gas in star-forming clumps weakly responds to I_FIR once the FUV radiation field becomes too intense (G0>1500). The different power law scalings (produced by different chemistries, densities, and line excitation regimes) in a single but spatially resolved GMC resemble the variety of Kennicutt-Schmidt law indexes found in galaxy averages. As a corollary for extragalactic studies, we conclude that high HCN/CO J=1-0 line intensity ratios do not always imply the presence of dense gas., Comment: accepted for publication in A&A. 24 pages, 18 figures, plus Appendix. Abridged Abstract

Published
2023
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30. Neural network-based emulation of interstellar medium models

Author

Palud, Pierre, Einig, Lucas, Petit, Franck Le, Bron, Emeric, Chainais, Pierre, Chanussot, Jocelyn, Pety, Jérôme, Thouvenin, Pierre-Antoine, Languignon, David, Bešlić, Ivana, Santa-Maria, Miriam G., Orkisz, Jan H., Ségal, Léontine E., Zakardjian, Antoine, Bardeau, Sébastien, Gerin, Maryvonne, Goicoechea, Javier R., Gratier, Pierre, Guzman, Viviana V., Hughes, Annie, Levrier, François, Liszt, Harvey S., Bourlot, Jacques Le, Roueff, Antoine, and Sievers, Albrecht

Subjects
Astrophysics - Astrophysics of Galaxies, Statistics - Applications
Abstract

The interpretation of observations of atomic and molecular tracers in the galactic and extragalactic interstellar medium (ISM) requires comparisons with state-of-the-art astrophysical models to infer some physical conditions. Usually, ISM models are too time-consuming for such inference procedures, as they call for numerous model evaluations. As a result, they are often replaced by an interpolation of a grid of precomputed models. We propose a new general method to derive faster, lighter, and more accurate approximations of the model from a grid of precomputed models. These emulators are defined with artificial neural networks (ANNs) designed and trained to address the specificities inherent in ISM models. Indeed, such models often predict many observables (e.g., line intensities) from just a few input physical parameters and can yield outliers due to numerical instabilities or physical bistabilities. We propose applying five strategies to address these characteristics: 1) an outlier removal procedure; 2) a clustering method that yields homogeneous subsets of lines that are simpler to predict with different ANNs; 3) a dimension reduction technique that enables to adequately size the network architecture; 4) the physical inputs are augmented with a polynomial transform to ease the learning of nonlinearities; and 5) a dense architecture to ease the learning of simple relations. We compare the proposed ANNs with standard classes of interpolation methods to emulate the Meudon PDR code, a representative ISM numerical model. Combinations of the proposed strategies outperform all interpolation methods by a factor of 2 on the average error, reaching 4.5% on the Meudon PDR code. These networks are also 1000 times faster than accurate interpolation methods and require ten to forty times less memory. This work will enable efficient inferences on wide-field multiline observations of the ISM.

Published
2023
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31. PDRs4All II: JWST's NIR and MIR imaging view of the Orion Nebula

Author

Habart, Emilie, Peeters, Els, Berné, Olivier, Trahin, Boris, Canin, Amélie, Chown, Ryan, Sidhu, Ameek, Van De Putte, Dries, Alarcón, Felipe, Schroetter, Ilane, Dartois, Emmanuel, Vicente, Sílvia, Abergel, Alain, Bergin, Edwin A., Bernard-Salas, Jeronimo, Boersma, Christiaan, Bron, Emeric, Cami, Jan, Cuadrado, Sara, Dicken, Daniel, Elyajouri, Meriem, Fuente, Asunción, Goicoechea, Javier R., Gordon, Karl D., Issa, Lina, Joblin, Christine, Kannavou, Olga, Khan, Baria, Lacinbala, Ozan, Languignon, David, Gal, Romane Le, Maragkoudakis, Alexandros, Meshaka, Raphael, Okada, Yoko, Onaka, Takashi, Pasquini, Sofia, Pound, Marc W., Robberto, Massimo, Röllig, Markus, Schefter, Bethany, Schirmer, Thiébaut, Tabone, Benoit, Tielens, Alexander G. G. M., Wolfire, Mark G., Zannese, Marion, Ysard, Nathalie, Miville-Deschenes, Marc-Antoine, Aleman, Isabel, Allamandola, Louis, Auchettl, Rebecca, Baratta, Giuseppe Antonio, Bejaoui, Salma, Bera, Partha P., Black, John H., Boulanger, Francois, Bouwman, Jordy, Brandl, Bernhard, Brechignac, Philippe, Brünken, Sandra, Buragohain, Mridusmita, Burkhardt, rew, Candian, Alessandra, Cazaux, Stéphanie, Cernicharo, Jose, Chabot, Marin, Chakraborty, Shubhadip, Champion, Jason, Colgan, Sean W. J., Cooke, Ilsa R., Coutens, Audrey, Cox, Nick L. J., Demyk, Karine, Meyer, Jennifer Donovan, Foschino, Sacha, García-Lario, Pedro, Gavilan, Lisseth, Gerin, Maryvonne, Gottlieb, Carl A., Guillard, Pierre, Gusdorf, Antoine, Hartigan, Patrick, He, Jinhua, Herbst, Eric, Hornekaer, Liv, Jäger, Cornelia, Janot-Pacheco, Eduardo, Kaufman, Michael, Kemper, Francisca, Kendrew, Sarah, Kirsanova, Maria S., Klaassen, Pamela, Kwok, Sun, Labiano, Álvaro, Lai, Thomas S. -Y., Lee, Timothy J., Lefloch, Bertrand, Petit, Franck Le, Li, Aigen, Linz, Hendrik, Mackie, Cameron J., Madden, Suzanne C., Mascetti, Joëlle, McGuire, Brett A., Merino, Pablo, Micelotta, Elisabetta R., Misselt, Karl, Morse, Jon A., Mulas, Giacomo, Neelamkodan, Naslim, Ohsawa, Ryou, Omont, Alain, Paladini, Roberta, Palumbo, Maria Elisabetta, Pathak, Amit, Pendleton, Yvonne J., Petrignani, Annemieke, Pino, Thomas, Puga, Elena, Rangwala, Naseem, Rapacioli, Mathias, Ricca, Alessandra, Roman-Duval, Julia, Roser, Joseph, Roueff, Evelyne, Rouillé, Gaël, Salama, Farid, Sales, Dinalva A., Sandstrom, Karin, Sarre, Peter, Sciamma-O'Brien, Ella, Sellgren, Kris, Shenoy, Sachindev S., Teyssier, David, Thomas, Richard D., Togi, Aditya, Verstraete, Laurent, Witt, Adolf N., Wootten, Alwyn, Zettergren, Henning, Zhang, Yong, Zhang, Ziwei E., and Zhen, Junfeng

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

The JWST has captured the most detailed and sharpest infrared images ever taken of the inner region of the Orion Nebula, the nearest massive star formation region, and a prototypical highly irradiated dense photo-dissociation region (PDR). We investigate the fundamental interaction of far-ultraviolet photons with molecular clouds. The transitions across the ionization front (IF), dissociation front (DF), and the molecular cloud are studied at high-angular resolution. These transitions are relevant to understanding the effects of radiative feedback from massive stars and the dominant physical and chemical processes that lead to the IR emission that JWST will detect in many Galactic and extragalactic environments. Due to the proximity of the Orion Nebula and the unprecedented angular resolution of JWST, these data reveal that the molecular cloud borders are hyper structured at small angular scales of 0.1-1" (0.0002-0.002 pc or 40-400 au at 414 pc). A diverse set of features are observed such as ridges, waves, globules and photoevaporated protoplanetary disks. At the PDR atomic to molecular transition, several bright features are detected that are associated with the highly irradiated surroundings of the dense molecular condensations and embedded young star. Toward the Orion Bar PDR, a highly sculpted interface is detected with sharp edges and density increases near the IF and DF. This was predicted by previous modeling studies, but the fronts were unresolved in most tracers. A complex, structured, and folded DF surface was traced by the H2 lines. This dataset was used to revisit the commonly adopted 2D PDR structure of the Orion Bar. JWST provides us with a complete view of the PDR, all the way from the PDR edge to the substructured dense region, and this allowed us to determine, in detail, where the emission of the atomic and molecular lines, aromatic bands, and dust originate.

Published
2023
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32. PDRs4All IV. An embarrassment of riches: Aromatic infrared bands in the Orion Bar

Author

Chown, Ryan, Sidhu, Ameek, Peeters, Els, Tielens, Alexander G. G. M., Cami, Jan, Berné, Olivier, Habart, Emilie, Alarcón, Felipe, Canin, Amélie, Schroetter, Ilane, Trahin, Boris, Van De Putte, Dries, Abergel, Alain, Bergin, Edwin A., Bernard-Salas, Jeronimo, Boersma, Christiaan, Bron, Emeric, Cuadrado, Sara, Dartois, Emmanuel, Dicken, Daniel, El-Yajouri, Meriem, Fuente, Asunción, Goicoechea, Javier R., Gordon, Karl D., Issa, Lina, Joblin, Christine, Kannavou, Olga, Khan, Baria, Lacinbala, Ozan, Languignon, David, Gal, Romane Le, Maragkoudakis, Alexandros, Meshaka, Raphael, Okada, Yoko, Onaka, Takashi, Pasquini, Sofia, Pound, Marc W., Robberto, Massimo, Röllig, Markus, Schefter, Bethany, Schirmer, Thiébaut, Vicente, Sílvia, Wolfire, Mark G., Zannese, Marion, Aleman, Isabel, Allamandola, Louis, Auchettl, Rebecca, Baratta, Giuseppe Antonio, Bejaoui, Salma, Bera, Partha P., Black, John H., Boulanger, Francois, Bouwman, Jordy, Brandl, Bernhard, Brechignac, Philippe, Brünken, Sandra, Buragohain, Mridusmita, Burkhardt, Andrew, Candian, Alessandra, Cazaux, Stéphanie, Cernicharo, Jose, Chabot, Marin, Chakraborty, Shubhadip, Champion, Jason, Colgan, Sean W. J., Cooke, Ilsa R., Coutens, Audrey, Cox, Nick L. J., Demyk, Karine, Meyer, Jennifer Donovan, Foschino, Sacha, García-Lario, Pedro, Gavilan, Lisseth, Gerin, Maryvonne, Gottlieb, Carl A., Guillard, Pierre, Gusdorf, Antoine, Hartigan, Patrick, He, Jinhua, Herbst, Eric, Hornekaer, Liv, Jäger, Cornelia, Janot-Pacheco, Eduardo, Kaufman, Michael, Kemper, Francisca, Kendrew, Sarah, Kirsanova, Maria S., Klaassen, Pamela, Kwok, Sun, Labiano, Álvaro, Lai, Thomas S. -Y., Lee, Timothy J., Lefloch, Bertrand, Petit, Franck Le, Li, Aigen, Linz, Hendrik, Mackie, Cameron J., Madden, Suzanne C., Mascetti, Joëlle, McGuire, Brett A., Merino, Pablo, Micelotta, Elisabetta R., Misselt, Karl, Morse, Jon A., Mulas, Giacomo, Neelamkodan, Naslim, Ohsawa, Ryou, Omont, Alain, Paladini, Roberta, Palumbo, Maria Elisabetta, Pathak, Amit, Pendleton, Yvonne J., Petrignani, Annemieke, Pino, Thomas, Puga, Elena, Rangwala, Naseem, Rapacioli, Mathias, Ricca, Alessandra, Roman-Duval, Julia, Roser, Joseph, Roueff, Evelyne, Rouillé, Gaël, Salama, Farid, Sales, Dinalva A., Sandstrom, Karin, Sarre, Peter, Sciamma-O'Brien, Ella, Sellgren, Kris, Shenoy, Sachindev S., Teyssier, David, Thomas, Richard D., Togi, Aditya, Verstraete, Laurent, Witt, Adolf N., Wootten, Alwyn, Zettergren, Henning, Zhang, Yong, Zhang, Ziwei E., and Zhen, Junfeng

Subjects
Astrophysics - Astrophysics of Galaxies, Astrophysics - Solar and Stellar Astrophysics
Abstract

(Abridged) Mid-infrared observations of photodissociation regions (PDRs) are dominated by strong emission features called aromatic infrared bands (AIBs). The most prominent AIBs are found at 3.3, 6.2, 7.7, 8.6, and 11.2 $\mu$m. The most sensitive, highest-resolution infrared spectral imaging data ever taken of the prototypical PDR, the Orion Bar, have been captured by JWST. We provide an inventory of the AIBs found in the Orion Bar, along with mid-IR template spectra from five distinct regions in the Bar: the molecular PDR, the atomic PDR, and the HII region. We use JWST NIRSpec IFU and MIRI MRS observations of the Orion Bar from the JWST Early Release Science Program, PDRs4All (ID: 1288). We extract five template spectra to represent the morphology and environment of the Orion Bar PDR. The superb sensitivity and the spectral and spatial resolution of these JWST observations reveal many details of the AIB emission and enable an improved characterization of their detailed profile shapes and sub-components. While the spectra are dominated by the well-known AIBs at 3.3, 6.2, 7.7, 8.6, 11.2, and 12.7 $\mu$m, a wealth of weaker features and sub-components are present. We report trends in the widths and relative strengths of AIBs across the five template spectra. These trends yield valuable insight into the photochemical evolution of PAHs, such as the evolution responsible for the shift of 11.2 $\mu$m AIB emission from class B$_{11.2}$ in the molecular PDR to class A$_{11.2}$ in the PDR surface layers. This photochemical evolution is driven by the increased importance of FUV processing in the PDR surface layers, resulting in a "weeding out" of the weakest links of the PAH family in these layers. For now, these JWST observations are consistent with a model in which the underlying PAH family is composed of a few species: the so-called 'grandPAHs'., Comment: 25 pages, 10 figures, to appear in A&A

Published
2023
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33. Measurements of the $\nu_{\mu}$ and $\bar{\nu}_{\mu}$-induced Coherent Charged Pion Production Cross Sections on $^{12}C$ by the T2K experiment

Author

Abe, K., Akhlaq, N., Akutsu, R., Ali, A., Monsalve, S. Alonso, Alt, C., Andreopoulos, C., Antonova, M., Aoki, S., Arihara, T., Asada, Y., Ashida, Y., Atkin, E. T., Barbi, M., Barker, G. J., Barr, G., Barrow, D., Batkiewicz-Kwasniak, M., Berardi, V., Berns, L., Bhadra, S., Blanchet, A., Blondel, A., Bolognesi, S., Bonus, T., Bordoni, S., Boyd, S. B., Bravar, A., Bronner, C., Bron, S., Bubak, A., Avanzini, M. Buizza, Caballero, J. A., Calabria, N. F., Cao, S., Carabadjac, D., Carter, A. J., Cartwright, S. L., Casado, M. P., Catanesi, M. G., Cervera, A., Chakrani, J., Cherdack, D., Chong, P. S., Christodoulou, G., Chvirova, A., Cicerchia, M., Coleman, J., Collazuol, G., Cook, L., Cudd, A., Dalmazzone, C., Daret, T., Davydov, Yu. I., De Roeck, A., De Rosa, G., Dealtry, T., Delogu, C. C., Densham, C., Dergacheva, A., Di Lodovico, F., Dolan, S., Douqa, D., Doyle, T. A., Drapier, O., Dumarchez, J., Dunne, P., Dygnarowicz, K., Eguchi, A., Emery-Schrenk, S., Erofeev, G., Ershova, A., Eurin, G., Fedorova, D., Fedotov, S., Feltre, M., Finch, A. J., Aguirre, G. A. Fiorentini, Fiorillo, G., Fitton, M. D., Patiño, J. M. Franco, Friend, M., Fujii, Y., Fukuda, Y., Furui, Y., Giannessi, L., Giganti, C., Glagolev, V., Gonin, M., Rosa, J. González, Goodman, E. A. G., Gorin, A., Grassi, M., Guigue, M., Hadley, D. R., Haigh, J. T., Hamacher-Baumann, P., Harris, D. A., Hartz, M., Hasegawa, T., Hassani, S., Hastings, N. C., Hayato, Y., Henaff, D., Hogan, M., Holeczek, J., Holin, A., Holvey, T., Van, N. T. Hong, Honjo, T., Ichikawa, A. K., Ikeda, M., Ishida, T., Ishitsuka, M., Israel, H. T., Izmaylov, A., Jakkapu, M., Jamieson, B., Jenkins, S. J., Jesús-Valls, C., Jiang, J. J., Ji, J. Y., Jonsson, P., Joshi, S., Jung, C. K., Jurj, P. B., Kabirnezhad, M., Kaboth, A. C., Kajita, T., Kakuno, H., Kameda, J., Kasetti, S. P., Kataoka, Y., Katori, T., Kawaue, M., Kearns, E., Khabibullin, M., Khotjantsev, A., Kikawa, T., King, S., Kiseeva, V., Kisiel, J., Kobayashi, H., Kobayashi, T., Koch, L., Kodama, S., Konaka, A., Kormos, L. L., Koshio, Y., Koto, T., Kowalik, K., Kudenko, Y., Kudo, Y., Kuribayashi, S., Kurjata, R., Kutter, T., Kuze, M., La Commara, M., Labarga, L., Lachner, K., Lagoda, J., Lakshmi, S. M., James, M. Lamers, Lamoureux, M., Langella, A., Laporte, J. -F., Last, D., Latham, N., Laveder, M., Lavitola, L., Lawe, M., Lee, Y., Lin, C., Lin, S. -K., Litchfield, R. P., Liu, S. L., Li, W., Longhin, A., Long, K. R., Moreno, A. Lopez, Ludovici, L., Lu, X., Lux, T., Machado, L. N., Magaletti, L., Mahn, K., Malek, M., Mandal, M., Manly, S., Marino, A. D., Marti-Magro, L., Martin, D. G. R., Martini, M., Martin, J. F., Maruyama, T., Matsubara, T., Matveev, V., Mauger, C., Mavrokoridis, K., Mazzucato, E., McCauley, N., McElwee, J., McFarland, K. S., McGrew, C., McKean, J., Mefodiev, A., Megias, G. D., Mehta, P., Mellet, L., Metelko, C., Mezzetto, M., Miller, E., Minamino, A., Mineev, O., Mine, S., Miura, M., Bueno, L. Molina, Moriyama, S., Morrison, P., Mueller, Th. A., Munford, D., Munteanu, L., Nagai, K., Nagai, Y., Nakadaira, T., Nakagiri, K., Nakahata, M., Nakajima, Y., Nakamura, A., Nakamura, H., Nakamura, K., Nakamura, K. D., Nakano, Y., Nakayama, S., Nakaya, T., Nakayoshi, K., Naseby, C. E. R., Ngoc, T. V., Nguyen, V. Q., Niewczas, K., Nishimori, S., Nishimura, Y., Nishizaki, K., Nosek, T., Nova, F., Novella, P., Nugent, J. C., O'Keeffe, H. M., O'Sullivan, L., Odagawa, T., Okinaga, W., Okumura, K., Okusawa, T., Ospina, N., Oyama, Y., Palladino, V., Paolone, V., Pari, M., Parlone, J., Pasternak, J., Pavin, M., Payne, D., Penn, G. C., Pershey, D., Pickering, L., Pidcott, C., Pintaudi, G., Pistillo, C., Popov, B., Porwit, K., Posiadala-Zezula, M., Prabhu, Y. S., Pupilli, F., Quilain, B., Radermacher, T., Radicioni, E., Radics, B., Ramírez, M. A., Ratoff, P. N., Reh, M., Riccio, C., Rondio, E., Roth, S., Roy, N., Rubbia, A., Ruggeri, A. C., Ruggles, C. A., Rychter, A., Sakashita, K., Sánchez, F., Schloesser, C. M., Scholberg, K., Scott, M., Seiya, Y., Sekiguchi, T., Sekiya, H., Sgalaberna, D., Shaikhiev, A., Shaker, F., Shiozawa, M., Shorrock, W., Shvartsman, A., Skrobova, N., Skwarczynski, K., Smyczek, D., Smy, M., Sobczyk, J. T., Sobel, H., Soler, F. J. P., Sonoda, Y., Speers, A. J., Spina, R., Suslov, I. A., Suvorov, S., Suzuki, A., Suzuki, S. Y., Suzuki, Y., Tada, M., Tairafune, S., Takayasu, S., Takeda, A., Takeuchi, Y., Takifuji, K., Tanaka, H. K., Tani, M., Teklu, A., Tereshchenko, V. V., Thamm, N., Thompson, L. F., Toki, W., Touramanis, C., Towstego, T., Tsui, K. M., Tsukamoto, T., Tzanov, M., Uchida, Y., Vagins, M., Vargas, D., Varghese, M., Vasseur, G., Vilela, C., Villa, E., Vinning, W. G. S., Virginet, U., Vladisavljevic, T., Wachala, T., Walsh, J. G., Wang, Y., Wan, L., Wark, D., Wascko, M. O., Weber, A., Wendell, R., Wilking, M. J., Wilkinson, C., Wilson, J. R., Wood, K., Wret, C., Xia, J., Xu, Y. -h., Yamamoto, K., Yamamoto, T., Yanagisawa, C., Yang, G., Yano, T., Yasutome, K., Yershov, N., Yevarouskaya, U., Yokoyama, M., Yoshimoto, Y., Yoshimura, N., Yu, M., Zaki, R., Zalewska, A., Zalipska, J., Zaremba, K., Zarnecki, G., Zhao, X., Zhu, T., Ziembicki, M., Zimmerman, E. D., Zito, M., and Zsoldos, S.

Subjects
High Energy Physics - Experiment
Abstract

We report an updated measurement of the $\nu_{\mu}$-induced, and the first measurement of the $\bar{\nu}_{\mu}$-induced coherent charged pion production cross section on $^{12}C$ nuclei in the T2K experiment. This is measured in a restricted region of the final-state phase space for which $p_{\mu,\pi} > 0.2$ GeV, $\cos(\theta_{\mu}) > 0.8$ and $\cos(\theta_{\pi}) > 0.6$, and at a mean (anti)neutrino energy of 0.85 GeV using the T2K near detector. The measured $\nu_{\mu}$ CC coherent pion production flux-averaged cross section on $^{12}C$ is $(2.98 \pm 0.37 (stat.) \pm 0.31 (syst.) \substack{ +0.49 \\ -0.00 } \mathrm{ (Q^2\,model)}) \times 10^{-40}~\mathrm{cm}^{2}$. The new measurement of the $\bar{\nu}_{\mu}$-induced cross section on $^{12}{C}$ is $(3.05 \pm 0.71 (stat.) \pm 0.39 (syst.) \substack{ +0.74 \\ -0.00 } \mathrm{(Q^2\,model)}) \times 10^{-40}~\mathrm{cm}^{2}$. The results are compatible with both the NEUT 5.4.0 Berger-Sehgal (2009) and GENIE 2.8.0 Rein-Sehgal (2007) model predictions.

Published
2023

34. An Interpretable Machine Learning Model with Deep Learning-based Imaging Biomarkers for Diagnosis of Alzheimer's Disease

Author

Kang, Wenjie, Li, Bo, Papma, Janne M., Jiskoot, Lize C., De Deyn, Peter Paul, Biessels, Geert Jan, Claassen, Jurgen A. H. R., Middelkoop, Huub A. M., van der Flier, Wiesje M., Ramakers, Inez H. G. B., Klein, Stefan, and Bron, Esther E.

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Machine learning methods have shown large potential for the automatic early diagnosis of Alzheimer's Disease (AD). However, some machine learning methods based on imaging data have poor interpretability because it is usually unclear how they make their decisions. Explainable Boosting Machines (EBMs) are interpretable machine learning models based on the statistical framework of generalized additive modeling, but have so far only been used for tabular data. Therefore, we propose a framework that combines the strength of EBM with high-dimensional imaging data using deep learning-based feature extraction. The proposed framework is interpretable because it provides the importance of each feature. We validated the proposed framework on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset, achieving accuracy of 0.883 and area-under-the-curve (AUC) of 0.970 on AD and control classification. Furthermore, we validated the proposed framework on an external testing set, achieving accuracy of 0.778 and AUC of 0.887 on AD and subjective cognitive decline (SCD) classification. The proposed framework significantly outperformed an EBM model using volume biomarkers instead of deep learning-based features, as well as an end-to-end convolutional neural network (CNN) with optimized architecture., Comment: 11 pages, 5 figures

Published
2023

36. Deep learning denoising by dimension reduction: Application to the ORION-B line cubes

Author

Einig, Lucas, Pety, Jérôme, Roueff, Antoine, Vandame, Paul, Chanussot, Jocelyn, Gerin, Maryvonne, Orkisz, Jan H., Palud, Pierre, Santa-Maria, Miriam Garcia, Magalhaes, Victor de Souza, Bešlić, Ivana, Bardeau, Sébastien, Bron, Emeric E., Chainais, Pierre, Goicoechea, Javier R, Gratier, Pierre, Veloso, Viviana Guzman, Hughes, Annie, Kainulainen, Jouni, Languignon, David, Lallement, Rosine, Levrier, François, Lis, Dariuscz C., Liszt, Harvey, Bourlot, Jacques Le, Petit, Franck Le, Öberg, Karin Danielsson, Peretto, Nicolas, Roueff, Evelyne, Sievers, Albrecht, Thouvenin, Pierre-Antoine, and Tremblin, Pascal

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

Context. The availability of large bandwidth receivers for millimeter radio telescopes allows the acquisition of position-position-frequency data cubes over a wide field of view and a broad frequency coverage. These cubes contain much information on the physical, chemical, and kinematical properties of the emitting gas. However, their large size coupled with inhomogenous signal-to-noise ratio (SNR) are major challenges for consistent analysis and interpretation.Aims. We search for a denoising method of the low SNR regions of the studied data cubes that would allow to recover the low SNR emission without distorting the signals with high SNR.Methods. We perform an in-depth data analysis of the 13 CO and C 17 O (1 -- 0) data cubes obtained as part of the ORION-B large program performed at the IRAM 30m telescope. We analyse the statistical properties of the noise and the evolution of the correlation of the signal in a given frequency channel with that of the adjacent channels. This allows us to propose significant improvements of typical autoassociative neural networks, often used to denoise hyperspectral Earth remote sensing data. Applying this method to the 13 CO (1 -- 0) cube, we compare the denoised data with those derived with the multiple Gaussian fitting algorithm ROHSA, considered as the state of the art procedure for data line cubes.Results. The nature of astronomical spectral data cubes is distinct from that of the hyperspectral data usually studied in the Earth remote sensing literature because the observed intensities become statistically independent beyond a short channel separation. This lack of redundancy in data has led us to adapt the method, notably by taking into account the sparsity of the signal along the spectral axis. The application of the proposed algorithm leads to an increase of the SNR in voxels with weak signal, while preserving the spectral shape of the data in high SNR voxels.Conclusions. The proposed algorithm that combines a detailed analysis of the noise statistics with an innovative autoencoder architecture is a promising path to denoise radio-astronomy line data cubes. In the future, exploring whether a better use of the spatial correlations of the noise may further improve the denoising performances seems a promising avenue. In addition

Published
2023
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37. The extremely sharp transition between molecular and ionized gas in the Horsehead nebula

Author

Hernández-Vera, C., Guzmán, V. V., Goicoechea, J. R., Maillard, V., Pety, J., Petit, F. Le, Gerin, M., Bron, E., Roueff, E., Abergel, A., Schirmer, T., Carpenter, J., Gratier, P., Gordon, K., and Misselt, K.

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

(Abridged) Massive stars can determine the evolution of molecular clouds with their strong ultraviolet (UV) radiation fields. Moreover, UV radiation is relevant in setting the thermal gas pressure in star-forming clouds, whose influence can extend from the rims of molecular clouds to entire star-forming galaxies. Probing the fundamental structure of nearby molecular clouds is therefore crucial to understand how massive stars shape their surrounding medium and how fast molecular clouds are destroyed, specifically at their UV-illuminated edges, where models predict an intermediate zone of neutral atomic gas between the molecular cloud and the surrounding ionized gas whose size is directly related to the exposed physical conditions. We present the highest angular resolution (~$0.5$", corresponding to $207$ au) and velocity-resolved images of the molecular gas emission in the Horsehead nebula, using CO J=3-2 and HCO$^+$ J=4-3 observations with ALMA. We find that CO and HCO$^+$ are present at the edge of the cloud, very close to the ionization (H$^+$/H) and dissociation fronts (H/H$_2$), suggesting a very thin layer of neutral atomic gas (<$650$ au) and a small amount of CO-dark gas ($A_V=0.006-0.26$ mag) for stellar UV illumination conditions typical of molecular clouds in the Milky Way. The new ALMA observations reveal a web of molecular gas filaments with an estimated thermal gas pressure of $P_{\mathrm{th}} = (2.3 - 4.0) \times 10^6$ K cm$^{-3}$, and the presence of a steep density gradient at the cloud edge that can be well explained by stationary isobaric PDR models with pressures consistent with our estimations. However, in the HII region and PDR interface, we find $P_{\mathrm{th,PDR}} > P_{\mathrm{th,HII}}$, suggesting the gas is slightly compressed. Therefore, dynamical effects cannot be completely ruled out and even higher angular observations will be needed to unveil their role., Comment: 15 pages, 1 table, 9 figures; Accepted for publication in A&A

Published
2023
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38. Observation of high-energy neutrinos from the Galactic plane

Author

Abbasi, R., Ackermann, M., Adams, J., Aguilar, J. A., Ahlers, M., Ahrens, M., Alameddine, J. M., Alves Jr., A. A., Amin, N. M., Andeen, K., Anderson, T., Anton, G., Argüelles, C., Ashida, Y., Athanasiadou, S., Axani, S., Bai, X., V., A. Balagopal, Barwick, S. W., Basu, V., Baur, S., Bay, R., Beatty, J. J., Becker, K. -H., Tjus, J. Becker, Beise, J., Bellenghi, C., Benda, S., BenZvi, S., Berley, D., Bernardini, E., Besson, D. Z., Binder, G., Bindig, D., Blaufuss, E., Blot, S., Boddenberg, M., Bontempo, F., Book, J. Y., Borowka, J., Böser, S., Botner, O., Böttcher, J., Bourbeau, E., Bradascio, F., Braun, J., Brinson, B., Bron, S., Brostean-Kaiser, J., Burley, R. T., Busse, R. S., Campana, M. A., Carnie-Bronca, E. G., Chen, C., Chen, Z., Chirkin, D., Choi, K., Clark, B. A., Clark, K., Classen, L., Coleman, A., Collin, G. H., Connolly, A., Conrad, J. M., Coppin, P., Correa, P., Cowen, D. F., Cross, R., Dappen, C., Dave, P., De Clercq, C., DeLaunay, J. J., López, D. Delgado, Dembinski, H., Deoskar, K., Desai, A., Desiati, P., de Vries, K. D., de Wasseige, G., DeYoung, T., Diaz, A., Díaz-Vélez, J. C., Dittmer, M., Dujmovic, H., Dunkman, M., DuVernois, M. A., Ehrhardt, T., Eller, P., Engel, R., Erpenbeck, H., Evans, J., Evenson, P. A., Fan, K. L., Fazely, A. R., Fedynitch, A., Feigl, N., Fiedlschuster, S., Fienberg, A. T., Finley, C., Fischer, L., Fox, D., Franckowiak, A., Friedman, E., Fritz, A., Fürst, P., Gaisser, T. K., Gallagher, J., Ganster, E., Garcia, A., Garrappa, S., Gerhardt, L., Ghadimi, A., Glaser, C., Glauch, T., Glüsenkamp, T., Goehlke, N., Goldschmidt, A., Gonzalez, J. G., Goswami, S., Grant, D., Grégoire, T., Griswold, S., Günther, C., Gutjahr, P., Haack, C., Hallgren, A., Halliday, R., Halve, L., Halzen, F., Minh, M. Ha, Hanson, K., Hardin, J., Harnisch, A. A., Haungs, A., Helbing, K., Henningsen, F., Hettinger, E. C., Hickford, S., Hignight, J., Hill, C., Hill, G. C., Hoffman, K. D., Hoshina, K., Hou, W., Huang, F., Huber, M., Huber, T., Hultqvist, K., Hünnefeld, M., Hussain, R., Hymon, K., In, S., Iovine, N., Ishihara, A., Jansson, M., Japaridze, G. S., Jeong, M., Jin, M., Jones, B. J. P., Kang, D., Kang, W., Kang, X., Kappes, A., Kappesser, D., Kardum, L., Karg, T., Karl, M., Karle, A., Katz, U., Kauer, M., Kellermann, M., Kelley, J. L., Kheirandish, A., Kin, K., Kiryluk, J., Klein, S. R., Kochocki, A., Koirala, R., Kolanoski, H., Kontrimas, T., Köpke, L., Kopper, C., Kopper, S., Koskinen, D. J., Koundal, P., Kovacevich, M., Kowalski, M., Kozynets, T., Krupczak, E., Kun, E., Kurahashi, N., Lad, N., Gualda, C. Lagunas, Lanfranchi, J. L., Larson, M. J., Lauber, F., Lazar, J. P., Lee, J. W., Leonard, K., Leszczyńska, A., Li, Y., Lincetto, M., Liu, Q. R., Liubarska, M., Lohfink, E., Mariscal, C. J. Lozano, Lu, L., Lucarelli, F., Ludwig, A., Luszczak, W., Lyu, Y., Ma, W. Y., Madsen, J., Mahn, K. B. M., Makino, Y., Mancina, S., Mariş, I. C., Martinez-Soler, I., Maruyama, R., McCarthy, S., McElroy, T., McNally, F., Mead, J. V., Meagher, K., Mechbal, S., Medina, A., Meier, M., Meighen-Berger, S., Merckx, Y., Micallef, J., Mockler, D., Montaruli, T., Moore, R. W., Morik, K., Morse, R., Moulai, M., Mukherjee, T., Naab, R., Nagai, R., Nahnhauer, R., Naumann, U., Necker, J., Nguyen, L. V., Niederhausen, H., Nisa, M. U., Nowicki, S. C., Nygren, D., Pollmann, A. Obertacke, Oehler, M., Oeyen, B., Olivas, A., O'Sullivan, E., Pandya, H., Pankova, D. V., Park, N., Parker, G. K., Paudel, E. N., Paul, L., Heros, C. Pérez de los, Peters, L., Peterson, J., Philippen, S., Pieper, S., Pizzuto, A., Plum, M., Popovych, Y., Porcelli, A., Rodriguez, M. Prado, Pries, B., Przybylski, G. T., Raab, C., Rack-Helleis, J., Raissi, A., Rameez, M., Rawlins, K., Rea, I. C., Rechav, Z., Rehman, A., Reichherzer, P., Reimann, R., Renzi, G., Resconi, E., Reusch, S., Rhode, W., Richman, M., Riedel, B., Roberts, E. J., Robertson, S., Roellinghoff, G., Rongen, M., Rott, C., Ruhe, T., Ryckbosch, D., Cantu, D. Rysewyk, Safa, I., Saffer, J., Salazar-Gallegos, D., Sampathkumar, P., Herrera, S. E. Sanchez, Sandrock, A., Santander, M., Sarkar, S., Satalecka, K., Schaufel, M., Schieler, H., Schindler, S., Schmidt, T., Schneider, A., Schneider, J., Schröder, F. G., Schumacher, L., Schwefer, G., Sclafani, S., Seckel, D., Seunarine, S., Sharma, A., Shefali, S., Shimizu, N., Silva, M., Skrzypek, B., Smithers, B., Snihur, R., Soedingrekso, J., Sogaard, A., Soldin, D., Spannfellner, C., Spiczak, G. M., Spiering, C., Stamatikos, M., Stanev, T., Stein, R., Stettner, J., Stezelberger, T., Stokstad, B., Stürwald, T., Stuttard, T., Sullivan, G. W., Taboada, I., Ter-Antonyan, S., Thwaites, J., Tilav, S., Tischbein, F., Tollefson, K., Tönnis, C., Toscano, S., Tosi, D., Trettin, A., Tselengidou, M., Tung, C. F., Turcati, A., Turcotte, R., Turley, C. F., Twagirayezu, J. P., Ty, B., Elorrieta, M. A. Unland, Valtonen-Mattila, N., Vandenbroucke, J., van Eijndhoven, N., Vannerom, D., van Santen, J., Veitch-Michaelis, J., Verpoest, S., Walck, C., Wang, W., Watson, T. B., Weaver, C., Weigel, P., Weindl, A., Weiss, M. J., Weldert, J., Wendt, C., Werthebach, J., Weyrauch, M., Whitehorn, N., Wiebusch, C. H., Willey, N., Williams, D. R., Wolf, M., Wrede, G., Wulff, J., Xu, X. W., Yanez, J. P., Yildizci, E., Yoshida, S., Yu, S., Yuan, T., Zhang, Z., and Zhelnin, P.

Subjects
Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Astrophysics of Galaxies, Computer Science - Machine Learning
Abstract

The origin of high-energy cosmic rays, atomic nuclei that continuously impact Earth's atmosphere, has been a mystery for over a century. Due to deflection in interstellar magnetic fields, cosmic rays from the Milky Way arrive at Earth from random directions. However, near their sources and during propagation, cosmic rays interact with matter and produce high-energy neutrinos. We search for neutrino emission using machine learning techniques applied to ten years of data from the IceCube Neutrino Observatory. We identify neutrino emission from the Galactic plane at the 4.5$\sigma$ level of significance, by comparing diffuse emission models to a background-only hypothesis. The signal is consistent with modeled diffuse emission from the Galactic plane, but could also arise from a population of unresolved point sources., Comment: Submitted on May 12th, 2022; Accepted on May 4th, 2023

Published
2023
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39. The genome of a bunyavirus cannot be defined at the level of the viral particle but only at the scale of the viral population.

Author

Dasgupta, Ranjit, Parker, Maxwell, Ben-Mahmoud, Sulley, Verdin, Eric, Gognalons, Patrick, Ancelin, Aurélie, Laï Kee Him, Joséphine, Girard, Justine, Vernerey, Marie-Stéphanie, Fernandez, Emmanuel, Filloux, Denis, Roumagnac, Philippe, Bron, Patrick, Michalakis, Yannis, Blanc, Stéphane, Yvon, Michel, German, Thomas, and Ullman, Diane

Subjects
Bunyavirales, genome formula, genome packaging, multipartite virus, orthotospovirus, Orthobunyavirus, RNA, Viral, Tospovirus, Genome, Viral, Virion
Abstract

Bunyaviruses are enveloped negative or ambisense single-stranded RNA viruses with a genome divided into several segments. The canonical view depicts each viral particle packaging one copy of each genomic segment in one polarity named the viral strand. Several opposing observations revealed nonequal ratios of the segments, uneven number of segments per virion, and even packaging of viral complementary strands. Unfortunately, these observations result from studies often addressing other questions, on distinct viral species, and not using accurate quantitative methods. Hence, what RNA segments and strands are packaged as the genome of any bunyavirus remains largely ambiguous. We addressed this issue by first investigating the virion size distribution and RNA content in populations of the tomato spotted wilt virus (TSWV) using microscopy and tomography. These revealed heterogeneity in viral particle volume and amount of RNA content, with a surprising lack of correlation between the two. Then, the ratios of all genomic segments and strands were established using RNA sequencing and qRT-PCR. Within virions, both plus and minus strands (but no mRNA) are packaged for each of the three L, M, and S segments, in reproducible nonequimolar proportions determined by those in total cell extracts. These results show that virions differ in their genomic content but together build up a highly reproducible genetic composition of the viral population. This resembles the genome formula described for multipartite viruses, with which some species of the order Bunyavirales may share some aspects of the way of life, particularly emerging properties at a supravirion scale.

Published
2023

40. OH as a probe of the warm-water cycle in planet-forming disks

Author

Zannese, Marion, Tabone, Benoît, Habart, Emilie, Goicoechea, Javier R., Zanchet, Alexandre, van Dishoeck, Ewine F., van Hemert, Marc C., Black, John H., Tielens, Alexander G. G. M., Veselinova, A., Jambrina, P. G., Menendez, M., Verdasco, E., Aoiz, F. J., Gonzalez-Sanchez, L., Trahin, Boris, Dartois, Emmanuel, Berné, Olivier, Peeters, Els, He, Jinhua, Sidhu, Ameek, Chown, Ryan, Schroetter, Ilane, Van De Putte, Dries, Canin, Amélie, Alarcón, Felipe, Abergel, Alain, Bergin, Edwin A., Bernard-Salas, Jeronimo, Boersma, Christiaan, Bron, Emeric, Cami, Jan, Dicken, Daniel, Elyajouri, Meriem, Fuente, Asunción, Gordon, Karl D., Issa, Lina, Joblin, Christine, Kannavou, Olga, Khan, Baria, Languignon, David, Le Gal, Romane, Maragkoudakis, Alexandros, Meshaka, Raphael, Okada, Yoko, Onaka, Takashi, Pasquini, Sofia, Pound, Marc W., Robberto, Massimo, Röllig, Markus, Schefter, Bethany, Schirmer, Thiébaut, Vicente, Sílvia, and Wolfire, Mark G.

Published
2024
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41. Prior-knowledge-informed deep learning for lacune detection and quantification using multi-site brain MRI

Author

Li, Bo, de Bresser, Jeroen, Niessen, Wiro, van Osch, Matthias, van der Flier, Wiesje M., Biessels, Geert Jan, Vernooij, Meike W., and Bron, Esther

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Lacunes of presumed vascular origin, also referred to as lacunar infarcts, are important to assess cerebral small vessel disease and cognitive diseases such as dementia. However, visual rating of lacunes from imaging data is challenging, time-consuming, and rater-dependent, owing to their small size, sparsity, and mimics. Whereas recent developments in automatic algorithms have shown to make the detection of lacunes faster while preserving sensitivity, they also showed a large number of false positives, which makes them impractical for use in clinical practice or large-scale studies. Here, we develop a novel framework that, in addition to lacune detection, outputs a categorical burden score. This score could provide a more practical estimate of lacune presence that simplifies and effectively accelerates the imaging assessment of lacunes. We hypothesize that the combination of detection and the categorical score makes the procedure less sensitive to noisy labels., Comment: Abstract presented at the 2022 annual meeting of the Organization for Human Brain Mapping (OHBM).Second place at the VALDO MICCAI challenge for cerebral lacune detection

Published
2023

42. Deep learning-based group-wise registration for longitudinal MRI analysis in glioma

Author

Hammecher, Claudia Chinea, van Garderen, Karin, Smits, Marion, Wesseling, Pieter, Westerman, Bart, French, Pim, Kouwenhoven, Mathilde, Verhaak, Roel, Vos, Frans, Bron, Esther, and Li, Bo

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

Glioma growth may be quantified with longitudinal image registration. However, the large mass-effects and tissue changes across images pose an added challenge. Here, we propose a longitudinal, learning-based, and groupwise registration method for the accurate and unbiased registration of glioma MRI. We evaluate on a dataset from the Glioma Longitudinal AnalySiS consortium and compare it to classical registration methods. We achieve comparable Dice coefficients, with more detailed registrations, while significantly reducing the runtime to under a minute. The proposed methods may serve as an alternative to classical toolboxes, to provide further insight into glioma growth., Comment: Digital poster presented at the annual meeting of the International Society for Magnetic Resonance in Medicine (ISMRM) 2023. A 6 minute video about this work is available for browsing by the conference website (Program number: 4361)

Published
2023

43. Dissociative recombination of N$_2$H$^+$: A revisited study

Author

Mezei, J. Zs, Ayouz, M. A., Orbán, A., Abdoulanziz, A., Talbi, D., Kashinski, D. O., Bron, E., Kokoouline, V., and Schneider, I. F.

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies, Physics - Atomic Physics
Abstract

Dissociative recombination of N$_2$H$^+$ is explored in a two-step theoretical study. In a first step, a diatomic (1D) rough model with frozen NN bond and frozen angles is adopted, in the framework of the multichannel quantum defect theory (MQDT). The importance of the indirect mechanism and of the bending mode is revealed, in spite of the disagreement between our cross section and the experimental one. In a second step, we use our recently elaborated 3D approach based on the normal mode approximation combined with R-matrix theory and MQDT. This approach results in satisfactory agreement with storage-ring measurements, significantly better at very low energy than the former calculations., Comment: 9 pages, 5 figures, 1 table

Published
2023
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44. Updated T2K measurements of muon neutrino and antineutrino disappearance using 3.6 $\times$ 10$^{21}$ protons on target

Author

Abe, K., Akhlaq, N., Akutsu, R., Alarakia-Charles, H., Ali, A., Hakim, Y. I. Alj, Monsalve, S. Alonso, Alt, C., Andreopoulos, C., Antonova, M., Aoki, S., Arihara, T., Asada, Y., Ashida, Y., Atkin, E. T., Barbi, M., Barker, G. J., Barr, G., Barrow, D., Batkiewicz-Kwasniak, M., Bench, F., Berardi, V., Berns, L., Bhadra, S., Blanchet, A., Blondel, A., Bolognesi, S., Bonus, T., Bordoni, S., Boyd, S. B., Bravar, A., Bronner, C., Bron, S., Bubak, A., Avanzini, M. Buizza, Caballero, J. A., Calabria, N. F., Cao, S., Carabadjac, D., Carter, A. J., Cartwright, S. L., Casado, M. P., Catanesi, M. G., Cervera, A., Chakrani, J., Cherdack, D., Chong, P. S., Christodoulou, G., Chvirova, A., Cicerchia, M., Coleman, J., Collazuol, G., Cook, L., Cudd, A., Dalmazzone, C., Daret, T., Dasgupta, P., Davydov, Yu. I., De Roeck, A., De Rosa, G., Dealtry, T., Delogu, C. C., Densham, C., Dergacheva, A., Di Lodovico, F., Dolan, S., Douqa, D., Doyle, T. A., Drapier, O., Dumarchez, J., Dunne, P., Dygnarowicz, K., Eguchi, A., Emery-Schrenk, S., Erofeev, G., Ershova, A., Eurin, G., Fedorova, D., Fedotov, S., Feltre, M., Finch, A. J., Aguirre, G. A. Fiorentini, Fiorillo, G., Fitton, M. D., Patiño, J. M. Franco, Friend, M., Fujii, Y., Fukuda, Y., Furui, Y., Fusshoeller, K., Giannessi, L., Giganti, C., Glagolev, V., Gonin, M., Rosa, J. González, Goodman, E. A. G., Gorin, A., Grassi, M., Guigue, M., Hadley, D. R., Haigh, J. T., Hamacher-Baumann, P., Harris, D. A., Hartz, M., Hasegawa, T., Hassani, S., Hastings, N. C., Hayato, Y., Henaff, D., Hiramoto, A., Hogan, M., Holeczek, J., Holin, A., Holvey, T., Van, N. T. Hong, Honjo, T., Iacob, F., Ichikawa, A. K., Ikeda, M., Ishida, T., Ishitsuka, M., Israel, H. T., Iwamoto, K., Izmaylov, A., Izumi, N., Jakkapu, M., Jamieson, B., Jenkins, S. J., Jesús-Valls, C., Jiang, J. J., Ji, J. Y., Jonsson, P., Joshi, S., Jung, C. K., Jurj, P. B., Kabirnezhad, M., Kaboth, A. C., Kajita, T., Kakuno, H., Kameda, J., Kasetti, S. P., Kataoka, Y., Katayama, Y., Katori, T., Kawaue, M., Kearns, E., Khabibullin, M., Khotjantsev, A., Kikawa, T., Kikutani, H., King, S., Kiseeva, V., Kisiel, J., Kobata, T., Kobayashi, H., Kobayashi, T., Koch, L., Kodama, S., Konaka, A., Kormos, L. L., Koshio, Y., Kostin, A., Koto, T., Kowalik, K., Kudenko, Y., Kudo, Y., Kuribayashi, S., Kurjata, R., Kutter, T., Kuze, M., La Commara, M., Labarga, L., Lachner, K., Lagoda, J., Lakshmi, S. M., James, M. Lamers, Lamoureux, M., Langella, A., Laporte, J. -F., Last, D., Latham, N., Laveder, M., Lavitola, L., Lawe, M., Lee, Y., Lin, C., Lin, S. -K., Litchfield, R. P., Liu, S. L., Li, W., Longhin, A., Long, K. R., Moreno, A. Lopez, Ludovici, L., Lu, X., Lux, T., Machado, L. N., Magaletti, L., Mahn, K., Malek, M., Mandal, M., Manly, S., Marino, A. D., Marti-Magro, L., Martin, D. G. R., Martini, M., Martin, J. F., Maruyama, T., Matsubara, T., Matveev, V., Mauger, C., Mavrokoridis, K., Mazzucato, E., McCauley, N., McElwee, J., McFarland, K. S., McGrew, C., McKean, J., Mefodiev, A., Megias, G. D., Mehta, P., Mellet, L., Metelko, C., Mezzetto, M., Miller, E., Minamino, A., Mineev, O., Mine, S., Miura, M., Bueno, L. Molina, Moriyama, S., Morrison, P., Mueller, Th. A., Munford, D., Munteanu, L., Nagai, K., Nagai, Y., Nakadaira, T., Nakagiri, K., Nakahata, M., Nakajima, Y., Nakamura, A., Nakamura, H., Nakamura, K., Nakamura, K. D., Nakano, Y., Nakayama, S., Nakaya, T., Nakayoshi, K., Naseby, C. E. R., Ngoc, T. V., Nguyen, V. Q., Niewczas, K., Nishimori, S., Nishimura, Y., Nishizaki, K., Nosek, T., Nova, F., Novella, P., Nugent, J. C., O'Keeffe, H. M., O'Sullivan, L., Odagawa, T., Ogawa, T., Okada, R., Okinaga, W., Okumura, K., Okusawa, T., Ospina, N., Osu, L., Owen, R. A., Oyama, Y., Palladino, V., Paolone, V., Pari, M., Parlone, J., Parsa, S., Pasternak, J., Pavin, M., Payne, D., Penn, G. C., Pershey, D., Pickering, L., Pidcott, C., Pintaudi, G., Pistillo, C., Popov, B., Yrey, A. J. Portocarrero, Porwit, K., Posiadala-Zezula, M., Prabhu, Y. S., Pupilli, F., Quilain, B., Radermacher, T., Radicioni, E., Radics, B., Ramírez, M. A., Ratoff, P. N., Reh, M., Riccio, C., Rondio, E., Roth, S., Roy, N., Rubbia, A., Ruggeri, A. C., Ruggles, C. A., Rychter, A., Sakashita, K., Sánchez, F., Santucci, G., Schefke, T., Schloesser, C. M., Scholberg, K., Scott, M., Seiya, Y., Sekiguchi, T., Sekiya, H., Sgalaberna, D., Shaikhiev, A., Shaker, F., Shiozawa, M., Shorrock, W., Shvartsman, A., Skrobova, N., Skwarczynski, K., Smyczek, D., Smy, M., Sobczyk, J. T., Sobel, H., Soler, F. J. P., Sonoda, Y., Speers, A. J., Spina, R., Suslov, I. A., Suvorov, S., Suzuki, A., Suzuki, S. Y., Suzuki, Y., Sztuc, A. A., Tada, M., Tairafune, S., Takayasu, S., Takeda, A., Takeuchi, Y., Takifuji, K., Tanaka, H. K., Tanigawa, H., Tanihara, Y., Tani, M., Teklu, A., Tereshchenko, V. V., Teshima, N., Thamm, N., Thompson, L. F., Toki, W., Touramanis, C., Towstego, T., Tsui, K. M., Tsukamoto, T., Tzanov, M., Uchida, Y., Vagins, M., Vargas, D., Varghese, M., Vasseur, G., Vilela, C., Villa, E., Vinning, W. G. S., Virginet, U., Vladisavljevic, T., Wachala, T., Wakabayashi, D., Walsh, J. G., Wang, Y., Wan, L., Wark, D., Wascko, M. O., Weber, A., Wendell, R., Wilking, M. J., Wilkinson, C., Wilson, J. R., Wood, K., Wret, C., Xia, J., Xu, Y. -h., Yamamoto, K., Yamamoto, T., Yanagisawa, C., Yang, G., Yano, T., Yasutome, K., Yershov, N., Yevarouskaya, U., Yokoyama, M., Yoshimoto, Y., Yoshimura, N., Yu, M., Zaki, R., Zalewska, A., Zalipska, J., Zaremba, K., Zarnecki, G., Zhao, X., Zhu, T., Ziembicki, M., Zimmerman, E. D., Zito, M., and Zsoldos, S.

Subjects
High Energy Physics - Experiment
Abstract

Muon neutrino and antineutrino disappearance probabilities are identical in the standard three-flavor neutrino oscillation framework, but CPT violation and non-standard interactions can violate this symmetry. In this work we report the measurements of $\sin^{2} \theta_{23}$ and $\Delta m_{32}^2$ independently for neutrinos and antineutrinos. The aforementioned symmetry violation would manifest as an inconsistency in the neutrino and antineutrino oscillation parameters. The analysis discussed here uses a total of 1.97$\times$10$^{21}$ and 1.63$\times$10$^{21}$ protons on target taken with a neutrino and antineutrino beam respectively, and benefits from improved flux and cross-section models, new near detector samples and more than double the data reducing the overall uncertainty of the result. No significant deviation is observed, consistent with the standard neutrino oscillation picture.

Published
2023

45. Imatinib Adherence and Persistence in Patients with Chronic Myeloid Leukemia in Belgium: Evidence from Real-World Data

Author

Michiels S, Tricas-Sauras S, Salaroli A, Bron D, Lewalle P, Vanschoenbeek K, Poirel HA, and Kirakoya-Samadoulougou F

Subjects
adherence, persistence, imatinib, chronic myeloid leukemia, pharmacy refills data, belgium, Medicine (General), R5-920
Abstract

Sandra Michiels,1– 3 Sandra Tricas-Sauras,2 Adriano Salaroli,3 Dominique Bron,3 Philippe Lewalle,3 Katrijn Vanschoenbeek,4 Hélène A Poirel,4 Fati Kirakoya-Samadoulougou1 1Center for Research in Epidemiology, Biostatistics and Clinical Research, School of Public Health, Université Libre de Bruxelles, Brussels, Belgium; 2Center for Research in Social Approaches to Health, School of Public Health, Université Libre de Bruxelles, Brussels, Belgium; 3Department of Hematology/Oncology, Institut Jules Bordet, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium; 4Belgian Cancer Registry, Brussels, BelgiumCorrespondence: Sandra Michiels, Email sandra.michiels@ulb.be; sandra.michiels@hubruxelles.bePurpose: Imatinib adherence and persistence are key components of the successful treatment of Chronic Myeloid Leukemia (CML). In Belgium, there is no study assessing these behaviors at a national level. Our study aimed to provide the first nationwide measure and to identify associated pharmacy-based predictors (age, gender, comorbidities). We also assessed mortality and transplantation incidence according to adherence status.Methods: Based on medico-administrative database linkage, we identified a retrospective Belgian cohort of 1194 patients diagnosed with CML between 2004 and 2016 and treated with imatinib. Adherence was measured over 24 months, considering the proportion of days covered (PDC). Persistence was measured as the time until discontinuation (gap of ≥ 90 days). Multivariable Poisson regression models with robust standard error were conducted to identify predictors associated with adherence (≥ 90% PDC). To identify factors associated with persistence, a multivariable Cox regression was performed.Results: At six months, 60.3% of patients were adherent, declining to 41.5% at 12 months, and to 30.1% at two-year follow-up (n=998). Adherence was greater at a younger age (eg 31– 40 years vs ≥ 75 years, adjusted prevalence ratio (aPR) 1.73; 95% confidence interval (CI): 1.09– 2.77) and among patients with no comorbidity (0 vs ≥ 2 comorbidities (aPR 1.56; 95% CI: 1.11– 2.19). The median persistence was 334.5 days (Q1:200–Q3:505.5); persistence at 24 months was 83.6% (n=998). Only age was associated with higher risk of discontinuation, with adjusted hazard ratio (aHR) of 6.05 for patients ≥ 75 years (95% CI: 5.52– 6.58). Transplants and deaths mainly occurred in patients defined as non-adherent at 24 months.Conclusion: This Belgian nationwide representative study revealed a critical low level of imatinib adherence, which decreased over time even though persistence was high at six months. We pinpointed pharmacy-based predictors that were easily identifiable by health care stakeholders in order to undertake interventions to improve adherence.Plain Language Summary: The introduction of imatinib, a new oral anticancer medication, has transformed chronic myeloid leukemia (CML) from a fatal disease to a chronic disease. However, the success of imatinib partly depends on how long a patient continues to take it (persistence) and the extent to which they take imatinib as prescribed (adherence). Over a 24-month follow-up period, this study aimed to provide an assessment of imatinib adherence and persistence for the first time and to identify associated risk factors. Using pharmacy dispensing data, our study revealed that whilst very few CML patients discontinued imatinib, a considerable proportion struggled to adhere to imatinib recommendations, with a decreasing rate of adherence and persistence over time. We have identified some demographic and clinical characteristics associated with higher risk of poor adherence and early discontinuation. The current study’s findings will help healthcare professionals to screen adherence behaviors prospectively and design specific interventions to maintain long-term optimal adherence to imatinib.Keywords: adherence, persistence, imatinib, chronic myeloid leukemia, pharmacy refills data, Belgium

Published
2024

46. Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon

Author

S. J. Salisbury, R. Ruiz Daniels, S. J. Monaghan, J. E. Bron, P. R. Villamayor, O. Gervais, M. D. Fast, L. Sveen, R. D. Houston, N. Robinson, and D. Robledo

Subjects
snRNAseq, Salmon, Aquaculture, Disease, Parasite, Sea lice, Biology (General), QH301-705.5
Abstract

Abstract Background Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. Results We characterized the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12 h, 24 h, 36 h, 48 h, and 60 h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. Conclusions Our results highlight the key role of keratinocytes in coho salmon’s sea lice resistance and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.

Published
2024
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47. The lactococcal ICE-ome encodes a repertoire of exchangeable traits with potential industrial relevance

Author

Simon van der Els, Jos Boekhorst, Peter A. Bron, and Michiel Kleerebezem

Subjects
Lactococcus lactis, Mobile genetic elements, Integrative conjugative element (ICE), Comparative genomics, ICE-cargo, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Dairy industries apply selected lactococcal strains and mixed cultures to produce diverse fermented products with distinctive flavor and texture properties. Innovation of the starter culture functionality in cheese applications embraces natural biodiversity of the Lactococcus species to identify novel strains with alternative flavor or texture forming capacities and/or increased processing robustness and phage resistance. Mobile genetic elements (MGE), like integrative conjugative elements (ICEs) play an important role in shaping the biodiversity of bacteria. Besides the genes involved in the conjugation of ICEs from donor to recipient strains, these elements also harbor cargo genes that encode a wide range of functions. The definition of such cargo genes can only be achieved by accurate identification of the ICE boundaries (delimiting). Here, we delimited 25 ICEs in lactococcal genome sequences with low contig numbers using insertion-sites flanking single-copy core-genome genes as markers for each of the distinct ICE-integrases we identified previously within the conserved ICE-core genes. For ICEs in strains for which genome information with large numbers of contigs is available, we exemplify that CRISPR-Cas9 driven ICE-curing, followed by resequencing, allows accurate delimitation and cargo definition of ICEs. Finally, we compare and contrast the cargo gene repertoire of the 26 delimited lactococcal ICEs, identifying high plasticity among the cargo of lactococccal ICEs and a range of encoded functions that is of apparent industrial interest, including restriction modification, abortive infection, and stress adaptation genes.

Published
2024
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48. First measurement of muon neutrino charged-current interactions on hydrocarbon without pions in the final state using multiple detectors with correlated energy spectra at T2K

Author

Abe, K., Akhlaq, N., Akutsu, R., Alarakia-Charles, H., Ali, A., Hakim, Y. I. Alj, Monsalve, S. Alonso, Alt, C., Andreopoulos, C., Antonova, M., Aoki, S., Arihara, T., Asada, Y., Ashida, Y., Atkin, E. T., Barbi, M., Barker, G. J., Barr, G., Barrow, D., Batkiewicz-Kwasniak, M., Bench, F., Berardi, V., Berns, L., Bhadra, S., Blanchet, A., Blondel, A., Bolognesi, S., Bonus, T., Bordoni, S., Boyd, S. B., Bravar, A., Bronner, C., Bron, S., Bubak, A., Avanzini, M. Buizza, Caballero, J. A., Calabria, N. F., Cao, S., Carabadjac, D., Carter, A. J., Cartwright, S. L., Casado, M. P., Catanesi, M. G., Cervera, A., Chakrani, J., Cherdack, D., Chong, P. S., Christodoulou, G., Chvirova, A., Cicerchia, M., Coleman, J., Collazuol, G., Cook, L., Cudd, A., Dalmazzone, C., Daret, T., Dasgupta, P., Davydov, Yu. I., De Roeck, A., De Rosa, G., Dealtry, T., Delogu, C. C., Densham, C., Dergacheva, A., Di Lodovico, F., Dolan, S., Douqa, D., Doyle, T. A., Drapier, O., Dumarchez, J., Dunne, P., Dygnarowicz, K., Eguchi, A., Emery-Schrenk, S., Erofeev, G., Ershova, A., Eurin, G., Fedorova, D., Fedotov, S., Feltre, M., Finch, A. J., Aguirre, G. A. Fiorentini, Fiorillo, G., Fitton, M. D., Patiño, J. M. Franco, Friend, M., Fujii, Y., Fukuda, Y., Furui, Y., Fusshoeller, K., Giannessi, L., Giganti, C., Glagolev, V., Gonin, M., Rosa, J. González, Goodman, E. A. G., Gorin, A., Grassi, M., Guigue, M., Hadley, D. R., Haigh, J. T., Hamacher-Baumann, P., Harris, D. A., Hartz, M., Hasegawa, T., Hassani, S., Hastings, N. C., Hayato, Y., Henaff, D., Hiramoto, A., Hogan, M., Holeczek, J., Holin, A., Holvey, T., Van, N. T. Hong, Honjo, T., Iacob, F., Ichikawa, A. K., Ikeda, M., Ishida, T., Ishitsuka, M., Israel, H. T., Izmaylov, A., Izumi, N., Jakkapu, M., Jamieson, B., Jenkins, S. J., Jesús-Valls, C., Jiang, J. J., Ji, J. Y., Jonsson, P., Joshi, S., Jung, C. K., Jurj, P. B., Kabirnezhad, M., Kaboth, A. C., Kajita, T., Kakuno, H., Kameda, J., Kasetti, S. P., Kataoka, Y., Katori, T., Kawaue, M., Kearns, E., Khabibullin, M., Khotjantsev, A., Kikawa, T., King, S., Kiseeva, V., Kisiel, J., Kobata, T., Kobayashi, H., Kobayashi, T., Koch, L., Kodama, S., Konaka, A., Kormos, L. L., Koshio, Y., Kostin, A., Koto, T., Kowalik, K., Kudenko, Y., Kudo, Y., Kuribayashi, S., Kurjata, R., Kutter, T., Kuze, M., La Commara, M., Labarga, L., Lachner, K., Lagoda, J., Lakshmi, S. M., James, M. Lamers, Lamoureux, M., Langella, A., Laporte, J. -F., Last, D., Latham, N., Laveder, M., Lavitola, L., Lawe, M., Lee, Y., Lin, C., Lin, S. -K., Litchfield, R. P., Liu, S. L., Li, W., Longhin, A., Long, K. R., Moreno, A. Lopez, Ludovici, L., Lu, X., Lux, T., Machado, L. N., Magaletti, L., Mahn, K., Malek, M., Mandal, M., Manly, S., Marino, A. D., Marti-Magro, L., Martin, D. G. R., Martini, M., Martin, J. F., Maruyama, T., Matsubara, T., Matveev, V., Mauger, C., Mavrokoridis, K., Mazzucato, E., McCauley, N., McElwee, J., McFarland, K. S., McGrew, C., McKean, J., Mefodiev, A., Megias, G. D., Mehta, P., Mellet, L., Metelko, C., Mezzetto, M., Miller, E., Minamino, A., Mineev, O., Mine, S., Miura, M., Bueno, L. Molina, Moriyama, S., Morrison, P., Mueller, Th. A., Munford, D., Munteanu, L., Nagai, K., Nagai, Y., Nakadaira, T., Nakagiri, K., Nakahata, M., Nakajima, Y., Nakamura, A., Nakamura, H., Nakamura, K., Nakamura, K. D., Nakano, Y., Nakayama, S., Nakaya, T., Nakayoshi, K., Naseby, C. E. R., Ngoc, T. V., Nguyen, V. Q., Niewczas, K., Nishimori, S., Nishimura, Y., Nishizaki, K., Nosek, T., Nova, F., Novella, P., Nugent, J. C., O'Keeffe, H. M., O'Sullivan, L., Odagawa, T., Ogawa, T., Okinaga, W., Okumura, K., Okusawa, T., Ospina, N., Osu, L., Owen, R. A., Oyama, Y., Palladino, V., Paolone, V., Pari, M., Parlone, J., Parsa, S., Pasternak, J., Pavin, M., Payne, D., Penn, G. C., Pershey, D., Pickering, L., Pidcott, C., Pintaudi, G., Pistillo, C., Popov, B., Yrey, A. J. Portocarrero, Porwit, K., Posiadala-Zezula, M., Prabhu, Y. S., Pupilli, F., Quilain, B., Radermacher, T., Radicioni, E., Radics, B., Ramírez, M. A., Ratoff, P. N., Reh, M., Riccio, C., Rondio, E., Roth, S., Roy, N., Rubbia, A., Ruggeri, A. C., Ruggles, C. A., Rychter, A., Sakashita, K., Sánchez, F., Santucci, G., Schefke, T., Schloesser, C. M., Scholberg, K., Scott, M., Seiya, Y., Sekiguchi, T., Sekiya, H., Sgalaberna, D., Shaikhiev, A., Shaker, F., Shiozawa, M., Shorrock, W., Shvartsman, A., Skrobova, N., Skwarczynski, K., Smyczek, D., Smy, M., Sobczyk, J. T., Sobel, H., Soler, F. J. P., Sonoda, Y., Speers, A. J., Spina, R., Suslov, I. A., Suvorov, S., Suzuki, A., Suzuki, S. Y., Suzuki, Y., Sztuc, A. A., Tada, M., Tairafune, S., Takayasu, S., Takeda, A., Takeuchi, Y., Takifuji, K., Tanaka, H. K., Tanigawa, H., Tani, M., Teklu, A., Tereshchenko, V. V., Teshima, N., Thamm, N., Thompson, L. F., Toki, W., Touramanis, C., Towstego, T., Tsui, K. M., Tsukamoto, T., Tzanov, M., Uchida, Y., Vagins, M., Vargas, D., Varghese, M., Vasseur, G., Vilela, C., Villa, E., Vinning, W. G. S., Virginet, U., Vladisavljevic, T., Wachala, T., Wakabayashi, D., Walsh, J. G., Wang, Y., Wan, L., Wark, D., Wascko, M. O., Weber, A., Wendell, R., Wilking, M. J., Wilkinson, C., Wilson, J. R., Wood, K., Wret, C., Xia, J., Xu, Y. -h., Yamamoto, K., Yamamoto, T., Yanagisawa, C., Yang, G., Yano, T., Yasutome, K., Yershov, N., Yevarouskaya, U., Yokoyama, M., Yoshimoto, Y., Yoshimura, N., Yu, M., Zaki, R., Zalewska, A., Zalipska, J., Zaremba, K., Zarnecki, G., Zhao, X., Zhu, T., Ziembicki, M., Zimmerman, E. D., Zito, M., and Zsoldos, S.

Subjects
High Energy Physics - Experiment
Abstract

This paper reports the first measurement of muon neutrino charged-current interactions without pions in the final state using multiple detectors with correlated energy spectra at T2K. The data was collected on hydrocarbon targets using the off-axis T2K near detector (ND280) and the on-axis T2K near detector (INGRID) with neutrino energy spectra peaked at 0.6 GeV and 1.1 GeV respectively. The correlated neutrino flux presents an opportunity to reduce the impact of the flux uncertainty and to study the energy dependence of neutrino interactions. The extracted double-differential cross sections are compared to several Monte Carlo neutrino-nucleus interaction event generators showing the agreement between both detectors individually and with the correlated result., Comment: Updated discussion in Sec. V-A; Updated author list

Published
2023
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49. Near-field imaging of domain switching in in-operando VO$_{2}$ devices

Author

Fernández, Sergio Salvía, Gao, Xing, Cassanelli, Silvia, Bron, Stephan, Hilgenkamp, Hans, and van Heumen, Erik

Subjects
Condensed Matter - Strongly Correlated Electrons, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Experimental insight in the nanoscale dynamics underlying switching in novel memristive devices is limited owing to the scarcity of techniques that can probe the electronic structure of these devices. Scattering scanning near-field optical microscopy is a relatively novel approach to probe the optical response of materials with a spatial resolution well below the diffraction limit. We use this non-invasive tool to demonstrate that it provides detailed information on the origin and memory behaviour of ultra-thin films of vanadium dioxide. Simultaneously recorded $I(V)$ characteristics and near-field maps show that discontinuities in the I(V) characteristics arise from the sudden switching of insulating domains to metallic domains. At the threshold voltage, the domains form a continuous current path. The metallic domains persist once the bias voltage is removed, but narrow monoclinic regions appear around the domain boundaries. The key advantage of our approach is that it provides detailed information on the electronic structure at length scales raging from tens of nanometers up to tens of microns and is easily applied under \textit{in operando} conditions., Comment: 5 pages, 3 figures

Published
2023

50. Measurements of neutrino oscillation parameters from the T2K experiment using $3.6\times10^{21}$ protons on target

Author

The T2K Collaboration, Abe, K., Akhlaq, N., Akutsu, R., Ali, A., Monsalve, S. Alonso, Alt, C., Andreopoulos, C., Antonova, M., Aoki, S., Arihara, T., Asada, Y., Ashida, Y., Atkin, E. T., Barbi, M., Barker, G. J., Barr, G., Barrow, D., Batkiewicz-Kwasniak, M., Bench, F., Berardi, V., Berns, L., Bhadra, S., Blanchet, A., Blondel, A., Bolognesi, S., Bonus, T., Bordoni, S., Boyd, S. B., Bravar, A., Bronner, C., Bron, S., Bubak, A., Avanzini, M. Buizza, Caballero, J. A., Calabria, N. F., Cao, S., Carabadjac, D., Carter, A. J., Cartwright, S. L., Catanesi, M. G., Cervera, A., Chakrani, J., Cherdack, D., Chong, P. S., Christodoulou, G., Chvirova, A., Cicerchia, M., Coleman, J., Collazuol, G., Cook, L., Cudd, A., Dalmazzone, C., Daret, T., Davydov, Yu. I., De Roeck, A., De Rosa, G., Dealtry, T., Delogu, C. C., Densham, C., Dergacheva, A., Di Lodovico, F., Dolan, S., Douqa, D., Doyle, T. A., Drapier, O., Dumarchez, J., Dunne, P., Dygnarowicz, K., Eguchi, A., Emery-Schrenk, S., Erofeev, G., Ershova, A., Eurin, G., Fedorova, D., Fedotov, S., Feltre, M., Finch, A. J., Aguirre, G. A. Fiorentini, Fiorillo, G., Fitton, M. D., Patiño, J. M. Franco, Friend, M., Fujii, Y., Fukuda, Y., Fusshoeller, K., Giannessi, L., Giganti, C., Glagolev, V., Gonin, M., Rosa, J. González, Goodman, E. A. G., Gorin, A., Grassi, M., Guigue, M., Hadley, D. R., Haigh, J. T., Hamacher-Baumann, P., Harris, D. A., Hartz, M., Hasegawa, T., Hassani, S., Hastings, N. C., Hayato, Y., Henaff, D., Hiramoto, A., Hogan, M., Holeczek, J., Holin, A., Holvey, T., Van, N. T. Hong, Honjo, T., Iacob, F., Ichikawa, A. K., Ikeda, M., Ishida, T., Ishitsuka, M., Israel, H. T., Iwamoto, K., Izmaylov, A., Izumi, N., Jakkapu, M., Jamieson, B., Jenkins, S. J., Jesús-Valls, C., Jiang, J. J., Jonsson, P., Joshi, S., Jung, C. K., Jurj, P. B., Kabirnezhad, M., Kaboth, A. C., Kajita, T., Kakuno, H., Kameda, J., Kasetti, S. P., Kataoka, Y., Katayama, Y., Katori, T., Kawaue, M., Kearns, E., Khabibullin, M., Khotjantsev, A., Kikawa, T., Kikutani, H., King, S., Kiseeva, V., Kisiel, J., Kobata, T., Kobayashi, H., Kobayashi, T., Koch, L., Kodama, S., Konaka, A., Kormos, L. L., Koshio, Y., Kostin, A., Koto, T., Kowalik, K., Kudenko, Y., Kudo, Y., Kuribayashi, S., Kurjata, R., Kutter, T., Kuze, M., La Commara, M., Labarga, L., Lachner, K., Lagoda, J., Lakshmi, S. M., James, M. Lamers, Lamoureux, M., Langella, A., Laporte, J. -F., Last, D., Latham, N., Laveder, M., Lavitola, L., Lawe, M., Lee, Y., Lin, C., Lin, S. -K., Litchfield, R. P., Liu, S. L., Li, W., Longhin, A., Long, K. R., Moreno, A. Lopez, Ludovici, L., Lu, X., Lux, T., Machado, L. N., Magaletti, L., Mahn, K., Malek, M., Mandal, M., Manly, S., Marino, A. D., Marti-Magro, L., Martin, D. G. R., Martini, M., Martin, J. F., Maruyama, T., Matsubara, T., Matveev, V., Mauger, C., Mavrokoridis, K., Mazzucato, E., McCauley, N., McElwee, J., McFarland, K. S., McGrew, C., McKean, J., Mefodiev, A., Megias, G. D., Mehta, P., Mellet, L., Metelko, C., Mezzetto, M., Miller, E., Minamino, A., Mineev, O., Mine, S., Miura, M., Bueno, L. Molina, Moriyama, S., Morrison, P., Mueller, Th. A., Munford, D., Munteanu, L., Nagai, K., Nagai, Y., Nakadaira, T., Nakagiri, K., Nakahata, M., Nakajima, Y., Nakamura, A., Nakamura, H., Nakamura, K., Nakamura, K. D., Nakano, Y., Nakayama, S., Nakaya, T., Nakayoshi, K., Naseby, C. E. R., Ngoc, T. V., Nguyen, V. Q., Niewczas, K., Nishimori, S., Nishimura, Y., Nishizaki, K., Nosek, T., Nova, F., Novella, P., Nugent, J. C., O'Keeffe, H. M., O'Sullivan, L., Odagawa, T., Ogawa, T., Okada, R., Okinaga, W., Okumura, K., Okusawa, T., Ospina, N., Owen, R. A., Oyama, Y., Palladino, V., Paolone, V., Pari, M., Parlone, J., Parsa, S., Pasternak, J., Pavin, M., Payne, D., Penn, G. C., Pershey, D., Pickering, L., Pidcott, C., Pintaudi, G., Pistillo, C., Popov, B., Porwit, K., Posiadala-Zezula, M., Prabhu, Y. S., Pupilli, F., Quilain, B., Radermacher, T., Radicioni, E., Radics, B., Ramírez, M. A., Ratoff, P. N., Reh, M., Riccio, C., Rondio, E., Roth, S., Roy, N., Rubbia, A., Ruggeri, A. C., Ruggles, C. A., Rychter, A., Sakashita, K., Sánchez, F., Santucci, G., Schloesser, C. M., Scholberg, K., Scott, M., Seiya, Y., Sekiguchi, T., Sekiya, H., Sgalaberna, D., Shaikhiev, A., Shaker, F., Shaykina, A., Shiozawa, M., Shorrock, W., Shvartsman, A., Skrobova, N., Skwarczynski, K., Smyczek, D., Smy, M., Sobczyk, J. T., Sobel, H., Soler, F. J. P., Sonoda, Y., Speers, A. J., Spina, R., Suslov, I. A., Suvorov, S., Suzuki, A., Suzuki, S. Y., Suzuki, Y., Sztuc, A. A., Tada, M., Tairafune, S., Takayasu, S., Takeda, A., Takeuchi, Y., Takifuji, K., Tanaka, H. K., Tanihara, Y., Tani, M., Teklu, A., Tereshchenko, V. V., Teshima, N., Thamm, N., Thompson, L. F., Toki, W., Touramanis, C., Towstego, T., Tsui, K. M., Tsukamoto, T., Tzanov, M., Uchida, Y., Vagins, M., Vargas, D., Varghese, M., Vasseur, G., Vilela, C., Villa, E., Vinning, W. G. S., Virginet, U., Vladisavljevic, T., Wachala, T., Walsh, J. G., Wang, Y., Wan, L., Wark, D., Wascko, M. O., Weber, A., Wendell, R., Wilking, M. J., Wilkinson, C., Wilson, J. R., Wood, K., Wret, C., Xia, J., Xu, Y. -h., Yamamoto, K., Yamamoto, T., Yanagisawa, C., Yang, G., Yano, T., Yasutome, K., Yershov, N., Yevarouskaya, U., Yokoyama, M., Yoshimoto, Y., Yoshimura, N., Yu, M., Zaki, R., Zalewska, A., Zalipska, J., Zaremba, K., Zarnecki, G., Zhao, X., Zhu, T., Ziembicki, M., Zimmerman, E. D., Zito, M., and Zsoldos, S.

Subjects
High Energy Physics - Experiment
Abstract

The T2K experiment presents new measurements of neutrino oscillation parameters using $19.7(16.3)\times10^{20}$ protons on target (POT) in (anti-)neutrino mode at the far detector (FD). Compared to the previous analysis, an additional $4.7\times10^{20}$ POT neutrino data was collected at the FD. Significant improvements were made to the analysis methodology, with the near-detector analysis introducing new selections and using more than double the data. Additionally, this is the first T2K oscillation analysis to use NA61/SHINE data on a replica of the T2K target to tune the neutrino flux model, and the neutrino interaction model was improved to include new nuclear effects and calculations. Frequentist and Bayesian analyses are presented, including results on $\sin^2\theta_{13}$ and the impact of priors on the $\delta_\mathrm{CP}$ measurement. Both analyses prefer the normal mass ordering and upper octant of $\sin^2\theta_{23}$ with a nearly maximally CP-violating phase. Assuming the normal ordering and using the constraint on $\sin^2\theta_{13}$ from reactors, $\sin^2\theta_{23}=0.561^{+0.021}_{-0.032}$ using Feldman--Cousins corrected intervals, and $\Delta{}m^2_{32}=2.494_{-0.058}^{+0.041}\times10^{-3}~\mathrm{eV^2}$ using constant $\Delta\chi^{2}$ intervals. The CP-violating phase is constrained to $\delta_\mathrm{CP}=-1.97_{-0.70}^{+0.97}$ using Feldman--Cousins corrected intervals, and $\delta_\mathrm{CP}=0,\pi$ is excluded at more than 90% confidence level. A Jarlskog invariant of zero is excluded at more than $2\sigma$ credible level using a flat prior in $\delta_\mathrm{CP}$, and just below $2\sigma$ using a flat prior in $\sin\delta_\mathrm{CP}$. When the external constraint on $\sin^2\theta_{13}$ is removed, $\sin^2\theta_{13}=28.0^{+2.8}_{-6.5}\times10^{-3}$, in agreement with measurements from reactor experiments. These results are consistent with previous T2K analyses.

Published
2023
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