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38,810 results on '"Lindahl, A."'

1. First Very Long Baseline Interferometry Detections at 870{\mu}m

Author

Raymond, Alexander W., Doeleman, Sheperd S., Asada, Keiichi, Blackburn, Lindy, Bower, Geoffrey C., Bremer, Michael, Broguiere, Dominique, Chen, Ming-Tang, Crew, Geoffrey B., Dornbusch, Sven, Fish, Vincent L., García, Roberto, Gentaz, Olivier, Goddi, Ciriaco, Han, Chih-Chiang, Hecht, Michael H., Huang, Yau-De, Janssen, Michael, Keating, Garrett K., Koay, Jun Yi, Krichbaum, Thomas P., Lo, Wen-Ping, Matsushita, Satoki, Matthews, Lynn D., Moran, James M., Norton, Timothy J., Patel, Nimesh, Pesce, Dominic W., Ramakrishnan, Venkatessh, Rottmann, Helge, Roy, Alan L., Sánchez, Salvador, Tilanus, Remo P. J., Titus, Michael, Torne, Pablo, Wagner, Jan, Weintroub, Jonathan, Wielgus, Maciek, Young, André, Akiyama, Kazunori, Albentosa-Ruíz, Ezequiel, Alberdi, Antxon, Alef, Walter, Algaba, Juan Carlos, Anantua, Richard, Azulay, Rebecca, Bach, Uwe, Baczko, Anne-Kathrin, Ball, David, Baloković, Mislav, Bandyopadhyay, Bidisha, Barrett, John, Bauböck, Michi, Benson, Bradford A., Bintley, Dan, Blundell, Raymond, Bouman, Katherine L., Boyce, Hope, Brissenden, Roger, Britzen, Silke, Broderick, Avery E., Bronzwaer, Thomas, Bustamante, Sandra, Carlstrom, John E., Chael, Andrew, Chan, Chi-kwan, Chang, Dominic O., Chatterjee, Koushik, Chatterjee, Shami, Chen, Yongjun, Cheng, Xiaopeng, Cho, Ilje, Christian, Pierre, Conroy, Nicholas S., Conway, John E., Crawford, Thomas M., Cruz-Osorio, Alejandro, Cui, Yuzhu, Dahale, Rohan, Davelaar, Jordy, De Laurentis, Mariafelicia, Deane, Roger, Dempsey, Jessica, Desvignes, Gregory, Dexter, Jason, Dhruv, Vedant, Dihingia, Indu K., Dzib, Sergio A., Eatough, Ralph P., Emami, Razieh, Falcke, Heino, Farah, Joseph, Fomalont, Edward, Fontana, Anne-Laure, Ford, H. Alyson, Foschi, Marianna, Fraga-Encinas, Raquel, Freeman, William T., Friberg, Per, Fromm, Christian M., Fuentes, Antonio, Galison, Peter, Gammie, Charles F., Georgiev, Boris, Gold, Roman, Gómez-Ruiz, Arturo I., Gómez, José L., Gu, Minfeng, Gurwell, Mark, Hada, Kazuhiro, Haggard, Daryl, Hesper, Ronald, Heumann, Dirk, Ho, Luis C., Ho, Paul, Honma, Mareki, Huang, Chih-Wei L., Huang, Lei, Hughes, David H., Ikeda, Shiro, Impellizzeri, C. M. Violette, Inoue, Makoto, Issaoun, Sara, James, David J., Jannuzi, Buell T., Jeter, Britton, Jiang, Wu, Jiménez-Rosales, Alejandra, Johnson, Michael D., Jorstad, Svetlana, Jones, Adam C., Joshi, Abhishek V., Jung, Taehyun, Karuppusamy, Ramesh, Kawashima, Tomohisa, Kettenis, Mark, Kim, Dong-Jin, Kim, Jae-Young, Kim, Jongsoo, Kim, Junhan, Kino, Motoki, Kocherlakota, Prashant, Kofuji, Yutaro, Koch, Patrick M., Koyama, Shoko, Kramer, Carsten, Kramer, Joana A., Kramer, Michael, Kubo, Derek, Kuo, Cheng-Yu, La Bella, Noemi, Lee, Sang-Sung, Levis, Aviad, Li, Zhiyuan, Lico, Rocco, Lindahl, Greg, Lindqvist, Michael, Lisakov, Mikhail, Liu, Jun, Liu, Kuo, Liuzzo, Elisabetta, Lobanov, Andrei P., Loinard, Laurent, Lonsdale, Colin J., Lowitz, Amy E., Lu, Ru-Sen, MacDonald, Nicholas R., Mahieu, Sylvain, Maier, Doris, Mao, Jirong, Marchili, Nicola, Markoff, Sera, Marrone, Daniel P., Marscher, Alan P., Martí-Vidal, Iván, Medeiros, Lia, Menten, Karl M., Mizuno, Izumi, Mizuno, Yosuke, Montgomery, Joshua, Moriyama, Kotaro, Moscibrodzka, Monika, Mulaudzi, Wanga, Müller, Cornelia, Müller, Hendrik, Mus, Alejandro, Musoke, Gibwa, Myserlis, Ioannis, Nagai, Hiroshi, Nagar, Neil M., Nakamura, Masanori, Narayanan, Gopal, Natarajan, Iniyan, Nathanail, Antonios, Fuentes, Santiago Navarro, Neilsen, Joey, Ni, Chunchong, Nowak, Michael A., Oh, Junghwan, Okino, Hiroki, Sánchez, Héctor Raúl Olivares, Oyama, Tomoaki, Özel, Feryal, Palumbo, Daniel C. M., Paraschos, Georgios Filippos, Park, Jongho, Parsons, Harriet, Pen, Ue-Li, Piétu, Vincent, PopStefanija, Aleksandar, Porth, Oliver, Prather, Ben, Principe, Giacomo, Psaltis, Dimitrios, Pu, Hung-Yi, Raffin, Philippe A., Rao, Ramprasad, Rawlings, Mark G., Ricarte, Angelo, Ripperda, Bart, Roelofs, Freek, Romero-Cañizales, Cristina, Ros, Eduardo, Roshanineshat, Arash, Ruiz, Ignacio, Ruszczyk, Chet, Rygl, Kazi L. J., Sánchez-Argüelles, David, Sánchez-Portal, Miguel, Sasada, Mahito, Satapathy, Kaushik, Savolainen, Tuomas, Schloerb, F. Peter, Schonfeld, Jonathan, Schuster, Karl-Friedrich, Shao, Lijing, Shen, Zhiqiang, Small, Des, Sohn, Bong Won, SooHoo, Jason, Salas, León David Sosapanta, Souccar, Kamal, Srinivasan, Ranjani, Stanway, Joshua S., Sun, He, Tazaki, Fumie, Tetarenko, Alexandra J., Tiede, Paul, Toma, Kenji, Toscano, Teresa, Traianou, Efthalia, Trent, Tyler, Trippe, Sascha, Turk, Matthew, van Bemmel, Ilse, van Langevelde, Huib Jan, van Rossum, Daniel R., Vos, Jesse, Ward-Thompson, Derek, Wardle, John, Washington, Jasmin E., Wharton, Robert, Wiik, Kaj, Witzel, Gunther, Wondrak, Michael F., Wong, George N., Wu, Qingwen, Yadlapalli, Nitika, Yamaguchi, Paul, Yfantis, Aristomenis, Yoon, Doosoo, Younsi, Ziri, Yu, Wei, Yuan, Feng, Yuan, Ye-Fei, Zensus, J. Anton, Zhang, Shuo, Zhao, Guang-Yao, and Zhao, Shan-Shan

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - High Energy Astrophysical Phenomena
Abstract

The first very long baseline interferometry (VLBI) detections at 870$\mu$m wavelength (345$\,$GHz frequency) are reported, achieving the highest diffraction-limited angular resolution yet obtained from the surface of the Earth, and the highest-frequency example of the VLBI technique to date. These include strong detections for multiple sources observed on inter-continental baselines between telescopes in Chile, Hawaii, and Spain, obtained during observations in October 2018. The longest-baseline detections approach 11$\,$G$\lambda$ corresponding to an angular resolution, or fringe spacing, of 19$\mu$as. The Allan deviation of the visibility phase at 870$\mu$m is comparable to that at 1.3$\,$mm on the relevant integration time scales between 2 and 100$\,$s. The detections confirm that the sensitivity and signal chain stability of stations in the Event Horizon Telescope (EHT) array are suitable for VLBI observations at 870$\mu$m. Operation at this short wavelength, combined with anticipated enhancements of the EHT, will lead to a unique high angular resolution instrument for black hole studies, capable of resolving the event horizons of supermassive black holes in both space and time., Comment: Corresponding author: S. Doeleman

Published
2024
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2. The need to implement FAIR principles in biomolecular simulations

Author

Amaro, Rommie, Åqvist, Johan, Bahar, Ivet, Battistini, Federica, Bellaiche, Adam, Beltran, Daniel, Biggin, Philip C., Bonomi, Massimiliano, Bowman, Gregory R., Bryce, Richard, Bussi, Giovanni, Carloni, Paolo, Case, David, Cavalli, Andrea, Chang, Chie-En A., Cheatham III, Thomas E., Cheung, Margaret S., Chipot, Cris, Chong, Lillian T., Choudhary, Preeti, Cisneros, Gerardo Andres, Clementi, Cecilia, Collepardo-Guevara, Rosana, Coveney, Peter, Covino, Roberto, Crawford, T. Daniel, Peraro, Matteo Dal, de Groot, Bert, Delemotte, Lucie, De Vivo, Marco, Essex, Jonathan, Fraternali, Franca, Gao, Jiali, Gelpí, Josep Lluís, Gervasio, Francesco Luigi, Gonzalez-Nilo, Fernando Danilo, Grubmüller, Helmut, Guenza, Marina, Guzman, Horacio V., Harris, Sarah, Head-Gordon, Teresa, Hernandez, Rigoberto, Hospital, Adam, Huang, Niu, Huang, Xuhui, Hummer, Gerhard, Iglesias-Fernández, Javier, Jensen, Jan H., Jha, Shantenu, Jiao, Wanting, Jorgensen, William L., Kamerlin, Shina Caroline Lynn, Khalid, Syma, Laughton, Charles, Levitt, Michael, Limongelli, Vittorio, Lindahl, Erik, Lindorff-Larsen, Kresten, Loverde, Sharon, Lundborg, Magnus, Luo, Yun Lyna, Luque, Francisco Javier, Lynch, Charlotte I., MacKerell, Alexander, Magistrato, Alessandra, Marrink, Siewert J., Martin, Hugh, McCammon, J. Andrew, Merz, Kenneth, Moliner, Vicent, Mulholland, Adrian, Murad, Sohail, Naganathan, Athi N., Nangia, Shikha, Noe, Frank, Noy, Agnes, Oláh, Julianna, O'Mara, Megan, Ondrechen, Mary Jo, Onuchic, José N., Onufriev, Alexey, Osuna, Silvia, Panchenko, Anna R., Pantano, Sergio, Parish, Carol, Parrinello, Michele, Perez, Alberto, Perez-Acle, Tomas, Perilla, Juan R., Pettitt, B. Montgomery, Pietropalo, Adriana, Piquemal, Jean-Philip, Poma, Adolfo, Praprotnik, Matej, Ramos, Maria J., Ren, Pengyu, Reuter, Nathalie, Roitberg, Adrian, Rosta, Edina, Rovira, Carme, Roux, Benoit, Röthlisberger, Ursula, Sanbonmatsu, Karissa Y., Schlick, Tamar, Shaytan, Alexey K., Simmerling, Carlos, Smith, Jeremy C., Sugita, Yuji, Świderek, Katarzyna, Taiji, Makoto, Tao, Peng, Tikhonova, Irina G., Tirado-Rives, Julian, Tunón, Inaki, Van Der Kamp, Marc W., Van der Spoel, David, Velankar, Sameer, Voth, Gregory A., Wade, Rebecca, Warshel, Ariel, Welborn, Valerie Vaissier, Wetmore, Stacey, Wong, Chung F., Yang, Lee-Wei, Zacharias, Martin, and Orozco, Modesto

Subjects
Quantitative Biology - Biomolecules
Abstract

This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and sustain a database that allows findability, accessibility, interoperability, and reusability of molecular dynamics simulation data. Such a development would democratize the field and significantly improve the impact of MD simulations on life science research. This will transform our working paradigm, pushing the field to a new frontier. We invite you to support our initiative at the MDDB community (https://mddbr.eu/community/)

Published
2024

3. Filler-Gap Dependencies and Islands in L2 English Production: Comparing Transfer from L1 Norwegian and L1 Swedish

Author

Dave Kush, Anne Dahl, and Filippa Lindahl

Abstract

Embedded questions (EQs) are islands for filler--gap dependency formation in English, but not in Norwegian. Kush and Dahl (2022) found that first language (L1) Norwegian participants often accepted filler-gap dependencies into EQs in second language (L2) English, and proposed that this reflected persistent transfer from Norwegian of the functional structure that licenses such filler-gap dependencies. However, their results do not conclusively establish that the judgment patterns were specific to transfer from L1 Norwegian and not a general L2 effect. To address this issue, we conducted elicited production tasks comparing how L1 Norwegian and L1 Swedish speakers complete dependencies into declarative complement clauses and EQs both in their native languages and L2 English. Despite its similarity to Norwegian, Swedish prohibits the filler-gap dependency into EQs that Norwegian allows. We expected participants to complete dependencies that they considered grammatical with gaps and to avoid gaps where they considered them ungrammatical. Our results clearly indicate transfer: L1 Norwegian participants overwhelmingly used gaps when completing dependencies into EQs in both L1 and L2, whereas Swedish participants almost never used gaps in either language. We interpret our results as support for models that allow transfer of functional heads and their associated features from L1 to L2, and suggest that such transfer persists when the L2 input does not provide relevant evidence for restructuring.

Published
2024
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4. GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability

Author

Alekseenko, Andrey, Páll, Szilárd, and Lindahl, Erik

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Computational Engineering, Finance, and Science, Computer Science - Performance, Physics - Computational Physics
Abstract

GROMACS is a widely-used molecular dynamics software package with a focus on performance, portability, and maintainability across a broad range of platforms. Thanks to its early algorithmic redesign and flexible heterogeneous parallelization, GROMACS has successfully harnessed GPU accelerators for more than a decade. With the diversification of accelerator platforms in HPC and no obvious choice for a multi-vendor programming model, the GROMACS project found itself at a crossroads. The performance and portability requirements, and a strong preference for a standards-based solution, motivated our choice to use SYCL on both new HPC GPU platforms: AMD and Intel. Since the GROMACS 2022 release, the SYCL backend has been the primary means to target AMD GPUs in preparation for exascale HPC architectures like LUMI and Frontier. SYCL is a cross-platform, royalty-free, C++17-based standard for programming hardware accelerators. It allows using the same code to target GPUs from all three major vendors with minimal specialization. While SYCL implementations build on native toolchains, performance of such an approach is not immediately evident. Biomolecular simulations have challenging performance characteristics: latency sensitivity, the need for strong scaling, and typical iteration times as short as hundreds of microseconds. Hence, obtaining good performance across the range of problem sizes and scaling regimes is particularly challenging. Here, we share the results of our work on readying GROMACS for AMD GPU platforms using SYCL, and demonstrate performance on Cray EX235a machines with MI250X accelerators. Our findings illustrate that portability is possible without major performance compromises. We provide a detailed analysis of node-level kernel and runtime performance with the aim of sharing best practices with the HPC community on using SYCL as a performance-portable GPU framework., Comment: 14 pages, 9 figures, presented at Cray User Group 2024

Published
2024

5. Broadband Multi-wavelength Properties of M87 during the 2018 EHT Campaign including a Very High Energy Flaring Episode

Author

Algaba, J. C., Balokovic, M., Chandra, S., Cheong, W. Y., Cui, Y. Z., D'Ammando, F., Falcone, A. D., Ford, N. M., Giroletti, M., Goddi, C., Gurwell, M. A., Hada, K., Haggard, D., Jorstad, S., Kaur, A., Kawashima, T., Kerby, S., Kim, J. Y., Kino, M., Kravchenko, E. V., Lee, S. S., Lu, R. S., Markoff, S., Michail, J., Neilsen, J., Nowak, M. A., Principe, G., Ramakrishnan, V., Ripperda, B., Sasada, M., Savchenko, S. S., Sheridan, C., Akiyama, K., Alberdi, A., Alef, W., Anantua, R., Asada, K., Azulay, R., Bach, U., Baczko, A. -K., Ball, D., Bandyopadhyay, B., Barrett, J., Bauböck, M., Benson, B. A., Bintley, D., Blackburn, L., Blundell, R., Bouman, K. L., Bower, G. C., Boyce, H., Bremer, M., Brissenden, R., Britzen, S., Broderick, A. E., Broguiere, D., Bronzwaer, T., Bustamante, S., Carlstrom, J. E., Chael, A., Chan, C. -K., Chang, D. O., Chatterjee, K., Chatterjee, S., Chen, M. -T., Chen, Y., Cheng, X., Cho, I., Christian, P., Conroy, N. S., Conway, J. E., Crawford, T. M., Crew, G. B., Cruz-Osorio, A., Dahale, R., Davelaar, J., De Laurentis, M., Deane, R., Dempsey, J., Desvignes, G., Dexter, J., Dhruv, V., Dihingia, I. K., Doeleman, S. S., Dzib, S. A., Eatough, R. P., Emami, R., Falcke, H., Farah, J., Fish, V. L., Fomalont, E., Ford, H. A., Foschi, M., Fraga-Encinas, R., Freeman, W. T., Friberg, P., Fromm, C. M., Fuentes, A., Galison, P., Gammie, C. F., García, R., Gentaz, O., Georgiev, B., Gold, R., Gómez-Ruiz, A. I., Gómez, J. L., Gu, M., Hesper, R., Heumann, D., Ho, L. C., Ho, P., Honma, M., Huang, C. -W. L., Huang, L., Hughes, D. H., Ikeda, S., Impellizzeri, C. M. V., Inoue, M., Issaoun, S., James, D. J., Jannuzi, B. T., Janssen, M., Jeter, B., Jiang, W., Jiménez-Rosales, A., Johnson, M. D., Jones, A. C., Joshi, A. V., Jung, T., Karuppusamy, R., Keating, G. K., Kettenis, M., Kim, D. -J., Kim, J., Koay, J. Y., Kocherlakota, P., Kofuji, Y., Koch, P. M., Koyama, S., Kramer, C., Kramer, J. A., Kramer, M., Krichbaum, T. P., Kuo, C. -Y., La Bella, N., Levis, A., Li, Z., Lico, R., Lindahl, G., Lindqvist, M., Lisakov, M., Liu, J., Liu, K., Liuzzo, E., Lo, W. -P., Lobanov, A. P., Loinard, L., Lonsdale, C. J., Lowitz, A. E., MacDonald, N. R., Mao, J., Marchili, N., Marrone, D. P., Marscher, A. P., Martí-Vidal, I., Matsushita, S., Matthews, L. D., Medeiros, L., Menten, K. M., Mizuno, I., Mizuno, Y., Montgomery, J., Moran, J. M., Moriyama, K., Moscibrodzka, M., Mulaudzi, W., Müller, C., Müller, H., Mus, A., Musoke, G., Myserlis, I., Nagai, H., Nagar, N. M., Nair, D. G., Nakamura, M., Narayanan, G., Natarajan, I., Nathanail, A., Fuentes, S. Navarro, Ni, C., Oh, J., Okino, H., Olivares, H., Oyama, T., Özel, F., Palumbo, D. C. M., Paraschos, G. Filippos, Park, J., Parsons, H., Patel, N., Pen, U. -L., Pesce, D. W., Piétu, V., PopStefanija, A., Porth, O., Prather, B., Psaltis, D., Pu, H. -Y., Rao, R., Rawlings, M. G., Raymond, A. W., Rezzolla, L., Ricarte, A., Roelofs, F., Romero-Cañizales, C., Ros, E., Roshanineshat, A., Rottmann, H., Roy, A. L., Ruiz, I., Ruszczyk, C., Rygl, K. L. J., Sánchez, S., Sánchez-Argüelles, D., Sánchez-Portal, M., Satapathy, K., Savolainen, T., Schloerb, F. P., Schonfeld, J., Schuster, K. -F., Shao, L., Shen, Z., Small, D., Sohn, B. W., SooHoo, J., Salas, L. D. Sosapanta, Souccar, K., Stanway, J. S., Sun, H., Tazaki, F., Tetarenko, A. J., Tiede, P., Tilanus, R. P. J., Titus, M., Toma, K., Torne, P., Toscano, T., Traianou, E., Trent, T., Trippe, S., Turk, M., van Bemmel, I., van Langevelde, H. J., van Rossum, D. R., Vos, J., Wagner, J., Ward-Thompson, D., Wardle, J., Washington, J. E., Weintroub, J., Wharton, R., Wielgus, M., Wiik, K., Witzel, G., Wondrak, M. F., Wong, G. N., Wu, Q., Yadlapalli, N., Yamaguchi, P., Yfantis, A., Yoon, D., Young, A., Younsi, Z., Yu, W., Yuan, F., Yuan, Y. -F., Zensus, J. A., Zhang, S., Zhao, G. -Y., Zhao, S. -S., Bellazzini, R., Berenji, B., Bissaldi, E., Blandford, R. D., Bonino, R., Bruel, P., Cameron, R. A., Caraveo, P. A., Cavazzuti, E., Cheung, C. C., Ciprini, S., Orestano, P. Cristarella, Cutini, S., Di Lalla, N., Dinesh, A., Di Venere, L., Domínguez, A., Fegan, S. J., Franckowiak, A., Fukazawa, Y., Fusco, P., Gargano, F., Gasbarra, C., Germani, S., Giliberti, M., Grenier, I. A., Hays, E., Horan, D., Kuss, M., Larsson, S., Liodakis, I., Longo, F., Loparco, F., Lovellette, M. N., Maldera, S., Mazziotta, M. N., Mereu, I., Michelson, P. F., Mirabal, N., Mizuno, T., Monzani, M. E., Morselli, A., Negro, M., Omodei, N., Orlando, E., Persic, M., Rainò, S., Rani, B., Reimer, A., Reimer, O., Sánchez-Conde, M., Parkinson, P. M. Saz, Sgrò, C., Siskind, E. J., Spinelli, P., Suson, D. J., Tajima, H., Torres, D. F., Zaharijas, G., Aharonian, F., Benkhali, F. Ait, Aschersleben, J., Ashkar, H., Backes, M., Martins, V. Barbosa, Batzofin, R., Becherini, Y., Berge, D., Böttcher, M., Boisson, C., Bolmont, J., de Lavergne, M. de Bony, Borowska, J., Bouyahiaoui, M., Bradascio, F., Brose, R., Brown, A., Bruno, B., Bulik, T., Burger-Scheidlin, C., Casanova, S., Cecil, R., Celic, J., Cerruti, M., Chand, T., Chen, A., Chibueze, J., Chibueze, O., Czerny, T., Dainotti, M., Dubus, F., Dumm, J., D'Urso, G., Drouhin, A., Durouchoux, P., Fabbian, D., Franczak, D., Funk, M., Gabanyi, J., Gaggero, G., Garcia, N., Geiger, A., Giorgi, M. G., Gleeson, S., Gonzalez, S., Gauthier, G. T., Grasso, P., Hovatta, T., Hyman, J., Kaaret, C., Kirk, D., Lal, S., Lesch, T. M., Lohmann, K., Massaro, C., Mayer, M., Meintjes, P. J., Miral, E., Mirra, A., Neronov, J., Padovani, E., Paccagnella, F., Parisi, E., Piotrowska, A., Pohl, S., Puga, G., Ramirez, L. R., Reville, S., Rowell, D. S., Rudge, M., Rybka, G., Schlenstedt, M. S., Seo, E. S., Svirski, J., Taylor, J. R., Torres, F., Tsujimoto, K., Tosti, F., Volpi, S., Walraven, N. A., Welker, L., Zietkiewicz, M., Abdalla, G., Aleva, C., Benkhali, H. A. Ait, Aldous, M., Amin, M., Aschieri, M. A., de Deus, E., Santos, J. de Los, Fontanot, D., Jorfi, S., Levens, P., Zwart, A. E. E., Oliviero, S., Puglisi, D., Thiel, M., Zaharijas, C., Amaral, F., Boella, L., Holincheck, L., Queiroz, R., Sofue, H., Tellis, G., Wagner, G., Wierzcholska, A., Zacharias, M., Zdziarski, A. A., Zech, A., Zywucka, N., Abe, S., Abhir, J., Abhishek, A., Acciari, V. A., Aguasca-Cabot, A., Agudo, I., Aniello, T., Ansoldi, S., Antonelli, L. A., Engels, A. Arbet, Arcaro, C., Artero, M., Asano, K., Babic, A., de Almeida, U. Barres, Barrio, J. A., Batkovic, I., Bautista, A., Baxter, J., González, J. Becerra, Bednarek, W., Bernardini, E., Bernete, J., Berti, A., Besenrieder, J., Bigongiari, C., Biland, A., Blanch, O., Bonnoli, G., Bosnjak, Z., Bronzini, E., Burelli, I., Busetto, G., Campoy-Ordaz, A., Carosi, A., Carosi, R., Carretero-Castrillo, M., Castro-Tirado, A. J., Cerasole, D., Ceribella, G., Chai, Y., Cifuentes, A., Colombo, E., Contreras, J. L., Cortina, J., Covino, S., D'Amico, G., D'Elia, V., Da Vela, P., Dazzi, F., De Angelis, A., De Lotto, B., de Menezes, R., Delfino, M., Delgado, J., Mendez, C. Delgado, Di Pierro, F., Di Tria, R., Prester, D. Dominis, Donini, A., Dorner, D., Doro, M., Elsaesser, D., Escudero, J., Fariña, L., Fattorini, A., Foffano, L., Font, L., Fröse, S., Fukami, S., López, R. J. García, Garczarczyk, M., Gasparyan, S., Gaug, M., Paiva, J. G. Giesbrecht, Giglietto, N., Giordano, F., Gliwny, P., Godinovic, N., Gradetzke, T., Grau, R., Green, D., Green, J. G., Günther, P., Hadasch, D., Hahn, A., Hassan, T., Heckmann, L., Llorente, J. Herrera, Hrupec, D., Imazawa, R., Ishio, K., Martínez, I. Jiménez, Jormanainen, J., Kayanoki, T., Kerszberg, D., Kluge, G. W., Kobayashi, Y., Kouch, P. M., Kubo, H., Kushida, J., Laínez, M., Lamastra, A., Leone, F., Lindfors, E., Lombardi, S., López-Coto, R., López-Moya, M., López-Oramas, A., Loporchio, S., Lorini, A., Lyard, E., Fraga, B. Machado de Oliveira, Majumdar, P., Makariev, M., Maneva, G., Manganaro, M., Mangano, S., Mannheim, K., Mariotti, M., Martínez, M., Martínez-Chicharro, M., Mas-Aguilar, A., Mazin, D., Menchiari, S., Mender, S., Miceli, D., Miener, T., Miranda, J. M., Mirzoyan, R., González, M. Molero, Molina, E., Mondal, H. A., Moralejo, A., Morcuende, D., Nakamori, T., Nanci, C., Neustroev, V., Nickel, L., Rosillo, M. Nievas, Nigro, C., Nikolic, L., Nilsson, K., Nishijima, K., Ekoume, T. Njoh, Noda, K., Nozaki, S., Ohtani, Y., Okumura, A., Otero-Santos, J., Paiano, S., Paneque, D., Paoletti, R., Paredes, J. M., Peresano, M., Pihet, M., Pirola, G., Podobnik, F., Moroni, P. G. Prada, Prandini, E., Priyadarshi, C., Ribó, M., Rico, J., Righi, C., Sahakyan, N., Saito, T., Saturni, F. G., Schmidt, K., Schmuckermaier, F., Schubert, J. L., Schweizer, T., Sciaccaluga, A., Silvestri, G., Sitarek, J., Sliusar, V., Sobczynska, D., Spolon, A., Stamerra, A., Strišković, J., Strom, D., Strzys, M., Suda, Y., Suutarinen, S., Takahashi, M., Takeishi, R., Tavecchio, F., Temnikov, P., Terauchi, K., Terzic, T., Teshima, M., Truzzi, S., Tutone, A., Ubach, S., van Scherpenberg, J., Acosta, M. Vazquez, Ventura, S., Verna, G., Viale, I., Vigorito, C. F., Vitale, V., Vovk, I., Walter, R., Will, M., Wunderlich, C., Yamamoto, T., Acharyya, A., Adams, C. B., Bangale, P., Bartkoske, J. T., Benbow, W., Christiansen, J. L., Duerr, A., Errando, M., Feng, Q., Foote, G. M., Fortson, L., Furniss, A., Hanlon, W., Hervet, O., Hinrichs, C. E., Holder, J., Humensky, T. B., Jin, W., Johnson, M. N., Kaaret, P., Kertzman, M., Kieda, D., Kleiner, T. K., Korzoun, N., Krennrich, F., Kumar, S., Lang, M. J., Lundy, M., Maier, G., McGrath, C. E., Millard, M. J., Mooney, C. L., Moriarty, P., Mukherjee, R., Ning, W., O'Brien, S., Ong, R. A., Pohl, M., Pueschel, E., Quinn, J., Ragan, K., Reynolds, P. T., Ribeiro, D., Roache, E., Ryan, J. L., Sadeh, I., Saha, L., Santander, M., Sembroski, G. H., Shang, R., Splettstoesser, M., Talluri, A. K., Tucci, J. V., Valverde, J., Vassiliev, V. V., Williams, D. A., Wong, S. L., Chen, Z., Cui, L., Hirota, T., Li, B., Li, G., Liu, Q., Liu, X., Liu, Z., Ma, J., Niinuma, K., Ro, H., Sakai, N., Sawada-Satoh, S., Wajima, K., Wang, J., Wang, N., Xia, B., Yan, H., Yonekura, Y., Zhang, H., Zhao, R., Zhong, W., group, The Event Horizon Telescope - Multi-wavelength science working, Collaboration, The Event Horizon Telescope, Collaboration, The Fermi Large Area Telescope, Collaboration, H. E. S. S., Collaboration, MAGIC, Collaboration, VERITAS, and Collaboration, EAVN

Subjects
Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Astrophysics of Galaxies
Abstract

The nearby elliptical galaxy M87 contains one of the only two supermassive black holes whose emission surrounding the event horizon has been imaged by the Event Horizon Telescope (EHT). In 2018, more than two dozen multi-wavelength (MWL) facilities (from radio to gamma-ray energies) took part in the second M87 EHT campaign. The goal of this extensive MWL campaign was to better understand the physics of the accreting black hole M87*, the relationship between the inflow and inner jets, and the high-energy particle acceleration. Understanding the complex astrophysics is also a necessary first step towards performing further tests of general relativity. The MWL campaign took place in April 2018, overlapping with the EHT M87* observations. We present a new, contemporaneous spectral energy distribution (SED) ranging from radio to very high energy (VHE) gamma-rays, as well as details of the individual observations and light curves. We also conduct phenomenological modelling to investigate the basic source properties. We present the first VHE gamma-ray flare from M87 detected since 2010. The flux above 350 GeV has more than doubled within a period of about 36 hours. We find that the X-ray flux is enhanced by about a factor of two compared to 2017, while the radio and millimetre core fluxes are consistent between 2017 and 2018. We detect evidence for a monotonically increasing jet position angle that corresponds to variations in the bright spot of the EHT image. Our results show the value of continued MWL monitoring together with precision imaging for addressing the origins of high-energy particle acceleration. While we cannot currently pinpoint the precise location where such acceleration takes place, the new VHE gamma-ray flare already presents a challenge to simple one-zone leptonic emission model approaches, and emphasises the need for combined image and spectral modelling., Comment: 46 pages, 23 figures, accepted by Astronomy & Astrophysics on August. 29, 2024

Published
2024

6. Atmospheric limitations for high-frequency ground-based VLBI

Author

Pesce, Dominic W., Blackburn, Lindy, Chaves, Ryan, Doeleman, Sheperd S., Freeman, Mark, Issaoun, Sara, Johnson, Michael D., Lindahl, Greg, Natarajan, Iniyan, Paine, Scott N., Palumbo, Daniel C. M., Roelofs, Freek, and Tiede, Paul

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

Very long baseline interferometry (VLBI) provides the highest-resolution images in astronomy. The sharpest resolution is nominally achieved at the highest frequencies, but as the observing frequency increases so too does the atmospheric contribution to the system noise, degrading the sensitivity of the array and hampering detection. In this paper, we explore the limits of high-frequency VLBI observations using ngehtsim, a new tool for generating realistic synthetic data. ngehtsim uses detailed historical atmospheric models to simulate observing conditions, and it employs heuristic visibility detection criteria that emulate single- and multi-frequency VLBI calibration strategies. We demonstrate the fidelity of ngehtsim's predictions using a comparison with existing 230 GHz data taken by the Event Horizon Telescope (EHT), and we simulate the expected performance of EHT observations at 345 GHz. Though the EHT achieves a nearly 100% detection rate at 230 GHz, our simulations indicate that it should expect substantially poorer performance at 345 GHz; in particular, observations of M87 at 345 GHz are predicted to achieve detection rates of $\lesssim$20% that may preclude imaging. Increasing the array sensitivity through wider bandwidths and/or longer integration times -- as enabled through, e.g., the simultaneous multi-frequency upgrades envisioned for the next-generation EHT -- can improve the 345 GHz prospects and yield detection levels that are comparable to those at 230 GHz. M87 and Sgr A* observations carried out in the atmospheric window around 460 GHz could expect to regularly achieve multiple detections on long baselines, but analogous observations at 690 and 875 GHz consistently obtain almost no detections at all., Comment: 29 pages, 12 figures, accepted for publication in ApJ

Published
2024

17. Ordered magnetic fields around the 3C 84 central black hole

Author

Paraschos, G. F., Kim, J. -Y., Wielgus, M., Röder, J., Krichbaum, T. P., Ros, E., Agudo, I., Myserlis, I., Moscibrodzka, M., Traianou, E., Zensus, J. A., Blackburn, L., Chan, C. -K., Issaoun, S., Janssen, M., Johnson, M. D., Fish, V. L., Akiyama, K., Alberdi, A., Alef, W., Algaba, J. C., Anantua, R., Asada, K., Azulay, R., Bach, U., Baczko, A. -K., Ball, D., Baloković, M., Barrett, J., Bauböck, M., Benson, B. A., Bintley, D., Blundell, R., Bouman, K. L., Bower, G. C., Boyce, H., Bremer, M., Brinkerink, C. D., Brissenden, R., Britzen, S., Broderick, A. E., Broguiere, D., Bronzwaer, T., Bustamante, S., Byun, D. -Y., Carlstrom, J. E., Ceccobello, C., Chael, A., Chang, D. O., Chatterjee, K., Chatterjee, S., Chen, M. T., Chen, Y., Cheng, X., Cho, I., Christian, P., Conroy, N. S., Conway, J. E., Cordes, J. M., Crawford, T. M., Crew, G. B., Cruz-Osorio, A., Cui, Y., Dahale, R., Davelaar, J., De Laurentis, M., Deane, R., Dempsey, J., Desvignes, G., Dexter, J., Dhruv, V., Doeleman, S. S., Dougal, S., Dzib, S. A., Eatough, R. P., Emami, R., Falcke, H., Farah, J., Fomalont, E., Ford, H. A., Foschi, M., Fraga-Encinas, R., Freeman, W. T., Friberg, P., Fromm, C. M., Fuentes, A., Galison, P., Gammie, C. F., García, R., Gentaz, O., Georgiev, B., Goddi, C., Gold, R., Gómez-Ruiz, A. I., Gómez, J. L., Gu, M., Gurwell, M., Hada, K., Haggard, D., Haworth, K., Hecht, M. H., Hesper, R., Heumann, D., Ho, L. C., Ho, P., Honma, M., Huang, C. L., Huang, L., Hughes, D. H., Ikeda, S., Impellizzeri, C. M. V., Inoue, M., James, D. J., Jannuzi, B. T., Jeter, B., Jaing, W., Jiménez-Rosales, A., Jorstad, S., Joshi, A. V., Jung, T., Karami, M., Karuppusamy, R., Kawashima, T., Keating, G. K., Kettenis, M., Kim, D. -J., Kim, J., Kino, M., Koay, J. Y., Kocherlakota, P., Kofuji, Y., Koch, P. M., Koyama, S., Kramer, C., Kramer, J. A., Kramer, M., Kuo, C. -Y., La Bella, N., Lauer, T. R., Lee, D., Lee, S. -S., Leung, P. K., Levis, A., Li, Z., Lico, R., Lindahl, G., Lindqvist, M., Lisakov, M., Liu, J., Liu, K., Liuzzo, E., Lo, W. -P., Lobanov, A. P., Loinard, L., Lonsdale, C. J., Lowitz, A. E., Lu, R. -S., MacDonald, N. R., Mao, J., Marchili, N., Markoff, S., Marrone, D. P., Marscher, A. P., Martí-Vidal, I., Matsushita, S., Matthews, L. D., Medeiros, L., Menten, K. M., Michalik, D., Mizuno, I., Mizuno, Y., Moran, J. M., Moriyama, K., Mulaudzi, W., Müller, C., Müller, H., Mus, A., Musoke, G., Nadolski, A., Nagai, H., Nagar, N. M., Nakamura, M., Narayanan, G., Natarajan, I., Nathanail, A., Fuentes, S. Navarro, Neilsen, J., Neri, R., Ni, C., Noutsos, A., Nowak, M. A., Oh, J., Okino, H., Olivares, H., Ortiz-León, G. N., Oyama, T., Özel, F., Palumbo, D. C. M., Park, J., Parsons, H., Patel, N., Pen, U. -L., Piétu, V., Plambeck, R., PopStefanija, A., Porth, O., Pötzl, F. M., Prather, B., Preciado-López, J. A., Psaltis, D., Pu, H. -Y., Ramakrishnan, V., Rao, R., Rawlings, M. G., Raymond, A. W., Rezzolla, L., Ricarte, A., Ripperda, B., Roelofs, F., Rogers, A., Romero-Cañizales, C., Roshanineshat, A., Rottmann, H., Roy, A. L., Ruiz, I., Ruszczyk, C., Rygl, K. L. J., Sánchez, S., Sánchez-Argüelles, D., Sánchez-Portal, M., Sasada, M., Satapathy, K., Savolainen, T., Schloerb, F. P., Schonfeld, J., Schuster, K., Shao, L., Shen, Z., Small, D., Sohn, B. W., SooHoo, J., Salas, L. D. Sosapanta, Souccar, K., Sun, H., Tazaki, F., Tetarenko, A. J., Tiede, P., Tilanus, R. P. J., Titus, M., Torne, P., Toscano, T., Trent, T., Trippe, S., Turk, M., van Bemmel, I., van Langevelde, H. J., van Rossum, D. R., Vos, J., Wagner, J., Ward-Thompson, D., Wardle, J., Washington, J. E., Weintroub, J., Wharton, R., Wiik, K., Witzel, G., Wondrak, M. F., Wong, G. N., Wu, Q., Yadlapalli, N., Yamaguchi, P., Yfantis, A., Yoon, D., Young, A., Young, K., Younsi, Z., Yu, W., Yuan, F., Yuan, Y. -F., Zhang, S., Zhao, G. Y., and Zhao, S. -S.

Subjects
Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Astrophysics of Galaxies
Abstract

3C84 is a nearby radio source with a complex total intensity structure, showing linear polarisation and spectral patterns. A detailed investigation of the central engine region necessitates the use of VLBI above the hitherto available maximum frequency of 86GHz. Using ultrahigh resolution VLBI observations at the highest available frequency of 228GHz, we aim to directly detect compact structures and understand the physical conditions in the compact region of 3C84. We used EHT 228GHz observations and, given the limited (u,v)-coverage, applied geometric model fitting to the data. We also employed quasi-simultaneously observed, multi-frequency VLBI data for the source in order to carry out a comprehensive analysis of the core structure. We report the detection of a highly ordered, strong magnetic field around the central, SMBH of 3C84. The brightness temperature analysis suggests that the system is in equipartition. We determined a turnover frequency of $\nu_m=(113\pm4)$GHz, a corresponding synchrotron self-absorbed magnetic field of $B_{SSA}=(2.9\pm1.6)$G, and an equipartition magnetic field of $B_{eq}=(5.2\pm0.6)$G. Three components are resolved with the highest fractional polarisation detected for this object ($m_\textrm{net}=(17.0\pm3.9)$%). The positions of the components are compatible with those seen in low-frequency VLBI observations since 2017-2018. We report a steeply negative slope of the spectrum at 228GHz. We used these findings to test models of jet formation, propagation, and Faraday rotation in 3C84. The findings of our investigation into different flow geometries and black hole spins support an advection-dominated accretion flow in a magnetically arrested state around a rapidly rotating supermassive black hole as a model of the jet-launching system in the core of 3C84. However, systematic uncertainties due to the limited (u,v)-coverage, however, cannot be ignored., Comment: 15 pages, 6 figures, published in A&A

Published
2024
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18. Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

Author

Auer, Lucas, Buée, Marc, Fauchery, Laure, Lombard, Vincent, Barry, Kerry W, Clum, Alicia, Copeland, Alex, Daum, Chris, Foster, Brian, LaButti, Kurt, Singan, Vasanth, Yoshinaga, Yuko, Martineau, Christine, Alfaro, Manuel, Castillo, Federico J, Imbert, J Bosco, Ramírez, Lucia, Castanera, Raúl, Pisabarro, Antonio G, Finlay, Roger, Lindahl, Björn, Olson, Ake, Séguin, Armand, Kohler, Annegret, Henrissat, Bernard, Grigoriev, Igor V, and Martin, Francis M

Subjects
Microbiology, Biological Sciences, Ecology, Genetics, Life on Land, Forests, Fungi, Soil Microbiology, Transcriptome, Mycorrhizae, Gene Expression Profiling, Gene Expression Regulation, Fungal, Nitrogen, Soil, Ecosystem, RNA, Messenger, forest soil, functional traits, fungal guilds, metatranscriptomics, organic matter degradation, Agricultural and Veterinary Sciences, Plant Biology & Botany, Plant biology, Climate change impacts and adaptation, Ecological applications
Abstract

Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.

Published
2024

20. AFLATOXIN B1 CONTAMINATION IN PORRIDGE FORMULATIONS FOR CHILDREN AND INGREDIENTS SOURCED FROM SELECTED MARKETS IN RWANDA

Author

Matabishi, M., Mutua, F., Lindahl, J.F., Hahirwa, I., Umugwaneza, M., Musafili, A., and Munyanshongore, C.

Subjects
Aflatoxins -- Health aspects, Porridge -- Contamination, Food contamination -- Analysis, Malnutrition in children -- Control, Agricultural industry, Food/cooking/nutrition, Health
Abstract

Providing safe and nutritious food for children globally is a challenge. In Rwanda, an initiative was introduced in 2018 to tackle chronic malnutrition by offering fortified porridge flour to economically disadvantaged families during critical periods. However, flour-based products in the sub-region have caused public health concerns following aflatoxin B1 (AFB1) contamination. This study analyzed the levels of AFB1 in 197 porridge formulations from health centers, and 248 samples of porridge ingredients from open markets in three districts of Rwanda. Samples were collected between June 2021 and December 2022 and analyzed using ultra-high-performance liquid chromatography. Of the 197 samples from health centers, 97.9 and 89.8% exceeded the European Union maximum limits for baby foods and foods for special medical purposes (0.1 [micro]g/kg), and cereals and nuts (2 [micro]g/kg), respectively with an average contamination level of 2.77 pg/kg ([+ or -]0.98). Only four samples exceeded the East African Community maximum limits of 5 [micro]g/kg for AFB1. Samples from open markets that exceeded the European Union and East African community limits of 0.1 [micro]g/kg, 2 [micro]g/kg, and 5 [micro]g/kg ranged from 17 to 100%, 0 to 100%, and 0 to 100%, respectively. Site and processing significantly influenced levels of AFB1 contamination in open-market samples. The mean AFB1 levels were 17.85 [micro]g/kg ([+ or -]70.25) in Burera District, 36.04 [micro]g/kg ([+ or -]85.59) in Huye District, and 9.01 [micro]g/kg ([+ or -]18.49) in Nyarugenge District. The average AFB1 levels significantly varied between different products. Peanut samples showed higher contamination levels of 56.79 and 99.08 [micro]g/kg for grain and flour, respectively. Flour samples in general had a higher mean of 51.65 [micro]g/kg ([+ or -]105.75), compared to grain samples, 16.5 [micro]g/kg ([+ or -]44). Thus, there are potential health risks associated with chronic exposure to AFB1 in children consuming flour-based foods from health centers and open markets. Interventions to mitigate AFB1 contamination and protect children should focus on food processing practices, implementing strict quality control measures, and raising awareness among stakeholders about the risks of AFB1 in flour-based products provided to children in Rwanda and similar settings. Key words: Flour-based porridge, contamination, aflatoxin B1, children, Rwanda, INTRODUCTION Safe and nutritious foods remain a challenge globally. Children are particularly vulnerable to malnutrition, which often leads to a higher incidence of diarrhea and hindered growth [1]. To ensure [...]

Published
2024
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21. Evolution of Approaches to Teacher Cognition and Teacher Identity: A Conceptual Conversation

Author

Yazan, Bedrettin and Lindahl, Kristen

Abstract

In this paper, as two TESOL practitioners, our purpose is to capture our reflections on how conceptual approaches to teacher learning have evolved over the years to highlight the interplay between teacher cognition and teacher identity. We also seek to decrease the distance between ourselves and our academic writing, essentially emerging from behind the conventions of academic writing to discuss concepts in a conversational tone, hopefully making them more accessible to a larger audience of practitioners and scholars. In discussing our ongoing negotiation of theoretical orientations, we have been able to reflect on the influence of the language teacher cognition research base on the wider field of language teacher identity research. The main take-away is that we can better illustrate the complexity involved in the practice of language teaching and the process of becoming language teachers if we combine the two in complementary ways: teachers' individual cognitive and metacognitive processes involved in their professional learning and their situatedness in social, cultural, political, and economic discourses.

Published
2023

35. Structural basis for the oligomerization-facilitated NLRP3 activation

Author

Yu, Xiaodi, Matico, Rosalie E., Miller, Robyn, Chauhan, Dhruv, Van Schoubroeck, Bertrand, Grauwen, Karolien, Suarez, Javier, Pietrak, Beth, Haloi, Nandan, Yin, Yanting, Tresadern, Gary John, Perez-Benito, Laura, Lindahl, Erik, Bottelbergs, Astrid, Oehlrich, Daniel, Van Opdenbosch, Nina, and Sharma, Sujata

Published
2024
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38. Symmetry-adapted Markov state models of closing, opening, and desensitizing in α 7 nicotinic acetylcholine receptors

Author

Yuxuan Zhuang, Rebecca J. Howard, and Erik Lindahl

Subjects
Science
Abstract

Abstract α7 nicotinic acetylcholine receptors (nAChRs) are homopentameric ligand-gated ion channels with critical roles in the nervous system. Recent studies have resolved and functionally annotated closed, open, and desensitized states of these receptors, providing insight into ion permeation and lipid binding. However, the process by which α7 nAChRs transition between states remains unclear. To understand gating and lipid modulation, we generated two ensembles of molecular dynamics simulations of apo α7 nAChRs, with or without cholesterol. Using symmetry-adapted Markov state modeling, we developed a five-state gating model. Free energies recapitulated functional behavior, with the closed state dominating in absence of agonist. Open-to-nonconducting transition rates corresponded to experimental open durations. Cholesterol relatively stabilized the desensitized state, and reduced open-desensitized barriers. These results establish plausible asymmetric transition pathways between states, define lipid modulation effects on the α7 nAChR conformational cycle, and provide an ensemble of structural models applicable to rational design of lipidic pharmaceuticals.

Published
2024
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39. A search for pulsars around Sgr A* in the first Event Horizon Telescope dataset

Author

Torne, Pablo, Liu, Kuo, Eatough, Ralph P., Wongphechauxsorn, Jompoj, Cordes, James M., Desvignes, Gregory, De Laurentis, Mariafelicia, Kramer, Michael, Ransom, Scott M., Chatterjee, Shami, Wharton, Robert, Karuppusamy, Ramesh, Blackburn, Lindy, Janssen, Michael, Chan, Chi-kwan, Crew, Geoffrey B., Matthews, Lynn D., Goddi, Ciriaco, Rottmann, Helge, Wagner, Jan, Sanchez, Salvador, Ruiz, Ignacio, Abbate, Federico, Bower, Geoffrey C., Salamanca, Juan J., Gomez-Ruiz, Arturo I., Herrera-Aguilar, Alfredo, Jiang, Wu, Lu, Ru-Sen, Pen, Ue-Li, Raymond, Alexander W., Shao, Lijing, Shen, Zhiqiang, Paubert, Gabriel, Sanchez-Portal, Miguel, Kramer, Carsten, Castillo, Manuel, Navarro, Santiago, John, David, Schuster, Karl-Friedrich, Johnson, Michael D., Rygl, Kazi L. J., Akiyama, Kazunori, Alberdi, Antxon, Alef, Walter, Algaba, Juan Carlos, Anantua, Richard, Asada, Keiichi, Azulay, Rebecca, Bach, Uwe, Baczko, Anne-Kathrin, Ball, David, Balokovic, Mislav, Barrett, John, Bauboeck, Michi, Benson, Bradford A., Bintley, Dan, Blundell, Raymond, Bouman, Katherine L., Boyce, Hope, Bremer, Michael, Brinkerink, Christiaan D., Brissenden, Roger, Britzen, Silke, Broderick, Avery E., Broguiere, Dominique, Bronzwaer, Thomas, Bustamante, Sandra, Byun, Do-Young, Carlstrom, John E., Ceccobello, Chiara, Chael, Andrew, Chang, Dominic O., Chatterjee, Koushik, Chen, Ming-Tang, Chen, Yongjun, Cheng, Xiaopeng, Cho, Ilje, Christian, Pierre, Conroy, Nicholas S., Conway, John E., Crawford, Thomas M., Cruz-Osorio, Alejandro, Cui, Yuzhu, Dahale, Rohan, Davelaar, Jordy, Deane, Roger, Dempsey, Jessica, Dexter, Jason, Dhruv, Vedant, Doeleman, Sheperd S., Dougal, Sean, Dzib, Sergio A., Emami, Razieh, Falcke, Heino, Farah, Joseph, Fish, Vincent L., Fomalont, Ed, Ford, H. Alyson, Foschi, Marianna, Fraga-Encinas, Raquel, Freeman, William T., Friberg, Per, Fromm, Christian M., Fuentes, Antonio, Galison, Peter, Gammie, Charles F., Garcia, Roberto, Gentaz, Olivier, Georgiev, Boris, Gold, Roman, Gomez, Jose L., Gu, Minfeng, Gurwell, Mark, Hada, Kazuhiro, Haggard, Daryl, Haworth, Kari, Hecht, Michael H., Hesper, Ronald, Heumann, Dirk, Ho, Luis C., Ho, Paul, Honma, Mareki, Huang, Chih-Wei L., Huang, Lei, Hughes, David H., Ikeda, Shiro, Impellizzeri, C. M. Violette, Inoue, Makoto, Issaoun, Sara, James, David J., Jannuzi, Buell T., Jeter, Britton, Jimenez-Rosales, Alejandra, Jorstad, Svetlana, Joshi, Abhishek V., Jung, Taehyun, Karami, Mansour, Kawashima, Tomohisa, Keating, Garrett K., Kettenis, Mark, Kim, Dong-Jin, Kim, Jae-Young, Kim, Jongsoo, Kim, Junhan, Kino, Motoki, Koay, Jun Yi, Kocherlakota, Prashant, Kofuji, Yutaro, Koyama, Shoko, Krichbaum, Thomas P., Kuo, Cheng-Yu, La Bella, Noemi, Lauer, Tod R., Lee, Daeyoung, Lee, Sang-Sung, Leung, Po Kin, Levis, Aviad, Li, Zhiyuan, Lico, Rocco, Lindahl, Greg, Lindqvist, Michael, Lisakov, Mikhail, Liu, Jun, Liuzzo, Elisabetta, Lo, Wen-Ping, Lobanov, Andrei P., Loinard, Laurent, Lonsdale, Colin J., MacDonald, Nicholas R., Mao, Jirong, Marchili, Nicola, Markoff, Sera, Marrone, Daniel P., Marscher, Alan P., Marti-Vidal, Ivan, Matsushita, Satoki, Medeiros, Lia, Menten, Karl M., Michalik, Daniel, Mizuno, Izumi, Mizuno, Yosuke, Moran, James M., Moriyama, Kotaro, Moscibrodzka, Monika, Muller, Cornelia, Muller, Hendrik, Mus, Alejandro, Musoke, Gibwa, Myserlis, Ioannis, Nadolski, Andrew, Nagai, Hiroshi, Nagar, Neil M., Nakamura, Masanori, Narayan, Ramesh, Narayanan, Gopal, Natarajan, Iniyan, Nathanail, Antonios, Neilsen, Joey, Neri, Roberto, Ni, Chunchong, Noutsos, Aristeidis, Nowak, Michael A., Oh, Junghwan, Okino, Hiroki, Olivares, Hector, Ortiz-Leon, Gisela N., Oyama, Tomoaki, Ozel, Feryal, Palumbo, Daniel C. M., Paraschos, Georgios Filippos, Park, Jongho, Parsons, Harriet, Patel, Nimesh, Pesce, Dominic W., Pietu, Vincent, Plambeck, Richard, PopStefanija, Aleksandar, Porth, Oliver, Potzl, Felix M., Prather, Ben, Preciado-Lopez, Jorge A., Psaltis, Dimitrios, Pu, Hung-Yi, Ramakrishnan, Venkatessh, Rao, Ramprasad, Rawlings, Mark G., Rezzolla, Luciano, Ricarte, Angelo, Ripperda, Bart, Roelofs, Freek, Rogers, Alan, Ros, Eduardo, Romero-Cañizales, Cristina, Roshanineshat, Arash, Roy, Alan L., Ruszczyk, Chet, Sanchez-Arguelles, David, Sasada, Mahito, Satapathy, Kaushik, Savolainen, Tuomas, Schloerb, F. Peter, Schonfeld, Jonathan, Small, Des, Sohn, Bong Won, SooHoo, Jason, Souccar, Kamal, Sun, He, Tetarenko, Alexandra J., Tiede, Paul, Tilanus, Remo P. J., Titus, Michael, Toscano, Teresa, Traianou, Efthalia, Trent, Tyler, Trippe, Sascha, Turk, Matthew, van Bemmel, Ilse, van Langevelde, Huib Jan, van Rossum, Daniel R., Vos, Jesse, Ward-Thompson, Derek, Wardle, John, Weintroub, Jonathan, Wex, Norbert, Wielgus, Maciek, Wiik, Kaj, Witzel, Gunther, Wondrak, Michael F., Wong, George N., Wu, Qingwen, Yadlapalli, Nitika, Yamaguchi, Paul, Yfantis, Aristomenis, Yoon, Doosoo, Young, Andre, Young, Ken, Younsi, Ziri, Yu, Wei, Yuan, Feng, Yuan, Ye-Fei, Zensus, J. Anton, Zhang, Shuo, Zhao, Guang-Yao, and Zhao, Shan-Shan

Subjects
Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

The Event Horizon Telescope (EHT) observed in 2017 the supermassive black hole at the center of the Milky Way, Sagittarius A* (Sgr A*), at a frequency of 228.1 GHz ($\lambda$=1.3 mm). The fundamental physics tests that even a single pulsar orbiting Sgr A* would enable motivate searching for pulsars in EHT datasets. The high observing frequency means that pulsars - which typically exhibit steep emission spectra - are expected to be very faint. However, it also negates pulse scattering, an effect that could hinder pulsar detections in the Galactic Center. Additionally, magnetars or a secondary inverse Compton emission could be stronger at millimeter wavelengths than at lower frequencies. We present a search for pulsars close to Sgr A* using the data from the three most-sensitive stations in the EHT 2017 campaign: the Atacama Large Millimeter/submillimeter Array, the Large Millimeter Telescope and the IRAM 30 m Telescope. We apply three detection methods based on Fourier-domain analysis, the Fast-Folding-Algorithm and single pulse search targeting both pulsars and burst-like transient emission; using the simultaneity of the observations to confirm potential candidates. No new pulsars or significant bursts were found. Being the first pulsar search ever carried out at such high radio frequencies, we detail our analysis methods and give a detailed estimation of the sensitivity of the search. We conclude that the EHT 2017 observations are only sensitive to a small fraction ($\lesssim$2.2%) of the pulsars that may exist close to Sgr A*, motivating further searches for fainter pulsars in the region., Comment: 33 pages, 7 figures, 6 Tables. Accepted for publication in ApJ

Published
2023

45. Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach

Author

Palermo, Gianluca, Accordi, Gianmarco, Gadioli, Davide, Vitali, Emanuele, Silvano, Cristina, Guindani, Bruno, Ardagna, Danilo, Beccari, Andrea R., Bonanni, Domenico, Talarico, Carmine, Lunghini, Filippo, Martinovic, Jan, Silva, Paulo, Bohm, Ada, Beranek, Jakub, Krenek, Jan, Jansik, Branislav, Crisci, Luigi, Biagio, Cosenza, Thoman, Peter, Salzmann, Philip, Fahringer, Thomas, Alexander, Leila, Tauriello, Gerardo, Schwede, Torsten, Durairaj, Janani, Emerson, Andrew, Ficarelli, Federico, Wingbermuhle, Sebastian, Lindahl, Eric, Gregori, Daniele, Sana, Emanuele, Coletti, Silvano, and Gschwandtner, Philip

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing
Abstract

Today digital revolution is having a dramatic impact on the pharmaceutical industry and the entire healthcare system. The implementation of machine learning, extreme-scale computer simulations, and big data analytics in the drug design and development process offers an excellent opportunity to lower the risk of investment and reduce the time to the patient. Within the LIGATE project, we aim to integrate, extend, and co-design best-in-class European components to design Computer-Aided Drug Design (CADD) solutions exploiting today's high-end supercomputers and tomorrow's Exascale resources, fostering European competitiveness in the field. The proposed LIGATE solution is a fully integrated workflow that enables to deliver the result of a virtual screening campaign for drug discovery with the highest speed along with the highest accuracy. The full automation of the solution and the possibility to run it on multiple supercomputing centers at once permit to run an extreme scale in silico drug discovery campaign in few days to respond promptly for example to a worldwide pandemic crisis., Comment: Paper Accepted to the 20th ACM International Conference on Computing Frontiers (CF'23)

Published
2023
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46. Divergent mechanisms of steroid inhibition in the human ρ1 GABAA receptor

Author

Chen Fan, John Cowgill, Rebecca J. Howard, and Erik Lindahl

Subjects
Science
Abstract

Abstract ρ-type γ-aminobutyric acid-A (GABAA) receptors are widely distributed in the retina and brain, and are potential drug targets for the treatment of visual, sleep and cognitive disorders. Endogenous neuroactive steroids including β-estradiol and pregnenolone sulfate negatively modulate the function of ρ1 GABAA receptors, but their inhibitory mechanisms are not clear. By combining five cryo-EM structures with electrophysiology and molecular dynamics simulations, we characterize binding sites and negative modulation mechanisms of β-estradiol and pregnenolone sulfate at the human ρ1 GABAA receptor. β-estradiol binds in a pocket at the interface between extracellular and transmembrane domains, apparently specific to the ρ subfamily, and disturbs allosteric conformational transitions linking GABA binding to pore opening. In contrast, pregnenolone sulfate binds inside the pore to block ion permeation, with a preference for activated structures. These results illuminate contrasting mechanisms of ρ1 inhibition by two different neuroactive steroids, with potential implications for subtype-specific gating and pharmacological design.

Published
2024
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47. Allosteric inhibition of CFTR gating by CFTRinh-172 binding in the pore

Author

Xiaolong Gao, Han-I Yeh, Zhengrong Yang, Chen Fan, Fan Jiang, Rebecca J. Howard, Erik Lindahl, John C. Kappes, and Tzyh-Chang Hwang

Subjects
Science
Abstract

Abstract Loss-of-function mutations of the CFTR gene cause the life-shortening genetic disease cystic fibrosis (CF), whereas overactivity of CFTR may lead to secretory diarrhea and polycystic kidney disease. While effective drugs targeting the CFTR protein have been developed for the treatment of CF, little progress has been made for diseases caused by hyper-activated CFTR. Here, we solve the cryo-EM structure of CFTR in complex with CFTRinh-172 (Inh-172), a CFTR gating inhibitor with promising potency and efficacy. We find that Inh-172 binds inside the pore of CFTR, interacting with amino acid residues from transmembrane segments (TMs) 1, 6, 8, 9, and 12 through mostly hydrophobic interactions and a salt bridge. Substitution of these residues lowers the apparent affinity of Inh-172. The inhibitor-bound structure reveals re-orientations of the extracellular segment of TMs 1, 8, and 12, supporting an allosteric modulation mechanism involving post-binding conformational changes. This allosteric inhibitory mechanism readily explains our observations that pig CFTR, which preserves all the amino acid residues involved in Inh-172 binding, exhibits a much-reduced sensitivity to Inh-172 and that the apparent affinity of Inh-172 is altered by the CF drug ivacaftor (i.e., VX-770) which enhances CFTR’s activity through binding to a site also comprising TM8.

Published
2024
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48. Hominin musical sound production: palaeoecological contexts and self domestication

Author

Gary Clark, Arthur Saniotis, Robert Bednarik, Malin Lindahl, and Maciej Henneberg

Subjects
evolution of music, evolution of dance, early hominins, bipedalism, paleoecology, locomotion, archaeology, ar. ramidus, self-domestication, Anthropology, GN1-890
Abstract

In this article we seek to integrate theories of music origins and dance with hominin fossil anatomy and the paleoecological contexts of hominin evolution. Based on the association between rhythm in music, dance and locomotion, we propose that early bipedal hominins may have evolved neurobiological substrates different from other great apes due to the rhythmic aspects of bipedal walking and running. Combined with the emancipation of the hands resulting from erect posture, we propose that the neurobiological changes necessary for technological innovation, cultural practices and human musical abilities may have evolved, at least in incipient form, much earlier than previously thought. The consequent ability to synchronize movement and sound production may have also proved beneficial as early bipedal hominins ventured out of late Miocene and early Pliocene woodland and forested habitats and into more open habitats with increased predation risk. We also postulate that, along with bipedalism, paedomorphic morphogenesis of the skull at the base of the hominin clade was a necessary prerequisite for the evolution of vocal modulation and singing in later varieties of hominin. To date research into the evolution of music and dance has yet to be integrated with the fossil and paleoecological evidence of early hominin evolution. This paper seeks to fill this lacuna in the extant literature on human evolution. We also suggest that autocatalytic feedback loops evolving synergistically with hominin erect posture, skull and hand morphology, neurochemical processes and the self-domestication syndrome, have been operative from early hominins some 6 Ma to the present. We document this process by reference to primatological, ethnographic, neurochemical and archaeological data.

Published
2024
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49. Study on the temporal and spatial distribution of Culex mosquitoes in Hanoi, Vietnam

Author

Janina Krambrich, Thang Nguyen-Tien, Long Pham-Thanh, Sinh Dang-Xuan, Ella Andersson, Patrick Höller, Duoc Trong Vu, Son Hai Tran, Lieu Thi Vu, Dario Akaberi, Jiaxin Ling, John H.-O. Pettersson, Jenny C. Hesson, Johanna F. Lindahl, and Åke Lundkvist

Subjects
Medicine, Science
Abstract

Abstract Arboviruses transmitted by mosquitoes, including Japanese encephalitis virus (JEV), present a substantial global health threat. JEV is transmitted by mosquitoes in the genus Culex, which are common in both urban and rural areas in Vietnam. In 2020, we conducted a 1-year survey of Culex mosquito abundance in urban, suburban, and peri-urban areas of Hanoi using CDC-light traps. Mosquitoes were identified to species and sorted into pools based on species, sex, and trap location. The mosquito pools were also investigated by RT-qPCR for detection of JEV. In total, 4829 mosquitoes were collected over a total of 455 trap-nights, across 13 months. Collected mosquitoes included Culex, Aedes, Anopheles, and Mansonia species. Culex mosquitoes, primarily Cx. quinquefasciatus, predominated, especially in peri-urban areas. Most Culex mosquitoes were caught in the early months of the year. The distribution and abundance of mosquitoes exhibited variations across urban, suburban, and peri-urban sites, emphasizing the influence of environmental factors such as degree of urbanization, temperature and humidity on Culex abundance. No JEV was detected in the mosquito pools. This study establishes baseline knowledge of Culex abundance and temporal variation, which is crucial for understanding the potential for JEV transmission in Hanoi.

Published
2024
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50. Perceptions and practices of Swedish wild boar hunters in relation to African swine fever before the first outbreak in Sweden

Author

Erika Chenais, Linda Ernholm, Annie Frisk Brunzell, Karl Mård, Lotta Svensson, Johanna F. Lindahl, and Susanna Sternberg Lewerin

Subjects
Focus group discussions, Questionnaire, Disease control, Hunting tourism, Veterinary medicine, SF600-1100
Abstract

Abstract Background The first outbreak of African Swine Fever (ASF) in Sweden was detected in 2023 in wild boar. This study was conducted before the first ASF outbreak with the objective of investigating Swedish hunters’ perceptions and practices pertaining to ASF ahead of any potential future outbreak. A mixed-methods interview study with Swedish wild boar hunters, consisting of focus group discussions and a questionnaire, was undertaken between October 2020 and December 2021. Six focus groups were conducted online, and an online questionnaire with questions related to practices and habits concerning hunting, the use of bait and hunting trips was sent to all members of the Swedish Hunting and Wildlife Association. A total of 3244 responses were received. Results Three general themes were identified in a thematic analysis of the data from the focus groups: hunters are willing to engage in ASF prevention and control, simplicity and feasibility are crucial for the implementation of reporting, sampling and control measures, and more information and the greater involvement of the authorities are required in ASF prevention and control. Results from the questionnaire showed that the use of bait was common. Products of animal origin were rarely used for baiting; the most common product used was maize. Hunting trips abroad, especially outside of the Nordic countries, were uncommon. Conclusions Hunting tourism and the use of bait do not seem to constitute a major risk for the introduction of ASF to wild boar populations in Sweden. The accessibility of relevant information for each concerned stakeholder and the ease of reporting and sampling are crucial to maintain the positive engagement of hunters.

Published
2024
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