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3,214 results on '"Brookes, A. J."'

1. Determining sensor geometry and gain in a wearable MEG system

Author

Hill, Ryan M., Rivero, Gonzalo Reina, Tyler, Ashley J., Schofield, Holly, Doyle, Cody, Osborne, James, Bobela, David, Rier, Lukas, Gibson, Joseph, Tanner, Zoe, Boto, Elena, Bowtell, Richard, Brookes, Matthew J., Shah, Vishal, and Holmes, Niall

Subjects
Physics - Medical Physics
Abstract

Optically pumped magnetometers (OPMs) are compact and lightweight sensors that can measure magnetic fields generated by current flow in neuronal assemblies in the brain. Such sensors enable construction of magnetoencephalography (MEG) instrumentation, with significant advantages over conventional MEG devices including adaptability to head size, enhanced movement tolerance, lower complexity and improved data quality. However, realising the potential of OPMs depends on our ability to perform system calibration, which means finding sensor locations, orientations, and the relationship between the sensor output and magnetic field (termed sensor gain). Such calibration is complex in OPMMEG since, for example, OPM placement can change from subject to subject (unlike in conventional MEG where sensor locations or orientations are fixed). Here, we present two methods for calibration, both based on generating well-characterised magnetic fields across a sensor array. Our first device (the HALO) is a head mounted system that generates dipole like fields from a set of coils. Our second (the matrix coil (MC)) generates fields using coils embedded in the walls of a magnetically shielded room. Our results show that both methods offer an accurate means to calibrate an OPM array (e.g. sensor locations within 2 mm of the ground truth) and that the calibrations produced by the two methods agree strongly with each other. When applied to data from human MEG experiments, both methods offer improved signal to noise ratio after beamforming suggesting that they give calibration parameters closer to the ground truth than factory settings and presumed physical sensor coordinates and orientations. Both techniques are practical and easy to integrate into real world MEG applications. This advances the field significantly closer to the routine use of OPMs for MEG recording., Comment: 36 pages, 10 figures

Published
2024

2. Genomic reanalysis of a pan-European rare-disease resource yields new diagnoses

Author

Laurie, Steven, Steyaert, Wouter, de Boer, Elke, Polavarapu, Kiran, Schuermans, Nika, Sommer, Anna K., Demidov, German, Ellwanger, Kornelia, Paramonov, Ida, Thomas, Coline, Aretz, Stefan, Baets, Jonathan, Benetti, Elisa, Bullich, Gemma, Chinnery, Patrick F., Clayton-Smith, Jill, Cohen, Enzo, Danis, Daniel, de Sainte Agathe, Jean-Madeleine, Denommé-Pichon, Anne-Sophie, Diaz-Manera, Jordi, Efthymiou, Stephanie, Faivre, Laurence, Fernandez-Callejo, Marcos, Freeberg, Mallory, Garcia-Pelaez, José, Guillot-Noel, Lena, Haack, Tobias B., Hanna, Mike, Hengel, Holger, Horvath, Rita, Houlden, Henry, Jackson, Adam, Johansson, Lennart, Johari, Mridul, Kamsteeg, Erik-Jan, Kellner, Melanie, Kleefstra, Tjitske, Lacombe, Didier, Lochmüller, Hanns, López-Martín, Estrella, Macaya, Alfons, Marcé-Grau, Anna, Maver, Aleš, Morsy, Heba, Muntoni, Francesco, Musacchia, Francesco, Nelson, Isabelle, Nigro, Vincenzo, Olimpio, Catarina, Oliveira, Carla, Paulasová Schwabová, Jaroslava, Pauly, Martje G., Peterlin, Borut, Peters, Sophia, Pfundt, Rolph, Piluso, Giulio, Piscia, Davide, Posada, Manuel, Reich, Selina, Renieri, Alessandra, Ryba, Lukas, Šablauskas, Karolis, Savarese, Marco, Schöls, Ludger, Schütz, Leon, Steinke-Lange, Verena, Stevanin, Giovanni, Straub, Volker, Sturm, Marc, Swertz, Morris A., Tartaglia, Marco, te Paske, Iris B. A. W., Thompson, Rachel, Torella, Annalaura, Trainor, Christina, Udd, Bjarne, Van de Vondel, Liedewei, van de Warrenburg, Bart, van Reeuwijk, Jeroen, Vandrovcova, Jana, Vitobello, Antonio, Vos, Janet, Vyhnálková, Emílie, Wijngaard, Robin, Wilke, Carlo, William, Doreen, Xu, Jishu, Yaldiz, Burcu, Zalatnai, Luca, Zurek, Birte, Brookes, Anthony J., Evangelista, Teresinha, Gilissen, Christian, Graessner, Holm, Hoogerbrugge, Nicoline, Ossowski, Stephan, Riess, Olaf, Schüle, Rebecca, Synofzik, Matthis, Verloes, Alain, Matalonga, Leslie, Brunner, Han G., Lohmann, Katja, de Voer, Richarda M., Töpf, Ana, Vissers, Lisenka E.L.M., Beltran, Sergi, and Hoischen, Alexander

Published
2025
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3. Offline tagging of radon-induced backgrounds in XENON1T and applicability to other liquid xenon detectors

Author

Aprile, E., Aalbers, J., Abe, K., Maouloud, S. Ahmed, Althueser, L., Andrieu, B., Angelino, E., Angevaare, J. R., Martin, D. Antón, Arneodo, F., Baudis, L., Baxter, A. L., Bazyk, M., Bellagamba, L., Biondi, R., Bismark, A., Brookes, E. J., Brown, A., Bruno, G., Budnik, R., Bui, T. K., Cardoso, J. M. R., Chavez, A. P. Cimental, Colijn, A. P., Conrad, J., Cuenca-García, J. J., D'Andrea, V., Garcia, L. C. Daniel, Decowski, M. P., Di Donato, C., Di Gangi, P., Diglio, S., Eitel, K., Elykov, A., Ferella, A. D., Ferrari, C., Fischer, H., Flehmke, T., Flierman, M., Fulgione, W., Fuselli, C., Gaemers, P., Gaior, R., Galloway, M., Gao, F., Ghosh, S., Glade-Beucke, R., Grandi, L., Grigat, J., Guan, H., Guida, M., Hammann, R., Higuera, A., Hils, C., Hoetzsch, L., Hood, N. F., Iacovacci, M., Itow, Y., Jakob, J., Joerg, F., Joy, A., Kaminaga, Y., Kara, M., Kavrigin, P., Kazama, S., Kobayashi, M., Kopec, A., Kuger, F., Landsman, H., Lang, R. F., Levinson, L., Li, I., Li, S., Liang, S., Lin, Y. T., Lindemann, S., Lindner, M., Liu, K., Loizeau, J., Lombardi, F., Long, J., Lopes, J. A. M., Luce, T., Ma, Y., Macolino, C., Mahlstedt, J., Mancuso, A., Manenti, L., Marignetti, F., Undagoitia, T. Marrodán, Martens, K., Masbou, J., Masson, E., Mastroianni, S., Melchiorre, A., Messina, M., Michael, A., Miuchi, K., Molinario, A., Moriyama, S., Morå, K., Mosbacher, Y., Murra, M., Müller, J., Ni, K., Oberlack, U., Paetsch, B., Palacio, J., Pan, Y., Pellegrini, Q., Peres, R., Peters, C., Pienaar, J., Pierre, M., Plante, G., Pollmann, T. R., Principe, L., Qi, J., Qin, J., García, D. Ramírez, Rajado, M., Shi, J., Singh, R., Sanchez, L., Santos, J. M. F. dos, Sarnoff, I., Sartorelli, G., Schreiner, J., Schulte, D., Schulte, P., Eißing, H. Schulze, Schumann, M., Lavina, L. Scotto, Selvi, M., Semeria, F., Shagin, P., Shi, S., Silva, M., Simgen, H., Takeda, A., Tan, P. -L., Terliuk, A., Thers, D., Toschi, F., Trinchero, G., Tunnell, C., Tönnies, F., Valerius, K., Vecchi, S., Vetter, S., Volta, G., Weinheimer, C., Weiss, M., Wenz, D., Wittweg, C., Wolf, T., Wu, V. H. S., Xing, Y., Xu, D., Xu, Z., Yamashita, M., Yang, L., Ye, J., Yuan, L., Zavattini, G., Zhong, M., and Zhu, T.

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

This paper details the first application of a software tagging algorithm to reduce radon-induced backgrounds in liquid noble element time projection chambers, such as XENON1T and XENONnT. The convection velocity field in XENON1T was mapped out using $^{222}\text{Rn}$ and $^{218}\text{Po}$ events, and the root-mean-square convection speed was measured to be $0.30 \pm 0.01$ cm/s. Given this velocity field, $^{214}\text{Pb}$ background events can be tagged when they are followed by $^{214}\text{Bi}$ and $^{214}\text{Po}$ decays, or preceded by $^{218}\text{Po}$ decays. This was achieved by evolving a point cloud in the direction of a measured convection velocity field, and searching for $^{214}\text{Bi}$ and $^{214}\text{Po}$ decays or $^{218}\text{Po}$ decays within a volume defined by the point cloud. In XENON1T, this tagging system achieved a $^{214}\text{Pb}$ background reduction of $6.2^{+0.4}_{-0.9}\%$ with an exposure loss of $1.8\pm 0.2 \%$, despite the timescales of convection being smaller than the relevant decay times. We show that the performance can be improved in XENONnT, and that the performance of such a software-tagging approach can be expected to be further improved in a diffusion-limited scenario. Finally, a similar method might be useful to tag the cosmogenic $^{137}\text{Xe}$ background, which is relevant to the search for neutrinoless double-beta decay., Comment: 17 pages, 19 figures

Published
2024
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4. The XENONnT Dark Matter Experiment

Author

XENON Collaboration, Aprile, E., Aalbers, J., Abe, K., Maouloud, S. Ahmed, Althueser, L., Andrieu, B., Angelino, E., Angevaare, J. R., Antochi, V. C., Martin, D. Antón, Arneodo, F., Balata, M., Baudis, L., Baxter, A. L., Bazyk, M., Bellagamba, L., Biondi, R., Bismark, A., Brookes, E. J., Brown, A., Bruenner, S., Bruno, G., Budnik, R., Bui, T. K., Cai, C., Cardoso, J. M. R., Cassese, F., Chiarini, A., Cichon, D., Chavez, A. P. Cimental, Colijn, A. P., Conrad, J., Corrieri, R., Cuenca-García, J. J., Cussonneau, J. P., Dadoun, O., D'Andrea, V., Decowski, M. P., De Fazio, B., Di Gangi, P., Diglio, S., Disdier, J. M., Douillet, D., Eitel, K., Elykov, A., Farrell, S., Ferella, A. D., Ferrari, C., Fischer, H., Flierman, M., Form, S., Front, D., Fulgione, W., Fuselli, C., Gaemers, P., Gaior, R., Rosso, A. Gallo, Galloway, M., Gao, F., Gardner, R., Garroum, N., Glade-Beucke, R., Grandi, L., Grigat, J., Guan, H., Guerzoni, M., Guida, M., Hammann, R., Higuera, A., Hils, C., Hoetzsch, L., Hood, N. F., Howlett, J., Huhmann, C., Iacovacci, M., Iaquaniello, G., Iven, L., Itow, Y., Jakob, J., Joerg, F., Joy, A., Kara, M., Kavrigin, P., Kazama, S., Kobayashi, M., Koltman, G., Kopec, A., Kuger, F., Landsman, H., Lang, R. F., Levinson, L., Li, I., Li, S., Liang, S., Lindemann, S., Lindner, M., Liu, K., Loizeau, J., Lombardi, F., Long, J., Lopes, J. A. M., Ma, Y., Macolino, C., Mahlstedt, J., Mancuso, A., Manenti, L., Marignetti, F., Undagoitia, T. Marrodán, Martella, P., Martens, K., Masbou, J., Masson, D., Masson, E., Mastroianni, S., Mele, E., Messina, M., Michinelli, R., Miuchi, K., Molinario, A., Moriyama, S., Morå, K., Mosbacher, Y., Murra, M., Müller, J., Ni, K., Nisi, S., Oberlack, U., Orlandi, D., Othegraven, R., Paetsch, B., Palacio, J., Parlati, S., Paschos, P., Pellegrini, Q., Peres, R., Peters, C., Pienaar, J., Pierre, M., Plante, G., Pollmann, T. R., Qi, J., Qin, J., García, D. Ramírez, Rynge, M., Shi, J., Singh, R., Sanchez, L., Santos, J. M. F. dos, Sarnoff, I., Sartorelli, G., Schreiner, J., Schulte, D., Schulte, P., Eißing, H. Schulze, Schumann, M., Lavina, L. Scotto, Selvi, M., Semeria, F., Shagin, P., Shi, S., Shockley, E., Silva, M., Simgen, H., Stephen, J., Stern, M., Stillwell, B. K., Takeda, A., Tan, P. -L., Tatananni, D., Terliuk, A., Thers, D., Toschi, F., Trinchero, G., Tunnell, C., Tönnies, F., Valerius, K., Volta, G., Weinheimer, C., Weiss, M., Wenz, D., Westermann, J., Wittweg, C., Wolf, T., Wu, V. H. S., Xing, Y., Xu, D., Xu, Z., Yamashita, M., Yang, L., Ye, J., Yuan, L., Zavattini, G., Zhong, M., and Zhu, T.

Subjects
Physics - Instrumentation and Detectors, Astrophysics - Instrumentation and Methods for Astrophysics, High Energy Physics - Experiment
Abstract

The multi-staged XENON program at INFN Laboratori Nazionali del Gran Sasso aims to detect dark matter with two-phase liquid xenon time projection chambers of increasing size and sensitivity. The XENONnT experiment is the latest detector in the program, planned to be an upgrade of its predecessor XENON1T. It features an active target of 5.9 tonnes of cryogenic liquid xenon (8.5 tonnes total mass in cryostat). The experiment is expected to extend the sensitivity to WIMP dark matter by more than an order of magnitude compared to XENON1T, thanks to the larger active mass and the significantly reduced background, improved by novel systems such as a radon removal plant and a neutron veto. This article describes the XENONnT experiment and its sub-systems in detail and reports on the detector performance during the first science run., Comment: 32 pages, 19 figures

Published
2024

5. Design and performance of the field cage for the XENONnT experiment

Author

Aprile, E., Abe, K., Maouloud, S. Ahmed, Althueser, L., Andrieu, B., Angelino, E., Angevaare, J. R., Antochi, V. C., Martin, D. Antón, Arneodo, F., Baudis, L., Baxter, A. L., Bazyk, M., Bellagamba, L., Biondi, R., Bismark, A., Brookes, E. J., Brown, A., Bruenner, S., Bruno, G., Budnik, R., Bui, T. K., Cai, C., Cardoso, J. M. R., Cichon, D., Chávez, A. P. Cimental, Colijn, A. P., Conrad, J., Cuenca-García, J. J., Cussonneau, J. P., DÁndrea, V., Decowski, M. P., Di Gangi, P., Diglio, S., Eitel, K., Elykov, A., Farrell, S., Ferella, A. D., Ferrari, C., Fischer, H., Flierman, M., Fulgione, W., Fuselli, C., Gaemers, P., Gaior, R., Rosso, A. Gallo, Galloway, M., Gao, F., Glade-Beucke, R., Grandi, L., Grigat, J., Guan, H., Guida, M., Hammann, R., Higuera, A., Hils, C., Hoetzsch, L., Hood, N. F., Howlett, J., Iacovacci, M., Itow, Y., Jakob, J., Joerg, F., Joy, A., Kara, M., Kavrigin, P., Kazama, S., Kobayashi, M., Koltman, G., Kopec, A., Kuger, F., Landsman, H., Lang, R. F., Levinson, L., Li, I., Li, S., Liang, S., Lindemann, S., Lindner, M., Liu, K., Loizeau, J., Lombardi, F., Long, J., Lopes, J. A. M., Ma, Y., Macolino, C., Mahlstedt, J., Mancuso, A., Manenti, L., Marignetti, F., Undagoitia, T. Marrodán, Martens, K., Masbou, J., Masson, D., Masson, E., Mastroianni, S., Messina, M., Miuchi, K., Molinario, A., Moriyama, S., Morå, K., Mosbacher, Y., Murra, M., Müller, J., Ni, K., Oberlack, U., Paetsch, B., Palacio, J., Pellegrini, Q., Peres, R., Peters, C., Pienaar, J., Pierre, M., Plante, G., Pollmann, T. R., Qi, J., Qin, J., García, D. Ramírez, Šarčević, N., Shi, J., Singh, R., Sanchez, L., Santos, J. M. F. dos, Sarnoff, I., Sartorelli, G., Schreiner, J., Schulte, D., Schulte, P., Eißing, H. Schulze, Schumann, M., Lavina, L. Scotto, Selvi, M., Semeria, F., Shagin, P., Shi, S., Shockley, E., Silva, M., Simgen, H., Takeda, A., Tan, P. -L., Terliuk, A., Thers, D., Toschi, F., Trinchero, G., Tunnell, C., Tönnies, F., Valerius, K., Volta, G., Weinheimer, C., Weiss, M., Wenz, D., Wittweg, C., Wolf, T., Wu, V. H. S., Xing, Y., Xu, D., Xu, Z., Yamashita, M., Yang, L., Ye, J., Yuan, L., Zavattini, G., Zhong, M., and Zhu, T.

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

The precision in reconstructing events detected in a dual-phase time projection chamber depends on an homogeneous and well understood electric field within the liquid target. In the XENONnT TPC the field homogeneity is achieved through a double-array field cage, consisting of two nested arrays of field shaping rings connected by an easily accessible resistor chain. Rather than being connected to the gate electrode, the topmost field shaping ring is independently biased, adding a degree of freedom to tune the electric field during operation. Two-dimensional finite element simulations were used to optimize the field cage, as well as its operation. Simulation results were compared to ${}^{83m}\mathrm{Kr}$ calibration data. This comparison indicates an accumulation of charge on the panels of the TPC which is constant over time, as no evolution of the reconstructed position distribution of events is observed. The simulated electric field was then used to correct the charge signal for the field dependence of the charge yield. This correction resolves the inconsistent measurement of the drift electron lifetime when using different calibrations sources and different field cage tuning voltages.

Published
2023
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6. Common conditions of use elements. Atomic concepts for consistent and effective information governance

Author

Sanchez Gonzalez, Maria del Carmen, Kamerling, Pim, Iermito, Mariapia, Casati, Sara, Riaz, Umar, Veal, Colin D., Maini, Monika, Jeanson, Francis, Benhamed, Oussama Mohammed, van Enckevort, Esther, Landi, Annalisa, Mimouni, Yanis, Le Cornec, Clèmence, Coviello, Domenico A., Franchin, Tiziana, Fusco, Francesca, Ramírez García, Jose Antonio, van der Zanden, Loes F. M., Bernier, Alexander, Wilkinson, Mark D., Mueller, Heimo, Gibson, Spencer J., and Brookes, Anthony J.

Published
2024
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7. Getting your DUCs in a row - standardising the representation of Digital Use Conditions

Author

Jeanson, Francis, Gibson, Spencer J., Alper, Pinar, Bernier, Alexander, Woolley, J. Patrick, Mietchen, Daniel, Strug, Andrzej, Becker, Regina, Kamerling, Pim, Sanchez Gonzalez, Maria del Carmen, Mah, Nancy, Novakowski, Ann, Wilkinson, Mark D., Benhamed, Oussama Mohammed, Landi, Annalisa, Krog, Georg Philip, Müller, Heimo, Riaz, Umar, Veal, Colin, Holub, Petr, van Enckevort, Esther, and Brookes, Anthony J.

Published
2024
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11. Cosmogenic background simulations for the DARWIN observatory at different underground locations

Author

Adrover, M., Althueser, L., Andrieu, B., Angelino, E., Angevaare, J. R., Antunovic, B., Aprile, E., Babicz, M., Bajpai, D., Barberio, E., Baudis, L., Bazyk, M., Bell, N., Bellagamba, L., Biondi, R., Biondi, Y., Bismark, A., Boehm, C., Breskin, A., Brookes, E. J., Brown, A., Bruno, G., Budnik, R., Capelli, C., Cardoso, J. M. R., Chauvin, A., Chavez, A. P. Cimental, Colijn, A. P., Conrad, J., Cuenca-García, J. J., D'Andrea, V., Decowski, M. P., Deisting, A., Di Gangi, P., Diglio, S., Doerenkamp, M., Drexlin, G., Eitel, K., Elykov, A., Engel, R., Farrell, S., Ferella, A. D., Ferrari, C., Fischer, H., Flierman, M., Fulgione, W., Gaemers, P., Gaior, R., Galloway, M., Garroum, N., Ghosh, S., Girard, F., Glade-Beucke, R., Glück, F., Grandi, L., Grigat, J., Größle, R., Guan, H., Guida, M., Hammann, R., Hannen, V., Hansmann-Menzemer, S., Hargittai, N., Hasegawa, T., Hils, C., Higuera, A., Hiraoka, K., Hoetzsch, L., Iacovacci, M., Itow, Y., Jakob, J., Jörg, F., Kara, M., Kavrigin, P., Kazama, S., Keller, M., Kilminster, B., Kleifges, M., Kobayashi, M., Kopec, A., von Krosigk, B., Kuger, F., Landsman, H., Lang, R. F., Li, I., Li, S., Liang, S., Lindemann, S., Lindner, M., Lombardi, F., Loizeau, J., Luce, T., Ma, Y., Macolino, C., Mahlstedt, J., Mancuso, A., Undagoitia, T. Marrodán, Lopes, J. A. M., Marignetti, F., Martens, K., Masbou, J., Mastroianni, S., Milutinovic, S., Miuchi, K., Miyata, R., Molinario, A., Monteiro, C. M. B., Morå, K., Morteau, E., Mosbacher, Y., Müller, J., Murra, M., Newstead, J. L., Ni, K., Oberlack, U. G., Ostrovskiy, I., Paetsch, B., Pandurovic, M., Pellegrini, Q., Peres, R., Pienaar, J., Pierre, M., Piotter, M., Plante, G., Pollmann, T. R., Principe, L., Qi, J., Qin, J., Silva, M. Rajado, García, D. Ramírez, Razeto, A., Sakamoto, S., Sanchez, L., Sanchez-Lucas, P., Santos, J. M. F. dos, Sartorelli, G., Scaffidi, A., Schulte, P., Schultz-Coulon, H. -C., Eißing, H. Schulze, Schumann, M., Lavina, L. Scotto, Selvi, M., Semeria, F., Shagin, P., Sharma, S., Shen, W., Silva, M., Simgen, H., Singh, R., Solmaz, M., Stanley, O., Steidl, M., Tan, P. L., Terliuk, A., Thers, D., Thümmler, T., Tönnies, F., Toschi, F., Trinchero, G., Trotta, R., Tunnell, C., Urquijo, P., Valerius, K., Vecchi, S., Vetter, S., Volta, G., Vorkapic, D., Wang, W., Weerman, K. M., Weinheimer, C., Weiss, M., Wenz, D., Wittweg, C., Wolf, J., Wolf, T., Wu, V. H. S., Wurm, M., Xing, Y., Yamashita, M., Ye, J., Zavattini, G., and Zuber, K.

Subjects
Physics - Instrumentation and Detectors
Abstract

Xenon dual-phase time projections chambers (TPCs) have proven to be a successful technology in studying physical phenomena that require low-background conditions. With 40t of liquid xenon (LXe) in the TPC baseline design, DARWIN will have a high sensitivity for the detection of particle dark matter, neutrinoless double beta decay ($0\nu\beta\beta$), and axion-like particles (ALPs). Although cosmic muons are a source of background that cannot be entirely eliminated, they may be greatly diminished by placing the detector deep underground. In this study, we used Monte Carlo simulations to model the cosmogenic background expected for the DARWIN observatory at four underground laboratories: Laboratori Nazionali del Gran Sasso (LNGS), Sanford Underground Research Facility (SURF), Laboratoire Souterrain de Modane (LSM) and SNOLAB. We determine the production rates of unstable xenon isotopes and tritium due to muon-included neutron fluxes and muon-induced spallation. These are expected to represent the dominant contributions to cosmogenic backgrounds and thus the most relevant for site selection.

Published
2023
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12. Search for events in XENON1T associated with Gravitational Waves

Author

XENON Collaboration, Aprile, E., Abe, K., Maouloud, S. Ahmed, Althueser, L., Andrieu, B., Angelino, E., Angevaare, J. R., Antochi, V. C., Martin, D. Antoń, Arneodo, F., Baudis, L., Baxter, A. L., Bazyk, M., Bellagamba, L., Biondi, R., Bismark, A., Brookes, E. J., Brown, A., Bruenner, S., Bruno, G., Budnik, R., Bui, T. K., Cai, C., Cardoso, J. M. R., Chavez, A. P. Cimental, Colijn, A. P., Conrad, J., Cuenca-García, J. J., D'Andrea, V., Decowski, M. P., Di Gangi, P., Diglio, S., Eitel, K., Elykov, A., Farrell, S., Ferella, A. D., Ferrari, C., Fischer, H., Flierman, M., Fulgione, W., Fuselli, C., Gaemers, P., Gaior, R., Rosso, A. Gallo, Galloway, M., Gao, F., Glade-Beucke, R., Grandi, L., Grigat, J., Guan, H., Guida, M., Hammann, R., Higuera, A., Hils, C., Hoetzsch, L., Hood, N. F., Howlett, J., Iacovacci, M., Itow, Y., Jakob, J., Joerg, F., Joy, A., Kara, M., Kavrigin, P., Kazama, S., Kobayashi, M., Koltman, G., Kopec, A., Kuger, F., Landsman, H., Lang, R. F., Carlos, D. G. Layos, Levinson, L., Li, I., Li, S., Liang, S., Lindemann, S., Lindner, M, Liu, K., Loizeau, J., Lombardi, F., Long, J., Lopes, J. A. M., Ma, Y., Macolino, C., Mahlstedt, J., Mancuso, A., Manenti, L., Marignetti, F., Undagoitia, T. Marrodán, Martens, K., Masbou, J., Masson, D., Masson, E., Mastroianni, S., Messina, M., Miuchi, K., Molinario, A., Moriyama, S., Morå, K., Mosbacher, Y., Murra, M., Müller, J., Ni, K., Oberlack, U., Paetsch, B., Palacio, J., Pellegrini, Q., Peres, R., Peters, C, Pienaar, J., Pierre, M., Plante, G., Pollmann, T. R., Qi, J., Qin, J., García, D. Ramírez, Shi, J., Singh, R., Sanchez, L., Santos, J. M. F. dos, Sarnoff, I., Sartorelli, G., Schreiner, J., Schulte, D., Schulte, P., Eißing, H. Schulze, Schumann, M., Lavina, L. Scotto, Selvi, M., Semeria, F., Shagin, P., Shi, S., Shockley, E., Silva, M., Simgen, H., Takeda, A., Tan, P. -L., Terliuk, A., Thers, D., Toschi, F., Trinchero, G., Tunnell, C., Tönnies, F., Valerius, K., Volta, G., Weinheimer, C., Weiss, M., Wenz, D., Wittweg, C., Wolf, T., Wu, V. H. S., Xing, Y., Xu, D., Xu, Z., Yamashita, M., Yang, L., Ye, J., Yuan, L., Zavattini, G., Zhong, M., and Zhu, T.

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

We perform a blind search for particle signals in the XENON1T dark matter detector that occur close in time to gravitational wave signals in the LIGO and Virgo observatories. No particle signal is observed in the nuclear recoil, electronic recoil, CE$\nu$NS, and S2-only channels within $\pm$ 500 seconds of observations of the gravitational wave signals GW170104, GW170729, GW170817, GW170818, and GW170823. We use this null result to constrain mono-energetic neutrinos and Beyond Standard Model particles emitted in the closest coalescence GW170817, a binary neutron star merger. We set new upper limits on the fluence (time-integrated flux) of coincident neutrinos down to 17 keV at 90% confidence level. Furthermore, we constrain the product of coincident fluence and cross section of Beyond Standard Model particles to be less than $10^{-29}$ cm$^2$/cm$^2$ in the [5.5-210] keV energy range at 90% confidence level.

Published
2023

13. Searching for Heavy Dark Matter near the Planck Mass with XENON1T

Author

Aprile, E., Abe, K., Maouloud, S. Ahmed, Althueser, L., Andrieu, B., Angelino, E., Angevaare, J. R., Antochi, V. C., Martin, D. Antón, Arneodo, F., Baudis, L., Baxter, A. L., Bazyk, M., Bellagamba, L., Biondi, R., Bismark, A., Brookes, E. J., Brown, A., Bruenner, S., Bruno, G., Budnik, R., Bui, T. K., Cai, C., Cardoso, J. M. R., Cichon, D., Chavez, A. P. Cimental, Clark, M., Colijn, A. P., Conrad, J., Cuenca-García, J. J., Cussonneau, J. P., D'Andrea, V., Decowski, M. P., Di Gangi, P., Di Pede, S., Diglio, S., Eitel, K., Elykov, A., Farrell, S., Ferella, A. D., Ferrari, C., Fischer, H., Flierman, M., Fulgione, W., Fuselli, C., Gaemers, P., Gaior, R., Rosso, A. Gallo, Galloway, M., Gao, F., Glade-Beucke, R., Grandi, L., Grigat, J., Guan, H., Guida, M., Hammann, R., Higuera, A., Hils, C., Hoetzsch, L., Hood, N. F., Howlett, J., Iacovacci, M., Itow, Y., Jakob, J., Joerg, F., Joy, A., Kato, N., Kara, M., Kavrigin, P., Kazama, S., Kobayashi, M., Koltman, G., Kopec, A., Kuger, F., Landsman, H., Lang, R. F., Levinson, L., Li, I., Li, S., Liang, S., Lindemann, S., Lindner, M., Liu, K., Loizeau, J., Lombardi, F., Long, J., Lopes, J. A. M., Ma, Y., Macolino, C., Mahlstedt, J., Mancuso, A., Manenti, L., Marignetti, F., Undagoitia, T. Marrodán, Martens, K., Masbou, J., Masson, D., Masson, E., Mastroianni, S., Messina, M., Miuchi, K., Mizukoshi, K., Molinario, A., Moriyama, S., Morå, K., Mosbacher, Y., Murra, M., Müller, J., Ni, K., Oberlack, U., Paetsch, B., Palacio, J., Pellegrini, Q., Peres, R., Peters, C., Pienaar, J., Pierre, M., Pizzella, V., Plante, G., Pollmann, T. R., Qi, J., Qin, J., García, D. Ramírez, Singh, R., Sanchez, L., Santos, J. M. F. dos, Sarnoff, I., Sartorelli, G., Schreiner, J., Schulte, D., Schulte, P., Eißing, H. Schulze, Schumann, M., Lavina, L. Scotto, Selvi, M., Semeria, F., Shagin, P., Shi, S., Shockley, E., Silva, M., Simgen, H., Takeda, A., Tan, P. -L., Terliuk, A., Thers, D., Toschi, F., Trinchero, G., Tunnell, C., Tönnies, F., Valerius, K., Volta, G., Weinheimer, C., Weiss, M., Wenz, D., Wittweg, C., Wolf, T., Wu, V. H. S., Xing, Y., Xu, D., Xu, Z., Yamashita, M., Yang, L., Ye, J., Yuan, L., Zavattini, G., Zhong, M., and Zhu, T.

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

Multiple viable theoretical models predict heavy dark matter particles with a mass close to the Planck mass, a range relatively unexplored by current experimental measurements. We use 219.4 days of data collected with the XENON1T experiment to conduct a blind search for signals from Multiply-Interacting Massive Particles (MIMPs). Their unique track signature allows a targeted analysis with only 0.05 expected background events from muons. Following unblinding, we observe no signal candidate events. This work places strong constraints on spin-independent interactions of dark matter particles with a mass between 1$\times$10$^{12}\,$GeV/c$^2$ and 2$\times$10$^{17}\,$GeV/c$^2$. In addition, we present the first exclusion limits on spin-dependent MIMP-neutron and MIMP-proton cross-sections for dark matter particles with masses close to the Planck scale., Comment: 7 pages, 6 figures

Published
2023
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14. Detector signal characterization with a Bayesian network in XENONnT

Author

XENON Collaboration, Aprile, E., Abe, K., Maouloud, S. Ahmed, Althueser, L., Andrieu, B., Angelino, E., Angevaare, J. R., Antochi, V. C., Martin, D. Antón, Arneodo, F., Baudis, L., Baxter, A. L., Bazyk, M., Bellagamba, L., Biondi, R., Bismark, A., Brookes, E. J., Brown, A., Bruenner, S., Bruno, G., Budnik, R., Bui, T. K., Cai, C., Cardoso, J. M. R., Cichon, D., Chavez, A. P. Cimental, Colijn, A. P., Conrad, J., Cuenca-García, J. J., Cussonneau, J. P., D'Andrea, V., Decowski, M. P., Di Gangi, P., Di Pede, S., Diglio, S., Eitel, K., Elykov, A., Farrell, S., Ferella, A. D., Ferrari, C., Fischer, H., Flierman, M., Fulgione, W., Fuselli, C., Gaemers, P., Gaior, R., Rosso, A. Gallo, Galloway, M., Gao, F., Glade-Beucke, R., Grandi, L., Grigat, J., Guan, H., Guida, M., Hammann, R., Higuera, A., Hils, C., Hoetzsch, L., Hood, N. F., Howlett, J., Iacovacci, M., Itow, Y., Jakob, J., Joerg, F., Joy, A., Kato, N., Kara, M., Kavrigin, P., Kazama, S., Kobayashi, M., Koltman, G., Kopec, A., Kuger, F., Landsman, H., Lang, R. F., Levinson, L., Li, I., Li, S., Liang, S., Lindemann, S., Lindner, M., Liu, K., Loizeau, J., Lombardi, F., Long, J., Lopes, J. A. M., Ma, Y., Macolino, C., Mahlstedt, J., Mancuso, A., Manenti, L., Marignetti, F., Undagoitia, T. Marrodán, Martens, K., Masbou, J., Masson, D., Masson, E., Mastroianni, S., Messina, M., Miuchi, K., Mizukoshi, K., Molinario, A., Moriyama, S., Morå, K., Mosbacher, Y., Murra, M., Müller, J., Ni, K., Oberlack, U., Paetsch, B., Palacio, J., Pellegrini, Q., Peres, R., Peters, C., Pienaar, J., Pierre, M., Pizzella, V., Plante, G., Pollmann, T. R., Qi, J., Qin, J., García, D. Ramírez, Singh, R., Sanchez, L., Santos, J. M. F. dos, Sarnoff, I., Sartorelli, G., Schreiner, J., Schulte, D., Schulte, P., Eißing, H. Schulze, Schumann, M., Lavina, L. Scotto, Selvi, M., Semeria, F., Shagin, P., Shi, S., Shockley, E., Silva, M., Simgen, H., Takeda, A., Tan, P. -L., Terliuk, A., Thers, D., Toschi, F., Trinchero, G., Tunnell, C., Tönnies, F., Valerius, K., Volta, G., Weinheimer, C., Weiss, M., Wenz, D., Wittweg, C., Wolf, T., Wu, V. H. S., Xing, Y., Xu, D., Xu, Z., Yamashita, M., Yang, L., Ye, J., Yuan, L., Zavattini, G., Zhong, M., and Zhu, T.

Subjects
High Energy Physics - Experiment
Abstract

We developed a detector signal characterization model based on a Bayesian network trained on the waveform attributes generated by a dual-phase xenon time projection chamber. By performing inference on the model, we produced a quantitative metric of signal characterization and demonstrate that this metric can be used to determine whether a detector signal is sourced from a scintillation or an ionization process. We describe the method and its performance on electronic-recoil (ER) data taken during the first science run of the XENONnT dark matter experiment. We demonstrate the first use of a Bayesian network in a waveform-based analysis of detector signals. This method resulted in a 3% increase in ER event-selection efficiency with a simultaneously effective rejection of events outside of the region of interest. The findings of this analysis are consistent with the previous analysis from XENONnT, namely a background-only fit of the ER data., Comment: 11 pages, 8 figures

Published
2023
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15. First Dark Matter Search with Nuclear Recoils from the XENONnT Experiment

Author

XENON Collaboration, Aprile, E., Abe, K., Agostini, F., Maouloud, S. Ahmed, Althueser, L., Andrieu, B., Angelino, E., Angevaare, J. R., Antochi, V. C., Martin, D. Antón, Arneodo, F., Baudis, L., Baxter, A. L., Bazyk, M., Bellagamba, L., Biondi, R., Bismark, A., Brookes, E. J., Brown, A., Bruenner, S., Bruno, G., Budnik, R., Bui, T. K., Cai, C., Cardoso, J. M. R., Cichon, D., Chavez, A. P. Cimental, Colijn, A. P., Conrad, J., Cuenca-García, J. J., Cussonneau, J. P., D'Andrea, V., Decowski, M. P., Di Gangi, P., Di Pede, S., Diglio, S., Eitel, K., Elykov, A., Farrell, S., Ferella, A. D., Ferrari, C., Fischer, H., Flierman, M., Fulgione, W., Fuselli, C., Gaemers, P., Gaior, R., Rosso, A. Gallo, Galloway, M., Gao, F., Glade-Beucke, R., Grandi, L., Grigat, J., Guan, H., Guida, M., Hammann, R., Higuera, A., Hils, C., Hoetzsch, L., Hood, N. F., Howlett, J., Iacovacci, M., Itow, Y., Jakob, J., Joerg, F., Joy, A., Kato, N., Kara, M., Kavrigin, P., Kazama, S., Kobayashi, M., Koltman, G., Kopec, A., Kuger, F., Landsman, H., Lang, R. F., Levinson, L., Li, I., Li, S., Liang, S., Lindemann, S., Lindner, M., Liu, K., Loizeau, J., Lombardi, F., Long, J., Lopes, J. A. M., Ma, Y., Macolino, C., Mahlstedt, J., Mancuso, A., Manenti, L., Marignetti, F., Undagoitia, T. Marrodán, Martens, K., Masbou, J., Masson, D., Masson, E., Mastroianni, S., Messina, M., Miuchi, K., Mizukoshi, K., Molinario, A., Moriyama, S., Morå, K., Mosbacher, Y., Murra, M., Müller, J., Ni, K., Oberlack, U., Paetsch, B., Palacio, J., Peres, R., Peters, C., Pienaar, J., Pierre, M., Pizzella, V., Plante, G., Qi, J., Qin, J., García, D. Ramírez, Singh, R., Sanchez, L., Santos, J. M. F. dos, Sarnoff, I., Sartorelli, G., Schreiner, J., Schulte, D., Schulte, P., Eißing, H. Schulze, Schumann, M., Lavina, L. Scotto, Selvi, M., Semeria, F., Shagin, P., Shi, S., Shockley, E., Silva, M., Simgen, H., Takeda, A., Tan, P. -L., Terliuk, A., Thers, D., Toschi, F., Trinchero, G., Tunnell, C., Tönnies, F., Valerius, K., Volta, G., Weinheimer, C., Weiss, M., Wenz, D., Wittweg, C., Wolf, T., Wu, V. H. S., Xing, Y., Xu, D., Xu, Z., Yamashita, M., Yang, L., Ye, J., Yuan, L., Zavattini, G., Zhong, M., and Zhu, T.

Subjects
High Energy Physics - Experiment, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, High Energy Physics - Phenomenology, Physics - Instrumentation and Detectors
Abstract

We report on the first search for nuclear recoils from dark matter in the form of weakly interacting massive particles (WIMPs) with the XENONnT experiment which is based on a two-phase time projection chamber with a sensitive liquid xenon mass of $5.9$ t. During the approximately 1.1 tonne-year exposure used for this search, the intrinsic $^{85}$Kr and $^{222}$Rn concentrations in the liquid target were reduced to unprecedentedly low levels, giving an electronic recoil background rate of $(15.8\pm1.3)~\mathrm{events}/(\mathrm{t\cdot y \cdot keV})$ in the region of interest. A blind analysis of nuclear recoil events with energies between $3.3$ keV and $60.5$ keV finds no significant excess. This leads to a minimum upper limit on the spin-independent WIMP-nucleon cross section of $2.58\times 10^{-47}~\mathrm{cm}^2$ for a WIMP mass of $28~\mathrm{GeV}/c^2$ at $90\%$ confidence level. Limits for spin-dependent interactions are also provided. Both the limit and the sensitivity for the full range of WIMP masses analyzed here improve on previous results obtained with the XENON1T experiment for the same exposure., Comment: Limit points are included in the submission file

Published
2023
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16. The Triggerless Data Acquisition System of the XENONnT Experiment

Author

Aprile, E., Aalbers, J., Abe, K., Agostini, F., Maouloud, S. Ahmed, Althueser, L., Andrieu, B., Angelino, E., Angevaare, J. R., Antochi, V. C., Martin, D. Antón, Arneodo, F., Baudis, L., Baxter, A. L., Bellagamba, L., Biondi, R., Bismark, A., Brookes, E. J., Brown, A., Bruenner, S., Bruno, G., Budnik, R., Bui, T. K., Cai, C., Cardoso, J. M. R., Cichon, D., Chavez, A. P. Cimental, Coderre, D., Colijn, A. P., Conrad, J., Cuenca-García, J. J., Cussonneau, J. P., D'Andrea, V., Decowski, M. P., Di Gangi, P., Di Pede, S., Diglio, S., Eitel, K., Elykov, A., Farrell, S., Ferella, A. D., Ferrari, C., Fischer, H., Flierman, M., Fulgione, W., Fuselli, C., Gaemers, P., Gaior, R., Rosso, A. Gallo, Galloway, M., Gao, F., Glade-Beucke, R., Grandi, L., Grigat, J., Guida, M., Hammann, R., Higuera, A., Hils, C., Hoetzsch, L., Hood, N. F., Howlett, J., Iacovacci, M., Itow, Y., Jakob, J., Joerg, F., Joy, A., Kato, N., Kara, M., Kavrigin, P., Kazama, S., Kobayashi, M., Koltman, G., Kopec, A., Kuger, F., Landsman, H., Lang, R. F., Levinson, L., Li, I., Li, S., Liang, S., Lindemann, S., Lindner, M., Liu, K., Loizeau, J., Lombardi, F., Long, J., Lopes, J. A. M., Ma, Y., Macolino, C., Mahlstedt, J., Mancuso, A., Manenti, L., Marignetti, F., Undagoitia, T. Marrodán, Martens, K., Masbou, J., Masson, D., Masson, E., Mastroianni, S., Messina, M., Miuchi, K., Mizukoshi, K., Molinario, A., Moriyama, S., Morå, K., Mosbacher, Y., Murra, M., Müller, J., Ni, K., Oberlack, U., Paetsch, B., Palacio, J., Peres, R., Peters, C., Pienaar, J., Pierre, M., Pizzella, V., Plante, G., Qi, J., Qin, J., García, D. Ramírez, Rocchetti, A., Sanchez, L., Sanchez-Lucas, P., Santos, J. M. F. dos, Sarnoff, I., Sartorelli, G., Schreiner, J., Schulte, D., Schulte, P., Eißing, H. Schulze, Schumann, M., Lavina, L. Scotto, Selvi, M., Semeria, F., Shagin, P., Shi, S., Shockley, E., Silva, M., Simgen, H., Takeda, A., Tan, P. -L., Terliuk, A., Thers, D., Toschi, F., Trinchero, G., Tunnell, C., Tönnies, F., Valerius, K., Volta, G., Weinheimer, C., Weiss, M., Wenz, D., Wittweg, C., Wolf, T., Xu, D., Xu, Z., Yamashita, M., Yang, L., Ye, J., Yuan, L., Zavattini, G., Zerbo, S., Zhong, M., and Zhu, T.

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

The XENONnT detector uses the latest and largest liquid xenon-based time projection chamber (TPC) operated by the XENON Collaboration, aimed at detecting Weakly Interacting Massive Particles and conducting other rare event searches. The XENONnT data acquisition (DAQ) system constitutes an upgraded and expanded version of the XENON1T DAQ system. For its operation, it relies predominantly on commercially available hardware accompanied by open-source and custom-developed software. The three constituent subsystems of the XENONnT detector, the TPC (main detector), muon veto, and the newly introduced neutron veto, are integrated into a single DAQ, and can be operated both independently and as a unified system. In total, the DAQ digitizes the signals of 698 photomultiplier tubes (PMTs), of which 253 from the top PMT array of the TPC are digitized twice, at $\times10$ and $\times0.5$ gain. The DAQ for the most part is a triggerless system, reading out and storing every signal that exceeds the digitization thresholds. Custom-developed software is used to process the acquired data, making it available within $\mathcal{O}\left(10\text{ s}\right)$ for live data quality monitoring and online analyses. The entire system with all the three subsystems was successfully commissioned and has been operating continuously, comfortably withstanding readout rates that exceed $\sim500$ MB/s during calibration. Livetime during normal operation exceeds $99\%$ and is $\sim90\%$ during most high-rate calibrations. The combined DAQ system has collected more than 2 PB of both calibration and science data during the commissioning of XENONnT and the first science run.

Published
2022
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17. Benchtop magnetic shielding for benchmarking atomic magnetometers

Author

Hobson, P. J., Holmes, N., Patel, P., Chalmers, J., Styles, B., Morley, C., Davis, A., Packer, M., Smith, T. X., Raudonyte, S., Holmes, D., Harrison, R., Woolger, D., Sims, D., Brookes, M. J., Bowtell, R. W., and Fromhold, T. M.

Subjects
Physics - Instrumentation and Detectors, Physics - Applied Physics
Abstract

Here, a benchtop hybrid magnetic shield containing four mumetal cylinders and nine internal flexible printed circuit boards is designed, constructed, tested, and operated. The shield is designed specifically as a test-bed for building and operating ultra-sensitive quantum magnetometers. The geometry and spacing of the mumetal cylinders are optimized to maximize shielding efficiency while maintaining Johnson noise $<15$ fT/$\sqrt{}$Hz. Experimental measurements at the shield's center show passive shielding efficiency of $\left(1.0\pm0.1\right){\times}10^6$ for a $0.2$ Hz oscillating field applied along the shield's axis. The nine flexible printed circuit boards generate three uniform fields, which all deviate from perfect uniformity by ${\leq}0.5$% along $50$% of the inner shield axis, and five linear field gradients and one second-order gradient, which all deviate by ${\leq}4$% from perfect linearity and curvature, respectively, over measured target regions. Together, the target field amplitudes are adjusted to minimize the remnant static field along $40$% of the inner shield axis, as mapped using an atomic magnetometer. In this region, the active null reduces the norm of the magnitudes of the three uniform fields and six gradients by factors of $19.5$ and $19.8$, respectively, thereby reducing the total static field from $1.68$ nT to $0.23$ nT., Comment: 8 pages, 9 figures; This work has been submitted to the IEEE for possible publication

Published
2022

18. The XENONnT dark matter experiment

Author

Aprile, E., Aalbers, J., Abe, K., Ahmed Maouloud, S., Althueser, L., Andrieu, B., Angelino, E., Angevaare, J. R., Antochi, V. C., Antón Martin, D., Arneodo, F., Balata, M., Baudis, L., Baxter, A. L., Bazyk, M., Bellagamba, L., Biondi, R., Bismark, A., Brookes, E. J., Brown, A., Bruenner, S., Bruno, G., Budnik, R., Bui, T. K., Cai, C., Cardoso, J. M. R., Cassese, F., Chiarini, A., Cichon, D., Cimental Chavez, A. P., Colijn, A. P., Conrad, J., Corrieri, R., Cuenca-García, J. J., Cussonneau, J. P., Dadoun, O., D’Andrea, V., Decowski, M. P., De Fazio, B., Gangi, P. Di, Diglio, S., Disdier, J. M., Douillet, D., Eitel, K., Elykov, A., Farrell, S., Ferella, A. D., Ferrari, C., Fischer, H., Flierman, M., Form, S., Front, D., Fulgione, W., Fuselli, C., Gaemers, P., Gaior, R., Rosso, A. Gallo, Galloway, M., Gao, F., Gardner, R., Garroum, N., Glade-Beucke, R., Grandi, L., Grigat, J., Guan, H., Guerzoni, M., Guida, M., Hammann, R., Higuera, A., Hils, C., Hoetzsch, L., Hood, N. F., Howlett, J., Huhmann, C., Iacovacci, M., Iaquaniello, G., Iven, L., Itow, Y., Jakob, J., Joerg, F., Joy, A., Kara, M., Kavrigin, P., Kazama, S., Kobayashi, M., Koltman, G., Kopec, A., Kuger, F., Landsman, H., Lang, R. F., Levinson, L., Li, I., Li, S., Liang, S., Lindemann, S., Lindner, M., Liu, K., Loizeau, J., Lombardi, F., Long, J., Lopes, J. A. M., Ma, Y., Macolino, C., Mahlstedt, J., Mancuso, A., Manenti, L., Marignetti, F., Marrodán Undagoitia, T., Martella, P., Martens, K., Masbou, J., Masson, D., Masson, E., Mastroianni, S., Mele, E., Messina, M., Michinelli, R., Miuchi, K., Molinario, A., Moriyama, S., Morå, K., Mosbacher, Y., Murra, M., Müller, J., Ni, K., Nisi, S., Oberlack, U., Orlandi, D., Othegraven, R., Paetsch, B., Palacio, J., Parlati, S., Paschos, P., Pellegrini, Q., Peres, R., Peters, C., Pienaar, J., Pierre, M., Plante, G., Pollmann, T. R., Qi, J., Qin, J., García, D. Ramírez, Rynge, M., Shi, J., Singh, R., Sanchez, L., Santos, J. M. F. dos, Sarnoff, I., Sartorelli, G., Schreiner, J., Schulte, D., Schulte, P., Schulze Eißing, H., Schumann, M., Scotto Lavina, L., Selvi, M., Semeria, F., Shagin, P., Shi, S., Shockley, E., Silva, M., Simgen, H., Stephen, J., Stern, M., Stillwell, B. K., Takeda, A., Tan, P.-L., Tatananni, D., Terliuk, A., Thers, D., Toschi, F., Trinchero, G., Tunnell, C., Tönnies, F., Valerius, K., Volta, G., Weinheimer, C., Weiss, M., Wenz, D., Westermann, J., Wittweg, C., Wolf, T., Wu, V. H. S., Xing, Y., Xu, D., Xu, Z., Yamashita, M., Yang, L., Ye, J., Yuan, L., Zavattini, G., Zhong, M., and Zhu, T.

Published
2024
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20. Validation, Deployment, and Real-World Implementation of a Modular Toolbox for Alzheimer’s Disease Detection and Dementia Risk Reduction: The AD-RIDDLE Project

Author

Malzbender, K., Barbarino, P., Ferrell, P. Barkman, Bradshaw, A., Brookes, A. J., Díaz, C., van der Flier, W. M., Georges, J., Hansson, O., Hartmanis, M., Jönsson, L., Krishnan, R., MacLeod, T., Mangialasche, F., Mecocci, P., Minguillon, C., Middleton, L., Pla, S., Sardi, S. P., Schöll, M., Suárez-Calvet, M., Weidner, W., Visser, P. J., Zetterberg, H., Bose, N., Solomon, A., and Kivipelto, Miia

Published
2024
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21. Bespoke magnetic field design for a magnetically shielded cold atom interferometer

Author

Hobson, P. J., Vovrosh, J., Stray, B., Packer, M., Winch, J., Holmes, N., Hayati, F., McGovern, K., Bowtell, R., Brookes, M. J., Bongs, K., Fromhold, T. M., and Holynski, M.

Subjects
Physics - Applied Physics
Abstract

Quantum sensors based on cold atoms are being developed which produce measurements of unprecedented accuracy. Due to shifts in atomic energy levels, quantum sensors often have stringent requirements on their internal magnetic field environment. Typically, background magnetic fields are attenuated using high permeability magnetic shielding, with the cancelling of residual and introduction of quantisation fields implemented with coils inside the shield. The high permeability shield, however, distorts all magnetic fields, including those generated inside the sensor. Here, we demonstrate a solution by designing multiple coils overlaid on a 3D-printed former to generate three uniform and three constant linear gradient magnetic fields inside the capped cylindrical magnetic shield of a cold atom interferometer. The fields are characterised in-situ and match their desired forms to high accuracy. For example, the uniform transverse field, $B_x$, deviates by less than $0.2$% over more than $40$% of the length of the shield. We also map the field directly using the cold atoms and investigate the potential of the coil system to reduce bias from the quadratic Zeeman effect. This coil design technology enables targeted field compensation over large spatial volumes and has the potential to reduce systematic shifts and noise in numerous cold atom systems., Comment: 12 pages, 9 figures

Published
2021
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23. New insights into the genetic etiology of Alzheimer’s disease and related dementias

Author

Bellenguez, Céline, Küçükali, Fahri, Jansen, Iris E, Kleineidam, Luca, Moreno-Grau, Sonia, Amin, Najaf, Naj, Adam C, Campos-Martin, Rafael, Grenier-Boley, Benjamin, Andrade, Victor, Holmans, Peter A, Boland, Anne, Damotte, Vincent, van der Lee, Sven J, Costa, Marcos R, Kuulasmaa, Teemu, Yang, Qiong, de Rojas, Itziar, Bis, Joshua C, Yaqub, Amber, Prokic, Ivana, Chapuis, Julien, Ahmad, Shahzad, Giedraitis, Vilmantas, Aarsland, Dag, Garcia-Gonzalez, Pablo, Abdelnour, Carla, Alarcón-Martín, Emilio, Alcolea, Daniel, Alegret, Montserrat, Alvarez, Ignacio, Álvarez, Victoria, Armstrong, Nicola J, Tsolaki, Anthoula, Antúnez, Carmen, Appollonio, Ildebrando, Arcaro, Marina, Archetti, Silvana, Pastor, Alfonso Arias, Arosio, Beatrice, Athanasiu, Lavinia, Bailly, Henri, Banaj, Nerisa, Baquero, Miquel, Barral, Sandra, Beiser, Alexa, Pastor, Ana Belén, Below, Jennifer E, Benchek, Penelope, Benussi, Luisa, Berr, Claudine, Besse, Céline, Bessi, Valentina, Binetti, Giuliano, Bizarro, Alessandra, Blesa, Rafael, Boada, Mercè, Boerwinkle, Eric, Borroni, Barbara, Boschi, Silvia, Bossù, Paola, Bråthen, Geir, Bressler, Jan, Bresner, Catherine, Brodaty, Henry, Brookes, Keeley J, Brusco, Luis Ignacio, Buiza-Rueda, Dolores, Bûrger, Katharina, Burholt, Vanessa, Bush, William S, Calero, Miguel, Cantwell, Laura B, Chene, Geneviève, Chung, Jaeyoon, Cuccaro, Michael L, Carracedo, Ángel, Cecchetti, Roberta, Cervera-Carles, Laura, Charbonnier, Camille, Chen, Hung-Hsin, Chillotti, Caterina, Ciccone, Simona, Claassen, Jurgen AHR, Clark, Christopher, Conti, Elisa, Corma-Gómez, Anaïs, Costantini, Emanuele, Custodero, Carlo, Daian, Delphine, Dalmasso, Maria Carolina, Daniele, Antonio, Dardiotis, Efthimios, Dartigues, Jean-François, de Deyn, Peter Paul, de Paiva Lopes, Katia, de Witte, Lot D, Debette, Stéphanie, Deckert, Jürgen, and del Ser, Teodoro

Subjects
Biochemistry and Cell Biology, Genetics, Biological Sciences, Dementia, Neurodegenerative, Prevention, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Alzheimer's Disease, Brain Disorders, Neurosciences, Aging, Acquired Cognitive Impairment, 2.1 Biological and endogenous factors, Neurological, Alzheimer Disease, Cognitive Dysfunction, Genome-Wide Association Study, Humans, tau Proteins, EADB, GR@ACE, DEGESCO, EADI, GERAD, Demgene, FinnGen, ADGC, CHARGE, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele.

Published
2022

24. Magnetic Field Design in a Cylindrical High-Permeability Shield: The Combination of Simple Building Blocks and a Genetic Algorithm

Author

Packer, M., Hobson, P. J., Davis, A., Holmes, N., Leggett, J., Glover, P., Hardwicke, N. L., Brookes, M. J., Bowtell, R., and Fromhold, T. M.

Subjects
Physics - Applied Physics
Abstract

Magnetically-sensitive experiments and newly-developed quantum technologies with integrated high-permeability magnetic shields require increasing control of their magnetic field environment and reductions in size, weight, power and cost. However, magnetic fields generated by active components are distorted by high-permeability magnetic shielding, particularly when they are close to the shield's surface. Here, we present an efficient design methodology for creating desired static magnetic field profiles by using discrete coils electromagnetically-coupled to a cylindrical passive magnetic shield. We utilize a modified Green's function solution that accounts for the interior boundary conditions on a closed finite-length high-permeability cylindrical magnetic shield, and determine simplified expressions when a cylindrical coil approaches the interior surface of the shield. We use an analytic formulation of simple discrete building blocks to provide a complete discrete coil basis to generate any physically-attainable magnetic field inside the shield. We then use a genetic algorithm to find optimized discrete coil structures composed of this basis. We use our methodology to generate an improved linear axial gradient field, $\mathrm{d}B_z/\mathrm{d}z$, and transverse bias field, $B_x$. These optimized structures increase, by a factor of seven and three compared to the standard configurations, the volume in which the desired and achieved fields agree within $1\%$ accuracy, respectively. This coil design method can be used to optimize active--passive magnetic field shaping systems that are compact and simple to manufacture, enabling accurate magnetic field control in spatially-confined experiments at low cost., Comment: The authors M. Packer and P. J. Hobson have contributed equally to this work. 24 pages, 16 figures

Published
2021
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25. Mechanisms and management of loss of response to anti-TNF therapy for patients with Crohn's disease: 3-year data from the prospective, multicentre PANTS cohort study

Author

Patel, Vinod, Mazhar, Zia, Saich, Rebecca, Colleypriest, Ben, Tham, Tony C, Iqbal, Tariq, Kaushik, Vishal, Murugesan, Senthil, Singh, Salil, Weaver, Sean, Preston, Cathryn, Butt, Assad, Smith, Melissa, Basude, Dharamveer, Beale, Amanda, Langlands, Sarah, Direkze, Natalie, Parkes, Miles, Torrente, Franco, De La Revella Negro, Juan, MacDonald, Chris Ewen, Evans, Stephen M, Gunasekera, Anton VJ, Thakur, Alka, Elphick, David, Shenoy, Achuth, Nwokolo, Chuka U, Dhar, Anjan, Cole, Andrew T, Agrawal, Anurag, Bridger, Stephen, Doherty, Julie, Cooper, Sheldon C, de Silva, Shanika, Mowat, Craig, Mayhead, Phillip, Lees, Charlie, Jones, Gareth, Ahmad, Tariq, Hart, James W, Kennedy, Nicholas A, Goodhand, James R, Lin, Simeng, Chanchlani, Neil, Nice, Rachel, McDonald, Timothy J, Bewshea, Claire, Al-Nuaimi, Yusur, Richards, Ellen, Haigh, Richard, Greenish, Huw, Heath, Harry, Gaya, Daniel R, Russell, Richard K, Gervais, Lisa, Dunckley, Paul, Mahmood, Tariq, Banim, Paul JR, Sonwalkar, Sunil, Ghosh, Deb, Phillips, Rosemary H, Azaz, Amer, Sebastian, Shaji, Shenderey, Richard, Armstrong, Lawrence, Bell, Claire, Hariraj, Radhakrishnan, Matthews, Helen, Jafferbhoy, Hasnain, Selinger, Christian P, Zamvar, Veena, De Caestecker, John S, Willmott, Anne, Miller, Richard, Babu, Palani Sathish, Tzivinikos, Christos, Bloom, Stuart L, Chung-Faye, Guy, Croft, Nicholas M, Fell, John ME, Harbord, Marcus, Hart, Ailsa, Hope, Ben, Irving, Peter M, Lindsay, James O, Mawdsley, Joel E, McNair, Alistair, Monahan, Kevin J, Murray, Charles D, Orchard, Timothy, Paul, Thankam, Pollok, Richard, Shah, Neil, Bouri, Sonia, Johnson, Matt W, Modi, Anita, Kabiru, Kasamu Dawa, Baburajan, B K, Bhaduri, Bim, Fagbemi, Andrew Adebayo, Levison, Scott, Limdi, Jimmy K, Watts, Gill, Foley, Stephen, Ramadas, Arvind, MacFaul, George, Mansfield, John, Grellier, Leonie, Morris, Mary-Anne, Tremelling, Mark, Hawkey, Chris, Kirkham, Sian, Charlton, Charles PJ, Rodrigues, Astor, Simmons, Alison, Lewis, Stephen J, Snook, Jonathon, Tighe, Mark, Goggin, Patrick M, De Silva, Aminda N, Lal, Simon, Smith, Mark S, Panter, Simon, Cummings, JR Fraser, Dharmisari, Suranga, Carter, Martyn, Watts, David, Mahmood, Zahid, McLain, Bruce, Sen, Sandip, Pigott, Anna J, Hobday, David, Wesley, Emma, Johnston, Richard, Edwards, Cathryn, Beckly, John, Vani, Deven, Ramakrishnan, Subramaniam, Chaudhary, Rakesh, Trudgill, Nigel J, Cooney, Rachel, Bell, Andy, Prasad, Neeraj, Gordon, John N, Brookes, Matthew J, Li, Andy, Gore, Stephen, Hamilton, Benjamin, Thomas, Amanda, Smith, Rebecca, Roberts, Christopher, Bishara, Maria, and Lees, Charlie W

Published
2024
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26. Planar Coil Optimization in a Magnetically Shielded Cylinder

Author

Packer, M., Hobson, P. J., Holmes, N., Leggett, J., Glover, P., Brookes, M. J., Bowtell, R., and Fromhold, T. M.

Subjects
Physics - Applied Physics
Abstract

Hybrid magnetic shields with both active field generating components and high-permeability magnetic shielding are increasingly needed for a variety of technologies and experiments that require precision-controlled magnetic field environments. However, the fields generated by the active components interact with the passive magnetic shield, distorting the desired field profiles. Consequently, optimization of the active components needed to generate user-specified target fields must include coupling to the high-permeability passive components. Here, we consider the optimization of planar active systems, on which an arbitrary static current flows, coupled to a closed high-permeability cylindrical shield. We modify the Green's function for the magnetic vector potential to match boundary conditions on the shield's interior surface, enabling us to construct an inverse optimization problem to design planar coils that generate user-specified magnetic fields inside high-permeability shields. We validate our methodology by designing two bi-planar hybrid active--passive systems, which generate a constant transverse field, $\mathbf{B}=\mathbf{\hat{x}}$, and a linear field gradient, $\mathbf{B}=(-x~\mathbf{\hat{x}}-y~\mathbf{\hat{y}}+2z~\mathbf{\hat{z}})$, respectively. For both systems, the inverse-optimized magnetic field profiles agree well with forward numerical simulations. Our design methodology is accurate and flexible, facilitating the miniaturization of high-performance hybrid magnetic field generating technologies with strict design constraints and spatial limitations., Comment: 24 pages, 10 figures

Published
2021
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27. Optimal Inverse Design of Magnetic Field Profiles in a Magnetically Shielded Cylinder

Author

Packer, M., Hobson, P. J., Holmes, N., Leggett, J., Glover, P., Brookes, M. J., Bowtell, R., and Fromhold, T. M.

Subjects
Physics - Applied Physics, Physics - Classical Physics
Abstract

Magnetic shields that use both active and passive components to enable the generation of a tailored low-field environment are required for many applications in science, engineering, and medical imaging. Until now, accurate field nulling, or field generation, has only been possible over a small fraction of the overall volume of the shield. This is due to the interaction between the active field-generating components and the surrounding high-permeability passive shielding material. In this paper, we formulate the interaction between an arbitrary static current flow on a cylinder and an exterior closed high-permeability cylinder. We modify the Green's function for the magnetic vector potential and match boundary conditions on the shield's interior surface to calculate the total magnetic field generated by the system. We cast this formulation into an inverse optimization problem to design active--passive magnetic field shaping systems that accurately generate any physical static magnetic field in the interior of a closed cylindrical passive shield. We illustrate this method by designing hybrid systems that generate a range of magnetic field profiles to high accuracy over large interior volumes, and simulate them in real-world shields whose passive components have finite permeability, thickness, and axial entry holes. Our optimization procedure can be adapted to design active--passive magnetic field shaping systems that accurately generate any physical user-specified static magnetic field in the interior of a closed cylindrical shield of any length, enabling the development and miniaturization of systems that require accurate magnetic shielding and control., Comment: 22 pages, 9 figures, 1 table

Published
2020
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28. GA4GH: International policies and standards for data sharing across genomic research and healthcare

Author

Rehm, Heidi L, Page, Angela JH, Smith, Lindsay, Adams, Jeremy B, Alterovitz, Gil, Babb, Lawrence J, Barkley, Maxmillian P, Baudis, Michael, Beauvais, Michael JS, Beck, Tim, Beckmann, Jacques S, Beltran, Sergi, Bernick, David, Bernier, Alexander, Bonfield, James K, Boughtwood, Tiffany F, Bourque, Guillaume, Bowers, Sarion R, Brookes, Anthony J, Brudno, Michael, Brush, Matthew H, Bujold, David, Burdett, Tony, Buske, Orion J, Cabili, Moran N, Cameron, Daniel L, Carroll, Robert J, Casas-Silva, Esmeralda, Chakravarty, Debyani, Chaudhari, Bimal P, Chen, Shu Hui, Cherry, J Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L, Cook-Deegan, Robert M, Courtot, Mélanie, Cunningham, Fiona, Cupak, Miro, Davies, Robert M, Denisko, Danielle, Doerr, Megan J, Dolman, Lena I, Dove, Edward S, Dursi, L Jonathan, Dyke, Stephanie OM, Eddy, James A, Eilbeck, Karen, Ellrott, Kyle P, Fairley, Susan, Fakhro, Khalid A, Firth, Helen V, Fitzsimons, Michael S, Fiume, Marc, Flicek, Paul, Fore, Ian M, Freeberg, Mallory A, Freimuth, Robert R, Fromont, Lauren A, Fuerth, Jonathan, Gaff, Clara L, Gan, Weiniu, Ghanaim, Elena M, Glazer, David, Green, Robert C, Griffith, Malachi, Griffith, Obi L, Grossman, Robert L, Groza, Tudor, Auvil, Jaime M Guidry, Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A, Hamosh, Ada, Hansen, David P, Hart, Reece K, Hartley, Dean Mitchell, Haussler, David, Hendricks-Sturrup, Rachele M, Ho, Calvin WL, Hobb, Ashley E, Hoffman, Michael M, Hofmann, Oliver M, Holub, Petr, Hsu, Jacob Shujui, Hubaux, Jean-Pierre, Hunt, Sarah E, Husami, Ammar, Jacobsen, Julius O, Jamuar, Saumya S, Janes, Elizabeth L, Jeanson, Francis, Jené, Aina, Johns, Amber L, Joly, Yann, Jones, Steven JM, Kanitz, Alexander, Kato, Kazuto, Keane, Thomas M, and Kekesi-Lafrance, Kristina

Subjects
Biological Sciences, Genetics, Biotechnology, Human Genome, 8.3 Policy, ethics, and research governance, Generic health relevance, Good Health and Well Being
Abstract

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

Published
2021

30. Questions and answers on iron deficiency treatment selection and the use of intravenous iron in routine clinical practice

Author

Richards, Toby, Breymann, Christian, Brookes, Matthew J, Lindgren, Stefan, Macdougall, Iain C, McMahon, Lawrence P, Munro, Malcolm G, Nemeth, Elizabeta, Rosano, Giuseppe MC, Schiefke, Ingolf, and Weiss, Günter

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Patient Safety, Prevention, Digestive Diseases, Nutrition, 2.1 Biological and endogenous factors, Aetiology, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Cardiovascular, Administration, Intravenous, Administration, Oral, Clinical Decision-Making, Consensus, Female, Humans, Iron Compounds, Iron Deficiencies, Male, Practice Guidelines as Topic, Pregnancy, Anaemia, iron-deficiency, cardiovascular diseases, erythrocyte transfusion, inflammatory bowel diseases, infusions, intravenous, iron, menorrhagia, renal insufficiency, chronic, pregnancy complications, Medical and Health Sciences, Cardiovascular System & Hematology, Biomedical and clinical sciences, Health sciences
Abstract

Iron deficiency is a common cause of morbidity and can arise as a consequence or complication from many diseases. The use of intravenous iron has increased significantly in the last decade, but concerns remain about indications and administration. Modern intravenous iron preparations can facilitate rapid iron repletion in one or two doses, both for absolute iron deficiency and, in the presence of inflammation, functional iron deficiency, where oral iron therapy is ineffective or has not worked. A multidisciplinary team of experts experienced in iron deficiency undertook a consensus review to support healthcare professionals with practical advice on managing iron deficiency in gastrointestinal, renal and cardiac disease, as well as; pregnancy, heavy menstrual bleeding, and surgery. We explain how intravenous iron may work where oral iron has not. We provide context on how and when intravenous iron should be administered, and informed opinion on potential benefits balanced with potential side-effects. We propose how intravenous iron side-effects can be anticipated in terms of what they may be and when they may occur. The aim of this consensus is to provide a practical basis for educating and preparing staff and patients on when and how iron infusions can be administered safely and efficiently. Key messages Iron deficiency treatment selection is driven by several factors, including the presence of inflammation, the time available for iron replenishment, and the anticipated risk of side-effects or intolerance. Intravenous iron preparations are indicated for the treatment of iron deficiency when oral preparations are ineffective or cannot be used, and therefore have applicability in a wide range of clinical contexts, including chronic inflammatory conditions, perioperative settings, and disorders associated with chronic blood loss. Adverse events occurring with intravenous iron can be anticipated according to when they typically occur, which provides a basis for educating and preparing staff and patients on how iron infusions can be administered safely and efficiently.

Published
2021

32. Effect on life expectancy of temporal sequence in a multimorbidity cluster of psychosis, diabetes, and congestive heart failure among 1·7 million individuals in Wales with 20-year follow-up: a retrospective cohort study using linked data

Author

Owen, Rhiannon K, Lyons, Jane, Akbari, Ashley, Guthrie, Bruce, Agrawal, Utkarsh, Alexander, Daniel C, Azcoaga-Lorenzo, Amaya, Brookes, Anthony J, Denaxas, Spiros, Dezateux, Carol, Fagbamigbe, Adeniyi Francis, Harper, Gill, Kirk, Paul D W, Özyiğit, Eda Bilici, Richardson, Sylvia, Staniszewska, Sophie, McCowan, Colin, Lyons, Ronan A, and Abrams, Keith R

Published
2023
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35. Clinical, genetic, epidemiologic, evolutionary, and functional delineation of TSPEAR-related autosomal recessive ectodermal dysplasia 14

Author

Ambrose, J.C., Arumugam, P., Bevers, R., Bleda, M., Boardman-Pretty, F., Boustred, C.R., Brittain, H., Brown, M.A., Caulfield, M.J., Chan, G.C., Giess, A., Griffin, J.N., Hamblin, A., Henderson, S., Hubbard, T.J.P., Jackson, R., Jones, L.J., Kasperaviciute, D., Kayikci, M., Kousathanas, A., Lahnstein, L., Lakey, A., Leigh, S.E.A., Leong, I.U.S., Lopez, F.J., Maleady-Crowe, F., McEntagart, M., Minneci, F., Mitchell, J., Moutsianas, L., Mueller, M., Murugaesu, N., Need, A.C., O‘Donovan, P., Odhams, C.A., Patch, C., Perez-Gil, D., Pereira, M.B., Pullinger, J., Rahim, T., Rendon, A., Rogers, T., Savage, K., Sawant, K., Scott, R.H., Siddiq, A., Sieghart, A., Smith, S.C., Sosinsky, A., Stuckey, A., Tanguy, M., Taylor Tavares, A.L., Thomas, E.R.A., Thompson, S.R., Tucci, A., Welland, M.J., Williams, E., Witkowska, K., Wood, S.M., Zarowiecki, M., Riess, Olaf, Haack, Tobias B., Graessner, Holm, Zurek, Birte, Ellwanger, Kornelia, Ossowski, Stephan, Demidov, German, Sturm, Marc, Schulze-Hentrich, Julia M., Schüle, Rebecca, Kessler, Christoph, Wayand, Melanie, Synofzik, Matthis, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Heutink, Peter, Brunner, Han, Scheffer, Hans, Hoogerbrugge, Nicoline, Hoischen, Alexander, ’t Hoen, Peter A.C., Vissers, Lisenka E.L.M., Gilissen, Christian, Steyaert, Wouter, Sablauskas, Karolis, de Voer, Richarda M., Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, Paske, Iris te, Janssen, Erik, de Boer, Elke, Steehouwer, Marloes, Yaldiz, Burcu, Kleefstra, Tjitske, Brookes, Anthony J., Veal, Colin, Gibson, Spencer, Wadsley, Marc, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Töpf, Ana, Straub, Volker, Bettolo, Chiara Marini, Specht, Sabine, Clayton-Smith, Jill, Banka, Siddharth, Alexander, Elizabeth, Jackson, Adam, Faivre, Laurence, Thauvin, Christel, Vitobello, Antonio, Denommé-Pichon, Anne-Sophie, Duffourd, Yannis, Tisserant, Emilie, Bruel, Ange-Line, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Laurie, Steven, Piscia, Davide, Matalonga, Leslie, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Garcia, Carles, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Paramonov, Ida, Lochmüller, Hanns, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hanauer, Marc, Olry, Annie, Lagorce, David, Havrylenko, Svitlana, Izem, Katia, Rigour, Fanny, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Bonne, Gisèle, Evangelista, Teresinha, Allamand, Valérie, Nelson, Isabelle, Ben Yaou, Rabah, Metay, Corinne, Eymard, Bruno, Cohen, Enzo, Atalaia, Antonio, Stojkovic, Tanya, Macek, Milan, Jr., Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Kremlik, Vlastimil, Parkinson, Helen, Keane, Thomas, Spalding, Dylan, Senf, Alexander, Robinson, Peter, Danis, Daniel, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Vandrovcova, Jana, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, Van de Vondel, Liedewei, Beijer, Danique, de Jonghe, Peter, Nigro, Vincenzo, Banfi, Sandro, Torella, Annalaura, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Rossi, Rachele, Neri, Marcella, Aretz, Stefan, Spier, Isabel, Sommer, Anna Katharina, Peters, Sophia, Oliveira, Carla, Pelaez, Jose Garcia, Matos, Ana Rita, José, Celina São, Ferreira, Marta, Gullo, Irene, Fernandes, Susana, Garrido, Luzia, Ferreira, Pedro, Carneiro, Fátima, Swertz, Morris A., Johansson, Lennart, van der Velde, Joeri K., van der Vries, Gerben, Neerincx, Pieter B., Roelofs-Prins, Dieuwke, Köhler, Sebastian, Metcalfe, Alison, Verloes, Alain, Drunat, Séverine, Rooryck, Caroline, Trimouille, Aurelien, Castello, Raffaele, Morleo, Manuela, Pinelli, Michele, Varavallo, Alessandra, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Martín, Estrella López, Delgado, Beatriz Martínez, Alonso García de la Rosa, F. Javier, Ciolfi, Andrea, Dallapiccola, Bruno, Pizzi, Simone, Radio, Francesca Clementina, Tartaglia, Marco, Renieri, Alessandra, Benetti, Elisa, Balicza, Peter, Molnar, Maria Judit, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, Macaya, Alfons, Marcé-Grau, Anna, Osorio, Andres Nascimiento, Natera de Benito, Daniel, Thompson, Rachel, Polavarapu, Kiran, Beeson, David, Cossins, Judith, Rodriguez Cruz, Pedro M., Hackman, Peter, Johari, Mridul, Savarese, Marco, Udd, Bjarne, Horvath, Rita, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Schröck, Evelin, Rump, Andreas, Lin, Sheng-Jia, Jones, Elizabeth A., Chandler, Kate E., Orr, David, Moss, Celia, Haider, Zahra, Ryan, Gavin, Holden, Simon, Harrison, Mike, Burrows, Nigel, Jones, Wendy D., Loveless, Mary, Petree, Cassidy, Stewart, Helen, Low, Karen, Donnelly, Deirdre, Lovell, Simon, Drosou, Konstantina, and Varshney, Gaurav K.

Published
2023
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36. A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Author

Abbott, Kristin M., Banka, Siddharth, de Boer, Elke, Ciolfi, Andrea, Clayton-Smith, Jill, Dallapiccola, Bruno, Denommé-Pichon, Anne-Sophie, Faivre, Laurence, Gilissen, Christian, Haack, Tobias B., Havlovicova, Marketa, Hoischen, Alexander, Jackson, Adam, Kerstjens, Mieke, Kleefstra, Tjitske, Martín, Estrella López, Macek, Milan, Jr., Matalonga, Leslie, Maystadt, Isabelle, Morleo, Manuela, Nigro, Vicenzo, Pinelli, Michele, Pizzi, Simone, Posada, Manuel, Radio, Francesca C., Renieri, Alessandra, Riess, Olaf, Rooryck, Caroline, Ryba, Lukas, Agathe, Jean-Madeleine de Sainte, Santen, Gijs W.E., Schwarz, Martin, Tartaglia, Marco, Thauvin, Christel, Torella, Annalaura, Trimouille, Aurélien, Verloes, Alain, Vissers, Lisenka, Vitobello, Antonio, Votypka, Pavel, Zguro, Kristina, Boer, Elke de, Cohen, Enzo, Danis, Daniel, Gao, Fei, Horvath, Rita, Johari, Mridul, Johanson, Lennart, Li, Shuang, Morsy, Heba, Nelson, Isabelle, Paramonov, Ida, te Paske, Iris B.A.W., Robinson, Peter, Savarese, Marco, Steyaert, Wouter, Töpf, Ana, van der Velde, Joeri K., Vandrovcova, Jana, Graessner, Holm, Zurek, Birte, Ellwanger, Kornelia, Ossowski, Stephan, Demidov, German, Sturm, Marc, Schulze-Hentrich, Julia M., Schüle, Rebecca, Xu, Jishu, Kessler, Christoph, Wayand, Melanie, Synofzik, Matthis, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Lerche, Holger, Kegele, Josua, Heutink, Peter, Brunner, Han, Scheffer, Hans, Hoogerbrugge, Nicoline, ‘t Hoen, Peter A.C., Vissers, Lisenka E.L.M., Sablauskas, Karolis, de Voer, Richarda M., Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, Paske, Iris te, Janssen, Erik, Steehouwer, Marloes, Yaldiz, Burcu, Brookes, Anthony J., Veal, Colin, Gibson, Spencer, Maddi, Vatsalya, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Straub, Volker, Bettolo, Chiara Marini, Manera, Jordi Diaz, Hambleton, Sophie, Engelhardt, Karin, Alexander, Elizabeth, Duffourd, Yannis, Bruel, Ange-Line, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Laurie, Steven, Piscia, Davide, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Lochmüller, Hanns, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hanauer, Marc, Lagorce, David, Hongnat, Oscar, Chahdil, Maroua, Lebreton, Emeline, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Bonne, Gisèle, Evangelista, Teresinha, Allamand, Valérie, Ben Yaou, Rabah, Metay, Corinne, Eymard, Bruno, Atalaia, Antonio, Stojkovic, Tanya, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Lišková, Petra, Doležalová, Pavla, Parkinson, Helen, Keane, Thomas, Freeberg, Mallory, Thomas, Coline, Spalding, Dylan, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Efthymiou, Stephanie, Cali, Elisa, Magrinelli, Francesca, Sisodiya, Sanjay M., Rohrer, Jonathan, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, de Vries, Geert, De Winter, Jonathan, Beijer, Danique, de Jonghe, Peter, Van de Vondel, Liedewei, De Ridder, Willem, Weckhuysen, Sarah, Nigro, Vincenzo, Mutarelli, Margherita, Varavallo, Alessandra, Banfi, Sandro, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Gualandi, Francesca, Bigoni, Stefania, Rossi, Rachele, Neri, Marcella, Aretz, Stefan, Spier, Isabel, Sommer, Anna Katharina, Peters, Sophia, Oliveira, Carla, Pelaez, Jose Garcia, Matos, Ana Rita, José, Celina São, Ferreira, Marta, Gullo, Irene, Fernandes, Susana, Garrido, Luzia, Ferreira, Pedro, Carneiro, Fátima, Swertz, Morris A., Johansson, Lennart, van der Vries, Gerben, Neerincx, Pieter B., Ruvolo, David, Kerstjens Frederikse, Wilhemina S., Zonneveld-Huijssoon, Eveline, Roelofs-Prins, Dieuwke, van Gijn, Marielle, Köhler, Sebastian, Metcalfe, Alison, Drunat, Séverine, Heron, Delphine, Mignot, Cyril, Keren, Boris, Lacombe, Didier, Trimouille, Aurelien, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Cilio, Maria-Roberta, Carpancea, Evelina, Depondt, Chantal, Lederer, Damien, Sznajer, Yves, Duerinckx, Sarah, Mary, Sandrine, Macaya, Alfons, Cazurro-Gutiérrez, Ana, Pérez-Dueñas, Belén, Munell, Francina, Jarava, Clara Franco, Masó, Laura Batlle, Marcé-Grau, Anna, Colobran, Roger, Hackman, Peter, Udd, Bjarne, Hemelsoet, Dimitri, Dermaut, Bart, Schuermans, Nika, Poppe, Bruce, Verdin, Hannah, Osorio, Andrés Nascimento, Depienne, Christel, Roos, Andreas, Cordts, Isabell, Deschauer, Marcus, Striano, Pasquale, Zara, Federico, Riva, Antonella, Iacomino, Michele, Uva, Paolo, Scala, Marcello, Scudieri, Paolo, Başak, Ayşe Nazlı, Claeys, Kristl, Boztug, Kaan, Haimel, Matthias, W.E, Gijs, Ruivenkamp, Claudia A.L., Natera de Benito, Daniel, Thompson, Rachel, Polavarapu, Kiran, Grimbacher, Bodo, Zaganas, Ioannis, Kokosali, Evgenia, Lambros, Mathioudakis, Evangeliou, Athanasios, Spilioti, Martha, Kapaki, Elisabeth, Bourbouli, Mara, Radio, Francesca Clementina, Balicza, Peter, Molnar, Maria Judit, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Delgado, Beatriz Martínez, Alonso García de la Rosa, F. Javier, Schröck, Evelin, Rump, Andreas, Mei, Davide, Vetro, Annalisa, Balestrini, Simona, Guerrini, Renzo, Chinnery, Patrick F., Ratnaike, Thiloka, Schon, Katherine, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, May, Patrick, Beeson, David, Cossins, Judith, Furini, Simone, Fallerini, Chiara, Benetti, Elisa, Afenjar, Alexandra, Goldenberg, Alice, Masurel, Alice, Phan, Alice, Dieux-Coeslier, Anne, Fargeot, Anne, Guerrot, Anne-Marie, Toutain, Annick, Molin, Arnaud, Sorlin, Arthur, Putoux, Audrey, Jouret, Béatrice, Laudier, Béatrice, Demeer, Bénédicte, Doray, Bérénice, Bonniaud, Bertille, Isidor, Bertrand, Gilbert-Dussardier, Brigitte, Leheup, Bruno, Reversade, Bruno, Paul, Carle, Vincent-Delorme, Catherine, Neiva, Cecilia, Poirsier, Céline, Quélin, Chloé, Chiaverini, Christine, Coubes, Christine, Francannet, Christine, Colson, Cindy, Desplantes, Claire, Wells, Constance, Goizet, Cyril, Sanlaville, Damien, Amram, Daniel, Lehalle, Daphné, Geneviève, David, Gaillard, Dominique, Zivi, Einat, Sarrazin, Elisabeth, Steichen, Elisabeth, Schaefer, Élise, Lacaze, Elodie, Jacquemin, Emmanuel, Bongers, Ernie, Kilic, Esra, Colin, Estelle, Giuliano, Fabienne, Prieur, Fabienne, Laffargue, Fanny, Morice-Picard, Fanny, Petit, Florence, Cartault, François, Feillet, François, Baujat, Geneviève, Morin, Gilles, Diene, Gwenaëlle, Journel, Hubert, Perthus, Isabelle, Lespinasse, James, Alessandri, Jean-Luc, Amiel, Jeanne, Martinovic, Jelena, Delanne, Julian, Albuisson, Juliette, Lambert, Laëtitia, Perrin, Laurence, Ousager, Lilian Bomme, Van Maldergem, Lionel, Pinson, Lucile, Ruaud, Lyse, Samimi, Mahtab, Bournez, Marie, Bonnet-Dupeyron, Marie Noëlle, Vincent, Marie, Jacquemont, Marie-Line, Cordier-Alex, Marie-Pierre, Gérard-Blanluet, Marion, Willems, Marjolaine, Spodenkiewicz, Marta, Doco-Fenzy, Martine, Rossi, Massimiliano, Renaud, Mathilde, Fradin, Mélanie, Mathieu, Michèle, Holder-Espinasse, Muriel H., Houcinat, Nada, Hanna, Nadine, Leperrier, Nathalie, Chassaing, Nicolas, Philip, Nicole, Boute, Odile, Van Kien, Philippe Khau, Parent, Philippe, Bitoun, Pierre, Sarda, Pierre, Vabres, Pierre, Jouk, Pierre-Simon, Touraine, Renaud, El Chehadeh, Salima, Whalen, Sandra, Marlin, Sandrine, Passemard, Sandrine, Grotto, Sarah, Bellanger, Séverine Audebert, Blesson, Sophie, Nambot, Sophie, Naudion, Sophie, Lyonnet, Stanislas, Odent, Sylvie, Attie-Bitach, Tania, Busa, Tiffany, Drouin-Garraud, Valérie, Layet, Valérie, Bizaoui, Varoona, Cusin, Véronica, Capri, Yline, Alembik, Yves, Jean-Marçais, Nolwenn, López-Martín, Estrella, Macek, Milan, Mencarelli, Maria Antonietta, Moutton, Sébastien, Pfundt, Rolph, Safraou, Hana, Thauvin-Robinet, Christel, Thevenon, Julien, Tran Mau-Them, Frédéric, de Vries, Bert B.A., Willemsen, Marjolein H., and Philippe, Christophe

Published
2023
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39. Publisher Correction: Federated discovery and sharing of genomic data using Beacons

Author

Fiume, Marc, Cupak, Miroslav, Keenan, Stephen, Rambla, Jordi, de la Torre, Sabela, Dyke, Stephanie OM, Brookes, Anthony J, Carey, Knox, Lloyd, David, Goodhand, Peter, Haeussler, Maximilian, Baudis, Michael, Stockinger, Heinz, Dolman, Lena, Lappalainen, Ilkka, Törnroos, Juha, Linden, Mikael, Spalding, J Dylan, Ur-Rehman, Saif, Page, Angela, Flicek, Paul, Sherry, Stephen, Haussler, David, Varma, Susheel, Saunders, Gary, and Scollen, Serena

Subjects
Information and Computing Sciences, Historical Studies, History, Heritage and Archaeology
Abstract

In the version of this article initially published, Lena Dolman's second affiliation was given as Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. The correct second affiliation is Ontario Institute for Cancer Research, Toronto, Ontario, Canada. The error has been corrected in the HTML and PDF versions of the article.

Published
2019

41. The families SHARE project: novel insights on recruiting and engaging Black men in a community-based genomic education program.

Author

Nummelin, Julia R., Brookes, Jama J., Bishop, Raegan A., Whitted, Calandra G., Dash, Chiranjeev, and Koehly, Laura M.

Subjects
*COMMUNITY-based programs, *FAMILY history (Medicine), *BLACK men, *PLACE-based education, *SOCIAL norms
Abstract

Background: Black Americans are disproportionately affected by a number of common complex conditions, such as cancer. Genomic tools like Family Health History (FHH) can be useful in guiding screening and behavior based on a person's risk for these conditions. Factors such as family communication and societal norms can influence individuals' knowledge of their FHH. Men, particularly Black men, are less likely than women to know FHH. Further, there is limited understanding of Black men's participation in FHH dissemination, as they are often underrepresented in biomedical research. Understanding Black men's perceptions of FHH sharing may help guide effective recruitment and retention efforts in future genomic research providing an opportunity to investigate their lack of engagement in FHH conversations. Aims: The purpose of this paper was two-fold: (1) Detail methods that were effective in recruiting and retaining Black men in community-based genomic research interventions, and (2) Evaluate the factors influencing men's participation in FHH gathering and sharing. Methods: This one-year, mixed methods study combined qualitative community-based education programs (n = 12) and semi-structured interviews (n = 27), with quantitative survey assessing participant characteristics and sex differences (n = 50). Transcripts from the program were coded by separate study team members for themes and provided insights into study participants' perceptions about FHH and their involvement in gathering and disseminating this information within their family. Results: Challenges in recruiting and retaining Black men prompted the study team to pivot recruitment strategies, including partnering with community-based organizations focused on men's health, growing the research team to include Black men, adapting to potential participants' time constraints, and creating opportunities to build trust. A thematic analysis of community education sessions and interviews identified five themes, including social role expectations and perceived family disconnectedness, that provide insights into potential barriers to participation. Qualitative data from participants suggests that beliefs and perceptions about the roles Black men play in health discussions within the family may influence their involvement, while community programs were seen as encouraging men to engage in these conversations. Conclusion: These lessons learned provide valuable perspectives on potential barriers to participation, which may inform future strategies that aim to engage Black men in family-oriented community education programs and genomic research. [ABSTRACT FROM AUTHOR]

Published
2025
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42. Carp carcass decomposition and water quality: implications for the release of CyHV-3 as a biocontrol agent for common carp in Australia.

Author

Walsh, Richard, Dornan, Tyler N., Upadhyay Stæhr, Sanjina, Brookes, Hamish J., Hipsey, Matthew R., Laws, Mark, Cassey, Phillip, and Brookes, Justin D.

Abstract

Context: In Australia's Murray–Darling Basin, the invasive common carp (Cyprinus carpio) poses a significant ecological threat. Efforts to manage their population include the potential use of cyprinid herpesvirus (CyHV-3) as a biological control agent. The environmental benefits of carp elimination could be substantial in the long term; our knowledge of the immediate ecological consequences resulting from large-scale fish die-offs remains limited. Aim: This study sought to investigate the effect of a large-scale fish-mortality event on water quality. Methods: Experiments of an increasing scale (bucket, mesocosm and whole wetland) were conducted to assess how decomposing carp carcasses alter dissolved oxygen and nutrient concentrations in water. Key results: In mesocosms, dead carp decayed more rapidly at 18 than 12°C, yielding oxygen demands of 1.022 ± 0.029 and 0.496 ± 0.239 mg kg−1 min−1 respectively. This carp decay released phosphorus, yielding 2121.1 ± 140.4 mg kg−1. In the wetland experiment, carp addition of 2400 kg ha−1 resulted in anoxic conditions over the following 2 weeks. The release of dissolved organic carbon and lipids led to a peak biological oxygen demand of 95.3 mg L−1. Conclusions: Carp decomposition considerably contributes to biological oxygen demand and algal growth through nutrient enrichment and is strongly influenced by carp density. Implications: The finding highlights key factors to consider before using biocontrol agents causing mass carp mortality, including hypoxia, anoxia and increased risk of harmful algal blooms. Investigations into the decomposition of common carp across three experiments of an increasing scale (bucket, mesocosm, wetland) showed a considerable release of phosphorus, with faster decomposition rates in warm conditions. The addition of 2400 kg ha−1 of carp induced anoxia in the wetland, underscoring essential considerations deploying biocontrol agents (e.g. cyprinid herpesvirus, CyHV-3) causing mass carp mortality. [ABSTRACT FROM AUTHOR]

Published
2025
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43. OAS1: A Protective Mechanism for Alzheimer's Disease? An Exploration of Data and Possible Mechanisms.

Author

Elsworthy, Richard J., Pearce, Alex, Masoudzadeh, Farnoush, Koska, Klaudia, Lodhiya, Honey, Meher, Gargi, Adjej, Jodelle, and Brookes, Keeley J.

Subjects
GENE expression, OLIGOADENYLATE synthetase, COVID-19 pandemic, ALZHEIMER'S disease, HAPLOTYPES
Abstract

The immune system and neuroinflammation are now well established in the aetiology of neurodegeneration. Previous studies of transcriptomic and gene association studies have highlighted the potential of the 2′–5′ oligoadenylate synthetase 1 (OAS1) to play a role in Alzheimer's disease. OAS1 is a viral response gene, interferon-induced, dsRNA activated enzyme, which binds RNase L to degrade dsRNA, and has been associated with COVID-19 response. This study explores whether a viral defence gene could play a vital role in neurodegeneration pathology. The genotyping of five SNPs across the OAS1 locus was conducted in the Brains for Dementia Research (BDR) Cohort for association with AD. RNA-sequencing data were explored for differences in OAS1 gene expression between phenotypes and genotypes. Finally, levels of dsRNA were measured in control cell lines, prior to and after exposure to amyloid oligomers and in cells harbouring a dementia-relevant mutation. No association of any of the OAS1 SNPs investigated were associated with the AD phenotype in the BDR cohort. However, gene expression data supported the previous observation that the minor allele haplotype was associated with higher levels of the OAS1 gene expression and the presence of an alternative transcript. Further to this, the presence of endogenous dsRNA was found to increase with exposure to amyloid oligomers and in the cell line with a dementia-relevant mutation. The data presented here suggest further exploration of the OAS1 gene in relation to dementia is warranted. Investigations of whether carriers of the protective OAS1 haplotype lower dsRNA presence and in turn lower inflammation and cell death are required to support the role of the gene as a moderator of neurodegeneration. [ABSTRACT FROM AUTHOR]

Published
2025
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44. Citric Acid and Sodium Bicarbonate as an Alternative Carbon Dioxide Source for Mosquito Surveillance.

Author

Hong, Christine, Brookes, Victoria J., Zadoks, Ruth N., and Webb, Cameron E.

Subjects
*DRY ice, *PUBLIC health surveillance, *COMPRESSED gas, *CULEX quinquefasciatus, *GAS cylinders
Abstract

Simple Summary: Trapping mosquitoes that are known vectors of pathogens of human health concern is essential for public health surveillance. Commonly deployed mosquito traps typically include carbon dioxide (CO2) supplied via compressed gas or dry ice, which can be expensive and difficult to transport. This study explored an alternative CO2 source for attracting mosquitoes using citric acid and baking soda (sodium bicarbonate) in a novel CO2 delivery system. Laboratory experiments assessed the effectiveness of CO2 production using citric acid and baking soda, followed by field trials in two locations to compare capture rates to dry ice traps. The findings showed that citric acid and baking soda could be an alternative to traditional CO2 sources in mosquito traps. Most mosquito surveillance programs rely on traps baited with carbon dioxide (CO2) to attract host-seeking mosquitoes. The source of CO2, traditionally dry ice or gas cylinders, poses operational challenges, especially in remote locations. CO2 production from citric acid and sodium bicarbonate (NaHCO3) using low-cost intravenous fluid bags ('acid traps') was evaluated in laboratory experiments. Field trials then compared the efficacy of these acid traps with dry ice traps. Using a 2 × 2 Latin square style design, trapping locations were established at two sites in Sydney, New South Wales, Australia (one urban and another peri-urban), to assess trap performance in diverse environments. The laboratory results showed CO2 production of sufficient amount and duration for overnight mosquito capture. Whilst field experiments showed that dry ice traps captured more mosquitoes (up to 59%) than acid traps, numbers were similar in the urban environment. At both sites, species composition was similar, with Culex quinquefasciatus, Aedes notoscriptus, and Aedes vigilax predominantly collected, and these are known species of pest and public health concern. Further modifications to the acid traps could further improve CO2 output and trap efficiency. [ABSTRACT FROM AUTHOR]

Published
2025
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45. The variation in post-endoscopy upper gastrointestinal cancer rates among endoscopy providers in England and associated factors: a population-based study.

Author

Kamran, Umair, Evison, Felicity, Morris, Eva Judith Ann, Brookes, Matthew J, Rutter, Matthew David, McCord, Mimi, Adderley, Nicola J, and Trudgill, Nigel

Subjects
BARRETT'S esophagus, GASTROINTESTINAL cancer, LOGISTIC regression analysis, NUMERIC databases, STOMACH ulcers, HOSPITAL statistics
Abstract

Background Post-endoscopy upper gastrointestinal cancer (PEUGIC) is an important key performance indicator for endoscopy quality. We examined variation in PEUGIC rates among endoscopy providers in England and explored associated factors. Methods The was a population-based, retrospective, case–control study, examining data from National Cancer Registration and Analysis Service and Hospital Episode Statistics databases for esophageal and gastric cancers diagnosed between 2009 and 2018 in England. PEUGIC were cancers diagnosed 6 to 36 months after an endoscopy that did not diagnose cancer. Associated factors were identified using multivariable logistic regression analyses. Results The national PEUGIC rate was 8.5%, varying from 5% to 13% among endoscopy providers. Factors associated with PEUGIC included: female sex (odds ratio [OR] 1.29 [95%CI 1.23–1.36]); younger age (age >80 years, OR 0.52 [0.48–0.56], compared with ≤60 years); increasing comorbidity (Charlson score >4, OR 5.06 [4.45–5.76]); history of esophageal ulcer (OR 3.30 [3.11–3.50]), Barrett's esophagus (OR 3.21 [3.02–3.42]), esophageal stricture (OR 1.28 [1.20–1.37]), or gastric ulcer (OR 1.55 [1.44–1.66]); squamous cell carcinoma (OR 1.50 [1.39–1.61]); and UK national endoscopy accreditation status – providers requiring improvement (OR 1.10 [1.01–1.20]), providers never assessed (OR 1.24 [1.04–1.47]). Conclusion PEUGIC rates varied threefold among endoscopy providers, suggesting unwarranted differences in endoscopy quality. PEUGIC was associated with endoscopy findings known to be associated with upper gastrointestinal cancer and a lack of national endoscopy provider accreditation. PEUGIC variations suggest an opportunity to raise performance standards to detect upper gastrointestinal cancers earlier and improve outcomes. [ABSTRACT FROM AUTHOR]

Published
2025
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46. Using OPM-MEG in contrasting magnetic environments

Author

Hill, Ryan M., Devasagayam, Jasen, Holmes, Niall, Boto, Elena, Shah, Vishal, Osborne, James, Safar, Kristina, Worcester, Frank, Mariani, Christopher, Dawson, Eliot, Woolger, David, Bowtell, Richard, Taylor, Margot J., and Brookes, Matthew J.

Published
2022
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49. Federated discovery and sharing of genomic data using Beacons

Author

Fiume, Marc, Cupak, Miroslav, Keenan, Stephen, Rambla, Jordi, de la Torre, Sabela, Dyke, Stephanie OM, Brookes, Anthony J, Carey, Knox, Lloyd, David, Goodhand, Peter, Haeussler, Maximilian, Baudis, Michael, Stockinger, Heinz, Dolman, Lena, Lappalainen, Ilkka, Törnroos, Juha, Linden, Mikael, Spalding, J Dylan, Ur-Rehman, Saif, Page, Angela, Flicek, Paul, Sherry, Stephen, Haussler, David, Varma, Susheel, Saunders, Gary, and Scollen, Serena

Subjects
Genomics, Humans, Information Dissemination, Information Storage and Retrieval
Published
2019

50. Registered access: authorizing data access

Author

Dyke, Stephanie OM, Linden, Mikael, Lappalainen, Ilkka, De Argila, Jordi Rambla, Carey, Knox, Lloyd, David, Spalding, J Dylan, Cabili, Moran N, Kerry, Giselle, Foreman, Julia, Cutts, Tim, Shabani, Mahsa, Rodriguez, Laura L, Haeussler, Maximilian, Walsh, Brian, Jiang, Xiaoqian, Wang, Shuang, Perrett, Daniel, Boughtwood, Tiffany, Matern, Andreas, Brookes, Anthony J, Cupak, Miro, Fiume, Marc, Pandya, Ravi, Tulchinsky, Ilia, Scollen, Serena, Törnroos, Juha, Das, Samir, Evans, Alan C, Malin, Bradley A, Beck, Stephan, Brenner, Steven E, Nyrönen, Tommi, Blomberg, Niklas, Firth, Helen V, Hurles, Matthew, Philippakis, Anthony A, Rätsch, Gunnar, Brudno, Michael, Boycott, Kym M, Rehm, Heidi L, Baudis, Michael, Sherry, Stephen T, Kato, Kazuto, Knoppers, Bartha M, Baker, Dixie, and Flicek, Paul

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Clinical Sciences, Genetics, 8.3 Policy, ethics, and research governance, Health and social care services research, Generic health relevance, Good Health and Well Being, Access to Information, Genetics, Medical, Genomics, Humans, Information Dissemination, Licensure, Practice Guidelines as Topic, Genetics & Heredity, Clinical sciences
Abstract

The Global Alliance for Genomics and Health (GA4GH) proposes a data access policy model-"registered access"-to increase and improve access to data requiring an agreement to basic terms and conditions, such as the use of DNA sequence and health data in research. A registered access policy would enable a range of categories of users to gain access, starting with researchers and clinical care professionals. It would also facilitate general use and reuse of data but within the bounds of consent restrictions and other ethical obligations. In piloting registered access with the Scientific Demonstration data sharing projects of GA4GH, we provide additional ethics, policy and technical guidance to facilitate the implementation of this access model in an international setting.

Published
2018

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