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1. How the Hidden Curriculum Reveals the Enculturation Experience of Underrepresented Students in Engineering.

Author: Kylee Shiekh, Dean Nieusma, Qin Zhu, and Stephen C. Rea
Published: 2023
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2. The Port Delivery System with ranibizumab: a new paradigm for long-acting retinal drug delivery

Author: Shrirang V. Ranade, Mark R. Wieland, Tammy Tam, Jennifer C. Rea, Judit Horvath, Aaron R. Hieb, Weitao Jia, Lori Grace, Giulio Barteselli, and Jay M. Stewart
Subjects: Ranibizumab, Port Delivery System, continuous drug delivery, nAMD, ocular implant, retina, Therapeutics. Pharmacology, RM1-950
Abstract: The Port Delivery System with ranibizumab (PDS) is an innovative intraocular drug delivery system designed for the continuous delivery of ranibizumab into the vitreous for 6 months and beyond. The PDS includes an ocular implant, a customized formulation of ranibizumab, and four dedicated ancillary devices for initial fill, surgical implantation, refill-exchange, and explantation, if clinically indicated. Ranibizumab is an ideal candidate for the PDS on account of its unique physicochemical stability and high solubility. Controlled release is achieved via passive diffusion through the porous release control element, which is tuned to specific drug characteristics to accomplish a therapeutic level of ranibizumab in the vitreous. To characterize drug release from the implant, release rate was measured in vitro with starting concentrations of ranibizumab 10, 40, and 100 mg/mL, with release of ranibizumab 40 and 100 mg/mL found to remain quantifiable after 6 months. Using a starting concentration of 100 mg/mL, active release rate at approximately 6 months was consistent after the initial fill and first, second, and third refills, demonstrating reproducibility between implants and between multiple refill-exchanges of the same implant. A refill-exchange performed with a single 100-µL stroke using the refill needle was shown to replace over 95% of the implant contents with fresh drug. In vitro data support the use of the PDS with fixed refill-exchange intervals of at least 6 months in clinical trials.
Published: 2022
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3. Embedded software of the KM3NeT central logic board.

Author: Sebastiano Aiello, Albert Akhriev, Sergio Alves Garre, Zineb Aly, A. Ambrosone, Fabrizio Ameli, Michel André 0002, E. Androutsou, Marco Anghinolfi, Mancia Anguita, L. Aphecetche, M. Ardid, S. Ardid, H. Atmani, Julien Aublin, Christos Bagatelas, L. Bailly-Salins, Z. Bardacová, Bruny Baret, S. Basegmez du Pree, Y. Becherini, M. Bendahman, F. Benfenati, M. Benhassi, D. M. Benoit, E. Berbee, V. Bertin, Vincent van Beveren, S. Biagi, M. Boettcher, J. Boumaaza, M. Bouta, M. Bouwhuis, C. Bozza, R. M. Bozza, H. Brânzas, F. Bretaudeau, R. Bruijn, J. Brunner, R. Bruno, E. Buis, R. Buompane, J. Busto, B. Caiffi, D. Calvo, S. Campion, A. Capone, F. Carenini, V. Carretero, T. Cartraud, P. Castaldi, V. Cecchini, S. Celli, L. Cerisy, M. Chabab, M. Chadolias, A. Chen, S. Cherubini, T. Chiarusi, M. Circella, R. Cocimano, J. A. B. Coelho, A. Coleiro, R. Coniglione, P. Coyle, A. Creusot, A. Cruz, G. Cuttone, R. Dallier, Y. Darras, A. De Benedittis, B. De Martino, V. Decoene, R. Del Burgo, L. S. Di Mauro, I. Di Palma, A. F. Díaz, D. Diego-Tortosa, C. Distefano, A. Domi, C. Donzaud, D. Dornic, M. Dörr, E. Drakopoulou, D. Drouhin, R. Dvornický, T. Eberl, E. Eckerová, A. Eddymaoui, T. van Eeden, M. Eff, D. van Eijk, I. El Bojaddaini, S. El Hedri, A. Enzenhöfer, G. Ferrara, M. D. Filipovic, F. Filippini, L. A. Fusco, O. Gabella, J. Gabriel, S. Gagliardini, T. Gal, J. García Méndez, A. Garcia Soto, C. Gatius Oliver, N. Geißelbrecht, H. Ghaddari, L. Gialanella, B. K. Gibson, E. Giorgio, A. Girardi, I. Goos, D. Goupilliere, S. R. Gozzini, R. Gracia, K. Graf, C. Guidi, B. Guillon, M. Gutiérrez, H. van Haren, A. Heijboer, A. Hekalo, L. Hennig, J. J. Hernández-Rey, F. Huang, W. Idrissi Ibnsalih, G. Illuminati, C. W. James, P. Jansweijer, M. de Jong, P. de Jong, B. J. Jung, P. Kalaczynski, O. Kalekin, U. F. Katz, N. R. Khan Chowdhury, A. Khatun, G. Kistauri, C. Kopper, A. Kouchner, V. Kulikovskiy, R. Kvatadze, M. Labalme, R. Lahmann, G. Larosa, C. Lastoria, A. Lazo, S. Le Stum, G. Lehaut, E. Leonora, N. Lessing, G. Levi, M. Lindsey Clark, Fabio Longhitano, J. Majumdar, L. Malerba, F. Mamedov, J. Manczak, A. Manfreda, M. Marconi, A. Margiotta, A. Marinelli, C. Markou, L. Martin, J. A. Martínez-Mora, F. Marzaioli, M. Mastrodicasa, S. Mastroianni, S. Miccichè, Gennaro Miele, P. Migliozzi, E. Migneco, S. Minutoli, M. L. Mitsou, C. M. Mollo, L. Morales-Gallegos, C. Morley-Wong, A. Mosbrugger, A. Moussa, I. Mozun Mateo, R. Muller, M. R. Musone, M. Musumeci, L. Nauta, S. Navas, A. Nayerhoda, C. A. Nicolau, B. Nkosi, B. ó Fearraigh, V. Oliviero, A. Orlando, E. Oukacha, J. Palacios González, G. Papalashvili, E. J. Pastor Gomez, A. M. Paun, G. E. Pavalas, S. Peña Martínez, M. Perrin-Terrin, J. Perronnel, V. Pestel, R. Pestes, P. Piattelli, C. Poirè, V. Popa, T. Pradier, S. Pulvirenti, G. Quéméner, C. Quiroz, U. Rahaman, N. Randazzo, S. Razzaque, I. C. Rea, Diego Real, S. Reck, Giorgio Riccobene, J. Robinson, A. Romanov, A. Saina, Francisco Salesa Greus, D. F. E. Samtleben, Agustín Sánchez Losa, M. Sanguineti, C. Santonastaso, D. Santonocito, P. Sapienza, Y. Scarpetta, J. Schnabel, M. F. Schneider, J. Schumann, H. M. Schutte, J. Seneca, B. Setter, I. Sgura, R. Shanidze, Y. Shitov, F. Simkovic, A. Simonelli, A. Sinopoulou, M. V. Smirnov, Bernardino Spisso, Maurizio Spurio, D. Stavropoulos, I. Stekl, M. Taiuti, Y. Tayalati, H. Tedjditi, H. Thiersen, I. Tosta e Melo, B. Trocme, S. Tsagkli, V. Tsourapis, E. Tzamariudaki, A. Vacheret, V. Valsecchi, V. Van Elewyck, G. Vannoye, G. Vasileiadis, F. Vazquez de Sola, C. Verilhac, A. Veutro, S. Viola, D. Vivolo, H. Warnhofer, J. Wilms, E. de Wolf, H. Yepes-Ramirez, G. Zarpapis, S. Zavatarelli, A. Zegarelli, D. Zito, J. D. Zornoza, Juan Zúñiga, and Natalia Zywucka
Published: 2024
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4. Low energy event reconstruction in IceCube DeepCore

Author: R. Abbasi, M. Ackermann, J. Adams, J. A. Aguilar, M. Ahlers, M. Ahrens, J. M. Alameddine, A. A. Alves, N. M. Amin, K. Andeen, T. Anderson, G. Anton, C. Argüelles, Y. Ashida, S. Axani, X. Bai, A. Balagopal V., S. W. Barwick, B. Bastian, V. Basu, S. Baur, R. Bay, J. J. Beatty, K.-H. Becker, J. Becker Tjus, J. Beise, C. Bellenghi, S. Benda, S. BenZvi, D. Berley, E. Bernardini, D. Z. Besson, G. Binder, D. Bindig, E. Blaufuss, S. Blot, M. Boddenberg, F. Bontempo, J. Y. Book, J. Borowka, S. Böser, O. Botner, J. Böttcher, E. Bourbeau, F. Bradascio, J. Braun, B. Brinson, S. Bron, J. Brostean-Kaiser, R. T. Burley, R. S. Busse, M. A. Campana, E. G. Carnie-Bronca, C. Chen, Z. Chen, D. Chirkin, K. Choi, B. A. Clark, K. Clark, L. Classen, A. Coleman, G. H. Collin, J. M. Conrad, P. Coppin, P. Correa, D. F. Cowen, R. Cross, C. Dappen, P. Dave, C. De Clercq, J. J. DeLaunay, D. Delgado López, H. Dembinski, K. Deoskar, A. Desai, P. Desiati, K. D. de Vries, G. de Wasseige, M. de With, T. De Young, A. Diaz, J. C. Díaz-Vélez, M. Dittmer, H. Dujmovic, M. Dunkman, M. A. DuVernois, T. Ehrhardt, P. Eller, R. Engel, H. Erpenbeck, J. Evans, P. A. Evenson, K. L. Fan, A. R. Fazely, A. Fedynitch, N. Feigl, S. Fiedlschuster, A. T. Fienberg, C. Finley, L. Fischer, D. Fox, A. Franckowiak, E. Friedman, A. Fritz, P. Fürst, T. K. Gaisser, J. Gallagher, E. Ganster, A. Garcia, S. Garrappa, L. Gerhardt, A. Ghadimi, C. Glaser, T. Glauch, T. Glüsenkamp, N. Goehlke, J. G. Gonzalez, S. Goswami, D. Grant, T. Grégoire, S. Griswold, C. Günther, P. Gutjahr, C. Haack, A. Hallgren, R. Halliday, L. Halve, F. Halzen, M. Ha Minh, K. Hanson, J. Hardin, A. A. Harnisch, A. Haungs, D. Hebecker, K. Helbing, F. Henningsen, E. C. Hettinger, S. Hickford, J. Hignight, C. Hill, G. C. Hill, K. D. Hoffman, R. Hoffmann, K. Hoshina, W. Hou, F. Huang, M. Huber, T. Huber, K. Hultqvist, M. Hünnefeld, R. Hussain, K. Hymon, S. In, N. Iovine, A. Ishihara, M. Jansson, G. S. Japaridze, M. Jeong, M. Jin, B. J. P. Jones, D. Kang, W. Kang, X. Kang, A. Kappes, D. Kappesser, L. Kardum, T. Karg, M. Karl, A. Karle, U. Katz, M. Kauer, M. Kellermann, J. L. Kelley, A. Kheirandish, K. Kin, T. Kintscher, J. Kiryluk, S. R. Klein, A. Kochocki, R. Koirala, H. Kolanoski, T. Kontrimas, L. Köpke, C. Kopper, S. Kopper, D. J. Koskinen, P. Koundal, M. Kovacevich, M. Kowalski, T. Kozynets, E. Krupczak, E. Kun, N. Kurahashi, N. Lad, C. Lagunas Gualda, J. L. Lanfranchi, M. J. Larson, F. Lauber, J. P. Lazar, J. W. Lee, K. Leonard, A. Leszczynska, Y. Li, M. Lincetto, Q. R. Liu, M. Liubarska, E. Lohfink, C. J. Lozano Mariscal, L. Lu, F. Lucarelli, A. Ludwig, W. Luszczak, Y. Lyu, W. Y. Ma, J. Madsen, K. B. M. Mahn, Y. Makino, S. Mancina, I. C. Maris, I. Martinez-Soler, R. Maruyama, S. McCarthy, T. McElroy, F. McNally, J. V. Mead, K. Meagher, S. Mechbal, A. Medina, M. Meier, S. Meighen-Berger, J. Micallef, D. Mockler, T. Montaruli, R. W. Moore, R. Morse, M. Moulai, T. Mukherjee, R. Naab, R. Nagai, U. Naumann, J. Necker, L. V. Nguyễn, H. Niederhausen, M. U. Nisa, S. C. Nowicki, A. Obertacke Pollmann, M. Oehler, B. Oeyen, A. Olivas, E. O’Sullivan, H. Pandya, D. V. Pankova, N. Park, G. K. Parker, E. N. Paudel, L. Paul, C. Pérez de los Heros, L. Peters, J. Peterson, S. Philippen, S. Pieper, A. Pizzuto, M. Plum, Y. Popovych, A. Porcelli, M. Prado Rodriguez, B. Pries, G. T. Przybylski, C. Raab, J. Rack-Helleis, A. Raissi, M. Rameez, K. Rawlins, I. C. Rea, Z. Rechav, A. Rehman, P. Reichherzer, R. Reimann, G. Renzi, E. Resconi, S. Reusch, W. Rhode, M. Richman, B. Riedel, E. J. Roberts, S. Robertson, G. Roellinghoff, M. Rongen, C. Rott, T. Ruhe, D. Ryckbosch, D. Rysewyk Cantu, I. Safa, J. Saffer, P. Sampathkumar, S. E. Sanchez Herrera, A. Sandrock, M. Santander, S. Sarkar, K. Satalecka, M. Schaufel, H. Schieler, S. Schindler, T. Schmidt, A. Schneider, J. Schneider, F. G. Schröder, L. Schumacher, G. Schwefer, S. Sclafani, D. Seckel, S. Seunarine, A. Sharma, S. Shefali, N. Shimizu, M. Silva, B. Skrzypek, B. Smithers, R. Snihur, J. Soedingrekso, D. Soldin, C. Spannfellner, G. M. Spiczak, C. Spiering, J. Stachurska, M. Stamatikos, T. Stanev, R. Stein, J. Stettner, T. Stezelberger, T. Stürwald, T. Stuttard, G. W. Sullivan, I. Taboada, S. Ter-Antonyan, J. Thwaites, S. Tilav, F. Tischbein, K. Tollefson, C. Tönnis, S. Toscano, D. Tosi, A. Trettin, M. Tselengidou, C. F. Tung, A. Turcati, R. Turcotte, C. F. Turley, J. P. Twagirayezu, B. Ty, M. A. Unland Elorrieta, N. Valtonen-Mattila, J. Vandenbroucke, N. van Eijndhoven, D. Vannerom, J. van Santen, J. Veitch-Michaelis, S. Verpoest, C. Walck, W. Wang, T. B. Watson, C. Weaver, P. Weigel, A. Weindl, M. J. Weiss, J. Weldert, C. Wendt, J. Werthebach, M. Weyrauch, N. Whitehorn, C. H. Wiebusch, N. Willey, D. R. Williams, M. Wolf, G. Wrede, J. Wulff, X. W. Xu, J. P. Yanez, E. Yildizci, S. Yoshida, S. Yu, T. Yuan, Z. Zhang, P. Zhelnin, and IceCube Collaboration
Subjects: Astrophysics, QB460-466, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract: Abstract The reconstruction of event-level information, such as the direction or energy of a neutrino interacting in IceCube DeepCore, is a crucial ingredient to many physics analyses. Algorithms to extract this high level information from the detector’s raw data have been successfully developed and used for high energy events. In this work, we address unique challenges associated with the reconstruction of lower energy events in the range of a few to hundreds of GeV and present two separate, state-of-the-art algorithms. One algorithm focuses on the fast directional reconstruction of events based on unscattered light. The second algorithm is a likelihood-based multipurpose reconstruction offering superior resolutions, at the expense of larger computational cost.
Published: 2022
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5. Hybrid deep learning architecture for general disruption prediction across tokamaks.

Author: J. X. Zhu, C. Rea, K. Montes, R. S. Granetz, R. Sweeney, and R. A. Tinguely
Published: 2020

6. Search for neutrinos from decaying dark matter with IceCube

Author: M. G. Aartsen, M. Ackermann, J. Adams, J. A. Aguilar, M. Ahlers, M. Ahrens, I. Al Samarai, D. Altmann, K. Andeen, T. Anderson, I. Ansseau, G. Anton, C. Argüelles, J. Auffenberg, S. Axani, P. Backes, H. Bagherpour, X. Bai, J. P. Barron, S. W. Barwick, V. Baum, R. Bay, J. J. Beatty, J. Becker Tjus, K.-H. Becker, S. BenZvi, D. Berley, E. Bernardini, D. Z. Besson, G. Binder, D. Bindig, E. Blaufuss, S. Blot, C. Bohm, M. Börner, F. Bos, S. Böser, O. Botner, E. Bourbeau, J. Bourbeau, F. Bradascio, J. Braun, M. Brenzke, H.-P. Bretz, S. Bron, J. Brostean-Kaiser, A. Burgman, R. S. Busse, T. Carver, E. Cheung, D. Chirkin, A. Christov, K. Clark, L. Classen, G. H. Collin, J. M. Conrad, P. Coppin, P. Correa, D. F. Cowen, R. Cross, P. Dave, M. Day, J. P. A. M. de André, C. De Clercq, J. J. DeLaunay, H. Dembinski, S. De Ridder, P. Desiati, K. D. de Vries, G. de Wasseige, M. de With, T. DeYoung, J. C. Díaz-Vélez, V. di Lorenzo, H. Dujmovic, J. P. Dumm, M. Dunkman, E. Dvorak, B. Eberhardt, T. Ehrhardt, B. Eichmann, P. Eller, P. A. Evenson, S. Fahey, A. R. Fazely, J. Felde, K. Filimonov, C. Finley, S. Flis, A. Franckowiak, E. Friedman, A. Fritz, T. K. Gaisser, J. Gallagher, E. Ganster, L. Gerhardt, K. Ghorbani, W. Giang, T. Glauch, T. Glüsenkamp, A. Goldschmidt, J. G. Gonzalez, D. Grant, Z. Griffith, C. Haack, A. Hallgren, L. Halve, F. Halzen, K. Hanson, D. Hebecker, D. Heereman, K. Helbing, R. Hellauer, S. Hickford, J. Hignight, G. C. Hill, K. D. Hoffman, R. Hoffmann, T. Hoinka, B. Hokanson-Fasig, K. Hoshina, F. Huang, M. Huber, K. Hultqvist, M. Hünnefeld, R. Hussain, S. In, N. Iovine, A. Ishihara, E. Jacobi, G. S. Japaridze, M. Jeong, K. Jero, B. J. P. Jones, P. Kalaczynski, W. Kang, A. Kappes, D. Kappesser, T. Karg, A. Karle, U. Katz, M. Kauer, A. Keivani, J. L. Kelley, A. Kheirandish, J. Kim, M. Kim, T. Kintscher, J. Kiryluk, T. Kittler, S. R. Klein, R. Koirala, H. Kolanoski, L. Köpke, C. Kopper, S. Kopper, J. P. Koschinsky, D. J. Koskinen, M. Kowalski, K. Krings, M. Kroll, G. Krückl, S. Kunwar, N. Kurahashi, T. Kuwabara, A. Kyriacou, M. Labare, J. L. Lanfranchi, M. J. Larson, F. Lauber, K. Leonard, M. Lesiak-Bzdak, M. Leuermann, Q. R. Liu, E. Lohfink, C. J. Lozano Mariscal, L. Lu, J. Lünemann, W. Luszczak, J. Madsen, G. Maggi, K. B. M. Mahn, S. Mancina, R. Maruyama, K. Mase, R. Maunu, K. Meagher, M. Medici, M. Meier, T. Menne, G. Merino, T. Meures, S. Miarecki, J. Micallef, G. Momenté, T. Montaruli, R. W. Moore, M. Moulai, R. Nahnhauer, P. Nakarmi, U. Naumann, G. Neer, H. Niederhausen, S. C. Nowicki, D. R. Nygren, A. Obertacke Pollmann, A. Olivas, A. O’Murchadha, E. O’Sullivan, T. Palczewski, H. Pandya, D. V. Pankova, P. Peiffer, J. A. Pepper, C. Pérez de los Heros, D. Pieloth, E. Pinat, M. Plum, P. B. Price, G. T. Przybylski, C. Raab, L. Rädel, M. Rameez, L. Rauch, K. Rawlins, I. C. Rea, R. Reimann, B. Relethford, M. Relich, E. Resconi, W. Rhode, M. Richman, S. Robertson, M. Rongen, C. Rott, T. Ruhe, D. Ryckbosch, D. Rysewyk, I. Safa, S. E. Sanchez Herrera, A. Sandrock, J. Sandroos, M. Santander, S. Sarkar, K. Satalecka, M. Schaufel, P. Schlunder, T. Schmidt, A. Schneider, S. Schoenen, S. Schöneberg, L. Schumacher, S. Sclafani, D. Seckel, S. Seunarine, J. Soedingrekso, D. Soldin, M. Song, G. M. Spiczak, C. Spiering, J. Stachurska, M. Stamatikos, T. Stanev, A. Stasik, R. Stein, J. Stettner, A. Steuer, T. Stezelberger, R. G. Stokstad, A. Stößl, N. L. Strotjohann, T. Stuttard, G. W. Sullivan, M. Sutherland, I. Taboada, J. Tatar, F. Tenholt, S. Ter-Antonyan, A. Terliuk, S. Tilav, P. A. Toale, M. N. Tobin, C. Tönnis, S. Toscano, D. Tosi, M. Tselengidou, C. F. Tung, A. Turcati, C. F. Turley, B. Ty, E. Unger, M. Usner, J. Vandenbroucke, W. Van Driessche, D. van Eijk, N. van Eijndhoven, S. Vanheule, J. van Santen, M. Vraeghe, C. Walck, A. Wallace, M. Wallraff, F. D. Wandler, N. Wandkowsky, A. Waza, C. Weaver, M. J. Weiss, C. Wendt, J. Werthebach, S. Westerhoff, B. J. Whelan, K. Wiebe, C. H. Wiebusch, L. Wille, D. R. Williams, L. Wills, M. Wolf, J. Wood, T. R. Wood, E. Woolsey, K. Woschnagg, G. Wrede, D. L. Xu, X. W. Xu, Y. Xu, J. P. Yanez, G. Yodh, S. Yoshida, and T. Yuan
Subjects: Astrophysics, QB460-466, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract: Abstract With the observation of high-energy astrophysical neutrinos by the IceCube Neutrino Observatory, interest has risen in models of PeV-mass decaying dark matter particles to explain the observed flux. We present two dedicated experimental analyses to test this hypothesis. One analysis uses 6 years of IceCube data focusing on muon neutrino ‘track’ events from the Northern Hemisphere, while the second analysis uses 2 years of ‘cascade’ events from the full sky. Known background components and the hypothetical flux from unstable dark matter are fitted to the experimental data. Since no significant excess is observed in either analysis, lower limits on the lifetime of dark matter particles are derived: we obtain the strongest constraint to date, excluding lifetimes shorter than $$10^{28}\hbox { s}$$ 1028s at 90% CL for dark matter masses above $$10~\hbox {TeV}$$ 10TeV .
Published: 2018
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7. Modulation of the gut microbiome with nisin

Author: Catherine O’Reilly, Ghjuvan M. Grimaud, Mairéad Coakley, Paula M. O’Connor, Harsh Mathur, Veronica L. Peterson, Ciara M. O’Donovan, Peadar G. Lawlor, Paul D. Cotter, Catherine Stanton, Mary C. Rea, Colin Hill, and R. Paul Ross
Subjects: Multidisciplinary
Abstract: Nisin is a broad spectrum bacteriocin used extensively as a food preservative that was identified in Lactococcus lactis nearly a century ago. We show that orally-ingested nisin survives transit through the porcine gastrointestinal tract intact (as evidenced by activity and molecular weight determination) where it impacts both the composition and functioning of the microbiota. Specifically, nisin treatment caused a reversible decrease in Gram positive bacteria, resulting in a reshaping of the Firmicutes and a corresponding relative increase in Gram negative Proteobacteria. These changes were mirrored by the modification in relative abundance of pathways involved in acetate, butyrate (decreased) and propionate (increased) synthesis which correlated with overall reductions in short chain fatty acid levels in stool. These reversible changes that occur as a result of nisin ingestion demonstrate the potential of bacteriocins like nisin to shape mammalian microbiomes and impact on the functionality of the community.
Published: 2023

8. A Live Bio-Therapeutic for Mastitis, Containing Lactococcus lactis DPC3147 With Comparable Efficacy to Antibiotic Treatment

Author: Michael Kitching, Harsh Mathur, James Flynn, Noel Byrne, Pat Dillon, Riona Sayers, Mary C. Rea, Colin Hill, and R. Paul Ross
Subjects: mastitis, emulsion, lacticin 3147, somatic cell counts, antibiotics, Microbiology, QR1-502
Abstract: Bovine mastitis is an ongoing significant concern in the dairy and agricultural industry resulting in substantial losses in milk production and revenue. Among the predominant etiological agents of bovine mastitis are Staphylococcus aureus, Streptococcus uberis, Streptococcus dysgalactiae, and Escherichia coli. Currently, the treatment of choice for bovine mastitis involves the use of commercial therapeutic antibiotic formulations such as TerrexineTM, containing both kanamycin and cephalexin. Such antibiotics are regularly administered in more than one dose resulting in the withholding of milk for processing for a number of days. Here, we describe the optimization of a formulation of Lactococcus lactis DPC3147, that produces the two-component bacteriocin lacticin 3147, in a liquid paraffin-based emulsion (formulation hereafter designated ‘live bio-therapeutic’) for the first time and compare it to the commercial antibiotic formulation TerrexineTM, with a view to treating cows with clinical/sub-clinical mastitis. Critically, in a field trial described here, this ‘ready-to-use’ emulsion containing live L. lactis DPC3147 cells exhibited comparable efficacy to TerrexineTM when used to treat mastitic cows. Furthermore, we found that the L. lactis cells within this novel emulsion-based formulation remained viable for up to 5 weeks, when stored at 4, 22, or 37°C. The relative ease and cost-effective nature of producing this ‘live bio-therapeutic’ formulation, in addition to its enhanced shelf life compared to previous aqueous-based formulations, indicate that this product could be a viable alternative therapeutic option for bovine mastitis. Moreover, the single-dose administration of this ‘live bio-therapeutic’ formulation is a further advantage, as it can expedite the return of the milk to the milk pool, in comparison to some commercial antibiotics. Overall, in this field trial, we show that the live bio-therapeutic formulation displayed a 47% cure rate compared to a 50% cure rate for a commercial antibiotic control, with respect to curing cows with clinical/sub-clinical mastitis. The study suggests that a larger field trial to further demonstrate efficacy is warranted.
Published: 2019
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9. Lactobacillus gasseri APC 678 Reduces Shedding of the Pathogen Clostridium difficile in a Murine Model

Author: Lisa Quigley, Mairéad Coakley, Debebe Alemayehu, Mary C. Rea, Patrick G. Casey, Órla O’Sullivan, Eileen Murphy, Barry Kiely, Paul D. Cotter, Colin Hill, and R. Paul Ross
Subjects: Lactobacillus gasseri, Clostridium difficile, C. difficile infection (CDI), murine model, live therapeutic agent, Microbiology, QR1-502
Abstract: Clostridium difficile is a common cause of health-care acquired diarrhea, resulting in a spectrum of disease from mild diarrhea to life-threatening illness. Sixty Lactobacillus strains were screened for anti-C. difficile activity using a co-culture method. Based on their ability to inhibit C. difficile, L. gasseri APC 678 and L. rhamnosus DPC 6111 were selected for study in a murine model of C. difficile infection. L. gasseri ATCC 33323, was included as a control. It was established that, relative to control mice not fed Lactobacillus, feeding with L. gasseri APC 678 resulted in a significant reduction by day 7 (8-fold, p = 0.017) of viable C. difficile VPI 10463 in the feces of mice. In contrast, neither L. rhamnosus DPC 6111 nor L. gasseri ATCC 33323 significantly reduced fecal C. difficile shedding. Sequencing of the cecal microbiota showed that in mice fed L. gasseri APC 678 there was a significant increase in bacterial diversity across a number of indices when compared to the control or other Lactobacillus-fed groups. There was no significant change in the relative abundance of Firmicutes or Bacteroidetes in the group fed L. gasseri APC 678 relative to the control, while the groups fed L. rhamnosus DPC 6111 or L. gasseri ATCC 33323 showed a significant decrease in the relative abundance of Firmicutes (p = 0.002 and p = 0.019, respectively) and a significant increase in Bacteroidetes (p = 0.002 and p = 0.023, respectively). These results highlight the potential of L. gasseri APC 678 as a live therapeutic agent to target C. difficile infection.
Published: 2019
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10. Teaching and confronting digital extremism: contexts, challenges and opportunities

Author: Stephen C. Rea
Subjects: Library and Information Sciences, Computer Science Applications, Education
Abstract: Purpose This paper aims to offer practical guidance on teaching about digital extremism – defined here as the intersection of digital disinformation campaigns with political extremism – by highlighting four pedagogical challenges: the danger of unintentionally “redpilling” students; the slippery slope to false equivalency and “bothsidesism” in turbulent partisan waters; the difficulty of separating empirical analyses from prescriptive debates circulating in popular media; and the trouble of getting students to understand digital extremism as a sociotechnical problem rather than as a social-or-technical problem. The conclusion proposes opportunities for educators to integrate practical approaches to confronting digital extremism with digital civics curricula. Design/methodology/approach This paper reviews pedagogical challenges and outlines a curricular program for teaching about digital extremism drawn from the author’s experience designing undergraduate courses and open teaching modules between 2016 and 2021. Findings Educators should shift focus from the substance of digital extremism to its tools – social media platforms’ surveillance and data-gathering methods, advertising technologies and monetized user-generated content, personalized recommendation algorithms and media manipulation strategies that amplify some narratives while suppressing others – and the media and political institutions that benefit most from it. Proposed lessons include: how digital extremists manipulate social media metadata; engagement with data creation and targeting practices; and analysis of information production, circulation and consumption exploring media manipulation tools and their effects. Originality/value This paper’s added values are the insights and practical recommendations for undergraduate educators teaching on a topic of urgent contemporary concern: digital extremism.
Published: 2022

11. Evaluation of the Potential of Lactobacillus paracasei Adjuncts for Flavor Compounds Development and Diversification in Short-Aged Cheddar Cheese

Author: Ewelina Stefanovic, Kieran N. Kilcawley, Clara Roces, Mary C. Rea, Maurice O'Sullivan, Jeremiah J. Sheehan, and Olivia McAuliffe
Subjects: Lactobacillus paracasei, dairy, cheese flavor, diversification, volatiles, Microbiology, QR1-502
Abstract: The non-starter microbiota of Cheddar cheese mostly comprises mesophilic lactobacilli, such as Lactobacillus casei, Lactobacillus paracasei, Lactobacillus rhamnosus, and Lactobacillus plantarum. These bacteria are recognized for their potential to improve Cheddar cheese flavor when used as adjunct cultures. In this study, three strains of L. paracasei (DPC2071, DPC4206, and DPC4536) were evaluated for their contribution to the enhancement and diversification of flavor in short-aged Cheddar cheese. The strains were selected based on their previously determined genomic diversity, variability in proteolytic enzyme activities and metabolic capability in cheese model systems. The addition of adjunct cultures did not affect the gross composition or levels of lipolysis of the cheeses. The levels of free amino acids (FAA) in cheeses showed a significant increase after 28 days of ripening. However, the concentrations of individual amino acids in the cheeses did not significantly differ except for some amino acids (aspartic acid, threonine, serine, and tryptophan) at Day 14. Volatile profile analysis revealed that the main compounds that differentiated the cheeses were of lipid origin, such as long chain aldehydes, acids, ketones, and lactones. This study demonstrated that the adjunct L. paracasei strains contributed to the development and diversification of compounds related to flavor in short-aged Cheddar cheeses.
Published: 2018
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12. Oral Delivery of Nisin in Resistant Starch Based Matrices Alters the Gut Microbiota in Mice

Author: Ronan Gough, Raúl Cabrera Rubio, Paula M. O'Connor, Fiona Crispie, André Brodkorb, Song Miao, Colin Hill, Reynolds P. Ross, Paul D. Cotter, Kanishka N. Nilaweera, and Mary C. Rea
Subjects: mouse, nisin, starch, resistant starch, microbiota, digestion, Microbiology, QR1-502
Abstract: There is a growing recognition of the role the gastrointestinal microbiota plays in health and disease. Ingested antimicrobial proteins and peptides have the potential to alter the gastrointestinal microbiota; particularly if protected from digestion. Nisin is an antimicrobial peptide that is used as a food preservative. This study examined the ability of nisin to affect the murine microbiota when fed to mice in two different starch based matrices; a starch dough comprising raw starch granules and a starch gel comprising starch that was gelatinized and retrograded. The effects of the two starch matrices by themselves on the microbiota were also examined. Following 16S rRNA compositional sequencing, beta diversity analysis highlighted a significant difference (p = 0.001, n = 10) in the murine microbiota between the four diet groups. The differences between the two nisin containing diets were mainly attributable to differences in the nisin release from the starch matrices while the differences between the carriers were mainly attributable to the type of resistant starch they possessed. Indeed, the differences in the relative abundance of several genera in the mice consuming the starch dough and starch gel diets, in particular Akkermansia, the relative abundance of which was 0.5 and 11.9%, respectively (p = 0.0002, n = 10), points to the potential value of resistance starch as a modulator of beneficial gut microbes. Intact nisin and nisin digestion products (in particular nisin fragment 22–31) were detected in the feces and the nisin was biologically active. However, despite a three-fold greater consumption of nisin in the group fed the nisin in starch dough diet, twice as much nisin was detected in the feces of the group which consumed the nisin in starch gel diet. In addition, the relative abundance of three times as many genera from the lower gastrointestinal tract (GIT) were significantly different (p < 0.001, n = 10) to the control for the group fed the nisin in starch gel diet, implying that the starch gel afforded a degree of protection from digestion to the nisin entrapped within it.
Published: 2018
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13. Bacteriocin-Antimicrobial Synergy: A Medical and Food Perspective

Author: Harsh Mathur, Des Field, Mary C. Rea, Paul D. Cotter, Colin Hill, and R. Paul Ross
Subjects: bacteriocins, antibiotic resistance, synergy, stressors, pathogens, antimicrobials, Microbiology, QR1-502
Abstract: The continuing emergence of multi-drug resistant pathogens has sparked an interest in seeking alternative therapeutic options. Antimicrobial combinatorial therapy is one such avenue. A number of studies have been conducted, involving combinations of bacteriocins with other antimicrobials, to circumvent the development of antimicrobial resistance and/or increase antimicrobial potency. Such bacteriocin-antimicrobial combinations could have tremendous value, in terms of reducing the likelihood of resistance development due to the involvement of two distinct mechanisms of antimicrobial action. Furthermore, antimicrobial synergistic interactions may also have potential financial implications in terms of decreasing the costs of treatment by reducing the concentration of an expensive antimicrobial and utilizing it in combination with an inexpensive one. In addition, combinatorial therapies with bacteriocins can broaden antimicrobial spectra and/or result in a reduction in the concentration of an antibiotic required for effective treatments to the extent that potentially toxic or adverse side effects can be reduced or eliminated. Here, we review studies in which bacteriocins were found to be effective in combination with other antimicrobials, with a view to targeting clinical and/or food-borne pathogens. Furthermore, we discuss some of the bottlenecks which are currently hindering the development of bacteriocins as viable therapeutic options, as well as addressing the need to exercise caution when attempting to predict clinical outcomes of bacteriocin-antimicrobial combinations.
Published: 2017
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14. Insights into the Mode of Action of the Sactibiotic Thuricin CD

Author: Colin Hill, R. Paul Ross, Harsh Mathur, Vincenzo Fallico, Paula M. O’Connor, Mary C. Rea, and Paul D. Cotter
Subjects: bacteriocin, mode of action, cytometry, membrane potential, viability, Microbiology, QR1-502
Abstract: Thuricin CD is a two-component bacteriocin, consisting of the peptides Trnα and Trnβ, and belongs to the newly designated sactibiotic subclass of bacteriocins. While it is clear from studies conducted thus far that it is a narrow-spectrum bacteriocin, requiring the synergistic activity of the two peptides, the precise mechanism of action of thuricin CD has not been elucidated. This study used a combination of flow cytometry and traditional culture-dependent assays to ascertain the effects of the thuricin CD peptides on the morphology, physiology and viability of sensitive Bacillus firmus DPC6349 cells. We show that both Trnα and Trnβ are membrane-acting and cause a collapse of the membrane potential, which could not be reversed even under membrane-repolarizing conditions. Furthermore, the depolarizing action of thuricin CD is accompanied by reductions in cell size and granularity, producing a pattern of physiological alterations in DPC6349 cells similar to those triggered by the pore-forming single-component bacteriocin Nisin A, and two-component lacticin 3147. Taken together, these results lead us to postulate that the lytic activity of thuricin CD involves the insertion of thuricin CD peptides into the membrane of target cells leading to permeabilization due to pore formation and consequent flux of ions across the membrane, resulting in membrane depolarization and eventual cell death.
Published: 2017
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15. Identification of ADS024, a newly characterized strain of Bacillus velezensis with direct Clostridiodes difficile killing and toxin degradation bio-activities

Author: Michelle M. O’Donnell, James W. Hegarty, Brian Healy, Sarah Schulz, Calum J. Walsh, Colin Hill, R. Paul Ross, Mary C. Rea, Ronald Farquhar, and Laurent Chesnel
Subjects: Multidisciplinary
Abstract: Clostridioides difficile infection (CDI) remains a significant health threat worldwide. C. difficile is an opportunistic, toxigenic pathogen that takes advantage of a disrupted gut microbiome to grow and produce signs and symptoms ranging from diarrhea to pseudomembranous colitis. Antibiotics used to treat C. difficile infection are usually broad spectrum and can further disrupt the commensal gut microbiota, leaving patients susceptible to recurrent C. difficile infection. There is a growing need for therapeutic options that can continue to inhibit the outgrowth of C. difficile after antibiotic treatment is completed. Treatments that degrade C. difficile toxins while having minimal collateral impact on gut bacteria are also needed to prevent recurrence. Therapeutic bacteria capable of producing a range of antimicrobial compounds, proteases, and other bioactive metabolites represent a potentially powerful tool for preventing CDI recurrence following resolution of symptoms. Here, we describe the identification and initial characterization of ADS024 (formerly ART24), a novel therapeutic bacterium that can kill C. difficile in vitro with limited impact on other commensal bacteria. In addition to directly killing C. difficile, ADS024 also produces proteases capable of degrading C. difficile toxins, the drivers of symptoms associated with most cases of CDI. ADS024 is in clinical development for the prevention of CDI recurrence as a single-strain live biotherapeutic product, and this initial data set supports further studies aimed at evaluating ADS024 in future human clinical trials.
Published: 2022

16. The law in computation: What machine learning, artificial intelligence, and big data mean for law and society scholarship

Author: John Emery, Evan Conaway, Tania DoCarmo, Noopur Raval, and Stephen C. Rea
Subjects: Sociology and Political Science, Computer science, business.industry, Computation, 05 social sciences, Big data, 050801 communication & media studies, 0506 political science, Scholarship, 0508 media and communications, 050602 political science & public administration, Artificial intelligence, business, Law
Published: 2021

17. Integrated deep learning framework for unstable event identification and disruption prediction of tokamak plasmas

Author: J.X. Zhu, C. Rea, R.S. Granetz, E.S. Marmar, R. Sweeney, K. Montes, and R.A. Tinguely
Subjects: Nuclear and High Energy Physics, Condensed Matter Physics
Abstract: The ability to identify underlying disruption precursors is key to disruption avoidance. In this paper, we present an integrated deep learning (DL) based model that combines disruption prediction with the identification of several disruption precursors like rotating modes, locked modes, H-to-L back transitions and radiative collapses. The first part of our study demonstrates that the DL-based unstable event identifier trained on 160 manually labeled DIII-D shots can achieve, on average, 84% event identification rate of various frequent unstable events (like H-L back transition, locked mode, radiative collapse, rotating MHD mode, large sawtooth crash), and the trained identifier can be adapted to label unseen discharges, thus expanding the original manually labeled database. Based on these results, the integrated DL-based framework is developed using a combined database of manually labeled and automatically labeled DIII-D data, and it shows state-of-the-art (AUC = 0.940) disruption prediction and event identification abilities on DIII-D. Through cross-machine numerical disruption prediction studies using this new integrated model and leveraging the C-Mod, DIII-D, and EAST disruption warning databases, we demonstrate the improved cross-machine disruption prediction ability and extended warning time of the new model compared with a baseline predictor. In addition, the trained integrated model shows qualitatively good cross-machine event identification ability. Given a labeled dataset, the strategy presented in this paper, i.e. one that combines a disruption predictor with an event identifier module, can be applied to upgrade any neural network based disruption predictor. The results presented here inform possible development strategies of machine learning based disruption avoidance algorithms for future tokamaks and highlight the importance of building comprehensive databases with unstable event information on current machines.
Published: 2023

18. DIII-D research advancing the physics basis for optimizing the tokamak approach to fusion energy

Author: M. E. Fenstermacher, J. Abbate, S. Abe, T. Abrams, M. Adams, B. Adamson, N. Aiba, T. Akiyama, P. Aleynikov, E. Allen, S. Allen, H. Anand, J. Anderson, Y. Andrew, T. Andrews, D. Appelt, R. Arbon, N. Ashikawa, A. Ashourvan, M. Aslin, Y. Asnis, M. Austin, D. Ayala, J. Bak, I. Bandyopadhyay, S. Banerjee, K. Barada, L. Bardoczi, J. Barr, E. Bass, D. Battaglia, A. Battey, W. Baumgartner, L. Baylor, J. Beckers, M. Beidler, E. Belli, J. Berkery, T. Bernard, N. Bertelli, M. Beurskens, R. Bielajew, S. Bilgili, B. Biswas, S. Blondel, J. Boedo, I. Bogatu, R. Boivin, T. Bolzonella, M. Bongard, X. Bonnin, P. Bonoli, M. Bonotto, A. Bortolon, S. Bose, N. Bosviel, S. Bouwmans, M. Boyer, W. Boyes, L. Bradley, R. Brambila, D. Brennan, S. Bringuier, L. Brodsky, M. Brookman, J. Brooks, D. Brower, G. Brown, W. Brown, M. Burke, K. Burrell, K. Butler, R. Buttery, I. Bykov, P. Byrne, A. Cacheris, K. Callahan, J. Callen, G. Campbell, J. Candy, J. Canik, P. Cano-Megias, N. Cao, L. Carayannopoulos, T. Carlstrom, W. Carrig, T. Carter, W. Cary, L. Casali, M. Cengher, G. Cespedes Paz, R. Chaban, V. Chan, B. Chapman, I. Char, A. Chattopadhyay, R. Chen, J. Chen, X. Chen, M. Chen, Z. Chen, M. Choi, W. Choi, G. Choi, L. Chousal, C. Chrobak, C. Chrystal, Y. Chung, R. Churchill, M. Cianciosa, J. Clark, M. Clement, S. Coda, A. Cole, C. Collins, W. Conlin, A. Cooper, J. Cordell, B. Coriton, T. Cote, J. Cothran, A. Creely, N. Crocker, C. Crowe, B. Crowley, T. Crowley, D. Cruz-Zabala, D. Cummings, M. Curie, D. Curreli, A. Dal Molin, B. Dannels, A. Dautt-Silva, K. Davda, G. De Tommasi, P. De Vries, G. Degrandchamp, J. Degrassie, D. Demers, S. Denk, S. Depasquale, E. Deshazer, A. Diallo, S. Diem, A. Dimits, R. Ding, S. Ding, W. Ding, T. Do, J. Doane, G. Dong, D. Donovan, J. Drake, W. Drews, J. Drobny, X. Du, H. Du, V. Duarte, D. Dudt, C. Dunn, J. Duran, A. Dvorak, F. Effenberg, N. Eidietis, D. Elder, D. Eldon, R. Ellis, W. Elwasif, D. Ennis, K. Erickson, D. Ernst, M. Fasciana, D. Fedorov, E. Feibush, N. Ferraro, J. Ferreira, J. Ferron, P. Fimognari, D. Finkenthal, R. Fitzpatrick, P. Fox, W. Fox, L. Frassinetti, H. Frerichs, H. Frye, Y. Fu, K. Gage, J. Galdon Quiroga, A. Gallo, Q. Gao, A. Garcia, M. Garcia Munoz, D. Garnier, A. Garofalo, A. Gattuso, D. Geng, K. Gentle, D. Ghosh, L. Giacomelli, S. Gibson, E. Gilson, C. Giroud, F. Glass, A. Glasser, D. Glibert, P. Gohil, R. Gomez, S. Gomez, X. Gong, E. Gonzales, A. Goodman, Y. Gorelov, V. Graber, R. Granetz, T. Gray, D. Green, C. Greenfield, M. Greenwald, B. Grierson, R. Groebner, W. Grosnickle, M. Groth, H. Grunloh, S. Gu, W. Guo, H. Guo, P. Gupta, J. Guterl, W. Guttenfelder, T. Guzman, S. Haar, R. Hager, S. Hahn, M. Halfmoon, T. Hall, K. Hallatschek, F. Halpern, G. Hammett, H. Han, E. Hansen, C. Hansen, M. Hansink, J. Hanson, M. Hanson, G. Hao, A. Harris, R. Harvey, S. Haskey, E. Hassan, A. Hassanein, D. Hatch, R. Hawryluk, W. Hayashi, W. Heidbrink, J. Herfindal, J. Hicok, D. Hill, E. Hinson, C. Holcomb, L. Holland, C. Holland, E. Hollmann, J. Hollocombe, A. Holm, I. Holmes, K. Holtrop, M. Honda, R. Hong, R. Hood, A. Horton, L. Horvath, M. Hosokawa, S. Houshmandyar, N. Howard, E. Howell, D. Hoyt, W. Hu, Y. Hu, Q. Hu, J. Huang, Y. Huang, J. Hughes, T. Human, D. Humphreys, P. Huynh, A. Hyatt, C. Ibanez, L. Ibarra, R. Icasas, K. Ida, V. Igochine, Y. In, S. Inoue, A. Isayama, O. Izacard, V. Izzo, A. Jackson, G. Jacobsen, A. Jaervinen, A. Jalalvand, J. Janhunen, S. Jardin, H. Jarleblad, Y. Jeon, H. Ji, X. Jian, E. Joffrin, A. Johansen, C. Johnson, T. Johnson, C. Jones, I. Joseph, D. Jubas, B. Junge, W. Kalb, R. Kalling, C. Kamath, J. Kang, D. Kaplan, A. Kaptanoglu, S. Kasdorf, J. Kates-Harbeck, P. Kazantzidis, A. Kellman, D. Kellman, C. Kessel, K. Khumthong, E. Kim, H. Kim, J. Kim, S. Kim, K. Kim, C. Kim, W. Kimura, M. King, J. King, J. Kinsey, A. Kirk, B. Kiyan, A. Kleiner, V. Klevarova, R. Knapp, M. Knolker, W. Ko, T. Kobayashi, E. Koch, M. Kochan, B. Koel, M. Koepke, A. Kohn, R. Kolasinski, E. Kolemen, E. Kostadinova, M. Kostuk, G. Kramer, D. Kriete, L. Kripner, S. Kubota, J. Kulchar, K. Kwon, R. La Haye, F. Laggner, H. Lan, R. Lantsov, L. Lao, A. Lasa Esquisabel, C. Lasnier, C. Lau, B. Leard, J. Lee, R. Lee, M. Lee, Y. Lee, C. Lee, S. Lee, M. Lehnen, A. Leonard, E. Leppink, M. Lesher, J. Lestz, J. Leuer, N. Leuthold, X. Li, K. Li, E. Li, G. Li, L. Li, Z. Li, J. Li, Y. Li, Z. Lin, D. Lin, X. Liu, J. Liu, Y. Liu, T. Liu, C. Liu, Z. Liu, D. Liu, A. Liu, A. Loarte-Prieto, L. Lodestro, N. Logan, J. Lohr, B. Lombardo, J. Lore, Q. Luan, T. Luce, T. Luda Di Cortemiglia, N. Luhmann, R. Lunsford, Z. Luo, A. Lvovskiy, B. Lyons, X. Ma, M. Madruga, B. Madsen, C. Maggi, K. Maheshwari, A. Mail, J. Mailloux, R. Maingi, M. Major, M. Makowski, R. Manchanda, C. Marini, A. Marinoni, A. Maris, T. Markovic, L. Marrelli, E. Martin, J. Mateja, G. Matsunaga, R. Maurizio, P. Mauzey, D. Mauzey, G. Mcardle, J. Mcclenaghan, K. Mccollam, C. Mcdevitt, K. Mckay, G. Mckee, A. Mclean, V. Mehta, E. Meier, J. Menard, O. Meneghini, G. Merlo, S. Messer, W. Meyer, C. Michael, C. Michoski, P. Milne, G. Minet, A. Misleh, Y. Mitrishkin, C. Moeller, K. Montes, M. Morales, S. Mordijck, D. Moreau, S. Morosohk, P. Morris, L. Morton, A. Moser, R. Moyer, C. Moynihan, T. Mrazkova, D. Mueller, S. Munaretto, J. Munoz Burgos, C. Murphy, K. Murphy, C. Muscatello, C. Myers, A. Nagy, G. Nandipati, M. Navarro, F. Nave, G. Navratil, R. Nazikian, A. Neff, G. Neilson, T. Neiser, W. Neiswanger, D. Nelson, A. Nelson, F. Nespoli, R. Nguyen, L. Nguyen, X. Nguyen, J. Nichols, M. Nocente, S. Nogami, S. Noraky, N. Norausky, M. Nornberg, R. Nygren, T. Odstrcil, D. Ogas, T. Ogorman, S. Ohdachi, Y. Ohtani, M. Okabayashi, M. Okamoto, L. Olavson, E. Olofsson, M. Omullane, R. Oneill, D. Orlov, W. Orvis, T. Osborne, D. Pace, G. Paganini Canal, A. Pajares Martinez, L. Palacios, C. Pan, Q. Pan, R. Pandit, M. Pandya, A. Pankin, Y. Park, J. Park, S. Parker, P. Parks, M. Parsons, B. Patel, C. Pawley, C. Paz-Soldan, W. Peebles, S. Pelton, R. Perillo, C. Petty, Y. Peysson, D. Pierce, A. Pigarov, L. Pigatto, D. Piglowski, S. Pinches, R. Pinsker, P. Piovesan, N. Piper, A. Pironti, R. Pitts, J. Pizzo, U. Plank, M. Podesta, E. Poli, F. Poli, D. Ponce, Z. Popovic, M. Porkolab, G. Porter, C. Powers, S. Powers, R. Prater, Q. Pratt, I. Pusztai, J. Qian, X. Qin, O. Ra, T. Rafiq, T. Raines, R. Raman, J. Rauch, A. Raymond, C. Rea, M. Reich, A. Reiman, S. Reinhold, M. Reinke, R. Reksoatmodjo, Q. Ren, Y. Ren, J. Ren, M. Rensink, J. Renteria, T. Rhodes, J. Rice, R. Roberts, J. Robinson, P. Rodriguez Fernandez, T. Rognlien, A. Rosenthal, S. Rosiello, J. Rost, J. Roveto, W. Rowan, R. Rozenblat, J. Ruane, D. Rudakov, J. Ruiz Ruiz, R. Rupani, S. Saarelma, S. Sabbagh, J. Sachdev, J. Saenz, S. Saib, M. Salewski, A. Salmi, B. Sammuli, C. Samuell, A. Sandorfi, C. Sang, J. Sarff, O. Sauter, K. Schaubel, L. Schmitz, O. Schmitz, J. Schneider, P. Schroeder, K. Schultz, E. Schuster, J. Schwartz, F. Sciortino, F. Scotti, J. Scoville, A. Seltzman, S. Seol, I. Sfiligoi, M. Shafer, S. Sharapov, H. Shen, Z. Sheng, T. Shepard, S. Shi, Y. Shibata, G. Shin, D. Shiraki, R. Shousha, H. Si, P. Simmerling, G. Sinclair, J. Sinha, P. Sinha, G. Sips, T. Sizyuk, C. Skinner, A. Sladkomedova, T. Slendebroek, J. Slief, R. Smirnov, J. Smith, S. Smith, D. Smith, J. Snipes, G. Snoep, A. Snyder, P. Snyder, E. Solano, W. Solomon, J. Song, A. Sontag, V. Soukhanovskii, J. Spendlove, D. Spong, J. Squire, C. Srinivasan, W. Stacey, G. Staebler, L. Stagner, T. Stange, P. Stangeby, R. Stefan, R. Stemprok, D. Stephan, J. Stillerman, T. Stoltzfus-Dueck, W. Stonecipher, S. Storment, E. Strait, D. Su, L. Sugiyama, Y. Sun, P. Sun, Z. Sun, A. Sun, D. Sundstrom, C. Sung, J. Sungcoco, W. Suttrop, Y. Suzuki, T. Suzuki, A. Svyatkovskiy, C. Swee, R. Sweeney, C. Sweetnam, G. Szepesi, M. Takechi, T. Tala, K. Tanaka, X. Tang, S. Tang, Y. Tao, R. Tao, D. Taussig, T. Taylor, K. Teixeira, K. Teo, A. Theodorsen, D. Thomas, K. Thome, A. Thorman, A. Thornton, A. Ti, M. Tillack, N. Timchenko, R. Tinguely, R. Tompkins, J. Tooker, A. Torrezan De Sousa, G. Trevisan, S. Tripathi, A. Trujillo Ochoa, D. Truong, C. Tsui, F. Turco, A. Turnbull, M. Umansky, E. Unterberg, P. Vaezi, P. Vail, J. Valdez, W. Valkis, B. Van Compernolle, J. Van Galen, R. Van Kampen, M. Van Zeeland, G. Verdoolaege, N. Vianello, B. Victor, E. Viezzer, S. Vincena, M. Wade, F. Waelbroeck, J. Wai, T. Wakatsuki, M. Walker, G. Wallace, R. Waltz, W. Wampler, L. Wang, H. Wang, Y. Wang, Z. Wang, G. Wang, S. Ward, M. Watkins, J. Watkins, W. Wehner, Y. Wei, M. Weiland, D. Weisberg, A. Welander, A. White, R. White, S. Wiesen, R. Wilcox, T. Wilks, M. Willensdorfer, H. Wilson, A. Wingen, M. Wolde, M. Wolff, K. Woller, A. Wolz, H. Wong, S. Woodruff, M. Wu, Y. Wu, S. Wukitch, G. Wurden, W. Xiao, R. Xie, Z. Xing, X. Xu, C. Xu, G. Xu, Z. Yan, X. Yang, S. Yang, T. Yokoyama, R. Yoneda, M. Yoshida, K. You, T. Younkin, J. Yu, M. Yu, G. Yu, Q. Yuan, L. Zaidenberg, L. Zakharov, A. Zamengo, S. Zamperini, M. Zarnstorff, E. Zeger, K. Zeller, L. Zeng, M. Zerbini, L. Zhang, X. Zhang, R. Zhang, B. Zhang, J. Zhang, L. Zhao, B. Zhao, Y. Zheng, L. Zheng, B. Zhu, J. Zhu, Y. Zhu, M. Zsutty, M. Zuin, Fenstermacher, M. 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Minet, G, Misleh, A, Mitrishkin, Y, Moeller, C, Montes, K, Morales, M, Mordijck, S, Moreau, D, Morosohk, S, Morris, P, Morton, L, Moser, A, Moyer, R, Moynihan, C, Mrazkova, T, Mueller, D, Munaretto, S, Burgos, J, Murphy, C, Murphy, K, Muscatello, C, Myers, C, Nagy, A, Nandipati, G, Navarro, M, Nave, F, Navratil, G, Nazikian, R, Neff, A, Neilson, G, Neiser, T, Neiswanger, W, Nelson, D, Nelson, A, Nespoli, F, Nguyen, R, Nguyen, L, Nguyen, X, Nichols, J, Nocente, M, Nogami, S, Noraky, S, Norausky, N, Nornberg, M, Nygren, R, Odstrcil, T, Ogas, D, Ogorman, T, Ohdachi, S, Ohtani, Y, Okabayashi, M, Okamoto, M, Olavson, L, Olofsson, E, Omullane, M, Oneill, R, Orlov, D, Orvis, W, Osborne, T, Pace, D, Canal, G, Martinez, A, Palacios, L, Pan, C, Pan, Q, Pandit, R, Pandya, M, Pankin, A, Park, Y, Park, J, Parker, S, Parks, P, Parsons, M, Patel, B, Pawley, C, Paz-Soldan, C, Peebles, W, Pelton, S, Perillo, R, Petty, C, Peysson, Y, Pierce, D, Pigarov, A, Pigatto, L, Piglowski, D, Pinches, S, Pinsker, R, Piovesan, P, Piper, N, Pironti, A, Pitts, R, Pizzo, J, Plank, U, Podesta, M, Poli, E, Poli, F, Ponce, D, Popovic, Z, Porkolab, M, Porter, G, Powers, C, Powers, S, Prater, R, Pratt, Q, Pusztai, I, Qian, J, Qin, X, Ra, O, Rafiq, T, Raines, T, Raman, R, Rauch, J, Raymond, A, Rea, C, Reich, M, Reiman, A, Reinhold, S, Reinke, M, Reksoatmodjo, R, Ren, Q, Ren, Y, Ren, J, Rensink, M, Renteria, J, Rhodes, T, Rice, J, Roberts, R, Robinson, J, Fernandez, P, Rognlien, T, Rosenthal, A, Rosiello, S, Rost, J, Roveto, J, Rowan, W, Rozenblat, R, Ruane, J, Rudakov, D, Ruiz, J, Rupani, R, Saarelma, S, Sabbagh, S, Sachdev, J, Saenz, J, Saib, S, Salewski, M, Salmi, A, Sammuli, B, Samuell, C, Sandorfi, A, Sang, C, Sarff, J, Sauter, O, Schaubel, K, Schmitz, L, Schmitz, O, Schneider, J, Schroeder, P, Schultz, K, Schuster, E, Schwartz, J, Sciortino, F, Scotti, F, Scoville, J, Seltzman, A, Seol, S, Sfiligoi, I, Shafer, M, Sharapov, S, Shen, H, Sheng, Z, Shepard, T, Shi, S, Shibata, Y, Shin, G, Shiraki, D, Shousha, R, Si, H, Simmerling, P, Sinclair, G, Sinha, J, Sinha, P, Sips, G, Sizyuk, T, Skinner, C, Sladkomedova, A, Slendebroek, T, Slief, J, Smirnov, R, Smith, J, Smith, S, Smith, D, Snipes, J, Snoep, G, Snyder, A, Snyder, P, Solano, E, Solomon, W, Song, J, Sontag, A, Soukhanovskii, V, Spendlove, J, Spong, D, Squire, J, Srinivasan, C, Stacey, W, Staebler, G, Stagner, L, Stange, T, Stangeby, P, Stefan, R, Stemprok, R, Stephan, D, Stillerman, J, Stoltzfus-Dueck, T, Stonecipher, W, Storment, S, Strait, E, Su, D, Sugiyama, L, Sun, Y, Sun, P, Sun, Z, Sun, A, Sundstrom, D, Sung, C, Sungcoco, J, Suttrop, W, Suzuki, Y, Suzuki, T, Svyatkovskiy, A, Swee, C, Sweeney, R, Sweetnam, C, Szepesi, G, Takechi, M, Tala, T, Tanaka, K, Tang, X, Tang, S, Tao, Y, Tao, R, Taussig, D, Taylor, T, Teixeira, K, Teo, K, Theodorsen, A, Thomas, D, Thome, K, Thorman, A, Thornton, A, Ti, A, Tillack, M, Timchenko, N, Tinguely, R, Tompkins, R, Tooker, J, De Sousa, A, Trevisan, G, Tripathi, S, Ochoa, A, Truong, D, Tsui, C, Turco, F, Turnbull, A, Umansky, M, Unterberg, E, Vaezi, P, Vail, P, Valdez, J, Valkis, W, Van Compernolle, B, Van Galen, J, Van Kampen, R, Van Zeeland, M, Verdoolaege, G, Vianello, N, Victor, B, Viezzer, E, Vincena, S, Wade, M, Waelbroeck, F, Wai, J, Wakatsuki, T, Walker, M, Wallace, G, Waltz, R, Wampler, W, Wang, L, Wang, H, Wang, Y, Wang, Z, Wang, G, Ward, S, Watkins, M, Watkins, J, Wehner, W, Wei, Y, Weiland, M, Weisberg, D, Welander, A, White, A, White, R, Wiesen, S, Wilcox, R, Wilks, T, Willensdorfer, M, Wilson, H, Wingen, A, Wolde, M, Wolff, M, Woller, K, Wolz, A, Wong, H, Woodruff, S, Wu, M, Wu, Y, Wukitch, S, Wurden, G, Xiao, W, Xie, R, Xing, Z, Xu, X, Xu, C, Xu, G, Yan, Z, Yang, X, Yang, S, Yokoyama, T, Yoneda, R, Yoshida, M, You, K, Younkin, T, Yu, J, Yu, M, Yu, G, Yuan, Q, Zaidenberg, L, Zakharov, L, Zamengo, A, Zamperini, S, Zarnstorff, M, Zeger, E, Zeller, K, Zeng, L, Zerbini, M, Zhang, L, Zhang, X, Zhang, R, Zhang, B, Zhang, J, Zhao, L, Zhao, B, Zheng, Y, Zheng, L, Zhu, B, Zhu, J, Zhu, Y, Zsutty, M, Zuin, M, Lawrence Livermore National Laboratory, Princeton Plasma Physics Laboratory, Princeton University, General Atomics, Max-Planck-Institut für Plasmaphysik, Imperial College London, National Institute for Fusion Science, Universidade de São Paulo, University of Texas at Austin, ITER, College of William and Mary, University of California Los Angeles, University of California San Diego, Columbia University, Massachusetts Institute of Technology, Oak Ridge National Laboratory, Eindhoven University of Technology, Oak Ridge Associated Universities, West Virginia University, University of Tennessee, Knoxville, National Research Council of Italy, Stony Brook University, Purdue University, University of Seville, University of Science and Technology of China, Carnegie Mellon University, Institute for Plasma Research, Peking University, University of California Davis, University of California Irvine, Commonwealth Fusion Systems, University of Liverpool, University of Illinois at Urbana-Champaign, University of Milan - Bicocca, Georgia Institute of Technology, Southwestern Institute of Physics, University of Toronto, Auburn University, Polytechnic University of Turin, Universidade Lisboa, Association CCFE, KTH Royal Institute of Technology, San Diego State University, Durham University, Lehigh University, Fusion and Plasma Physics, University of Washington, Department of Applied Physics, Sandia National Laboratories, Ghent University, Technical University of Denmark, CEA, University of Colorado Boulder, Harvard University, National Technical University of Athens, Coventry University, University of Stuttgart, Czech Academy of Sciences, Harvey Mudd College, Seoul National University, Donghua University, University of York, Dalian University of Technology, University of California Berkeley, Los Alamos National Laboratory, United States Department of Energy, University of British Columbia, Pacific Northwest National Laboratory, University of Wisconsin, Michigan State University, University of Strathclyde, Pennsylvania State University, Rensselaer Polytechnic Institute, University of Southern California, Chalmers University of Technology, University of Virginia, University of Naples Federico II, University of Oxford, VTT Technical Research Centre of Finland, National Institute of Technology, University of Connecticut, DIFFER, CIEMAT, Hanyang University, Brigham Young University, UiT The Arctic University of Norway, Australian National University, Russian Research Centre Kurchatov Institute, Forschungszentrum Jülich, Zhejiang University, The University of Tokyo, University of Michigan, Agenzia nazionale per le nuove tecnologie, l'energia e lo sviluppo economico sostenibile, Aalto-yliopisto, Aalto University, DIII-D Team, Complex Ionized Media, Elementary Processes in Gas Discharges, Applied Physics and Science Education, Science and Technology of Nuclear Fusion, and Control Systems Technology
Subjects: Nuclear and High Energy Physics, Tokamak, Technology and Engineering, DIII-D, Nuclear engineering, TOKAMAKS, MITIGATION, law.invention, Plasma physics, mitigation, law, plasma physic, tokamak, Physics, Core-edge integration, Basis (linear algebra), plasma physics, core-edge integration, scenarios, Fusion power, Condensed Matter Physics, SCENARIOS, fusion energy, Fusion energy
Abstract: Funding Information: This material is based upon work supported by the US Department of Energy, Office of Science, Office of Fusion Energy Sciences, using the DIII-D National Fusion Facility, a DOE Office of Science user facility, under Awards DE-FC02-04ER54698 and DE-AC52-07NA27344. Publisher Copyright: © 2022 IAEA, Vienna. DIII-D physics research addresses critical challenges for the operation of ITER and the next generation of fusion energy devices. This is done through a focus on innovations to provide solutions for high performance long pulse operation, coupled with fundamental plasma physics understanding and model validation, to drive scenario development by integrating high performance core and boundary plasmas. Substantial increases in off-axis current drive efficiency from an innovative top launch system for EC power, and in pressure broadening for Alfven eigenmode control from a co-/counter-I p steerable off-axis neutral beam, all improve the prospects for optimization of future long pulse/steady state high performance tokamak operation. Fundamental studies into the modes that drive the evolution of the pedestal pressure profile and electron vs ion heat flux validate predictive models of pedestal recovery after ELMs. Understanding the physics mechanisms of ELM control and density pumpout by 3D magnetic perturbation fields leads to confident predictions for ITER and future devices. Validated modeling of high-Z shattered pellet injection for disruption mitigation, runaway electron dissipation, and techniques for disruption prediction and avoidance including machine learning, give confidence in handling disruptivity for future devices. For the non-nuclear phase of ITER, two actuators are identified to lower the L-H threshold power in hydrogen plasmas. With this physics understanding and suite of capabilities, a high poloidal beta optimized-core scenario with an internal transport barrier that projects nearly to Q = 10 in ITER at ∼8 MA was coupled to a detached divertor, and a near super H-mode optimized-pedestal scenario with co-I p beam injection was coupled to a radiative divertor. The hybrid core scenario was achieved directly, without the need for anomalous current diffusion, using off-axis current drive actuators. Also, a controller to assess proximity to stability limits and regulate β N in the ITER baseline scenario, based on plasma response to probing 3D fields, was demonstrated. Finally, innovative tokamak operation using a negative triangularity shape showed many attractive features for future pilot plant operation.
Published: 2022

19. Crowdsourcing as a Tool for Research: Methodological, Fair, and Political Considerations

Author: Qin Zhu, Stephen C. Rea, Benjamin Gilbert, Chuan Yue, and Hanzelle Kleeman
Subjects: Research ethics, business.industry, 05 social sciences, General Engineering, 020207 software engineering, 02 engineering and technology, Crowdsourcing, Politics, 0202 electrical engineering, electronic engineering, information engineering, 0501 psychology and cognitive sciences, Engineering ethics, Sociology, business, 050107 human factors, Social Sciences (miscellaneous), Ethics of technology
Abstract: Crowdsourcing platforms are powerful tools for academic researchers. Proponents claim that crowdsourcing helps researchers quickly and affordably recruit enough human subjects with diverse backgrounds to generate significant statistical power, while critics raise concerns about unreliable data quality, labor exploitation, and unequal power dynamics between researchers and workers. We examine these concerns along three dimensions: methods, fairness, and politics. We find that researchers offer vastly different compensation rates for crowdsourced tasks, and address potential concerns about data validity by using platform-specific tools and user verification methods. Additionally, workers depend upon crowdsourcing platforms for a significant portion of their income, are motivated more by fear of losing access to work than by specific compensation rates, and are frustrated by a lack of transparency and occasional unfair treatment from job requesters. Finally, we discuss critical computing scholars’ proposals to address crowdsourcing’s problems, challenges with implementing these resolutions, and potential avenues for future research.
Published: 2020

20. The synthesis of xyloglucan, an abundant plant cell wall polysaccharide, requires CSLC function

Author: Anne C. Rea, Sang Jin Kim, Kenneth Keegstra, Linda Danhof, Federica Brandizzi, Starla Zemelis-Durfee, Markus Pauly, Zachary S. Shepard, Balakumaran Chandrasekar, and Nicholas Thrower
Subjects: 0106 biological sciences, 0301 basic medicine, CSLC, Mutant, Arabidopsis, Plant Biology, 01 natural sciences, Gene Expression Regulation, Enzymologic, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, xyloglucan, Cell Wall, Gene Expression Regulation, Plant, Plant Cells, Glucans, Gene, Phylogeny, Multidisciplinary, biology, Arabidopsis Proteins, Biological Sciences, biology.organism_classification, glucan synthase, Phenotype, Reverse genetics, Xyloglucan, 030104 developmental biology, chemistry, Biochemistry, Glucosyltransferases, Mutation, Xylans, Function (biology), 010606 plant biology & botany
Abstract: Significance Plant cells have a polysaccharide-based wall that maintains their structural and functional integrity and determines their shape. Reorganization of wall components is required to allow growth and differentiation. One matrix polysaccharide that is postulated to play an important role in this reorganization is xyloglucan (XyG). While the structure of XyG is well understood, its biosynthesis is not. Through genetic studies with Arabidopsis CSLC genes, we demonstrate that they are responsible for the synthesis of the XyG glucan backbone. A quintuple cslc mutant is able to grow and develop normally but lacks detectable XyG. These results raise important questions regarding cell wall structure and its reorganization during growth. The series of cslc mutants will be valuable tools for investigating these questions., Xyloglucan (XyG) is an abundant component of the primary cell walls of most plants. While the structure of XyG has been well studied, much remains to be learned about its biosynthesis. Here we employed reverse genetics to investigate the role of Arabidopsis cellulose synthase like-C (CSLC) proteins in XyG biosynthesis. We found that single mutants containing a T-DNA in each of the five Arabidopsis CSLC genes had normal levels of XyG. However, higher-order cslc mutants had significantly reduced XyG levels, and a mutant with disruptions in all five CSLC genes had no detectable XyG. The higher-order mutants grew with mild tissue-specific phenotypes. Despite the apparent lack of XyG, the cslc quintuple mutant did not display significant alteration of gene expression at the whole-genome level, excluding transcriptional compensation. The quintuple mutant could be complemented by each of the five CSLC genes, supporting the conclusion that each of them encodes a XyG glucan synthase. Phylogenetic analyses indicated that the CSLC genes are widespread in the plant kingdom and evolved from an ancient family. These results establish the role of the CSLC genes in XyG biosynthesis, and the mutants described here provide valuable tools with which to study both the molecular details of XyG biosynthesis and the role of XyG in plant cell wall structure and function.
Published: 2020

21. Search for High-energy Neutrino Emission from Galactic X-Ray Binaries with IceCube

Author: R. Abbasi, M. Ackermann, J. Adams, J. A. Aguilar, M. Ahlers, M. Ahrens, J. M. Alameddine, A. A. Alves, N. M. Amin, K. Andeen, T. Anderson, G. Anton, C. Argüelles, Y. Ashida, S. Axani, X. Bai, A. Balagopal V., S. W. Barwick, B. Bastian, V. Basu, S. Baur, R. Bay, J. J. Beatty, K.-H. Becker, J. Becker Tjus, J. Beise, C. Bellenghi, S. Benda, S. BenZvi, D. Berley, E. Bernardini, D. Z. Besson, G. Binder, D. Bindig, E. Blaufuss, S. Blot, M. Boddenberg, F. Bontempo, J. Borowka, S. Böser, O. Botner, J. Böttcher, E. Bourbeau, F. Bradascio, J. Braun, B. Brinson, S. Bron, J. Brostean-Kaiser, S. Browne, A. Burgman, R. T. Burley, R. S. Busse, M. A. Campana, E. G. Carnie-Bronca, C. Chen, Z. Chen, D. Chirkin, K. Choi, B. A. Clark, K. Clark, L. Classen, A. Coleman, G. H. Collin, J. M. Conrad, P. Coppin, P. Correa, D. F. Cowen, R. Cross, C. Dappen, P. Dave, C. De Clercq, J. J. DeLaunay, D. Delgado López, H. Dembinski, K. Deoskar, A. Desai, P. Desiati, K. D. de Vries, G. de Wasseige, M. de With, T. DeYoung, A. Diaz, J. C. Díaz-Vélez, M. Dittmer, H. Dujmovic, M. Dunkman, M. A. DuVernois, T. Ehrhardt, P. Eller, R. Engel, H. Erpenbeck, J. Evans, P. A. Evenson, K. L. Fan, A. R. Fazely, A. Fedynitch, N. Feigl, S. Fiedlschuster, A. T. Fienberg, C. Finley, L. Fischer, D. Fox, A. Franckowiak, E. Friedman, A. Fritz, P. Fürst, T. K. Gaisser, J. Gallagher, E. Ganster, A. Garcia, S. Garrappa, L. Gerhardt, A. Ghadimi, C. Glaser, T. Glauch, T. Glüsenkamp, J. G. Gonzalez, S. Goswami, D. Grant, T. Grégoire, S. Griswold, C. Günther, P. Gutjahr, C. Haack, A. Hallgren, R. Halliday, L. Halve, F. Halzen, M. Ha Minh, K. Hanson, J. Hardin, A. A. Harnisch, A. Haungs, D. Hebecker, K. Helbing, F. Henningsen, E. C. Hettinger, S. Hickford, J. Hignight, C. Hill, G. C. Hill, K. D. Hoffman, R. Hoffmann, K. Hoshina, F. Huang, M. Huber, T. Huber, K. Hultqvist, M. Hünnefeld, R. Hussain, K. Hymon, S. In, N. Iovine, A. Ishihara, M. Jansson, G. S. Japaridze, M. Jeong, M. Jin, B. J. P. Jones, D. Kang, W. Kang, X. Kang, A. Kappes, D. Kappesser, L. Kardum, T. Karg, M. Karl, A. Karle, U. Katz, M. Kauer, M. Kellermann, J. L. Kelley, A. Kheirandish, K. Kin, T. Kintscher, J. Kiryluk, S. R. Klein, A. Kochocki, R. Koirala, H. Kolanoski, T. Kontrimas, L. Köpke, C. Kopper, S. Kopper, D. J. Koskinen, P. Koundal, M. Kovacevich, M. Kowalski, T. Kozynets, E. Krupczak, E. Kun, N. Kurahashi, N. Lad, C. Lagunas Gualda, J. L. Lanfranchi, M. J. Larson, F. Lauber, J. P. Lazar, J. W. Lee, K. Leonard, A. Leszczyńska, Y. Li, M. Lincetto, Q. R. Liu, M. Liubarska, E. Lohfink, C. J. Lozano Mariscal, L. Lu, F. Lucarelli, A. Ludwig, W. Luszczak, Y. Lyu, W. Y. Ma, J. Madsen, K. B. M. Mahn, Y. Makino, S. Mancina, I. C. Mariş, I. Martinez-Soler, R. Maruyama, S. McCarthy, T. McElroy, F. McNally, J. V. Mead, K. Meagher, S. Mechbal, A. Medina, M. Meier, S. Meighen-Berger, J. Micallef, D. Mockler, T. Montaruli, R. W. Moore, R. Morse, M. Moulai, R. Naab, R. Nagai, U. Naumann, J. Necker, L. V. Nguyễn, H. Niederhausen, M. U. Nisa, S. C. Nowicki, A. Obertacke Pollmann, M. Oehler, B. Oeyen, A. Olivas, E. O’Sullivan, H. Pandya, D. V. Pankova, N. Park, G. K. Parker, E. N. Paudel, L. Paul, C. Pérez de los Heros, L. Peters, J. Peterson, S. Philippen, S. Pieper, M. Pittermann, A. Pizzuto, M. Plum, Y. Popovych, A. Porcelli, M. Prado Rodriguez, B. Pries, G. T. Przybylski, C. Raab, J. Rack-Helleis, A. Raissi, M. Rameez, K. Rawlins, I. C. Rea, Z. Rechav, A. Rehman, P. Reichherzer, R. Reimann, G. Renzi, E. Resconi, S. Reusch, W. Rhode, M. Richman, B. Riedel, E. J. Roberts, S. Robertson, G. Roellinghoff, M. Rongen, C. Rott, T. Ruhe, D. Ryckbosch, D. Rysewyk Cantu, I. Safa, J. Saffer, S. E. Sanchez Herrera, A. Sandrock, M. Santander, S. Sarkar, K. Satalecka, M. Schaufel, H. Schieler, S. Schindler, T. Schmidt, A. Schneider, J. Schneider, F. G. Schröder, L. Schumacher, G. Schwefer, S. Sclafani, D. Seckel, S. Seunarine, A. Sharma, S. Shefali, N. Shimizu, M. Silva, B. Skrzypek, B. Smithers, R. Snihur, J. Soedingrekso, D. Soldin, C. Spannfellner, G. M. Spiczak, C. Spiering, J. Stachurska, M. Stamatikos, T. Stanev, R. Stein, J. Stettner, T. Stezelberger, T. Stürwald, T. Stuttard, G. W. Sullivan, I. Taboada, S. Ter-Antonyan, J. Thwaites, S. Tilav, F. Tischbein, K. Tollefson, C. Tönnis, S. Toscano, D. Tosi, A. Trettin, M. Tselengidou, C. F. Tung, A. Turcati, R. Turcotte, C. F. Turley, J. P. Twagirayezu, B. Ty, M. A. Unland Elorrieta, N. Valtonen-Mattila, J. Vandenbroucke, N. van Eijndhoven, D. Vannerom, J. van Santen, J. Veitch-Michaelis, S. Verpoest, C. Walck, W. Wang, T. B. Watson, C. Weaver, P. Weigel, A. Weindl, M. J. Weiss, J. Weldert, C. Wendt, J. Werthebach, M. Weyrauch, N. Whitehorn, C. H. Wiebusch, N. Willey, D. R. Williams, M. Wolf, G. Wrede, J. Wulff, X. W. Xu, J. P. Yanez, E. Yildizci, S. Yoshida, S. Yu, T. Yuan, Z. Zhang, P. Zhelnin, Vriendenkring VUB, Elementary Particle Physics, and Physics
Subjects: interaction [cosmic radiation], pole, 330, High-Energy Phenomena and Fundamental Physics, cosmic radiation: interaction, neutrino: flux, MICROQUASAR, IceCube, Subatomär fysik, star, Astronomi, astrofysik och kosmologi, Subatomic Physics, site, ABSORPTION, Astronomy, Astrophysics and Cosmology, binary [X-ray], detector [neutrino], neutrino: potential, astro-ph.HE, High Energy Astrophysical Phenomena (astro-ph.HE), Physics, CATALOG, ddc, neutrino: detector, LIGHT, acceleration [cosmic radiation], X-ray: binary, Astrophysics - High Energy Astrophysical Phenomena, FLUX, Astrophysics::High Energy Astrophysical Phenomena, FOS: Physical sciences, Astrophysics::Cosmology and Extragalactic Astrophysics, gas, quasar, ddc:530, cosmic radiation: acceleration, Astrophysics::Galaxy Astrophysics, ANTARES, CONSTRAINTS, Astronomy and Astrophysics, flux [neutrino], sensitivity, GALAXY, Physics and Astronomy, Space and Planetary Science, atmosphere, JETS, ddc:520, time dependence, galaxy, potential [neutrino]
Abstract: The astrophysical journal / 2 930, L24 (2022). doi:10.3847/2041-8213/ac67d8, We present the first comprehensive search for high-energy neutrino emission from high- and low-mass X-ray binaries conducted by IceCube. Galactic X-ray binaries are long-standing candidates for the source of Galactic hadronic cosmic rays and neutrinos. The compact object in these systems can be the site of cosmic-ray acceleration, and neutrinos can be produced by interactions of cosmic rays with radiation or gas, in the jet of a microquasar, in the stellar wind, or in the atmosphere of the companion star. We study X-ray binaries using 7.5 yr of IceCube data with three separate analyses. In the first, we search for periodic neutrino emission from 55 binaries in the Northern Sky with known orbital periods. In the second, the X-ray light curves of 102 binaries across the entire sky are used as templates to search for time-dependent neutrino emission. Finally, we search for time-integrated emission of neutrinos for a list of 4 notable binaries identified as microquasars. In the absence of a significant excess, we place upper limits on the neutrino flux for each hypothesis and compare our results with theoretical predictions for several binaries. In addition, we evaluate the sensitivity of the next generation neutrino telescope at the South Pole, IceCube-Gen2, and demonstrate its power to identify potential neutrino emission from these binary sources in the Galaxy., Published by Institute of Physics Publ., London
Published: 2022

22. Continuous positive airway pressure and adverse cardiovascular events in obstructive sleep apnea: are participants of randomized trials representative of sleep clinic patients?

Author: Chi-Hang Lee, Ulysses J. Magalang, Peter R. Eastwood, Jennifer H. Walsh, David R. Hillman, Diego R. Mazzotti, Bhajan Singh, Ayesha Reynor, Brendan T. Keenan, Allan I. Pack, Bindiya Shenoy, Siobhan C Rea, Greg Maislin, Ivan T Ling, Satvinder S. Dhaliwal, Kathleen J. Maddison, and Nigel McArdle
Subjects: Adult, Male, medicine.medical_specialty, medicine.medical_treatment, Polysomnography, law.invention, Hypoxemia, Randomized controlled trial, law, Physiology (medical), Internal medicine, Humans, Medicine, Continuous positive airway pressure, Randomized Controlled Trials as Topic, Sleep Apnea, Obstructive, Continuous Positive Airway Pressure, medicine.diagnostic_test, business.industry, medicine.disease, nervous system diseases, respiratory tract diseases, Obstructive sleep apnea, Apnea–hypopnea index, Cardiovascular Diseases, Propensity score matching, Female, Observational study, Neurology (clinical), medicine.symptom, business
Abstract: Study Objectives Randomized controlled trials (RCTs) have shown no reduction in adverse cardiovascular (CV) events in patients randomized to continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea (OSA). This study examined whether randomized study populations were representative of OSA patients attending a sleep clinic. Methods Sleep clinic patients were 3,965 consecutive adults diagnosed with OSA by in-laboratory polysomnography from 2006 to 2010 at a tertiary hospital sleep clinic. Characteristics of these patients were compared with participants of five recent RCTs examining the effect of CPAP on adverse CV events in OSA. The percentage of patients with severe (apnea-hypopnea index, [AHI] ≥ 30 events/h) or any OSA (AHI ≥ 5 events/h) who met the eligibility criteria of each RCT was determined, and those criteria that excluded the most patients identified. Results Compared to RCT participants, sleep clinic OSA patients were younger, sleepier, more likely to be female and less likely to have established CV disease. The percentage of patients with severe or any OSA who met the RCT eligibility criteria ranged from 1.2% to 20.9% and 0.8% to 21.9%, respectively. The eligibility criteria that excluded most patients were preexisting CV disease, symptoms of excessive sleepiness, nocturnal hypoxemia and co-morbidities. Conclusions A minority of sleep clinic patients diagnosed with OSA meet the eligibility criteria of RCTs of CPAP on adverse CV events in OSA. OSA populations in these RCTs differ considerably from typical sleep clinic OSA patients. This suggests that the findings of such OSA treatment-related RCTs are not generalizable to sleep clinic OSA patients. Randomized Intervention with Continuous Positive Airway Pressure in CAD and OSA (RICCADSA) trial, https://clinicaltrials.gov/ct2/show/NCT00519597, ClinicalTrials.gov number, NCT00519597. Usefulness of Nasal Continuous Positive Airway Pressure (CPAP) Treatment in Patients with a First Ever Stroke and Sleep Apnea Syndrome, https://clinicaltrials.gov/ct2/show/NCT00202501, ClinicalTrials.gov number, NCT00202501. Effect of Continuous Positive Airway Pressure (CPAP) on Hypertension and Cardiovascular Morbidity-Mortality in Patients with Sleep Apnea and no Daytime Sleepiness, https://clinicaltrials.gov/ct2/show/NCT00127348, ClinicalTrials.gov number, NCT00127348. Continuous Positive Airway Pressure (CPAP) in Patients with Acute Coronary Syndrome and Obstructive Sleep Apnea (OSA) (ISAACC), https://clinicaltrials.gov/ct2/show/NCT01335087, ClinicalTrials.gov number, NCT01335087.
Published: 2021

23. Nisin in Combination with Cinnamaldehyde and EDTA to Control Growth of Escherichia coli Strains of Swine Origin

Author: Des Field, Inès Baghou, Mary C. Rea, Gillian E. Gardiner, R. Paul Ross, and Colin Hill
Subjects: antimicrobial resistance, antibiotics, antimicrobial peptide, enterotoxigenic E. coli, nisin, bacteriocin, essential oil, cinnamaldehyde, EDTA, Therapeutics. Pharmacology, RM1-950
Abstract: Post-weaning diarrhoea (PWD) due to enterotoxigenic Escherichia coli (ETEC) is an economically important disease in pig production worldwide. Although antibiotics have contributed significantly to mitigate the economic losses caused by PWD, there is major concern over the increased incidence of antimicrobial resistance among bacteria isolated from pigs. Consequently, suitable alternatives that are safe and effective are urgently required. Many naturally occurring compounds, including the antimicrobial peptide nisin and a number of plant essential oils, have been widely studied and are reported to be effective as antimicrobial agents against pathogenic microorganisms. Here, we evaluate the potential of nisin in combination with the essential oil cinnamaldehyde and ethylenediaminetetraacetic acid (EDTA) to control the growth of E. coli strains of swine origin including two characterized as ETEC. The results reveal that the use of nisin (10 μM) with low concentrations of trans-cinnamaldehyde (125 μg/mL) and EDTA (0.25–2%) resulted in extended lag phases of growth compared to when either antimicrobial is used alone. Further analysis through kill curves revealed that an approximate 1-log reduction in E. coli cell counts was observed against the majority of targets tested following 3 h incubation. These results highlight the potential benefits of combining the natural antimicrobial nisin with trans-cinnamaldehyde and EDTA as a new approach for the inhibition of E. coli strains of swine origin.
Published: 2017
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24. Free-water imaging of the cholinergic basal forebrain and pedunculopontine nucleus in Parkinson's disease

Author: Nicola J Ray, Rachael A Lawson, Sarah L Martin, Hilmar P Sigurdsson, Joanna Wilson, Brook Galna, Sue Lord, Lisa Alcock, Gordon W Duncan, Tien K Khoo, John T O’Brien, David J Burn, John-Paul Taylor, River C Rea, Maurizio Bergamino, Lynn Rochester, and Alison J Yarnall
Subjects: Neurology (clinical)
Abstract: Free-water imaging can predict and monitor dopamine system degeneration in people with Parkinson’s disease. It can also enhance the sensitivity of traditional diffusion tensor imaging (DTI) metrics for indexing neurodegeneration. However, these tools are yet to be applied to investigate cholinergic system degeneration in Parkinson’s disease, which involves both the pedunculopontine nucleus and cholinergic basal forebrain. Free-water imaging, free-water-corrected DTI and volumetry were used to extract structural metrics from the cholinergic basal forebrain and pedunculopontine nucleus in 99 people with Parkinson’s disease and 46 age-matched controls. Cognitive ability was tracked over 4.5 years. Pearson’s partial correlations revealed that free-water-corrected DTI metrics in the pedunculopontine nucleus were associated with performance on cognitive tasks that required participants to make rapid choices (behavioural flexibility). Volumetric, free-water content and DTI metrics in the cholinergic basal forebrain were elevated in a sub-group of people with Parkinson’s disease with evidence of cognitive impairment, and linear mixed modelling revealed that these metrics were differently associated with current and future changes to cognition. Free water and free-water-corrected DTI can index cholinergic degeneration that could enable stratification of patients in clinical trials of cholinergic interventions for cognitive decline. In addition, degeneration of the pedunculopontine nucleus impairs behavioural flexibility in Parkinson’s disease, which may explain this region’s role in increased risk of falls.
Published: 2021

25. Identification of ADS024, a newly characterized strain of Bacillus velezensis with direct Clostridiodes difficile killing and toxin degradation bio-activities

Author: Michelle M, O'Donnell, James W, Hegarty, Brian, Healy, Sarah, Schulz, Calum J, Walsh, Colin, Hill, R Paul, Ross, Mary C, Rea, Ronald, Farquhar, and Laurent, Chesnel
Subjects: Clostridioides difficile, Clostridium Infections, Humans, Bacillus, Anti-Bacterial Agents, Peptide Hydrolases
Abstract: Clostridioides difficile infection (CDI) remains a significant health threat worldwide. C. difficile is an opportunistic, toxigenic pathogen that takes advantage of a disrupted gut microbiome to grow and produce signs and symptoms ranging from diarrhea to pseudomembranous colitis. Antibiotics used to treat C. difficile infection are usually broad spectrum and can further disrupt the commensal gut microbiota, leaving patients susceptible to recurrent C. difficile infection. There is a growing need for therapeutic options that can continue to inhibit the outgrowth of C. difficile after antibiotic treatment is completed. Treatments that degrade C. difficile toxins while having minimal collateral impact on gut bacteria are also needed to prevent recurrence. Therapeutic bacteria capable of producing a range of antimicrobial compounds, proteases, and other bioactive metabolites represent a potentially powerful tool for preventing CDI recurrence following resolution of symptoms. Here, we describe the identification and initial characterization of ADS024 (formerly ART24), a novel therapeutic bacterium that can kill C. difficile in vitro with limited impact on other commensal bacteria. In addition to directly killing C. difficile, ADS024 also produces proteases capable of degrading C. difficile toxins, the drivers of symptoms associated with most cases of CDI. ADS024 is in clinical development for the prevention of CDI recurrence as a single-strain live biotherapeutic product, and this initial data set supports further studies aimed at evaluating ADS024 in future human clinical trials.
Published: 2021

26. Seagrass spatial data synthesis from north‐east Australia, Torres Strait and Gulf of Carpentaria, 1983 to 2022

Author: A Carter, S McKenna, MA Rasheed, H Taylor, C van deWetering, K Chartrand, C Reason, C Collier, L Shepherd, J Mellors, L McKenzie, NC Duke, A Roelofs, N Smit, R Groom, D Barrett, S Evans, R Pitcher, N Murphy, M Carlisle, M David, S Lui, Torres Strait Indigenous Rangers, and RG Coles
Subjects: Oceanography, GC1-1581
Abstract: Abstract The Gulf of Carpentaria and Torres Strait in north‐eastern Australia support globally significant seagrass ecosystems that underpin fishing and cultural heritage of the region. Reliable data on seagrass distribution are critical to understanding how these ecosystems are changing, while managing for resilience. Spatial data on seagrass have been collected since the early 1980s, but the early data were poorly curated. Some was not publicly available, and some already lost. We validated and synthesized historical seagrass spatial data to create a publicly available database. We include a site layer of 48,612 geolocated data points including information on seagrass presence/absence, sediment, collection date, and data custodian. We include a polygon layer with 641 individual seagrass meadows. Thirteen seagrass species are identified in depths ranging from intertidal to 38 m below mean sea level. Our synthesis includes scientific survey data from 1983 to 2022 and provides an important evidence base for marine resource management.
Published: 2024
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27. Impact of nisin on Clostridioides difficile and microbiota composition in a faecal fermentation model of the human colon

Author: R. Paul Ross, Paula M. O'Connor, Colin Hill, Mary C. Rea, Orla O'Sullivan, and Catherine O’Reilly
Subjects: Risk, Diarrhea, Intestinal microbiota, Bacteriocin, Colon, medicine.disease_cause, Applied Microbiology and Biotechnology, Microbiology, Minimum inhibitory concentration, chemistry.chemical_compound, Feces, Antibiotics, Pregnancy, Escherichia, RNA, Ribosomal, 16S, polycyclic compounds, medicine, Humans, Shigella, Nisin, Diversity, biology, Clostridioides difficile, food and beverages, General Medicine, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Gastrointestinal Microbiome, chemistry, Therapies, Fermentation, Clostridium Infections, bacteria, Bacteroides, Narrow-spectrum, Infection, Bacteria, Biotechnology
Abstract: Aims: Nisin is a bacteriocin with a broad spectrum of activity against Gram-positive bacteria. The aims were to assess nisin activity against Clostridioides difficile in a complex microbial environment and determine the minimum inhibitory concentration at which C. difficile growth is suppressed whilst having minimal impact on the faecal microbiota. Methods and Results: Faecal slurries were prepared from fresh faecal samples and spiked with C. difficile (10(6) CFU per ml). Nisin was added to each fermentation at a range of concentrations from 0 to 500 mu M. Following 24 h, 16S rRNA gene sequencing was performed, and the presence of viable C. difficile was assessed. There was no viable C. difficile detected in the presence of 50-500 mu M nisin. There was a decrease in the diversity of the microbiota in a nisin dose-dependent manner. Nisin predominantly depleted the relative abundance of the Gram-positive bacteria whilst the relative abundance of Gram-negative bacteria such as Escherichia Shigella and Bacteroides increased. Conclusions: Using an ex vivo model of the colon, this study demonstrates the ability of purified nisin to selectively deplete C. difficile in a faecal microbial environment and establishes the minimum concentration at which this occurs whilst having a minimal impact on the composition of the microbiota. Significance and Impact of the Study: This study opens up the potential to use nisin as a therapeutic for clostridial gut infections.
Published: 2021

28. Quantitative EEG and cholinergic basal forebrain atrophy in Parkinson's disease and mild cognitive impairment

Author: David J. Wright, Sarah L Martin, River C. Rea, Chesney E. Craig, Paul S. Holmes, Rok Berlot, Jurij Bon, Nicola J. Ray, and Zvezdan Pirtošek
Subjects: Male, 0301 basic medicine, Aging, medicine.medical_specialty, Parkinson's disease, Basal Forebrain, Electroencephalography, Nucleus basalis, 03 medical and health sciences, 0302 clinical medicine, Atrophy, Internal medicine, mental disorders, medicine, Humans, Dementia, Cognitive Dysfunction, Aged, Basal forebrain, Lewy body, medicine.diagnostic_test, business.industry, General Neuroscience, Parkinson Disease, Organ Size, Middle Aged, medicine.disease, Magnetic Resonance Imaging, Cholinergic Neurons, 030104 developmental biology, Endocrinology, Cholinergic, Female, Neurology (clinical), Geriatrics and Gerontology, business, 030217 neurology & neurosurgery, Developmental Biology
Abstract: Cholinergic degeneration is a key feature of dementia in neurodegenerative conditions including Alzheimer's disease (AD) and Parkinson's disease (PD). Quantitative electro-encephalography (EEG) metrics are altered in both conditions from early stages, and recent research in people with Lewy body and AD dementia suggests these changes may be associated with atrophy in cholinergic basal forebrain nuclei (cBF). To determine if these relationships exist in predementia stages of neurodegenerative conditions, we studied resting-state EEG and in vivo cBF volumes in 31 people with PD (without dementia), 21 people with mild cognitive impairment (MCI), and 21 age-matched controls. People with PD showed increased power in slower frequencies and reduced alpha reactivity compared to controls. Volumes of cholinergic cell clusters corresponding to the medial septum and vertical and horizontal limb of the diagonal band, and the posterior nucleus basalis of Meynert, correlated positively with; alpha reactivity in people with PD (p< 0.01); and pre-alpha power in people with MCI (p< 0.05). These results suggest that alpha reactivity and pre-alpha power are related to changes in cBF volumes in MCI and PD without dementia.
Published: 2021

29. Chronotopes and Social Types in South Korean Digital Gaming

Author: Stephen C. Rea
Subjects: 060201 languages & linguistics, Cultural Studies, Linguistics and Language, 060101 anthropology, Visual Arts and Performing Arts, Communication, 05 social sciences, Perspective (graphical), Media studies, 06 humanities and the arts, Language and Linguistics, 0602 languages and literature, 0601 history and archaeology, Sociology, Chronotope
Abstract: This article examines a South Korean cultural chronotope from the perspective of Korea’s world-renowned digital gaming culture, including its professional electronic sports (e-sports) scene...
Published: 2019

30. Nisin variants from Streptococcus and Staphylococcus successfully express in NZ9800

Author: Des Field, Paula M. O'Connor, Julie N O'Sullivan, R.P. Ross, Mary C. Rea, and Colin Hill
Subjects: Staphylococcus, medicine.disease_cause, Applied Microbiology and Biotechnology, Microbiology, Streptococcus agalactiae, 03 medical and health sciences, chemistry.chemical_compound, Bacteriocin, Bacteriocins, polycyclic compounds, medicine, Nisin, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Lactococcus lactis, Structural gene, food and beverages, Streptococcus, General Medicine, biochemical phenomena, metabolism, and nutrition, Lantibiotics, biology.organism_classification, Genetically modified organism, Staphylococcus capitis, Anti-Bacterial Agents, chemistry, bacteria, lipids (amino acids, peptides, and proteins), Biotechnology
Abstract: AIMS Increases in antimicrobial resistance have meant that the antimicrobial potential of lantibiotics is now being investigated irrespective of the nature of the producing organism. The aim of this study was to investigate whether natural nisin variants produced by non-Generally Recognized as Safe (GRAS) strains, such as nisin H, nisin J and nisin P, could be expressed in a well-characterized GRAS host. METHODS AND RESULTS This study involved cloning the nisin A promoter and leader sequence fused to nisin H, nisin J or nisin P structural gene sequences originally produced by Streptococcus hyointestinalis DPC 6484, Staphylococcus capitis APC 2923 and Streptococcus agalactiae DPC 7040, respectively. This resulted in their expression in Lactococcus lactis NZ9800, a genetically modified strain that does not produce nisin A. CONCLUSIONS Induction of the nisin controlled gene expression system demonstrates that these three nisin variants could be acted on by nisin A machinery provided by the host strain. SIGNIFICANCE AND IMPACT OF THE STUDY Describes the first successful heterologous production of three natural nisin variants by a GRAS strain, and demonstrates how such systems could be harnessed not only for lantibiotic production but also in the expansion of their structural diversity and development for use as future biotherapeutics.
Published: 2021

31. The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes

Author: Colin Hill, Paul D. Cotter, Beatriz Gómez-Sala, R. Paul Ross, Mary C. Rea, Calum J. Walsh, Kristján Kristjánsson, Finlay Burns, Klara B. Jakobsdóttir, D. Stokes, Elena Guijarro-García, and Fergus W. J. Collins
Subjects: 0301 basic medicine, Microbiology (medical), antibiotic resistance, Zoology, microbiome, Sede Central IEO, RC799-869, Biology, Microbiology, Deep sea, 03 medical and health sciences, 0302 clinical medicine, Antibiotic resistance, Bacterial Proteins, Drug Resistance, Bacterial, Deep sea fish, Pressure, Animals, Microbiome, Atlantic Ocean, Ecosystem, Phylogeny, deep-sea, Bacteria, Fishes, Deep-sea, Gastroenterology, Genomics, Diseases of the digestive system. Gastroenterology, Anti-Bacterial Agents, Gastrointestinal Microbiome, Intestines, 030104 developmental biology, Infectious Diseases, Habitat, %22">Fish , 030211 gastroenterology & hepatology, Cell, Bioluminescence, Adaptation, Research Article, Research Paper, Antibiotic resistance genes
Abstract: Adaptation to life in the deep-sea can be dramatic, with fish displaying behaviors and appearances unlike those seen in any other aquatic habitat. However, the extent of which adaptations may have developed at a microbial scale is not as clear. Shotgun metagenomic sequencing of the intestinal microbiome of 32 species of deep-sea fish from across the Atlantic Ocean revealed that many of the associated microbes differ extensively from those previously identified in reference databases. 111 individual metagenome-assembled genomes (MAGs) were constructed representing individual microbial species from the microbiomes of these fish, many of which are potentially novel bacterial taxa and provide a window into the microbial diversity in this underexplored environment. These MAGs also demonstrate how these microbes have adapted to deep-sea life by encoding a greater capacity for several cellular processes such as protein folding and DNA replication that can be inhibited by high pressure. Another intriguing feature was the almost complete lack of genes responsible for acquired resistance to known antibiotics in many of the samples. This highlights that deep-sea fish microbiomes may represent one of few animal-associated microbiomes with little influence from human activity. The ability of the microbes in these samples to bioluminesce is lower than expected given predictions that this trait has an important role in their life cycle at these depths. The study highlights the uniqueness, complexity and adaptation of microbial communities living in one of the largest and harshest environments on Earth., Sí
Published: 2021

32. Comparative survival analysis of multiparametric tests-when molecular tests disagree-A TEAM Pathology study

Author: Bartlett, John M. S. Bayani, Jane Kornaga, Elizabeth Xu, Keying Pond, Greg R. Piper, Tammy Mallon, Elizabeth Yao, Cindy Q. Boutros, Paul C. Hasenburg, Annette Dunn, J. A. and Markopoulos, Christos Dirix, Luc Seynaeve, Caroline van de Velde, Cornelis J. H. Stein, Robert C. Rea, Daniel
Subjects: education
Abstract: Multiparametric assays for risk stratification are widely used in the management of both node negative and node positive hormone receptor positive invasive breast cancer. Recent data from multiple sources suggests that different tests may provide different risk estimates at the individual patient level. The TEAM pathology study consists of 3284 postmenopausal ER+ve breast cancers treated with endocrine therapy Using genes comprising the following multi-parametric tests OncotypeDx(R), Prosigna (TM) and MammaPrint(R) signatures were trained to recapitulate true assay results. Patients were then classified into risk groups and survival assessed. Whilst likelihood chi(2) ratios suggested limited value for combining tests, Kaplan-Meier and LogRank tests within risk groups suggested combinations of tests provided statistically significant stratification of potential clinical value. Paradoxically whilst Prosigna-trained results stratified Oncotype-trained subgroups across low and intermediate risk categories, only intermediate risk Prosigna-trained cases were further stratified by Oncotype-trained results. Both Oncotype-trained and Prosigna-trained results further stratified MammaPrint-trained low risk cases, and MammaPrint-trained results also stratified Oncotype-trained low and intermediate risk groups but not Prosigna-trained results. Comparisons between existing multiparametric tests are challenging, and evidence on discordance between tests in risk stratification presents further dilemmas. Detailed analysis of the TEAM pathology study suggests a complex inter-relationship between test results in the same patient cohorts which requires careful evaluation regarding test utility. Further prognostic improvement appears both desirable and achievable.
Published: 2021

33. Search for multi-flare neutrino emissions in 10 yr of IceCube data from a catalog of sources

Author: R. Abbasi, M. Ackermann, J. Adams, J. A. Aguilar, M. Ahlers, M. Ahrens, C. Alispach, A. A. Alves, N. M. Amin, R. An, K. Andeen, T. Anderson, G. Anton, C. Argüelles, Y. Ashida, S. Axani, X. Bai, A. Balagopal V., A. Barbano, S. W. Barwick, B. Bastian, V. Basu, S. Baur, R. Bay, J. J. Beatty, K.-H. Becker, J. Becker Tjus, C. Bellenghi, S. BenZvi, D. Berley, E. Bernardini, D. Z. Besson, G. Binder, D. Bindig, E. Blaufuss, S. Blot, M. Boddenberg, F. Bontempo, J. Borowka, S. Böser, O. Botner, J. Böttcher, E. Bourbeau, F. Bradascio, J. Braun, S. Bron, J. Brostean-Kaiser, S. Browne, A. Burgman, R. T. Burley, R. S. Busse, M. A. Campana, E. G. Carnie-Bronca, C. Chen, D. Chirkin, K. Choi, B. A. Clark, K. Clark, L. Classen, A. Coleman, G. H. Collin, J. M. Conrad, P. Coppin, P. Correa, D. F. Cowen, R. Cross, C. Dappen, P. Dave, C. De Clercq, J. J. DeLaunay, H. Dembinski, K. Deoskar, S. De Ridder, A. Desai, P. Desiati, K. D. de Vries, G. de Wasseige, M. de With, T. DeYoung, S. Dharani, A. Diaz, J. C. Díaz-Vélez, M. Dittmer, H. Dujmovic, M. Dunkman, M. A. DuVernois, E. Dvorak, T. Ehrhardt, P. Eller, R. Engel, H. Erpenbeck, J. Evans, P. A. Evenson, K. L. Fan, A. R. Fazely, S. Fiedlschuster, A. T. Fienberg, K. Filimonov, C. Finley, L. Fischer, D. Fox, A. Franckowiak, E. Friedman, A. Fritz, P. Fürst, T. K. Gaisser, J. Gallagher, E. Ganster, A. Garcia, S. Garrappa, L. Gerhardt, A. Ghadimi, C. Glaser, T. Glauch, T. Glüsenkamp, A. Goldschmidt, J. G. Gonzalez, S. Goswami, D. Grant, T. Grégoire, S. Griswold, M. Gündüz, C. Günther, C. Haack, A. Hallgren, R. Halliday, L. Halve, F. Halzen, M. Ha Minh, K. Hanson, J. Hardin, A. A. Harnisch, A. Haungs, S. Hauser, D. Hebecker, K. Helbing, F. Henningsen, E. C. Hettinger, S. Hickford, J. Hignight, C. Hill, G. C. Hill, K. D. Hoffman, R. Hoffmann, T. Hoinka, B. Hokanson-Fasig, K. Hoshina, F. Huang, M. Huber, T. Huber, K. Hultqvist, M. Hünnefeld, R. Hussain, S. In, N. Iovine, A. Ishihara, M. Jansson, G. S. Japaridze, M. Jeong, B. J. P. Jones, D. Kang, W. Kang, X. Kang, A. Kappes, D. Kappesser, T. Karg, M. Karl, A. Karle, U. Katz, M. Kauer, M. Kellermann, J. L. Kelley, A. Kheirandish, K. Kin, T. Kintscher, J. Kiryluk, S. R. Klein, R. Koirala, H. Kolanoski, T. Kontrimas, L. Köpke, C. Kopper, S. Kopper, D. J. Koskinen, P. Koundal, M. Kovacevich, M. Kowalski, T. Kozynets, E. Kun, N. Kurahashi, N. Lad, C. Lagunas Gualda, J. L. Lanfranchi, M. J. Larson, F. Lauber, J. P. Lazar, J. W. Lee, K. Leonard, A. Leszczyńska, Y. Li, M. Lincetto, Q. R. Liu, M. Liubarska, E. Lohfink, C. J. Lozano Mariscal, L. Lu, F. Lucarelli, A. Ludwig, W. Luszczak, Y. Lyu, W. Y. Ma, J. Madsen, K. B. M. Mahn, Y. Makino, S. Mancina, I. C. Mariş, R. Maruyama, K. Mase, T. McElroy, F. McNally, J. V. Mead, K. Meagher, A. Medina, M. Meier, S. Meighen-Berger, J. Micallef, D. Mockler, T. Montaruli, R. W. Moore, R. Morse, M. Moulai, R. Naab, R. Nagai, U. Naumann, J. Necker, L. V. Nguyễn, H. Niederhausen, M. U. Nisa, S. C. Nowicki, D. R. Nygren, A. Obertacke Pollmann, M. Oehler, B. Oeyen, A. Olivas, E. O’Sullivan, H. Pandya, D. V. Pankova, N. Park, G. K. Parker, E. N. Paudel, L. Paul, C. Pérez de los Heros, L. Peters, J. Peterson, S. Philippen, D. Pieloth, S. Pieper, M. Pittermann, A. Pizzuto, M. Plum, Y. Popovych, A. Porcelli, M. Prado Rodriguez, P. B. Price, B. Pries, G. T. Przybylski, C. Raab, A. Raissi, M. Rameez, K. Rawlins, I. C. Rea, A. Rehman, P. Reichherzer, R. Reimann, G. Renzi, E. Resconi, S. Reusch, W. Rhode, M. Richman, B. Riedel, E. J. Roberts, S. Robertson, G. Roellinghoff, M. Rongen, C. Rott, T. Ruhe, D. Ryckbosch, D. Rysewyk Cantu, I. Safa, J. Saffer, S. E. Sanchez Herrera, A. Sandrock, J. Sandroos, M. Santander, S. Sarkar, K. Satalecka, M. Scharf, M. Schaufel, H. Schieler, S. Schindler, P. Schlunder, T. Schmidt, A. Schneider, J. Schneider, F. G. Schröder, L. Schumacher, G. Schwefer, S. Sclafani, D. Seckel, S. Seunarine, A. Sharma, S. Shefali, M. Silva, B. Skrzypek, B. Smithers, R. Snihur, J. Soedingrekso, D. Soldin, C. Spannfellner, G. M. Spiczak, C. Spiering, J. Stachurska, M. Stamatikos, T. Stanev, R. Stein, J. Stettner, A. Steuer, T. Stezelberger, T. Stürwald, T. Stuttard, G. W. Sullivan, I. Taboada, F. Tenholt, S. Ter-Antonyan, S. Tilav, F. Tischbein, K. Tollefson, L. Tomankova, C. Tönnis, S. Toscano, D. Tosi, A. Trettin, M. Tselengidou, C. F. Tung, A. Turcati, R. Turcotte, C. F. Turley, J. P. Twagirayezu, B. Ty, M. A. Unland Elorrieta, N. Valtonen-Mattila, J. Vandenbroucke, N. van Eijndhoven, D. Vannerom, J. van Santen, S. Verpoest, M. Vraeghe, C. Walck, T. B. Watson, C. Weaver, P. Weigel, A. Weindl, M. J. Weiss, J. Weldert, C. Wendt, J. Werthebach, M. Weyrauch, N. Whitehorn, C. H. Wiebusch, D. R. Williams, M. Wolf, K. Woschnagg, G. Wrede, J. Wulff, X. W. Xu, Y. Xu, J. P. Yanez, S. Yoshida, S. Yu, T. Yuan, Z. Zhang, Faculty of Sciences and Bioengineering Sciences, Physics, Elementary Particle Physics, and Vriendenkring VUB
Subjects: BLAZAR TXS 0506+056, High-energy astronomy, Population, M87, FOS: Physical sciences, Binomial test, Astrophysics, 030226 pharmacology & pharmacy, 01 natural sciences, ASTROPHYSICAL SOURCES, law.invention, 03 medical and health sciences, 0302 clinical medicine, law, 0103 physical sciences, education, 010303 astronomy & astrophysics, High Energy Astrophysical Phenomena (astro-ph.HE), Astroparticle physics, Physics, astro-ph.HE, COINCIDENT, education.field_of_study, Northern Hemisphere, Astronomy and Astrophysics, MODEL, Physics and Astronomy, Space and Planetary Science, JETS, Neutrino, Neutrino astronomy, Astrophysics - High Energy Astrophysical Phenomena, Flare
Abstract: A recent time-integrated analysis of a catalog of 110 candidate neutrino sources revealed a cumulative neutrino excess in the data collected by IceCube between April 6, 2008 and July 10, 2018. This excess, inconsistent with the background hypothesis in the Northern hemisphere at the $3.3~\sigma$ level, is associated with four sources: NGC 1068, TXS 0506+056, PKS 1424+240 and GB6 J1542+6129. This letter presents two time-dependent neutrino emission searches on the same data sample and catalog: a point-source search that looks for the most significant time-dependent source of the catalog by combining space, energy and time information of the events, and a population test based on binomial statistics that looks for a cumulative time-dependent neutrino excess from a subset of sources. Compared to previous time-dependent searches, these analyses enable a feature to possibly find multiple flares from a single direction with an unbinned maximum-likelihood method. M87 is found to be the most significant time-dependent source of this catalog at the level of $1.7~\sigma$ post-trial, and TXS 0506+056 is the only source for which two flares are reconstructed. The binomial test reports a cumulative time-dependent neutrino excess in the Northern hemisphere at the level of $3.0~\sigma$ associated with four sources: M87, TXS 0506+056, GB6 J1542+6129 and NGC 1068.
Published: 2021

34. Got Rosettes? Phenotype Them Fast, Accurately, and Easily with ARADEEPOPSIS!

Author: Anne C. Rea
Subjects: 0106 biological sciences, 0301 basic medicine, Marketing buzz, business.industry, Deep learning, Cell Biology, Plant Science, Biology, Plant biology, 01 natural sciences, In Brief, 03 medical and health sciences, 030104 developmental biology, Artificial intelligence, business, 010606 plant biology & botany
Abstract: “Deep learning” is a buzz term that seems to be cropping up in plant biology research these days. Originally reserved, perhaps, for computer nerds rather than us biology ones, deep learning is a type of machine learning used in the field of artificial intelligence. Modeled on the human brain
Published: 2020

35. Realism in Theology and Metaphysics

Author: Michael C. Rea
Abstract: Since the early 2000s, increasing attention has been paid in two separate disciplines to questions about realism and ontological commitment. The disciplines are analytic metaphysics on the one hand, and theology on the other. Chapter 1 discusses two arguments for the conclusion that realism in theology and metaphysics—that is, a realist treatment of doctrines in theology and metaphysics—is untenable. The first is due to Peter Byrne, the second to Bas van Fraassen. The chapter concludes that practitioners of metaphysics and theology ought simply to ignore this conclusion. Those who are already sceptical of theology or metaphysics or both will find in the objections plenty to agree with. But they should not convince the unconvinced.
Published: 2020

36. God beyond Being

Author: Michael C. Rea
Subjects: Transcendence (religion), Philosophy, media_common.quotation_subject, media_common, Epistemology
Abstract: Theologians divide as to how best to understand God’s transcendence. Famously, towards the end of his Mystical Theology, Pseudo-Dionysius characterized God’s transcendence by saying that God is ‘beyond every denial, beyond every assertion’ and that God ‘lies beyond thought and beyond being’. Many in his wake have followed him in these affirmations. Contemporary analytic philosophers commonly dismiss such claims as unintelligible or inconsistent with basic doctrines of Christianity (e.g. that God exists, is personal, became incarnate). But they are so deeply entrenched in the tradition that it seems a worthwhile effort to try to do them justice. This chapter develops an intelligible account of divine transcendence that accommodates the language of beyondness while at the same time remaining consistent with the truth of central Christian doctrines.
Published: 2020

37. Gender as a Divine Attribute

Author: Michael C. Rea
Abstract: It is standard within the Christian tradition to characterize God in predominantly masculine terms. Let ‘traditionalism’ refer to the view that this pattern of characterization is theologically mandatory. This chapter seeks to undercut the main motivations for traditionalism by showing that it is not more accurate to characterize God as masculine rather than feminine (or vice versa). The novelty of the argument lies in the fact that it presupposes neither theological anti-realism nor a robust doctrine of divine transcendence, but instead rests heavy theoretical weight on the imago Dei doctrine and the method of perfect-being theology. The chapter closes by examining the implications of its main argument for the moral and liturgical propriety of characterizing God in predominantly masculine terms.
Published: 2020

38. Polytheism and Christian Belief

Author: Michael C. Rea
Abstract: Christian philosophers and theologians have long been concerned with the question of how to reconcile their belief in three fully divine Persons with their commitment to monotheism. The most popular strategy for doing this—the social trinitarian strategy—argues that, though the divine Persons are in no sense the same God, monotheism is secured by certain relations that obtain among them. It is argued that if the social trinitarian understanding of the doctrine of the Trinity is correct, then Christianity is not interestingly different from the polytheistic Amun-Re theology of Egypt’s New Kingdom period. Thus, social trinitarianism should be classified as a version of polytheism rather than monotheism.
Published: 2020

39. Introduction

Author: Michael C. Rea
Abstract: This chapter introduces the volume. The chapters in the first part of the volume deal with metatheological issues pertaining to discourse about God and the authority of scripture; the chapters in the second part focus on divine attributes; and the chapters in the third part discuss the doctrine of the trinity and related issues. The section headings of this introduction match the part divisions of the book, but it is not the aim here to summarize the chapters included in each section’s corresponding part. Instead, this introduction aims to supplement those papers with a more general discussion of some of the author’s past and current thinking on the various loci covered by the chapters in the volume.
Published: 2020

40. The Metaphysics of Original Sin

Author: Michael C. Rea
Abstract: This chapter argues that there is no straightforward conflict between the doctrine of original sin (construed as including the doctrine of original guilt) and the following thesis, which is taken to be the primary source of philosophical objection to that doctrine: (MR) A person P is morally responsible for the obtaining of a state of affairs S only if S obtains (or obtained) and P could have prevented S from obtaining. After surveying a variety of different construals of the doctrine of original sin, the chapter shows that the main source of tension with MR is the further assumption that no human being who was born after the commission of first sin could have done anything to prevent that first sin; and no human being who is born corrupt could have done anything to prevent her own corruption. The chapter then discusses different ways in which this assumption might be resisted.
Published: 2020

41. Authority and Truth

Author: Michael C. Rea
Abstract: Chapter 3 is divided into three sections. The first attempts to clarify what might be meant in calling a text authoritative. The second draws distinctions between different things that might be meant by saying that a text is truthful. The goal in both of these parts is to arrive at some general conclusions about texts, rather than specific conclusions about the Bible. Consequently, the chapter refrains from making assumptions about (e.g.) biblical interpretation or about the truth of particular biblical texts. Indeed, for much of the discussion, the Bible is not even directly in view. The third section draws out some of the implications of the discussions in the first two sections for the question of how textual authority and textual truth are connected to one another. It also comments on the significance of these conclusions for discussions about the relation between biblical authority and biblical inerrancy.
Published: 2020

42. Theology without Idolatry or Violence

Author: Michael C. Rea
Abstract: In Theology without Metaphysics, Kevin Hector offers a broadly Wittgensteinian theory about the nature and deployment of human concepts and predicates with the goal of showing how both can be applied to God in a non-metaphysical way. In this way, he hopes to show that cataphatic theology is not inherently metaphysical, and that one can therefore engage in it without falling into idolatry or violence. After brief clarification of the ‘idolatry’ and ‘violence’ objections against metaphysics, followed by an explanation of the way in which Hector’s proposal is supposed to provide a non-metaphysical way of doing substantive, cataphatic theology, this chapter identifies five difficulties that beset Hector’s view.
Published: 2020

43. Essays in Analytic Theology

Author: Michael C. Rea
Abstract: This book is the first of two volumes collecting together the most substantial work in analytic theology that I have done between 2003 and 2018. The essays in this volume focus on the nature of God, whereas the essays in the companion volume focus on humanity and the human condition. The essays in the first part of this volume deal with issues in the philosophy of theology having to do with discourse about God and the authority of scripture; the essays in the second part focus on divine attributes; and the essays in the third part discuss the doctrine of the trinity and related issues. The book includes one new essay, another essay that was previously published only in German translation, and new postscripts to two of the essays.
Published: 2020

44. Divine Attributes as a Topic in Analytic Theology

Author: Michael C. Rea
Subjects: Philosophy, Theology
Abstract: Analytic theology differs from other forms of theology primarily in its methodology: its ambitions, its style, its conversation partners, and so on. This is where the most interesting differences between analytic philosophical discussions of the divine attributes and contemporary theological discussions of that topic are to be found. The main positive thesis of this chapter is that the most distinctive features of the approach to divine attributes that one finds in the analytic philosophical literature are simply instances of more general distinctives of analytic theology. The chapter focuses on some of the distinguishing features of the way in which the topic of divine attributes is approached in analytic philosophy of religion as contrasted with the way(s) in which many contemporary theologians are inclined to approach it. The end result is a clearer picture both of the nature of analytic theology in general and of the distinctive character of an analytic approach to the topic of divine attributes.
Published: 2020

45. Hylomorphism and the Incarnation

Author: Michael C. Rea
Abstract: This chapter offers a metaphysical account of the incarnation that starts from substantive assumptions about the nature of natures and about the metaphysics of the Trinity and develops in light of these a story about the relations among the elements involved in the incarnation. Central to the view described are two features of Aristotle’s metaphysics: (i) a hylomorphic understanding of material objects, (ii) a doctrine of numerical sameness without identity, and (iii) the view that the nature of a thing can appropriately be identified with its form. These ideas, along with other important aspects of the metaphysical framework which are discussed, form the bulk of the chapter. They are followed by a brief sketch of the account of the Trinity that the author and Jeffrey Brower have presented in detail elsewhere. In the final section, the author’s account of the incarnation is presented.
Published: 2020

46. In Defence of Sceptical Theism

Author: Michael C. Rea
Subjects: media_common.quotation_subject, Philosophy, Theism, Theology, Skepticism, media_common
Abstract: Some evidential arguments from evil rely on an inference of the following sort: ‘If, after thinking hard, we can’t think of any God-justifying reason for permitting some horrific evil then it is likely that there is no such reason.’ Sceptical theists, ourselves included, say that this inference is not a good one and that evidential arguments from evil that depend on it are, as a result, unsound. Michael Almeida and Graham Oppy have argued that Michael Bergmann’s way of developing the sceptical theist response to such arguments fails because it commits those who endorse it to a sort of scepticism that undermines ordinary moral practice. This chapter defends Bergmann’s sceptical theist response against this charge.
Published: 2020

47. Material Constitution and the Trinity [with Jeffrey Brower]

Author: Michael C. Rea
Subjects: Constitution, Philosophy, media_common.quotation_subject, Theology, media_common
Abstract: The Christian doctrine of the Trinity poses a serious philosophical problem. On the one hand, it seems to imply that there is exactly one divine being. On the other hand, it seems to imply that there are three divine beings. There is another well-known philosophical problem that presents us with a similar sort of tension: the problem of material constitution. This chapter argues that a relatively neglected solution to the problem of material constitution—an appeal to the Aristotelian doctrine of numerical sameness without identity—can be developed into a novel solution to the problem of the Trinity.
Published: 2020

48. Hiddenness and Transcendence

Author: Michael C. Rea
Abstract: For over two decades, the philosophical literature on divine hiddenness has been concerned with just one problem about divine hiddenness that arises out of one very particular concept of God. The problem—call it the Schellenberg problem—has J. L. Schellenberg as both its inventor and its most ardent defender. This chapter argues that the Schellenberg problem is an attack on a straw deity. More specifically, it proposes that Schellenberg’s argument against the existence of God depends on certain theological claims that are not commitments of traditional Christian theology and that would, furthermore, be repudiated by many of the most important and influential theologians in the Christian tradition. The chapter closes with some very brief remarks about the implications of this conclusion for what is taken to be the real import of the Schellenberg problem.
Published: 2020

49. The Trinity

Author: Michael C. Rea
Abstract: The Christian doctrine of the Trinity poses a serious philosophical problem. On the one hand, it seems to imply that there is exactly one divine being; on the other hand, it seems to imply that there are three. There is another well-known philosophical problem that presents us with a similar sort of tension: the problem of material constitution. After an examination of two classificatory schemes (the Latin tradition which traces its historical roots through the western church. and the Greek tradition which traces its roots through the eastern church) this chapter argues that a relatively neglected solution to the problem of material constitution can be developed into a novel solution to the problem of the Trinity.
Published: 2020

50. Wright on Theodicy

Author: Michael C. Rea
Subjects: ComputingMilieux_THECOMPUTINGPROFESSION, GeneralLiterature_MISCELLANEOUS
Abstract: In Evil and the Justice of God, N. T. Wright suggests that attempting to solve the philosophical problem of evil is an immature response to the existence of evil—one that belittles the real problem, which is just that evil is bad and needs to be dealt with. If he is correct, then the vast majority of work on the problem of evil in the analytic philosophical tradition has been worthless at best, and possibly even pernicious (by virtue of trivializing a serious theological issue). This chapter identifies a kernel of truth in Wright’s objection to philosophical attempts to solve the problem of evil, and goes on to argue that some such attempts avoid Wright’s objection.
Published: 2020

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