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3. Index

Author

Dunne, Matthew

Published
2013

5. Cover

Author

Dunne, Matthew

Published
2013

10. Back Cover

Author

Dunne, Matthew

Published
2013

14. Notes

Author

Dunne, Matthew

Published
2013

19. Combining imitation and deep reinforcement learning to accomplish human-level performance on a virtual foraging task

Author

Giammarino, Vittorio, Dunne, Matthew F, Moore, Kylie N, Hasselmo, Michael E, Stern, Chantal E, and Paschalidis, Ioannis Ch.

Subjects
Computer Science - Machine Learning, Electrical Engineering and Systems Science - Systems and Control
Abstract

We develop a simple framework to learn bio-inspired foraging policies using human data. We conduct an experiment where humans are virtually immersed in an open field foraging environment and are trained to collect the highest amount of rewards. A Markov Decision Process (MDP) framework is introduced to model the human decision dynamics. Then, Imitation Learning (IL) based on maximum likelihood estimation is used to train Neural Networks (NN) that map human decisions to observed states. The results show that passive imitation substantially underperforms humans. We further refine the human-inspired policies via Reinforcement Learning (RL) using the on-policy Proximal Policy Optimization (PPO) algorithm which shows better stability than other algorithms and can steadily improve the policies pretrained with IL. We show that the combination of IL and RL can match human results and that good performance strongly depends on combining the allocentric information with an egocentric representation of the environment., Comment: 24 pages, 15 figures more...

Published
2022

21. Engineered reporter phages for detection of Escherichia coli, Enterococcus, and Klebsiella in urine

Author

Meile, Susanne, Du, Jiemin, Staubli, Samuel, Grossmann, Sebastian, Koliwer-Brandl, Hendrik, Piffaretti, Pietro, Leitner, Lorenz, Matter, Cassandra I., Baggenstos, Jasmin, Hunold, Laura, Milek, Sonja, Guebeli, Christian, Kozomara-Hocke, Marko, Neumeier, Vera, Botteon, Angela, Klumpp, Jochen, Marschall, Jonas, McCallin, Shawna, Zbinden, Reinhard, Kessler, Thomas M., Loessner, Martin J., Dunne, Matthew, and Kilcher, Samuel more...

Published
2023
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24. Target highlights in CASP13: Experimental target structures through the eyes of their authors

Author

Lepore, Rosalba, Kryshtafovych, Andriy, Alahuhta, Markus, Veraszto, Harshul A, Bomble, Yannick J, Bufton, Joshua C, Bullock, Alex N, Caba, Cody, Cao, Hongnan, Davies, Owen R, Desfosses, Ambroise, Dunne, Matthew, Fidelis, Krzysztof, Goulding, Celia W, Gurusaran, Manickam, Gutsche, Irina, Harding, Christopher J, Hartmann, Marcus D, Hayes, Christopher S, Joachimiak, Andrzej, Leiman, Petr G, Loppnau, Peter, Lovering, Andrew L, Lunin, Vladimir V, Michalska, Karolina, Mir‐Sanchis, Ignacio, Mitra, AK, Moult, John, Phillips, George N, Pinkas, Daniel M, Rice, Phoebe A, Tong, Yufeng, Topf, Maya, Walton, Jonathan D, and Schwede, Torsten more...

Subjects
Biochemistry and Cell Biology, Biological Sciences, Arabidopsis, Bacterial Proteins, Computational Biology, Crystallography, X-Ray, Humans, Models, Molecular, Protein Conformation, Proteins, CASP, protein structure prediction, cryo-EM, X-ray crystallography, CASP, protein structure prediction, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Mathematical sciences
Abstract

The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment. more...

Published
2019

28. Personalized bacteriophage therapy outcomes for 100 consecutive cases:a multicentre, multinational, retrospective observational study

Author

Pirnay, Jean Paul, Djebara, Sarah, Steurs, Griet, Griselain, Johann, Cochez, Christel, De Soir, Steven, Glonti, Tea, Spiessens, An, Vanden Berghe, Emily, Green, Sabrina, Wagemans, Jeroen, Lood, Cédric, Schrevens, Eddie, Chanishvili, Nina, Kutateladze, Mzia, de Jode, Mathieu, Ceyssens, Pieter Jan, Draye, Jean Pierre, Verbeken, Gilbert, De Vos, Daniel, Rose, Thomas, Onsea, Jolien, Van Nieuwenhuyse, Brieuc, Soentjens, Patrick, Lavigne, Rob, Merabishvili, Maya, Pang, Kim Win, Metsemakers, Willem Jan, Van der Linden, Dimitri, Chatzis, Olga, Eskenazi, Anaïs, Lopez, Angel, De Voeght, Adrien, Rousseau, Anne Françoise, Tilmanne, Anne, Vens, Daphne, Gérain, Jean, Layeux, Brice, Vlieghe, Erika, Baar, Ingrid, Van Ierssel, Sabrina, Van Laethem, Johan, Guiot, Julien, De Roock, Sophie, Jennes, Serge, Uyttebroek, Saartje, Van Gerven, Laura, Hellings, Peter W., Dupont, Lieven, Debaveye, Yves, Devolder, David, Spriet, Isabel, De Munter, Paul, Depypere, Melissa, Vanfleteren, Michiel, Cornu, Olivier, Verhulst, Stijn, Boiy, Tine, Lamote, Stoffel, Van Zele, Thibaut, Wieërs, Grégoire, Courtin, Cécile, Lebeaux, David, Sartre, Jacques, Ferry, Tristan, Laurent, Frédéric, Paul, Kevin, Di Luca, Mariagrazia, Gottschlich, Stefan, Tkhilaishvili, Tamta, Cesta, Novella, Racenis, Karlis, Barbosa, Telma, López-Cortés, Luis Eduardo, Tomás, Maria, Hübner, Martin, Pham, Truong Thanh, Nagtegaal, Paul, Ten Oever, Jaap, Daniels, Johannes, Loubert, Maartje, Iheb, Ghariani, Jones, Joshua, Hall, Lesley, Young, Matthew, Balarjishvili, Nana, Tediashvili, Marina, Tong, Yigang, Rohde, Christine, Wittmann, Johannes, Hazan, Ronen, Nir-Paz, Ran, Azeredo, Joana, Krylov, Victor, Cameron, David, Pitton, Melissa, Que, Yok Ai, Resch, Gregory, McCallin, Shawna, Dunne, Matthew, Kilcher, Samuel, Pirnay, Jean Paul, Djebara, Sarah, Steurs, Griet, Griselain, Johann, Cochez, Christel, De Soir, Steven, Glonti, Tea, Spiessens, An, Vanden Berghe, Emily, Green, Sabrina, Wagemans, Jeroen, Lood, Cédric, Schrevens, Eddie, Chanishvili, Nina, Kutateladze, Mzia, de Jode, Mathieu, Ceyssens, Pieter Jan, Draye, Jean Pierre, Verbeken, Gilbert, De Vos, Daniel, Rose, Thomas, Onsea, Jolien, Van Nieuwenhuyse, Brieuc, Soentjens, Patrick, Lavigne, Rob, Merabishvili, Maya, Pang, Kim Win, Metsemakers, Willem Jan, Van der Linden, Dimitri, Chatzis, Olga, Eskenazi, Anaïs, Lopez, Angel, De Voeght, Adrien, Rousseau, Anne Françoise, Tilmanne, Anne, Vens, Daphne, Gérain, Jean, Layeux, Brice, Vlieghe, Erika, Baar, Ingrid, Van Ierssel, Sabrina, Van Laethem, Johan, Guiot, Julien, De Roock, Sophie, Jennes, Serge, Uyttebroek, Saartje, Van Gerven, Laura, Hellings, Peter W., Dupont, Lieven, Debaveye, Yves, Devolder, David, Spriet, Isabel, De Munter, Paul, Depypere, Melissa, Vanfleteren, Michiel, Cornu, Olivier, Verhulst, Stijn, Boiy, Tine, Lamote, Stoffel, Van Zele, Thibaut, Wieërs, Grégoire, Courtin, Cécile, Lebeaux, David, Sartre, Jacques, Ferry, Tristan, Laurent, Frédéric, Paul, Kevin, Di Luca, Mariagrazia, Gottschlich, Stefan, Tkhilaishvili, Tamta, Cesta, Novella, Racenis, Karlis, Barbosa, Telma, López-Cortés, Luis Eduardo, Tomás, Maria, Hübner, Martin, Pham, Truong Thanh, Nagtegaal, Paul, Ten Oever, Jaap, Daniels, Johannes, Loubert, Maartje, Iheb, Ghariani, Jones, Joshua, Hall, Lesley, Young, Matthew, Balarjishvili, Nana, Tediashvili, Marina, Tong, Yigang, Rohde, Christine, Wittmann, Johannes, Hazan, Ronen, Nir-Paz, Ran, Azeredo, Joana, Krylov, Victor, Cameron, David, Pitton, Melissa, Que, Yok Ai, Resch, Gregory, McCallin, Shawna, Dunne, Matthew, and Kilcher, Samuel more...

Abstract

In contrast to the many reports of successful real-world cases of personalized bacteriophage therapy (BT), randomized controlled trials of non-personalized bacteriophage products have not produced the expected results. Here we present the outcomes of a retrospective observational analysis of the first 100 consecutive cases of personalized BT of difficult-to-treat infections facilitated by a Belgian consortium in 35 hospitals, 29 cities and 12 countries during the period from 1 January 2008 to 30 April 2022. We assessed how often personalized BT produced a positive clinical outcome (general efficacy) and performed a regression analysis to identify functional relationships. The most common indications were lower respiratory tract, skin and soft tissue, and bone infections, and involved combinations of 26 bacteriophages and 6 defined bacteriophage cocktails, individually selected and sometimes pre-adapted to target the causative bacterial pathogens. Clinical improvement and eradication of the targeted bacteria were reported for 77.2% and 61.3% of infections, respectively. In our dataset of 100 cases, eradication was 70% less probable when no concomitant antibiotics were used (odds ratio = 0.3; 95% confidence interval = 0.127–0.749). In vivo selection of bacteriophage resistance and in vitro bacteriophage–antibiotic synergy were documented in 43.8% (7/16 patients) and 90% (9/10) of evaluated patients, respectively. We observed a combination of antibiotic re-sensitization and reduced virulence in bacteriophage-resistant bacterial isolates that emerged during BT. Bacteriophage immune neutralization was observed in 38.5% (5/13) of screened patients. Fifteen adverse events were reported, including seven non-serious adverse drug reactions suspected to be linked to BT. While our analysis is limited by the uncontrolled nature of these data, it indicates that BT can be effective in combination with antibiotics and can inform the design of future controlled clinical trials. B more...

Published
2024

30. NATURAL JUSTICE.

Author

DUNNE, MATTHEW

Subjects
*ANIMAL welfare, *CRIMINAL investigation, *ENVIRONMENTAL crimes, *WILDLIFE crimes, *BIRDS of prey
Abstract

The article discusses recent trials in Victoria where individuals were charged with killing protected wedge-tailed eagles. The cases highlighted the lengthy process of prosecuting wildlife crimes, with one individual confessing to killing over 400 eagles by lacing animal carcasses with poison. The community was shocked and outraged by these crimes, which were reminiscent of past practices where eagles were considered vermin and legally killed. Investigations into these crimes are challenging due to the need for strong evidence, and community witnesses play a crucial role in holding perpetrators accountable. [Extracted from the article] more...

Published
2024

31. Heterodimerization of Endolysin Isoforms During Bacterial Infection by Staphylococcal Phage φ2638A

Author

Zinsli, Léa V., primary, Sobieraj, Anna M., additional, Ernst, Patrick, additional, Meile, Susanne, additional, Kilcher, Samuel, additional, Iseli, Cedric, additional, Keller, Anja, additional, Dreier, Birgit, additional, Mittl, Peer R. E., additional, Plückthun, Andreas, additional, Loessner, Martin J., additional, Schmelcher, Mathias, additional, and Dunne, Matthew, additional more...

Published
2024
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33. Combining imitation and deep reinforcement learning to human-level performance on a virtual foraging task.

Author

Giammarino, Vittorio, Dunne, Matthew F, Moore, Kylie N, Hasselmo, Michael E, Stern, Chantal E, and Paschalidis, Ioannis Ch

Abstract

We develop a framework to learn bio-inspired foraging policies using human data. We conduct an experiment where humans are virtually immersed in an open field foraging environment and are trained to collect the highest amount of rewards. A Markov Decision Process (MDP) framework is introduced to model the human decision dynamics. Then, Imitation Learning (IL) based on maximum likelihood estimation is used to train Neural Networks (NN) that map human decisions to observed states. The results show that passive imitation substantially underperforms humans. We further refine the human-inspired policies via Reinforcement Learning (RL) using the on-policy Proximal Policy Optimization (PPO) algorithm which shows better stability than other algorithms and can steadily improve the policies pre-trained with IL. We show that the combination of IL and RL match human performance and that the artificial agents trained with our approach can quickly adapt to reward distribution shift. We finally show that good performance and robustness to reward distribution shift strongly depend on combining allocentric information with an egocentric representation of the environment. [ABSTRACT FROM AUTHOR] more...

Published
2024
Full Text
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36. Nanoscale clustering by O-antigen-Secretory Immunoglobulin-A binding limits outer membrane diffusion by encaging individualSalmonellacells

Author

Hockenberry, Alyson, primary, Radiom, Milad, additional, Arnoldini, Markus, additional, Turgay, Yagmur, additional, Dunne, Matthew, additional, Adamcik, Jozef, additional, Stadtmueller, Beth, additional, Mezzenga, Raffaele, additional, Ackermann, Martin, additional, and Slack, Emma, additional more...

Published
2023
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39. Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps

Author

Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Gonzalez-Serrano, Rafael, Rosselli, Riccardo, Roda-Garcia, Juan J., Martín Cuadrado, Ana Belén, Rodriguez-Valera, Francisco, Dunne, Matthew, Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Gonzalez-Serrano, Rafael, Rosselli, Riccardo, Roda-Garcia, Juan J., Martín Cuadrado, Ana Belén, Rodriguez-Valera, Francisco, and Dunne, Matthew more...

Published
2023

40. Enhancing bacteriophage therapeutics through in situ production and release of heterologous antimicrobial effectors

Author

Du, Jiemin; https://orcid.org/0000-0002-1246-6508, Meile, Susanne; https://orcid.org/0000-0001-8786-7157, Baggenstos, Jasmin, Jäggi, Tobias, Piffaretti, Pietro; https://orcid.org/0000-0001-7621-0475, Hunold, Laura, Matter, Cassandra I; https://orcid.org/0000-0002-5450-8614, Leitner, Lorenz; https://orcid.org/0000-0001-5764-3494, Kessler, Thomas M; https://orcid.org/0000-0002-1991-5919, Loessner, Martin J; https://orcid.org/0000-0002-8162-2631, Kilcher, Samuel; https://orcid.org/0000-0002-1162-6549, Dunne, Matthew; https://orcid.org/0000-0002-2329-8183, Du, Jiemin; https://orcid.org/0000-0002-1246-6508, Meile, Susanne; https://orcid.org/0000-0001-8786-7157, Baggenstos, Jasmin, Jäggi, Tobias, Piffaretti, Pietro; https://orcid.org/0000-0001-7621-0475, Hunold, Laura, Matter, Cassandra I; https://orcid.org/0000-0002-5450-8614, Leitner, Lorenz; https://orcid.org/0000-0001-5764-3494, Kessler, Thomas M; https://orcid.org/0000-0002-1991-5919, Loessner, Martin J; https://orcid.org/0000-0002-8162-2631, Kilcher, Samuel; https://orcid.org/0000-0002-1162-6549, and Dunne, Matthew; https://orcid.org/0000-0002-2329-8183 more...

Abstract

Bacteriophages operate via pathogen-specific mechanisms of action distinct from conventional, broad-spectrum antibiotics and are emerging as promising alternative antimicrobials. However, phage-mediated killing is often limited by bacterial resistance development. Here, we engineer phages for target-specific effector gene delivery and host-dependent production of colicin-like bacteriocins and cell wall hydrolases. Using urinary tract infection (UTI) as a model, we show how heterologous effector phage therapeutics (HEPTs) suppress resistance and improve uropathogen killing by dual phage- and effector-mediated targeting. Moreover, we designed HEPTs to control polymicrobial uropathogen communities through production of effectors with cross-genus activity. Using phage-based companion diagnostics, we identified potential HEPT responder patients and treated their urine ex vivo. Compared to wildtype phage, a colicin E7-producing HEPT demonstrated superior control of patient E. coli bacteriuria. Arming phages with heterologous effectors paves the way for successful UTI treatment and represents a versatile tool to enhance and adapt phage-based precision antimicrobials. more...

Published
2023

41. Engineered reporter phages for detection of Escherichia coli, Enterococcus, and Klebsiella in urine

Author

Meile, Susanne; https://orcid.org/0000-0001-8786-7157, Du, Jiemin; https://orcid.org/0000-0002-1246-6508, Staubli, Samuel; https://orcid.org/0009-0009-0984-1889, Grossmann, Sebastian; https://orcid.org/0000-0002-4141-079X, Koliwer-Brandl, Hendrik; https://orcid.org/0000-0003-1613-5615, Piffaretti, Pietro; https://orcid.org/0000-0001-7621-0475, Leitner, Lorenz; https://orcid.org/0000-0001-5764-3494, Matter, Cassandra I; https://orcid.org/0000-0002-5450-8614, Baggenstos, Jasmin, Hunold, Laura, Milek, Sonja, Guebeli, Christian; https://orcid.org/0000-0002-1706-0187, Kozomara-Hocke, Marko, Neumeier, Vera; https://orcid.org/0000-0002-8149-3710, Botteon, Angela, Klumpp, Jochen; https://orcid.org/0000-0003-3410-2702, Marschall, Jonas; https://orcid.org/0000-0002-0052-3210, McCallin, Shawna; https://orcid.org/0000-0002-4277-7753, Zbinden, Reinhard, Kessler, Thomas M; https://orcid.org/0000-0002-1991-5919, Loessner, Martin J; https://orcid.org/0000-0002-8162-2631, Dunne, Matthew; https://orcid.org/0000-0002-2329-8183, Kilcher, Samuel; https://orcid.org/0000-0002-1162-6549, Meile, Susanne; https://orcid.org/0000-0001-8786-7157, Du, Jiemin; https://orcid.org/0000-0002-1246-6508, Staubli, Samuel; https://orcid.org/0009-0009-0984-1889, Grossmann, Sebastian; https://orcid.org/0000-0002-4141-079X, Koliwer-Brandl, Hendrik; https://orcid.org/0000-0003-1613-5615, Piffaretti, Pietro; https://orcid.org/0000-0001-7621-0475, Leitner, Lorenz; https://orcid.org/0000-0001-5764-3494, Matter, Cassandra I; https://orcid.org/0000-0002-5450-8614, Baggenstos, Jasmin, Hunold, Laura, Milek, Sonja, Guebeli, Christian; https://orcid.org/0000-0002-1706-0187, Kozomara-Hocke, Marko, Neumeier, Vera; https://orcid.org/0000-0002-8149-3710, Botteon, Angela, Klumpp, Jochen; https://orcid.org/0000-0003-3410-2702, Marschall, Jonas; https://orcid.org/0000-0002-0052-3210, McCallin, Shawna; https://orcid.org/0000-0002-4277-7753, Zbinden, Reinhard, Kessler, Thomas M; https://orcid.org/0000-0002-1991-5919, Loessner, Martin J; https://orcid.org/0000-0002-8162-2631, Dunne, Matthew; https://orcid.org/0000-0002-2329-8183, and Kilcher, Samuel; https://orcid.org/0000-0002-1162-6549 more...

Abstract

The rapid detection and species-level differentiation of bacterial pathogens facilitates antibiotic stewardship and improves disease management. Here, we develop a rapid bacteriophage-based diagnostic assay to detect the most prevalent pathogens causing urinary tract infections: Escherichia coli, Enterococcus spp., and Klebsiella spp. For each uropathogen, two virulent phages were genetically engineered to express a nanoluciferase reporter gene upon host infection. Using 206 patient urine samples, reporter phage-induced bioluminescence was quantified to identify bacteriuria and the assay was benchmarked against conventional urinalysis. Overall, E. coli, Enterococcus spp., and Klebsiella spp. were each detected with high sensitivity (68%, 78%, 87%), specificity (99%, 99%, 99%), and accuracy (90%, 94%, 98%) at a resolution of ≥10$^{3}$ CFU/ml within 5 h. We further demonstrate how bioluminescence in urine can be used to predict phage antibacterial activity, demonstrating the future potential of reporter phages as companion diagnostics that guide patient-phage matching prior to therapeutic phage application. more...

Published
2023

44. Engineered reporter phages for rapid detection ofEscherichia coli, Klebsiellaspp., andEnterococcusspp. in urine

Author

Meile, Susanne, primary, Du, Jiemin, additional, Staubli, Samuel, additional, Grossman, Sebastian, additional, Koliwer-Brandl, Hendrik, additional, Piffaretti, Pietro, additional, Leitner, Lorenz, additional, Matter, Cassandra I., additional, Baggenstos, Jasmin, additional, Hunold, Laura, additional, Milek, Sonja, additional, Gübeli, Christian, additional, Kozomara-Hocke, Marko, additional, Neumeier, Vera, additional, Botteon, Angela, additional, Klumpp, Jochen, additional, Marschall, Jonas, additional, McCallin, Shawna, additional, Zbinden, Reinhard, additional, Kessler, Thomas M., additional, Loessner, Martin J., additional, Dunne, Matthew, additional, and Kilcher, Samuel, additional more...

Published
2022
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48. International Trade

Author

Dunne, Matthew S., Balsanek, Kristy, Barclay, Dean, Ewart, Andrea, Fernandez, Julio, Lalonde, Paul, Martino, Laura, Neir, Ann, and Rhodes, James

Published
2005

49. Enhancing bacteriophage therapeutics throughin situproduction and release of heterologous antimicrobial effectors

Author

Du, Jiemin, primary, Meile, Susanne, additional, Baggenstos, Jasmin, additional, Jäggi, Tobias, additional, Piffaretti, Pietro, additional, Hunold, Laura, additional, Matter, Cassandra I., additional, Leitner, Lorenz, additional, Kessler, Thomas M., additional, Loessner, Martin J., additional, Kilcher, Samuel, additional, and Dunne, Matthew, additional more...

Published
2022
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