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1. Health and economic impacts of Lassa vaccination campaigns in West Africa

Author

Smith, David R. M., Turner, Joanne, Fahr, Patrick, Attfield, Lauren A., Bessell, Paul R., Donnelly, Christl A., Gibb, Rory, Jones, Kate E., Redding, David W., Asogun, Danny, Ayodeji, Oladele Oluwafemi, Azuogu, Benedict N., Fischer, II, William A., Jan, Kamji, Olayinka, Adebola T., Wohl, David A., Torkelson, Andrew A., Dinkel, Katelyn A., Nixon, Emily J., Pouwels, Koen B., and Hollingsworth, T. Déirdre

Published
2024
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2. Human movement and environmental barriers shape the emergence of dengue

Author

Harish, Vinyas, Colón-González, Felipe J., Moreira, Filipe R. R., Gibb, Rory, Kraemer, Moritz U. G., Davis, Megan, Reiner, Jr., Robert C., Pigott, David M., Perkins, T. Alex, Weiss, Daniel J., Bogoch, Isaac I., Vazquez-Prokopec, Gonzalo, Saide, Pablo Manrique, Barbosa, Gerson L., Sabino, Ester C., Khan, Kamran, Faria, Nuno R., Hay, Simon I., Correa-Morales, Fabián, Chiaravalloti-Neto, Francisco, and Brady, Oliver J.

Published
2024
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3. Network embedding unveils the hidden interactions in the mammalian virome

Author

Poisot, Timothée, Ouellet, Marie-Andrée, Mollentze, Nardus, Farrell, Maxwell J., Becker, Daniel J., Brierly, Liam, Albery, Gregory F., Gibb, Rory J., Seifert, Stephanie N., and Carlson, Colin J.

Subjects
Quantitative Biology - Quantitative Methods
Abstract

At most 1-2% of the global virome has been sampled to date. Recent work has shown that predicting which host-virus interactions are possible but undiscovered or unrealized is, fundamentally, a network science problem. Here, we develop a novel method that combines a coarse recommender system (Linear Filtering; LF) with an imputation algorithm based on low-rank graph embedding (Singular Value Decomposition; SVD) to infer host-virus associations. This combination of techniques results in informed initial guesses based on directly measurable network properties (density, degree distribution) that are refined through SVD (which is able to leverage emerging features). Using this method, we recovered highly plausible undiscovered interactions with a strong signal of viral coevolutionary history, and revealed a global hotspot of unusually unique but unsampled (or unrealized) host-virus interactions in the Amazon rainforest. We develop several tests for quantifying the bias and realism of these predictions, and show that the LF-SVD method is robust in each aspect. We finally show that graph embedding of the imputed network can be used to improve predictions of human infection from viral genome features, showing that the global structure of the mammal-virus network provides additional insights into human disease emergence., Comment: 35 pages, 2 figures, 9 extended data figures, 7 extended data tables

Published
2021

4. Interactions between climate change, urban infrastructure and mobility are driving dengue emergence in Vietnam

Author

Gibb, Rory, Colón-González, Felipe J., Lan, Phan Trong, Huong, Phan Thi, Nam, Vu Sinh, Duoc, Vu Trong, Hung, Do Thai, Dong, Nguyễn Thanh, Chien, Vien Chinh, Trang, Ly Thi Thuy, Kien Quoc, Do, Hoa, Tran Minh, Tai, Nguyen Hữu, Hang, Tran Thi, Tsarouchi, Gina, Ainscoe, Eleanor, Harpham, Quillon, Hofmann, Barbara, Lumbroso, Darren, Brady, Oliver J., and Lowe, Rachel

Published
2023
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7. Understanding and predicting effects of global environmental change on zoonotic disease

Author

Gibb, Rory James

Subjects
616.9
Abstract

Global environmental change is increasingly recognized to influence risk of numerous zoonotic (animal-borne) infectious diseases. There is a fast-growing body of research into climate change effects on zoonotic risks, but broad-scale studies have rarely investigated how climate interacts with other key drivers, in particular land use change. Here, I evaluate effects of land use and climate on zoonotic disease risk, both generally and in a case study disease, by integrating multiple data types (ecological, epidemiological, satellite) and tools from biodiversity science, spatiotemporal epidemiology and land use modelling. First, I compile and analyse a global database of local species communities and their pathogens, and show that ecological communities in anthropogenic land uses globally are increasingly dominated by zoonotic host species, including mammalian reservoirs of globally-significant zoonoses, and that these trends are likely mediated by species traits. Second, I examine interacting effects of land, climate and socioeconomic factors on Lassa fever (LF), a neglected rodent-borne viral zoonosis that is a significant public health concern in West Africa, focusing on disease risk projection at both short (interannual) and long (multi-decadal) time horizons. In an epidemiological analysis of case surveillance time series from Nigeria, I show that present-day human LF incidence is associated with climate, agriculture and poverty, that periodic surges in LF cases are predicted by seasonal climate-vegetation dynamics, and that recent emergence trends are most likely underpinned by improving surveillance. At longer timescales, I then couple a mechanistic disease risk model with a dynamic land change model and climate projections, to show that different economic and climate policy futures (Shared Socioeconomic Pathways) may result in markedly different outcomes for LF risk and burden by 2030 and 2050 across West Africa. Finally, I synthesise the implications of these results for our understanding of the global change ecology of zoonotic disease, the epidemiology and control of LF, and for broader Planetary Health perspectives on managing zoonotic risks.

Published
2020

13. The anthropogenic fingerprint on emerging infectious diseases

Author

Gibb, Rory, primary, Ryan, Sadie J., additional, Pigott, David, additional, Fernandez, Maria del Pilar, additional, Muylaert, Renata L., additional, Albery, Gregory F., additional, Becker, Daniel J., additional, Blackburn, Jason K., additional, Caceres-Escobar, Hernan, additional, Celone, Michael, additional, Eskew, Evan A., additional, Frank, Hannah K., additional, Han, Barbara A., additional, Hulland, Erin N., additional, Jones, Kate E., additional, Katz, Rebecca, additional, Kucharski, Adam, additional, Limmathurotsakul, Direk, additional, Lippi, Catherine A., additional, Longbottom, Joshua, additional, Martinez, Juan Fernando, additional, Messina, Jane P., additional, Nsoesie, Elaine O., additional, Redding, David W., additional, Romero-Alvarez, Daniel, additional, Schmid, Boris V., additional, Seifert, Stephanie N., additional, Sinchi, Anabel, additional, Trisos, Christopher H., additional, Wille, Michelle, additional, and Carlson, Colin J., additional

Published
2024
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15. Projecting health and economic impacts of Lassa vaccination campaigns in West Africa

Author

Smith, David R M, primary, Turner, Joanne, additional, Fahr, Patrick, additional, Attfield, Lauren A, additional, Bessell, Paul R, additional, Donnelly, Christl A, additional, Gibb, Rory, additional, Jones, Kate E, additional, Redding, David W, additional, Asogun, Danny, additional, Ayodeji, Oladele Oluwafemi, additional, Azuogu, Benedict N, additional, Fischer, William A, additional, Jan, Kamji, additional, Olayinka, Adebola T, additional, Wohl, David A, additional, Torkelson, Andrew A, additional, Dinkel, Katelyn A, additional, Nixon, Emily J, additional, Pouwels, Koen B, additional, and Hollingsworth, T Déirdre, additional

Published
2024
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16. Designing and describing climate change impact attribution studies: a guide to common approaches

Author

Carlson, Colin, primary, Mitchell, Dann, additional, Carleton, Tamma, additional, Chersich, Matthew, additional, Gibb, Rory, additional, Lavelle, Torre, additional, Lukas-Sithole, Megan, additional, North, Michelle, additional, Lippi, Catherine, additional, New, Mark, additional, Ryan, Sadie, additional, Shumba, Stella, additional, and Trisos, Christopher, additional

Published
2024
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19. Interactions between climate change, urban infrastructure and mobility are driving dengue emergence in Vietnam

Author

Gibb, Rory, primary, Colón-González, Felipe J., additional, Lan, Phan Trong, additional, Huong, Phan Thi, additional, Nam, Vu Sinh, additional, Duoc, Vu Trong, additional, Hung, Do Thai, additional, Dong, Nguyễn Thanh, additional, Chien, Vien Chinh, additional, Trang, Ly Thi Thuy, additional, Quoc, Do Kien, additional, Hoa, Tran Minh, additional, Tai, Nguyen Hữu, additional, Hang, Tran Thi, additional, Tsarouchi, Gina, additional, Ainscoe, Eleanor, additional, Harpham, Quillon, additional, Hofmann, Barbara, additional, Lumbroso, Darren, additional, Brady, Oliver J., additional, and Lowe, Rachel, additional

Published
2023
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21. Projecting the future incidence and burden of dengue in Southeast Asia

Author

Barcelona Supercomputing Center, Colón González, Felipe J., Gibb, Rory, Khan, Kamran, Watts, Alexander, Lowe, Rachel, Brady, Oliver J., Barcelona Supercomputing Center, Colón González, Felipe J., Gibb, Rory, Khan, Kamran, Watts, Alexander, Lowe, Rachel, and Brady, Oliver J.

Abstract

The recent global expansion of dengue has been facilitated by changes in urbanisation, mobility, and climate. In this work, we project future changes in dengue incidence and case burden to 2099 under the latest climate change scenarios. We fit a statistical model to province-level monthly dengue case counts from eight countries across Southeast Asia, one of the worst affected regions. We project that dengue incidence will peak this century before declining to lower levels with large variations between and within countries. Our findings reveal that northern Thailand and Cambodia will show the biggest decreases and equatorial areas will show the biggest increases. The impact of climate change will be counterbalanced by income growth, with population growth having the biggest influence on increasing burden. These findings can be used for formulating mitigation and adaptation interventions to reduce the immediate growing impact of dengue virus in the region., F.J.C.-G., R.G., R.L. and O.J.B. were supported by the UK Space Agency Dengue Forecasting Model Satellite-based System (D-MOSS). R.L. was supported by a Royal Society Dorothy Hodgkin Fellowship., Peer Reviewed, Postprint (published version)

Published
2023

22. Interactions between climate change, urban infrastructure and mobility are driving dengue emergence in Vietnam

Author

Barcelona Supercomputing Center, Gibb, Rory, Colón González, Felipe J, Lan, Phan Trong, Huong, Phan Thi, Nam, Vu Sinh, Lowe, Rachel, Barcelona Supercomputing Center, Gibb, Rory, Colón González, Felipe J, Lan, Phan Trong, Huong, Phan Thi, Nam, Vu Sinh, and Lowe, Rachel

Abstract

Dengue is expanding globally, but how dengue emergence is shaped locally by interactions between climatic and socio-environmental factors is not well understood. Here, we investigate the drivers of dengue incidence and emergence in Vietnam, through analysing 23 years of district-level case data spanning a period of significant socioeconomic change (1998-2020). We show that urban infrastructure factors (sanitation, water supply, long-term urban growth) predict local spatial patterns of dengue incidence, while human mobility is a more influential driver in subtropical northern regions than the endemic south. Temperature is the dominant factor shaping dengue’s distribution and dynamics, and using long-term reanalysis temperature data we show that warming since 1950 has expanded transmission risk throughout Vietnam, and most strongly in current dengue emergence hotspots (e.g., southern central regions, Ha Noi). In contrast, effects of hydrometeorology are complex, multi-scalar and dependent on local context: risk increases under either short-term precipitation excess or long-term drought, but improvements in water supply mitigate drought-associated risks except under extreme conditions. Our findings challenge the assumption that dengue is an urban disease, instead suggesting that incidence peaks in transitional landscapes with intermediate infrastructure provision, and provide evidence that interactions between recent climate change and mobility are contributing to dengue’s expansion throughout Vietnam., The authors thank Colin Carlson for the insightful discussion of early results. This research was supported by the UK Space Agency-funded International Partnership Programme 2 D-MOSS project “An integrated dengue early warning system driven by Earth Observations in Vietnam” (all authors), as well as a Royal Society Dorothy Hodgkin Fellowship (R.L.), a Wellcome Trust Sir Henry Wellcome Fellowship (206471/Z/17/Z) and a UK Medical Research Council Career Development Award (MR/V031112/1, both O.B.)., Peer Reviewed, "Article signat per 21 autors/es: Rory Gibb, Felipe J. Colón-González, Phan Trong Lan, Phan Thi Huong, Vu Sinh Nam, Vu Trong Duoc, Hung Do Thai, Nguyễn Thanh Dong, Vien Chinh Chien, Ly Thi Thuy Trang, Do Kien Quoc, Tran Minh Hoa, Nguyen Hữu Tai, Tran Thi Hang, Gina Tsarouchi, Eleanor Ainscoe, Quillon Harpham, Barbara Hofmann, Darren Lumbroso, Oliver J. Brady & Rachel Lowe ", Postprint (published version)

Published
2023

24. MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Author

Grilo, Clara, Afonso, Beatriz C., Afonso, Filipe, Alexandre, Marta, Aliácar, Sara, Almeida, Ana, Alonso, Ivan Prego, Álvares, Francisco, Alves, Paulo, Alves, Paulo Célio, Alves, Pedro, Duarte, Beatriz, Duro, Virginia, Encarnação, Cláudia, Eufrázio, Sofia, Fael, António, Falé, João Salvador, Faria, Sandra, Fernandes, C, Fernandes, Margarida, Lopes, Susana, Rosalino, L. M., Costa, Gonçalo Ferrão, Ferreira, Clara, Ferreira, Diogo F., Ferreira, Eduardo, Ferreira, Joaquim Pedro, Ferreira, João, Ferreira, Diana, Fonseca, Carlos, Fontes, Inês, Fragoso, Ricardo, Rosário, Inês T., López-Baucells, Adrià, Franco, Claudia, Freitas, Tamira, Gabriel, Sofia I., Gibb, Rory, Gil, Patricia, Gomes, Carla Patricia Jorge, Horta, Pedro, Gomes, Pedro, Gomes, Verónica, Rossa, Mariana, Grilo, Ana Filipa, Amado, Anabela, Guedes, Américo, Guilherme, Filipa, Gutiérrez, Iván, Harper, Henry, Herrera, José M., Hipólito, Dário, Infante, Samuel, Jesus, José, Russo, Danilo, Loureiro, Armando, Loureiro, Filipa, Lourenço, Rui, Lourenço, Sofia, Lucas, Paula, Magalhães, Ana, Maldonado, Cristina, Marcolin, Fabio, Marques, Sara, Marques, J. Tiago, Sá, Pedro, Amendoeira, Vitor, Marques, Carina, Marques, Paulo, Marrecas, Pedro Caetano, Martins, Frederico, Martins, Raquel, Mascarenhas, Miguel, Mata, Vanessa A., Mateus, Ana Rita, Matos, Milene, Sabino‐Marques, Helena, Medinas, Denis, Amorim, Francisco, Mendes, Tiago, Mendes, Gabriel, Mestre, Frederico, Milhinhas, Catarina, Mira, António, Monarca, Rita I., Monteiro, Norberto, Monteiro, Barbara, Salgueiro, Vânia, Monterroso, Pedro, Nakamura, Mónia, Silva Aparício, Guilherme, Negrões, Nuno, Nóbrega, Eva K., Nóvoa, Miguel, Nunes, Manuel, Nunes, Nuno Jardim, Oliveira, Flávio, Oliveira, José Miguel, Santos, Helena, M. Palmeirim, Jorge, Pargana, João, Paula, Anabela, Araújo, Ricardo, Paupério, Joana, Pedroso, Nuno M., Pereira, Guilherme, Pereira, Pedro F., Pereira, José, Pereira, Maria João Ramos, Santos, Joana, Petrucci-Fonseca, Francisco, Pimenta, Miguel, Pinto, Sara, Pinto, Nuno, Ascensão, Fernando, Pires, Rosa, Pita, Ricardo, Pontes, Carlos, Quaresma, Marisa, Queirós, João, Barbosa, A. Márcia, Queirós, Luís, Rainho, Ana, Graça Ramalhinho, Maria, Ramalho, Patrícia, Raposeira, Helena, Augusto, Margarida, Rasteiro, Francisco, Rebelo, Hugo, Regala, Frederico Tátá, Reto, Dyana, Jones, Kate E., Ribeiro, Sérgio Bruno, Rio‐Maior, Helena, Rocha, Ricardo, Rocha, Rita Gomes, Rodrigues, Luísa, Román, Jacinto, Bandeira, Victor, Roque, Sara, Santos, João P. V., Santos, Nuno, Santos, Sara, Santos, Carlos Pedro, Santos-Reis, Margarida, Serronha, Ana, Sierra, Pablo, Silva, Bruno, Silva, Carla S. G. M., Silva, Clara, Laborde, Marina I., Barbosa, Soraia, Silva, Diogo, Silva, Luís P., Silva, Ricardo, Silva, Carmen, Silva Júnior, Flavio Manoel Rodrigues, Sousa, Pedro, Sousa‐Guedes, Diana, Spadoni, Giulia, Tapisso, Joaquim T., Oliveira, Luís Lamas, Teixeira, Daniela, Barbosa, Sérgio, Teixeira, Sérgio, Teixeira, Nuno, Torres, Rita T., Travassos, Paulo, Vale‐Gonçalves, Hélia, Cidraes‐Vieira, Nuno, Merten, Sophie, Luz Mathias, Maria, Leitão, Inês, Barreiro, Silvia, Barros, Paulo, Barros, Tânia, Barros, Filomena, Pinto Basto, Mafalda, Bernardino, Joana, Bicho, Sara, Biedma, Luis Eduardo, Borges, Marta, Braz, Luis, Lemos, Rita, Brito, José Carlos, Brito, Tiago, Cabral, João Alexandre, Calzada, Javier, Camarinha, Cláudia, Carapuço, Mafalda, Cardoso, Paulo, Carmo, Mário, Carrapato, Carlos, Silva Carrilho, Maílis, Lima, Cátia, Carvalho, Diogo Filipe T. C. S., Carvalho, Filipe, Carvalho, João, Castro, Diana, Castro, Guilherme, Castro, Joana, Castro, Luis Roma, Catry, Filipe Xavier, Cerveira, Ana M., Cid, André, Linck, Paloma, Clarke, Rafael, Conde, Conceição, Conde, José, Costa, Jorge, Costa, Mafalda, Costa, Pedro, Costa, Cristina, Couto, André Pedro, Craveiro, João, Dias, Marta, Lopes, Hugo, Dias, Sofia, and Repositório da Universidade de Lisboa

Abstract

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.

Published
2022

25. The Global Virome in One Network (VIRION): an Atlas of Vertebrate-Virus Associations

Author

Carlson, Colin J., primary, Gibb, Rory J., additional, Albery, Gregory F., additional, Brierley, Liam, additional, Connor, Ryan P., additional, Dallas, Tad A., additional, Eskew, Evan A., additional, Fagre, Anna C., additional, Farrell, Maxwell J., additional, Frank, Hannah K., additional, Muylaert, Renata L., additional, Poisot, Timothée, additional, Rasmussen, Angela L., additional, Ryan, Sadie J., additional, and Seifert, Stephanie N., additional

Published
2022
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26. MAMMALS IN PORTUGAL: A data set of terrestrial, volant, and marine mammal occurrences in Portugal

Author

Grilo, Clara, primary, Afonso, Beatriz C., additional, Afonso, Filipe, additional, Alexandre, Marta, additional, Aliácar, Sara, additional, Almeida, Ana, additional, Alonso, Ivan Prego, additional, Álvares, Francisco, additional, Alves, Paulo, additional, Alves, Paulo Célio, additional, Alves, Pedro, additional, Amado, Anabela, additional, Amendoeira, Vitor, additional, Amorim, Francisco, additional, da Silva Aparício, Guilherme, additional, Araújo, Ricardo, additional, Ascensão, Fernando, additional, Augusto, Margarida, additional, Bandeira, Victor, additional, Barbosa, A. Márcia, additional, Barbosa, Soraia, additional, Barbosa, Sérgio, additional, Barreiro, Silvia, additional, Barros, Paulo, additional, Barros, Tânia, additional, Barros, Filomena, additional, Basto, Mafalda, additional, Bernardino, Joana, additional, Bicho, Sara, additional, Biedma, Luis Eduardo, additional, Borges, Marta, additional, Braz, Luis, additional, Brito, José Carlos, additional, Brito, Tiago, additional, Cabral, João Alexandre, additional, Calzada, Javier, additional, Camarinha, Cláudia, additional, Carapuço, Mafalda, additional, Cardoso, Paulo, additional, Carmo, Mário, additional, Carrapato, Carlos, additional, da Silva Carrilho, Maílis, additional, Carvalho, Diogo Filipe T. C. S., additional, Carvalho, Filipe, additional, Carvalho, João, additional, Castro, Diana, additional, Castro, Guilherme, additional, Castro, Joana, additional, Castro, Luis Roma, additional, Catry, Filipe Xavier, additional, Cerveira, Ana M., additional, Cid, André, additional, Clarke, Rafael, additional, Conde, Conceição, additional, Conde, José, additional, Costa, Jorge, additional, Costa, Mafalda, additional, Costa, Pedro, additional, Costa, Cristina, additional, do Couto, André Pedro, additional, Craveiro, João, additional, Dias, Marta, additional, Dias, Sofia, additional, Duarte, Beatriz, additional, Duro, Virginia, additional, Encarnação, Cláudia, additional, Eufrázio, Sofia, additional, Fael, António, additional, Falé, João Salvador, additional, Faria, Sandra, additional, Fernandes, Carlos, additional, Fernandes, Margarida, additional, da Costa, Gonçalo Ferrão, additional, Ferreira, Clara, additional, Ferreira, Diogo F., additional, Ferreira, Eduardo, additional, Ferreira, Joaquim Pedro, additional, Ferreira, João, additional, Ferreira, Diana, additional, Fonseca, Carlos, additional, Fontes, Inês, additional, Fragoso, Ricardo, additional, Franco, Claudia, additional, Freitas, Tamira, additional, Gabriel, Sofia I., additional, Gibb, Rory, additional, Gil, Patricia, additional, Gomes, Carla Patricia Jorge, additional, Horta, Pedro, additional, Gomes, Pedro, additional, Gomes, Verónica, additional, Grilo, Filipa, additional, Guedes, Américo, additional, Guilherme, Filipa, additional, Gutiérrez, Iván, additional, Harper, Henry, additional, Herrera, José M., additional, Hipólito, Dário, additional, Infante, Samuel, additional, Jesus, José, additional, Jones, Kate E., additional, Laborde, Marina I., additional, de Oliveira, Luís Lamas, additional, Leitão, Inês, additional, Lemos, Rita, additional, Lima, Cátia, additional, Linck, Paloma, additional, Lopes, Hugo, additional, Lopes, Susana, additional, López‐Baucells, Adrià, additional, Loureiro, Armando, additional, Loureiro, Filipa, additional, Lourenço, Rui, additional, Lourenço, Sofia, additional, Lucas, Paula, additional, Magalhães, Ana, additional, Maldonado, Cristina, additional, Marcolin, Fabio, additional, Marques, Sara, additional, Marques, J. Tiago, additional, Marques, Carina, additional, Marques, Paulo, additional, Marrecas, Pedro Caetano, additional, Martins, Frederico, additional, Martins, Raquel, additional, Mascarenhas, Miguel, additional, Mata, Vanessa A., additional, Mateus, Ana Rita, additional, Matos, Milene, additional, Medinas, Denis, additional, Mendes, Tiago, additional, Mendes, Gabriel, additional, Mestre, Frederico, additional, Milhinhas, Catarina, additional, Mira, António, additional, Monarca, Rita I., additional, Monteiro, Norberto, additional, Monteiro, Barbara, additional, Monterroso, Pedro, additional, Nakamura, Mónia, additional, Negrões, Nuno, additional, Nóbrega, Eva K., additional, Nóvoa, Miguel, additional, Nunes, Manuel, additional, Nunes, Nuno Jardim, additional, Oliveira, Flávio, additional, Oliveira, José Miguel, additional, Palmeirim, Jorge M., additional, Pargana, João, additional, Paula, Anabela, additional, Paupério, Joana, additional, Pedroso, Nuno M., additional, Pereira, Guilherme, additional, Pereira, Pedro F., additional, Pereira, José, additional, Pereira, Maria João Ramos, additional, Petrucci‐Fonseca, Francisco, additional, Pimenta, Miguel, additional, Pinto, Sara, additional, Pinto, Nuno, additional, Pires, Rosa, additional, Pita, Ricardo, additional, Pontes, Carlos, additional, Quaresma, Marisa, additional, Queirós, João, additional, Queirós, Luís, additional, Rainho, Ana, additional, da Graça Ramalhinho, Maria, additional, Ramalho, Patrícia, additional, Raposeira, Helena, additional, Rasteiro, Francisco, additional, Rebelo, Hugo, additional, Regala, Frederico Tátá, additional, Reto, Dyana, additional, Ribeiro, Sérgio Bruno, additional, Rio‐Maior, Helena, additional, Rocha, Ricardo, additional, Rocha, Rita Gomes, additional, Rodrigues, Luísa, additional, Román, Jacinto, additional, Roque, Sara, additional, Rosalino, Luís Miguel, additional, do Rosário, Inês T., additional, Rossa, Mariana, additional, Russo, Danilo, additional, Sá, Pedro, additional, Sabino‐Marques, Helena, additional, Salgueiro, Vânia, additional, Santos, Helena, additional, Santos, Joana, additional, Santos, João P. V., additional, Santos, Nuno, additional, Santos, Sara, additional, Santos, Carlos Pedro, additional, Santos‐Reis, Margarida, additional, Serronha, Ana, additional, Sierra, Pablo, additional, Silva, Bruno, additional, Silva, Carla S. G. M., additional, Silva, Clara, additional, Silva, Diogo, additional, da Silva, Luís P., additional, Silva, Ricardo, additional, Silva, Carmen, additional, da Silva Júnior, Flavio Manoel Rodrigues, additional, Sousa, Pedro, additional, Sousa‐Guedes, Diana, additional, Spadoni, Giulia, additional, Tapisso, Joaquim T., additional, Teixeira, Daniela, additional, Teixeira, Sérgio, additional, Teixeira, Nuno, additional, Torres, Rita T., additional, Travassos, Paulo, additional, Vale‐Gonçalves, Hélia, additional, Cidraes‐Vieira, Nuno, additional, von Merten, Sophie, additional, and da Luz Mathias, Maria, additional

Published
2022
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30. The future of zoonotic risk prediction

Author

Carlson, Colin J., primary, Farrell, Maxwell J., additional, Grange, Zoe, additional, Han, Barbara A., additional, Mollentze, Nardus, additional, Phelan, Alexandra L., additional, Rasmussen, Angela L., additional, Albery, Gregory F., additional, Bett, Bernard, additional, Brett-Major, David M., additional, Cohen, Lily E., additional, Dallas, Tad, additional, Eskew, Evan A., additional, Fagre, Anna C., additional, Forbes, Kristian M., additional, Gibb, Rory, additional, Halabi, Sam, additional, Hammer, Charlotte C., additional, Katz, Rebecca, additional, Kindrachuk, Jason, additional, Muylaert, Renata L., additional, Nutter, Felicia B., additional, Ogola, Joseph, additional, Olival, Kevin J., additional, Rourke, Michelle, additional, Ryan, Sadie J., additional, Ross, Noam, additional, Seifert, Stephanie N., additional, Sironen, Tarja, additional, Standley, Claire J., additional, Taylor, Kishana, additional, Venter, Marietjie, additional, and Webala, Paul W., additional

Published
2021
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31. Data Proliferation, Reconciliation, and Synthesis in Viral Ecology

Author

Gibb, Rory, primary, Albery, Gregory F, additional, Becker, Daniel J, additional, Brierley, Liam, additional, Connor, Ryan, additional, Dallas, Tad A, additional, Eskew, Evan A, additional, Farrell, Maxwell J, additional, Rasmussen, Angela L, additional, Ryan, Sadie J, additional, Sweeny, Amy, additional, Carlson, Colin J, additional, and Poisot, Timothée, additional

Published
2021
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33. The Global Virome in One Network (VIRION): an atlas of vertebrate-virus associations

Author

Carlson, Colin J., primary, Gibb, Rory J., additional, Albery, Gregory F., additional, Brierley, Liam, additional, Connor, Ryan P., additional, Dallas, Tad A., additional, Eskew, Evan A., additional, Fagre, Anna C., additional, Farrell, Maxwell J., additional, Frank, Hannah K., additional, Muylaert, Renata L., additional, Poisot, Timothée, additional, Rasmussen, Angela L., additional, Ryan, Sadie J., additional, and Seifert, Stephanie N., additional

Published
2021
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35. Zoonotic Risk Technology Enters the Viral Emergence Toolkit

Author

Carlson, Colin, primary, Farrell, Maxwell, additional, Grange, Zoe, additional, Han, Barbara, additional, Mollentze, Nardus, additional, Phelan, Alexandra, additional, Rasmussen, Angela, additional, Albery, Gregory, additional, Bett, Bernard, additional, Brett-Major, David, additional, Cohen, Lily, additional, Dallas, Tad, additional, Eskew, Evan, additional, Fagre, Anna, additional, Forbes, Kristian, additional, Gibb, Rory, additional, Halabi, Sam, additional, Hammer, Charlotte, additional, Katz, Rebecca, additional, Kindrachuk, Jason, additional, Muylaert, Renata, additional, Nutter, Felicia, additional, Ogola, Joseph, additional, Olival, Kevin, additional, Rourke, Michelle, additional, Ryan, Sadie, additional, Ross, Noam, additional, Seifert, Stephanie, additional, Sironen, Tarja, additional, Standley, Claire, additional, Taylor, Kishana, additional, Venter, Marietje, additional, and Webala, Paul, additional

Published
2021
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37. Spatiotemporal analysis of surveillance data enables climate-based forecasting of Lassa fever

Author

Redding, David W., primary, Gibb, Rory, additional, Dan-Nwafor, Chioma C., additional, Ilori, Elsie A., additional, Usman, Yashe Rimamdeyati, additional, Saliu, Oladele H., additional, Michael, Amedu O., additional, Akanimo, Iniobong, additional, Ipadeola, Oladipupo B., additional, Enright, Lauren, additional, Donnelly, Christl A., additional, Abubakar, Ibrahim, additional, Jones, Kate E., additional, and Ihekweazu, Chikwe, additional

Published
2020
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38. Bat detective—Deep learning tools for bat acoustic signal detection

Author

Mac Aodha, Oisin, Gibb, Rory, Barlow, Kate E., Browning, Ella, Firman, Michael, Freeman, Robin, Harder, Briana, Kinsey, Libby, Mead, Gary R., Newson, Stuart E., Pandourski, Ivan, Parsons, Stuart, Russ, Jon, Szodoray-Paradi, Abigel, Szodoray-Paradi, Farkas, Tilova, Elena, Girolami, Mark, Brostow, Gabriel, and Jones, Kate E.

Subjects
Computer and Information Sciences, Neural Networks, Physiology, Audio Signal Processing, Sensory Physiology, Research and Analysis Methods, Machine Learning, Chiroptera, Bats, Acoustic Signals, Medicine and Health Sciences, Animals, Animal Signaling and Communication, Mammals, Behavior, Animal Behavior, Physics, Applied Mathematics, Simulation and Modeling, Endangered Species, Organisms, Biology and Life Sciences, Eukaryota, Computational Biology, Signal Processing, Computer-Assisted, Acoustics, Sensory Systems, Auditory System, Echolocation, Physical Sciences, Vertebrates, Amniotes, Signal Processing, Engineering and Technology, Animal Migration, Neural Networks, Computer, Zoology, Bioacoustics, Mathematics, Algorithms, Research Article, Animal Navigation, Neuroscience, Environmental Monitoring
Abstract

Passive acoustic sensing has emerged as a powerful tool for quantifying anthropogenic impacts on biodiversity, especially for echolocating bat species. To better assess bat population trends there is a critical need for accurate, reliable, and open source tools that allow the detection and classification of bat calls in large collections of audio recordings. The majority of existing tools are commercial or have focused on the species classification task, neglecting the important problem of first localizing echolocation calls in audio which is particularly problematic in noisy recordings. We developed a convolutional neural network based open-source pipeline for detecting ultrasonic, full-spectrum, search-phase calls produced by echolocating bats. Our deep learning algorithms were trained on full-spectrum ultrasonic audio collected along road-transects across Europe and labelled by citizen scientists from www.batdetective.org. When compared to other existing algorithms and commercial systems, we show significantly higher detection performance of search-phase echolocation calls with our test sets. As an example application, we ran our detection pipeline on bat monitoring data collected over five years from Jersey (UK), and compared results to a widely-used commercial system. Our detection pipeline can be used for the automatic detection and monitoring of bat populations, and further facilitates their use as indicator species on a large scale. Our proposed pipeline makes only a small number of bat specific design decisions, and with appropriate training data it could be applied to detecting other species in audio. A crucial novelty of our work is showing that with careful, non-trivial, design and implementation considerations, state-of-the-art deep learning methods can be used for accurate and efficient monitoring in audio., Author summary There is a critical need for robust and accurate tools to scale up biodiversity monitoring and to manage the impact of anthropogenic change. For example, the monitoring of bat species and their population dynamics can act as an important indicator of ecosystem health as they are particularly sensitive to habitat conversion and climate change. In this work we propose a fully automatic and efficient method for detecting bat echolocation calls in noisy audio recordings. We show that our approach is more accurate compared to existing algorithms and other commercial tools. Our method enables us to automatically estimate bat activity from multi-year, large-scale, audio monitoring programmes.

Published
2018

39. Climate and land-use change homogenise terrestrial biodiversity, with consequences for ecosystem functioning and human well-being

Author

Newbold, Tim, additional, Adams, Georgina L., additional, Albaladejo Robles, Gonzalo, additional, Boakes, Elizabeth H., additional, Braga Ferreira, Guilherme, additional, Chapman, Abbie S. A., additional, Etard, Adrienne, additional, Gibb, Rory, additional, Millard, Joseph, additional, Outhwaite, Charlotte L., additional, and Williams, Jessica J., additional

Published
2019
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47. Bat Detective - Deep Learning Tools for Bat Acoustic Signal Detection

Author

Aodha, Oisin Mac, primary, Gibb, Rory, additional, Barlow, Kate E., additional, Browning, Ella, additional, Firman, Michael, additional, Freeman, Robin, additional, Harder, Briana, additional, Kinsey, Libby, additional, Mead, Gary R., additional, Newson, Stuart E., additional, Pandourski, Ivan, additional, Parsons, Stuart, additional, Russ, Jon, additional, Szodoray-Paradi, Abigel, additional, Szodoray-Paradi, Farkas, additional, Tilova, Elena, additional, Girolami, Mark, additional, Brostow, Gabriel, additional, and Jones, Kate E., additional

Published
2017
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48. Emerging opportunities and challenges for passive acoustics in ecological assessment and monitoring.

Author

Gibb, Rory, Browning, Ella, Glover‐Kapfer, Paul, Jones, Kate E., and Börger, Luca

Subjects
ACOUSTICS, ACOUSTIC transducers, ENVIRONMENTAL monitoring, BIODIVERSITY, MACHINE learning
Abstract

High‐throughput environmental sensing technologies are increasingly central to global monitoring of the ecological impacts of human activities. In particular, the recent boom in passive acoustic sensors has provided efficient, noninvasive, and taxonomically broad means to study wildlife populations and communities, and monitor their responses to environmental change. However, until recently, technological costs and constraints have largely confined research in passive acoustic monitoring (PAM) to a handful of taxonomic groups (e.g., bats, cetaceans, birds), often in relatively small‐scale, proof‐of‐concept studies.The arrival of low‐cost, open‐source sensors is now rapidly expanding access to PAM technologies, making it vital to evaluate where these tools can contribute to broader efforts in ecology and biodiversity research. Here, we synthesise and critically assess the current emerging opportunities and challenges for PAM for ecological assessment and monitoring of both species populations and communities.We show that terrestrial and marine PAM applications are advancing rapidly, facilitated by emerging sensor hardware, the application of machine learning innovations to automated wildlife call identification, and work towards developing acoustic biodiversity indicators. However, the broader scope of PAM research remains constrained by limited availability of reference sound libraries and open‐source audio processing tools, especially for the tropics, and lack of clarity around the accuracy, transferability and limitations of many analytical methods.In order to improve possibilities for PAM globally, we emphasise the need for collaborative work to develop standardised survey and analysis protocols, publicly archived sound libraries, multiyear audio datasets, and a more robust theoretical and analytical framework for monitoring vocalising animal communities. [ABSTRACT FROM AUTHOR]

Published
2019
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50. Frontline Politics.

Author

Gibb, Rory

Abstract

The article discusses the musical style of underground artist Gaika Tavares, while also discussing his second mixtape titled 'Security'.

Published
2016

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