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Number of items: 60.
2024
Davis, Christopher N., Crump, Ronald E., Sutherland, Samuel A., Spencer, Simon E. F., Corbella, Alice, Chansey, Shampa, Lebuki, Junior, Miaka, Erick Mwamba and Rock, Kat S. (2024) Comparison of stochastic and deterministic models for gambiense sleeping sickness at different spatial scales : a health area analysis in the DRC. PLoS Computational Biology, 20 (4). e1011993. doi:10.1371/journal.pcbi.1011993 ISSN 1553-7358.
Monod, MΓ©lodie, Brizzi, Andrea, Galiwango, Ronald M., Ssekubugu, Robert, Chen, Yu, Xi, Xiaoyue, Kankaka, Edward Nelson, Ssempijja, Victor, Abeler DΓΆrner, Lucie, Akullian, Adam et al.
(2024)
Longitudinal population-level HIV epidemiological and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda.
Nature Microbiology, 9
.
pp. 35-54.
doi:10.1038/s41564-023-01530-8
ISSN 2058-5276.
2023
Crellen, Thomas, Haswell, Melissa, Sithithaworn, Paiboon, Sayasone, Somphou, Odermatt, Peter, Lamberton, Poppy H. L., Spencer, Simon E. F. and DΓ©irdre Hollingsworth, T. (2023) Diagnosis of helminths depends on worm fecundity and the distribution of parasites within hosts. Proceedings of the Royal Society B: Biological Sciences, 290 (1991). 20222204. doi:10.1098/rspb.2022.2204 ISSN 0962-8452.
2022
Corbella, Alice, Spencer, Simon E. F. and Roberts, Gareth O. (2022) Automatic Zig Zag sampling in practice. Statistics and Computing, 32 . 107. doi:10.1007/s11222-022-10142-x ISSN 0960-3174.
Iacovidou, Melissa, Barreaux, Priscille, Spencer, Simon E. F., Thomas, Matthew B., Gorsich, Erin E. and Rock, Kat S. (2022) Omitting age-dependent mosquito mortality in malaria models underestimates the effectiveness of insecticide-treated nets. PLoS Computational Biology, 18 (9). e1009540. doi:10.1371/journal.pcbi.1009540 ISSN 1553-7358.
Crump, Ronald E., Huang, Ching-I, Spencer, Simon E. F., Brown, Paul E., Shampa, Chansy, Mwamba Miaka, Erick and Rock, Kat S. (2022) Modelling to infer the role of animals in gambiense human African trypanosomiasis transmission and elimination in the DRC. PLOS Neglected Tropical Diseases, 16 (7). e0010599. doi:10.1371/journal.pntd.0010599 ISSN 1935-2735.
Rakai Health Sciences Program and PANGEA-HIV (Including: Xi, Xiaoyue, Spencer, Simon E. F., Hall, Matthew, Grabowski, M. Kate, Kagaayi, Joseph and Ratmann, Oliver). (2022) Inferring the sources of HIV infection in Africa from deep-sequence data with semi-parametric Bayesian Poisson flow models. Journal of the Royal Statistical Society: Series C (Applied Statistics), 71 (3). pp. 517-540. doi:10.1111/rssc.12544 ISSN 0035-9254.
Palacio Lozano, Diana Catalina, Jones, Hugh E., Gavard, Remy, Thomas, Mary J., RamΓrez, Claudia , Wootton, Christopher, Sarmiento Chaparro, JosΓ© AristΓ³bulo, OβConnor, Peter B., Spencer, Simon E. F., Rossell, David, Mejia-Ospino, Enrique, Witt, Matthias and Barrow, Mark P. (2022) Revealing the reactivity of individual chemical entities in complex mixtures : the chemistry behind bio-oil upgrading. Analytical Chemistry, 94 (21). pp. 7536-7544. doi:10.1021/acs.analchem.2c00261 ISSN 1520-6882.
Huang, Ching-I, Crump, Ronald E., Brown, Paul E., Spencer, Simon E. F., Mwamba Miaka, Erick, Shampa, Chansy, Keeling, Matthew James and Rock, Kat S. (2022) Identifying regions for enhanced control of gambiense sleeping sickness in the Democratic Republic of Congo. Nature Communications, 13 (1). 1448. doi:10.1038/s41467-022-29192-w ISSN 2041-1723.
2021
Retkute, Renata, Touloupou, Panayiota, BasÑñez, Maria-Gloria, Hollingsworth, T. Deirdre and Spencer, Simon E. F. (2021) Integrating geostatistical maps and infectious disease transmission models using adaptive multiple importance sampling. Annals of Applied Statistics, 15 (4). pp. 1980-1998. doi:10.1214/21-AOAS1486 ISSN 1932-6157.
Das, Aatreyee M., Chitnis, Nakul, Burri, Christian, Paris, Daniel H., Patel, Swati, Spencer, Simon E. F., Miaka, Erick M. and Castano, Soledad (2021) Modelling the impact of fexinidazole use on human African trypanosomiasis (HAT) transmission in the Democratic Republic of the Congo. PLoS Neglected Tropical Diseases, 15 (11). e0009992. doi:10.1371/journal.pntd.0009992 ISSN 1935-2727.
Tennant, Warren, Cardinale, Eric, CΓͺtre-Sossah, Catherine, Moutroifi, Youssouf, Le Godais, Gilles, Colombi, Davide, Spencer, Simon E. F., Tildesley, Michael J., Keeling, Matt J., Charafouddine, Onzade, Colizza, Vittoria, Edmunds, W. John and MΓ©tras, RaphaΓ«lle (2021) Modelling the persistence and control of Rift Valley fever virus in a spatially heterogeneous landscape. Nature Communications, 12 (1). 5593. doi:10.1038/s41467-021-25833-8 ISSN 2041-1723.
Spencer, Simon E. F. (2021) Accelerating adaptation in the adaptive Metropolis-Hastings random walk algorithm. The Australian & New Zealand Journal of Statistics, 63 (3). pp. 468-484. doi:10.1111/anzs.12344 ISSN 1369-1473.
Davis, Christopher N., Castano, Maria Soledad, Aliee, Maryam, Patel, Swati, Miaka, Erick Mwamba, Keeling, Matthew James, Spencer, Simon E. F., Chitnis, Nakul and Rock, Kat S. (2021) Modelling to quantify the likelihood that local elimination of transmission has occurred using routine gambiense human African trypanosomiasis surveillance data. Clinical Infectious Diseases . ciab190. doi:10.1093/cid/ciab190 ISSN 1058-4838.
Toor, Jaspreet, Adams, Emily R., Aliee, Maryam, Amoah, Benjamin, Anderson, Roy M., Ayabina, Diepreye, Bailey, Robin, BasÑñez, Maria-Gloria, Blok, David J., Blumberg, Seth et al.
(2021)
Predicted impact of COVID-19 on neglected tropical disease programs and the opportunity for innovation.
Clinical Infectious Diseases, 72
(8).
pp. 1463-1466.
doi:10.1093/cid/ciaa933
ISSN 1058-4838.
Aliee, Maryam, CastaΓ±o, Soledad, Davis, Christopher N., Patel, Swati, Miaka, Erick Mwamba, Spencer, Simon E. F., Keeling, Matt J., Chitnis, Nakul and Rock, Kat S. (2021) Predicting the impact of COVID-19 interruptions on transmission of gambiense human African trypanosomiasis in two health zones of the Democratic Republic of Congo. Transactions of the Royal Society of Tropical Medicine and Hygiene, 115 (3). pp. 245-252. trab019. doi:10.1093/trstmh/trab019 ISSN 0035-9203.
Benschop, Jackie, Nisa, Shahista and Spencer, Simon E. F. (2021) Still 'dairy farm fever'? A Bayesian model for Leptospirosis notification data in New Zealand. Journal of The Royal Society Interface, 18 (175). 20200964. doi:10.1098/rsif.2020.0964 ISSN 1742-5689.
Crump, Ronald E., Huang, Ching-I, Knock, Edward, Spencer, Simon E. F., Brown, Paul E., Mwamba Miaka, Erick, Shampa, Chansy, Keeling, Matthew James and Rock, Kat S. (2021) Quantifying epidemiological drivers of gambiense human African Trypanosomiasis across the Democratic Republic of Congo. PLoS Computational Biology, 17 (1). e1008532. doi:10.1371/journal.pcbi.1008532 ISSN 1553-7358.
Spencer, Simon E. F., Franco, Jacopo and Rodger, Alison (2021) Bayesian inference assessment of protein secondary structure analysis using circular dichroism data β how much structural information is contained in protein circular dichroism spectra? Analytical Methods, 13 (3). pp. 359-368. doi:10.1039/D0AY01645D ISSN 1759-9660.
2020
Touloupou, Panayiota, FinkenstΓ€dt, BΓ€rbel, Besser, Thomas E., French, Nigel P. and Spencer, Simon E. F. (2020) Bayesian inference for multi-strain epidemics with application to Escherichia coli O157 : H7 in feedlot cattle. The Annals of Applied Statistics, 14 (4). pp. 1925-1944. doi:10.1214/20-AOAS1366 ISSN 1932-6157.
Griffin, Adam, Roberts, Gareth O. and Spencer, Simon E. F. (2020) An epidemic model for an evolving pathogen with strain-dependent immunity. Mathematical Biosciences, 330 . 108480. doi:10.1016/j.mbs.2020.108480 ISSN 0025-5564.
Touloupou, Panayiota, Retkute, Renata, Hollingsworth, T. DΓ©irdre and Spencer, Simon E. F. (2020) Statistical methods for linking geostatistical maps and transmission models : application to lymphatic filariasis in East Africa. Spatial and Spatio-temporal Epidemiology, 41 . 100391. doi:10.1016/j.sste.2020.100391 ISSN 1877-5845.
Gavard, Remy, Jones, Hugh E., Palacio Lozano, Diana Catalina, Thomas, Mary Joanna, Rossell, David, Spencer, Simon E.F. and Barrow, Mark P. (2020) KairosMS : a new solution for the processing of hyphenated ultrahigh resolution mass spectrometry data. Analytical Chemistry, 92 (5). pp. 3775-3786. doi:10.1021/acs.analchem.9b05113 ISSN 0003-2700.
Rakai Health Sciences Program, Pangea HIV Consortium (Including:
Ratmann, Oliver, Kagaayi, Joseph, Hall, Matthew, Golubchick, Tanya, Kigozi, Godfrey, Xi, Xiaoyue, Wymant, Chris, Nakigozi, Gertrude, Abeler-DΓΆrner, Lucie, Bonsall, David et al.
).
(2020)
Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities : a population-based study in Rakai, Uganda.
The Lancet HIV, 7
(3).
e173-e183.
doi:10.1016/S2352-3018(19)30378-9
ISSN 2352-3018.
Chapman, Lloyd A. C., Spencer, Simon E. F., Pollington, Timothy M., Jewell, Chris P., Mondal, Dinesh, Alvar, Jorge, Hollingsworth, T. Deirdre, Cameron, Mary M., Bern, Caryn and Medley, Graham (2020) Inferring transmission trees to guide targeting of interventions against visceral leishmaniasis and post-kala-azar dermal leishmaniasis. Proceedings of the National Academy of Sciences, 117 (41). pp. 25742-25750. doi:10.1073/pnas.2002731117 ISSN 0027-8424.
Tennant, Warren, Tildesley, Michael J., Spencer, Simon E. F. and Keeling, Matthew James (2020) Climate drivers of plague epidemiology in British India, 1898β1949. Proceedings of the Royal Society B: Biological Sciences, 287 (1928). 20200538. doi:10.1098/rspb.2020.0538 ISSN 0962-8452.
Touloupou, P., Finkenstadt-Rand, B. F. and Spencer, Simon E. F. (2020) Scalable Bayesian inference for coupled hidden Markov and semi-Markov models. Journal for Computational and Graphical Statistics, 29 (2). pp. 238-249. doi:10.1080/10618600.2019.1654880 ISSN 1061-8600.
Touloupou, Panayiota, FinkenstΓ€dt, BΓ€rbel and Spencer, Simon E. F. (2020) Scalable Bayesian inference for coupled hidden Markov and semi-Markov models. Journal of Computational and Graphical Statistics, 29 (2). 238-249 . doi:10.1080/10618600.2019.1654880 ISSN 1537-2715.
2019
Gavard, Remy, Palacio Lozano, Diana Catalina, Guzman, Alexander, Rossell, David, Spencer, Simon E. F. and Barrow, Mark P. (2019) Rhapso : automatic stitching of mass segments from fourier transform ion cyclotron resonance mass spectra. Analytical Chemistry, 91 (23). pp. 15130-15137. doi:10.1021/acs.analchem.9b03846 ISSN 0003-2700.
McKinley, Trevelyan J., Neal, Peter, Spencer, Simon E. F., Conlan, Andrew J. K. and Tiley, Laurence (2019) Efficient Bayesian model choice for partially observed processes : with application to an experimental transmission study of an infectious disease. Bayesian Analysis . doi:10.1214/19-BA1174 ISSN 1931-6690.
Touloupou, Panayiota, FinkenstΓ€dt, BΓ€rbel and Spencer, Simon E. F. (2019) Data for Scalable Bayesian inference for coupled hidden Markov and semi-Markov models. [Dataset]
Palacio Lozano, Diana Catalina, Gavard, Remy, Arenas-Diaz, Juan P., Thomas, Mary J., Stranz, David D., Meija-Ospino, Enrique, Guzman, Alexander, Spencer, Simon E. F., Rossell, David and Barrow, Mark P. (2019) Pushing the analytical limits : new insights into complex mixtures using mass spectra segments of constant ultrahigh resolving power. Chemical Science, 10 (29). pp. 6966-6978. doi:10.1039/C9SC02903F ISSN 2041-6520.
2018
Chapman, Lloyd A. C., Jewell, Chris P., Spencer, Simon E. F., Pellis, Lorenzo, Datta, Samik, Chowdhury, Rajib, Bern, Caryn, Medley, Graham and Hollingsworth, T. DΓ©irdre (2018) The role of case proximity in transmission of visceral leishmaniasis in a highly endemic village in Bangladesh. PLoS Neglected Tropical Diseases, 12 (10). e0006453. doi:10.1371/journal.pntd.0006453 ISSN 1935-2727.
Spencer, Rachel A., Spencer, Simon E. F., Rodgers, Sarah, Campbell, Stephen and Avery, Anthony (2018) Processing of discharge summaries in general practice : a retrospective record review. British Journal of General Practice, 68 (673). e576-e585. doi:10.3399/bjgp18X697877 ISSN 0960-1643.
Spencer, Rachel, Spencer, Simon E. F., Rodgers, Sarah, Campbell, Stephen M. and Avery, Anthony John (2018) Processing of discharge summaries in general practice : a retrospective record review. British Journal of General Practice, 68 (673). e576-e585. doi:10.3399/bjgp18X697877 ISSN 0960-1643.
Alzahrani, Naif, Neal, Peter, Spencer, Simon E. F., McKinley, Trevelyan J. and Touloupou, Panayiota (2018) Model selection for time series of count data. Computational Statistics & Data Analysis, 122 . pp. 33-44. doi:10.1016/j.csda.2018.01.002 ISSN 0167-9473.
Touloupou, Panayiota, Alzahrani, Naif, Neal, Peter, Spencer, Simon E. F. and McKinley, Trevelyan J. (2018) Efficient model comparison techniques for models requiring large scale data augmentation. Bayesian Analysis, 13 (2). pp. 437-459. doi:10.1214/17-BA1057 ISSN 1931-6690.
2017
Ahlstrom, Christina, Muellner, Petra, Spencer, Simon E. F., Hong, Samuel, Saupe, Amy, Rovira, Albert, Hedberg, Craig, Perez, Andres, Muellner, Ulrich and Alvarez, Julio (2017) Inferring source attribution from a multi-year multi-source dataset of Salmonella in Minnesota. Zoonoses and Public Health, 64 (8). pp. 589-598. doi:10.1111/zph.12351 ISSN 1863-1959.
Gavard, Remy, Rossell, David, Spencer, Simon E. F. and Barrow, Mark P. (2017) Themis : batch preprocessing for ultrahigh-resolution mass spectra of complex mixtures. Analytical Chemistry, 89 (21). pp. 11383-11390. doi:10.1021/acs.analchem.7b02345 ISSN 0003-2700.
Griffin, Adam, Jenkins, Paul, Roberts, Gareth O. and Spencer, Simon E. F. (2017) Simulation from quasi-stationary distributions on reducible state spaces. Advances in Applied Probability, 49 (3). pp. 960-980. doi:10.1017/apr.2017.28 ISSN 0001-8678.
Hill, Steven M. (Mark), Nesser, Nicole K., Johnson-Camacho, Katie, Jeffress, Mara, Johnson, Aimee, Boniface, Chris, Spencer, Simon E. F., Lu, Yiling, Heiser, Laura M., Lawrence, Yancey, Pande, Nupur T., Korkola, James, Gray, Joe W., Mills, Gordon B., Mukherjee, Sach and Spellman, Paul T. (2017) Context-specificity in causal signaling networks revealed by phosphoprotein profiling. Cell Systems, 4 (1). 73-83.e10. doi:10.1016/j.cels.2016.11.013 ISSN 2405-4712.
2015
Spencer, Simon E. F., Besser, Thomas E., Cobbold, Rowland N. and French, Nigel P. (2015) βSuper' or just βabove average'? Supershedders and the transmission of Escherichia coli O157:H7 among feedlot cattle. Journal of The Royal Society Interface, 12 (110). 20150446. doi:10.1098/rsif.2015.0446 ISSN 1742-5689.
Barry, Nicolas P. E., Pitto-Barry, AnaΓ―s, Tran, Johanna, Spencer, Simon E. F., Johansen, Adam M., Sanchez, Ana M., Dove, Andrew P., OβReilly, Rachel K., Deeth, Robert J., Beanland, R. and Sadler, P. J. (2015) Osmium atoms and Os2 molecules move faster on selenium-doped compared to sulfur-doped boronic graphenic surfaces. Chemistry of Materials, 27 (14). pp. 5100-5105. doi:10.1021/acs.chemmater.5b01853 ISSN 0897-4756.
Pellis, Lorenzo, Spencer, Simon E. F. and House, Thomas A. (2015) Real-time growth rate for general stochastic SIR epidemics on unclustered networks. Mathematical Biosciences, 265 . pp. 65-81. doi:10.1016/j.mbs.2015.04.006 ISSN 0025-5564.
Spencer, Simon E. F., Hill, Steven M. (Mark) and Mukherjee, Sach (2015) Inferring network structure from interventional time-course experiments. Annals of Applied Statistics, Volume 9 (Number 1). pp. 507-524. doi:10.1214/15-AOAS806 ISSN 1932-6157.
2014
Oates, Chris J., Amos, Richard and Spencer, Simon E. F. (2014) Quantifying the multi-scale performance of network inference algorithms. Statistical Applications in Genetics and Molecular Biology, Volume 13 (Number 5). pp. 611-631. doi:10.1515/sagmb-2014-0012 ISSN 1544-6115.
Spencer, Simon E. F. (2014) InterventionalDBN : Interventional Inference for Dynamic Bayesian Networks. [Dataset]
2013
Spencer, Simon E. F. and OβNeill, Philip D. (2013) Assessing the impact of intervention delays on stochastic epidemics. Methodology and Computing in Applied Probability, Volume 15 (Number 4). pp. 803-820. doi:10.1007/s11009-012-9278-7 ISSN 1387-5841.
2012
Spencer, Simon E. F., Marshall, J., Pirie, R., Campbell, D., Baker, M. G. and French, N. P. (2012) The spatial and temporal determinants of campylobacteriosis notifications in New Zealand, 2001β2007. Epidemiology and Infection, Vol.140 (No.9). pp. 1663-1677. doi:10.1017/S0950268811002159 ISSN 0950-2688.
2011
Spencer, Simon E. F. and O'Neill, P. D. (2011) The probability of containment for multitype branching process models for emerging epidemics. Journal of Applied Probability, Vol.48 (No.1). pp. 173-188. doi:10.1239/jap/1300198143 ISSN 0021-9002.
Muellner, P., Marshall, J. C., Spencer, Simon E. F., Noble, A. D., Shadbolt, T., Collins-Emerson, J. M., Midwinter, A. C., Carter, P. E., Pirie, R., Wilson, D. J., Campbell, D. M., Stevenson, M. A. and French, N. P. (2011) Utilizing a combination of molecular and spatial tools to assess the effect of a public health intervention. Preventive Veterinary Medicine, Vol.102 (No.3). pp. 242-253. doi:10.1016/j.prevetmed.2011.07.011 ISSN 0167-5877.
Spencer, Simon E. F., Marshall, Jonathan, Pirie, Ruth, Campbell, Donald and French, Nigel P. (2011) The detection of spatially localised outbreaks in campylobacteriosis notification data. Spatial and Spatio-temporal Epidemiology, Vol.2 (No.3). pp. 173-183. doi:10.1016/j.sste.2011.07.008 ISSN 1877-5845.
Muellner, Petra, Zadoks, Ruth N., Perez, Andres M., Spencer, Simon E. F., Schukken, Ynte H. and French, Nigel P. (2011) The integration of molecular tools into veterinary and spatial epidemiology. Spatial and Spatio-temporal Epidemiology, Vol.2 (No.3). pp. 159-171. doi:10.1016/j.sste.2011.07.005 ISSN 1877-5845.
2010
Benschop, J., Spencer, Simon E. F., Alban, L., Stevenson, M. and French, N. (2010) Bayesian zero-inflated predictive modelling of herd-level salmonella prevalence for risk-based surveillance. Zoonoses and Public Health, Vol.57 (Suppl.1). pp. 60-70. doi:10.1111/j.1863-2378.2010.01355.x ISSN 1863-1959.
Mullner, P., Shadbolt, T., Collins-Emerson, J. M., Midwinter, A. C., Spencer, Simon E. F., Marshall, J., Carter, P. E., Campbell, D. M., Wilson, D. J., Hathaway, S., Pirie, R. and French, N. P. (2010) Molecular and spatial epidemiology of human campylobacteriosis : source association and genotype-related risk factors. Epidemiology and Infection, Vol.138 (No.10). pp. 1372-1383. doi:10.1017/S0950268809991579 ISSN 0950-2688.
Mullner, P., Collins-Emerson, J. M., Midwinter, A. C., Carter, P., Spencer, Simon E. F., van der Logt, P., Hathaway, S. and French, N. P. (2010) Molecular epidemiology of campylobacter jejuni in a geographically isolated country with a uniquely structured poultry industry. Applied and Environmental Microbiology, Vol.76 (No.7). pp. 2145-2154. doi:10.1128/AEM.00862-09 ISSN 0099-2240.
2009
Mullner, Petra, Spencer, Simon E. F., Wilson, Daniel J., Jones, Geoff, Noble, Alasdair D., Midwinter, Anne C., Collins-Emerson, Julie M., Carter, Philip, Hathaway, Steve and French, Nigel P. (2009) Assigning the source of human campylobacteriosis in New Zealand : a comparative genetic and epidemiological approach. Infection, Genetics and Evolution , Vol.9 (No.6). pp. 1311-1319. doi:10.1016/j.meegid.2009.09.003 ISSN 1567-1348.
Mullner, Petra, Jones, Geoff, Noble, Alasdair, Spencer, Simon E. F., Hathaway, Steve and French, Nigel Peter (2009) Source attribution of food-borne zoonoses in New Zealand : a modified Hald Model. Risk Analysis, Vol.29 (No.7). pp. 970-984. doi:10.1111/j.1539-6924.2009.01224.x ISSN 0272-4332.
2008
Mullner, P., Collins-Emerson, J., Midwinter, A., Spencer, Simon E. F. and French, N. (2008) Molecular and modeling tools for campylobacter source attribution. In: UNSPECIFIED. Published in: Proceedings of the Food Safety, Animal Welfare & Biosecurity, Epidemiology & Animal Health Management, and Industry branches of the NZVA - Proceedings of the Food Safety, Animal Welfare & Biosecurity Branch of the NZVA (No.273). pp. 83-90.
Mullner, P., Pleydell, Eve, Shadbolt, Tui, Collins-Emerson, Julie, Midwinter, Anne, Spencer, Simon E. F. and French, Nigel P. (2008) Working at the human and animal health interface - a multidisciplinary team approach towards reducing New Zealand's Campylobacteriosis problem. In: UNSPECIFIED. Published in: Proceedings of the Food Safety, Animal Welfare & Biosecurity, Epidemiology & Animal Health Management, and Industry branches of the NZVA - Proceedings of the Food Safety, Animal Welfare & Biosecurity Branch of the NZVA (No.273). pp. 11-15.
This list was generated on Mon Apr 22 23:51:01 2024 BST.