Author: "Christopher R. Jones" - Searchworks@Jio Institute Digital Library Search Results

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1. Application of a new MDCKII-MDR1 cell model to measure the extent of drug distribution in vitro at equilibrium for prediction of in vivo unbound brain-to-plasma drug distribution

Author: Kristine Langthaler, Christopher R. Jones, Lasse Saaby, Christoffer Bundgaard, and Birger Brodin
Subjects: Neurology. Diseases of the nervous system, RC346-429
Abstract: Abstract Intro: Reliable estimates of drug uptake from blood to brain parenchyma are crucial in CNS drug discovery and development. While in vivo Kp,uu,brain estimates are the gold standard for investigating brain drug disposition, animal usage is a limitation to high throughput application. This study investigates an in vitro model using P-gp expressing MDCKII-MDR1 cells for predicting in vivo brain drug penetration. Methods: In vitro equilibrium distribution studies were conducted in apical and basolateral solutions with high protein content to estimate Kp,brain and Kp,uu,brain values. The correlation between in vitro and in vivo Kp,brain values for a set of compounds was examined. Results: We observed a good correlation between in vitro and in vivo Kp,brain values (R2 = 0.69, Slope: 1.6), indicating that the in vitro model could predict in vivo drug brain penetration. The ‘unilateral (Uni-L)’ in vitro setup correctly classified 5 out of 5 unrestricted compounds and 3 out of 5 restricted compounds. Possible reasons for the observed disparities for some compounds have been discussed, such as difference in transport areas between in vitro and in vivo settings and effect of pH changes. Conclusion: The in vitro assay setup developed in this study holds promise for predicting in vivo drug brain penetration in CNS drug discovery. The correlation between in vitro and in vivo Kp,brain values, underscores that the model may have potential for early-stage screening. With minor refinements, this in vitro approach could reduce the reliance on in vivo experiments, accelerating the pace of CNS drug discovery and promoting a more ethical research approach.
Published: 2024
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2. Modelling Public Intentions to Use Innovative EV Chargers Employing Hybrid Energy Storage Systems: A UK Case Study Based upon the Technology Acceptance Model

Author: Christopher R. Jones, Herman Elgueta, Nikita Chudasama, Daphne Kaklamanou, Duncan East, and Andrew J. Cruden
Subjects: electric vehicles, charging infrastructure, technology acceptance model, mobility, public acceptance, Technology
Abstract: The current study investigates public intentions to use an innovative, off-grid renewably powered EV charging technology called FEVER (Future Electric Vehicle Energy networks supporting Renewables). We report the findings of a questionnaire-based survey (QBS) conducted at a zoo in the south of England, exploring the prospect of demonstrating FEVER. The QBS was designed around a context-specific technology acceptance model (TAM) and administered both face-to-face (n = 63) and online (n = 158) from April to May 2023. The results indicate that most participants were willing to pay to use FEVER, particularly where revenue would benefit the zoo. The participants agreed they intended to use the chargers, and that they would be useful and easy to use. The participants agreed that there would be normative pressure to use the chargers, but that their use would be enjoyable. Of greatest concern was that the chargers would be blocked by others. The participants were ambivalent about concerns over charging duration and charge sufficiency. Structural equation modelling confirmed that the context-specific TAM explained 58% of people’s use intentions. The core relationships of the TAM were confirmed, with ‘perceived usefulness’ additionally predicted by subjective norms and ‘perceived ease of use’ additionally predicted by anticipated enjoyment. Of the other variables, only concern that the chargers would be blocked was retained as a marginal predictor of ‘perceived ease of use’. The implications of these findings for the co-design and demonstration of FEVER are discussed.
Published: 2024
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3. Modeling Land‐Atmosphere Coupling at Cloud‐Resolving Scale Within the Multiple Atmosphere Multiple Land (MAML) Framework in SP‐E3SM

Author: Guangxing Lin, L. Ruby Leung, Jungmin Lee, Bryce E. Harrop, Ian T. Baker, Mark D. Branson, A. Scott Denning, Christopher R. Jones, Mikhail Ovchinnikov, David A. Randall, and Zhao Yang
Subjects: land‐atmosphere coupling, Earth system modeling, super‐parameterization, precipitation, cloud‐resolving model, Physical geography, GB3-5030, Oceanography, GC1-1581
Abstract: Abstract Representing subgrid variabilities of land surface processes and their upscaled effects is crucial for global climate modeling. Here, we implement a multiple atmosphere multiple land (MAML) framework in the superparamaterized version of E3SM (SP‐E3SM) to explicitly simulate the subgrid variabilities of land states and fluxes at cloud‐resolving scale and their interactions with atmosphere. Comparing to the standard SP‐E3SM in which all the atmospheric columns of the cloud resolving model embedded within the global atmospheric model grid interact with the same land surface (i.e., multiple atmosphere single land (MASL)), the impact of MAML on the strength of land‐atmosphere coupling is limited, partly because the current implementation mainly facilitates one‐way coupling between the cloud‐resolving model and the land surface model. Despite such limitation, MAML increases the surface latent heat flux at the expense of sensible heat flux, and increases precipitation in India, Amazon, and Central Africa, reducing the model dry bias compared to the standard SP‐E3SM. By employing a normalized gross moist stability (NGMS) diagnostic framework, we find that the increase in precipitation minus evaporation (P‐E) is primarily driven by the change in large‐scale moisture convergence, particularly by the increase of water vapor in the lower atmosphere, while the local effect of total surface energy flux plays a minor role in the P‐E change. More specifically, MAML changes the surface energy partitioning (evaporative fraction), increases the atmosphere water vapor, and further increases P‐E by decreasing the NGMS. Finally, future development in the MAML framework is discussed.
Published: 2023
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4. Understanding lay-public perceptions of energy storage technologies: Preliminary results of a questionnaire conducted in Canada

Author: James Gaede, Christopher R. Jones, Sara Ganowski, and Ian H. Rowlands
Subjects: Energy storage, Public perceptions, Attitudes, Acceptance, Electrical engineering. Electronics. Nuclear engineering, TK1-9971
Abstract: ‘Grid-scale’ energy storage technologies (ESTs) provide energy storage at scales, capacity and power levels necessary to support the operation of electricity grids, particularly those with substantial renewable (e.g., wind and solar) generation capacity. Public perceptions of new and innovative technologies are known to influence their commercial success, yet there is little existing literature into perceptions and antecedents of grid-scale electricity storage among the general public. In this paper, we report on the findings of an online survey distributed to a diverse sample of the Canadian public (N=1, 022), focusing on perceptions of four specific ESTs (i.e., compressed air energy storage, flywheels, lithium ion batteries, and pumped hydro storage) and the factors that influence intentions to accept ESTs. This research is part of a larger joint-project between researchers at the University of Waterloo and the University of Surrey designed to investigate the similarities and differences in public perceptions of grid-scale ESTs in Canada and the UK. This paper compliments an earlier one that presented the findings for the same survey conducted on a diverse sample of the UK public.
Published: 2020
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5. Activity-State Dependent Reversal of Ketamine-Induced Resting State EEG Effects by Clozapine and Naltrexone in the Freely Moving Rat

Author: Christien Bowman, Ulrike Richter, Christopher R. Jones, Claus Agerskov, and Kjartan Frisch Herrik
Subjects: NMDAR (NMDA receptor), resting state EEG, translational biomarker, schizophrenia, antidepressant, naltrexone, Psychiatry, RC435-571
Abstract: Ketamine is a non-competitive N-Methyl-D-aspartate receptor (NMDAR) antagonist used in the clinic to initiate and maintain anaesthesia; it induces dissociative states and has emerged as a breakthrough therapy for major depressive disorder. Using local field potential recordings in freely moving rats, we studied resting state EEG profiles induced by co-administering ketamine with either: clozapine, a highly efficacious antipsychotic; or naltrexone, an opioid receptor antagonist reported to block the acute antidepressant effects of ketamine. As human electroencephalography (EEG) is predominantly recorded in a passive state, head-mounted accelerometers were used with rats to determine active and passive states at a high temporal resolution to offer the highest translatability. In general, pharmacological effects for the three drugs were more pronounced in (or restricted to) the passive state. Specifically, during inactive periods clozapine induced increases in delta (0.1–4 Hz), gamma (30–60 Hz) and higher frequencies (>100 Hz). Importantly, it reversed the ketamine-induced reduction in low beta power (10–20 Hz) and potentiated ketamine-induced increases in gamma and high frequency oscillations (130–160 Hz). Naltrexone inhibited frequencies above 50 Hz and significantly reduced the ketamine-induced increase in high frequency oscillations. However, some frequency band changes, such as clozapine-induced decreases in delta power, were only seen in locomoting rats. These results emphasise the potential in differentiating between activity states to capture drug effects and translate to human resting state EEG. Furthermore, the differential reversal of ketamine-induced EEG effects by clozapine and naltrexone may have implications for the understanding of psychotomimetic as well as rapid antidepressant effects of ketamine.
Published: 2022
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6. Mesoscale Convective Systems in a Superparameterized E3SM Simulation at High Resolution

Author: Guangxing Lin, Christopher R. Jones, L. Ruby Leung, Zhe Feng, and Mikhail Ovchinnikov
Subjects: super‐parameterization, global climate model, precipitation, mesoscle convective system, convection, clouds, Physical geography, GB3-5030, Oceanography, GC1-1581
Abstract: Abstract Accurately representing mesoscale convective systems (MCSs) is crucial to simulating the energy and water cycles in global climate models. Using a novel MCS identification and tracking algorithm applied to observations and model simulations, we evaluate how well the Energy Exascale Earth System Model (E3SM) simulates MCSs over the central US. Simulations performed by E3SM at 25 km grid spacing with and without superparameterization (SP) are compared and evaluated against observations using multiple metrics highlighting important MCS characteristics. Compared to E3SM, the superparameterized model (SP‐E3SM) better simulates MCS number and MCS precipitation amount, diurnal cycle, propagation, and the probability distribution of precipitation rate in both spring and summer. The improvement from SP is partly contributed by improvement in simulating the large‐scale environments, featuring enhanced atmospheric low‐level moisture and larger moisture transport to the central US relative to E3SM. However, SP‐E3SM still underestimates MCS precipitation amount, particularly in summer. This underestimation is closely related to the negative bias in MCS precipitation intensity, although the drier environments simulated during summer also contributes to underestimation of MCS frequency. Without SP, the larger bias in MCS precipitation amount is closely related to the negative bias in MCS frequency, while the substantial dry bias in the large‐scale environments also contributes to underestimation of MCS intensity. Our results suggest that SP improves MCS simulation by improving modeling of the large‐scale environments and convection initiation, which are both major limiting factors in E3SM even at 25 km grid spacing where deep convection is represented by a cumulus parameterization.
Published: 2022
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7. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

Author: Thushan I. de Silva, Guihai Liu, Benjamin B. Lindsey, Danning Dong, Shona C. Moore, Nienyun Sharon Hsu, Dhruv Shah, Dannielle Wellington, Alexander J. Mentzer, Adrienn Angyal, Rebecca Brown, Matthew D. Parker, Zixi Ying, Xuan Yao, Lance Turtle, Susanna Dunachie, Mala K. Maini, Graham Ogg, Julian C. Knight, Yanchun Peng, Sarah L. Rowland-Jones, Tao Dong, David M. Aanensen, Khalil Abudahab, Helen Adams, Alexander Adams, Safiah Afifi, Dinesh Aggarwal, Shazaad S.Y. Ahmad, Louise Aigrain, Adela Alcolea-Medina, Nabil-Fareed Alikhan, Elias Allara, Roberto Amato, Tara Annett, Stephen Aplin, Cristina V. Ariani, Hibo Asad, Amy Ash, Paula Ashfield, Fiona Ashford, Laura Atkinson, Stephen W. Attwood, Cressida Auckland, Alp Aydin, David J. Baker, Paul Baker, Carlos E. Balcazar, Jonathan Ball, Jeffrey C. Barrett, Magdalena Barrow, Edward Barton, Matthew Bashton, Andrew R. Bassett, Rahul Batra, Chris Baxter, Nadua Bayzid, Charlotte Beaver, Angela H. Beckett, Shaun M. Beckwith, Luke Bedford, Robert Beer, Andrew Beggs, Katherine L. Bellis, Louise Berry, Beatrice Bertolusso, Angus Best, Emma Betteridge, David Bibby, Kelly Bicknell, Debbie Binns, Alec Birchley, Paul W. Bird, Chloe Bishop, Rachel Blacow, Victoria Blakey, Beth Blane, Frances Bolt, James Bonfield, Stephen Bonner, David Bonsall, Tim Boswell, Andrew Bosworth, Yann Bourgeois, Olivia Boyd, Declan T. Bradley, Cassie Breen, Catherine Bresner, Judith Breuer, Stephen Bridgett, Iraad F. Bronner, Ellena Brooks, Alice Broos, Julianne R. Brown, Giselda Bucca, Sarah L. Buchan, David Buck, Matthew Bull, Phillipa J. Burns, Shirelle Burton-Fanning, Timothy Byaruhanga, Matthew Byott, Sharon Campbell, Alessandro M. Carabelli, James S. Cargill, Matthew Carlile, Silvia F. Carvalho, Anna Casey, Anibolina Castigador, Jana Catalan, Vicki Chalker, Nicola J. Chaloner, Meera Chand, Joseph G. Chappell, Themoula Charalampous, Wendy Chatterton, Yasmin Chaudhry, Carol M. Churcher, Gemma Clark, Phillip Clarke, Benjamin J. Cogger, Kevin Cole, Jennifer Collins, Rachel Colquhoun, Thomas R. Connor, Kate F. Cook, Jason Coombes, Sally Corden, Claire Cormie, Nicholas Cortes, Marius Cotic, Seb Cotton, Simon Cottrell, Lindsay Coupland, MacGregor Cox, Alison Cox, Noel Craine, Liam Crawford, Aidan Cross, Matthew R. Crown, Dorian Crudgington, Nicola Cumley, Tanya Curran, Martin D. Curran, Ana da Silva Filipe, Gavin Dabrera, Alistair C. Darby, Rose K. Davidson, Alisha Davies, Robert M. Davies, Thomas Davis, Daniela de Angelis, Elen De Lacy, Leonardo de Oliveira Martins, Johnny Debebe, Rebecca Denton-Smith, Samir Dervisevic, Rebecca Dewar, Jayasree Dey, Joana Dias, Donald Dobie, Matthew J. Dorman, Fatima Downing, Megan Driscoll, Louis du Plessis, Nichola Duckworth, Jillian Durham, Kirstine Eastick, Lisa J. Easton, Richard Eccles, Jonathan Edgeworth, Sue Edwards, Kate El Bouzidi, Sahar Eldirdiri, Nicholas Ellaby, Scott Elliott, Gary Eltringham, Leah Ensell, Michelle J. Erkiert, Marina Escalera Zamudio, Sarah Essex, Johnathan M. Evans, Cariad Evans, William Everson, Derek J. Fairley, Karlie Fallon, Arezou Fanaie, Ben W. Farr, Christopher Fearn, Theresa Feltwell, Lynne Ferguson, Laia Fina, Flavia Flaviani, Vicki M. Fleming, Sally Forrest, Ebenezer Foster-Nyarko, Benjamin H. Foulkes, Luke Foulser, Mireille Fragakis, Dan Frampton, Sarah Francois, Christophe Fraser, Timothy M. Freeman, Helen Fryer, Marc Fuchs, William Fuller, Kavitha Gajee, Katerina Galai, Abbie Gallagher, Eileen Gallagher, Michael D. Gallagher, Marta Gallis, Amy Gaskin, Bree Gatica-Wilcox, Lily Geidelberg, Matthew Gemmell, Iliana Georgana, Ryan P. George, Laura Gifford, Lauren Gilbert, Sophia T. Girgis, Sharon Glaysher, Emily J. Goldstein, Tanya Golubchik, Andrea N. Gomes, Sónia Gonçalves, Ian G. Goodfellow, Scott Goodwin, Salman Goudarzi, Marina Gourtovaia, Clive Graham, Lee Graham, Paul R. Grant, Luke R. Green, Angie Green, Jane Greenaway, Richard Gregory, Martyn Guest, Rory N. Gunson, Ravi K. Gupta, Bernardo Gutierrez, Sam T. Haldenby, William L. Hamilton, Samantha E. Hansford, Tanzina Haque, Kathryn A. Harris, Ian Harrison, Ewan M. Harrison, Jennifer Hart, John A. Hartley, William T. Harvey, Matthew Harvey, Mohammed O. Hassan-Ibrahim, Judith Heaney, Thomas Helmer, John H. Henderson, Andrew R. Hesketh, Jessica Hey, David Heyburn, Ellen E. Higginson, Verity Hill, Jack D. Hill, Rachel A. Hilson, Ember Hilvers, Matthew T.G. Holden, Amy Hollis, Christopher W. Holmes, Nadine Holmes, Alison H. Holmes, Richard Hopes, Hailey R. Hornsby, Myra Hosmillo, Catherine Houlihan, Hannah C. Howson-Wells, Jonathan Hubb, Hannah Huckson, Warwick Hughes, Joseph Hughes, Margaret Hughes, Stephanie Hutchings, Giles Idle, Chris J. Illingworth, Robert Impey, Dianne Irish-Tavares, Miren Iturriza-Gomara, Rhys Izuagbe, Chris Jackson, Ben Jackson, Leigh M. Jackson, Kathryn A. Jackson, David K. Jackson, Aminu S. Jahun, Victoria James, Keith James, Christopher Jeanes, Aaron R. Jeffries, Sarah Jeremiah, Andrew Jermy, Michaela John, Rob Johnson, Kate Johnson, Ian Johnston, Owen Jones, Sophie Jones, Hannah Jones, Christopher R. Jones, Neil Jones, Amelia Joseph, Sarah Judges, Gemma L. Kay, Sally Kay, Jon-Paul Keatley, Alexander J. Keeley, Anita Kenyon, Leanne M. Kermack, Manjinder Khakh, Stephen P. Kidd, Maimuna Kimuli, Stuart Kirk, Christine Kitchen, Katie Kitchman, Bridget A. Knight, Cherian Koshy, Moritz U.G. Kraemer, Sara Kumziene-Summerhayes, Dominic Kwiatkowski, Angie Lackenby, Kenneth G. Laing, Temi Lampejo, Cordelia F. Langford, Deborah Lavin, Andrew I. Lawton, Jack Lee, David Lee, Stefanie V. Lensing, Steven Leonard, Lisa J. Levett, Thanh Le-Viet, Jonathan Lewis, Kevin Lewis, Jennifier Liddle, Steven Liggett, Patrick J. Lillie, Michelle M. Lister, Rich Livett, Stephanie Lo, Nicholas J. Loman, Matthew W. Loose, Stavroula F. Louka, Katie F. Loveson, Sarah Lowdon, Hannah Lowe, Helen L. Lowe, Anita O. Lucaci, Catherine Ludden, Jessica Lynch, Ronan A. Lyons, Katrina Lythgoe, Nicholas W. Machin, George MacIntyre-Cockett, Andrew Mack, Ben Macklin, Alasdair Maclean, Emily Macnaughton, Pinglawathee Madona, Mailis Maes, Laurentiu Maftei, Adhyana I.K. Mahanama, Tabitha W. Mahungu, Daniel Mair, Joshua Maksimovic, Cassandra S. Malone, Daniel Maloney, Nikos Manesis, Robin Manley, Anna Mantzouratou, Angela Marchbank, Arun Mariappan, Inigo Martincorena, Rocio T. Martinez Nunez, Alison E. Mather, Patrick Maxwell, Megan Mayhew, Tamyo Mbisa, Clare M. McCann, Shane A. McCarthy, Kathryn McCluggage, Patrick C. McClure, J.T. McCrone, Martin P. McHugh, James P. McKenna, Caoimhe McKerr, Georgina M. McManus, Claire L. McMurray, Claire McMurray, Alan McNally, Lizzie Meadows, Nathan Medd, Oliver Megram, Mirko Menegazzo, Ian Merrick, Stephen L. Michell, Michelle L. Michelsen, Mariyam Mirfenderesky, Jeremy Mirza, Julia Miskelly, Emma Moles-Garcia, Robin J. Moll, Zoltan Molnar, Irene M. Monahan, Matteo Mondani, Siddharth Mookerjee, Christopher Moore, Jonathan Moore, Nathan Moore, Catherine Moore, Helen Morcrette, Sian Morgan, Mari Morgan, Matilde Mori, Arthur Morriss, Samuel Moses, Craig Mower, Peter Muir, Afrida Mukaddas, Florence Munemo, Robert Munn, Abigail Murray, Leanne J. Murray, Darren R. Murray, Manasa Mutingwende, Richard Myers, Eleni Nastouli, Gaia Nebbia, Andrew Nelson, Charlotte Nelson, Sam Nicholls, Jenna Nichols, Roberto Nicodemi, Kyriaki Nomikou, Justin O’Grady, Sarah O'Brien, Mina Odedra, Natasha Ohemeng-Kumi, Karen Oliver, Richard J. Orton, Husam Osman, xeine O'Toole, Nicole Pacchiarini, Debra Padgett, Andrew J. Page, Emily J. Park, Naomi R. Park, Surendra Parmar, David G. Partridge, David Pascall, Amita Patel, Bindi Patel, Steve Paterson, Brendan A.I. Payne, Sharon J. Peacock, Clare Pearson, Emanuela Pelosi, Benita Percival, Jon Perkins, Malorie Perry, Malte L. Pinckert, Steven Platt, Olga Podplomyk, Manoj Pohare, Marcus Pond, Cassie F. Pope, Radoslaw Poplawski, Jessica Powell, Jennifer Poyner, Liam Prestwood, Anna Price, James R. Price, Jacqui A. Prieto, David T. Pritchard, Sophie J. Prosolek, Georgia Pugh, Monika Pusok, Oliver G. Pybus, Hannah M. Pymont, Michael A. Quail, Joshua Quick, Clara Radulescu, Jayna Raghwani, Manon Ragonnet-Cronin, Lucille Rainbow, Diana Rajan, Shavanthi Rajatileka, Newara A. Ramadan, Andrew Rambaut, John Ramble, Paul A. Randell, Paul Randell, Liz Ratcliffe, Veena Raviprakash, Mohammad Raza, Nicholas M. Redshaw, Sara Rey, Nicola Reynolds, Alex Richter, David L. Robertson, Esther Robinson, Samuel C. Robson, Fiona Rogan, Stefan Rooke, Will Rowe, Sunando Roy, Steven Rudder, Chris Ruis, Steven Rushton, Felicity Ryan, Kordo Saeed, Buddhini Samaraweera, Christine M. Sambles, Roy Sanderson, Theo Sanderson, Fei Sang, Thea Sass, Emily Scher, Garren Scott, Carol Scott, Jasveen Sehmi, Sharif Shaaban, Divya Shah, Jessica Shaw, Ekaterina Shelest, James G. Shepherd, Liz A. Sheridan, Nicola Sheriff, Lesley Shirley, John Sillitoe, Siona Silviera, David A. Simpson, Aditi Singh, Dawn Singleton, Timofey Skvortsov, Tim J. Sloan, Graciela Sluga, Ken Smith, Kim S. Smith, Perminder Smith, Darren L. Smith, Louise Smith, Colin P. Smith, Nikki Smith, Katherine L. Smollett, Luke B. Snell, Thomas Somassa, Joel Southgate, Karla Spellman, Michael H. Spencer Chapman, Lewis G. Spurgin, Moira J. Spyer, Rachael Stanley, William Stanley, Thomas D. Stanton, Igor Starinskij, Joanne Stockton, Susanne Stonehouse, Nathaniel Storey, David J. Studholme, Malur Sudhanva, Emma Swindells, Yusri Taha, Ngee Keong Tan, Julian W. Tang, Miao Tang, Ben E.W. Taylor, Joshua F. Taylor, Sarah Taylor, Ben Temperton, Kate E. Templeton, Claire Thomas, Laura Thomson, Emma C. Thomson, Alicia Thornton, Scott A.J. Thurston, John A. Todd, Rachael Tomb, Lily Tong, Gerry Tonkin-Hill, M. Estee Torok, Jaime M. Tovar-Corona, Amy Trebes, Alexander J. Trotter, Ioulia Tsatsani, Robyn Turnbull, Katherine A. Twohig, Helen Umpleby, Anthony P. Underwood, Edith E. Vamos, Tetyana I. Vasylyeva, Sreenu Vattipally, Gabrielle Vernet, Barry B. Vipond, Erik M. Volz, Sarah Walsh, Dennis Wang, Ben Warne, Joanna Warwick-Dugdale, Elizabeth Wastnedge, Joanne Watkins, Louisa K. Watson, Sheila Waugh, Hermione J. Webster, Danni Weldon, Elaine Westwick, Thomas Whalley, Helen Wheeler, Mark Whitehead, Max Whiteley, Andrew Whitwham, Claudia Wierzbicki, Nicholas J. Willford, Lesley-Anne Williams, Rebecca Williams, Cheryl Williams, Chris Williams, Charlotte A. Williams, Rachel J. Williams, Thomas Williams, Catryn Williams, Kathleen A. Williamson, Eleri Wilson-Davies, Eric Witele, Karen T. Withell, Adam A. Witney, Paige Wolverson, Nick Wong, Trudy Workman, Victoria Wright, Derek W. Wright, Tim Wyatt, Sarah Wyllie, Li Xu-McCrae, Mehmet Yavus, Geraldine Yaze, Corin A. Yeats, Gonzalo Yebra, Wen C. Yew, Gregory R. Young, Jamie Young, Alex E. Zarebski, Peijun Zhang, J. Kenneth Baillie, Malcolm G. Semple, Peter J.M. Openshaw, Gail Carson, Beatrice Alex, Petros Andrikopoulos, Benjamin Bach, Wendy S. Barclay, Debby Bogaert, Kanta Chechi, Graham S. Cooke, Annemarie B. Docherty, Gonçalo dos Santos Correia, Marc-Emmanuel Dumas, Jake Dunning, Tom Fletcher, Christopher A. Green, William Greenhalf, Julian L. Griffin, Rishi K. Gupta, Ewen M. Harrison, Julian A. Hiscox, Antonia Ying Wai Ho, Peter W. Horby, Samreen Ijaz, Saye Khoo, Paul Klenerman, Andrew Law, Matthew R. Lewis, Sonia Liggi, Wei Shen Lim, Lynn Maslen, Laura Merson, Alison M. Meynert, Mahdad Noursadeghi, Michael Olanipekun, Anthonia Osagie, Massimo Palmarini, Carlo Palmieri, William A. Paxton, Georgios Pollakis, Nicholas Price, Clark D. Russell, Vanessa Sancho-Shimizu, Caroline J. Sands, Janet T. Scott, Louise Sigfrid, Tom Solomon, Shiranee Sriskandan, David Stuart, Charlotte Summers, Olivia V. Swann, Zoltan Takats, Panteleimon Takis, Richard S. Tedder, A.A. Roger Thompson, Ryan S. Thwaites, Maria Zambon, Hayley Hardwick, Chloe Donohue, Fiona Griffiths, Wilna Oosthuyzen, Cara Donegan, Rebecca G. Spencer, Jo Dalton, Michelle Girvan, Egle Saviciute, Stephanie Roberts, Janet Harrison, Laura Marsh, Marie Connor, Sophie Halpin, Clare Jackson, Carrol Gamble, Daniel Plotkin, James Lee, Gary Leeming, Murray Wham, Sara Clohisey, Ross Hendry, James Scott-Brown, Victoria Shaw, Sarah E. McDonald, Seán Keating, Katie A. Ahmed, Jane A. Armstrong, Milton Ashworth, Innocent G. Asiimwe, Siddharth Bakshi, Samantha L. Barlow, Laura Booth, Benjamin Brennan, Katie Bullock, Benjamin W.A. Catterall, Jordan J. Clark, Emily A. Clarke, Sarah Cole, Louise Cooper, Helen Cox, Christopher Davis, Oslem Dincarslan, Chris Dunn, Philip Dyer, Angela Elliott, Anthony Evans, Lorna Finch, Lewis W.S. Fisher, Terry Foster, Isabel Garcia-Dorival, Philip Gunning, Catherine Hartley, Rebecca L. Jensen, Christopher B. Jones, Trevor R. Jones, Shadia Khandaker, Katharine King, Robyn T. Kiy, Chrysa Koukorava, Annette Lake, Suzannah Lant, Diane Latawiec, Lara Lavelle-Langham, Daniella Lefteri, Lauren Lett, Lucia A. Livoti, Maria Mancini, Sarah McDonald, Laurence McEvoy, John McLauchlan, Soeren Metelmann, Nahida S. Miah, Joanna Middleton, Joyce Mitchell, Ellen G. Murphy, Rebekah Penrice-Randal, Jack Pilgrim, Tessa Prince, Will Reynolds, P. Matthew Ridley, Debby Sales, Victoria E. Shaw, Rebecca K. Shears, Benjamin Small, Krishanthi S. Subramaniam, Agnieska Szemiel, Aislynn Taggart, Jolanta Tanianis-Hughes, Jordan Thomas, Erwan Trochu, Libby van Tonder, Eve Wilcock, J. Eunice Zhang, Lisa Flaherty, Nicole Maziere, Emily Cass, Alejandra Doce Carracedo, Nicola Carlucci, Anthony Holmes, Hannah Massey, Lee Murphy, Nicola Wrobel, Sarah McCafferty, Kirstie Morrice, Alan MacLean, Kayode Adeniji, Daniel Agranoff, Ken Agwuh, Dhiraj Ail, Erin L. Aldera, Ana Alegria, Sam Allen, Brian Angus, Abdul Ashish, Dougal Atkinson, Shahedal Bari, Gavin Barlow, Stella Barnass, Nicholas Barrett, Christopher Bassford, Sneha Basude, David Baxter, Michael Beadsworth, Jolanta Bernatoniene, John Berridge, Colin Berry, Nicola Best, Pieter Bothma, David Chadwick, Robin Brittain-Long, Naomi Bulteel, Tom Burden, Andrew Burtenshaw, Vikki Caruth, Duncan Chambler, Nigel Chee, Jenny Child, Srikanth Chukkambotla, Tom Clark, Paul Collini, Catherine Cosgrove, Jason Cupitt, Maria-Teresa Cutino-Moguel, Paul Dark, Chris Dawson, Phil Donnison, Sam Douthwaite, Andrew Drummond, Ingrid DuRand, Ahilanadan Dushianthan, Tristan Dyer, Chi Eziefula, Chrisopher Fegan, Adam Finn, Duncan Fullerton, Sanjeev Garg, Atul Garg, Effrossyni Gkrania-Klotsas, Jo Godden, Arthur Goldsmith, Elaine Hardy, Stuart Hartshorn, Daniel Harvey, Peter Havalda, Daniel B. Hawcutt, Maria Hobrok, Luke Hodgson, Anil Hormis, Michael Jacobs, Susan Jain, Paul Jennings, Agilan Kaliappan, Vidya Kasipandian, Stephen Kegg, Michael Kelsey, Jason Kendall, Caroline Kerrison, Ian Kerslake, Oliver Koch, Gouri Koduri, George Koshy, Shondipon Laha, Steven Laird, Susan Larkin, Tamas Leiner, Patrick Lillie, James Limb, Vanessa Linnett, Jeff Little, Mark Lyttle, Michael MacMahon, Emily MacNaughton, Ravish Mankregod, Huw Masson, Elijah Matovu, Katherine McCullough, Ruth McEwen, Manjula Meda, Gary Mills, Jane Minton, Kavya Mohandas, Quen Mok, James Moon, Elinoor Moore, Patrick Morgan, Craig Morris, Katherine Mortimore, Mbiye Mpenge, Rohinton Mulla, Michael Murphy, Megan Nagel, Thapas Nagarajan, Mark Nelson, Lillian Norris, Matthew K. O'Shea, Igor Otahal, Marlies Ostermann, Mark Pais, Selva Panchatsharam, Danai Papakonstantinou, Hassan Paraiso, Brij Patel, Natalie Pattison, Justin Pepperell, Mark Peters, Mandeep Phull, Stefania Pintus, Jagtur Singh Pooni, Tim Planche, Frank Post, David Price, Rachel Prout, Nikolas Rae, Henrik Reschreiter, Tim Reynolds, Neil Richardson, Mark Roberts, Devender Roberts, Alistair Rose, Guy Rousseau, Bobby Ruge, Brendan Ryan, Taranprit Saluja, Matthias L. Schmid, Aarti Shah, Prad Shanmuga, Anil Sharma, Anna Shawcross, Jeremy Sizer, Manu Shankar-Hari, Richard Smith, Catherine Snelson, Nick Spittle, Nikki Staines, Tom Stambach, Richard Stewart, Pradeep Subudhi, Tamas Szakmany, Kate Tatham, Jo Thomas, Chris Thompson, Robert Thompson, Ascanio Tridente, Darell Tupper-Carey, Mary Twagira, Nick Vallotton, Rama Vancheeswaran, Lisa Vincent-Smith, Shico Visuvanathan, Alan Vuylsteke, Sam Waddy, Rachel Wake, Andrew Walden, Ingeborg Welters, Tony Whitehouse, Paul Whittaker, Ashley Whittington, Padmasayee Papineni, Meme Wijesinghe, Martin Williams, Lawrence Wilson, Stephen Winchester, Martin Wiselka, Adam Wolverson, Daniel G. Wootton, Andrew Workman, Bryan Yates, and Peter Young
Subjects: Phylogenetics, Molecular biology, Immunology, Immune response, Virology, Science
Abstract: Summary: We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.
Published: 2021
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8. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

Author: Bo Meng, Steven A. Kemp, Guido Papa, Rawlings Datir, Isabella A.T.M. Ferreira, Sara Marelli, William T. Harvey, Spyros Lytras, Ahmed Mohamed, Giulia Gallo, Nazia Thakur, Dami A. Collier, Petra Mlcochova, Lidia M. Duncan, Alessandro M. Carabelli, Julia C. Kenyon, Andrew M. Lever, Anna De Marco, Christian Saliba, Katja Culap, Elisabetta Cameroni, Nicholas J. Matheson, Luca Piccoli, Davide Corti, Leo C. James, David L. Robertson, Dalan Bailey, Ravindra K. Gupta, Samuel C. Robson, Nicholas J. Loman, Thomas R. Connor, Tanya Golubchik, Rocio T. Martinez Nunez, Catherine Ludden, Sally Corden, Ian Johnston, David Bonsall, Colin P. Smith, Ali R. Awan, Giselda Bucca, M. Estee Torok, Kordo Saeed, Jacqui A. Prieto, David K. Jackson, William L. Hamilton, Luke B. Snell, Catherine Moore, Ewan M. Harrison, Sonia Goncalves, Derek J. Fairley, Matthew W. Loose, Joanne Watkins, Rich Livett, Samuel Moses, Roberto Amato, Sam Nicholls, Matthew Bull, Darren L. Smith, Jeff Barrett, David M. Aanensen, Martin D. Curran, Surendra Parmar, Dinesh Aggarwal, James G. Shepherd, Matthew D. Parker, Sharon Glaysher, Matthew Bashton, Anthony P. Underwood, Nicole Pacchiarini, Katie F. Loveson, Kate E. Templeton, Cordelia F. Langford, John Sillitoe, Thushan I. de Silva, Dennis Wang, Dominic Kwiatkowski, Andrew Rambaut, Justin O’Grady, Simon Cottrell, Matthew T.G. Holden, Emma C. Thomson, Husam Osman, Monique Andersson, Anoop J. Chauhan, Mohammed O. Hassan-Ibrahim, Mara Lawniczak, Alex Alderton, Meera Chand, Chrystala Constantinidou, Meera Unnikrishnan, Alistair C. Darby, Julian A. Hiscox, Steve Paterson, Inigo Martincorena, Erik M. Volz, Andrew J. Page, Oliver G. Pybus, Andrew R. Bassett, Cristina V. Ariani, Michael H. Spencer Chapman, Kathy K. Li, Rajiv N. Shah, Natasha G. Jesudason, Yusri Taha, Martin P. McHugh, Rebecca Dewar, Aminu S. Jahun, Claire McMurray, Sarojini Pandey, James P. McKenna, Andrew Nelson, Gregory R. Young, Clare M. McCann, Scott Elliott, Hannah Lowe, Ben Temperton, Sunando Roy, Anna Price, Sara Rey, Matthew Wyles, Stefan Rooke, Sharif Shaaban, Mariateresa de Cesare, Laura Letchford, Siona Silveira, Emanuela Pelosi, Eleri Wilson-Davies, Myra Hosmillo, Áine O’Toole, Andrew R. Hesketh, Richard Stark, Louis du Plessis, Chris Ruis, Helen Adams, Yann Bourgeois, Stephen L. Michell, Dimitris Gramatopoulos, Jonathan Edgeworth, Judith Breuer, John A. Todd, Christophe Fraser, David Buck, Michaela John, Gemma L. Kay, Steve Palmer, Sharon J. Peacock, David Heyburn, Danni Weldon, Esther Robinson, Alan McNally, Peter Muir, Ian B. Vipond, John Boyes, Venkat Sivaprakasam, Tranprit Salluja, Samir Dervisevic, Emma J. Meader, Naomi R. Park, Karen Oliver, Aaron R. Jeffries, Sascha Ott, Ana da Silva Filipe, David A. Simpson, Chris Williams, Jane A.H. Masoli, Bridget A. Knight, Christopher R. Jones, Cherian Koshy, Amy Ash, Anna Casey, Andrew Bosworth, Liz Ratcliffe, Li Xu-McCrae, Hannah M. Pymont, Stephanie Hutchings, Lisa Berry, Katie Jones, Fenella Halstead, Thomas Davis, Christopher Holmes, Miren Iturriza-Gomara, Anita O. Lucaci, Paul Anthony Randell, Alison Cox, Pinglawathee Madona, Kathryn Ann Harris, Julianne Rose Brown, Tabitha W. Mahungu, Dianne Irish-Tavares, Tanzina Haque, Jennifer Hart, Eric Witele, Melisa Louise Fenton, Steven Liggett, Clive Graham, Emma Swindells, Jennifer Collins, Gary Eltringham, Sharon Campbell, Patrick C. McClure, Gemma Clark, Tim J. Sloan, Carl Jones, Jessica Lynch, Ben Warne, Steven Leonard, Jillian Durham, Thomas Williams, Sam T. Haldenby, Nathaniel Storey, Nabil-Fareed Alikhan, Nadine Holmes, Christopher Moore, Matthew Carlile, Malorie Perry, Noel Craine, Ronan A. Lyons, Angela H. Beckett, Salman Goudarzi, Christopher Fearn, Kate Cook, Hannah Dent, Hannah Paul, Robert Davies, Beth Blane, Sophia T. Girgis, Mathew A. Beale, Katherine L. Bellis, Matthew J. Dorman, Eleanor Drury, Leanne Kane, Sally Kay, Samantha McGuigan, Rachel Nelson, Liam Prestwood, Shavanthi Rajatileka, Rahul Batra, Rachel J. Williams, Mark Kristiansen, Angie Green, Anita Justice, Adhyana I.K. Mahanama, Buddhini Samaraweera, Nazreen F. Hadjirin, Joshua Quick, Radoslaw Poplawski, Leanne M. Kermack, Nicola Reynolds, Grant Hall, Yasmin Chaudhry, Malte L. Pinckert, Iliana Georgana, Robin J. Moll, Alicia Thornton, Richard Myers, Joanne Stockton, Charlotte A. Williams, Wen C. Yew, Alexander J. Trotter, Amy Trebes, George MacIntyre-Cockett, Alec Birchley, Alexander Adams, Amy Plimmer, Bree Gatica-Wilcox, Caoimhe McKerr, Ember Hilvers, Hannah Jones, Hibo Asad, Jason Coombes, Johnathan M. Evans, Laia Fina, Lauren Gilbert, Lee Graham, Michelle Cronin, Sara Kumziene-Summerhayes, Sarah Taylor, Sophie Jones, Danielle C. Groves, Peijun Zhang, Marta Gallis, Stavroula F. Louka, Igor Starinskij, Chris Jackson, Marina Gourtovaia, Gerry Tonkin-Hill, Kevin Lewis, Jaime M. Tovar-Corona, Keith James, Laura Baxter, Mohammad T. Alam, Richard J. Orton, Joseph Hughes, Sreenu Vattipally, Manon Ragonnet-Cronin, Fabricia F. Nascimento, David Jorgensen, Olivia Boyd, Lily Geidelberg, Alex E. Zarebski, Jayna Raghwani, Moritz U.G. Kraemer, Joel Southgate, Benjamin B. Lindsey, Timothy M. Freeman, Jon-Paul Keatley, Joshua B. Singer, Leonardo de Oliveira Martins, Corin A. Yeats, Khalil Abudahab, Ben E.W. Taylor, Mirko Menegazzo, John Danesh, Wendy Hogsden, Sahar Eldirdiri, Anita Kenyon, Jenifer Mason, Trevor I. Robinson, Alison Holmes, James Price, John A. Hartley, Tanya Curran, Alison E. Mather, Giri Shankar, Rachel Jones, Robin Howe, Sian Morgan, Elizabeth Wastenge, Michael R. Chapman, Siddharth Mookerjee, Rachael Stanley, Wendy Smith, Timothy Peto, David Eyre, Derrick Crook, Gabrielle Vernet, Christine Kitchen, Huw Gulliver, Ian Merrick, Martyn Guest, Robert Munn, Declan T. Bradley, Tim Wyatt, Charlotte Beaver, Luke Foulser, Sophie Palmer, Carol M. Churcher, Ellena Brooks, Kim S. Smith, Katerina Galai, Georgina M. McManus, Frances Bolt, Francesc Coll, Lizzie Meadows, Stephen W. Attwood, Alisha Davies, Elen De Lacy, Fatima Downing, Sue Edwards, Garry P. Scarlett, Sarah Jeremiah, Nikki Smith, Danielle Leek, Sushmita Sridhar, Sally Forrest, Claire Cormie, Harmeet K. Gill, Joana Dias, Ellen E. Higginson, Mailis Maes, Jamie Young, Michelle Wantoch, Dorota Jamrozy, Stephanie Lo, Minal Patel, Verity Hill, Claire M. Bewshea, Sian Ellard, Cressida Auckland, Ian Harrison, Chloe Bishop, Vicki Chalker, Alex Richter, Andrew Beggs, Angus Best, Benita Percival, Jeremy Mirza, Oliver Megram, Megan Mayhew, Liam Crawford, Fiona Ashcroft, Emma Moles-Garcia, Nicola Cumley, Richard Hopes, Patawee Asamaphan, Marc O. Niebel, Rory N. Gunson, Amanda Bradley, Alasdair Maclean, Guy Mollett, Rachel Blacow, Paul Bird, Thomas Helmer, Karlie Fallon, Julian Tang, Antony D. Hale, Louissa R. Macfarlane-Smith, Katherine L. Harper, Holli Carden, Nicholas W. Machin, Kathryn A. Jackson, Shazaad S.Y. Ahmad, Ryan P. George, Lance Turtle, Elaine O’Toole, Joanne Watts, Cassie Breen, Angela Cowell, Adela Alcolea-Medina, Themoula Charalampous, Amita Patel, Lisa J. Levett, Judith Heaney, Aileen Rowan, Graham P. Taylor, Divya Shah, Laura Atkinson, Jack C.D. Lee, Adam P. Westhorpe, Riaz Jannoo, Helen L. Lowe, Angeliki Karamani, Leah Ensell, Wendy Chatterton, Monika Pusok, Ashok Dadrah, Amanda Symmonds, Graciela Sluga, Zoltan Molnar, Paul Baker, Stephen Bonner, Sarah Essex, Edward Barton, Debra Padgett, Garren Scott, Jane Greenaway, Brendan A.I. Payne, Shirelle Burton-Fanning, Sheila Waugh, Veena Raviprakash, Nicola Sheriff, Victoria Blakey, Lesley-Anne Williams, Jonathan Moore, Susanne Stonehouse, Louise Smith, Rose K. Davidson, Luke Bedford, Lindsay Coupland, Victoria Wright, Joseph G. Chappell, Theocharis Tsoleridis, Jonathan Ball, Manjinder Khakh, Vicki M. Fleming, Michelle M. Lister, Hannah C. Howson-Wells, Louise Berry, Tim Boswell, Amelia Joseph, Iona Willingham, Nichola Duckworth, Sarah Walsh, Emma Wise, Nathan Moore, Matilde Mori, Nick Cortes, Stephen Kidd, Rebecca Williams, Laura Gifford, Kelly Bicknell, Sarah Wyllie, Allyson Lloyd, Robert Impey, Cassandra S. Malone, Benjamin J. Cogger, Nick Levene, Lynn Monaghan, Alexander J. Keeley, David G. Partridge, Mohammad Raza, Cariad Evans, Kate Johnson, Emma Betteridge, Ben W. Farr, Scott Goodwin, Michael A. Quail, Carol Scott, Lesley Shirley, Scott A.J. Thurston, Diana Rajan, Iraad F. Bronner, Louise Aigrain, Nicholas M. Redshaw, Stefanie V. Lensing, Shane McCarthy, Alex Makunin, Carlos E. Balcazar, Michael D. Gallagher, Kathleen A. Williamson, Thomas D. Stanton, Michelle L. Michelsen, Joanna Warwick-Dugdale, Robin Manley, Audrey Farbos, James W. Harrison, Christine M. Sambles, David J. Studholme, Angie Lackenby, Tamyo Mbisa, Steven Platt, Shahjahan Miah, David Bibby, Carmen Manso, Jonathan Hubb, Gavin Dabrera, Mary Ramsay, Daniel Bradshaw, Ulf Schaefer, Natalie Groves, Eileen Gallagher, David Lee, David Williams, Nicholas Ellaby, Hassan Hartman, Nikos Manesis, Vineet Patel, Juan Ledesma, Katherine A. Twohig, Elias Allara, Clare Pearson, Jeffrey K.J. Cheng, Hannah E. Bridgewater, Lucy R. Frost, Grace Taylor-Joyce, Paul E. Brown, Lily Tong, Alice Broos, Daniel Mair, Jenna Nichols, Stephen N. Carmichael, Katherine L. Smollett, Kyriaki Nomikou, Elihu Aranday-Cortes, Natasha Johnson, Seema Nickbakhsh, Edith E. Vamos, Margaret Hughes, Lucille Rainbow, Richard Eccles, Charlotte Nelson, Mark Whitehead, Richard Gregory, Matthew Gemmell, Claudia Wierzbicki, Hermione J. Webster, Chloe L. Fisher, Adrian W. Signell, Gilberto Betancor, Harry D. Wilson, Gaia Nebbia, Flavia Flaviani, Alberto C. Cerda, Tammy V. Merrill, Rebekah E. Wilson, Marius Cotic, Nadua Bayzid, Thomas Thompson, Erwan Acheson, Steven Rushton, Sarah O’Brien, David J. Baker, Steven Rudder, Alp Aydin, Fei Sang, Johnny Debebe, Sarah Francois, Tetyana I. Vasylyeva, Marina Escalera Zamudio, Bernardo Gutierrez, Angela Marchbank, Joshua Maksimovic, Karla Spellman, Kathryn McCluggage, Mari Morgan, Robert Beer, Safiah Afifi, Trudy Workman, William Fuller, Catherine Bresner, Adrienn Angyal, Luke R. Green, Paul J. Parsons, Rachel M. Tucker, Rebecca Brown, Max Whiteley, James Bonfield, Christoph Puethe, Andrew Whitwham, Jennifier Liddle, Will Rowe, Igor Siveroni, Thanh Le-Viet, Amy Gaskin, Rob Johnson, Irina Abnizova, Mozam Ali, Laura Allen, Ralph Anderson, Cristina Ariani, Siobhan Austin-Guest, Sendu Bala, Jeffrey Barrett, Andrew Bassett, Kristina Battleday, James Beal, Mathew Beale, Sam Bellany, Tristram Bellerby, Katie Bellis, Duncan Berger, Matt Berriman, Paul Bevan, Simon Binley, Jason Bishop, Kirsty Blackburn, Nick Boughton, Sam Bowker, Timothy Brendler-Spaeth, Iraad Bronner, Tanya Brooklyn, Sarah Kay Buddenborg, Robert Bush, Catarina Caetano, Alex Cagan, Nicola Carter, Joanna Cartwright, Tiago Carvalho Monteiro, Liz Chapman, Tracey-Jane Chillingworth, Peter Clapham, Richard Clark, Adrian Clarke, Catriona Clarke, Daryl Cole, Elizabeth Cook, Maria Coppola, Linda Cornell, Clare Cornwell, Craig Corton, Abby Crackett, Alison Cranage, Harriet Craven, Sarah Craw, Mark Crawford, Tim Cutts, Monika Dabrowska, Matt Davies, Joseph Dawson, Callum Day, Aiden Densem, Thomas Dibling, Cat Dockree, David Dodd, Sunil Dogga, Matthew Dorman, Gordon Dougan, Martin Dougherty, Alexander Dove, Lucy Drummond, Monika Dudek, Laura Durrant, Elizabeth Easthope, Sabine Eckert, Pete Ellis, Ben Farr, Michael Fenton, Marcella Ferrero, Neil Flack, Howerd Fordham, Grace Forsythe, Matt Francis, Audrey Fraser, Adam Freeman, Anastasia Galvin, Maria Garcia-Casado, Alex Gedny, Sophia Girgis, James Glover, Oliver Gould, Andy Gray, Emma Gray, Coline Griffiths, Yong Gu, Florence Guerin, Will Hamilton, Hannah Hanks, Ewan Harrison, Alexandria Harrott, Edward Harry, Julia Harvison, Paul Heath, Anastasia Hernandez-Koutoucheva, Rhiannon Hobbs, Dave Holland, Sarah Holmes, Gary Hornett, Nicholas Hough, Liz Huckle, Lena Hughes-Hallet, Adam Hunter, Stephen Inglis, Sameena Iqbal, Adam Jackson, David Jackson, Carlos Jimenez Verdejo, Matthew Jones, Kalyan Kallepally, Keely Kay, Jon Keatley, Alan Keith, Alison King, Lucy Kitchin, Matt Kleanthous, Martina Klimekova, Petra Korlevic, Ksenia Krasheninnkova, Greg Lane, Cordelia Langford, Adam Laverack, Katharine Law, Stefanie Lensing, Amanah Lewis-Wade, Jennifer Liddle, Quan Lin, Sarah Lindsay, Sally Linsdell, Rhona Long, Jamie Lovell, Jon Lovell, James Mack, Mark Maddison, Aleksei Makunin, Irfan Mamun, Jenny Mansfield, Neil Marriott, Matt Martin, Matthew Mayho, Jo McClintock, Sandra McHugh, Liz MapcMinn, Carl Meadows, Emily Mobley, Robin Moll, Maria Morra, Leanne Morrow, Kathryn Murie, Sian Nash, Claire Nathwani, Plamena Naydenova, Alexandra Neaverson, Ed Nerou, Jon Nicholson, Tabea Nimz, Guillaume G. Noell, Sarah O’Meara, Valeriu Ohan, Charles Olney, Doug Ormond, Agnes Oszlanczi, Yoke Fei Pang, Barbora Pardubska, Naomi Park, Aaron Parmar, Gaurang Patel, Maggie Payne, Sharon Peacock, Arabella Petersen, Deborah Plowman, Tom Preston, Michael Quail, Richard Rance, Suzannah Rawlings, Nicholas Redshaw, Joe Reynolds, Mark Reynolds, Simon Rice, Matt Richardson, Connor Roberts, Katrina Robinson, Melanie Robinson, David Robinson, Hazel Rogers, Eduardo Martin Rojo, Daljit Roopra, Mark Rose, Luke Rudd, Ramin Sadri, Nicholas Salmon, David Saul, Frank Schwach, Phil Seekings, Alison Simms, Matt Sinnott, Shanthi Sivadasan, Bart Siwek, Dale Sizer, Kenneth Skeldon, Jason Skelton, Joanna Slater-Tunstill, Lisa Sloper, Nathalie Smerdon, Chris Smith, Christen Smith, James Smith, Katie Smith, Michelle Smith, Sean Smith, Tina Smith, Leighton Sneade, Carmen Diaz Soria, Catarina Sousa, Emily Souster, Andrew Sparkes, Michael Spencer-Chapman, Janet Squares, Robert Stanley, Claire Steed, Tim Stickland, Ian Still, Mike Stratton, Michelle Strickland, Allen Swann, Agnieszka Swiatkowska, Neil Sycamore, Emma Swift, Edward Symons, Suzanne Szluha, Emma Taluy, Nunu Tao, Katy Taylor, Sam Taylor, Stacey Thompson, Mark Thompson, Mark Thomson, Nicholas Thomson, Scott Thurston, Dee Toombs, Benjamin Topping, Jaime Tovar-Corona, Daniel Ungureanu, James Uphill, Jana Urbanova, Philip Jansen Van, Valerie Vancollie, Paul Voak, Danielle Walker, Matthew Walker, Matt Waller, Gary Ward, Charlie Weatherhogg, Niki Webb, Alan Wells, Eloise Wells, Luke Westwood, Theo Whipp, Thomas Whiteley, Georgia Whitton, Sara Widaa, Mia Williams, Mark Wilson, and Sean Wright
Subjects: SARS-CoV-2, COVID-19, antibody escape, neutralizing antibodies, infectivity, spike mutation, Biology (General), QH301-705.5
Abstract: Summary: We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted.
Published: 2021
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9. Social Identity and the Use of Ideological Categorization in Political Evaluation

Author: Ingrid J. Haas, Christopher R. Jones, and Russell H. Fazio
Subjects: political cognition, political attitudes, political identity, evaluation, social identity, social categorization, Psychology, BF1-990
Abstract: In this research, we address a longstanding question concerning how individuals evaluate social and political issues. We focus on the role that political self-identification plays when individuals evaluate policy statements. In a laboratory setting, participants completed a task facilitation procedure, in which they made paired sets of judgments about a series of policy statements. Relative to a control task, ideological categorization of policy statements as liberal or conservative influenced the ease of evaluation. On experimental trials that began with ideological categorization, policy evaluations that were consistent with the participant’s own ideology were made more quickly than responses that were ideologically inconsistent and more quickly than responses following a control judgment. In three experiments, we show that this effect is stronger for individuals with more accessible ideological identification (Experiment 1) and more extreme ideological identification (Experiment 2), and that it holds when examining partisan instead of ideological identification (Experiment 3). The findings suggest that the use of ideological category information can facilitate and interfere with evaluative judgments of political issues, and that the use of such categories varies as a function of individual differences in the strength of political identification.
Published: 2019
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10. National Institute for Health Research Health Informatics Collaborative: development of a pipeline to collate electronic clinical data for viral hepatitis research

Author: Jim Davies, Charles Crichton, Eleanor Barnes, Ben Glampson, Abdulrahim Mulla, Kerrie Woods, Kosh Agarwal, David Anthony Smith, Tingyan Wang, Oliver Freeman, Hizni Salih, Philippa Clare Matthews, Kinga Anna Várnai, Christopher R. Jones, Luca Mercuri, A. Torm Shaw, Lydia N Drumright, Luis Romão, David Ramlakan, Finola Higgins, Alistair Weir, Eleni Nastouli, William Gelson, and Graham S. Cooke
Subjects: Computer applications to medicine. Medical informatics, R858-859.7
Abstract: Objective The National Institute for Health Research (NIHR) Health Informatics Collaborative (HIC) is a programme of infrastructure development across NIHR Biomedical Research Centres. The aim of the NIHR HIC is to improve the quality and availability of routinely collected data for collaborative, cross-centre research. This is demonstrated through research collaborations in selected therapeutic areas, one of which is viral hepatitis.Design The collaboration in viral hepatitis identified a rich set of datapoints, including information on clinical assessment, antiviral treatment, laboratory test results and health outcomes. Clinical data from different centres were standardised and combined to produce a research-ready dataset; this was used to generate insights regarding disease prevalence and treatment response.Results A comprehensive database has been developed for potential viral hepatitis research interests, with a corresponding data dictionary for researchers across the centres. An initial cohort of 960 patients with chronic hepatitis B infections and 1404 patients with chronic hepatitis C infections has been collected.Conclusion For the first time, large prospective cohorts are being formed within National Health Service (NHS) secondary care services that will allow research questions to be rapidly addressed using real-world data. Interactions with industry partners will help to shape future research and will inform patient-stratified clinical practice. An emphasis on NHS-wide systems interoperability, and the increased utilisation of structured data solutions for electronic patient records, is improving access to data for research, service improvement and the reduction of clinical data gaps.
Published: 2020
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11. Editorial: Methodological, Theoretical and Applied Advances in Behavioral Spillover

Author: Christopher R. Jones, Lorraine Whitmarsh, Katarzyna Byrka, Stuart Capstick, Amanda R. Carrico, Matteo M. Galizzi, Daphne Kaklamanou, and David Uzzell
Subjects: attitude, identity, behavior, spillover, theory, method, Psychology, BF1-990
Published: 2019
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12. Treatment optimisation for hepatitis C in the era of combination direct-acting antiviral therapy: a systematic review and meta-analysis [version 1; peer review: 2 approved]

Author: Christopher R. Jones, Barnaby F. Flower, Ella Barber, Bryony Simmons, and Graham S. Cooke
Subjects: Medicine, Science
Abstract: Background: Prior to direct-acting antiviral (DAA) therapy, personalised medicine played an important role in the treatment of hepatitis C virus (HCV). Whilst simplified treatment strategies are central to treatment scale-up, some patients will benefit from treatment optimisation. This systematic review and meta-analysis explores treatment optimisation strategies in the DAA era. Methods: We systematically searched Medline, Embase, and Web of Science for studies that adopted a stratified or personalised strategy using a licensed combination DAA regimen, alone or with additional agents. We performed a thematic analysis to classify optimisation strategies and a meta-analysis of sustained virologic response rates (SVR), exploring heterogeneity with subgroup analyses and meta-regression. Results: We included 64 studies (9450 participants). Thematic analysis found evidence of three approaches: duration, combination, and/or dose optimisation. We separated strategies into those aiming to maintain SVR in the absence of predictors of failure, and those aiming to improve SVR in the presence of predictors of failure. Shortened duration regimens achieve pooled SVR rates of 94.2% (92.3-95.9%) for 8 weeks, 81.1% (75.1-86.6%) for 6 weeks, and 63.1% (39.9-83.7%) for ≤4 weeks. Personalised strategies (100% vs 87.6%; p
Published: 2019
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13. Understanding Contextual Spillover: Using Identity Process Theory as a Lens for Analyzing Behavioral Responses to a Workplace Dietary Choice Intervention

Author: Caroline Verfuerth, Christopher R. Jones, Diana Gregory-Smith, and Caroline Oates
Subjects: contextual spillover, identity process theory, behavior change, workplace, identity, Psychology, BF1-990
Abstract: Spillover occurs when one environmentally sustainable behavior leads to another, often initiated by a behavior change intervention. A number of studies have investigated positive and negative spillover effects, but empirical evidence is mixed, showing evidence for both positive and negative spillover effects, and lack of spillover altogether. Environmental identity has been identified as an influential factor for spillover effects. Building on identity process theory the current framework proposes that positive, negative, and a lack of spillover are determined by perceived threat of initial behavior and identity process mechanisms evaluating the behavior. It is proposed, that an environmental behavior change intervention may threaten one's existing identities, leading to either (a) integration, (b) compartmentalization, or (c) conflict between one's environmental identity and non-environmental identities. Initial evidence for the proposed framework is based on a field intervention which included a meat reduction programme in a canteen of a medium size private sector company. Semi-structured interviews and an explorative visualization method that aimed at assessing identity change were implemented with thirteen employees (i.e., intervention participants) before and after the intervention. The qualitative data was analyzed by using thematic analysis via NVivo12. Results of the visualization task and interview method provided initial evidence of direct and indirect positive contextual spillover effects, with comparatively less evidence a lack of spillover and a relative absence of reported negative spillover. This paper provides a novel theoretical approach, centered on identity process theory to enhance understanding of positive spillover, negative spillover, and the lack of spillover.
Published: 2019
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14. WindNet: Improving the impact assessment of wind power projects

Author: Christopher R. Jones, Eckart Lange, Jian Kang, Aki Tsuchiya, Robert Howell, Aidan While, Richard J. Crisp, John Steel, Keelan Meade, Fei Qu, Danial Sturge, and Agnes Bray
Subjects: wind power, environmental impact assessment, planning, public acceptance, cumulative effects assessment, visual impact, noise impact, health and wellbeing, Production of electric energy or power. Powerplants. Central stations, TK1001-1841, Renewable energy sources, TJ807-830
Abstract: Growing international demand for renewable energy has led to rapid growth in the wind power sector and wind farms are becoming an increasingly common feature of landscapes and seascapes in many countries. However, as the most appropriate locations within established markets are taken up, and as wind power penetrates new markets, there is an increasing likelihood that proposed projects will encroach on sensitive landscapes and residential areas. This will present challenges for the industry, particularly due to the impact that public opinion can have upon the outcomes of planning decisions about specific projects. This article introduces the four key dimensions of the WindNet programme, which are helping to elucidate some of the socio-technical debates that will likely shape the future of the wind power sector. The article outlines studies investigating (1) public responses to cumulative landscape and visual impacts, (2) the auditory impact of wind power projects on human health, (3) the science of wind farm design and its implications for planning, and (4) the relevance of the democratic deficit explanation of the so-called "social gap" in wind farm siting. The outcomes of the research being conducted by WindNet stand to help reduce uncertainty within the planning process and assist in providing a more comprehensive and fairer assessment of the possible impacts associated with wind power project development.
Published: 2014
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15. The Social Acceptance of Carbon Dioxide Utilisation: A Review and Research Agenda

Author: Christopher R. Jones, Barbara Olfe-Kräutlein, Henriette Naims, and Katy Armstrong
Subjects: carbon dioxide utilisation, carbon capture and utilisation, social acceptance, public perception, review, General Works
Abstract: CO2 utilisation technologies—also called carbon dioxide utilisation (CDU) and carbon capture and utilisation (CCU)—convert CO2via physical, chemical, or biological processes into carbon-based products. CO2 utilisation technologies are viewed as a means of helping to address climate change and broadening the raw material base for commodities that can be sold to generate economic revenue. However, while technical research and development into the feasibility of CO2 utilisation options are accelerating rapidly; at present, there has been limited research into the social acceptance of the technology and CO2-derived products. This review article outlines and explores three key dimensions of social acceptance (i.e., socio-political, market, and community acceptance) pertaining to innovation within CO2 utilisation. The article highlights the importance of considering issues of social acceptance as an aspect of the research, development, demonstration, and deployment process for CO2 utilisation and explores how key stakeholders operating on each dimension might affect the innovation pathways, investment, and siting decisions relating to CO2 utilisation facilities and CO2-derived products. Beyond providing a state-of-the-art review of current research into the social acceptance of CO2 utilisation, this article also outlines an agenda for future research in the field.
Published: 2017
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16. Mechanisms of marine low cloud sensitivity to idealized climate perturbations: A single‐LES exploration extending the CGILS cases

Author: Christopher S. Bretherton, Peter N. Blossey, and Christopher R. Jones
Subjects: cloud feedbacks, LES, climate sensitivity, boundary‐layer cloud, Physical geography, GB3-5030, Oceanography, GC1-1581
Abstract: Climate change sensitivities of subtropical cloud‐topped marine boundary layers are analyzed using large‐eddy simulation (LES) of three CGILS cases of well‐mixed stratocumulus, cumulus under stratocumulus, and shallow cumulus cloud regimes, respectively. For each case, a steadily forced control simulation on a small horizontally doubly periodic domain is run 10–20 days into quasi‐steady state. The LES is rerun to steady state with forcings perturbed by changes in temperature, free‐tropospheric relative humidity (RH), CO2 concentration, subsidence, inversion stability, and wind speed; cloud responses to combined forcings superpose approximately linearly. For all three cloud regimes and 2× CO2 forcing perturbations estimated from the CMIP3 multimodel mean, the LES predicts positive shortwave cloud feedback, like most CMIP3 global climate models. At both stratocumulus locations, the cloud remains overcast but thins in the warmer, moister, CO2‐enhanced climate, due to the combined effects of an increased lower‐tropospheric vertical humidity gradient and an enhanced free‐tropospheric greenhouse effect that reduces the radiative driving of turbulence. Reduced subsidence due to weakening of tropical overturning circulations partly counteracts these two factors by raising the inversion and allowing the cloud layer to deepen. These compensating mechanisms may explain the large scatter in low cloud feedbacks predicted by climate models. CMIP3‐predicted changes in wind speed, inversion stability, and free‐tropospheric RH have lesser impacts on the cloud thickness. In the shallow cumulus regime, precipitation regulates the simulated boundary‐layer depth and vertical structure. Cloud‐droplet (aerosol) concentration limits the boundary‐layer depth and affects the simulated cloud feedbacks.
Published: 2013
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17. Attitude Formation Through Exploration

Author: Christopher R. Jones and J. Richard Eiser
Subjects: History of scholarship and learning. The humanities, AZ20-999, Social Sciences
Abstract: Little experimental research has investigated how attitudes are formed via direct personal experience within risky environments. This report summarizes the development of Treasure Island (TI), an attitude learning paradigm based on BeanFest . Two studies are reported: The first designed to compare the outcomes of TI with BeanFest ; the second to show how a manipulation of risk predictability would affect attitude learning within the paradigm. Study 1 demonstrated sampling and learning asymmetries similar to those seen in BeanFest , although the magnitude of these asymmetries was attenuated by the opportunity for participants to landmark decisions. The manipulation of risk predictability in Study 2 led participants to seemingly form a less accurate representation of the underlying pay-off contingencies; however, a significant negative learning asymmetry did persist. The findings of this research (a) identify TI as a versatile paradigm for the investigation of attitude learning within risky environments and (b) confirm the robust nature of the negative learning asymmetry in contingent-learning settings; but (c) assert that care should be taken when generalizing the findings of BeanFest to ostensibly more variable contexts.
Published: 2014
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18. Impact Electrochemistry of MoS2: Electrocatalysis and Hydrogen Generation at Low Overpotentials

Author: Tshiamo Manyepedza, James M. Courtney, Abigail Snowden, Christopher R. Jones, and Neil V. Rees
Subjects: General Energy, Physical and Theoretical Chemistry, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials
Published: 2022

19. Understanding public perceptions of chemical recycling: A comparative study of public attitudes towards coal and waste gasification in Germany and the United Kingdom

Author: Christopher R. Jones, Roh Pin Lee, Daphne Kaklamanou, and Publica
Subjects: Chemical recycling, Environmental Engineering, Public perception, Renewable Energy, Sustainability and the Environment, Attitudes, Environmental Chemistry, Technology acceptance, Industrial and Manufacturing Engineering, Gasification
Abstract: Despite the recognised importance of public acceptance for the success of industrial technologies, little is known about public attitudes towards chemical recycling. We address this gap by investigating the nature of public attitudes towards gasification. Gasification, a form of chemical recycling, can be used to convert carbonaceous wastes into feedstocks that can be used to produce a variety of products (e.g., plastics and transportation fuels) and is seen as a means of supporting the transition towards a circular carbon economy. Using an online questionnaire distributed to diverse samples of the public in Germany (n = 318) and the UK (n = 327), we assessed participants' attitudes towards gasification after exposure to a short informative video about either coal- or waste-based gasification. These countries were selected as both have advanced chemical recycling industries, but also evidence historic differences in public perceptions of carbon-related technologies. Results show that initial self-reported awareness and knowledge of gasification were very low, although improved by the video. Participants in both countries were generally positive about gasification, particularly waste-based gasification. Mediation analysis indicated that this preference was explained by a stronger positive and weaker negative affective response to the technology, as well as a stronger belief that waste-based gasification is a ‘green’ technology option that was worthy of investment. Trust in developers was identified as a direct predictor of attitudes towards gasification. The study complements the ongoing techno-economic-ecological evaluations of gasification technologies and has implications for the development of public engagement and communication efforts.
Published: 2022

20. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Author: S. Cotton, M.P. McHugh, R. Dewar, J.G. Haas, K. Templeton, Samuel C. Robson, Thomas R. Connor, Nicholas J. Loman, Tanya Golubchik, Rocio T. Martinez Nunez, David Bonsall, Andrew Rambaut, Luke B. Snell, Rich Livett, Catherine Ludden, Sally Corden, Eleni Nastouli, Gaia Nebbia, Ian Johnston, Jacqui A. Prieto, Kordo Saeed, David K. Jackson, Catherine Houlihan, Dan Frampton, William L. Hamilton, Adam A. Witney, Giselda Bucca, Cassie F. Pope, Catherine Moore, Emma C. Thomson, Teresa Cutino-Moguel, Ewan M. Harrison, Colin P. Smith, Fiona Rogan, Shaun M. Beckwith, Abigail Murray, Dawn Singleton, Kirstine Eastick, Liz A. Sheridan, Paul Randell, Leigh M. Jackson, Cristina V. Ariani, Sónia Gonçalves, Derek J. Fairley, Matthew W. Loose, Joanne Watkins, Samuel Moses, Sam Nicholls, Matthew Bull, Roberto Amato, Darren L. Smith, David M. Aanensen, Jeffrey C. Barrett, Beatrix Kele, Dinesh Aggarwal, James G. Shepherd, Martin D. Curran, Surendra Parmar, Matthew D. Parker, Catryn Williams, Sharon Glaysher, Anthony P. Underwood, Matthew Bashton, Nicole Pacchiarini, Katie F. Loveson, Matthew Byott, Alessandro M. Carabelli, Kate E. Templeton, Sharon J. Peacock, Thushan I. de Silva, Dennis Wang, Cordelia F. Langford, John Sillitoe, Rory N. Gunson, Simon Cottrell, Justin O’Grady, Dominic Kwiatkowski, Patrick J. Lillie, Nicholas Cortes, Nathan Moore, Claire Thomas, Phillipa J. Burns, Tabitha W. Mahungu, Steven Liggett, Angela H. Beckett, Matthew TG. Holden, Lisa J. Levett, Husam Osman, Mohammed O. Hassan-Ibrahim, David A. Simpson, Meera Chand, Ravi K. Gupta, Alistair C. Darby, Steve Paterson, Oliver G. Pybus, Erik M. Volz, Daniela de Angelis, David L. Robertson, Andrew J. Page, Inigo Martincorena, Louise Aigrain, Andrew R. Bassett, Nick Wong, Yusri Taha, Michelle J. Erkiert, Michael H. Spencer Chapman, Rebecca Dewar, Martin P. McHugh, Siddharth Mookerjee, Stephen Aplin, Matthew Harvey, Thea Sass, Helen Umpleby, Helen Wheeler, James P. McKenna, Ben Warne, Joshua F. Taylor, Yasmin Chaudhry, Rhys Izuagbe, Aminu S. Jahun, Gregory R. Young, Claire McMurray, Clare M. McCann, Andrew Nelson, Scott Elliott, Hannah Lowe, Anna Price, Matthew R. Crown, Sara Rey, Sunando Roy, Ben Temperton, Sharif Shaaban, Andrew R. Hesketh, Kenneth G. Laing, Irene M. Monahan, Judith Heaney, Emanuela Pelosi, Siona Silviera, Eleri Wilson-Davies, Helen Fryer, Helen Adams, Louis du Plessis, Rob Johnson, William T. Harvey, Joseph Hughes, Richard J. Orton, Lewis G. Spurgin, Yann Bourgeois, Chris Ruis, Áine O'Toole, Marina Gourtovaia, Theo Sanderson, Christophe Fraser, Jonathan Edgeworth, Judith Breuer, Stephen L. Michell, John A. Todd, Michaela John, David Buck, Kavitha Gajee, Gemma L. Kay, David Heyburn, Themoula Charalampous, Adela Alcolea-Medina, Katie Kitchman, Alan McNal, David T. Pritch, Samir Dervisevic, Peter Muir, Esther Robinson, Barry B. Vipond, Newara A. Ramadan, Christopher Jeanes, Danni Weldon, Jana Catalan, Neil Jones, Ana da Silva Filipe, Chris Williams, Marc Fuchs, Julia Miskelly, Aaron R. Jeffries, Karen Oliver, Naomi R. Park, Amy Ash, Cherian Koshy, Magdalena Barrow, Sarah L. Buchan, Anna Mantzouratou, Gemma Clark, Christopher W. Holmes, Sharon Campbell, Thomas Davis, Ngee Keong Tan, Julianne R. Brown, Kathryn A. Harris, Stephen P. Kidd, Paul R. Grant, Li Xu-McCrae, Alison Cox, Pinglawathee Madona, Marcus Pond, Paul A. Randell, Karen T. Withell, Cheryl Williams, Clive Graham, Rebecca Denton-Smith, Emma Swindells, Robyn Turnbull, Tim J. Sloan, Andrew Bosworth, Stephanie Hutchings, Hannah M. Pymont, Anna Casey, Liz Ratcliffe, Christopher R. Jones, Bridget A. Knight, Tanzina Haque, Jennifer Hart, Dianne Irish-Tavares, Eric Witele, Craig Mower, Louisa K. Watson DipHE, Jennifer Collins, Gary Eltringham, Dorian Crudgington, Ben Macklin, Miren Iturriza-Gomara, Anita O. Lucaci, Patrick C. McClure, Matthew Carlile, Nadine Holmes, Christopher Moore, Nathaniel Storey, Stefan Rooke, Gonzalo Yebra, Noel Craine, Malorie Perry, Nabil-Fareed Alikhan, Stephen Bridgett, Kate F. Cook, Christopher Fearn, Salman Goudarzi, Ronan A. Lyons, Thomas Williams, Sam T. Haldenby, Jillian Durham, Steven Leonard, Robert M. Davies, Rahul Batra, Beth Blane, Moira J. Spyer, Perminder Smith, Mehmet Yavus, Rachel J. Williams, Adhyana IK. Mahanama, Buddhini Samaraweera, Sophia T. Girgis, Samantha E. Hansford, Angie Green, Charlotte Beaver, Katherine L. Bellis, Matthew J. Dorman, Sally Kay, Liam Prestwood, Shavanthi Rajatileka, Joshua Quick, Radoslaw Poplawski, Nicola Reynolds, Andrew Mack, Arthur Morriss, Thomas Whalley, Bindi Patel, Iliana Georgana, Myra Hosmillo, Malte L. Pinckert, Joanne Stockton, John H. Henderson, Amy Hollis, William Stanley, Wen C. Yew, Richard Myers, Alicia Thornton, Alexander Adams, Tara Annett, Hibo Asad, Alec Birchley, Jason Coombes, Johnathan M. Evans, Laia Fina, Bree Gatica-Wilcox, Lauren Gilbert, Lee Graham, Jessica Hey, Ember Hilvers, Sophie Jones, Hannah Jones, Sara Kumziene-Summerhayes, Caoimhe McKerr, Jessica Powell, Georgia Pugh, Sarah Taylor, Alexander J. Trotter, Charlotte A. Williams, Leanne M. Kermack, Benjamin H. Foulkes, Marta Gallis, Hailey R. Hornsby, Stavroula F. Louka, Manoj Pohare, Paige Wolverson, Peijun Zhang, George MacIntyre-Cockett, Amy Trebes, Robin J. Moll, Lynne Ferguson, Emily J. Goldstein, Alasdair Maclean, Rachael Tomb, Igor Starinskij, Laura Thomson, Joel Southgate, Moritz UG. Kraemer, Jayna Raghwani, Alex E. Zarebski, Olivia Boyd, Lily Geidelberg, Chris J. Illingworth, Chris Jackson, David Pascall, Sreenu Vattipally, Timothy M. Freeman, Sharon N. Hsu, Benjamin B. Lindsey, Keith James, Kevin Lewis, Gerry Tonkin-Hill, Jaime M. Tovar-Corona, MacGregor Cox, Khalil Abudahab, Mirko Menegazzo, Ben EW. Taylor, Corin A. Yeats, Afrida Mukaddas, Derek W. Wright, Leonardo de Oliveira Martins, Rachel Colquhoun, Verity Hill, Ben Jackson, J.T. McCrone, Nathan Medd, Emily Scher, Jon-Paul Keatley, Tanya Curran, Sian Morgan, Patrick Maxwell, Ken Smith, Sahar Eldirdiri, Anita Kenyon, Alison H. Holmes, James R. Price, Tim Wyatt, Alison E. Mather, Timofey Skvortsov, John A. Hartley, Martyn Guest, Christine Kitchen, Ian Merrick, Robert Munn, Beatrice Bertolusso, Jessica Lynch, Gabrielle Vernet, Stuart Kirk, Elizabeth Wastnedge, Rachael Stanley, Giles Idle, Declan T. Bradley, Nicholas F. Killough, Jennifer Poyner, Matilde Mori, Owen Jones, Victoria Wright, Ellena Brooks, Carol M. Churcher, Laia Delgado Callico, Mireille Fragakis, Katerina Galai, Andrew Jermy, Sarah Judges, Anna Markov, Georgina M. McManus, Kim S. Smith, Peter MD. Thomas-McEwen, Elaine Westwick, Stephen W. Attwood, Frances Bolt, Alisha Davies, Elen De Lacy, Fatima Downing, Sue Edwards, Lizzie Meadows, Sarah Jeremiah, Nikki Smith, Luke Foulser, Amita Patel, Louise Berry, Tim Boswell, Vicki M. Fleming, Hannah C. Howson-Wells, Amelia Joseph, Manjinder Khakh, Michelle M. Lister, Paul W. Bird, Karlie Fallon, Thomas Helmer, Claire L. McMurray, Mina Odedra, Jessica Shaw, Julian W. Tang, Nicholas J. Willford, Victoria Blakey, Veena Raviprakash, Nicola Sheriff, Lesley-Anne Williams, Theresa Feltwell, Luke Bedford, James S. Cargill, Warwick Hughes, Jonathan Moore, Susanne Stonehouse, Laura Atkinson, Jack CD. Lee, Divya Shah, Natasha Ohemeng-Kumi, John Ramble, Jasveen Sehmi, Rebecca Williams, Wendy Chatterton, Monika Pusok, William Everson, Anibolina Castigador, Emily Macnaughton, Kate El Bouzidi, Temi Lampejo, Malur Sudhanva, Cassie Breen, Graciela Sluga, Shazaad SY. Ahmad, Ryan P. George, Nicholas W. Machin, Debbie Binns, Victoria James, Rachel Blacow, Lindsay Coupland, Louise Smith, Edward Barton, Debra Padgett, Garren Scott, Aidan Cross, Mariyam Mirfenderesky, Jane Greenaway, Kevin Cole, Phillip Clarke, Nichola Duckworth, Sarah Walsh, Kelly Bicknell, Robert Impey, Sarah Wyllie, Richard Hopes, Chloe Bishop, Vicki Chalker, Ian Harrison, Laura Gifford, Zoltan Molnar, Cressida Auckland, Cariad Evans, Kate Johnson, David G. Partridge, Mohammad Raza, Paul Baker, Stephen Bonner, Sarah Essex, Leanne J. Murray, Andrew I. Lawton, Shirelle Burton-Fanning, Brendan AI. Payne, Sheila Waugh, Andrea N. Gomes, Maimuna Kimuli, Darren R. Murray, Paula Ashfield, Donald Dobie, Fiona Ashford, Angus Best, Liam Crawford, Nicola Cumley, Megan Mayhew, Oliver Megram, Jeremy Mirza, Emma Moles-Garcia, Benita Percival, Megan Driscoll, Leah Ensell, Helen L. Lowe, Laurentiu Maftei, Matteo Mondani, Nicola J. Chaloner, Benjamin J. Cogger, Lisa J. Easton, Hannah Huckson, Jonathan Lewis, Sarah Lowdon, Cassandra S. Malone, Florence Munemo, Manasa Mutingwende, Roberto Nicodemi, Olga Podplomyk FD, Thomas Somassa, Andrew Beggs, Alex Richter, Claire Cormie, Joana Dias, Sally Forrest, Ellen E. Higginson, Mailis Maes, Jamie Young, Rose K. Davidson, Kathryn A. Jackson, Alexander J. Keeley, Jonathan Ball, Timothy Byaruhanga, Joseph G. Chappell, Jayasree Dey, Jack D. Hill, Emily J. Park, Arezou Fanaie, Rachel A. Hilson, Geraldine Yaze, Stephanie Lo, Safiah Afifi, Robert Beer, Joshua Maksimovic, Kathryn McCluggage, Karla Spellman, Catherine Bresner, William Fuller, Angela Marchbank, Trudy Workma, Ekaterina Shelest, Johnny Debebe, Fei Sang, Sarah Francois, Bernardo Gutierrez, Tetyana I. Vasylyeva, Flavia Flaviani, Manon Ragonnet-Cronin, Katherine L. Smollett, Alice Broos, Daniel Mair, Jenna Nichols, Kyriaki Nomikou, Lily Tong, Ioulia Tsatsani, Sarah O'Brien, Steven Rushton, Roy Sanderson, Jon Perkins, Seb Cotton, Abbie Gallagher, Elias Allara, Clare Pearson, David Bibby, Gavin Dabrer, Nicholas Ellaby, Eileen Gallagher, Jonathan Hubb, Angie Lackenby, David Lee, Nikos Manesis, Tamyo Mbisa, Steven Platt, Katherine A. Twohig, Mari Morgan, Alp Aydin, David J. Baker, Ebenezer Foster-Nyarko, Sophie J. Prosolek, Steven Rudder, Chris Baxter, Sílvia F. Carvalho, Deborah Lavin, Arun Mariappan, Clara Radulescu, Aditi Singh, Miao Tang, Helen Morcrette, Nadua Bayzid, Marius Cotic, Carlos E. Balcazar, Michael D. Gallagher, Daniel Maloney, Thomas D. Stanton, Kathleen A. Williamson, Robin Manley, Michelle L. Michelsen, Christine M. Sambles, David J. Studholme, Joanna Warwick-Dugdale, Richard Eccles, Matthew Gemmell, Richard Gregory, Margaret Hughes, Charlotte Nelson, Lucille Rainbow, Edith E. Vamos, Hermione J. Webster, Mark Whitehead, Claudia Wierzbicki, Adrienn Angyal, Luke R. Green, Max Whiteley, Emma Betteridge, Iraad F. Bronner, Ben W. Farr, Scott Goodwin, Stefanie V. Lensing, Shane A. McCarthy, Michael A. Quail, Diana Rajan, Nicholas M. Redshaw, Carol Scott, Lesley Shirley, Scott AJ. Thurston, Will Rowe, Amy Gaskin, Thanh Le-Viet, James Bonfield, Jennifier Liddle, Andrew Whitwham, University of St Andrews. School of Medicine, University of St Andrews. Infection and Global Health Division, and Apollo - University of Cambridge Repository
Subjects: Microbiology (medical), MCC, Introduction, SARS-CoV-2, NDAS, COVID-19, Care homes, General Medicine, NIS, Patient Discharge, Hospitals, Hospitalization, Infectious Diseases, SDG 3 - Good Health and Well-being, RA0421, RA0421 Public health. Hygiene. Preventive Medicine, Humans, Hospital discharge
Abstract: COG-UK is supported by funding from the MRC part of UK Research & Innovation, the National Institute of Health Research (Grant code MC_PC_19027), and Genome Research Limited, operating as the Welcome Sanger Institute. Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine. Publisher PDF
Published: 2023

21. The Aryne Ene Reaction

Author: Christopher R. Jones and Yun Yang
Subjects: Organic Chemistry, Catalysis
Abstract: Intermolecular aryne ene reactions present opportunities to arylate a wide range of unsaturated substrates in a single step, whilst intramolecular reactions provide expedient access to valuable benzofused carbo- and heterocyclic frameworks. This short review will chart the development of the aryne ene reaction from initial reports that rationalise unexpected byproduct formation in competing [4+2] and [2+2] cycloadditions through to its exploitation in contemporary synthetic methodology.1 Introduction2 Alkene Ene Reactions2.1 Intermolecular2.2 Intramolecular3 Alkyne Ene Reactions3.1 Intermolecular3.2 Intramolecular4 Allene Ene Reactions5 Aromatic Ene Reactions6 Hetero Ene Reactions6.1 Enols6.2 Enamines6.3 Imines7 Conclusions
Published: 2022

22. Better calibration of cloud parameterizations and subgrid effects increases the fidelity of the E3SM Atmosphere Model version 1

Author: Po-Lun Ma, Bryce E. Harrop, Vincent E. Larson, Richard B. Neale, Andrew Gettelman, Hugh Morrison, Hailong Wang, Kai Zhang, Stephen A. Klein, Mark D. Zelinka, Yuying Zhang, Yun Qian, Jin-Ho Yoon, Christopher R. Jones, Meng Huang, Sheng-Lun Tai, Balwinder Singh, Peter A. Bogenschutz, Xue Zheng, Wuyin Lin, Johannes Quaas, Hélène Chepfer, Michael A. Brunke, Xubin Zeng, Johannes Mülmenstädt, Samson Hagos, Zhibo Zhang, Hua Song, Xiaohong Liu, Michael S. Pritchard, Hui Wan, Jingyu Wang, Qi Tang, Peter M. Caldwell, Jiwen Fan, Larry K. Berg, Jerome D. Fast, Mark A. Taylor, Jean-Christophe Golaz, Shaocheng Xie, Philip J. Rasch, and L. Ruby Leung
Abstract: Realistic simulation of the Earth's mean-state climate remains a major challenge, and yet it is crucial for predicting the climate system in transition. Deficiencies in models' process representations, propagation of errors from one process to another, and associated compensating errors can often confound the interpretation and improvement of model simulations. These errors and biases can also lead to unrealistic climate projections and incorrect attribution of the physical mechanisms governing past and future climate change. Here we show that a significantly improved global atmospheric simulation can be achieved by focusing on the realism of process assumptions in cloud calibration and subgrid effects using the Energy Exascale Earth System Model (E3SM) Atmosphere Model version 1 (EAMv1). The calibration of clouds and subgrid effects informed by our understanding of physical mechanisms leads to significant improvements in clouds and precipitation climatology, reducing common and long-standing biases across cloud regimes in the model. The improved cloud fidelity in turn reduces biases in other aspects of the system. Furthermore, even though the recalibration does not change the global mean aerosol and total anthropogenic effective radiative forcings (ERFs), the sensitivity of clouds, precipitation, and surface temperature to aerosol perturbations is significantly reduced. This suggests that it is possible to achieve improvements to the historical evolution of surface temperature over EAMv1 and that precise knowledge of global mean ERFs is not enough to constrain historical or future climate change. Cloud feedbacks are also significantly reduced in the recalibrated model, suggesting that there would be a lower climate sensitivity when it is run as part of the fully coupled E3SM. This study also compares results from incremental changes to cloud microphysics, turbulent mixing, deep convection, and subgrid effects to understand how assumptions in the representation of these processes affect different aspects of the simulated atmosphere as well as its response to forcings. We conclude that the spectral composition and geographical distribution of the ERFs and cloud feedback, as well as the fidelity of the simulated base climate state, are important for constraining the climate in the past and future.
Published: 2022

23. Practical Application of Rodent Transporter Knockout Models to Assess Brain Penetration in Drug Discovery

Author: Elin, Eneberg, Christopher R, Jones, Thomas, Jensen, Kristine, Langthaler, and Christoffer, Bundgaard
Subjects: Blood-Brain Barrier, Drug Discovery, ATP Binding Cassette Transporter, Subfamily G, Member 2, Animals, Brain, Humans, Membrane Transport Proteins, Rodentia, Neoplasm Proteins
Abstract: Background & Objective: Compound X is a drug candidate for the treatment of neurodegenerative diseases. Its brain distribution was evaluated as part of the lead identification and optimization activities undertaken in early drug discovery. Methods: The brain distribution of compound X was studied in genetic transporter knockout rodent models, in vivo models with a chemical inhibitor, and in vitro transporter cell systems. Results: Compound X was found to be a substrate for human Breast Cancer-Resistance Protein (BCRP) in vitro (efflux ratio 8.1) and rodent Bcrp in vivo (Kp, uuKO/Kp, uuWT = 0.15/0.057 = 2.7, p< 0.05) but not a substrate for human P-glycoprotein (P-gp) in vitro (efflux ratio 1.0) nor rodent P-gp in vivo (Kp, uuKO/Kp, uuWT = 0.056/ 0.051 = 1.1, p> 0.05). When both transporters were knocked out in vivo, Kp, uu increased to 0.51±0.02. A similar pattern observed across compounds with related chemistry corroborating the structure-activity relationship. Conclusion: While in vitro assays showed compound X to be a substrate for human BCRP and not P-gp, in vivo studies indicated a synergistic effect between rodent efflux transporters. However, this only accounted for ~50% of restricted BBB-transport, suggesting involvement of other efflux transporters. Considering Kp, uu as a key criterion for assessing the technical quality of CNS candidates before progression into clinical development, it is important to identify relevant screening assays for a better understanding of low Kp, uu and brain distribution in pre-clinical models for translation to humans.
Published: 2022

24. Corrosion inhibition and disinfection of central heating and cooling water systems using in situ generated hydrogen peroxide

Author: Ye Cao, Yue Xu, Qi Li, Ruth-Sarah Rose, Isaac Abrahams, Christopher R. Jones, and Tippu S. Sheriff
Subjects: Materials Chemistry, General Chemistry, Catalysis
Abstract: MnCl2·4H2O and Tiron (disodium 4,5-dihydroxy-1,3-benzenedisulfonate) rapidly remove O2 from aqueous solution at pH 7.50–11.0 and 20–50 °C using hydroxylamine (NH2OH) as reducing substrate and acts as an anti-corrosion and anti-bacterial formulation.
Published: 2022

25. Quantifying the Mechanical Properties of Yeast Candida albicans Using Atomic Force Microscopy-based Force Spectroscopy

Author: Christopher R. Jones, Zhenyu Jason Zhang, and Hung-Ji Tsai
Published: 2023

26. A change would do you good: advances in research impact in sustainable tourism and some ‘home truths’ for the sector

Author: Christopher R. Jones and Andreas Walmsley
Subjects: Economic growth, Higher education, business.industry, Tourism, Leisure and Hospitality Management, Political science, Socio economic impact, Geography, Planning and Development, business, Discipline, Economic benefits, Tourism, Sustainable tourism
Abstract: There is a growing impetus on academics working in higher education to evidence the wider impact (i.e. the social and economic benefits) of their research. As academic disciplines, tourism in gener...
Published: 2021

27. Developmental and reproductive safety of AZD1222 (ChAdOx1 nCoV-19) in mice

Author: Jayne Harris, Chi Man Tang, Anna Karin Maguire, Vicky Skellett, Shaun Maguire, Richard Stebbings, Joanne Goodman, Christopher R. Jones, and Gillian Armour
Subjects: COVID-19 Vaccines, Placenta, media_common.quotation_subject, Breastfeeding, Physiology, Gestational Age, Fertility, Antibodies, Viral, Toxicology, Risk Assessment, Mice, Fetus, Immunogenicity, Vaccine, Pregnancy, ChAdOx1 nCoV-19, Animals, Lactation, Medicine, Seroconversion, Maternal-Fetal Exchange, reproductive and urinary physiology, media_common, business.industry, Vaccination, Gestational age, medicine.disease, Prenatal Exposure Delayed Effects, Gestation, Female, business, Reproductive toxicity, Biomarkers
Abstract: AZD1222 (ChAdOx1 nCoV-19) is a COVID-19 vaccine that is not yet licensed for use during pregnancy. To support the inclusion of pregnant and breastfeeding people in AZD1222 clinical studies, a non-clinical developmental and reproductive toxicity study was performed to evaluate its effects on fertility and reproductive processes of female CD-1 mice during the embryofetal development phase, and postnatal outcomes during the littering phase. Immunogenicity assessments were also made in dams, fetuses, and pups. There were no vaccine-related unscheduled deaths throughout the study. Furthermore, there were no vaccine-related effects on female reproduction, fetal or pup survival, fetal external, visceral, or skeletal findings, pup physical development, and no abnormal gross pathology findings in pups or dams. Antibody responses raised in dams were maintained throughout gestation and postnatal periods, and seroconversion in fetuses and pups indicate placental and lactational transfer of immunoglobulins. Together with clinical data from non-pregnant people, these results support the inclusion of pregnant and breastfeeding people in AZD1222 clinical studies.
Published: 2021

28. Quantifying the mechanical properties of yeastCandida albicansusing atomic force microscopy-based force spectroscopy

Author: Christopher R. Jones, Zhenyu Jason Zhang, and Hung-Ji Tsai
Abstract: Fungi can adapt to a wide range of environmental stress in the wild and host milieu by employing their plastic genome and great diversity in morphology. Among different adaptive strategies, mechanical stimuli, such as changes in osmotic pressure, surface remodelling, hyphal formation, and cell divisions, could guide the physical cues into physiological responses through complex signalling network. While fungal pathogens require a pressure-driven force to expand and penetrate host tissues, quantitatively studying the biophysical properties at the host-fungal interface is critical to understand the development of fungal diseases. Microscopy-based techniques have enabled researchers to monitor the dynamic mechanics on fungal cell surface in responses to the host stress and antifungal drugs. Here, we describe a label-free, high-resolution method based on atomic force microscopy, with a step-by-step protocol to measure the physical properties in human fungal pathogenCandida albicans.
Published: 2022

29. Perceptions of accountability and trust in the regulatory governance of wood burning stove sustainability: Survey evidence from the post-Brexit UK

Author: Matthew Wood, Chantelle Wood, Peter Styring, Christopher R. Jones, Jeffery K. Smith, Marianne Day, Rohit Chakraborty, and Gloria Mensah
Subjects: General Energy, Management, Monitoring, Policy and Law
Published: 2023

30. Collaboration and the net generation: the changing characteristics of first year university students.

Author: Christopher R. Jones 0002 and Ruslan Ramanau
Published: 2009

31. Construction of Protograph LDPC Codes with Linear Minimum Distance.

Author: Dariush Divsalar, Sam Dolinar, and Christopher R. Jones 0001
Published: 2006
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32. Characterisation of intravenous pharmacokinetics in Göttingen minipig and clearance prediction using established

Author: Kristine, Langthaler, Christopher R, Jones, Rasmus B, Christensen, Elin, Eneberg, Birger, Brodin, and Christoffer, Bundgaard
Subjects: Kinetics, Liver, Pharmaceutical Preparations, Metabolic Clearance Rate, Swine, Hepatocytes, Animals, Humans, Swine, Miniature, Pharmacokinetics, Models, Biological
Abstract: The use of the Göttingen minipig as an animal model for drug safety testing and prediction of human pharmacokinetics (PK) continues to gain momentum in pharmaceutical research and development. The aim of this study was to evaluate
Published: 2022

33. Constructing LDPC codes from simple loop-free encoding modules.

Author: Dariush Divsalar, Samuel Dolinar, Jeremy Thorpe, and Christopher R. Jones 0001
Published: 2005
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34. Low-rate LDPC codes with simple protograph structure.

Author: Dariush Divsalar, Sam Dolinar, and Christopher R. Jones 0001
Published: 2005
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35. CSCL - the next ten years: a view from Europe.

Author: Christopher R. Jones 0002, Lone Dirckinck-Holmfeld, and Berner Lindström
Published: 2005

36. Reducing meat consumption at work and at home: facilitators and barriers that influence contextual spillover

Author: Panayiota J. Alevizou, Caroline Verfuerth, Diana Gregory-Smith, Christopher R. Jones, and Caroline Oates
Subjects: Marketing, Consumption (economics), Typology, White meat, Strategy and Management, 05 social sciences, food and beverages, Social marketing, Spillover effect, Work (electrical), Intervention (counseling), 0502 economics and business, Red meat, 050211 marketing, Psychology, 050203 business & management
Abstract: This study contributes to conflicting knowledge on contextual spillover effects from the workplace to the home setting (i.e. knock-on effects of one behaviour to another). A social marketing intervention was staged in a canteen in which red meat meals were replaced with white meat and plant-based alternatives, together with an information campaign. Thirteen employees were interviewed twice (pre- and post-intervention totalling 26 interviews). The findings indicated a two-way pathway framework (for positive and lack of spillover) which is supported by a range of factors. The findings allowed the grouping of factors into facilitators and barriers of contextual spillover and a three-dimensional typology. Overall, the findings showed that a social marketing intervention in a workplace can lead to sustainable food consumption at home. These effects are influenced by barriers and facilitators which can lead to the manifestation of other types of behaviour or a lack thereof. Resulting practical implications are discussed.
Published: 2021

37. A Flexible Hardware Encoder for Low-Density Parity-Check Codes.

Author: Dong-U Lee, Wayne Luk, Connie Wang, Christopher R. Jones 0001, Michael Smith 0020, and John D. Villasenor
Published: 2004
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38. Construction of irregular LDPC codes with low error floors.

Author: Tao Tian, Christopher R. Jones 0001, John D. Villasenor, and Richard D. Wesel
Published: 2003
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39. Robustness of LDPC codes on periodic fading channels.

Author: Christopher R. Jones 0001, Tao Tian, Adina Matache, Richard D. Wesel, and John D. Villasenor
Published: 2002
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40. Applying Design Thinking in Health Care: Reflections of Nursing Honors Program Students

Author: Bethany R. Pittman, Sigrid Ladores, Trevor Purter, Nancy P. Wingo, Christopher R. Jones, Madeline Russell, and Janet Brown
Subjects: Adult, Male, Models, Educational, Quality management, media_common.quotation_subject, Empathy, Clinical settings, Design thinking, Professional Competence, Nursing, Health care, Humans, Models, Nursing, Curriculum, Problem Solving, General Nursing, media_common, business.industry, Nursing research, Identifying problems, Education, Nursing, Baccalaureate, Quality Improvement, Nursing Research, Alabama, Female, Students, Nursing, business, Psychology
Abstract: Nursing faculty at the University of Alabama at Birmingham (UAB) incorporated design thinking (DT) into the curriculum of the UAB School of Nursing Honors Program as a framework for undergraduate students' immersion into research experiences. This article describes the experiences of students who participated in the first honors class that used DT and discusses how to incorporate DT into nursing research and quality improvement projects. Active learning strategies provided students various opportunities to conceptualize and apply the five-step DT process by identifying possible solutions to problems in clinical settings. Three major themes emerged from these reflections: trusting the process, cultivating empathy, and applying DT in the future. Students found that trusting the process of learning about DT facilitated their understanding of empathy's role in health care as they recognized DT's far-reaching applications beyond the honors program. A pragmatic, intuitive, and innovative approach to identifying problems and solutions, DT empowers nurses to creatively and confidently address issues they encounter to improve outcomes for their patients, health-care systems, and communities.
Published: 2020

41. Characterisation of intravenous pharmacokinetics in Göttingen minipig and clearance prediction using established in vitro to in vivo extrapolation methodologies

Author: Kristine Langthaler, Christopher R. Jones, Rasmus B. Christensen, Elin Eneberg, Birger Brodin, and Christoffer Bundgaard
Subjects: Pharmacology, Health, Toxicology and Mutagenesis, General Medicine, Toxicology, Biochemistry
Abstract: 1. The use of the Göttingen minipig as an animal model for drug safety testing and prediction of human pharmacokinetics (PK) continues to gain momentum in pharmaceutical research and development. The aim of this study was to evaluate in vitro to in vivo extrapolation (IVIVE) methodologies for prediction of hepatic, metabolic clearance (CL hep,met) in Göttingen minipig, using a comprehensive set of compounds. 2. In vivo clearance was determined in Göttingen minipig by intravenous cassette dosing and hepatocyte intrinsic clearance, plasma protein binding and non-specific incubation binding were determined in vitro. Prediction of CL hep,met was performed by IVIVE using conventional and adapted formats of the well-stirred liver model.3. The best prediction of in vivo CL hep,met from scaled in vitro kinetic data was achieved using an empirical correction factor based on a 'regression offset' of the IVIV relationship.4. In summary, these results expand the in vitro and in vivo PK knowledge in Göttingen minipig. We show regression corrected IVIVE provides superior prediction of in vivo CL hep,met in minipig offering a practical, unified scaling approach to address systematic under-predictions. Finally, we propose a reference set for researchers to establish their own 'lab-specific' regression correction for IVIVE in minipig.
Published: 2022

42. Mesoscale Convective Systems in a Superparameterized E3SM Simulation at High Resolution

Author: Guangxing Lin, Christopher R. Jones, L. Ruby Leung, Zhe Feng, and Mikhail Ovchinnikov
Subjects: Physical geography, Global and Planetary Change, super‐parameterization, global climate model, General Earth and Planetary Sciences, Environmental Chemistry, clouds, GC1-1581, precipitation, Oceanography, convection, mesoscle convective system, GB3-5030
Abstract: Accurately representing mesoscale convective systems (MCSs) is crucial to simulating the energy and water cycles in global climate models. Using a novel MCS identification and tracking algorithm applied to observations and model simulations, we evaluate how well the Energy Exascale Earth System Model (E3SM) simulates MCSs over the central US. Simulations performed by E3SM at 25 km grid spacing with and without superparameterization (SP) are compared and evaluated against observations using multiple metrics highlighting important MCS characteristics. Compared to E3SM, the superparameterized model (SP‐E3SM) better simulates MCS number and MCS precipitation amount, diurnal cycle, propagation, and the probability distribution of precipitation rate in both spring and summer. The improvement from SP is partly contributed by improvement in simulating the large‐scale environments, featuring enhanced atmospheric low‐level moisture and larger moisture transport to the central US relative to E3SM. However, SP‐E3SM still underestimates MCS precipitation amount, particularly in summer. This underestimation is closely related to the negative bias in MCS precipitation intensity, although the drier environments simulated during summer also contributes to underestimation of MCS frequency. Without SP, the larger bias in MCS precipitation amount is closely related to the negative bias in MCS frequency, while the substantial dry bias in the large‐scale environments also contributes to underestimation of MCS intensity. Our results suggest that SP improves MCS simulation by improving modeling of the large‐scale environments and convection initiation, which are both major limiting factors in E3SM even at 25 km grid spacing where deep convection is represented by a cumulus parameterization.
Published: 2021

43. Configurable computing solutions for automatic target recognition.

Author: John D. Villasenor, Brian Schoner, Kang-Ngee Chia, Charles Zapata, Hea Joung Kim, Christopher R. Jones 0001, Shane Lansing, and Bill Mangione-Smith
Published: 1996
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44. Issues in wireless video coding using run-time-reconfigurable FPGAs.

Author: Brian Schoner, Christopher R. Jones 0001, and John D. Villasenor
Published: 1995
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45. Impact of the COVID-19 pandemic on routine surveillance for adults with chronic hepatitis B virus (HBV) infection in the UK

Author: Afzal N. Chaudhry, Steve Harris, Theresa Noble, Frazer Warricker, Eleni Nastouli, Vince Taylor, Hang Phan, Eleanor Barnes, Gail Roadknight, William Gelson, Jim Davies, Kinga A Várnai, Stephanie Little, Monique Andersson, Luis Romão, Paul Klenerman, Tingyan Wang, Josune Olza, David Smith, Dimitri Papadimitriou, David Ramlakhan, Ben Glampson, Graham S Cooke, Cori Campbell, Philippa C Matthews, Hizni Salih, Christopher R. Jones, Kerrie Woods, Oliver Freeman, Jane Collier, Louise English, Salim I. Khakoo, Florina Borca, and Luca Mercuri
Subjects: education.field_of_study, medicine.medical_specialty, Coronavirus disease 2019 (COVID-19), business.industry, Population, Health informatics, Virus, Chronic hepatitis, Electronic health record, Pandemic, Emergency medicine, Medicine, business, education, Viral load
Abstract: Background and aimsTo determine the impact of the COVID-19 pandemic on the population with chronic Hepatitis B virus (HBV) infection under hospital follow-up in the UK, we quantified the coverage and frequency of measurements of biomarkers used for routine surveillance (ALT and HBV viral load).MethodsWe used anonymised electronic health record data from the National Institute for Health Research (NIHR) Health Informatics Collaborative (HIC) pipeline representing five UK NHS Trusts.ResultsWe report significant reductions in surveillance of both biomarkers during the pandemic compared to pre-COVID years, both in terms of the proportion of patients who had ≥1 measurement annually, and the mean number of measurements per patient.ConclusionsFurther investigation is required to determine whether these disruptions will be associated with increased rates of adverse chronic HBV outcomes.
Published: 2021

46. Variable short duration treatment versus standard treatment, with and without adjunctive ribavirin, for chronic hepatitis C: the STOP-HCV-1 non-inferiority, factorial RCT

Author: Richard Gilson, Rachel Halford, Graham S Cooke, AS Walker, Aftab Ala, Sumita Verma, Helen Ainscough, Christopher R. Jones, Leanne McCabe, Daniel M. Forton, Chin Lye Ch’ng, Sanjay Bhagani, Stuart McPherson, Eleanor Barnes, Fleur Hudson, Benjamin Stone, Dung Nguyen, Martin Wiselka, Jane Collier, M. Azim Ansari, Stephen T. Barclay, Stephen D. Ryder, David Smith, Sarah Pett, Emily Dennis, and Mark Nelson
Subjects: Ledipasvir, medicine.medical_specialty, Sofosbuvir, business.industry, Standard treatment, Ribavirin, precision medicine, Hepatitis C, medicine.disease, Confidence interval, Ombitasvir, chemistry.chemical_compound, chemistry, Paritaprevir, Internal medicine, medicine, Medicine, hepatitis c, business, direct-acting antivirals, medicine.drug
Abstract: Background High cure rates with licensed durations of therapy for chronic hepatitis C virus suggest that many patients are overtreated. New strategies in individuals who find it challenging to adhere to standard treatment courses could significantly contribute to the elimination agenda. Objectives To compare cure rates using variable ultrashort first-line treatment stratified by baseline viral load followed by retreatment, with a fixed 8-week first-line treatment with retreatment with or without adjunctive ribavirin. Design An open-label, multicentre, factorial randomised controlled trial. Randomisation Randomisation was computer generated, with patients allocated in a 1 : 1 ratio using a factorial design to each of biomarker-stratified variable ultrashort strategy or fixed duration and adjunctive ribavirin (or not), using a minimisation algorithm with a probabilistic element. Setting NHS. Participants A total of 202 adults (aged ≥ 18 years) infected with chronic hepatitis C virus genotype 1a/1b or 4 for ≥ 6 months, with a detectable plasma hepatitis C viral load and no significant fibrosis [FibroScan® (Echosens, Paris, France) score F0–F1 or biopsy-proven minimal fibrosis], a hepatitis C virus viral load 24 weeks on anti-human immunodeficiency virus drugs. Interventions Fixed-duration 8-week first-line therapy compared with variable ultrashort first-line therapy, initially for 4–6 weeks (continuous scale) stratified by screening viral load (variable ultrashort strategy 1, mean 32 days of treatment) and then, subsequently, for 4–7 weeks (variable ultrashort strategy 2 mean 39 days of duration), predominantly with ombitasvir, paritaprevir, ritonavir (Viekirax®; AbbVie, Chicago, IL, USA), and dasabuvir (Exviera®; AbbVie, Chicago, IL, USA) or ritonavir. All patients in whom first-line treatment was unsuccessful were immediately retreated with 12 weeks’ sofosbuvir, ledipasvir (Harvoni®, Gilead Sciences, Inc., Foster City, CA, USA) and ribavirin. Main outcome measure The primary outcome was overall sustained virological response (persistently undetectable) 12 weeks after the end of therapy (SVR12). Results A total of 202 patients were analysed. All patients in whom the primary outcome was evaluable achieved SVR12 overall [100% (197/197), 95% confidence interval 86% to 100%], demonstrating non-inferiority between fixed- and variable-duration strategies (difference 0%, 95% confidence interval –3.8% to 3.7%, prespecified non-inferiority margin 4%). A SVR12 following first-line treatment was achieved in 91% (92/101; 95% confidence interval 86% to 97%) of participants randomised to the fixed-duration strategy and by 48% (47/98; 95% confidence interval 39% to 57%) allocated to the variable-duration strategy. However, the proportion achieving SVR12 was significantly higher among those allocated to variable ultrashort strategy 2 [72% (23/32), 95% confidence interval 56% to 87%] than among those allocated to variable ultrashort strategy 1 [36% (24/66), 95% confidence interval 25% to 48%]. Overall, a SVR12 following first-line treatment was achieved by 72% (70/101) (95% confidence interval 65% to 78%) of patients treated with ribavirin and by 68% (69/98) (95% confidence interval 61% to 76%) of those not treated with ribavirin. A SVR12 with variable ultrashort strategies 1 and 2 was 52% (25/48) (95% confidence interval 38% to 65%) with ribavirin, compared with 44% (22/50) (95% confidence interval 31% to 56) without. However, at treatment failure, the emergence of viral resistance was lower with ribavirin [12% (3/26), 95% confidence interval 2% to 30%] than without [38% (11/29), 95% confidence interval 21% to 58%; p = 0.01]. All 10 individuals who became undetectable at day 3 of treatment achieved first-line SVR12 regardless of treatment duration. Five participants in the variable-duration arm and five in the fixed-duration arm experienced serious adverse events (p = 0.69), as did five participants receiving ribavirin and five participants receiving no ribavirin. Conclusions SVR12 rates were significantly higher when ultrashort treatment varied between 4 and 7 weeks, rather than between 4 and 6 weeks. We found no evidence of ribavirin significantly affecting first-line SVR12, with unsuccessful first-line short-course therapy also not compromising subsequent retreatment with sofosbuvir, ledipasvir and ribavirin. Future work A priority for future work needs to be the development and evaluation of robust predictive measures to identify those patients who can be cured with ultrashort courses of therapy. Trial registration Current Controlled Trials ISRCTN37915093, EudraCT 2015-005004-28 and CTA 19174/0370/001-0001. Funding This project was funded by the Efficacy and Mechanism Evaluation programme, a MRC and National Institute for Health Research (NIHR) partnership. This will be published in full in Efficacy and Mechanism Evaluation; Vol. 8, No. 17. See the NIHR Journals Library website for further project information.
Published: 2021

47. Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

Author: Mohammad Raza, Alison E. Mather, Gilberto Betancor, Ian Merrick, Ben Taylor, Mathew A. Beale, Helen Ward, Samir Dervisevic, Michelle Cronin, Aaron R. Jeffries, Louise Smith, Steven Rudder, Mara K. N. Lawniczak, Sascha Ott, Ashok Dadrah, Luke Bedford, Gabrielle Vernet, Erik M. Volz, Rahul Batra, Johnny Debebe, Caoimhe McKerr, Samantha McGuigan, Oliver Megram, Katie Jones, Mailis Maes, Rebecca Dewar, Emma Swindells, Robert E. Johnson, Myra Hosmillo, Wen C Yew, Vineet Patel, Scott Aj Thurston, Matthew Bashton, Luke B Snell, Lynn Monaghan, David Buck, Gregory R Young, Garren Scott, Louis du Plessis, Sara Kumziene-Summerhayes, David M. Aanensen, Carl Jones, Nadine Holmes, Bernardo Gutierrez, Elizabeth Wastenge, Stavroula F Louka, Dennis Wang, Richard I. Gregory, M. Estée Török, Alistair C. Darby, Ulf Schaefer, Marc Niebel, David Robertson, E. Thomson, Carol Churcher, Patrick C McClure, Scott Elliott, Sarah Jeremiah, Katerina Galai, Matthew W. Loose, Megan Mayhew, Adhyana I K Mahanama, Angeliki Karamani, Naomi R Park, David J. Williams, Lance Turtle, Lucy R. Frost, Alicia Thornton, Jennifier Liddle, M Morgan, Tim Wyatt, Paul W Bird, Chloe Bishop, Esther Robinson, Alasdair MacLean, Inigo Martincorena, Bridget A. Knight, Emma Meader, Thomas R. Connor, Hermione J. Webster, Peter Muir, Sarah Walsh, Stephanie W. Lo, Andrew Bosworth, Hannah E Bridgewater, David Simpson, Radoslaw Poplawski, Angus I. Best, David Baker, Laura Letchford, Cassie Breen, Yann Bourgeois, Matthew Gemmell, Nikki Smith, Alison Holmes, Iliana Georgana, Christophe Fraser, Natasha Jesudason, Johnathan M Evans, Rachael Stanley, Lesley-Anne Williams, Jessica Lynch, Hannah Lowe, Eleri Wilson-Davies, Paul A. Baker, Alex Makunin, James Bonfield, Helen Adams, Christopher Fearn, Peter J. Diggle, Harry D Wilson, Carmen F. Manso, Nichola Duckworth, D Haw, Anna L. Casey, Audrey Farbos, Sam Haldenby, Vicki Chalker, Roberto Amato, Elen De Lacy, Ben Farr, Eric Witele, Buddhini Samaraweera, G MacIntyre-Cockett, Husam Osman, Jane Greenaway, Justin O'Grady, Sally Forrest, Andrew Nelson, Monika Pusok, A Lloyd, Edward Barton, James W. Harrison, Sophie Palmer, Amanda Symmonds, James Shepherd, Nazreen F. Hadjirin, Stephen L. Michell, Mohammed O Hassan-Ibrahim, Fiona Ashcroft, Daniel Mair, Richard H. Myers, Dianne Irish-Tavares, Hannah C. Howson-Wells, Jacqui Prieto, Christine Sambles, Andrew Hesketh, Alp Aydin, Sónia Gonçalves, Tabitha Mahungu, Tanzina Haque, Nicholas Ellaby, Karen Oliver, Hannah Paul, Joanne Watts, Claire McMurray, Lisa J Levett, Darren Smith, Simon Cottrell, Joanna Warwick-Dugdale, Pinglawathee Madona, Matthew J. Dorman, Lizzie Meadows, Ali R Awan, Leanne M Kermack, Jennifer Hart, Angie Lackenby, Carol Scott, Michael Spencer Chapman, Lucille Rainbow, Kyriaki Nomikou, Julianne R Brown, Juan Ledesma, Adam P Westhorpe, Giri Shankar, Karlie Fallon, Tim J Sloan, Joanne Watkins, Robert Impey, Sue Edwards, Rebecca C H Brown, Robin J Moll, Karla Spellman, Laura Gifford, Jamie Young, Adrienn Angyal, Graham Phillip Taylor, Robin Manley, Gavin Dabrera, Michelle Wantoch, Rachel Williams, David Heyburn, Mirko Menegazzo, Derrick W. Crook, Gaia Nebbia, Rachel Nelson, Elaine O'Toole, Luke Foulser, Katherine L Harper, Fatima Downing, Hassan Hartman, Nathan Moore, Gemma L. Kay, Matthew Wyles, Thanh Le-Viet, Edith Vamos, John Sillitoe, Lesley Shirley, Nicholas J. Loman, Iona Willingham, Elihu Aranday-Cortes, Ian B Vipond, Jeremy Mirza, Alberto C Cerda, Michelle L Michelsen, Steven Riley, Alison Cox, Igor Siveroni, Nadua Bayzid, Shavanthi Rajatileka, Giselda Bucca, Benjamin J Cogger, Tim Boswell, Matthew J. Bull, Stephen Carmichael, Lisa Berry, Frances Bolt, Kylie E. C. Ainslie, Martyn Guest, Sarojini Pandey, Katherine L. Bellis, Shane A. McCarthy, Christopher Ruis, Fei Sang, David Bonsall, Danni Weldon, Alex Alderton, Lee Graham, Amy Trebes, Sally Corden, Adrian W Signell, Tanya Golubchik, Huw Gulliver, Rocio Martinez Nunez, Dinesh Aggarwal, Tanya Curran, Jonathan K. Ball, Sharif Shaaban, Paul Randell, Jillian Durham, Alec Birchley, Matilde Mori, Joana Dias, Katherine A Twohig, Grant Hall, Antony D Hale, Alan McNally, Jonathan D. Edgeworth, Safiah Afifi, Andrew Rambaut, Katherine Smollett, David N. Lee, Tamyo Mbisa, Shahjahan Miah, Steven Rushton, Grace Taylor-Joyce, Hannah M Pymont, Chloe L Fisher, Cordelia Langford, Alex G. Richter, Jane A. H. Masoli, Michael Gallagher, Vicki M. Fleming, Kathleen A. Williamson, Anna Price, Holli Carden, Khalil Abudahab, Joanne D. Stockton, Meera Unnikrishnan, Jennifer Collins, Emma Moles-Garcia, Michaela John, Christine Kitchen, Tranprit Saluja, Ian Harrison, Lily Tong, Thomas G. Thompson, Thomas Helmer, Amita Patel, Siona Silveira, Deborah Ashby, Claire M Bewshea, Anita Justice, Brendan A I Payne, Alexander J. Trotter, Nikos Manesis, Katie F. Loveson, Cristina V. Ariani, Wendy Chatterton, Robert J. Munn, Julian A. Hiscox, Robert Beer, Judith Breuer, Caroline E. Walters, Liam Crawford, Ara Darzi, Will P. M. Rowe, Cariad Evans, Matthew Parker, Tammy V Merrill, Louise Aigrain, Joshua Quick, Leigh M Jackson, Samuel M. Nicholls, Jonathan W. Moore, John A Hartley, Graham P. Taylor, Cherian Koshy, Shirelle Burton-Fanning, Sheila Waugh, Catherine Moore, Danielle C. Groves, Peijun Zhang, Sahar Eldirdiri, Derek Fairley, Tim E. A. Peto, Jack Cd Lee, Sharon Glaysher, Liam Prestwood, Hannah Dent, Anita Kenyon, Stephen P. Kidd, Nick Levene, Igor Starinskij, Joseph G. Chappell, Steve Paterson, Gary Eltringham, Laia Fina, Angela Marchbank, Daniel Bradshaw, Marina Escalera Zamudio, Scott Goodwin, Andrew D Beggs, Seema Nickbakhsh, Trevor Robinson, Christina Atchison, David K. Jackson, Kathy Li, Rory Gunson, Sunando Roy, Graham S Cooke, Steven Liggett, Yasmin Chaudhry, Anoop Chauhan, Ben Temperton, Mariateresa de Cesare, Paul E Brown, Li Xu-McCrae, Martin P McHugh, Catherine Ludden, Wendy Smith, Danielle Leek, Divya K. Shah, Judith Heaney, Dominic P. Kwiatkowski, Kate M. Johnson, Robin Howe, Malorie Perry, Tetyana I. Vasylyeva, David F. Bibby, Haowei Wang, Steve Palmer, Nicholas W Machin, Charlotte A Williams, Bree Gatica-Wilcox, Angie Green, John A. Todd, Paul Elliott, Noel Craine, Jeffrey K. J. Cheng, Kate Templeton, Jonathan Hubb, Joshua Maksimovic, Christl A. Donnelly, Monique Andersson, Christopher Holmes, Dimitris Grammatopoulos, Christopher B. Williams, David G Partridge, Aminu S Jahun, Alexander Adams, Marius Cotic, Sarah Essex, Christopher J. Moore, Trudy Workman, Nicola Sheriff, Helen L Lowe, Ewan M. Harrison, Dorota Jamrozy, Rachel Jones, Ellen Higginson, Erwan Acheson, Christopher R. Jones, Oliver G. Pybus, Francesc Coll, Sian Morgan, Paul J. Parsons, Patawee Asamaphan, Veena Raviprakash, Andrew R. Bassett, Declan Bradley, Laura Atkinson, Anthony Underwood, Graciela Sluga, Sally Kay, Ellena Brooks, Oliver Eales, Andrew Whitwham, Surendra Parmar, Angela Cowell, Nicole Pacchiarini, Theocharis Tsoleridis, Jason Coombes, Robert Davies, Flavia Flaviani, Benita Percival, Jenna Nichols, Natasha M. Johnson, Salman Goudarzi, Hibo Asad, Amanda Bradley, Hannah Jones, Chrystala Constantinidou, Georgina M McManus, Minal Patel, Steven Leonard, Rebecca Williams Bmbs, Andrew J. Page, Christoph Puethe, Nicola Reynolds, Amy Ash, John Danesh, Corin Yeats, Claudia Wierzbicki, Kordo Saeed, John Boyes, Michael A. Quail, Sharon J. Peacock, Nabil-Fareed Alikhan, Jon-Paul Keatley, Claudio Fronterre, Garry Scarlett, James McKenna, Thushan I de Silva, Malte L Pinckert, Kate B. Cook, Amy Gaskin, Rajiv Shah, Matthew T. G. Holden, Sophie J Prosolek, Nathaniel Storey, Ryan P George, Lindsay Coupland, Jenifer Mason, Matthew Carlile, Thomas D Stanton, Guy Mollett, Siddharth Mookerjee, Mary Ramsay, Steven Platt, Stephen W Attwood, Susanne Stonehouse, Sophie Jones, Venkat Sivaprakasam, Amy Plimmer, Mark Whitehead, Catherine Bresner, Stefanie V Lensing, Louissa R Macfarlane-Smith, Colin P. Smith, Wendy Hogsden, Charlotte Nelson, Ian Johnston, Jeffrey C. Barrett, Joshua B Singer, Samuel Robson, Zoltán Molnár, Emma L. Wise, Sian Ellard, Kim S Smith, Alice Broos, Manjinder Khakh, Kathryn A Jackson, Claire Cormie, Rachel Tucker, Ian Goodfellow, S.E. Moses, Nicola Cumley, Meera Chand, Debra Padgett, Cassandra S Malone, James V. Price, Themoula Charalampous, Ronan A Lyons, Natalie Groves, Stefan Rooke, Rebekah E Wilson, Stephen Bonner, Richard Stark, Sharon Campbell, Michelle Lister, Carlos Balcazar, Ana da Silva Filipe, Ben Warne, Thomas N. Williams, Marta Gallis, Lauren Gilbert, Rose K Davidson, Angela Helen Beckett, Ember Hilvers, Kathryn McCluggage, Eileen Gallagher, Charlotte Beaver, Nick Cortes, Alisha Davies, Yusri Taha, Leah Ensell, Emanuela Pelosi, Elias Allara, Cressida Auckland, Eleanor Drury, Richard Eccles, Adela Alcolea-Medina, William L Hamilton, Rich Livett, Rachel Blacow, Margaret Hughes, Sarah François, Melisa Louise Fenton, Liz Ratcliffe, Verity Hill, Stephanie Hutchings, Kathryn Ann Harris, Emma Betteridge, William D. Fuller, Sophia T Girgis, Louise Berry, Gemma Clark, Nicholas M Redshaw, Richard Hopes, Leonardo de Oliveira Martins, Alexander J Keeley, Beth Blane, Wendy S. Barclay, Victoria Wright, Anita Lucaci, Luke R. Green, Fenella D. Halstead, Sarah Wyllie, Iraad F. Bronner, Áine O'Toole, Ravi Gupta, Leanne Kane, Clare M. McCann, Michael R Chapman, David W Eyre, Kelly Bicknell, Aileen G. Rowan, Sara Rey, Shazaad Ahmad, Diana Rajan, S Taylor, Sarah J. O'Brien, Alessandro M Carabelli, Amelia Joseph, Max Whiteley, Riaz Jannoo, Victoria Blakey, Martin D. Curran, David J. Studholme, Harmeet K Gill, Thomas R. A. Davis, Sushmita Sridhar, Clive Graham, Julian Tang, Clare Pearson, Mark Kristiansen, Miren Iturriza-Gomara, National Institute for Health Research, and UK Research and Innovation
Subjects: Delta, Adult, Male, 2019-20 coronavirus outbreak, COVID-19 Vaccines, Vaccination Coverage, Coronavirus disease 2019 (COVID-19), Adolescent, General Science & Technology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Vaccine Efficacy, Biology, Young Adult, Exponential growth, Ethnicity, Prevalence, Humans, Child, Aged, Family Characteristics, Multidisciplinary, High prevalence, COVID-19 Genomics UK (COG-UK) Consortium11‡, SARS-CoV-2, Age Factors, COVID-19, Middle Aged, Virology, Hospitalization, England, Socioeconomic Factors, COVID-19 Nucleic Acid Testing, Child, Preschool, Female, Self Report
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were rising during early summer 2021 in many countries as a result of the Delta variant. We assessed reverse transcription polymerase chain reaction swab positivity in the Real-time Assessment of Community Transmission–1 (REACT-1) study in England. During June and July 2021, we observed sustained exponential growth with an average doubling time of 25 days, driven by complete replacement of the Alpha variant by Delta and by high prevalence at younger, less-vaccinated ages. Prevalence among unvaccinated people [1.21% (95% credible interval 1.03%, 1.41%)] was three times that among double-vaccinated people [0.40% (95% credible interval 0.34%, 0.48%)]. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.
Published: 2021

48. Cohort Profile: National Institute for Health Research Health Informatics Collaborative: Hepatitis B Virus (NIHR HIC HBV) Research Dataset

Author: Eleanor Barnes, Ben Glampson, Gail Roadknight, William Gelson, Eleni Nastouli, Salim I. Khakoo, Florina Borca, Luis Romão, Luca Mercuri, Steve Harris, Theresa Noble, Josune Olza, Vince Taylor, Zuzana Moysova, Afzal N. Chaudhry, Jane Collier, David Ramlakhan, Philippa C Matthews, Stephanie Little, Graham S Cooke, Paul Klenerman, Jim Davies, Christopher R. Jones, Hang Phan, Louise English, Hizni Salih, David Smith, Tingyan Wang, Monique Andersson, Dimitri Papadimitriou, Kinga A Várnai, Frazer Warricker, Cori Campbell, Kerrie Woods, and Oliver Freeman
Subjects: Hepatitis B virus, education.field_of_study, medicine.medical_specialty, HBsAg, business.industry, Population, medicine.disease, medicine.disease_cause, Health informatics, Family medicine, Epidemiology, Cohort, medicine, education, Viral hepatitis, business, Viral load
Abstract: PurposeThe National Institute for Health Research (NIHR) Health Informatics Collaborative (HIC) was established to enable re-use of routinely collected clinical data across National Health Service (NHS) Trusts in the United Kingdom to support translational research. Viral hepatitis is one of the first five exemplar themes and hepatitis B virus (HBV) is the current focus of the theme. The NIHR HIC HBV dataset, derived from the central data repository of NIHR HIC viral hepatitis theme, aims to describe and characterise HBV infection in secondary care in the United Kingdom, and provides a resource for translational research.ParticipantsThe dataset comprises >5000 individuals (99% adults aged ≥18, 1% children aged Findings to dateData on demographics, laboratory tests, antiviral treatment, elastography scores, imaging/biopsy reports, death information, and potential risk factors for liver disease have been collected. Data are captured by electronic patient record (EPR) systems, and records are updated prospectively as new results are added. This cohort profile describes the dataset in its current form. Among the adults, 55% are male, and the median age at index date (defined as the first recorded positive hepatitis B virus surface antigen (HBsAg) or HBV DNA in EPR systems) was 40 years (interquartile range [IQR]: 32-50). For those individuals with ethnicity reported, 30% were Asian, 24% were Black, 30% were White, and the remaining 16% were mixed or other ethnic groups. Currently, the median follow-up duration of the adult patients in this dataset was 5.0 (IQR: 2.7-7.5) years, with 9.3 (95% CI: 8.2-10.5) deaths per 1,000 person-years. We have already conducted several analyses using subsets of this dataset including an evaluation of distribution and trajectories of HBsAg and HBV viral load in CHB, reviewing the use of antiviral treatment, quantifying the burden of liver disease in the untreated population, and studying the use of laboratory biomarkers to improve stratification and surveillance.Future plansLongitudinal data collection is continuing, with the sample growing in size, more parameters being collected, average follow-up increasing, and more NHS Trusts participating. This dataset offers important opportunities for epidemiological studies and biomedical informatics research, as well as characterising an HBV population for clinical trials through external collaborations with industry.
Published: 2021

49. Cohort Profile: The National Institute for Health Research Health Informatics Collaborative: Hepatitis B Virus (NIHR HIC HBV) research dataset

Author: Tingyan Wang, David A Smith, Cori Campbell, Oliver Freeman, Zuzana Moysova, Theresa Noble, Kinga A Várnai, Steve Harris, Hizni Salih, Gail Roadknight, Stephanie Little, Ben Glampson, Luca Mercuri, Dimitri Papadimitriou, Christopher R Jones, Vince Taylor, Afzal Chaudhry, Hang Phan, Florina Borca, Josune Olza, Frazer Warricker, Luis Romão, David Ramlakhan, Louise English, Paul Klenerman, Monique Andersson, Jane Collier, Alexander J Stockdale, Stacy Todd, Karl McIntyre, Andrew Frankland, Eleni Nastouli, Salim I Khakoo, William Gelson, Graham S Cooke, Kerrie Woods, Jim Davies, Eleanor Barnes, and Philippa C Matthews
Subjects: Epidemiology, FOS: Clinical medicine, Immunology, Infectious Disease, General Medicine, Genetics & Genomics
Abstract: No description supplied
Published: 2021

50. Better calibration of cloud parameterizations and subgrid effects increases the fidelity of E3SM Atmosphere Model version 1

Author: Po-Lun Ma, Bryce E. Harrop, Vincent E. Larson, Richard Neale, Andrew Gettelman, Hugh Morrison, Hailong Wang, Kai Zhang, Stephen A. Klein, Mark D. Zelinka, Yuying Zhang, Yun Qian, Jin-Ho Yoon, Christopher R. Jones, Meng Huang, Sheng-Lun Tai, Balwinder Singh, Peter A. Bogenschutz, Xue Zheng, Wuyin Lin, Johannes Quaas, Hélène Chepfer, Michael A. Brunke, Xubin Zeng, Johannes Mülmenstädt, Samson Hagos, Zhibo Zhang, Hua Song, Xiaohong Liu, Hui Wan, Jingyu Wang, Qi Tang, Peter M. Caldwell, Jiwen Fan, Larry K. Berg, Jerome D. Fast, Mark A. Taylor, Jean-Christophe Golaz, Shaocheng Xie, Philip J. Rasch, and L. Ruby Leung
Abstract: Realistic simulation of the Earth’s mean state climate remains a major challenge and yet it is crucial for predicting the climate system in transition. Deficiencies in models’ process representations, propagation of errors from one process to another, and associated compensating errors can often confound the interpretation and improvement of model simulations. These errors and biases can also lead to unrealistic climate projections as well as incorrect attribution of the physical mechanisms governing the past and future climate change. Here we show that a significantly improved global atmospheric simulation can be achieved by focusing on the realism of process assumptions in cloud calibration and subgrid effects using the Energy Exascale Earth System Model (E3SM) Atmosphere Model version 1 (EAMv1). The calibration of clouds and subgrid effects informed by our understanding of physical mechanisms leads to significant improvements in clouds and precipitation climatology, reducing common and longstanding biases across cloud regimes in the model. The improved cloud fidelity in turn reduces biases in other aspects of the system. Furthermore, even though the recalibration does not change the global mean aerosol and total anthropogenic effective radiative forcings (ERFs), the sensitivity of clouds, precipitation, and surface temperature to aerosol perturbations is significantly reduced. This suggests that it is possible to achieve improvements to the historical evolution of surface temperature over EAMv1 and that precise knowledge of global mean ERFs is not enough to constrain historical or future climate change. Cloud feedbacks are also significantly reduced in the recalibrated model, suggesting that there would be a lower climate sensitivity when running as part of the fully coupled E3SM. This study also compares results from incremental changes to cloud microphysics, turbulent mixing, deep convection, and subgrid effects to understand how assumptions in the representation of these processes affect different aspects of the simulated atmosphere as well as its response to forcings. We conclude that the spectral composition and geographical distribution of the ERFs and cloud feedback as well as the fidelity of the simulated base climate state are important for constraining the climate in the past and future.
Published: 2021

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