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1. The Far-INfrarEd Spectrometer for Surface Emissivity (FINESSE) – Part 1: Instrument description and level 1 radiances

Author: J. E. Murray, L. Warwick, H. Brindley, A. Last, P. Quigley, A. Rochester, A. Dewar, and D. Cummins
Subjects: Environmental engineering, TA170-171, Earthwork. Foundations, TA715-787
Abstract: The Far-INfrarEd Spectrometer for Surface Emissivity (FINESSE) instrument combines a commercial Bruker EM27 spectrometer with a front-end viewing and calibration rig developed at Imperial College London. FINESSE is specifically designed to enable accurate measurements of surface emissivity, covering the range 400–1600 cm−1, and, as part of this remit, can obtain views over the full 360° angular range. In this part, Part 1, we describe the system configuration, outlining the instrument spectral characteristics, our data acquisition methodology, and the calibration strategy. As part of the process, we evaluate the stability of the system, including the impact of knowledge of blackbody (BB) target emissivity and temperature. We also establish a numerical description of the instrument line shape (ILS), which shows strong frequency-dependent asymmetry. We demonstrate why it is important to account for these effects by assessing their impact on the overall uncertainty budget on the level 1 radiance products from FINESSE. Initial comparisons of observed spectra with simulations show encouraging performance given the uncertainty budget.
Published: 2024
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2. Long-term impact of COVID-19 hospitalisation among individuals with pre-existing airway diseases in the UK: a multicentre, longitudinal cohort study – PHOSP-COVID

Author: Omer Elneima, John R. Hurst, Carlos Echevarria, Jennifer K. Quint, Samantha Walker, Salman Siddiqui, Petr Novotny, Paul E. Pfeffer, Jeremy S. Brown, Manu Shankar-Hari, Hamish J.C. McAuley, Olivia C. Leavy, Aarti Shikotra, Amisha Singapuri, Marco Sereno, Matthew Richardson, Ruth M. Saunders, Victoria C. Harris, Linzy Houchen-Wolloff, Neil J. Greening, Ewen M. Harrison, Annemarie B. Docherty, Nazir I. Lone, James D. Chalmers, Ling-Pei Ho, Alex Horsley, Michael Marks, Krisnah Poinasamy, Betty Raman, Rachael A. Evans, Louise V. Wain, Aziz Sheikh, Chris E. Brightling, Anthony De Soyza, Liam G. Heaney, J.K. Baillie, N.I. Lone, E. Pairo-Castineira, N. Avramidis, K. Rawlik, S Jones, L. Armstrong, B. Hairsine, H. Henson, C. Kurasz, A. Shaw, L. Shenton, H. Dobson, A. Dell, S. Fairbairn, N. Hawkings, J. Haworth, M. Hoare, V. Lewis, A. Lucey, G. Mallison, H. Nassa, C. Pennington, A. Price, C. Price, A. Storrie, G. Willis, S. Young, K. Poinasamy, S. Walker, I. Jarrold, A. Sanderson, K. Chong-James, C. David, W.Y. James, P. Pfeffer, O. Zongo, A. Martineau, C. Manisty, C. Armour, V. Brown, J. Busby, B. Connolly, T. Craig, S. Drain, L.G. Heaney, B. King, N. Magee, E. Major, D. McAulay, L. McGarvey, J. McGinness, T. Peto, R. Stone, A. Bolger, F. Davies, A. Haggar, J. Lewis, A. Lloyd, R. Manley, E. McIvor, D. Menzies, K. Roberts, W. Saxon, D. Southern, C. Subbe, V. Whitehead, A. Bularga, N.L. Mills, J. Dawson, H. El-Taweel, L. Robinson, L. Brear, K. Regan, D. Saralaya, K. Storton, S. Amoils, A. Bermperi, I. Cruz, K. Dempsey, A. Elmer, J. Fuld, H. Jones, S. Jose, S. Marciniak, M. Parkes, C. Ribeiro, J. Taylor, M. Toshner, L. Watson, J. Worsley, L. Broad, T. Evans, M. Haynes, L. Jones, L. Knibbs, A. McQueen, C. Oliver, K. Paradowski, R. Sabit, J. Williams, I. Jones, L. Milligan, E. Harris, C. Sampson, E. Davies, C. Evenden, A. Hancock, K. Hancock, C. Lynch, M. Rees, L. Roche, N. Stroud, T. Thomas-Woods, S. Heller, T. Chalder, K. Shah, E. Robertson, B. Young, M. Babores, M. Holland, N. Keenan, S. Shashaa, H. Wassall, L. Austin, E. Beranova, T. Cosier, J. Deery, T. Hazelton, H. Ramos, R. Solly, S. Turney, H. Weston, M. Ralser, L. Pearce, S. Pugmire, W. Stoker, A. Wilson, W. McCormick, E. Fraile, J. Ugoji, L. Aguilar Jimenez, G. Arbane, S. Betts, K. Bisnauthsing, A. Dewar, N. Hart, G. Kaltsakas, H. Kerslake, M.M. Magtoto, P. Marino, L.M. Martinez, M. Ostermann, J. Rossdale, T.S. Solano, M. Alvarez Corral, A. Arias, E. Bevan, D. Griffin, J. Martin, J. Owen, S. Payne, A. Prabhu, A. Reed, W. Storrar, N. Williams, C. Wrey Brown, T. Burdett, J. Featherstone, C. Lawson, A. Layton, C. Mills, L. Stephenson, Y. Ellis, P. Atkin, K. Brindle, M.G. Crooks, K. Drury, N. Easom, R. Flockton, L. Holdsworth, A. Richards, D.L. Sykes, S. Thackray-Nocera, C. Wright, S. Coetzee, K. Davies, R. Hughes, R. Loosley, H. McGuinness, A. Mohamed, L. O'Brien, Z. Omar, E. Perkins, J. Phipps, G. Ross, A. Taylor, H. Tench, R. Wolf-Roberts, L. Burden, E. Calvelo, B. Card, C. Carr, E.R. Chilvers, D. Copeland, P. Cullinan, P. Daly, L. Evison, T. Fayzan, H. Gordon, S. Haq, R.G. Jenkins, C. King, O. Kon, K. March, M. Mariveles, L. McLeavey, N. Mohamed, S. Moriera, U. Munawar, J. Nunag, U. Nwanguma, L. Orriss-Dib, A. Ross, M. Roy, E. Russell, K. Samuel, J. Schronce, N. Simpson, L. Tarusan, D.C. Thomas, C. Wood, N. Yasmin, D. Altmann, L.S. Howard, D. Johnston, A. Lingford-Hughes, W.D-C. Man, J. Mitchell, P.L. Molyneaux, C. Nicolaou, D.P. O'Regan, L. Price, J. Quint, D. Smith, R.S. Thwaites, J. Valabhji, S. Walsh, C.M. Efstathiou, F. Liew, A. Frankel, L. Lightstone, S. McAdoo, M. Wilkins, M. Willicombe, R. Touyz, A-M. Guerdette, M. Hewitt, R. Reddy, K. Warwick, S. White, A. McMahon, M. Malim, K. Bramham, M. Brown, K. Ismail, T. Nicholson, C. Pariante, C. Sharpe, S. Wessely, J. Whitney, O. Adeyemi, R. Adrego, H. Assefa-Kebede, J. Breeze, S. Byrne, P. Dulawan, A. Hoare, C.J. Jolley, A. Knighton, S. Patale, I. Peralta, N. Powell, A. Ramos, K. Shevket, F. Speranza, A. Te, A. Shah, A. Chiribiri, C. O'Brien, A. Hayday, A. Ashworth, P. Beirne, J. Clarke, C. Coupland, M. Dalton, C. Favager, J. Glossop, J. Greenwood, L. Hall, T. Hardy, A. Humphries, J. Murira, D. Peckham, S. Plein, J. Rangeley, G. Saalmink, A.L. Tan, E. Wade, B. Whittam, N. Window, J. Woods, G. Coakley, L. Turtle, L. Allerton, A.M. Allt, M. Beadsworth, A. Berridge, J. Brown, S. Cooper, A. Cross, S. Defres, S.L. Dobson, J. Earley, N. French, W. Greenhalf, K. Hainey, H.E. Hardwick, J. Hawkes, V. Highett, S. Kaprowska, A.L. Key, L. Lavelle-Langham, N. Lewis-Burke, G. Madzamba, F. Malein, S. Marsh, C. Mears, L. Melling, M.J. Noonan, L. Poll, J. Pratt, E. Richardson, A. Rowe, M.G. Semple, V. Shaw, K.A. Tripp, L.O. Wajero, S.A. Williams-Howard, D.G. Wootton, J. Wyles, S.N. Diwanji, S. Gurram, P. Papineni, S. Quaid, G.F. Tiongson, E. Watson, A. Briggs, M. Marks, C. Hastie, N. Rogers, N. Smith, D. Stensel, L. Bishop, K. McIvor, P. Rivera-Ortega, B. Al-Sheklly, C. Avram, J. Blaikely, M. Buch, N. Choudhury, D. Faluyi, T. Felton, T. Gorsuch, N.A. Hanley, A. Horsley, T. Hussell, Z. Kausar, N. Odell, R. Osbourne, K. Piper Hanley, K. Radhakrishnan, S. Stockdale, T. Kabir, J.T. Scott, P.J.M. Openshaw, I.D. Stewart, D. Burn, A. Ayoub, G. Burns, G. Davies, A. De Soyza, C. Echevarria, H. Fisher, C. Francis, A. Greenhalgh, P. Hogarth, J. Hughes, K. Jiwa, G. Jones, G. MacGowan, D. Price, A. Sayer, J. Simpson, H. Tedd, S. Thomas, S. West, M. Witham, S. Wright, A. Young, M.J. McMahon, P. Neill, D. Anderson, N. Basu, H. Bayes, A. Brown, A. Dougherty, K. Fallon, L. Gilmour, D. Grieve, K. Mangion, A. Morrow, R. Sykes, C. Berry, I.B. McInnes, K. Scott, F. Barrett, A. Donaldson, E.K. Sage, D. Bell, R. Hamil, K. Leitch, L. Macliver, M. Patel, J. Quigley, A. Smith, B. Welsh, G. Choudhury, S. Clohisey, A. Deans, A.B. Docherty, J. Furniss, E.M. Harrison, S. Kelly, A. Sheikh, J.D. Chalmers, D. Connell, C. Deas, A. Elliott, J. George, S. Mohammed, J. Rowland, A.R. Solstice, D. Sutherland, C.J. Tee, J. Bunker, R. Gill, R. Nathu, K. Holmes, H. Adamali, D. Arnold, S. Barratt, A. Dipper, S. Dunn, N. Maskell, A. Morley, L. Morrison, L. Stadon, S. Waterson, H. Welch, B. Jayaraman, T. Light, I. Vogiatzis, P. Almeida, C.E. Bolton, A. Hosseini, L. Matthews, R. Needham, K. Shaw, A.K. Thomas, J. Bonnington, M. Chrystal, C. Dupont, P.L. Greenhaff, A. Gupta, W. Jang, S. Linford, A. Nikolaidis, S. Prosper, A. Burns, N. Kanellakis, V.M. Ferreira, C. Nikolaidou, C. Xie, M. Ainsworth, A. Alamoudi, A. Bloss, P. Carter, M. Cassar, J. Chen, F. Conneh, T. Dong, R.I. Evans, E. Fraser, J.R. Geddes, F. Gleeson, P. Harrison, M. Havinden-Williams, L.P. Ho, P. Jezzard, I. Koychev, P. Kurupati, H. McShane, C. Megson, S. Neubauer, D. Nicoll, G. Ogg, E. Pacpaco, M. Pavlides, Y. Peng, N. Petousi, J. Pimm, N.M. Rahman, B. Raman, M.J. Rowland, K. Saunders, M. Sharpe, N. Talbot, E.M. Tunnicliffe, A. Korszun, S. Kerr, R.E. Barker, D. Cristiano, N. Dormand, P. George, M. Gummadi, S. Kon, K. Liyanage, C.M. Nolan, B. Patel, S. Patel, O. Polgar, P. Shah, S. Singh, J.A. Walsh, M. Gibbons, S. Ahmad, S. Brill, J. Hurst, H. Jarvis, L. Lim, S. Mandal, D. Matila, O. Olaosebikan, C. Singh, C. Laing, H. Baxendale, L. Garner, C. Johnson, J. Mackie, A. Michael, J. Newman, J. Pack, K. Paques, H. Parfrey, J. Parmar, A. Reddy, M. Halling-Brown, P. Dark, N. Diar-Bakerly, D. Evans, E. Hardy, A. Harvey, D. Holgate, S. Knight, N. Mairs, N. Majeed, L. McMorrow, J. Oxton, J. Pendlebury, C. Summersgill, R. Ugwuoke, S. Whittaker, W. Matimba-Mupaya, S. Strong-Sheldrake, P. Chowienczyk, J. Bagshaw, M. Begum, K. Birchall, R. Butcher, H. Carborn, F. Chan, K. Chapman, Y. Cheng, L. Chetham, C. Clark, Z. Coburn, J. Cole, M. Dixon, A. Fairman, J. Finnigan, H. Foot, D. Foote, A. Ford, R. Gregory, K. Harrington, L. Haslam, L. Hesselden, J. Hockridge, A. Holbourn, B. Holroyd-Hind, L. Holt, A. Howell, E. Hurditch, F. Ilyas, C. Jarman, A. Lawrie, J-H. Lee, E. Lee, R. Lenagh, A. Lye, I. Macharia, M. Marshall, A. Mbuyisa, J. McNeill, S. Megson, J. Meiring, L. Milner, S. Misra, H. Newell, T. Newman, C. Norman, L. Nwafor, D. Pattenadk, M. Plowright, J. Porter, P. Ravencroft, C. Roddis, J. Rodger, S.L. Rowland-Jones, P. Saunders, J. Sidebottom, J. Smith, L. Smith, N. Steele, G. Stephens, R. Stimpson, B. Thamu, A.A.R. Thompson, N. Tinker, K. Turner, H. Turton, P. Wade, J. Watson, I. Wilson, A. Zawia, L. Allsop, K. Bennett, P. Buckley, M. Flynn, M. Gill, C. Goodwin, M. Greatorex, H. Gregory, C. Heeley, L. Holloway, M. Holmes, J. Hutchinson, J. Kirk, W. Lovegrove, T.A. Sewell, S. Shelton, D. Sissons, K. Slack, S. Smith, D. Sowter, S. Turner, V. Whitworth, I. Wynter, J. Tomlinson, L. Warburton, S. Painter, S. Palmer, D. Redwood, J. Tilley, C. Vickers, T. Wainwright, G. Breen, M. Hotopf, R. Aul, D. Forton, M. Ali, A. Dunleavy, M. Mencias, N. Msimanga, T. Samakomva, S. Siddique, V. Tavoukjian, J. Teixeira, R. Ahmed, R. Francis, L. Connor, A. Cook, G.A. Davies, T. Rees, F. Thaivalappil, C. Thomas, M. McNarry, K.E. Lewis, M. Coulding, S. Kilroy, J. McCormick, J. McIntosh, V. Turner, J. Vere, A. Butt, H. Savill, S.S. Kon, G. Landers, H. Lota, S. Portukhay, M. Nasseri, A. Daniels, A. Hormis, J. Ingham, L. Zeidan, M. Chablani, L. Osborne, S. Aslani, A. Banerjee, R. Batterham, G. Baxter, R. Bell, A. David, E. Denneny, A.D. Hughes, W. Lilaonitkul, P. Mehta, A. Pakzad, B. Rangelov, B. Williams, J. Willoughby, M. Xu, N. Ahwireng, D. Bang, D. Basire, J.S. Brown, R.C. Chambers, A. Checkley, R. Evans, M. Heightman, T. Hillman, J. Jacob, R. Jastrub, M. Lipman, S. Logan, D. Lomas, M. Merida Morillas, H. Plant, J.C. Porter, K. Roy, E. Wall, T. Treibel, N. Ahmad Haider, C. Atkin, R. Baggott, M. Bates, A. Botkai, A. Casey, B. Cooper, J. Dasgin, C. Dawson, K. Draxlbauer, N. Gautam, J. Hazeldine, T. Hiwot, S. Holden, K. Isaacs, T. Jackson, V. Kamwa, D. Lewis, J.M. Lord, S. Madathil, C. McGhee, K. McGee, A. Neal, A. Newton-Cox, J. Nyaboko, D. Parekh, Z. Peterkin, H. Qureshi, L. Ratcliffe, E. Sapey, J. Short, T. Soulsby, J. Stockley, Z. Suleiman, T. Thompson, M. Ventura, S. Walder, C. Welch, D. Wilson, S. Yasmin, K.P. Yip, N. Chaudhuri, C. Childs, R. Djukanovic, S. Fletcher, M. Harvey, M.G. Jones, E. Marouzet, B. Marshall, R. Samuel, T. Sass, T. Wallis, H. Wheeler, R. Steeds, P. Beckett, C. Dickens, U. Nanda, M. Aljaroof, N. Armstrong, H. Arnold, H. Aung, M. Bakali, M. Bakau, E. Baldry, M. Baldwin, C. Bourne, M. Bourne, C.E. Brightling, N. Brunskill, P. Cairns, L. Carr, A. Charalambou, C. Christie, M.J. Davies, E. Daynes, S. Diver, R. Dowling, S. Edwards, C. Edwardson, O. Elneima, H. Evans, R.A. Evans, J. Finch, S. Finney, S. Glover, N. Goodman, B. Gooptu, N.J. Greening, K. Hadley, P. Haldar, B. Hargadon, V.C. Harris, L. Houchen-Wolloff, W. Ibrahim, L. Ingram, K. Khunti, A. Lea, D. Lee, H.J.C. McAuley, G.P. McCann, P. McCourt, T. McNally, G. Mills, W. Monteiro, M. Pareek, S. Parker, A. Prickett, I.N. Qureshi, A. Rowland, R. Russell, M. Sereno, A. Shikotra, S. Siddiqui, A. Singapuri, S.J. Singh, J. Skeemer, M. Soares, E. Stringer, S. Terry, T. Thornton, M. Tobin, T.J.C. Ward, F. Woodhead, T. Yates, A.J. Yousuf, B. Guillen Guiio, O.C. Leavy, L.V. Wain, M. Broome, P. McArdle, D. Thickett, R. Upthegrove, D. Wilkinson, P. Moss, D. Wraith, J. Evans, E. Bullmore, J.L. Heeney, C. Langenberg, W. Schwaeble, C. Summers, J. Weir McCall, D. Adeloye, D.E. Newby, R. Pius, I. Rudan, M. Shankar-Hari, C.L. Sudlow, M. Thorpe, S. Walmsley, B. Zheng, L. Allan, C. Ballard, A. McGovern, J. Dennis, J. Cavanagh, S. MacDonald, K. O'Donnell, J. Petrie, N. Sattar, M. Spears, E. Guthrie, M. Henderson, R.J. Allen, M. Bingham, T. Brugha, R. Free, D. Jones, L. Gardiner, A.J. Moss, E. Mukaetova-Ladinska, P. Novotny, C. Overton, J.E. Pearl, T. Plekhanova, M. Richardson, N. Samani, J. Sargent, M. Sharma, M. Steiner, C. Taylor, C. Tong, E. Turner, J. Wormleighton, B. Zhao, K. Ntotsis, R.M. Saunders, D. Lozano-Rojas, D. Cuthbertson, G. Kemp, A. McArdle, B. Michael, W. Reynolds, L.G. Spencer, B. Vinson, M. Ashworth, K. Abel, H. Chinoy, B. Deakin, M. Harvie, C.A. Miller, S. Stanel, P. Barran, D. Trivedi, H. McAllister-Williams, S. Paddick, A. Rostron, J.P. Taylor, D. Baguley, C. Coleman, E. Cox, L. Fabbri, S. Francis, I. Hall, E. Hufton, S. Johnson, F. Khan, P. Kitterick, R. Morriss, N. Selby, L. Wright, C. Antoniades, A. Bates, M. Beggs, K. Bhui, K. Breeze, K.M. Channon, D. Clark, X. Fu, M. Husain, X. Li, E. Lukaschuk, C. McCracken, K. McGlynn, R. Menke, K. Motohashi, T.E. Nichols, G. Ogbole, S. Piechnik, I. Propescu, J. Propescu, A.A. Samat, Z.B. Sanders, L. Sigfrid, M. Webster, L. Kingham, P. Klenerman, H. Lamlum, G. Carson, M. Taquet, L. Finnigan, L.C. Saunders, J.M. Wild, P.C. Calder, N. Huneke, G. Simons, D. Baldwin, S. Bain, L. Daines, E. Bright, P. Crisp, R. Dharmagunawardena, M. Stern, L. Bailey, A. Reddington, A. Wight, A. Ashish, J. Cooper, E. Robinson, A. Broadley, L. Barman, C. Brookes, K. Elliott, L. Griffiths, Z. Guy, K. Howard, D. Ionita, H. Redfearn, C. Sarginson, and A. Turnbull
Subjects: Medicine
Abstract: Background The long-term outcomes of COVID-19 hospitalisation in individuals with pre-existing airway diseases are unknown. Methods Adult participants hospitalised for confirmed or clinically suspected COVID-19 and discharged between 5 March 2020 and 31 March 2021 were recruited to the Post-hospitalisation COVID-19 (PHOSP-COVID) study. Participants attended research visits at 5 months and 1 year post discharge. Clinical characteristics, perceived recovery, burden of symptoms and health-related quality of life (HRQoL) of individuals with pre-existing airway disease (i.e., asthma, COPD or bronchiectasis) were compared to the non-airways group. Results A total of 615 out of 2697 (22.8%) participants had a history of pre-existing airway diseases (72.0% diagnosed with asthma, 22.9% COPD and 5.1% bronchiectasis). At 1 year, the airways group participants were less likely to feel fully recovered (20.4% versus 33.2%, p
Published: 2024
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3. Prevalence of physical frailty, including risk factors, up to 1 year after hospitalisation for COVID-19 in the UK: a multicentre, longitudinal cohort studyResearch in context

Author: Hamish J.C. McAuley, Rachael A. Evans, Charlotte E. Bolton, Christopher E. Brightling, James D. Chalmers, Annemarie B. Docherty, Omer Elneima, Paul L. Greenhaff, Ayushman Gupta, Victoria C. Harris, Ewen M. Harrison, Ling-Pei Ho, Alex Horsley, Linzy Houchen-Wolloff, Caroline J. Jolley, Olivia C. Leavy, Nazir I. Lone, William D-C Man, Michael Marks, Dhruv Parekh, Krisnah Poinasamy, Jennifer K. Quint, Betty Raman, Matthew Richardson, Ruth M. Saunders, Marco Sereno, Aarti Shikotra, Amisha Singapuri, Sally J. Singh, Michael Steiner, Ai Lyn Tan, Louise V. Wain, Carly Welch, Julie Whitney, Miles D. Witham, Janet Lord, Neil J. Greening, K. Abel, H. Adamali, D. Adeloye, O. Adeyemi, R. Adrego, L.A. Aguilar Jimenez, S. Ahmad, N. Ahmad Haider, R. Ahmed, N. Ahwireng, M. Ainsworth, B. Al-Sheklly, A. Alamoudi, M. Ali, M. Aljaroof, A.M. All, L. Allan, R.J. Allen, L. Allerton, L. Allsop, P. Almeida, D. Altmann, M. Alvarez Corral, S. Amoils, D. Anderson, C. Antoniades, G. Arbane, A. Arias, C. Armour, L. Armstrong, N. Armstrong, D. Arnold, H. Arnold, A. Ashish, A. Ashworth, M. Ashworth, S. Aslani, H. Assefa-Kebede, C. Atkin, P. Atkin, R. Aul, H. Aung, L. Austin, C. Avram, A. Ayoub, M. Babores, R. Baggott, J. Bagshaw, D. Baguley, L. Bailey, J.K. Baillie, S. Bain, M. Bakali, M. Bakau, E. Baldry, D. Baldwin, M. Baldwin, C. Ballard, A. Banerjee, B. Bang, R.E. Barker, L. Barman, S. Barratt, F. Barrett, D. Basire, N. Basu, M. Bates, A. Bates, R. Batterham, H. Baxendale, H. Bayes, M. Beadsworth, P. Beckett, M. Beggs, M. Begum, P. Beirne, D. Bell, R. Bell, K. Bennett, E. Beranova, A. Bermperi, A. Berridge, C. Berry, S. Betts, E. Bevan, K. Bhui, M. Bingham, K. Birchall, L. Bishop, K. Bisnauthsing, J. Blaikely, A. Bloss, A. Bolger, C.E. Bolton, J. Bonnington, A. Botkai, C. Bourne, M. Bourne, K. Bramham, L. Brear, G. Breen, J. Breeze, A. Briggs, E. Bright, C.E. Brightling, S. Brill, K. Brindle, L. Broad, A. Broadley, C. Brookes, M. Broome, A. Brown, J. Brown, J.S. Brown, M. Brown, V. Brown, T. Brugha, N. Brunskill, M. Buch, P. Buckley, A. Bularga, E. Bullmore, L. Burden, T. Burdett, D. Burn, G. Burns, A. Burns, J. Busby, R. Butcher, A. Butt, S. Byrne, P. Cairns, P.C. Calder, E. Calvelo, H. Carborn, B. Card, C. Carr, L. Carr, G. Carson, P. Carter, A. Casey, M. Cassar, J. Cavanagh, M. Chablani, T. Chalder, J.D. Chalmers, R.C. Chambers, F. Chan, K.M. Channon, K. Chapman, A. Charalambou, N. Chaudhuri, A. Checkley, J. Chen, Y. Cheng, L. Chetham, C. Childs, E.R. Chilvers, H. Chinoy, A. Chiribiri, K. Chong-James, G. Choudhury, N. Choudhury, P. Chowienczyk, C. Christie, M. Chrystal, D. Clark, C. Clark, J. Clarke, S. Clohisey, G. Coakley, Z. Coburn, S. Coetzee, J. Cole, C. Coleman, F. Conneh, D. Connell, B. Connolly, L. Connor, A. Cook, B. Cooper, J. Cooper, S. Cooper, D. Copeland, T. Cosier, M. Coulding, C. Coupland, E. Cox, T. Craig, P. Crisp, D. Cristiano, M.G. Crooks, A. Cross, I. Cruz, P. Cullinan, D. Cuthbertson, L. Daines, M. Dalton, P. Daly, A. Daniels, P. Dark, J. Dasgin, A. David, C. David, E. Davies, F. Davies, G. Davies, G.A. Davies, K. Davies, M.J. Davies, J. Dawson, E. Daynes, A. De Soyza, B. Deakin, A. Deans, C. Deas, J. Deery, S. Defres, A. Dell, K. Dempsey, E. Denneny, J. Dennis, A. Dewar, R. Dharmagunawardena, N. Diar-Bakerly, C. Dickens, A. Dipper, S. Diver, S.N. Diwanji, M. Dixon, R. Djukanovic, H. Dobson, S.L. Dobson, A.B. Docherty, A. Donaldson, T. Dong, N. Dormand, A. Dougherty, R. Dowling, S. Drain, K. Draxlbauer, K. Drury, H.J.C. Drury, P. Dulawan, A. Dunleavy, S. Dunn, C. Dupont, J. Earley, N. Easom, C. Echevarria, S. Edwards, C. Edwardson, H. El-Taweel, A. Elliott, K. Elliott, Y. Ellis, A. Elmer, O. Elneima, D. Evans, H. Evans, J. Evans, R. Evans, R.A. Evans, R.I. Evans, T. Evans, C. Evenden, L. Evison, L. Fabbri, S. Fairbairn, A. Fairman, K. Fallon, D. Faluyi, C. Favager, T. Fayzan, J. Featherstone, T. Felton, J. Finch, S. Finney, J. Finnigan, L. Finnigan, H. Fisher, S. Fletcher, R. Flockton, M. Flynn, H. Foot, D. Foote, A. Ford, D. Forton, E. Fraile, C. Francis, R. Francis, S. Francis, A. Frankel, E. Fraser, R. Free, N. French, X. Fu, J. Fuld, J. Furniss, L. Garner, N. Gautam, J.R. Geddes, J. George, P. George, M. Gibbons, M. Gill, L. Gilmour, F. Gleeson, J. Glossop, S. Glover, N. Goodman, C. Goodwin, B. Gooptu, H. Gordon, T. Gorsuch, M. Greatorex, P.L. Greenhaff, W. Greenhalf, A. Greenhalgh, N.J. Greening, J. Greenwood, H. Gregory, R. Gregory, D. Grieve, D. Griffin, L. Griffiths, A.-M. Guerdette, B. Guillen Guio, M. Gummadi, A. Gupta, S. Gurram, E. Guthrie, Z. Guy, H.H. Henson, K. Hadley, A. Haggar, K. Hainey, B. Hairsine, P. Haldar, I. Hall, L. Hall, M. Halling-Brown, R. Hamil, A. Hancock, K. Hancock, N.A. Hanley, S. Haq, H.E. Hardwick, E. Hardy, T. Hardy, B. Hargadon, K. Harrington, E. Harris, V.C. Harris, E.M. Harrison, P. Harrison, N. Hart, A. Harvey, M. Harvey, M. Harvie, L. Haslam, M. Havinden-Williams, J. Hawkes, N. Hawkings, J. Haworth, A. Hayday, M. Haynes, J. Hazeldine, T. Hazelton, L.G. Heaney, C. Heeley, J.L. Heeney, M. Heightman, S. Heller, M. Henderson, L. Hesselden, M. Hewitt, V. Highett, T. Hillman, T. Hiwot, L.P. Ho, A. Hoare, M. Hoare, J. Hockridge, P. Hogarth, A. Holbourn, S. Holden, L. Holdsworth, D. Holgate, M. Holland, L. Holloway, K. Holmes, M. Holmes, B. Holroyd-Hind, L. Holt, A. Hormis, A. Horsley, A. Hosseini, M. Hotopf, L. Houchen-Wolloff, K. Howard, L.S. Howard, A. Howell, E. Hufton, A.D. Hughes, J. Hughes, R. Hughes, A. Humphries, N. Huneke, E. Hurditch, J. Hurst, M. Husain, T. Hussell, J. Hutchinson, W. Ibrahim, F. Ilyas, J. Ingham, L. Ingram, D. Ionita, K. Isaacs, K. Ismail, T. Jackson, J. Jacob, W.Y. James, W. Jang, C. Jarman, I. Jarrold, H. Jarvis, R. Jastrub, B. Jayaraman, R.G. Jenkins, P. Jezzard, K. Jiwa, C. Johnson, S. Johnson, D. Johnston, C.J. Jolley, D. Jones, G. Jones, H. Jones, I. Jones, L. Jones, M.G. Jones, S. Jones, S. Jose, T. Kabir, G. Kaltsakas, V. Kamwa, N. Kanellakis, S. Kaprowska, Z. Kausar, N. Keenan, S. Kelly, G. Kemp, S. Kerr, H. Kerslake, A.L. Key, F. Khan, K. Khunti, S. Kilroy, B. King, C. King, L. Kingham, J. Kirk, P. Kitterick, P. Klenerman, L. Knibbs, S. Knight, A. Knighton, O. Kon, S. Kon, S.S. Kon, S. Koprowska, A. Korszun, I. Koychev, C. Kurasz, P. Kurupati, C. Laing, H. Lamlum, G. Landers, C. Langenberg, D. Lasserson, L. Lavelle-Langham, A. Lawrie, C. Lawson, A. Layton, A. Lea, O.C. Leavy, D. Lee, J.-H. Lee, E. Lee, K. Leitch, R. Lenagh, D. Lewis, J. Lewis, K.E. Lewis, V. Lewis, N. Lewis-Burke, X. Li, T. Light, L. Lightstone, W. Lilaonitkul, L. Lim, S. Linford, A. Lingford-Hughes, M. Lipman, K. Liyanage, A. Lloyd, S. Logan, D. Lomas, N.I. Lone, R. Loosley, J.M. Lord, H. Lota, W. Lovegrove, A. Lucey, E. Lukaschuk, A. Lye, C. Lynch, S. MacDonald, G. MacGowan, I. Macharia, J. Mackie, L. Macliver, S. Madathil, G. Madzamba, N. Magee, M.M. Magtoto, N. Mairs, N. Majeed, E. Major, F. Malein, M. Malim, G. Mallison, W. D-C Man, S. Mandal, K. Mangion, C. Manisty, R. Manley, K. March, S. Marciniak, P. Marino, M. Mariveles, M. Marks, E. Marouzet, S. Marsh, B. Marshall, M. Marshall, J. Martin, A. Martineau, L.M. Martinez, N. Maskell, D. Matila, W. Matimba-Mupaya, L. Matthews, A. Mbuyisa, S. McAdoo, H. McAllister-Williams, A. McArdle, P. McArdle, D. McAulay, G.P. McCann, J. McCormick, W. McCormick, P. McCourt, L. McGarvey, C. McGee, K. Mcgee, J. McGinness, K. McGlynn, A. McGovern, H. McGuinness, I.B. McInnes, J. McIntosh, E. McIvor, K. McIvor, L. McLeavey, A. McMahon, M.J. McMahon, L. McMorrow, T. Mcnally, M. McNarry, J. McNeill, A. McQueen, H. McShane, C. Mears, C. Megson, S. Megson, P. Mehta, J. Meiring, L. Melling, M. Mencias, D. Menzies, M. Merida Morillas, A. Michael, C. Miller, L. Milligan, C. Mills, G. Mills, N.L. Mills, L. Milner, S. Misra, J. Mitchell, A. Mohamed, N. Mohamed, S. Mohammed, P.L. Molyneaux, W. Monteiro, S. Moriera, A. Morley, L. Morrison, R. Morriss, A. Morrow, A.J. Moss, P. Moss, K. Motohashi, N. Msimanga, E. Mukaetova-Ladinska, U. Munawar, J. Murira, U. Nanda, H. Nassa, M. Nasseri, A. Neal, R. Needham, P. Neill, S. Neubauer, D.E. Newby, H. Newell, T. Newman, J. Newman, A. Newton-Cox, T. Nicholson, D. Nicoll, A. Nikolaidis, C.M. Nolan, M.J. Noonan, C. Norman, P. Novotny, J. Nunag, L. Nwafor, U. Nwanguma, J. Nyaboko, C. O'Brien, K. O'Donnell, D. O'Regan, L. O’Brien, N. Odell, G. Ogg, O. Olaosebikan, C. Oliver, Z. Omar, P.J.M. Openshaw, L. Orriss-Dib, L. Osborne, R. Osbourne, M. Ostermann, C. Overton, J. Owen, J. Oxton, J. Pack, E. Pacpaco, S. Paddick, S. Painter, A. Pakzad, S. Palmer, P. Papineni, K. Paques, K. Paradowski, M. Pareek, D. Parekh, H. Parfrey, C. Pariante, S. Parker, M. Parkes, J. Parmar, S. Patale, B. Patel, M. Patel, S. Patel, D. Pattenadk, M. Pavlides, S. Payne, L. Pearce, J.E. Pearl, D. Peckham, J. Pendlebury, Y. Peng, C. Pennington, I. Peralta, E. Perkins, Z. Peterkin, T. Peto, N. Petousi, J. Petrie, P. Pfeffer, J. Phipps, J. Pimm, K. Piper Hanley, R. Pius, H. Plant, S. Plein, T. Plekhanova, M. Plowright, K. Poinasamy, O. Polgar, L. Poll, J.C. Porter, J. Porter, S. Portukhay, N. Powell, A. Prabhu, J. Pratt, A. Price, C. Price, D. Price, L. Price, A. Prickett, J. Propescu, S. Prosper, S. Pugmire, S. Quaid, J. Quigley, J. Quint, H. Qureshi, I.N. Qureshi, K. Radhakrishnan, N.M. Rahman, M. Ralser, B. Raman, A. Ramos, H. Ramos, J. Rangeley, B. Rangelov, L. Ratcliffe, P. Ravencroft, A. Reddington, R. Reddy, A. Reddy, H. Redfearn, D. Redwood, A. Reed, M. Rees, T. Rees, K. Regan, W. Reynolds, C. Ribeiro, A. Richards, E. Richardson, M. Richardson, P. Rivera-Ortega, K. Roberts, E. Robertson, E. Robinson, L. Robinson, L. Roche, C. Roddis, J. Rodger, A. Ross, G. Ross, J. Rossdale, A. Rostron, A. Rowe, A. Rowland, J. Rowland, M.J. Rowland, S.L. Rowland-Jones, K. Roy, M. Roy, I. Rudan, R. Russell, E. Russell, G. Saalmink, R. Sabit, E.K. Sage, T. Samakomva, N. Samani, C. Sampson, K. Samuel, R. Samuel, A. Sanderson, E. Sapey, D. Saralaya, J. Sargant, C. Sarginson, T. Sass, N. Sattar, K. Saunders, R.M. Saunders, P. Saunders, L.C. Saunders, H. Savill, W. Saxon, A. Sayer, J. Schronce, W. Schwaeble, J.T. Scott, K. Scott, N. Selby, M.G. Semple, M. Sereno, T.A. Sewell, A. Shah, K. Shah, P. Shah, M. Shankar-Hari, M. Sharma, C. Sharpe, M. Sharpe, S. Shashaa, A. Shaw, K. Shaw, V. Shaw, A. Sheikh, S. Shelton, L. Shenton, K. Shevket, A. Shikotra, J. Short, S. Siddique, S. Siddiqui, J. Sidebottom, L. Sigfrid, G. Simons, J. Simpson, N. Simpson, A. Singapuri, C. Singh, S. Singh, S.J. Singh, D. Sissons, J. Skeemer, K. Slack, A. Smith, D. Smith, S. Smith, J. Smith, L. Smith, M. Soares, T.S. Solano, R. Solly, A.R. Solstice, T. Soulsby, D. Southern, D. Sowter, M. Spears, L.G. Spencer, F. Speranza, L. Stadon, S. Stanel, N. Steele, M. Steiner, D. Stensel, G. Stephens, L. Stephenson, M. Stern, I. Stewart, R. Stimpson, S. Stockdale, J. Stockley, W. Stoker, R. Stone, W. Storrar, A. Storrie, K. Storton, E. Stringer, S. Strong-Sheldrake, N. Stroud, C. Subbe, C.L. Sudlow, Z. Suleiman, C. Summers, C. Summersgill, D. Sutherland, D.L. Sykes, R. Sykes, N. Talbot, A.L. Tan, L. Tarusan, V. Tavoukjian, A. Taylor, C. Taylor, J. Taylor, A. Te, H. Tedd, C.J. Tee, J. Teixeira, H. Tench, S. Terry, S. Thackray-Nocera, F. Thaivalappil, B. Thamu, D. Thickett, C. Thomas, D.C. Thomas, S. Thomas, A.K. Thomas, T. Thomas-Woods, T. Thompson, A.A.R. Thompson, T. Thornton, M. Thorpe, R.S. Thwaites, J. Tilley, N. Tinker, G.F. Tiongson, M. Tobin, J. Tomlinson, C. Tong, M. Toshner, R. Touyz, K.A. Tripp, E. Tunnicliffe, A. Turnbull, E. Turner, S. Turner, V. Turner, K. Turner, S. Turney, L. Turtle, H. Turton, J. Ugoji, R. Ugwuoke, R. Upthegrove, J. Valabhji, M. Ventura, J. Vere, C. Vickers, B. Vinson, E. Wade, P. Wade, L.V. Wain, T. Wainwright, L.O. Wajero, S. Walder, S. Walker, E. Wall, T. Wallis, S. Walmsley, J.A. Walsh, S. Walsh, L. Warburton, T.J.C. Ward, K. Warwick, H. Wassall, S. Waterson, E. Watson, L. Watson, J. Watson, J. Weir McCall, C. Welch, H. Welch, B. Welsh, S. Wessely, S. West, H. Weston, H. Wheeler, S. White, V. Whitehead, J. Whitney, S. Whittaker, B. Whittam, V. Whitworth, A. Wight, J. Wild, M. Wilkins, D. Wilkinson, B. Williams, N. Williams, J. Williams, S.A. Williams-Howard, M. Willicombe, G. Willis, J. Willoughby, A. Wilson, D. Wilson, I. Wilson, N. Window, M. Witham, R. Wolf-Roberts, C. Wood, F. Woodhead, J. Woods, D.G. Wootton, J. Wormleighton, J. Worsley, D. Wraith, C. Wrey Brown, C. Wright, L. Wright, S. Wright, J. Wyles, I. Wynter, M. Xu, N. Yasmin, S. Yasmin, T. Yates, K.P. Yip, B. Young, S. Young, A. Young, A.J. Yousuf, A. Zawia, L. Zeidan, B. Zhao, B. Zheng, and O. Zongo
Subjects: COVID-19, Physical frailty, Long-COVID, Fried's frailty phenotype, Hospitalisation, Medicine (General), R5-920
Abstract: Summary: Background: The scale of COVID-19 and its well documented long-term sequelae support a need to understand long-term outcomes including frailty. Methods: This prospective cohort study recruited adults who had survived hospitalisation with clinically diagnosed COVID-19 across 35 sites in the UK (PHOSP-COVID). The burden of frailty was objectively measured using Fried's Frailty Phenotype (FFP). The primary outcome was the prevalence of each FFP group—robust (no FFP criteria), pre-frail (one or two FFP criteria) and frail (three or more FFP criteria)—at 5 months and 1 year after discharge from hospital. For inclusion in the primary analysis, participants required complete outcome data for three of the five FFP criteria. Longitudinal changes across frailty domains are reported at 5 months and 1 year post-hospitalisation, along with risk factors for frailty status. Patient-perceived recovery and health-related quality of life (HRQoL) were retrospectively rated for pre-COVID-19 and prospectively rated at the 5 month and 1 year visits. This study is registered with ISRCTN, number ISRCTN10980107. Findings: Between March 5, 2020, and March 31, 2021, 2419 participants were enrolled with FFP data. Mean age was 57.9 (SD 12.6) years, 933 (38.6%) were female, and 429 (17.7%) had received invasive mechanical ventilation. 1785 had measures at both timepoints, of which 240 (13.4%), 1138 (63.8%) and 407 (22.8%) were frail, pre-frail and robust, respectively, at 5 months compared with 123 (6.9%), 1046 (58.6%) and 616 (34.5%) at 1 year. Factors associated with pre-frailty or frailty were invasive mechanical ventilation, older age, female sex, and greater social deprivation. Frail participants had a larger reduction in HRQoL compared with before their COVID-19 illness and were less likely to describe themselves as recovered. Interpretation: Physical frailty and pre-frailty are common following hospitalisation with COVID-19. Improvement in frailty was seen between 5 and 12 months although two-thirds of the population remained pre-frail or frail. This suggests comprehensive assessment and interventions targeting pre-frailty and frailty beyond the initial illness are required. Funding: UK Research and Innovation and National Institute for Health Research.
Published: 2023
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4. Spanning disks in triangulations of surfaces

Author: Clinch, Katie, Dewar, Sean, Fuladi, Niloufar, Gorsky, Maximilian, Huynh, Tony, Kastis, Eleftherios, Nixon, Anthony, and Servatius, Brigitte
Subjects: Mathematics - Combinatorics, Computer Science - Discrete Mathematics, 57Kxx, 05C10, G.2.2
Abstract: Given a triangulation $G$ of a surface $\mathbb{D}$, a spanning disk is a disk $\mathbb{D} \subseteq \mathbb{S}$ containing all the vertices of $G$ such that the boundary of $\mathbb{D}$ is a cycle of $G$. In this paper, we consider the question of when a triangulation of a surface contains a spanning disk. We give a very short proof that every triangulation of the torus contains a spanning disk, which strengthens a theorem of Nevo and Tarabykin. For arbitrary surfaces, we prove that triangulations with sufficiently high facewidth always contain spanning disks. Finally, we exhibit triangulations which do not have spanning disks. This shows that a minimum facewidth condition is necessary. Our results are motivated by and have applications for rigidity questions in the plane., Comment: 7 pages, 2 figures
Published: 2024

5. Constructing reflection-symmetric flexible realisations of graphs

Author: Dewar, Sean, Grasegger, Georg, and Legerský, Jan
Subjects: Mathematics - Combinatorics, 52C25, 70B15, 05C70
Abstract: We study reflection-symmetric realisations of symmetric graphs in the plane that allow a continuous symmetry and edge-length preserving deformation. To do so, we identify a necessary combinatorial condition on graphs with reflection-symmetric flexible realisations. This condition is based on a specific type of edge colouring, where edges are assigned one of three colours in a symmetric way. From some of these colourings we also construct concrete reflection-symmetric realisations with their corresponding symmetry preserving motion. We study also a specific class of reflection-symmetric realisations consisting of triangles and parallelograms.
Published: 2024

6. Single-cell 3D genome reconstruction in the haploid setting using rigidity theory

Author: Dewar, Sean, Grasegger, Georg, Kubjas, Kaie, Mohammadi, Fatemeh, and Nixon, Anthony
Subjects: Quantitative Biology - Genomics, Mathematics - Combinatorics, Mathematics - Metric Geometry, Mathematics - Optimization and Control
Abstract: This article considers the problem of 3-dimensional genome reconstruction for single-cell data, and the uniqueness of such reconstructions in the setting of haploid organisms. We consider multiple graph models as representations of this problem, and use techniques from graph rigidity theory to determine identifiability. Biologically, our models come from Hi-C data, microscopy data, and combinations thereof. Mathematically, we use unit ball and sphere packing models, as well as models consisting of distance and inequality constraints. In each setting, we describe and/or derive new results on realisability and uniqueness. We then propose a 3D reconstruction method based on semidefinite programming and apply it to synthetic and real data sets using our models.
Published: 2024

7. Edge-length preserving embeddings of graphs between normed spaces

Author: Dewar, Sean, Kastis, Eleftherios, Kitson, Derek, and Sims, William
Subjects: Mathematics - Metric Geometry, Mathematics - Combinatorics, 05C10 (Primary) 52A21, 52C25 (Secondary)
Abstract: The concept of graph flattenability, initially formalized by Belk and Connelly and later expanded by Sitharam and Willoughby, extends the question of embedding finite metric spaces into a given normed space. A finite simple graph $G=(V,E)$ is said to be $(X,Y)$-flattenable if any set of induced edge lengths from an embedding of $G$ into a normed space $Y$ can also be realised by an embedding of $G$ into a normed space $X$. This property, being minor-closed, can be characterized by a finite list of forbidden minors. Following the establishment of fundamental results about $(X,Y)$-flattenability, we identify sufficient conditions under which it implies independence with respect to the associated rigidity matroids for $X$ and $Y$. We show that the spaces $\ell_2$ and $\ell_\infty$ serve as two natural extreme spaces of flattenability and discuss $(X, \ell_p )$-flattenability for varying $p$. We provide a complete characterization of $(X,Y)$-flattenable graphs for the specific case when $X$ is 2-dimensional and $Y$ is infinite-dimensional., Comment: 21 pages, 3 figures
Published: 2024

8. Angular constraints on planar frameworks

Author: Dewar, Sean, Grasegger, Georg, Nixon, Anthony, Rosen, Zvi, Sims, William, Sitharam, Meera, and Urizar, David
Subjects: Mathematics - Combinatorics, Mathematics - Metric Geometry, 52C25 (Primary) 05C10, 52C35 (Secondary)
Abstract: Consider a collection of points and the sets of slopes or directions of the lines between pairs of points. It is known that the algebraic matroid on this set of elements is the well studied 2-dimensional rigidity matroid. This article analyzes a construction on top of the set of slopes given by an angle constraint system of incidences and angles. In this setting we provide a matricial rigidity formulation of the problem for colored graphs, an algebro-geometric reformulation, precise necessary conditions and a combinatorial characterization of the generic behaviour for a special case., Comment: 27 pages, 7 figures, 3 tables
Published: 2024

9. Extremal decompositions of tropical varieties and relations with rigidity theory

Author: Babaee, Farhad, Dewar, Sean, and Maxwell, James
Subjects: Mathematics - Algebraic Geometry, Mathematics - Combinatorics, Mathematics - Metric Geometry, 14T10 (Primary) 14T15, 52C25 (Secondary)
Abstract: Extremality and irreducibility constitute fundamental concepts in mathematics, particularly within tropical geometry. While extremal decomposition is typically computationally hard, this article presents a fast algorithm for identifying the extremal decomposition of tropical varieties with rational balanced weightings. Additionally, we explore connections and applications related to rigidity theory. In particular, we prove that a tropical hypersurface is extremal if and only if it has a unique reciprocal diagram up to homothety., Comment: 30 pages, 12 figures
Published: 2024

10. Provincial Archdeacon for reconciliation collated at St Paul’s Melbourne

Author: Dewar, Marion
Published: 2024

11. Rigidity of nearly planar classes of graphs

Author: Dewar, Sean, Grasegger, Georg, Kastis, Eleftherios, Nixon, Anthony, and Servatius, Brigitte
Subjects: Mathematics - Combinatorics, Mathematics - Metric Geometry, 52C25 (Primary) O5C10, 62H22 (Secondary)
Abstract: We explore the rigidity of generic frameworks in 3-dimensions whose underlying graph is close to being planar. Specifically we consider apex graphs, edge-apex graphs and their variants and prove independence results in the generic 3-dimensional rigidity matroid adding to the short list of graph classes for which 3-dimensional rigidity is understood. We then analyse global rigidity for these graph classes and use our results to deduce bounds on the maximum likelihood threshold of graphs in these nearly planar classes., Comment: 29 pages, 9 figures, 4 tables
Published: 2024

12. Rigid frameworks with dilation constraints

Author: Dewar, Sean, Nixon, Anthony, and Sainsbury, Andrew
Subjects: Mathematics - Combinatorics, Mathematics - Metric Geometry
Abstract: We consider the rigidity and global rigidity of bar-joint frameworks in Euclidean $d$-space under additional dilation constraints in specified coordinate directions. In this setting we obtain a complete characterisation of generic rigidity. We then consider generic global rigidity. In particular, we provide an algebraic sufficient condition and a weak necessary condition. We also construct a large family of globally rigid frameworks and conjecture a combinatorial characterisation when most coordinate directions have dilation constraints., Comment: 15 pages, 1 figure
Published: 2024

13. Self-interacting dark matter solves the final parsec problem of supermassive black hole mergers

Author: Alonso-Álvarez, Gonzalo, Cline, James M., and Dewar, Caitlyn
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - High Energy Astrophysical Phenomena, General Relativity and Quantum Cosmology, High Energy Physics - Phenomenology
Abstract: Evidence for a stochastic gravitational wave (GW) background, plausibly originating from the merger of supermassive black holes (SMBHs), is accumulating with observations from pulsar timing arrays. An outstanding question is how inspiraling SMBHs get past the "final parsec" of separation, where they have a tendency to stall before GW emission alone can make the binary coalesce. We argue that dynamical friction from the dark matter (DM) spike surrounding the black holes is sufficient to resolve this puzzle, if the DM has a self-interaction cross section of order $\,$cm$^2$/g. The same effect leads to a softening of the GW spectrum at low frequencies as suggested by the current data. For collisionless cold DM, the friction deposits so much energy that the spike is disrupted and cannot bridge the final parsec, while for self-interacting DM, the isothermal core of the halo can act as a reservoir for the energy liberated from the SMBH orbits. A realistic velocity dependence, such as generated by the exchange of a massive mediator like a dark photon, is favored to give a good fit to the GW spectrum while providing a large enough core. A similar velocity dependence has been advocated for solving the small-scale structure problems of cold DM., Comment: 5 pages + appendices, 7 figures; v2: added EPTA data, references; v3: Dynamical friction formula modified to include the DM velocity dispersion, derivation detailed in new appendix. Other minor updates implemented. Quantitative results are slightly modified, but qualitative conclusions are unchanged. Matches published version
Published: 2024

14. DNA replication recruits a friend to overcome a challenging break-up

Author: Dewar, James M
Published: 2024
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15. Continuing a vibrant floral tradition in Leongatha

Author: Stuchbury, Joanne and Dewar, Marion
Published: 2024

16. Exploring the use of Rasch modelling in “common content” items for multi-site and multi-year assessment

Author: Hope, David, Kluth, David, Homer, Matthew, Dewar, Avril, Goddard-Fuller, Rikki, Jaap, Alan, and Cameron, Helen
Published: 2024
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17. A common flanking variant is associated with enhanced stability of the FGF14-SCA27B repeat locus

Author: Pellerin, David, Del Gobbo, Giulia F., Couse, Madeline, Dolzhenko, Egor, Nageshwaran, Sathiji K., Cheung, Warren A., Xu, Isaac R. L., Dicaire, Marie-Josée, Spurdens, Guinevere, Matos-Rodrigues, Gabriel, Stevanovski, Igor, Scriba, Carolin K., Rebelo, Adriana, Roth, Virginie, Wandzel, Marion, Bonnet, Céline, Ashton, Catherine, Agarwal, Aman, Peter, Cyril, Hasson, Dan, Tsankova, Nadejda M., Dewar, Ken, Lamont, Phillipa J., Laing, Nigel G., Renaud, Mathilde, Houlden, Henry, Synofzik, Matthis, Usdin, Karen, Nussenzweig, Andre, Napierala, Marek, Chen, Zhao, Jiang, Hong, Deveson, Ira W., Ravenscroft, Gianina, Akbarian, Schahram, Eberle, Michael A., Boycott, Kym M., Pastinen, Tomi, Brais, Bernard, Zuchner, Stephan, and Danzi, Matt C.
Published: 2024
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18. Control of DNA replication in vitro using a reversible replication barrier

Author: Vontalge, Emma J., Kavlashvili, Tamar, Dahmen, Steven N., Cranford, Matthew T., and Dewar, James M.
Published: 2024
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19. The number of realisations of a rigid graph in Euclidean and spherical geometries

Author: Dewar, Sean and Grasegger, Georg
Subjects: Mathematics - Combinatorics, Mathematics - Algebraic Geometry, 52C25 (Primary) 05C30, 68R10, 68R12 (Secondary)
Abstract: A graph is $d$-rigid if for any generic realisation of the graph in $\mathbb{R}^d$ (equivalently, the $d$-dimensional sphere $\mathbb{S}^d$), there are only finitely many non-congruent realisations in the same space with the same edge lengths. By extending this definition to complex realisations in a natural way, we define $c_d(G)$ to be the number of equivalent $d$-dimensional complex realisations of a $d$-rigid graph $G$ for a given generic realisation, and $c^*_d(G)$ to be the number of equivalent $d$-dimensional complex spherical realisations of $G$ for a given generic spherical realisation. Somewhat surprisingly, these two realisation numbers are not always equal. Recently developed algorithms for computing realisation numbers determined that the inequality $c_2(G) \leq c_2^*(G)$ holds for any minimally 2-rigid graph $G$ with 12 vertices or less. In this paper we confirm that, for any dimension $d$, the inequality $c_d(G) \leq c_d^*(G)$ holds for every $d$-rigid graph $G$. This result is obtained via new techniques involving coning, the graph operation that adds an extra vertex adjacent to all original vertices of the graph., Comment: 33 pages, 8 figures
Published: 2023

20. Genes for cooperation are not more likely to be carried by plasmids.

Author: Dewar, Anna, Belcher, Laurence, West, Stuart, and Scott, Thomas
Subjects: comparative genomics, horizontal gene transfer, phylogenetic comparative methods, social evolution, Plasmids, Genome, Bacterial, Bacteria, Genomics, Gene Transfer, Horizontal
Abstract: Cooperation is prevalent across bacteria, but risks being exploited by non-cooperative cheats. Horizontal gene transfer, particularly via plasmids, has been suggested as a mechanism to stabilize cooperation. A key prediction of this hypothesis is that genes which are more likely to be transferred, such as those on plasmids, should be more likely to code for cooperative traits. Testing this prediction requires identifying all genes for cooperation in bacterial genomes. However, previous studies used a method which likely misses some of these genes for cooperation. To solve this, we used a new genomics tool, SOCfinder, which uses three distinct modules to identify all kinds of genes for cooperation. We compared where these genes were located across 4648 genomes from 146 bacterial species. In contrast to the prediction of the hypothesis, we found no evidence that plasmid genes are more likely to code for cooperative traits. Instead, we found the opposite-that genes for cooperation were more likely to be carried on chromosomes. Overall, the vast majority of genes for cooperation are not located on plasmids, suggesting that the more general mechanism of kin selection is sufficient to explain the prevalence of cooperation across bacteria.
Published: 2024

21. Divergent responses of highly migratory species to climate change in the California Current

Author: Lezama‐Ochoa, Nerea, Brodie, Stephanie, Welch, Heather, Jacox, Michael G, Buil, Mercedes Pozo, Fiechter, Jerome, Cimino, Megan, Muhling, Barbara, Dewar, Heidi, Becker, Elizabeth A, Forney, Karin A, Costa, Daniel, Benson, Scott R, Farchadi, Nima, Braun, Camrin, Lewison, Rebecca, Bograd, Steven, and Hazen, Elliott L
Subjects: Environmental Sciences, Biological Sciences, Environmental Management, Life on Land, Climate Action, California Current System, centre of gravity, climate change, downscaled ocean projections, earth system model, habitat suitability index, species distribution model, Ecology, Biological sciences, Environmental sciences
Abstract: Aim: Marine biodiversity faces unprecedented threats from anthropogenic climate change. Ecosystem responses to climate change have exhibited substantial variability in the direction and magnitude of redistribution, posing challenges for developing effective climate-adaptive marine management strategies. Location: The California Current Ecosystem (CCE), USA. Methods: We project suitable habitat for 10 highly migratory species in the California Current System using an ensemble of three high-resolution (~10 km) downscaled ocean projections under the Representative Concentration Pathway 8.5 (RCP8.5). Spanning the period from 1980 to 2100, our analysis focuses on assessing the direction and distance of distributional shifts, as well as changes in core habitat area for each species. Results: Our findings reveal a divergent response among species to climate impacts. Specifically, four species were projected to undergo significant poleward shifts exceeding 100 km, and gain habitat (~7%–60%) in response to climate change. Conversely, six species were projected to shift towards the coast, resulting in a loss of habitat ranging from 10% to 66% by the end of the century. These divergent responses could typically be characterized by the mode of thermoregulation (i.e. ectotherm vs. endotherm) and species' affiliations with cool and productive upwelled waters that are characteristic of the region. Furthermore, our study highlights an increase in niche overlap between protected species and those targeted by fisheries, which may lead to increased human interaction events under climate change. Main Conclusions: By providing valuable species distribution projections, our research contributes to the understanding of climate change effects on marine biodiversity and offers critical insight and support for developing climate-ready management of protected and fished species.
Published: 2024

22. State of the California Current Ecosystem report in 2022: a tale of two La Niñas

Author: Thompson, Andrew R, Swalethorp, Rasmus, Alksne, Michaela, Santora, Jarrod A, Hazen, Elliott L, Leising, Andrew, Satterthwaite, Erin, Sydeman, William J, Anderson, Clarissa R, Auth, Toby D, Baumann-Pickering, Simone, Baumgardner, Timothy, Bjorkstedt, Eric P, Bograd, Steven J, Bowlin, Noelle M, Burke, Brian J, Daly, Elizabeth A, Dewar, Heidi, Field, John C, Fisher, Jennifer L, Garfield, Newell, Gidding, Ashlyn, Goericke, Ralf, Golightly, Richard, Gómez-Ocampo, Eliana, Gomez-Valdes, Jose, Hildebrand, John A, Jacobson, Kym C, Jacox, Michael G, Jahncke, Jaime, Johns, Michael, Jones, Joshua M, Lavaniegos, Bertha, Mantua, Nate, McChesney, Gerard J, Medina, Megan E, Melin, Sharon R, Miranda, Luis Erasmo, Morgan, Cheryl A, Nickels, Catherine F, Orben, Rachael A, Porquez, Jessica M, Preti, Antonella, Robertson, Roxanne R, Rudnick, Daniel L, Sakuma, Keith M, Schacter, Carley R, Schroeder, Isaac D, Scopel, Lauren, Snodgrass, Owyn E, Thompson, Sarah Ann, Warzybok, Pete, Whitaker, Katherine, Watson, William, Weber, Edward D, and Wells, Brian
Subjects: Earth Sciences, Oceanography, Biological Sciences, Ecology, California Current, marine heatwave, La Nina/El Nino, California Cooperative Oceanic Fisheries Investigation, global warming, Geology
Abstract: 2022 marked the third consecutive La Niña and extended the longest consecutive stretch of negative Oceanic Niño Index since 1998-2001. While physical and biological conditions in winter and spring largely adhered to prior La Niña conditions, summer and fall were very different. Similar to past La Niña events, in winter and spring coastal upwelling was either average or above average, temperature average or below average, salinity generally above average. In summer and fall, however, upwelling and temperature were generally average or slightly below average, salinity was close to average and chlorophyll a was close to average. Again, as during prior La Niña events, biomass of northern/southern copepods was above/below average off Oregon in winter, and body size of North Pacific krill in northern California was above average in winter. By contrast, later in the year the abundance of northern krill dropped off Oregon while southern copepods increased and body sizes of North Pacific krill fell in northern California. Off Oregon and Washington abundances of market squid and Pacific pompano (indicators of warm, non-typical La Niña conditions) were high. In the 20th century, Northern anchovy recruitment tended to be high during cold conditions, but despite mostly warm conditions from 2015-2021 anchovy populations boomed and remained high in 2022. Resident seabird reproductive success, which tended in the past to increase during productive La Niña conditions was highly variable throughout the system as common murre and pelagic cormorant, experienced complete reproductive failure at Yaquina Head, Oregon while Brandt’s cormorant reproduction was average. At three sampling locations off central California, however, common murre reproduction was close to or above average while both pelagic and Brandt’s cormorant were above average. California sealion reproduction has been above average each year since 2016, and pup weight was also above average in 2022, likely in response not to La Niña or El Niño but continuous high abundance of anchovy. The highly variable and often unpredictable physical and biological conditions in 2022 highlight a growing recognition of disconnects between basin-scale indices and local conditions in the CCE. “July-December 2022 is the biggest outlier from individual “strong” La Niña (events) ever going back to the 50s.” – Nate Mantua
Published: 2024

23. Novel subtypes of severe COVID-19 respiratory failure based on biological heterogeneity: a secondary analysis of a randomized controlled trial

Author: Alipanah-Lechner, Narges, Hurst-Hopf, James, Delucchi, Kevin, Swigart, Lamorna, Willmore, Andrew, LaCombe, Benjamin, Dewar, Robin, Lane, H Clifford, Lallemand, Perrine, Liu, Kathleen D, Esserman, Laura, Matthay, Michael A, and Calfee, Carolyn S
Subjects: Biomedical and Clinical Sciences, Clinical Sciences, Coronaviruses, Rare Diseases, Acute Respiratory Distress Syndrome, Emerging Infectious Diseases, Clinical Research, Clinical Trials and Supportive Activities, Infectious Diseases, Lung, 4.1 Discovery and preclinical testing of markers and technologies, 2.1 Biological and endogenous factors, Respiratory, Good Health and Well Being, Adult, Humans, Male, Middle Aged, Aged, Female, COVID-19, SARS-CoV-2, Inflammation, Respiratory Distress Syndrome, Oxygen, Respiratory Insufficiency, Biomarkers, Hypoxemic respiratory failure, Latent class analysis, Phenotyping, Biological heterogeneity, Protein biomarkers, I-SPY COVID Consortium, Medical and Health Sciences, Emergency & Critical Care Medicine, Biomedical and clinical sciences, Health sciences
Abstract: BackgroundDespite evidence associating inflammatory biomarkers with worse outcomes in hospitalized adults with COVID-19, trials of immunomodulatory therapies have met with mixed results, likely due in part to biological heterogeneity of participants. Latent class analysis (LCA) of clinical and protein biomarker data has identified two subtypes of non-COVID acute respiratory distress syndrome (ARDS) with different clinical outcomes and treatment responses. We studied biological heterogeneity and clinical outcomes in a multi-institutional platform randomized controlled trial of adults with severe COVID-19 hypoxemic respiratory failure (I-SPY COVID).MethodsClinical and plasma protein biomarker data were analyzed from 400 trial participants enrolled from September 2020 until October 2021 with severe COVID-19 requiring ≥ 6 L/min supplemental oxygen. Seventeen hypothesis-directed protein biomarkers were measured at enrollment using multiplex Luminex panels or single analyte enzyme linked immunoassay methods (ELISA). Biomarkers and clinical variables were used to test for latent subtypes and longitudinal biomarker changes by subtype were explored. A validated parsimonious model using interleukin-8, bicarbonate, and protein C was used for comparison with non-COVID hyper- and hypo-inflammatory ARDS subtypes.ResultsAverage participant age was 60 ± 14 years; 67% were male, and 28-day mortality was 25%. At trial enrollment, 85% of participants required high flow oxygen or non-invasive ventilation, and 97% were receiving dexamethasone. Several biomarkers of inflammation (IL-6, IL-8, IL-10, sTNFR-1, TREM-1), epithelial injury (sRAGE), and endothelial injury (Ang-1, thrombomodulin) were associated with 28- and 60-day mortality. Two latent subtypes were identified. Subtype 2 (27% of participants) was characterized by persistent derangements in biomarkers of inflammation, endothelial and epithelial injury, and disordered coagulation and had twice the mortality rate compared with Subtype 1. Only one person was classified as hyper-inflammatory using the previously validated non-COVID ARDS model.ConclusionsWe discovered evidence of two novel biological subtypes of severe COVID-19 with significantly different clinical outcomes. These subtypes differed from previously established hyper- and hypo-inflammatory non-COVID subtypes of ARDS. Biological heterogeneity may explain inconsistent findings from trials of hospitalized patients with COVID-19 and guide treatment approaches.
Published: 2024

24. 7 Corridors of Jurisdiction: The Role of Aquatic Spaces in Sovereign Claims-Making in New France (1600s–1620s)

Author: Dewar, Helen, primary
Published: 2024
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25. 'What Do I Stand For?' - A Phenomenological Account of an Identity Crisis in the Climate Classroom

Author: Virginie F. C. Servant-Miklos and Eleanor F. Dewar
Abstract: This single-participant idiographic study examines the implications of a student's identity crisis in the climate classroom through the lens of existential phenomenology. The study analyses the ontological sense-making process of a mixed-race, bisexual female student reckoning with the racial dimensions of climate change during an environmental course in a liberal arts college in the Netherlands. By delving into the ontological implications of the participant's experience of the course, the analysis shows that environmental education can meaningfully impact the mind-body relationship and self-identification of students with marginalized identities. The findings challenge some of the assumptions of popular frameworks for understanding marginalization in environmental education, like intersectionality, and post-humanist perspectives. The authors conclude that attending to human sense-making in environmental education can benefit students with marginalized identities by grounding environmental education in practices that make space for these identities.
Published: 2024
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26. On the uniqueness of collections of pennies and marbles

Author: Dewar, Sean, Grasegger, Georg, Kubjas, Kaie, Mohammadi, Fatemeh, and Nixon, Anthony
Subjects: Mathematics - Combinatorics, Mathematics - Metric Geometry, 05C10, 52C25, 52C17
Abstract: In this note we study the uniqueness problem for collections of pennies and marbles. More generally, consider a collection of unit $d$-spheres that may touch but not overlap. Given the existence of such a collection, one may analyse the contact graph of the collection. In particular we consider the uniqueness of the collection arising from the contact graph. Using the language of graph rigidity theory, we prove a precise characterisation of uniqueness (global rigidity) in dimensions 2 and 3 when the contact graph is additionally chordal. We then illustrate a wide range of examples in these cases. That is, we illustrate collections of marbles and pennies that can be perturbed continuously (flexible), are locally unique (rigid) and are unique (globally rigid). We also contrast these examples with the usual generic setting of graph rigidity., Comment: 9 pages, 11 figures
Published: 2023

27. Letter to the editor

Author: Dewar, Marion
Published: 2024

28. A shallow scattering layer structures the energy seascape of an open ocean predator.

Author: Arostegui, Martin, Muhling, Barbara, Culhane, Emmett, Dewar, Heidi, Koch, Stephanie, and Braun, Camrin
Abstract: Large predators frequent the open ocean where subsurface light drives visually based trophic interactions. However, we lack knowledge on how predators achieve energy balance in the unproductive open ocean where prey biomass is minimal in well-lit surface waters but high in dim midwaters in the form of scattering layers. We use an interdisciplinary approach to assess how the bioenergetics of scattering layer forays by a model predator vary across biomes. We show that the mean metabolic cost rate of daytime deep foraging dives to scattering layers decreases as much as 26% from coastal to pelagic biomes. The more favorable energetics offshore are enabled by the addition of a shallow scattering layer that, if not present, would otherwise necessitate costlier dives to deeper layers. The unprecedented importance of this shallow scattering layer challenges assumptions that the globally ubiquitous primary deep scattering layer constitutes the only mesopelagic resource regularly targeted by apex predators.
Published: 2023

29. Juvenile Albacore tuna (Thunnus alalunga) foraging ecology varies with environmental conditions in the California Current Large Marine Ecosystem

Author: Nickels, Catherine F, Portner, Elan J, Snodgrass, Owyn, Muhling, Barbara, and Dewar, Heidi
Subjects: Earth Sciences, Oceanography, Agricultural, Veterinary and Food Sciences, Fisheries Sciences, Life Below Water, classification and regression tree, diet, environmental drivers, fisheries interactions, foraging strategy, prey, stomach contents, Fisheries, Fisheries sciences
Abstract: Juvenile North Pacific Albacore tuna (Thunnus alalunga) support commercial and recreational fisheries in the California Current Large Marine Ecosystem (CCLME), where they forage during summer and fall. The distributions of the commercial and recreational fisheries and estimates of forage availability have varied substantially over the past century. Time-series quantifying Albacore diet can help link forage composition to variability in Albacore abundance and distribution and, consequently, their availability to fishers. Previous diet studies in the CCLME are of relatively short duration, and long-term variability in Albacore diet remains poorly understood. We describe the diets of juvenile Albacore from three regions in the CCLME from 2007 to 2019 and use classification and regression tree analysis to explore environmental drivers of variability. Important prey include Northern Anchovy (Engraulis mordax), rockfishes (Sebastes spp.), Boreal Clubhook Squid (Onychoteuthis borealijaponica), euphausiids (Order: Euphausiidae), and amphipods (Order: Amphipoda), each contributing >5% mean proportional abundance. Most prey items were short lived species or young-of-the-year smaller than 10 cm. Diet variability was related to environmental conditions over the first 6 months of the year (PDO, sea surface temperature, and NPGO) and conditions concurrent with Albacore capture (region and surface nitrate flux). We describe foraging flexibility over regional and annual scales associated with these environmental influences. Continuous, long-term studies offer the opportunity to identify flexibility in Albacore foraging behavior and begin to make a predictive link between environmental conditions early in the year and Albacore foraging during summer and fall.
Published: 2023

30. Evaluation of a hospital-initiated tobacco dependence treatment service: uptake, smoking cessation, readmission and mortality

Author: Robins, John, Patel, Irem, McNeill, Ann, Moxham, John, Woodhouse, Arran, Absalom, Gareth, Shehu, Buljana, Bruce, Geraldine, Dewar, Amy, Molloy, Alanna, Duckworth Porras, Stephanie, Waring, Michael, Stock, Andrew, and Robson, Debbie
Published: 2024
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31. Rural-urban difference in the prevalence of hypertension in West Africa: a systematic review and meta-analysis

Author: Sani, Ruqayya Nasir, Connelly, Paul J., Toft, Mette, Rowa-Dewar, Neneh, Delles, Christian, Gasevic, Danijela, and Karaye, Kamilu Musa
Published: 2024
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32. Rigid graphs in cylindrical normed spaces

Author: Dewar, Sean and Kitson, Derek
Subjects: Mathematics - Metric Geometry, Mathematics - Combinatorics, 52C25 (Primary) 52A21, 05C50 (Secondary)
Abstract: We characterise rigid graphs for cylindrical normed spaces $Z=X\oplus_\infty \mathbb{R}$ where $X$ is a finite dimensional real normed linear space and $Z$ is endowed with the product norm. In particular, we obtain purely combinatorial characterisations of minimal rigidity for a large class of 3-dimensional cylindrical normed spaces; for example, when $X$ is an $\ell_p$-plane with $p\in (1,\infty)$. We combine these results with recent work of Cros et al. to characterise rigid graphs in the 4-dimensional cylindrical space $(\mathbb{R}^2\oplus_1\mathbb{R})\oplus_\infty\mathbb{R}$. These are among the first combinatorial characterisations of rigid graphs in normed spaces of dimension greater than 2. Examples of rigid graphs are presented and algorithmic aspects are discussed., Comment: 28 pages
Published: 2023

33. A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection

Author: Augusto, Danillo G, Murdolo, Lawton D, Chatzileontiadou, Demetra SM, Sabatino, Joseph J, Yusufali, Tasneem, Peyser, Noah D, Butcher, Xochitl, Kizer, Kerry, Guthrie, Karoline, Murray, Victoria W, Pae, Vivian, Sarvadhavabhatla, Sannidhi, Beltran, Fiona, Gill, Gurjot S, Lynch, Kara L, Yun, Cassandra, Maguire, Colin T, Peluso, Michael J, Hoh, Rebecca, Henrich, Timothy J, Deeks, Steven G, Davidson, Michelle, Lu, Scott, Goldberg, Sarah A, Kelly, J Daniel, Martin, Jeffrey N, Vierra-Green, Cynthia A, Spellman, Stephen R, Langton, David J, Dewar-Oldis, Michael J, Smith, Corey, Barnard, Peter J, Lee, Sulggi, Marcus, Gregory M, Olgin, Jeffrey E, Pletcher, Mark J, Maiers, Martin, Gras, Stephanie, and Hollenbach, Jill A
Subjects: Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Emerging Infectious Diseases, Vaccine Related, Clinical Research, Pneumonia, Biodefense, Lung, Pneumonia & Influenza, Infectious Diseases, Prevention, Aetiology, 2.1 Biological and endogenous factors, Infection, Good Health and Well Being, Humans, Alleles, Asymptomatic Infections, COVID-19, Epitopes, T-Lymphocyte, Peptides, SARS-CoV-2, HLA-B Antigens, Cohort Studies, T-Lymphocytes, Immunodominant Epitopes, Cross Reactions, Spike Glycoprotein, Coronavirus, General Science & Technology
Abstract: Studies have demonstrated that at least 20% of individuals infected with SARS-CoV-2 remain asymptomatic1-4. Although most global efforts have focused on severe illness in COVID-19, examining asymptomatic infection provides a unique opportunity to consider early immunological features that promote rapid viral clearance. Here, postulating that variation in the human leukocyte antigen (HLA) loci may underly processes mediating asymptomatic infection, we enrolled 29,947 individuals, for whom high-resolution HLA genotyping data were available, in a smartphone-based study designed to track COVID-19 symptoms and outcomes. Our discovery cohort (n = 1,428) comprised unvaccinated individuals who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci with disease course and identified a strong association between HLA-B*15:01 and asymptomatic infection, observed in two independent cohorts. Suggesting that this genetic association is due to pre-existing T cell immunity, we show that T cells from pre-pandemic samples from individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 S-derived peptide NQKLIANQF. The majority of the reactive T cells displayed a memory phenotype, were highly polyfunctional and were cross-reactive to a peptide derived from seasonal coronaviruses. The crystal structure of HLA-B*15:01-peptide complexes demonstrates that the peptides NQKLIANQF and NQKLIANAF (from OC43-CoV and HKU1-CoV) share a similar ability to be stabilized and presented by HLA-B*15:01. Finally, we show that the structural similarity of the peptides underpins T cell cross-reactivity of high-affinity public T cell receptors, providing the molecular basis for HLA-B*15:01-mediated pre-existing immunity.
Published: 2023

34. Is cooperation favored by horizontal gene transfer?

Author: Scott, Thomas, West, Stuart, Dewar, Anna, and Wild, Geoff
Subjects: altruism, cooperation, evolutionary theory, horizontal gene transfer, plasmid, population genetics
Abstract: It has been hypothesized that horizontal gene transfer on plasmids can facilitate the evolution of cooperation, by allowing genes to jump between bacteria, and hence increase genetic relatedness at the cooperative loci. However, we show theoretically that horizontal gene transfer only appreciably increases relatedness when plasmids are rare, where there are many plasmid-free cells available to infect (many opportunities for horizontal gene transfer). In contrast, when plasmids are common, there are few opportunities for horizontal gene transfer, meaning relatedness is not appreciably increased, and so cooperation is not favored. Plasmids, therefore, evolve to be rare and cooperative, or common and noncooperative, meaning plasmid frequency and cooperativeness are never simultaneously high. The overall level of plasmid-mediated cooperation, given by the product of plasmid frequency and cooperativeness, is therefore consistently negligible or low.
Published: 2023

35. Identifying contact graphs of sphere packings with generic radii

Author: Dewar, Sean
Subjects: Mathematics - Combinatorics, Mathematics - Metric Geometry, 05B40 (Primary) 52C17, 52C25 (Secondary)
Abstract: Ozkan et al. conjectured that any packing of $n$ spheres with generic radii will be stress-free, and hence will have at most $3n-6$ contacts. In this paper we prove that this conjecture is true for any sphere packing with contact graph of the form $G \oplus K_2$, i.e., the graph formed by connecting every vertex in a graph $G$ to every vertex in the complete graph with two vertices. We also prove the converse of the conjecture holds in this special case: specifically, a graph $G \oplus K_2$ is the contact graph of a generic radii sphere packing if and only if $G$ is a penny graph with no cycles., Comment: 22 pages, 2 figures. Correction made to Lemma 3.1 (now Lemma 3.2) and Corollary 1.3 replaced by Conjecture 5.1
Published: 2023

36. Hepatobiliary System

Author: Rubin, Erin, primary, Dewar, James Park, additional, Schmolze, Daniel, additional, and Zheng, Wei, additional
Published: 2024
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37. 69 Fakamae

Author: Dewar, Amy, primary and Matariki, Jack, additional
Published: 2024
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38. Engagement matters in a post-pandemic world

Author: Dewar, John
Published: 2022

39. Urban Slum as a Hotspot for Pandemic in India

Author: Swaminathan, Jose, Rajan, Anand Prem, Zachariah, Hanna, Bhattacharyya, Snigdha, Rico-Bautista, Nolfer, Bayona-Ibáñez, Eduar, Rico-Bautista, Dewar, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Nagar, Atulya K., editor, Jat, Dharm Singh, editor, Mishra, Durgesh Kumar, editor, and Joshi, Amit, editor
Published: 2024
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40. Effective Supply Chain During Natural Disasters

Author: Swaminathan, Jose, Jose, Esther, Krishna, Gopi, Medina-Cárdenas, Yurley, Rico-Bautista, Dewar, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Nagar, Atulya K., editor, Jat, Dharm Singh, editor, Mishra, Durgesh, editor, and Joshi, Amit, editor
Published: 2024
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41. Survey Based Analysis on Processed Food and Organic Consumption Pattern in India

Author: Jain, Kushi, Swaminathan, Jose, Rico-Bautista, Dewar, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Guarda, Teresa, editor, Portela, Filipe, editor, and Diaz-Nafria, Jose Maria, editor
Published: 2024
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42. Clean Architecture: Impact on Performance and Maintainability of Native Android Projects

Author: Santiago-Salazar, Javier Alfonso, Rico-Bautista, Dewar, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Tabares, Marta, editor, Vallejo, Paola, editor, Suarez, Biviana, editor, Suarez, Marco, editor, Ruiz, Oscar, editor, and Aguilar, Jose, editor
Published: 2024
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43. Instructional Strategies for Performance Improvement in Algebra: A Systematic Mapping

Author: Garcia-Carrascal, Shirley Tatiana, Sepulveda-Vega, Laura Daniela, Rico-Bautista, Dewar, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Tabares, Marta, editor, Vallejo, Paola, editor, Suarez, Biviana, editor, Suarez, Marco, editor, Ruiz, Oscar, editor, and Aguilar, Jose, editor
Published: 2024
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44. Are smartphone use and nature contact predictive of depression in a UK university population?

Author: Dewar, Ethan and Catling, Jonathan
Published: 2024
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45. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes.

Author: Cotton, S, McHugh, M, Dewar, R, Haas, J, and Templeton, K
Subjects: Care homes, Hospital discharge, Introduction, SARS-CoV-2, Humans, SARS-CoV-2, COVID-19, Patient Discharge, Hospitalization, Hospitals
Abstract: 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.
Published: 2023

46. Computing maximum likelihood thresholds using graph rigidity

Author: Bernstein, Daniel Irving, Dewar, Sean, Gortler, Steven J., Nixon, Anthony, Sitharam, Meera, and Theran, Louis
Subjects: Mathematics - Combinatorics, Mathematics - Metric Geometry, Mathematics - Statistics Theory, 62H12 (Primary), 52C25 (Secondary)
Abstract: The maximum likelihood threshold (MLT) of a graph $G$ is the minimum number of samples to almost surely guarantee existence of the maximum likelihood estimate in the corresponding Gaussian graphical model. Recently a new characterization of the MLT in terms of rigidity-theoretic properties of $G$ was proved \cite{Betal}. This characterization was then used to give new combinatorial lower bounds on the MLT of any graph. We continue this line of research by exploiting combinatorial rigidity results to compute the MLT precisely for several families of graphs. These include graphs with at most $9$ vertices, graphs with at most 24 edges, every graph sufficiently close to a complete graph and graphs with bounded degrees., Comment: 15 pages, 5 figures. arXiv admin note: substantial text overlap with arXiv:2108.02185
Published: 2022
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47. How many contacts can exist between oriented squares of various sizes?

Author: Dewar, Sean
Subjects: Mathematics - Combinatorics, Mathematics - Metric Geometry, 05B40 (Primary) 52C15, 52C05 (Secondary)
Abstract: A homothetic packing of squares is any set of various-size squares with the same orientation where no two squares have overlapping interiors. If all $n$ squares have the same size then we can have up to roughly $4n$ contacts by arranging the squares in a grid formation. The maximum possible number of contacts for a set of $n$ squares will drop drastically, however, if the size of each square is chosen more-or-less randomly. In the following paper we describe a necessary and sufficient condition for determining if a set of $n$ squares with fixed sizes can be arranged into a homothetic square packing with more than $2n-2$ contacts. Using this, we then prove that any (possibly not homothetic) packing of $n$ squares will have at most $2n-2$ face-to-face contacts if the various widths of the squares do not satisfy a finite set of linear equations., Comment: 24 pages, 7 figures
Published: 2022

48. On the relationship between the multi-region relaxed variational principle and resistive inner layer theory

Author: Kumar, A., Loizu, J., Hole, M. J., Qu, Z., Hudson, S. R., and Dewar, R. L
Subjects: Physics - Plasma Physics
Abstract: We show that the variational energy principle of multi-region relaxed magnetohydrodynamic (MRxMHD) model can be used to predict finite-pressure linear tearing instabilities. In this model, the plasma volume is sliced into sub-volumes separated by "ideal interfaces", and in each volume the magnetic field relaxes to a Taylor state where the pressure gradient $\nabla p = 0$. The MRxMHD model is implemented in the SPEC code so that the equilibrium solution in each region is computed while the preserving force balance across the interfaces. As SPEC computes the Hessian matrix (a discretized stability matrix), the stability of an MRxMHD equilibrium can also be computed with SPEC. In this article, using SPEC, we investigate the effect of local pressure gradients and the $\nabla p = 0$ in the vicinity of the resonant surface of a tearing mode. For low beta plasma, we have been able to illustrate a relationship between the resistive singular layer theory [Coppi et al. (1966) Nucl. Fusion 6 101, Glasser et al. The Physics of Fluids 18, 875-888 (1975)], and the MRxMHD model. Within the singular layer, the volume-averaged magnetic helicity and the flux-averaged toroidal flux are shown to be the invariants for the linear tearing modes in SPEC simulations. Our technique to compute MRxMHD stability is first tested numerically in cylindrical tokamak and its application in toroidal geometry is demonstrated. We demonstrate an agreement between the stability boundary obtained with SPEC simulation and the resistive inner layer theories., Comment: 10 pages, 6 figures
Published: 2022
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49. Facilitating Faculty Getting Started in SoTL: Reflections by Two Carnegie Scholars

Author: Dewar, Jacqueline and Perkins, Kathleen
Abstract: SoTL has been embraced as a viable approach to professional development for higher education faculty. Workshops and programs of various types and lengths have offered guidance and provided mentorship for SoTL novices. Many books, manuals, and websites describe how to undertake a SoTL investigation, but far fewer sources of advice exist for those assisting faculty beginning in SoTL. In this article, two Carnegie scholars reflect on their experiences and lessons learned helping others join the SoTL community. They discuss common characteristics of the new scholars they encountered and the types of assistance, both intellectual and institutional, that the scholars needed. They offer advice and suggest resources for working with new SoTL scholars and describe some of the benefits that accrue from this work.
Published: 2021

50. Uniquely realisable graphs in analytic normed planes

Author: Dewar, Sean, Hewetson, John, and Nixon, Anthony
Subjects: Mathematics - Combinatorics, Mathematics - Metric Geometry, 52C25, 05C10, 52A21, 53A35, 52B40
Abstract: A bar-joint framework $(G,p)$ in the Euclidean space $\mathbb{E}^d$ is globally rigid if it is the unique realisation, up to rigid congruences, of $G$ in $\mathbb{E}^d$ with the edge lengths of $(G,p)$. Building on key results of Hendrickson and Connelly, Jackson and Jord\'{a}n gave a complete combinatorial characterisation of when a generic framework is global rigidity in $\mathbb{E}^2$. We prove an analogous result when the Euclidean norm is replaced by any norm that is analytic on $\mathbb{R}^2 \setminus \{0\}$. More precisely, we show that a graph $G=(V,E)$ is globally rigid in a non-Euclidean analytic normed plane if and only if $G$ is 2-connected and $G-e$ contains 2 edge-disjoint spanning trees for all $e\in E$. The main technical tool is a recursive construction of 2-connected and redundantly rigid graphs in analytic normed planes. We also obtain some sufficient conditions for global rigidity as corollaries of our main result and prove that the analogous necessary conditions hold in $d$-dimensional analytic normed spaces., Comment: 40 pages, 16 figures
Published: 2022

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