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351. The Atacama Cosmology Telescope: Detection of the pairwise kinematic Sunyaev-Zel’dovich effect with SDSS DR15 galaxies ()

Author: Calafut, V, Gallardo, P, Vavagiakis, E, Amodeo, S, Aiola, S, Austermann, J, Battaglia, N, Battistelli, E, Beall, J, Bean, R, Bond, J, Calabrese, E, Choi, S, Cothard, N, Devlin, M, Duell, C, Duff, S, Duivenvoorden, A, Dunkley, J, Dunner, R, Ferraro, S, Guan, Y, Hill, J, Hilton, G, Hilton, M, Hlozek, R, Huber, Z, Hubmayr, J, Huffenberger, K, Hughes, J, Koopman, B, Kosowsky, A, Li, Y, Lokken, M, Madhavacheril, M, Mcmahon, J, Moodley, K, Naess, S, Nati, F, Newburgh, L, Niemack, M, Page, L, Partridge, B, Schaan, E, Schillaci, A, Sifon, C, Spergel, D, Staggs, S, Ullom, J, Vale, L, Van Engelen, A, Van Lanen, J, Wollack, E, Xu, Z, Calafut V., Gallardo P. A., Vavagiakis E. M., Amodeo S., Aiola S., Austermann J. E., Battaglia N., Battistelli E. S., Beall J. A., Bean R., Bond J. R., Calabrese E., Choi S. K., Cothard N. F., Devlin M. J., Duell C. J., Duff S. M., Duivenvoorden A. J., Dunkley J., Dunner R., Ferraro S., Guan Y., Hill J. C., Hilton G. C., Hilton M., Hlozek R., Huber Z. B., Hubmayr J., Huffenberger K. M., Hughes J. P., Koopman B. J., Kosowsky A., Li Y., Lokken M., Madhavacheril M., McMahon J., Moodley K., Naess S., Nati F., Newburgh L. B., Niemack M. D., Page L. A., Partridge B., Schaan E., Schillaci A., Sifon C., Spergel D. N., Staggs S. T., Ullom J. N., Vale L. R., Van Engelen A., Van Lanen J., Wollack E. J., Xu Z., Calafut, V, Gallardo, P, Vavagiakis, E, Amodeo, S, Aiola, S, Austermann, J, Battaglia, N, Battistelli, E, Beall, J, Bean, R, Bond, J, Calabrese, E, Choi, S, Cothard, N, Devlin, M, Duell, C, Duff, S, Duivenvoorden, A, Dunkley, J, Dunner, R, Ferraro, S, Guan, Y, Hill, J, Hilton, G, Hilton, M, Hlozek, R, Huber, Z, Hubmayr, J, Huffenberger, K, Hughes, J, Koopman, B, Kosowsky, A, Li, Y, Lokken, M, Madhavacheril, M, Mcmahon, J, Moodley, K, Naess, S, Nati, F, Newburgh, L, Niemack, M, Page, L, Partridge, B, Schaan, E, Schillaci, A, Sifon, C, Spergel, D, Staggs, S, Ullom, J, Vale, L, Van Engelen, A, Van Lanen, J, Wollack, E, Xu, Z, Calafut V., Gallardo P. A., Vavagiakis E. M., Amodeo S., Aiola S., Austermann J. E., Battaglia N., Battistelli E. S., Beall J. A., Bean R., Bond J. R., Calabrese E., Choi S. K., Cothard N. F., Devlin M. J., Duell C. J., Duff S. M., Duivenvoorden A. J., Dunkley J., Dunner R., Ferraro S., Guan Y., Hill J. C., Hilton G. C., Hilton M., Hlozek R., Huber Z. B., Hubmayr J., Huffenberger K. M., Hughes J. P., Koopman B. J., Kosowsky A., Li Y., Lokken M., Madhavacheril M., McMahon J., Moodley K., Naess S., Nati F., Newburgh L. B., Niemack M. D., Page L. A., Partridge B., Schaan E., Schillaci A., Sifon C., Spergel D. N., Staggs S. T., Ullom J. N., Vale L. R., Van Engelen A., Van Lanen J., Wollack E. J., and Xu Z.
Abstract: We present a detection of the pairwise kinematic Sunyaev-Zeldovich (kSZ) effect using Atacama Cosmology Telescope (ACT) and Planck CMB observations in combination with Luminous Red Galaxy samples from the Sloan Digital Sky Survey (SDSS) DR15 catalog. Results are obtained using three ACT CMB maps: co-added 150 and 98 GHz maps, combining observations from 2008-2018 (ACT DR5), which overlap with SDSS DR15 over 3,700 sq. deg., and a component-separated map using night-time only observations from 2014-2015 (ACT DR4), overlapping with SDSS DR15 over 2,089 sq. deg. Comparisons of the results from these three maps provide consistency checks in relation to potential frequency-dependent foreground contamination. A total of 343,647 galaxies are used as tracers to identify and locate galaxy groups and clusters from which the kSZ signal is extracted using aperture photometry. We consider the impact of various aperture photometry assumptions and covariance estimation methods on the signal extraction. Theoretical predictions of the pairwise velocities are used to obtain best-fit, mass-averaged, optical depth estimates for each of five luminosity-selected tracer samples. A comparison of the kSZ-derived optical depth measurements obtained here to those derived from the thermal SZ effect for the same sample is presented in a companion paper.
Published: 2021

352. Probing Galaxy Evolution in Massive Clusters Using ACT and DES: Splashback as a Cosmic Clock

Author: Adhikari, S, Shin, T, Jain, B, Hilton, M, Baxter, E, Chang, C, Wechsler, R, Battaglia, N, Bond, J, Bocquet, S, Choi, S, Derose, J, Devlin, M, Dunkley, J, Evrard, A, Ferraro, S, Hill, J, Hughes, J, Gallardo, P, Lokken, M, Macinnis, A, Madhavacheril, M, Mcmahon, J, Nati, F, Newburgh, L, Niemack, M, Page, L, Palmese, A, Partridge, B, Rozo, E, Rykoff, E, Salatino, M, Schillaci, A, Sehgal, N, Sifon, C, To, C, Wollack, E, Wu, H, Xu, Z, Aguena, M, Allam, S, Amon, A, Annis, J, Avila, S, Bacon, D, Bertin, E, Bhargava, S, Brooks, D, Burke, D, Rosell, A, Kind, M, Carretero, J, Castander, F, Choi, A, Costanzi, M, Da Costa, L, Vicente, J, Desai, S, Diehl, T, Doel, P, Everett, S, Ferrero, I, Ferte, A, Flaugher, B, Fosalba, P, Frieman, J, Garcia-Bellido, J, Gaztanaga, E, Gruen, D, Gruendl, R, Gschwend, J, Gutierrez, G, Hartley, W, Hinton, S, Hollowood, D, Honscheid, K, James, D, Jeltema, T, Kuehn, K, Kuropatkin, N, Lahav, O, Lima, M, Maia, M, Marshall, J, Martini, P, Melchior, P, Menanteau, F, Miquel, R, Morgan, R, L. C. Ogando, R, Paz-Chinchon, F, Malagon, A, Sanchez, E, Santiago, B, Scarpine, V, Serrano, S, Sevilla-Noarbe, I, Smith, M, Soares-Santos, M, Suchyta, E, E. C. Swanson, M, Varga, T, Wilkinson, R, Zhang, Y, Austermann, J, Beall, J, Becker, D, Denison, E, Duff, S, Hilton, G, Hubmayr, J, Ullom, J, Lanen, J, Vale, L, Adhikari S., Shin T. -H., Jain B., Hilton M., Baxter E., Chang C., Wechsler R. H., Battaglia N., Bond J. R., Bocquet S., Choi S. K., Derose J., Devlin M., Dunkley J., Evrard A. E., Ferraro S., Hill J. C., Hughes J. P., Gallardo P. A., Lokken M., Macinnis A., Madhavacheril M. S., McMahon J., Nati F., Newburgh L. B., Niemack M. D., Page L. A., Palmese A., Partridge B., Rozo E., Rykoff E., Salatino M., Schillaci A., Sehgal N., Sifon C., To C. -H., Wollack E., Wu H. -Y., Xu Z., Aguena M., Allam S., Amon A., Annis J., Avila S., Bacon D., Bertin E., Bhargava S., Brooks D., Burke D. L., Rosell A. C., Kind M. C., Carretero J., Castander F. J., Choi A., Costanzi M., Da Costa L. N., Vicente J. D., Desai S., Diehl T. H., Doel P., Everett S., Ferrero I., Ferte A., Flaugher B., Fosalba P., Frieman J., Garcia-Bellido J., Gaztanaga E., Gruen D., Gruendl R. A., Gschwend J., Gutierrez G., Hartley W. G., Hinton S. R., Hollowood D. L., Honscheid K., James D. J., Jeltema T., Kuehn K., Kuropatkin N., Lahav O., Lima M., Maia M. A. G., Marshall J. L., Martini P., Melchior P., Menanteau F., Miquel R., Morgan R., L. C. Ogando R., Paz-Chinchon F., Malagon A. P., Sanchez E., Santiago B., Scarpine V., Serrano S., Sevilla-Noarbe I., Smith M., Soares-Santos M., Suchyta E., E. C. Swanson M., Varga T. N., Wilkinson R. D., Zhang Y., Austermann J. E., Beall J. A., Becker D. T., Denison E. V., Duff S. M., Hilton G. C., Hubmayr J., Ullom J. N., Lanen J. V., Vale L. R., Adhikari, S, Shin, T, Jain, B, Hilton, M, Baxter, E, Chang, C, Wechsler, R, Battaglia, N, Bond, J, Bocquet, S, Choi, S, Derose, J, Devlin, M, Dunkley, J, Evrard, A, Ferraro, S, Hill, J, Hughes, J, Gallardo, P, Lokken, M, Macinnis, A, Madhavacheril, M, Mcmahon, J, Nati, F, Newburgh, L, Niemack, M, Page, L, Palmese, A, Partridge, B, Rozo, E, Rykoff, E, Salatino, M, Schillaci, A, Sehgal, N, Sifon, C, To, C, Wollack, E, Wu, H, Xu, Z, Aguena, M, Allam, S, Amon, A, Annis, J, Avila, S, Bacon, D, Bertin, E, Bhargava, S, Brooks, D, Burke, D, Rosell, A, Kind, M, Carretero, J, Castander, F, Choi, A, Costanzi, M, Da Costa, L, Vicente, J, Desai, S, Diehl, T, Doel, P, Everett, S, Ferrero, I, Ferte, A, Flaugher, B, Fosalba, P, Frieman, J, Garcia-Bellido, J, Gaztanaga, E, Gruen, D, Gruendl, R, Gschwend, J, Gutierrez, G, Hartley, W, Hinton, S, Hollowood, D, Honscheid, K, James, D, Jeltema, T, Kuehn, K, Kuropatkin, N, Lahav, O, Lima, M, Maia, M, Marshall, J, Martini, P, Melchior, P, Menanteau, F, Miquel, R, Morgan, R, L. C. Ogando, R, Paz-Chinchon, F, Malagon, A, Sanchez, E, Santiago, B, Scarpine, V, Serrano, S, Sevilla-Noarbe, I, Smith, M, Soares-Santos, M, Suchyta, E, E. C. Swanson, M, Varga, T, Wilkinson, R, Zhang, Y, Austermann, J, Beall, J, Becker, D, Denison, E, Duff, S, Hilton, G, Hubmayr, J, Ullom, J, Lanen, J, Vale, L, Adhikari S., Shin T. -H., Jain B., Hilton M., Baxter E., Chang C., Wechsler R. H., Battaglia N., Bond J. R., Bocquet S., Choi S. K., Derose J., Devlin M., Dunkley J., Evrard A. E., Ferraro S., Hill J. C., Hughes J. P., Gallardo P. A., Lokken M., Macinnis A., Madhavacheril M. S., McMahon J., Nati F., Newburgh L. B., Niemack M. D., Page L. A., Palmese A., Partridge B., Rozo E., Rykoff E., Salatino M., Schillaci A., Sehgal N., Sifon C., To C. -H., Wollack E., Wu H. -Y., Xu Z., Aguena M., Allam S., Amon A., Annis J., Avila S., Bacon D., Bertin E., Bhargava S., Brooks D., Burke D. L., Rosell A. C., Kind M. C., Carretero J., Castander F. J., Choi A., Costanzi M., Da Costa L. N., Vicente J. D., Desai S., Diehl T. H., Doel P., Everett S., Ferrero I., Ferte A., Flaugher B., Fosalba P., Frieman J., Garcia-Bellido J., Gaztanaga E., Gruen D., Gruendl R. A., Gschwend J., Gutierrez G., Hartley W. G., Hinton S. R., Hollowood D. L., Honscheid K., James D. J., Jeltema T., Kuehn K., Kuropatkin N., Lahav O., Lima M., Maia M. A. G., Marshall J. L., Martini P., Melchior P., Menanteau F., Miquel R., Morgan R., L. C. Ogando R., Paz-Chinchon F., Malagon A. P., Sanchez E., Santiago B., Scarpine V., Serrano S., Sevilla-Noarbe I., Smith M., Soares-Santos M., Suchyta E., E. C. Swanson M., Varga T. N., Wilkinson R. D., Zhang Y., Austermann J. E., Beall J. A., Becker D. T., Denison E. V., Duff S. M., Hilton G. C., Hubmayr J., Ullom J. N., Lanen J. V., and Vale L. R.
Abstract: We measure the projected number density profiles of galaxies and the splashback feature in clusters selected by the Sunyaev-Zel'dovich effect from the Advanced Atacama Cosmology Telescope (AdvACT) survey using galaxies observed by the Dark Energy Survey (DES). The splashback radius is consistent with CDM-only simulations and is located at 2.4-0.4+0.3 Mpc h-1. We split the galaxies on color and find significant differences in their profile shapes. Red and green-valley galaxies show a splashback-like minimum in their slope profile consistent with theory, while the bluest galaxies show a weak feature at a smaller radius. We develop a mapping of galaxies to subhalos in simulations and assign colors based on infall time onto their hosts. We find that the shift in location of the steepest slope and different profile shapes can be mapped to the average time of infall of galaxies of different colors. The steepest slope traces a discontinuity in the phase space of dark matter halos. By relating spatial profiles to infall time, we can use splashback as a clock to understand galaxy quenching. We find that red galaxies have on average been in clusters over 3.2 Gyr, green galaxies about 2.2 Gyr, while blue galaxies have been accreted most recently and have not reached apocenter. Using the full radial profiles, we fit a simple quenching model and find that the onset of galaxy quenching occurs after a delay of about a gigayear and that galaxies quench rapidly thereafter with an exponential timescale of 0.6 Gyr.
Published: 2021

353. Insights from Monitoring Aspirin Adherence: A Medication Adherence Cascade Tool

Author: Wheat HL, Irani E, Hughes J, Josephson R, and Dolansky MA
Subjects: Medicine (General), R5-920, aspirin, cardiovascular disease, medication adherence
Abstract: Heather L Wheat, 1 Elliane Irani, 2 Joel Hughes, 3 Richard Josephson, 4, 5 Mary A Dolansky 2 1Department of Medicine, Case Western Reserve University, University Hospitals Cleveland Medical Center, Cleveland, OH, USA; 2Frances Payne Bolton School of Nursing, Case Western Reserve University, Cleveland, OH, USA; 3Department of Psychological Sciences, Kent State University, Kent, OH, USA; 4School of Medicine, Case Western Reserve University, Cleveland, OH, USA; 5Department of Medicine, Division of Cardiology, Case Western Reserve University, Harrington Heart & Vascular Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USACorrespondence: Heather L WheatDepartment of Medicine, Case Western Reserve University, University Hospitals Cleveland Medical Center, 11100 Euclid Ave, Cleveland, OH, 44106, USATel +1 216 844-8447Email Heather.Wheat@UHhospitals.orgBackground: Adherence to recommended medications is a key issue in the care of patients with cardiovascular disease (CVD) and barriers to adherence are well established during the medication adherence cascade, the processes of prescribing, obtaining, taking, and maintaining medication use. Aspirin avoids many of the barriers in the medication adherence cascade as it does not require a prescription (prescribing) and is inexpensive, easily accessible (obtaining), prescribed once-daily (taking) as an over-the-counter medication and is generally perceived by patients as safe (maintaining). The purpose of this paper is to report aspirin adherence and propose the Medication Adherence Cascade Tool to assist clinicians to consider all aspects of medication adherence.Methods: Adherence to aspirin was monitored with an electronic pillbox. Frequency analysis, independent T-tests, and ANOVA were completed on 151 patients with underlying heart failure who were prescribed aspirin within a larger parent study. Chi-square tests were completed to assess differences in baseline demographic characteristics.Findings: Mean aspirin adherence was 82.2% overall, with 11.9% of sample with adherence 50%, 18.5% with adherence 50– 80%, and 69.5% with adherence ≥ 80%. Greater adherence was observed in self-identified White as compared to Black patients (84.47% vs 73.53%; p = 0.014), and patients ≥ 70 years of age compared to < 70 years (87.00% vs 77.49%; p = 0.009).Interpretation: Aspirin adherence was suboptimal despite the fact that it addresses most of the barriers on the medication adherence cascade (ie, relatively easy access, low cost, and low risk). A Medication Adherence Cascade Tool (MACT) is proposed as a clinical guide to facilitate patient–provider co-production of strategies to address medication adherence. The tool can assist patients and providers to co-produce adherence to achieve optimal medication benefits.Keywords: medication adherence, aspirin, cardiovascular disease
Published: 2021

354. Effects of Computer Simulation Training on In Vivo Discrete Trial Teaching

Author: Eldevik, Sigmund, Ondire, Iwona, and Hughes, J. Carl
Abstract: Although Discrete-trial Teaching (DTT) is effective in teaching a many skills to children with autism, its proper implementation requires rigorous staff training. This study used an interactive computer simulation program ("DTkid") to teach staff relevant DTT skills. Participants (N = 12) completed two sets of pre-tests either once (n = 7) or twice (n = 5) before brief DTkid training. These evaluated (a) simulated interactive teaching using DTkid and (b) in vivo teaching of three basic skills (receptive and expressive labeling; verbal imitation) to children with autism. Post-tests showed that DTkid training, rather than repeated testing, was significantly associated with improvements in staff's ability to implement DTT both within the simulation and in vivo, and that the skills acquired showed both stimulus and response generalization.
Published: 2013
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355. The timber roofs of York Minster

Author: Hughes, J. Quentin, primary
Published: 2017
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356. List of Contributors

Author: Aalhus, J.L., primary, Berhe, D.T., additional, Bertram, H.C., additional, Bonny, S., additional, Bruce, H.L., additional, Dalrymple, B.P., additional, De Backer, C.J.S., additional, Dragsted, L.O., additional, Egelandsdal, B., additional, England, E.M., additional, Enser, M., additional, Estévez, M., additional, Faucitano, L., additional, Frank, D., additional, Gagaoua, M., additional, Gerrard, D.E., additional, Grandin, T., additional, Greaser, M.L., additional, Guo, B., additional, Guo, W., additional, Ha, M., additional, Haug, A., additional, Henchion, M., additional, Hocquette, J.-F., additional, Hollung, K., additional, Hudders, L., additional, Hughes, J., additional, López-Campos, Ó., additional, Lametsch, R., additional, Lanusse, C., additional, Martelli, G., additional, Matarneh, S.K., additional, Matthews, K., additional, Miklos, R., additional, Moreno, L., additional, Nair, M.N., additional, Namvar, A., additional, Nannoni, E., additional, Nishimura, T., additional, Oksbjerg, N., additional, Oostindjer, M., additional, Oytam, Y., additional, Paulsen, J.E., additional, Pereira, P.C., additional, Pethick, D., additional, Picard, B., additional, Polkinghorne, R., additional, Post, M.J., additional, Puolanne, E., additional, Purslow, P.P., additional, Sødring, M., additional, Scheffler, T.L., additional, Scollan, N., additional, Sikes, A., additional, Strydom, P., additional, Suman, S.P., additional, Therkildsen, M., additional, van Huis, A., additional, Vaskoska, R., additional, Vicente, F., additional, Warner, R., additional, Warriner, K., additional, Webb, E.C., additional, Webb, E.M., additional, Widowski, T., additional, and Wood, J.D., additional
Published: 2017
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357. Sensory Perceptions and New Consumer Attitudes to Meat

Author: Frank, D., primary, Oytam, Y., additional, and Hughes, J., additional
Published: 2017
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358. Early lung cancer team intervention in emergency admissions: P266

Author: Dunbar, J, Walshaw, M, Ledson, M, McIver, A, Hughes, J, Maddock, N, and Smyth, C
Published: 2017
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359. Rethinking the 'one-stop' neck lump clinic: a novel pathway beyond coronavirus disease 2019.

Author: Hariri, A, Jawad, S, Otero, S, Lechner, M, Morley, S, Beale, T, Hughes, J, Stimpson, P, Dwivedi, R, and Vaz, F
Subjects: HEAD & neck cancer, MEDICAL care, UNNECESSARY surgery, CANCER patients, MEDICAL care use, MEDICAL referrals, MEDICAL appointments, COVID-19 pandemic, CANCER patient medical care
Abstract: Objectives: UK guidelines advocate 'one-stop' neck lump assessment for cancer referrals. This paper reports the pilot of a novel pre-clinic ultrasound pathway, presents outcomes, and discusses strengths and limitations in the context of the coronavirus disease 2019 pandemic. Methods: Two-week-wait cancer referral patients with a neck lump were allocated a pre-clinic ultrasound scan followed by a clinic appointment. Demographic, patient journey and outcome data were collected and analysed. Results: Ninety-nine patients underwent ultrasound assessment with or without biopsy on average 8 days following referral. Patients were followed up on average 14.1 days (range, 2–26 days) after initial referral. At the first clinic appointment, 45 patients were discharged, 10 were scheduled for surgery, 12 were diagnosed with cancer, 6 were referred to another specialty and cancer was excluded in 19 patients. Retrospectively, four ultrasounds were performed unnecessarily. Conclusion: Pre-clinic ultrasound scanning is an alternative to the one-stop neck lump pathway. This study demonstrates fewer clinic visits, faster diagnosis and a low proportion of unnecessary scans, whilst minimising face-to-face consultations and aerosol-generating procedures. [ABSTRACT FROM AUTHOR]
Published: 2023
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360. Model-Driven Development For PDS4 Software And Services

Author: Padams, Jordan, Hardman, Sean, Joyners, Ronald, Cayanan, Michael, Algermissen, Stirling, Crichton, Daniel, and Hughes, J. Steven
Abstract: Software and services that access Planetary Data System (PDS) PDS4 data products need to parse product labels to retrieve, interpret, and process the referenced digital objects. Under PDS4 a driving principle is that the product label provide all of the information necessary for these functions to be performed accurately. However, significantly more information is available in the PDS4 Information Model (IM)[1], the controlling document used to define, create, and syntactically and semantically verify the product labels. This additional information in the IM is made available for use, by both software and services, to configure, promote resiliency, and improve interoperability.
Published: 2018

361. Model-Driven Development For PDS4 Software And Services

Author: Hughes, J. Steven, Crichton, Daniel, Algermissen, Stirling, Cayanan, Michael, Joyners, Ronald, Hardman, Sean, and Padams, Jordan
Published: 2018

362. Common interoperable protocols and interface specifications for repositories

Author: Hughes, J. Steven
Published: 2018

363. A retrospective report (2003–2013) of the complications associated with the use of a one-man (head and tail) rope recovery system in horses following general anaesthesia

Author: Niimura del Barrio, Maria Chie, David, Florent, Hughes, J. M. Lynne, Clifford, David, Wilderjans, Hans, and Bennett, Rachel
Published: 2018
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364. Six Years of Chandra Observations of Supernova Remnants

Author: Weisskopf, M. C., Hughes, J. P., and Mason, John W., editor
Published: 2006
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365. Broadband Terahertz Emission From Ion-Implanted Semiconductors

Author: Lloyd-Hughes, J., Castro-Camus, E., Fraser, M. D., Tan, H. H., Jagadish, C., Johnston, M. B., Saraniti, M., editor, and Ravaioli, U., editor
Published: 2006
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366. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2

Author: Eales, O, Page, AJ, de Oliveira Martins, L, Wang, H, Bodinier, B, Haw, D, Jonnerby, J, Atchison, C, Robson, SC, Connor, TR, Loman, NJ, Golubchik, T, Nunez, RTM, Bonsall, D, Rambaut, A, Snell, LB, Livett, R, Ludden, C, Corden, S, Nastouli, E, Nebbia, G, Johnston, I, Lythgoe, K, Torok, ME, Goodfellow, IG, Prieto, JA, Saeed, K, Jackson, DK, Houlihan, C, Frampton, D, Hamilton, WL, Witney, AA, Bucca, G, Pope, CF, Moore, C, Thomson, EC, Harrison, EM, Smith, CP, Rogan, F, Beckwith, SM, Murray, A, Singleton, D, Eastick, K, Sheridan, LA, Randell, P, Jackson, LM, Ariani, CV, Gonçalves, S, Fairley, DJ, Loose, MW, Watkins, J, Moses, S, Nicholls, S, Bull, M, Amato, R, Smith, DL, Aanensen, DM, Barrett, JC, Aggarwal, D, Shepherd, JG, Curran, MD, Parmar, S, Parker, MD, Williams, C, Glaysher, S, Underwood, AP, Bashton, M, Pacchiarini, N, Loveson, KF, Byott, M, Carabelli, AM, Templeton, KE, de Silva, TI, Wang, D, Langford, CF, Sillitoe, J, Gunson, RN, Cottrell, S, O’Grady, J, Kwiatkowski, D, Lillie, PJ, Cortes, N, Moore, N, Thomas, C, Burns, PJ, Mahungu, TW, Liggett, S, Beckett, AH, Holden, MTG, Levett, LJ, Osman, H, Hassan-Ibrahim, MO, Simpson, DA, Chand, M, Gupta, RK, Darby, AC, Paterson, S, Pybus, OG, Volz, EM, de Angelis, D, Robertson, DL, Martincorena, I, Aigrain, L, Bassett, AR, Wong, N, Taha, Y, Erkiert, MJ, Chapman, MHS, Dewar, R, McHugh, MP, Mookerjee, S, Aplin, S, Harvey, M, Sass, T, Umpleby, H, Wheeler, H, McKenna, JP, Warne, B, Taylor, JF, Chaudhry, Y, Izuagbe, R, Jahun, AS, Young, GR, McMurray, C, McCann, CM, Nelson, A, Elliott, S, Lowe, H, Price, A, Crown, MR, Rey, S, Roy, S, Temperton, B, Shaaban, S, Hesketh, AR, Laing, KG, Monahan, IM, Heaney, J, Pelosi, E, Silviera, S, Wilson-Davies, E, Fryer, H, Adams, H, du Plessis, L, Johnson, R, Harvey, WT, Hughes, J, Orton, RJ, Spurgin, LG, Bourgeois, Y, Ruis, C, O’Toole, Á, Gourtovaia, M, Sanderson, T, Fraser, C, Edgeworth, J, Breuer, J, Michell, SL, Todd, JA, John, M, Buck, D, Gajee, K, Kay, GL, Peacock, SJ, Heyburn, D, Kitchman, K, McNally, A, Pritchard, DT, Dervisevic, S, Muir, P, Robinson, E, Vipond, BB, Ramadan, NA, Jeanes, C, Weldon, D, Catalan, J, Jones, N, da Silva Filipe, A, Fuchs, M, Miskelly, J, Jeffries, AR, Oliver, K, Park, NR, Ash, A, Koshy, C, Barrow, M, Buchan, SL, Mantzouratou, A, Clark, G, Holmes, CW, Campbell, S, Davis, T, Tan, NK, Brown, JR, Harris, KA, Kidd, SP, Grant, PR, Xu-McCrae, L, Cox, A, Madona, P, Pond, M, Randell, PA, Withell, KT, Graham, C, Denton-Smith, R, Swindells, E, Turnbull, R, Sloan, TJ, Bosworth, A, Hutchings, S, Pymont, HM, Casey, A, Ratcliffe, L, Jones, CR, Knight, BA, Haque, T, Hart, J, Irish-Tavares, D, Witele, E, Mower, C, Watson, LK, Collins, J, Eltringham, G, Crudgington, D, Macklin, B, Iturriza-Gomara, M, Lucaci, AO, McClure, PC, Carlile, M, Holmes, N, Storey, N, Rooke, S, Yebra, G, Craine, N, Perry, M, Alikhan, N - F, Bridgett, S, Cook, KF, Fearn, C, Goudarzi, S, Lyons, RA, Williams, T, Haldenby, ST, Durham, J, Leonard, S, Davies, RM, Batra, R, Blane, B, Spyer, MJ, Smith, P, Yavus, M, Williams, RJ, Mahanama, AIK, Samaraweera, B, Girgis, ST, Hansford, SE, Green, A, Beaver, C, Bellis, KL, Dorman, MJ, Kay, S, Prestwood, L, Rajatileka, S, Quick, J, Poplawski, R, Reynolds, N, Mack, A, Morriss, A, Whalley, T, Patel, B, Georgana, I, Hosmillo, M, Pinckert, ML, Stockton, J, Henderson, JH, Hollis, A, Stanley, W, Yew, WC, Myers, R, Thornton, A, Adams, A, Annett, T, Asad, H, Birchley, A, Coombes, J, Evans, JM, Fina, L, Gatica-Wilcox, B, Gilbert, L, Graham, L, Hey, J, Hilvers, E, Jones, S, Jones, H, Kumziene-Summerhayes, S, McKerr, C, Powell, J, Pugh, G, Taylor, S, Trotter, AJ, Williams, CA, Kermack, LM, Foulkes, BH, Gallis, M, Hornsby, HR, Louka, SF, Pohare, M, Wolverson, P, Zhang, P, MacIntyre-Cockett, G, Trebes, A, Moll, RJ, Ferguson, L, Goldstein, EJ, Maclean, A, Tomb, R, Starinskij, I, Thomson, L, Southgate, J, Kraemer, MUG, Raghwani, J, Zarebski, AE, Boyd, O, Geidelberg, L, Illingworth, CJ, Jackson, C, Pascall, D, Vattipally, S, Freeman, TM, Hsu, SN, Lindsey, BB, James, K, Lewis, K, Tonkin-Hill, G, Tovar-Corona, JM, Cox, MG, Abudahab, K, Menegazzo, M, MEng, BEWT, Yeats, CA, Mukaddas, A, Wright, DW, Colquhoun, R, Hill, V, Jackson, B, McCrone, JT, Medd, N, Scher, E, Keatley, J - P, Curran, T, Morgan, S, Maxwell, P, Smith, K, Eldirdiri, S, Kenyon, A, Holmes, AH, Price, JR, Wyatt, T, Mather, AE, Skvortsov, T, Hartley, JA, Guest, M, Kitchen, C, Merrick, I, Munn, R, Bertolusso, B, Lynch, J, Vernet, G, Kirk, S, Wastnedge, E, Stanley, R, Idle, G, Bradley, DT, Poyner, J, Mori, M, Jones, O, Wright, V, Brooks, E, Churcher, CM, Fragakis, M, Galai, K, Jermy, A, Judges, S, McManus, GM, Smith, KS, Westwick, E, Attwood, SW, Bolt, F, Davies, A, De Lacy, E, Downing, F, Edwards, S, Meadows, L, Jeremiah, S, Smith, N, Foulser, L, Charalampous, T, Patel, A, Berry, L, Boswell, T, Fleming, VM, Howson-Wells, HC, Joseph, A, Khakh, M, Lister, MM, Bird, PW, Fallon, K, Helmer, T, McMurray, CL, Odedra, M, Shaw, J, Tang, JW, Willford, NJ, Blakey, V, Raviprakash, V, Sheriff, N, Williams, L - A, Feltwell, T, Bedford, L, Cargill, JS, Hughes, W, Moore, J, Stonehouse, S, Atkinson, L, Lee, JCD, Shah, D, Alcolea-Medina, A, Ohemeng-Kumi, N, Ramble, J, Sehmi, J, Williams, R, Chatterton, W, Pusok, M, Everson, W, Castigador, A, Macnaughton, E, Bouzidi, KE, Lampejo, T, Sudhanva, M, Breen, C, Sluga, G, Ahmad, SSY, George, RP, Machin, NW, Binns, D, James, V, Blacow, R, Coupland, L, Smith, L, Barton, E, Padgett, D, Scott, G, Cross, A, Mirfenderesky, M, Greenaway, J, Cole, K, Clarke, P, Duckworth, N, Walsh, S, Bicknell, K, Impey, R, Wyllie, S, Hopes, R, Bishop, C, Chalker, V, Harrison, I, Gifford, L, Molnar, Z, Auckland, C, Evans, C, Johnson, K, Partridge, DG, Raza, M, Baker, P, Bonner, S, Essex, S, Murray, LJ, Lawton, AI, Burton-Fanning, S, Payne, BAI, Waugh, S, Gomes, AN, Kimuli, M, Murray, DR, Ashfield, P, Dobie, D, Ashford, F, Best, A, Crawford, L, Cumley, N, Mayhew, M, Megram, O, Mirza, J, Moles-Garcia, E, Percival, B, Driscoll, M, Ensell, L, Lowe, HL, Maftei, L, Mondani, M, Chaloner, NJ, Cogger, BJ, Easton, LJ, Huckson, H, Lewis, J, Lowdon, S, Malone, CS, Munemo, F, Mutingwende, M, Nicodemi, R, Podplomyk, O, Somassa, T, Beggs, A, Richter, A, Cormie, C, Dias, J, Forrest, S, Higginson, EE, Maes, M, Young, J, Davidson, RK, Jackson, KA, Turtle, L, Keeley, AJ, Ball, J, Byaruhanga, T, Chappell, JG, Dey, J, Hill, JD, Park, EJ, Fanaie, A, Hilson, RA, Yaze, G, Lo, S, Afifi, S, Beer, R, Maksimovic, J, McCluggage, K, Spellman, K, Bresner, C, Fuller, W, Marchbank, A, Workman, T, Shelest, E, Debebe, J, Sang, F, Zamudio, ME, Francois, S, Gutierrez, B, Vasylyeva, TI, Flaviani, F, Ragonnet-Cronin, M, Smollett, KL, Broos, A, Mair, D, Nichols, J, Nomikou, K, Tong, L, Tsatsani, I, O’Brien, PS, Rushton, S, Sanderson, R, Perkins, J, Cotton, S, Gallagher, A, Allara, E, Pearson, C, Bibby, D, Dabrera, G, Ellaby, N, Gallagher, E, Hubb, J, Lackenby, A, Lee, D, Manesis, N, Mbisa, T, Platt, S, Twohig, KA, Morgan, M, Aydin, A, Baker, DJ, Foster-Nyarko, E, Prosolek, SJ, Rudder, S, Baxter, C, Carvalho, SF, Lavin, D, Mariappan, A, Radulescu, C, Singh, A, Tang, M, Morcrette, H, Bayzid, N, Cotic, M, Balcazar, CE, Gallagher, MD, Maloney, D, Stanton, TD, Williamson, KA, Manley, R, Michelsen, ML, Sambles, CM, Studholme, DJ, Warwick-Dugdale, J, Eccles, R, Gemmell, M, Gregory, R, Hughes, M, Nelson, C, Rainbow, L, Vamos, EE, Webster, HJ, Whitehead, M, Wierzbicki, C, Angyal, A, Green, LR, Whiteley, M, Betteridge, E, Bronner, IF, Farr, BW, Goodwin, S, Lensing, SV, McCarthy, SA, Quail, MA, Rajan, D, Redshaw, NM, Scott, C, Shirley, L, Thurston, SAJ, Rowe, W, Gaskin, A, Le-Viet, T, Bonfield, J, Liddle, J, Whitwham, A, Ashby, D, Barclay, W, Taylor, G, Cooke, G, Ward, H, Darzi, A, Riley, S, Chadeau-Hyam, M, Donnelly, CA, Elliott, P, The COVID-19 Genomics UK (COG-UK) Consortium, Department of Health, Imperial College Healthcare NHS Trust- BRC Funding, Medical Research Council (MRC), Cancer Research UK, Commission of the European Communities, Wellcome Trust, National Institute for Health Research, and Imperial College Healthcare NHS Trust: Research Capability Funding (RCF)
Subjects: Delta variant, Science & Technology, SARS-CoV-2, COVID-19, 1103 Clinical Sciences, C500, Microbiology, Genetic diversity, B900, Infectious Diseases, England, COVID-19 Genomics UK (COG-UK) Consortium, 1108 Medical Microbiology, Mutation, Humans, Transmission advantage, Life Sciences & Biomedicine, Phylogeny, 0605 Microbiology
Abstract: Background Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detecting emerging variants that can more successfully navigate the immune landscape. Methods We present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. During round 14 (9 September–27 September 2021) and 15 (19 October–5 November 2021) lineages were determined for 1322 positive individuals, with 27.1% of those which reported their symptom status reporting no symptoms in the previous month. Results We identified 44 unique lineages, all of which were Delta or Delta sub-lineages, and found a reduction in their mutation rate over the study period. The proportion of the Delta sub-lineage AY.4.2 was increasing, with a reproduction number 15% (95% CI 8–23%) greater than the most prevalent lineage, AY.4. Further, AY.4.2 was less associated with the most predictive COVID-19 symptoms (p = 0.029) and had a reduced mutation rate (p = 0.050). Both AY.4.2 and AY.4 were found to be geographically clustered in September but this was no longer the case by late October/early November, with only the lineage AY.6 exhibiting clustering towards the South of England. Conclusions As SARS-CoV-2 moves towards endemicity and new variants emerge, genomic data obtained from random community samples can augment routine surveillance data without the potential biases introduced due to higher sampling rates of symptomatic individuals.
Published: 2022

367. Cancer, Fertility and Me : Developing and Testing a Novel Fertility Preservation Patient Decision Aid to Support Women at Risk of Losing Their Fertility Because of Cancer Treatment

Author: Jones, G.L., Moss, R.H., Darby, F., Mahmoodi, N., Phillips, B., Hughes, J., Vogt, K.S., Greenfield, D.M., Brauten-Smith, G., Gath, J., Campbell, T., Stark, D., Velikova, G., Snowden, J.A., Baskind, E., Mascerenhas, M., Yeomanson, D., Skull, J., Lane, S., Bekker, H.L., and Anderson, R.A.
Subjects: Cancer Research, Oncology, patient decision aid, fertility preservation, cancer, women, gonadotoxic treatment, survivorship, mixed-method study
Abstract: BackgroundWomen with a new cancer diagnosis face complex decisions about interventions aiming to preserve their fertility. Decision aids are more effective in supporting decision making than traditional information provision. We describe the development and field testing of a novel patient decision aid designed to support women to make fertility preservation treatment decisions around cancer diagnosis.MethodsA prospective, mixed-method, three stage study involving: 1) co-development of the resource in collaboration with a multi-disciplinary group of key stakeholders including oncology and fertility healthcare professionals and patient partners (n=24), 2) alpha testing with a group of cancer patients who had faced a fertility preservation treatment decision in the past (n=11), and oncology and fertility healthcare professionals and stakeholders (n=14) and, 3) beta testing with women in routine care who had received a recent diagnosis of cancer and were facing a fertility preservation treatment decision (n=41) and their oncology and fertility healthcare professionals (n=3). Ten service users recruited from a closed Breast Cancer Now Facebook group and the support group Cancer and Fertility UK also provided feedback on CFM via an online survey.ResultsA 60-page paper prototype of the Cancer, Fertility and Me patient decision aid was initially developed. Alpha testing of the resource found that overall, it was acceptable to cancer patients, healthcare professionals and key stakeholders and it was considered a useful resource to support fertility preservation treatment decision-making. However, the healthcare professionals felt that the length of the patient decision aid, and elements of its content may be a barrier to its use. Subsequently, the prototype was reduced to 40 pages. During beta testing of the shortened version in routine care, women who received the resource described its positive impact on their ability to make fertility preservation decisions and support them at a stressful time. However, practical difficulties emerged which impacted upon its wider dissemination in clinical practice and limited some elements of the evaluation planned.DiscussionWomen receiving the decision aid within the cancer treatment pathway found it helped them engage with decisions about fertility preservation, and make better informed, values-based care plans with oncology and fertility teams. More work is needed to address access and implementation of this resource as part of routine oncology care pathways.
Published: 2022

368. PostCog: A tool for interdisciplinary research into underground forums at scale

Author: Pete, I, Hughes, J, Caines, A, Vu, AV, Gupta, H, Hutchings, A, Anderson, R, and Buttery, P
Subjects: cybercrime, data analysis, interdisciplinary research tools, forums
Abstract: Underground forums provide useful insights into cybercrime, where researchers analyse underlying economies, key actors, their discussions and interactions, as well as different types of cybercrime. This interdisciplinary topic of study incorporates expertise from diverse areas, including computer science, criminology, economics, psychology, and other social sciences. Historically, there were significant challenges around access to data, but there are now research datasets of millions of messages scraped from underground forums. The problems now stem from the size of these datasets and the technical nature of methods and tools available for data sampling and analysis at scale, which make data exploration difficult for non-technical users. POSTCOG has been developed to solve this problem. We first provide a survey of prior work into underground forums; this was used to understand the requirements and functionalities valued by researchers, and to inform the design of a data exploration tool. We then describe POSTCOG, a web application developed to support users from both technical and non-technical backgrounds in forum analyses, such as search, information extraction and cross-forum comparison. The prototype’s usability is then evalu- ated through two user studies with expert users of the CRIMEBB dataset. POSTCOG is made available for academic research upon signing an agreement with the Cambridge Cybercrime Centre.
Published: 2022

369. Technical and Clinical Outcomes Following Colonic Stenting: A Seven-Year Analysis of 268 Procedures

Author: Little, M. W., Oakley, T., Briggs, J. H., Sutcliffe, J. A., Allouni, A. K., Makris, G., Bratby, M. J., Tapping, C. R., Patel, R., Wigham, A., Anthony, S., Phillips-Hughes, J., and Uberoi, R.
Published: 2016
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370. A Method for comprehensively Assessing Economic Trade-Offs of New Irrigation Developments

Author: Petheram, C., Hughes, J., McKellar, L., Kim, S., Holz, L., Poulton, P., Kehoe, M., Podger, S., Podger, G., McJannet, D., and Hornbuckle, J.
Published: 2016
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371. Advanced ACTPol Cryogenic Detector Arrays and Readout

Author: Henderson, S. W., Allison, R., Austermann, J., Baildon, T., Battaglia, N., Beall, J. A., Becker, D., De Bernardis, F., Bond, J. R., Calabrese, E., Choi, S. K., Coughlin, K. P., Crowley, K. T., Datta, R., Devlin, M. J., Duff, S. M., Dunkley, J., Dünner, R., van Engelen, A., Gallardo, P. A., Grace, E., Hasselfield, M., Hills, F., Hilton, G. C., Hincks, A. D., Hloẑek, R., Ho, S. P., Hubmayr, J., Huffenberger, K., Hughes, J. P., Irwin, K. D., Koopman, B. J., Kosowsky, A. B., Li, D., McMahon, J., Munson, C., Nati, F., Newburgh, L., Niemack, M. D., Niraula, P., Page, L. A., Pappas, C. G., Salatino, M., Schillaci, A., Schmitt, B. L., Sehgal, N., Sherwin, B. D., Sievers, J. L., Simon, S. M., Spergel, D. N., Staggs, S. T., Stevens, J. R., Thornton, R., Van Lanen, J., Vavagiakis, E. M., Ward, J. T., and Wollack, E. J.
Published: 2016
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372. Venues for Meeting Sex Partners and Partner HIV Risk Characteristics: HIV Prevention Trials Network (HPTN064) Women’s HIV Seroincidence Study (ISIS)

Author: Roman Isler, M., Golin, C., Wang, J., Hughes, J., Justman, J., Haley, D., Kuo, I., Adimora, A., Chege, W., Hodder, S., and HIV Prevention Trials Network (HPTN064) Women’s HIV SeroIncidence Study (ISIS)
Published: 2016
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373. Auditory canal exostoses in Irish surfers

Author: Lennon, P., Murphy, C., Fennessy, B., and Hughes, J. P.
Published: 2016
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374. The PDS4 Information Model and its role in agile science data curation

Author: Crichton, Daniel J and Hughes, J. Steven
Abstract: UNKNOWN
Published: 2017

375. The PDS4 Information Model and its role in agile science data curation

Author: Hughes, J. Steven and Crichton, Daniel J
Published: 2017

376. Evidence-Based Infection Control in the Intensive Care Unit

Author: Hughes, J., Taylor, N., Cerda, E., de la Cal, M.A., Gullo, Antonino, editor, van Saene, H. K. F., editor, De La Cal, M. A., editor, and Silvestri, L., editor
Published: 2005
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377. The Greening of World History

Author: Hughes, J. Donald and Hughes-Warrington, Marnie, editor
Published: 2005
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378. Emerging infectious diseases: the public’s view of the problem and what should be expected from the public health community

Author: Hughes, J. M., Peters, C. J., editor, and Calisher, Charles H., editor
Published: 2005
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379. ABA and Diverse Cultural and Linguistic Environments: A Welsh Perspective

Author: Jones, E. W., Hoerger, M., Hughes, J. C., Williams, B. M., Jones, B., Moseley, Y., Hughes, D. R., and Prys, D.
Abstract: Gwynedd Local Education Authority (LEA) in North West Wales, UK, is funding a small-scale autism-specific specialist education service using ABA methodology. The program is available through the medium of Welsh, English or bilingually, depending on the individual needs of the child (Jones and Hoerger in Eur J Behav Anal 10:249-253, "2009"). Delivering an ABA curriculum within a Welsh context raises issues regarding how ABA interventions work in a non-Anglo-American cultural and linguistic context. We describe one part of the program, as well as the mechanics of translation and interpretation: How ABA fits conceptually in a different language, how Skinner's original ideas about developing a scientific terminology to describe behavior can be applied to a different cultural and linguistic tradition, and cultural variation in reinforcement practices.
Published: 2011
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380. A prenylated dsRNA sensor protects against severe COVID-19

Author: Wickenhagen, A, Sugrue, E, Lytras, S, Kuchi, S, Noerenberg, M, Turnbull, ML, Loney, C, Herder, V, Allan, J, Jarmson, I, Cameron-Ruiz, N, Varjak, M, Pinto, RM, Lee, JY, Iselin, L, Palmalux, N, Stewart, DG, Swingler, S, Greenwood, EJD, Crozier, TWM, Gu, Q, Davies, EL, Clohisey, S, Wang, B, Trindade Maranhão Costa, F, Freire Santana, M, de Lima Ferreira, LC, Murphy, L, Fawkes, A, Meynert, A, Grimes, G, Da Silva Filho, JL, Marti, M, Hughes, J, Stanton, RJ, Wang, ECY, Ho, A, Davis, I, Jarrett, RF, Castello, A, Robertson, DL, Semple, MG, Openshaw, PJM, Palmarini, M, Lehner, PJ, Baillie, JK, Rihn, SJ, Wilson, SJ, ISARIC4C Investigators, Carson, G, Alex, B, Bach, B, Barclay, WS, Bogaert, D, Chand, M, Cooke, GS, Docherty, AB, Dunning, J, da Silva Filipe, A, Fletcher, T, Green, CA, Harrison, EM, Ho, AYW, Horby, PW, Ijaz, S, Khoo, S, Klenerman, P, Law, A, Lim, WS, Mentzer, AJ, Merson, L, Meynert, AM, Noursadeghi, M, Moore, SC, Paxton, WA, Pollakis, G, Price, N, Rambaut, A, Russell, CD, Sancho-Shimizu, V, Scott, JT, de Silva, T, Sigfrid, L, Solomon, T, Sriskandan, S, Stuart, D, Summers, C, Tedder, RS, Thomson, EC, Thompson, AAR, Thwaites, RS, Turtle, LCW, Gupta, RK, Palmieri, C, Swann, OV, Zambon, M, Dumas, M-E, Griffin, JL, Takats, Z, Chechi, K, Andrikopoulos, P, Osagie, A, Olanipekun, M, Liggi, S, Lewis, MR, Dos Santos Correia, G, Sands, CJ, Takis, P, Maslen, L, Hardwick, H, Donohue, C, Griffiths, F, Oosthuyzen, W, Donegan, C, Spencer, RG, Norman, L, Pius, R, Drake, TM, Fairfield, CJ, Knight, SR, Mclean, KA, Murphy, D, Shaw, CA, Dalton, J, Girvan, M, Saviciute, E, Roberts, S, Harrison, J, Marsh, L, Connor, M, Halpin, S, Jackson, C, Gamble, C, Plotkin, D, Lee, J, Leeming, G, Wham, M, Hendry, R, Scott-Brown, J, Greenhalf, W, Shaw, V, McDonald, SE, Keating, S, Ahmed, KA, Armstrong, JA, Ashworth, M, Asiimwe, IG, Bakshi, S, Barlow, SL, Booth, L, Brennan, B, Bullock, K, Catterall, BWA, Clark, JJ, Clarke, EA, Cole, S, Cooper, L, Cox, H, Davis, C, Dincarslan, O, Dunn, C, Dyer, P, Elliott, A, Evans, A, Finch, L, Fisher, LWS, Foster, T, Garcia-Dorival, I, Gunning, P, Hartley, C, Jensen, RL, Jones, CB, Jones, TR, Khandaker, S, King, K, Kiy, RT, Koukorava, C, Lake, A, Lant, S, Latawiec, D, Lavelle-Langham, L, Lefteri, D, Lett, L, Livoti, LA, Mancini, M, McDonald, S, McEvoy, L, McLauchlan, J, Metelmann, S, Miah, NS, Middleton, J, Mitchell, J, Murphy, EG, Penrice-Randal, R, Pilgrim, J, Prince, T, Reynolds, W, Ridley, PM, Sales, D, Shaw, VE, Shears, RK, Small, B, Subramaniam, KS, Szemiel, A, Taggart, A, Tanianis-Hughes, J, Thomas, J, Trochu, E, van Tonder, L, Wilcock, E, Zhang, JE, Flaherty, L, Maziere, N, Cass, E, Carracedo, AD, Carlucci, N, Holmes, A, Massey, H, Wrobel, N, McCafferty, S, Morrice, K, MacLean, A, Adeniji, K, Agranoff, D, Agwuh, K, Ail, D, Aldera, EL, Alegria, A, Allen, S, Angus, B, Ashish, A, Atkinson, D, Bari, S, Barlow, G, Barnass, S, Barrett, N, Bassford, C, Basude, S, Baxter, D, Beadsworth, M, Bernatoniene, J, Berridge, J, Berry, C, Best, N, Bothma, P, Chadwick, D, Brittain-Long, R, Bulteel, N, Burden, T, Burtenshaw, A, Caruth, V, Chambler, D, Chee, N, Child, J, Chukkambotla, S, Clark, T, Collini, P, Cosgrove, C, Cupitt, J, Cutino-Moguel, M-T, Dark, P, Dawson, C, Dervisevic, S, Donnison, P, Douthwaite, S, Drummond, A, DuRand, I, Dushianthan, A, Dyer, T, Evans, C, Eziefula, C, Fegan, C, Finn, A, Fullerton, D, Garg, S, Garg, A, Gkrania-Klotsas, E, Godden, J, Goldsmith, A, Graham, C, Hardy, E, Hartshorn, S, Harvey, D, Havalda, P, Hawcutt, DB, Hobrok, M, Hodgson, L, Hormis, A, Jacobs, M, Jain, S, Jennings, P, Kaliappan, A, Kasipandian, V, Kegg, S, Kelsey, M, Kendall, J, Kerrison, C, Kerslake, I, Koch, O, Koduri, G, Koshy, G, Laha, S, Laird, S, Larkin, S, Leiner, T, Lillie, P, Limb, J, Linnett, V, Little, J, Lyttle, M, MacMahon, M, MacNaughton, E, Mankregod, R, Masson, H, Matovu, E, McCullough, K, McEwen, R, Meda, M, Mills, G, Minton, J, Mirfenderesky, M, Mohandas, K, Mok, Q, Moon, J, Moore, E, Morgan, P, Morris, C, Mortimore, K, Moses, S, Mpenge, M, Mulla, R, Murphy, M, Nagel, M, Nagarajan, T, Nelson, M, Norris, L, O'Shea, MK, Otahal, I, Ostermann, M, Pais, M, Panchatsharam, S, Papakonstantinou, D, Paraiso, H, Patel, B, Pattison, N, Pepperell, J, Peters, M, Phull, M, Pintus, S, Singh Pooni, J, Planche, T, Post, F, Price, D, Prout, R, Rae, N, Reschreiter, H, Reynolds, T, Richardson, N, Roberts, M, Roberts, D, Rose, A, Rousseau, G, Ruge, B, Ryan, B, Saluja, T, Schmid, ML, Shah, A, Shanmuga, P, Sharma, A, Shawcross, A, Sizer, J, Shankar-Hari, M, Smith, R, Snelson, C, Spittle, N, Staines, N, Stambach, T, Stewart, R, Subudhi, P, Szakmany, T, Tatham, K, Thompson, C, Thompson, R, Tridente, A, Tupper-Carey, D, Twagira, M, Vallotton, N, Vancheeswaran, R, Vincent-Smith, L, Visuvanathan, S, Vuylsteke, A, Waddy, S, Wake, R, Walden, A, Welters, I, Whitehouse, T, Whittaker, P, Whittington, A, Papineni, P, Wijesinghe, M, Williams, M, Wilson, L, Winchester, S, Wiselka, M, Wolverson, A, Wootton, DG, Workman, A, Yates, B, Young, P, Division of Computational and Systems Medicine, Imperial College London, London, SW7 2AZ, UK, Imperial College London - National Heart and Lung Institute, Centre National de la Recherche Scientifique (CNRS), MRC - University of Glasgow Centre for Virus Research, University of Kent [Canterbury], University of Glasgow, National Institute for Health Research, UK Research and Innovation, UKRI MRC COVID-19 Rapid Response Call, Mentzer, AJ, Investigators, ISARIC4C, Lee, J, and Angus, B
Subjects: 2',5'-Oligoadenylate Synthetase/genetics, L PATHWAY, viruses, SINGLE-NUCLEOTIDE POLYMORPHISM, RNASE-L, RNA, Viral/chemistry, RNA, Double-Stranded/chemistry, Virus Replication, Severity of Illness Index, COVID-19/enzymology, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Chiroptera, Sense (molecular biology), 2',5'-Oligoadenylate Synthetase, MESH: COVID-19, MESH: Animals, MESH: Interferons, ENZYME-ACTIVITY, MESH: 2',5'-Oligoadenylate Synthetase, Endoribonucleases/metabolism, 0303 health sciences, MESH: Protein Prenylation, Multidisciplinary, I INTERFERON, Coronaviridae/enzymology, MESH: Polymorphism, Single Nucleotide, 030302 biochemistry & molecular biology, MESH: Chiroptera, CORONAVIRUS REPLICATION, 3. Good health, Cell biology, Multidisciplinary Sciences, Isoenzymes, RNA silencing, VIRUS NS1 PROTEIN, MESH: RNA, Viral, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Isoenzymes, Science & Technology - Other Topics, RNA, Viral, MESH: 5' Untranslated Regions, [SDV.IMM]Life Sciences [q-bio]/Immunology, SARS-CORONAVIRUS, Gene isoform, MESH: Endoribonucleases, Retroelements, RNase P, Coronaviridae, General Science & Technology, Protein Prenylation, Biology, Polymorphism, Single Nucleotide, Chiroptera/genetics, 03 medical and health sciences, MESH: RNA, Double-Stranded, MESH: Retroelements, SARS-CoV-2/genetics, MESH: Severity of Illness Index, Endoribonucleases, Animals, Humans, MESH: SARS-CoV-2, Interferons/immunology, Gene, ISARIC4C Investigators, 030304 developmental biology, RNA, Double-Stranded, Science & Technology, MESH: Humans, ACCEPTOR SITE, Phosphoric Diester Hydrolases, SARS-CoV-2, fungi, MESH: Virus Replication, RNA, COVID-19, Phosphoric Diester Hydrolases/genetics, Viral replication, A549 Cells, Protein prenylation, SPLICE-SITE POLYMORPHISM, Interferons, MESH: A549 Cells, 5' Untranslated Regions, MESH: Phosphoric Diester Hydrolases, Isoenzymes/genetics, MESH: Coronaviridae
Abstract: International audience; INTRODUCTIONInterferons (IFNs) are cytokines that are rapidly deployed in response to invading pathogens. By initiating a signaling cascade that stimulates the expression of hundreds of genes, IFNs create an antiviral state in host cells. Because IFNs heavily influence COVID-19 outcomes, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication can be inhibited by the antiviral state, it is important to understand how the individual antiviral effectors encoded by IFN-stimulated genes (ISGs) inhibit SARS-CoV-2.RATIONALEWe hypothesized that IFN-stimulated antiviral effectors can inhibit SARS-CoV-2, and that variation at the loci encoding these defenses underlies why some people are more susceptible to severe COVID-19.RESULTSWe used arrayed ISG expression screening to reveal that 2′-5′-oligoadenylate synthetase 1 (OAS1) consistently inhibited SARS-CoV-2 in different contexts. Using CRISPR-Cas9, we found that endogenous OAS1 makes a substantial contribution to the antiviral state by recognizing short stretches of double-stranded RNA (dsRNA) and activating RNase L. We globally mapped where OAS1 binds to SARS-CoV-2 viral RNAs and found that OAS1 binding is remarkably specific, with two conserved stem loops in the SARS-CoV-2 5′-untranslated region (UTR) constituting the principal viral target.OAS1 expression was readily detectable at the sites of infection in individuals who died of COVID-19, and specific OAS1 alleles are known to be associated with altered susceptibility to infection and severe disease. It had previously been reported that alleles containing a common splice-acceptor single nucleotide polymorphism in OAS1 (Rs10774671) were associated with less severe COVID-19. We determined that people with at least one allele with a G at this position could express a prenylated form of OAS1 (p46), whereas other individuals could not. Using a series of mutants, we found that C-terminal prenylation was necessary for OAS1 to initiate a block to SARS-CoV-2. Furthermore, confocal microscopy revealed that prenylation targeted OAS1 to perinuclear structures rich in viral dsRNA, whereas non-prenylated OAS1 was diffusely localized and unable to initiate a detectable block to SARS-CoV-2 replication.The realization that prenylation is essential for OAS1-mediated sensing of SARS-CoV-2 allowed us to examine the transcriptome of infected patients and investigate whether there was a link between the expression of prenylated OAS1 and SARS-CoV-2 disease progression. Analysis of the OAS1 transcripts from 499 hospitalized COVID-19 patients revealed that expressing prenylated OAS1 was associated with protection from severe COVID-19.Because prenylated OAS1 was so important in human cases, we wanted to determine whether horseshoe bats, the likely source of SARS-CoV-2, possessed the same defense. When we examined the genomic region where the prenylation signal should reside, retrotransposition of a long terminal repeat sequence had ablated this signal, preventing the expression of prenylated anti-CoV OAS1 in these bats.CONCLUSIONC-terminal prenylation targets OAS1 to intracellular sites rich in viral dsRNA, which are likely the SARS-CoV-2 replicative organelles. Once in the right place, OAS1 binds to dsRNA structures in the SARS-CoV-2 5′-UTR and initiates a potent block to SARS-CoV-2 replication. Thus, the correct targeting of OAS1 and the subsequent inhibition of SARS-CoV-2 likely underpins the genetic association of alleles containing a G at Rs10774671 with reduced susceptibility to infection and severe disease in COVID-19. Moreover, the conspicuous absence of this antiviral defense in horseshoe bats potentially explains why SARS-CoV-2 is so sensitive to this defense in humans.
Published: 2021

381. Temperature-Dependent Dielectric Properties of Human Bone Constituents at THz Frequencies: Contrast Mechanisms and Bound Water Dynamics

Author: Chopra, N., primary, Shaw, N., additional, Lotkowska, L., additional, Sui, C., additional, Navarro-Cia, M., additional, and Lloyd-Hughes, J., additional
Published: 2022
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382. Rapid s- & p- polarised THz spectroscopy for in-vivo measurements using a handheld scanner

Author: Ou, H., primary, Stantchev, R. I., additional, Deveikis, J., additional, Chopra, N., additional, Serrano, A. I. H., additional, Lloyd-Hughes, J., additional, and Pickwell-MacPherson, E., additional
Published: 2022
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383. Deep Learning Electrocardiographic Analysis for Detection of Left-Sided Valvular Heart Disease

Author: Elias, Pierre, primary, Poterucha, Timothy J., additional, Rajaram, Vijay, additional, Moller, Luca Matos, additional, Rodriguez, Victor, additional, Bhave, Shreyas, additional, Hahn, Rebecca T., additional, Tison, Geoffrey, additional, Abreau, Sean A., additional, Barrios, Joshua, additional, Torres, Jessica Nicole, additional, Hughes, J. Weston, additional, Perez, Marco V., additional, Finer, Joshua, additional, Kodali, Susheel, additional, Khalique, Omar, additional, Hamid, Nadira, additional, Schwartz, Allan, additional, Homma, Shunichi, additional, Kumaraiah, Deepa, additional, Cohen, David J., additional, Maurer, Mathew S., additional, Einstein, Andrew J., additional, Nazif, Tamim, additional, Leon, Martin B., additional, and Perotte, Adler J., additional
Published: 2022
Full Text: View/download PDF

384. Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study

Author: Evans, R A, primary, Leavy, O C, additional, Richardson, M, additional, Elneima, O, additional, McAuley, H J C, additional, Shikotra, A, additional, Singapuri, A, additional, Sereno, M, additional, Saunders, R M, additional, Harris, V C, additional, Houchen-Wolloff, L, additional, Aul, R, additional, Beirne, P, additional, Bolton, C E, additional, Brown, J S, additional, Choudhury, G, additional, Diar-Bakerly, N, additional, Easom, N, additional, Echevarria, C, additional, Fuld, J, additional, Hart, N, additional, Hurst, J, additional, Jones, M G, additional, Parekh, D, additional, Pfeffer, P, additional, Rahman, N M, additional, Rowland-Jones, S L, additional, Shah, A M, additional, Wootton, D G, additional, Chalder, T, additional, Davies, M J, additional, De Soyza, A, additional, Geddes, J R, additional, Greenhalf, W, additional, Greening, N J, additional, Heaney, L G, additional, Heller, S, additional, Howard, L S, additional, Jacob, J, additional, Jenkins, R G, additional, Lord, J M, additional, Man, W D-C, additional, McCann, G P, additional, Neubauer, S, additional, Openshaw, P J M, additional, Porter, J C, additional, Rowland, M J, additional, Scott, J T, additional, Semple, M G, additional, Singh, S J, additional, Thomas, D C, additional, Toshner, M, additional, Lewis, K E, additional, Thwaites, R S, additional, Briggs, A, additional, Docherty, A B, additional, Kerr, S, additional, Lone, N I, additional, Quint, J, additional, Sheikh, A, additional, Thorpe, M, additional, Zheng, B, additional, Chalmers, J D, additional, Ho, L P, additional, Horsley, A, additional, Marks, M, additional, Poinasamy, K, additional, Raman, B, additional, Harrison, E M, additional, Wain, L V, additional, Brightling, C E, additional, Abel, K, additional, Adamali, H, additional, Adeloye, D, additional, Adeyemi, O, additional, Adrego, R, additional, Aguilar Jimenez, L A, additional, Ahmad, S, additional, Ahmad Haider, N, additional, Ahmed, R, additional, Ahwireng, N, 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additional, Lynch, C, additional, MacDonald, S, additional, MacGowan, G, additional, Macharia, I, additional, Mackie, J, additional, Macliver, L, additional, Madathil, S, additional, Madzamba, G, additional, Magee, N, additional, Magtoto, M M, additional, Mairs, N, additional, Majeed, N, additional, Major, E, additional, Malein, F, additional, Malim, M, additional, Mallison, G, additional, Mandal, S, additional, Mangion, K, additional, Manisty, C, additional, Manley, R, additional, March, K, additional, Marciniak, S, additional, Marino, P, additional, Mariveles, M, additional, Marouzet, E, additional, Marsh, S, additional, Marshall, B, additional, Marshall, M, additional, Martin, J, additional, Martineau, A, additional, Martinez, L M, additional, Maskell, N, additional, Matila, D, additional, Matimba-Mupaya, W, additional, Matthews, L, additional, Mbuyisa, A, additional, McAdoo, S, additional, Weir McCall, J, additional, McAllister-Williams, H, additional, McArdle, A, additional, 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Mitchell, J, additional, Mohamed, A, additional, Mohamed, N, additional, Mohammed, S, additional, Molyneaux, P L, additional, Monteiro, W, additional, Moriera, S, additional, Morley, A, additional, Morrison, L, additional, Morriss, R, additional, Morrow, A, additional, Moss, A J, additional, Moss, P, additional, Motohashi, K, additional, Msimanga, N, additional, Mukaetova-Ladinska, E, additional, Munawar, U, additional, Murira, J, additional, Nanda, U, additional, Nassa, H, additional, Nasseri, M, additional, Neal, A, additional, Needham, R, additional, Neill, P, additional, Newell, H, additional, Newman, T, additional, Newton-Cox, A, additional, Nicholson, T, additional, Nicoll, D, additional, Nolan, C M, additional, Noonan, M J, additional, Norman, C, additional, Novotny, P, additional, Nunag, J, additional, Nwafor, L, additional, Nwanguma, U, additional, Nyaboko, J, additional, O'Donnell, K, additional, O'Brien, C, additional, O'Brien, L, additional, O'Regan, D, additional, Odell, N, additional, Ogg, G, additional, Olaosebikan, O, additional, Oliver, C, additional, Omar, Z, additional, Orriss-Dib, L, additional, Osborne, L, additional, Osbourne, R, additional, Ostermann, M, additional, Overton, C, additional, Owen, J, additional, Oxton, J, additional, Pack, J, additional, Pacpaco, E, additional, Paddick, S, additional, Painter, S, additional, Pakzad, A, additional, Palmer, S, additional, Papineni, P, additional, Paques, K, additional, Paradowski, K, additional, Pareek, M, additional, Parfrey, H, additional, Pariante, C, additional, Parker, S, additional, Parkes, M, additional, Parmar, J, additional, Patale, S, additional, Patel, B, additional, Patel, M, additional, Patel, S, additional, Pattenadk, D, additional, Pavlides, M, additional, Payne, S, additional, Pearce, L, additional, Pearl, J E, additional, Peckham, D, additional, Pendlebury, J, additional, Peng, Y, additional, Pennington, C, additional, Peralta, I, additional, Perkins, E, additional, Peterkin, Z, additional, Peto, T, additional, Petousi, N, additional, Petrie, J, additional, Phipps, J, additional, Pimm, J, additional, Piper Hanley, K, additional, Pius, R, additional, Plant, H, additional, Plein, S, additional, Plekhanova, T, additional, Plowright, M, additional, Polgar, O, additional, Poll, L, additional, Porter, J, additional, Portukhay, S, additional, Powell, N, additional, Prabhu, A, additional, Pratt, J, additional, Price, A, additional, Price, C, additional, Price, D, additional, Price, L, additional, Prickett, A, additional, Propescu, J, additional, Pugmire, S, additional, Quaid, S, additional, Quigley, J, additional, Qureshi, H, additional, Qureshi, I N, additional, Radhakrishnan, K, additional, Ralser, M, additional, Ramos, A, additional, Ramos, H, additional, Rangeley, J, additional, Rangelov, B, additional, Ratcliffe, L, additional, Ravencroft, P, additional, Reddington, A, additional, Reddy, R, additional, Redfearn, H, additional, Redwood, D, additional, Reed, A, additional, Rees, M, additional, Rees, T, additional, Regan, K, additional, Reynolds, W, additional, Ribeiro, C, additional, Richards, A, additional, Richardson, E, additional, Rivera-Ortega, P, additional, Roberts, K, additional, Robertson, E, additional, Robinson, E, additional, Robinson, L, additional, Roche, L, additional, Roddis, C, additional, Rodger, J, additional, Ross, A, additional, Ross, G, additional, Rossdale, J, additional, Rostron, A, additional, Rowe, A, additional, Rowland, A, additional, Rowland, J, additional, Roy, K, additional, Roy, M, additional, Rudan, I, additional, Russell, R, additional, Russell, E, additional, Saalmink, G, additional, Sabit, R, additional, Sage, E K, additional, Samakomva, T, additional, Samani, N, additional, Sampson, C, additional, Samuel, K, additional, Samuel, R, additional, Sanderson, A, additional, Sapey, E, additional, Saralaya, D, additional, Sargant, J, additional, Sarginson, C, additional, Sass, T, additional, Sattar, N, additional, Saunders, K, additional, Saunders, P, additional, Saunders, L C, additional, Savill, H, additional, Saxon, W, additional, Sayer, A, additional, Schronce, J, additional, Schwaeble, W, additional, Scott, K, additional, Selby, N, additional, Sewell, T A, additional, Shah, K, additional, Shah, P, additional, Shankar-Hari, M, additional, Sharma, M, additional, Sharpe, C, additional, Sharpe, M, additional, Shashaa, S, additional, Shaw, A, additional, Shaw, K, additional, Shaw, V, additional, Shelton, S, additional, Shenton, L, additional, Shevket, K, additional, Short, J, additional, Siddique, S, additional, Siddiqui, S, additional, Sidebottom, J, additional, Sigfrid, L, additional, Simons, G, additional, Simpson, J, additional, Simpson, N, additional, Singh, C, additional, Singh, S, additional, Sissons, D, additional, Skeemer, J, additional, Slack, K, additional, Smith, A, additional, Smith, D, additional, Smith, S, additional, Smith, J, additional, Smith, L, additional, Soares, M, additional, Solano, T S, additional, Solly, R, additional, Solstice, AR, additional, Soulsby, T, additional, Southern, D, additional, Sowter, D, additional, Spears, M, additional, Spencer, L G, additional, Speranza, F, additional, Stadon, L, additional, Stanel, S, additional, Steele, N, additional, Steiner, M, additional, Stensel, D, additional, Stephens, G, additional, Stephenson, L, additional, Stern, M, additional, Stewart, I, additional, Stimpson, R, additional, Stockdale, S, additional, Stockley, J, additional, Stoker, W, additional, Stone, R, additional, Storrar, W, additional, Storrie, A, additional, Storton, K, additional, Stringer, E, additional, Strong-Sheldrake, S, additional, Stroud, N, additional, Subbe, C, additional, Sudlow, C L, additional, Suleiman, Z, additional, Summers, C, additional, Summersgill, C, additional, Sutherland, D, additional, Sykes, D L, additional, Sykes, R, additional, Talbot, N, additional, Tan, A L, additional, Tarusan, L, additional, Tavoukjian, V, additional, Taylor, A, additional, Taylor, C, additional, Taylor, J, additional, Te, A, additional, Tedd, H, additional, Tee, CJ, additional, Teixeira, J, additional, Tench, H, additional, Terry, S, additional, Thackray-Nocera, S, additional, Thaivalappil, F, additional, Thamu, B, additional, Thickett, D, additional, Thomas, C, additional, Thomas, S, additional, Thomas, A K, additional, Thomas-Woods, T, additional, Thompson, T, additional, Thompson, A A R, additional, Thornton, T, additional, Tilley, J, additional, Tinker, N, additional, Tiongson, G F, additional, Tobin, M, additional, Tomlinson, J, additional, Tong, C, additional, Touyz, R, additional, Tripp, K A, additional, Tunnicliffe, E, additional, Turnbull, A, additional, Turner, E, additional, Turner, S, additional, Turner, V, additional, Turner, K, additional, Turney, S, additional, Turtle, L, additional, Turton, H, additional, Ugoji, J, additional, Ugwuoke, R, additional, Upthegrove, R, additional, Valabhji, J, additional, Ventura, M, additional, Vere, J, additional, Vickers, C, additional, Vinson, B, additional, Wade, E, additional, Wade, P, additional, Wainwright, T, additional, Wajero, L O, additional, Walder, S, additional, Walker, S, additional, Wall, E, additional, Wallis, T, additional, Walmsley, S, additional, Walsh, J A, additional, Walsh, S, additional, Warburton, L, additional, Ward, T J C, additional, Warwick, K, additional, Wassall, H, additional, Waterson, S, additional, Watson, E, additional, Watson, L, additional, Watson, J, additional, Welch, C, additional, Welch, H, additional, Welsh, B, additional, Wessely, S, additional, West, S, additional, Weston, H, additional, Wheeler, H, additional, White, S, additional, Whitehead, V, additional, Whitney, J, additional, Whittaker, S, additional, Whittam, B, additional, Whitworth, V, additional, Wight, A, additional, Wild, J, additional, Wilkins, M, additional, Wilkinson, D, additional, Williams, N, additional, Williams, J, additional, Williams-Howard, S A, additional, Willicombe, M, additional, Willis, G, additional, Willoughby, J, additional, Wilson, A, additional, Wilson, D, additional, Wilson, I, additional, Window, N, additional, Witham, M, additional, Wolf-Roberts, R, additional, Wood, C, additional, Woodhead, F, additional, Woods, J, additional, Wormleighton, J, additional, Worsley, J, additional, Wraith, D, additional, Wrey Brown, C, additional, Wright, C, additional, Wright, L, additional, Wright, S, additional, Wyles, J, additional, Wynter, I, additional, Xu, M, additional, Yasmin, N, additional, Yasmin, S, additional, Yates, T, additional, Yip, K P, additional, Young, B, additional, Young, S, additional, Young, A, additional, Yousuf, A J, additional, Zawia, A, additional, Zeidan, L, additional, Zhao, B, additional, and Zongo, O, additional
Published: 2022
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385. Peer Review #2 of "Assessing availability of European plant protection product data: an example evaluating basic area treated (v0.1)"

Author: Hughes, J, additional
Published: 2022
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386. Superclustering with the Atacama Cosmology Telescope and Dark Energy Survey. I. Evidence for Thermal Energy Anisotropy Using Oriented Stacking

Author: Lokken, M., primary, Hložek, R., additional, Engelen, A. van, additional, Madhavacheril, M., additional, Baxter, E., additional, DeRose, J., additional, Doux, C., additional, Pandey, S., additional, Rykoff, E. S., additional, Stein, G., additional, To, C., additional, Abbott, T. M. C., additional, Adhikari, S., additional, Aguena, M., additional, Allam, S., additional, Andrade-Oliveira, F., additional, Annis, J., additional, Battaglia, N., additional, Bernstein, G. M., additional, Bertin, E., additional, Bond, J. R., additional, Brooks, D., additional, Calabrese, E., additional, Rosell, A. Carnero, additional, Kind, M. Carrasco, additional, Carretero, J., additional, Cawthon, R., additional, Choi, A., additional, Costanzi, M., additional, Crocce, M., additional, Costa, L. N. da, additional, Pereira, M. E. da Silva, additional, Vicente, J. De, additional, Desai, S., additional, Dietrich, J. P., additional, Doel, P., additional, Dunkley, J., additional, Everett, S., additional, Evrard, A. E., additional, Ferraro, S., additional, Flaugher, B., additional, Fosalba, P., additional, Frieman, J., additional, Gallardo, P. A., additional, García-Bellido, J., additional, Gaztanaga, E., additional, Gerdes, D. W., additional, Giannantonio, T., additional, Gruen, D., additional, Gruendl, R. A., additional, Gschwend, J., additional, Gutierrez, G., additional, Hill, J. C., additional, Hilton, M., additional, Hincks, A. D., additional, Hinton, S. R., additional, Hollowood, D. L., additional, Honscheid, K., additional, Hoyle, B., additional, Huang, Z., additional, Hughes, J. P., additional, Huterer, D., additional, Jain, B., additional, James, D. J., additional, Jeltema, T., additional, Kuehn, K., additional, Lima, M., additional, Maia, M. A. G., additional, Marshall, J. L., additional, McMahon, J., additional, Melchior, P., additional, Menanteau, F., additional, Miquel, R., additional, Mohr, J. J., additional, Moodley, K., additional, Morgan, R., additional, Nati, F., additional, Page, L., additional, Ogando, R. L. C., additional, Palmese, A., additional, Paz-Chinchón, F., additional, Malagón, A. A. Plazas, additional, Pieres, A., additional, Romer, A. K., additional, Rozo, E., additional, Sanchez, E., additional, Scarpine, V., additional, Schillaci, A., additional, Schubnell, M., additional, Serrano, S., additional, Sevilla-Noarbe, I., additional, Sheldon, E., additional, Shin, T., additional, Sifón, C., additional, Smith, M., additional, Soares-Santos, M., additional, Suchyta, E., additional, Swanson, M. E. C., additional, Tarle, G., additional, Thomas, D., additional, Tucker, D. L., additional, Varga, T. N., additional, Weller, J., additional, Wechsler, R. H., additional, Wilkinson, R. D., additional, Wollack, E. J., additional, and Xu, Z., additional
Published: 2022
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387. Deep modeling of plasma and neutral fluctuations from gas puff turbulence imaging

Author: Mathews, A., primary, Terry, J. L., additional, Baek, S. G., additional, Hughes, J. W., additional, Kuang, A. Q., additional, LaBombard, B., additional, Miller, M. A., additional, Stotler, D., additional, Reiter, D., additional, Zholobenko, W., additional, and Goto, M., additional
Published: 2022
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388. P-226 Outcomes using induction chemotherapy followed by long-course chemoradiotherapy as total neoadjuvant therapy for locally advanced rectal cancer

Author: Gatfield, E., primary, Hughes, J., additional, Kumaran, M., additional, Doherty, G., additional, Daly, M., additional, Stancliffe, M., additional, Jephcott, C., additional, Wilson, C., additional, Smith, S., additional, and Jadon, R., additional
Published: 2022
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389. A Science Data System Architecture for Information Retrieval

Author: Crichton, Daniel J., Hughes, J. Steven, Kelly, Sean, Du, Ding-Zhu, editor, Raghavendra, Cauligi, editor, Wu, Weili, Xiong, Hui, and Shekhar, Shashi
Published: 2004
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390. Using Participant Data to Extend the Evidence Base for Intensive Behavioral Intervention for Children with Autism

Author: Eldevik, Sigmund, Hastings, Richard P., and Hughes, J. Carl
Abstract: We gathered individual participant data from 16 group design studies on behavioral intervention for children with autism. In these studies, 309 children received behavioral intervention, 39 received comparison interventions, and 105 were in a control group. More children who underwent behavioral intervention achieved reliable change in IQ (29.8%) compared with 2.6% and 8.7% for comparison and control groups, respectively, and reliable change in adaptive behavior was achieved for 20.6% versus 5.7% and 5.1%, respectively. These results equated to a number needed to treat of 5 for IQ and 7 for adaptive behavior and absolute risk reduction of 23% and 16%, respectively. Within the behavioral intervention sample, IQ and adaptive behavior at intake predicted gains in adaptive behavior. Intensity of intervention predicted gains in both IQ and adaptive behavior.
Published: 2010
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391. Percutaneous cholecystostomy: The radiologist's role in treating acute cholecystitis

Author: Little, M.W., Briggs, J.H., Tapping, C.R., Bratby, M.J., Anthony, S., Phillips-Hughes, J., and Uberoi, R.
Published: 2013
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392. Atacama Cosmology Telescope: Component-separated maps of CMB temperature and the thermal Sunyaev-Zel'dovich effect

Author: Madhavacheril, M, Hill, J, Naess, S, Addison, G, Aiola, S, Baildon, T, Battaglia, N, Bean, R, Bond, J, Calabrese, E, Calafut, V, Choi, S, Darwish, O, Datta, R, Devlin, M, Dunkley, J, Dunner, R, Ferraro, S, Gallardo, P, Gluscevic, V, Halpern, M, Han, D, Hasselfield, M, Hilton, M, Hincks, A, Hlozek, R, Ho, S, Huffenberger, K, Hughes, J, Koopman, B, Kosowsky, A, Lokken, M, Louis, T, Lungu, M, Macinnis, A, Maurin, L, Mcmahon, J, Moodley, K, Nati, F, Niemack, M, Page, L, Partridge, B, Robertson, N, Sehgal, N, Schaan, E, Schillaci, A, Sherwin, B, Sifon, C, Simon, S, Spergel, D, Staggs, S, Storer, E, Van Engelen, A, Vavagiakis, E, Wollack, E, Xu, Z, Madhavacheril M. S., Hill J. C., Naess S., Addison G. E., Aiola S., Baildon T., Battaglia N., Bean R., Bond J. R., Calabrese E., Calafut V., Choi S. K., Darwish O., Datta R., Devlin M. J., Dunkley J., Dunner R., Ferraro S., Gallardo P. A., Gluscevic V., Halpern M., Han D., Hasselfield M., Hilton M., Hincks A. D., HloZek R., Ho S. -P. P., Huffenberger K. M., Hughes J. P., Koopman B. J., Kosowsky A., Lokken M., Louis T., Lungu M., Macinnis A., Maurin L., McMahon J. J., Moodley K., Nati F., Niemack M. D., Page L. A., Partridge B., Robertson N., Sehgal N., Schaan E., Schillaci A., Sherwin B. D., Sifon C., Simon S. M., Spergel D. N., Staggs S. T., Storer E. R., Van Engelen A., Vavagiakis E. M., Wollack E. J., Xu Z., Madhavacheril, M, Hill, J, Naess, S, Addison, G, Aiola, S, Baildon, T, Battaglia, N, Bean, R, Bond, J, Calabrese, E, Calafut, V, Choi, S, Darwish, O, Datta, R, Devlin, M, Dunkley, J, Dunner, R, Ferraro, S, Gallardo, P, Gluscevic, V, Halpern, M, Han, D, Hasselfield, M, Hilton, M, Hincks, A, Hlozek, R, Ho, S, Huffenberger, K, Hughes, J, Koopman, B, Kosowsky, A, Lokken, M, Louis, T, Lungu, M, Macinnis, A, Maurin, L, Mcmahon, J, Moodley, K, Nati, F, Niemack, M, Page, L, Partridge, B, Robertson, N, Sehgal, N, Schaan, E, Schillaci, A, Sherwin, B, Sifon, C, Simon, S, Spergel, D, Staggs, S, Storer, E, Van Engelen, A, Vavagiakis, E, Wollack, E, Xu, Z, Madhavacheril M. S., Hill J. C., Naess S., Addison G. E., Aiola S., Baildon T., Battaglia N., Bean R., Bond J. R., Calabrese E., Calafut V., Choi S. K., Darwish O., Datta R., Devlin M. J., Dunkley J., Dunner R., Ferraro S., Gallardo P. A., Gluscevic V., Halpern M., Han D., Hasselfield M., Hilton M., Hincks A. D., HloZek R., Ho S. -P. P., Huffenberger K. M., Hughes J. P., Koopman B. J., Kosowsky A., Lokken M., Louis T., Lungu M., Macinnis A., Maurin L., McMahon J. J., Moodley K., Nati F., Niemack M. D., Page L. A., Partridge B., Robertson N., Sehgal N., Schaan E., Schillaci A., Sherwin B. D., Sifon C., Simon S. M., Spergel D. N., Staggs S. T., Storer E. R., Van Engelen A., Vavagiakis E. M., Wollack E. J., and Xu Z.
Abstract: Optimal analyses of many signals in the cosmic microwave background (CMB) require map-level extraction of individual components in the microwave sky, rather than measurements at the power spectrum level alone. To date, nearly all map-level component separation in CMB analyses has been performed exclusively using satellite data. In this paper, we implement a component separation method based on the internal linear combination (ILC) approach which we have designed to optimally account for the anisotropic noise (in the 2D Fourier domain) often found in ground-based CMB experiments. Using this method, we combine multifrequency data from the Planck satellite and the Atacama Cosmology Telescope Polarimeter (ACTPol) to construct the first wide-area (≈2100 sq. deg.), arcminute-resolution component-separated maps of the CMB temperature anisotropy and the thermal Sunyaev-Zel'dovich (tSZ) effect sourced by the inverse-Compton scattering of CMB photons off hot, ionized gas. Our ILC pipeline allows for explicit deprojection of various contaminating signals, including a modified blackbody approximation of the cosmic infrared background (CIB) spectral energy distribution. The cleaned CMB maps will be a useful resource for CMB lensing reconstruction, kinematic SZ cross-correlations, and primordial non-Gaussianity studies. The tSZ maps will be used to study the pressure profiles of galaxies, groups, and clusters through cross-correlations with halo catalogs, with dust contamination controlled via CIB deprojection. The data products described in this paper are available on LAMBDA.
Published: 2020

393. The Atacama Cosmology Telescope: Weighing Distant Clusters with the Most Ancient Light

Author: Madhavacheril, M, Sifon, C, Battaglia, N, Aiola, S, Amodeo, S, Austermann, J, Beall, J, Becker, D, Richard Bond, J, Calabrese, E, Choi, S, Denison, E, Devlin, M, Dicker, S, Duff, S, Duivenvoorden, A, Dunkley, J, Dunner, R, Ferraro, S, Gallardo, P, Guan, Y, Han, D, Colin Hill, J, Hilton, G, Hilton, M, Hubmayr, J, Huffenberger, K, Hughes, J, Koopman, B, Kosowsky, A, van Lanen, J, Lee, E, Louis, T, Macinnis, A, Mcmahon, J, Moodley, K, Naess, S, Namikawa, T, Nati, F, Newburgh, L, Niemack, M, Page, L, Partridge, B, Qu, F, Robertson, N, Salatino, M, Schaan, E, Schillaci, A, Schmitt, B, Sehgal, N, Sherwin, B, Simon, S, Spergel, D, Staggs, S, Storer, E, Ullom, J, Vale, L, van Engelen, A, Vavagiakis, E, Wollack, E, Xu, Z, Madhavacheril M. S., Sifon C., Battaglia N., Aiola S., Amodeo S., Austermann J. E., Beall J. A., Becker D. T., Richard Bond J., Calabrese E., Choi S. K., Denison E. V., Devlin M. J., Dicker S. R., Duff S. M., Duivenvoorden A. J., Dunkley J., Dunner R., Ferraro S., Gallardo P. A., Guan Y., Han D., Colin Hill J., Hilton G. C., Hilton M., Hubmayr J., Huffenberger K. M., Hughes J. P., Koopman B. J., Kosowsky A., van Lanen J., Lee E., Louis T., MacInnis A., McMahon J., Moodley K., Naess S., Namikawa T., Nati F., Newburgh L., Niemack M. D., Page L. A., Partridge B., Qu F. J., Robertson N. C., Salatino M., Schaan E., Schillaci A., Schmitt B. L., Sehgal N., Sherwin B. D., Simon S. M., Spergel D. N., Staggs S., Storer E. R., Ullom J. N., Vale L. R., van Engelen A., Vavagiakis E. M., Wollack E. J., Xu Z., Madhavacheril, M, Sifon, C, Battaglia, N, Aiola, S, Amodeo, S, Austermann, J, Beall, J, Becker, D, Richard Bond, J, Calabrese, E, Choi, S, Denison, E, Devlin, M, Dicker, S, Duff, S, Duivenvoorden, A, Dunkley, J, Dunner, R, Ferraro, S, Gallardo, P, Guan, Y, Han, D, Colin Hill, J, Hilton, G, Hilton, M, Hubmayr, J, Huffenberger, K, Hughes, J, Koopman, B, Kosowsky, A, van Lanen, J, Lee, E, Louis, T, Macinnis, A, Mcmahon, J, Moodley, K, Naess, S, Namikawa, T, Nati, F, Newburgh, L, Niemack, M, Page, L, Partridge, B, Qu, F, Robertson, N, Salatino, M, Schaan, E, Schillaci, A, Schmitt, B, Sehgal, N, Sherwin, B, Simon, S, Spergel, D, Staggs, S, Storer, E, Ullom, J, Vale, L, van Engelen, A, Vavagiakis, E, Wollack, E, Xu, Z, Madhavacheril M. S., Sifon C., Battaglia N., Aiola S., Amodeo S., Austermann J. E., Beall J. A., Becker D. T., Richard Bond J., Calabrese E., Choi S. K., Denison E. V., Devlin M. J., Dicker S. R., Duff S. M., Duivenvoorden A. J., Dunkley J., Dunner R., Ferraro S., Gallardo P. A., Guan Y., Han D., Colin Hill J., Hilton G. C., Hilton M., Hubmayr J., Huffenberger K. M., Hughes J. P., Koopman B. J., Kosowsky A., van Lanen J., Lee E., Louis T., MacInnis A., McMahon J., Moodley K., Naess S., Namikawa T., Nati F., Newburgh L., Niemack M. D., Page L. A., Partridge B., Qu F. J., Robertson N. C., Salatino M., Schaan E., Schillaci A., Schmitt B. L., Sehgal N., Sherwin B. D., Simon S. M., Spergel D. N., Staggs S., Storer E. R., Ullom J. N., Vale L. R., van Engelen A., Vavagiakis E. M., Wollack E. J., and Xu Z.
Abstract: We use gravitational lensing of the cosmic microwave background (CMB) to measure the mass of the most distant blindly selected sample of galaxy clusters on which a lensing measurement has been performed to date. In CMB data from the the Atacama Cosmology Telescope and the Planck satellite, we detect the stacked lensing effect from 677 near-infrared-selected galaxy clusters from the Massive and Distant Clusters of WISE Survey (MaDCoWS), which have a mean redshift of zñ = 1.08. There are currently no representative optical weak lensing measurements of clusters that match the distance and average mass of this sample. We detect the lensing signal with a significance of 4.2s. We model the signal with a halo model framework to find the mean mass of the population from which these clusters are drawn. Assuming that the clusters follow Navarro–Frenk–White (NFW) density profiles, we infer a mean mass of M500cñ = (1.7 + 0.4) ́ 1014 M*. We consider systematic uncertainties from cluster redshift errors, centering errors, and the shape of the NFW profile. These are all smaller than 30% of our reported uncertainty. This work highlights the potential of CMB lensing to enable cosmological constraints from the abundance of distant clusters populating ever larger volumes of the observable universe, beyond the capabilities of optical weak lensing measurements.
Published: 2020

394. Other legumes : Faba bean, chickpea, lentil, pigeonpea, mungbean, blackgram, lima bean, horsegram, bambara groundnut and winged bean

Author: Makkouk, K. M., Kumari, S. G., Hughes, J. d’A., Muniyappa, V., Kulkarni, N. K., Loebenstein, Gad, editor, and Thottappilly, George, editor
Published: 2003
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395. Meta-Analysis of Early Intensive Behavioral Intervention for Children with Autism

Author: Eldevik, Sigmund, Hastings, Richard P., Hughes, J. Carl, Jahr, Erik, Eikeseth, Svein, and Cross, Scott
Abstract: A systematic literature search for studies reporting effects of Early Intensive Behavioral Intervention identified 34 studies, 9 of which were controlled designs having either a comparison or a control group. We completed a meta-analysis yielding a standardized mean difference effect size for two available outcome measures: change in full-scale intelligence and/or adaptive behavior composite. Effect sizes were computed using Hedges's "g." The average effect size was 1.10 for change in full-scale intelligence (95% confidence interval = 0.87, 1.34) and 0.66 (95% confidence interval = 0.41, 0.90) for change in adaptive behavior composite. These effect sizes are generally considered to be large and moderate, respectively. Our results support the clinical implication that at present, and in the absence of other interventions with established efficacy, Early Intensive Behavioral Intervention should be an intervention of choice for children with autism. (Contains 1 table and 3 figures.)
Published: 2009
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396. Regional panmixia in the mullet 'Mugil cephalus' along the coast of Eastern Queensland; revealed using six highly polymorphic microsatellite loci

Author: Huey, JA, Espinoza, T, and Hughes, J M
Published: 2013

397. In-Situ Treatment Technologies

Author: Ward, C. H., Hughes, J. B., Pope, G. A., Delshad, M., Dwaranath, V., Spain, J., Nishino, S., Fruchter, J. S., Vermeul, V. R., Williams, M. D., Szecsody, J. E., Reible, Danny, editor, and Demnerova, Katerina, editor
Published: 2002
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398. Organizational Transition to Object Technology: Theory and Practice

Author: Serour, M. K., Henderson-Sellers, B., Hughes, J., Winder, D., Chow, L., Goos, G., editor, Hartmanis, J., editor, van Leeuwen, J., editor, Bellahsène, Zohra, editor, Patel, Dilip, editor, and Rolland, Colette, editor
Published: 2002
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399. Measurements of Neutral Density in the Alcator C-Mod Tokamak

Author: Boivin, R. L., Hughes, J. W., LaBombard, B., Mossessian, D., Terry, J. L., Stott, Peter E., editor, Wootton, Alan, editor, Gorini, Giuseppe, editor, Sindoni, Elio, editor, and Batani, Dimitri, editor
Published: 2002
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400. SARS-CoV-2 evolution during treatment of chronic infection

Author: Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., Hosmillo, M., Rees-Spear, C., Mlcochova, P., Lumb, I. U., Roberts, D. J., Chandra, A., Temperton, N., Baker, S., Dougan, G., Hess, C., Kingston, N., Lehner, P. J., Lyons, P. A., Matheson, N. J., Owehand, W. H., Saunders, C., Summers, C., Thaventhiran, J. E. D., Toshner, M., Weekes, M. P., Bucke, A., Calder, J., Canna, L., Domingo, J., Elmer, A., Fuller, S., Harris, J., Hewitt, S., Kennet, J., Jose, S., Kourampa, J., Meadows, A., O'Brien, C., Price, J., Publico, C., Rastall, R., Ribeiro, C., Rowlands, J., Ruffolo, V., Tordesillas, H., Bullman, B., Dunmore, B. J., Fawke, S., Graf, S., Hodgson, J., Huang, C., Hunter, K., Jones, E., Legchenko, E., Matara, C., Martin, J., Mescia, F., O'Donnell, C., Pointon, L., Pond, N., Shih, J., Sutcliffe, R., Tilly, T., Treacy, C., Tong, Z., Wood, J., Wylot, M., Bergamaschi, L., Betancourt, A., Bower, G., Cossetti, C., De Sa, A., Epping, M., Gleadall, N., Grenfell, R., Hinch, A., Huhn, O., Jackson, S., Jarvis, I., Lewis, D., Marsden, J., Nice, F., Okecha, G., Omarjee, O., Perera, M., Richoz, N., Romashova, V., Yarkoni, N. S., Sharma, R., Stefanucci, L., Stephens, J., Strezlecki, M., Turner, L., De Bie, E. M. D. D., Bunclark, K., Josipovic, M., Mackay, M., Rossi, S., Selvan, M., Spencer, S., Yong, C., Ansaripour, A., Michael, A., Mwaura, L., Patterson, C., Polwarth, G., Polgarova, P., di Stefano, G., Fahey, C., Michel, R., Bong, S. -H., Coudert, J. D., Holmes, E., Allison, J., Butcher, H., Caputo, D., Clapham-Riley, D., Dewhurst, E., Furlong, A., Graves, B., Gray, J., Ivers, T., Kasanicki, M., Le Gresley, E., Linger, R., Meloy, S., Muldoon, F., Ovington, N., Papadia, S., Phelan, I., Stark, H., Stirrups, K. E., Townsend, P., Walker, N., Webster, J., Robson, S. C., Loman, N. J., Connor, T. R., Golubchik, T., Martinez Nunez, R. T., Ludden, C., Corden, S., Johnston, I., Bonsall, D., Smith, C. P., Awan, A. R., Bucca, G., Estee Torok, M., Saeed, K., Prieto, J. A., Jackson, D. K., Hamilton, W. L., Snell, L. B., Moore, C., Harrison, E. M., Goncalves, S., Fairley, D. J., Loose, M. W., Watkins, J., Livett, R., Moses, S., Amato, R., Nicholls, S., Bull, M., Smith, D. L., Barrett, J., Aanensen, D. M., Curran, M. D., Parmar, S., Aggarwal, D., Shepherd, J. G., Parker, M. D., Glaysher, S., Bashton, M., Underwood, A. P., Pacchiarini, N., Loveson, K. F., Carabelli, A. M., Templeton, K. E., Langford, C. F., Sillitoe, J., de Silva, T. I., Wang, D., Kwiatkowski, D., Rambaut, A., O'Grady, J., Cottrell, S., Holden, M. T. G., Thomson, E. C., Osman, H., Andersson, M., Chauhan, A. J., Hassan-Ibrahim, M. O., Lawniczak, M., Alderton, A., Chand, M., Constantinidou, C., Unnikrishnan, M., Darby, A. C., Hiscox, J. A., Paterson, S., Martincorena, I., Robertson, D. L., Volz, E. M., Page, A. J., Pybus, O. G., Bassett, A. R., Ariani, C. V., Spencer Chapman, M. H., K. K., Li, Shah, R. N., Jesudason, N. G., Taha, Y., Mchugh, M. P., Dewar, R., Jahun, A. S., Mcmurray, C., Pandey, S., Mckenna, J. P., Nelson, A., Young, G. R., Mccann, C. M., Elliott, S., Lowe, H., Temperton, B., Roy, S., Price, A., Rey, S., Wyles, M., Rooke, S., Shaaban, S., de Cesare, M., Letchford, L., Silveira, S., Pelosi, E., Wilson-Davies, E., O'Toole, A., Hesketh, A. R., Stark, R., du Plessis, L., Ruis, C., Adams, H., Bourgeois, Y., Michell, S. L., Gramatopoulos, D., Edgeworth, J., Breuer, J., Todd, J. A., Fraser, C., Buck, D., John, M., Kay, G. L., Palmer, S., Peacock, S. J., Heyburn, D., Weldon, D., Robinson, E., Mcnally, A., Muir, P., Vipond, I. B., Boyes, J., Sivaprakasam, V., Salluja, T., Dervisevic, S., Meader, E. J., Park, N. R., Oliver, K., Jeffries, A. R., Ott, S., da Silva Filipe, A., Simpson, D. A., Williams, C., Masoli, J. A. H., Knight, B. A., Jones, C. R., Koshy, C., Ash, A., Casey, A., Bosworth, A., Ratcliffe, L., Xu-McCrae, L., Pymont, H. M., Hutchings, S., Berry, L., Jones, K., Halstead, F., Davis, T., Holmes, C., Iturriza-Gomara, M., Lucaci, A. O., Randell, P. A., Cox, A., Madona, P., Harris, K. A., Brown, J. R., Mahungu, T. W., Irish-Tavares, D., Haque, T., Hart, J., Witele, E., Fenton, M. L., Liggett, S., Graham, C., Swindells, E., Collins, J., Eltringham, G., Campbell, S., Mcclure, P. C., Clark, G., Sloan, T. J., Jones, C., Lynch, J., Warne, B., Leonard, S., Durham, J., Williams, T., Haldenby, S. T., Storey, N., Alikhan, N. -F., Holmes, N., Carlile, M., Perry, M., Craine, N., Lyons, R. A., Beckett, A. H., Goudarzi, S., Fearn, C., Cook, K., Dent, H., Paul, H., Davies, R., Blane, B., Girgis, S. T., Beale, M. A., Bellis, K. L., Dorman, M. J., Drury, E., Kane, L., Kay, S., Mcguigan, S., Nelson, R., Prestwood, L., Rajatileka, S., Batra, R., Williams, R. J., Kristiansen, M., Green, A., Justice, A., Mahanama, A. I. K., Samaraweera, B., Hadjirin, N. F., Quick, J., Poplawski, R., Kermack, L. M., Reynolds, N., Hall, G., Chaudhry, Y., Pinckert, M. L., Georgana, I., Moll, R. J., Thornton, A., Myers, R., Stockton, J., Williams, C. A., Yew, W. C., Trotter, A. J., Trebes, A., MacIntyre-Cockett, G., Birchley, A., Adams, A., Plimmer, A., Gatica-Wilcox, B., Mckerr, C., Hilvers, E., Jones, H., Asad, H., Coombes, J., Evans, J. M., Fina, L., Gilbert, L., Graham, L., Cronin, M., Kumziene-Summerhayes, S., Taylor, S., Jones, S., Groves, D. C., Zhang, P., Gallis, M., Louka, S. F., Starinskij, I., Jackson, C., Gourtovaia, M., Tonkin-Hill, G., Lewis, K., Tovar-Corona, J. M., James, K., Baxter, L., Alam, M. T., Orton, R. J., Hughes, J., Vattipally, S., Ragonnet-Cronin, M., Nascimento, F. F., Jorgensen, D., Boyd, O., Geidelberg, L., Zarebski, A. E., Raghwani, J., Kraemer, M. U. G., Southgate, J., Lindsey, B. B., Freeman, T. M., Keatley, J. -P., Singer, J. B., de Oliveira Martins, L., Yeats, C. A., Abudahab, K., Taylor, B. E. W., Menegazzo, M., Danesh, J., Hogsden, W., Eldirdiri, S., Kenyon, A., Mason, J., Robinson, T. I., Holmes, A., Hartley, J. A., Curran, T., Mather, A. E., Shankar, G., Jones, R., Howe, R., Morgan, S., Wastenge, E., Chapman, M. R., Mookerjee, S., Stanley, R., Smith, W., Peto, T., Eyre, D., Crook, D., Vernet, G., Kitchen, C., Gulliver, H., Merrick, I., Guest, M., Munn, R., Bradley, D. T., Wyatt, T., Beaver, C., Foulser, L., Churcher, C. M., Brooks, E., Smith, K. S., Galai, K., Mcmanus, G. M., Bolt, F., Coll, F., Meadows, L., Attwood, S. W., Davies, A., De Lacy, E., Downing, F., Edwards, S., Scarlett, G. P., Jeremiah, S., Smith, N., Leek, D., Sridhar, S., Forrest, S., Cormie, C., Gill, H. K., Dias, J., Higginson, E. E., Maes, M., Young, J., Wantoch, M., Jamrozy, D., Lo, S., Patel, M., Hill, V., Bewshea, C. M., Ellard, S., Auckland, C., Harrison, I., Bishop, C., Chalker, V., Richter, A., Beggs, A., Best, A., Percival, B., Mirza, J., Megram, O., Mayhew, M., Crawford, L., Ashcroft, F., Moles-Garcia, E., Cumley, N., Hopes, R., Asamaphan, P., Niebel, M. O., Gunson, R. N., Bradley, A., Maclean, A., Mollett, G., Blacow, R., Bird, P., Helmer, T., Fallon, K., Tang, J., Hale, A. D., Macfarlane-Smith, L. R., Harper, K. L., Carden, H., Machin, N. W., Jackson, K. A., Ahmad, S. S. Y., George, R. P., Turtle, L., O'Toole, E., Watts, J., Breen, C., Cowell, A., Alcolea-Medina, A., Charalampous, T., Patel, A., Levett, L. J., Heaney, J., Rowan, A., Taylor, G. P., Shah, D., Atkinson, L., Lee, J. C. D., Westhorpe, A. P., Jannoo, R., Lowe, H. L., Karamani, A., Ensell, L., Chatterton, W., Pusok, M., Dadrah, A., Symmonds, A., Sluga, G., Molnar, Z., Baker, P., Bonner, S., Essex, S., Barton, E., Padgett, D., Scott, G., Greenaway, J., Payne, B. A. I., Burton-Fanning, S., Waugh, S., Raviprakash, V., Sheriff, N., Blakey, V., Williams, L. -A., Moore, J., Stonehouse, S., Smith, L., Davidson, R. K., Bedford, L., Coupland, L., Wright, V., Chappell, J. G., Tsoleridis, T., Ball, J., Khakh, M., Fleming, V. M., Lister, M. M., Howson-Wells, H. C., Boswell, T., Joseph, A., Willingham, I., Duckworth, N., Walsh, S., Wise, E., Moore, N., Mori, M., Cortes, N., Kidd, S., Williams, R., Gifford, L., Bicknell, K., Wyllie, S., Lloyd, A., Impey, R., Malone, C. S., Cogger, B. J., Levene, N., Monaghan, L., Keeley, A. J., Partridge, D. G., Raza, M., Evans, C., Johnson, K., Abnizova, I., Aigrain, L., Ali, M., Allen, L., Anderson, R., Ariani, C., Austin-Guest, S., Bala, S., Bassett, A., Battleday, K., Beal, J., Beale, M., Bellany, S., Bellerby, T., Bellis, K., Berger, D., Berriman, M., Betteridge, E., Bevan, P., Binley, S., Bishop, J., Blackburn, K., Bonfield, J., Boughton, N., Bowker, S., Brendler-Spaeth, T., Bronner, I., Brooklyn, T., Buddenborg, S. K., Bush, R., Caetano, C., Cagan, A., Carter, N., Cartwright, J., Monteiro, T. C., Chapman, L., Chillingworth, T. -J., Clapham, P., Clark, R., Clarke, A., Clarke, C., Cole, D., Cook, E., Coppola, M., Cornell, L., Cornwell, C., Corton, C., Crackett, A., Cranage, A., Craven, H., Craw, S., Crawford, M., Cutts, T., Dabrowska, M., Davies, M., Dawson, J., Day, C., Densem, A., Dibling, T., Dockree, C., Dodd, D., Dogga, S., Dougherty, M., Dove, A., Drummond, L., Dudek, M., Durrant, L., Easthope, E., Eckert, S., Ellis, P., Farr, B., Fenton, M., Ferrero, M., Flack, N., Fordham, H., Forsythe, G., Francis, M., Fraser, A., Freeman, A., Galvin, A., Garcia-Casado, M., Gedny, A., Girgis, S., Glover, J., Goodwin, S., Gould, O., Gray, A., Gray, E., Griffiths, C., Gu, Y., Guerin, F., Hamilton, W., Hanks, H., Harrison, E., Harrott, A., Harry, E., Harvison, J., Heath, P., Hernandez-Koutoucheva, A., Hobbs, R., Holland, D., Holmes, S., Hornett, G., Hough, N., Huckle, L., Hughes-Hallet, L., Hunter, A., Inglis, S., Iqbal, S., Jackson, A., Jackson, D., Verdejo, C. J., Jones, M., Kallepally, K., Kay, K., Keatley, J., Keith, A., King, A., Kitchin, L., Kleanthous, M., Klimekova, M., Korlevic, P., Krasheninnkova, K., Lane, G., Langford, C., Laverack, A., Law, K., Lensing, S., Lewis-Wade, A., Liddle, J., Lin, Q., Lindsay, S., Linsdell, S., Long, R., Lovell, J., Mack, J., Maddison, M., Makunin, A., Mamun, I., Mansfield, J., Marriott, N., Martin, M., Mayho, M., Mccarthy, S., Mcclintock, J., Mchugh, S., Mcminn, L., Meadows, C., Mobley, E., Moll, R., Morra, M., Morrow, L., Murie, K., Nash, S., Nathwani, C., Naydenova, P., Neaverson, A., Nerou, E., Nicholson, J., Nimz, T., Noell, G. G., O'Meara, S., Ohan, V., Olney, C., Ormond, D., Oszlanczi, A., Pang, Y. F., Pardubska, B., Park, N., Parmar, A., Patel, G., Payne, M., Peacock, S., Petersen, A., Plowman, D., Preston, T., Puethe, C., Quail, M., Rajan, D., Rance, R., Rawlings, S., Redshaw, N., Reynolds, J., Reynolds, M., Rice, S., Richardson, M., Roberts, C., Robinson, K., Robinson, M., Robinson, D., Rogers, H., Rojo, E. M., Roopra, D., Rose, M., Rudd, L., Sadri, R., Salmon, N., Saul, D., Schwach, F., Scott, C., Seekings, P., Shirley, L., Simms, A., Sinnott, M., Sivadasan, S., Siwek, B., Sizer, D., Skeldon, K., Skelton, J., Slater-Tunstill, J., Sloper, L., Smerdon, N., Smith, C., Smith, J., Smith, K., Smith, M., Smith, S., Smith, T., Sneade, L., Soria, C. D., Sousa, C., Souster, E., Sparkes, A., Spencer-Chapman, M., Squares, J., Steed, C., Stickland, T., Still, I., Stratton, M., Strickland, M., Swann, A., Swiatkowska, A., Sycamore, N., Swift, E., Symons, E., Szluha, S., Taluy, E., Tao, N., Taylor, K., Thompson, S., Thompson, M., Thomson, M., Thomson, N., Thurston, S., Toombs, D., Topping, B., Tovar-Corona, J., Ungureanu, D., Uphill, J., Urbanova, J., Jansen Van, P., Vancollie, V., Voak, P., Walker, D., Walker, M., Waller, M., Ward, G., Weatherhogg, C., Webb, N., Wells, A., Wells, E., Westwood, L., Whipp, T., Whiteley, T., Whitton, G., Whitwham, A., Widaa, S., Williams, M., Wilson, M., Wright, S., Farr, B. W., Quail, M. A., Thurston, S. A. J., Bronner, I. F., Redshaw, N. M., Lensing, S. V., Balcazar, C. E., Gallagher, M. D., Williamson, K. A., Stanton, T. D., Michelsen, M. L., Warwick-Dugdale, J., Manley, R., Farbos, A., Harrison, J. W., Sambles, C. M., Studholme, D. J., Lackenby, A., Mbisa, T., Platt, S., Miah, S., Bibby, D., Manso, C., Hubb, J., Dabrera, G., Ramsay, M., Bradshaw, D., Schaefer, U., Groves, N., Gallagher, E., Lee, D., Williams, D., Ellaby, N., Hartman, H., Manesis, N., Patel, V., Ledesma, J., Twohig, K. A., Allara, E., Pearson, C., Cheng, J. K. J., Bridgewater, H. E., Frost, L. R., Taylor-Joyce, G., Brown, P. E., Tong, L., Broos, A., Mair, D., Nichols, J., Carmichael, S. N., Smollett, K. L., Nomikou, K., Aranday-Cortes, E., Johnson, N., Nickbakhsh, S., Vamos, E. E., Hughes, M., Rainbow, L., Eccles, R., Nelson, C., Whitehead, M., Gregory, R., Gemmell, M., Wierzbicki, C., Webster, H. J., Fisher, C. L., Signell, A. W., Betancor, G., Wilson, H. D., Nebbia, G., Flaviani, F., Cerda, A. C., Merrill, T. V., Wilson, R. E., Cotic, M., Bayzid, N., Thompson, T., Acheson, E., Rushton, S., O'Brien, S., Baker, D. J., Rudder, S., Aydin, A., Sang, F., Debebe, J., Francois, S., Vasylyeva, T. I., Zamudio, M. E., Gutierrez, B., Marchbank, A., Maksimovic, J., Spellman, K., Mccluggage, K., Morgan, M., Beer, R., Afifi, S., Workman, T., Fuller, W., Bresner, C., Angyal, A., Green, L. R., Parsons, P. J., Tucker, R. M., Brown, R., Whiteley, M., Rowe, W., Siveroni, I., Le-Viet, T., Gaskin, A., Johnson, R., Sharrocks, K., Blane, E., Modis, Y., Leigh, K. E., Briggs, J. A. G., van Gils, M. J., Smith, K. G. C., Bradley, J. R., Doffinger, R., Ceron-Gutierrez, L., Barcenas-Morales, G., Pollock, D. D., Goldstein, R. A., Smielewska, A., Skittrall, J. P., Gouliouris, T., Goodfellow, I. G., Gkrania-Klotsas, E., Illingworth, C. J. R., Mccoy, L. E., Gupta, R. K., Medical Microbiology and Infection Prevention, AII - Infectious diseases, Collier, Dami A [0000-0001-5446-4423], Jahun, Aminu [0000-0002-4585-1701], Temperton, Nigel [0000-0002-7978-3815], Modis, Yorgo [0000-0002-6084-0429], Briggs, John AG [0000-0003-3990-6910], Goldstein, Richard A [0000-0001-5148-4672], Skittrall, Jordan P [0000-0002-8228-3758], Gkrania-Klotsas, Effrossyni [0000-0002-0930-8330], McCoy, Laura E [0000-0001-9503-7946], Gupta, Ravindra K [0000-0001-9751-1808], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, Male, Time Factors, viruses, Passive, Antibodies, Viral, CITIID-NIHR BioResource COVID-19 Collaboration, 2.1 Biological and endogenous factors, Viral, Aetiology, Neutralizing, Lung, Phylogeny, neutralising antibodies, Infectivity, education.field_of_study, Genome, Multidisciplinary, Alanine, biology, High-Throughput Nucleotide Sequencing, Viral Load, Spike Glycoprotein, Virus Shedding, Adenosine Monophosphate, Aged, Antibodies, Neutralizing, COVID-19, Chronic Disease, Genome, Viral, Humans, Immune Evasion, Immune Tolerance, Immunization, Passive, Immunosuppression Therapy, Mutagenesis, Mutant Proteins, Mutation, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Evolution, Molecular, Infectious Diseases, Pneumonia & Influenza, Antibody, Infection, Viral load, Biotechnology, Evolution, General Science & Technology, antibody escape, Convalescent plasma, 030106 microbiology, Population, evasion, Antibodies, Virus, Article, Vaccine Related, resistance, 03 medical and health sciences, Immune system, COVID-19 Genomics UK (COG-UK) Consortium, Biodefense, Genetics, Viral shedding, education, COVID-19 Serotherapy, QR355, Prevention, Wild type, Molecular, Pneumonia, Virology, COVID-19 Drug Treatment, Coronavirus, Emerging Infectious Diseases, Good Health and Well Being, 030104 developmental biology, biology.protein, Immunization, immune suppression, mutation
Abstract: The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for virus infection through the engagement of the human ACE2 protein1 and is a major antibody target. Here we show that chronic infection with SARS-CoV-2 leads to viral evolution and reduced sensitivity to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma, by generating whole-genome ultra-deep sequences for 23 time points that span 101 days and using in vitro techniques to characterize the mutations revealed by sequencing. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (ΔH69/ΔV70) in the S1 N-terminal domain of the spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype were reduced in frequency, before returning during a final, unsuccessful course of convalescent plasma treatment. In vitro, the spike double mutant bearing both ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. The spike deletion mutant ΔH69/ΔV70 had a twofold higher level of infectivity than wild-type SARS-CoV-2, possibly compensating for the reduced infectivity of the D796H mutation. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals.
Published: 2021

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