Author: "McHugh, Martin P" / Publication Type: Academic Journals - Searchworks@Jio Institute Digital Library Search Results

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1. An Observational Narrative of Student Reaction to Video Hooks

Author: McCauley, Veronica and McHugh, Martin
Abstract: Digital video has become a dominant form of student learning in and beyond the classroom, and thus its pervasive nature in contemporary learning environments commands scholarly inquiry. In this paper we explore a participatory design-based research approach to the integration of video hook technology in the post-primary science classroom (students aged 12-15). Video hooks were designed with the intention of engaging students and augmenting their interest in science. Teachers across ten schools voluntarily agreed to implement the video hooks, and with their students (N = 128) engage in a qualitative, observational methodology to ascertain their effect. Triangulated data was collected through teacher interviews (N = 10), structured lesson observation and researcher journal documentation. Results reveal that student reaction was instant and impactful with evidence of both triggered and maintained student interest.
Published: 2021

2. Genomic reconstruction of the SARS-CoV-2 epidemic in England

Author: Robson, Samuel C, Connor, Thomas R, Loman, Nicholas J, Golubchik, Tanya, Martinez Nunez, Rocio T, Bonsall, David, Rambaut, Andrew, Snell, Luke B, Ludden, Catherine, Corden, Sally, Nastouli, Eleni, Nebbia, Gaia, Lythgoe, Katrina, Torok, M Estee, Goodfellow, Ian G, Prieto, Jacqui A, Saeed, Kordo, Houlihan, Catherine, Frampton, Dan, Hamilton, William L, Witney, Adam A, Bucca, Giselda, Pope, Cassie F, Moore, Catherine, Thomson, Emma C, Harrison, Ewan M, Smith, Colin P, Rogan, Fiona, Beckwith, Shaun M, Murray, Abigail, Singleton, Dawn, Eastick, Kirstine, Sheridan, Liz A, Randell, Paul, Jackson, Leigh M, Gonçalves, Sónia, Fairley, Derek J, Loose, Matthew W, Watkins, Joanne, Moses, Samuel, Nicholls, Sam, Bull, Matthew, Smith, Darren L, Aanensen, David M, Aggarwal, Dinesh, Shepherd, James G, Curran, Martin D, Parmar, Surendra, Parker, Matthew D, Williams, Catryn, Glaysher, Sharon, Underwood, Anthony P, Bashton, Matthew, Pacchiarini, Nicole, Loveson, Katie F, Byott, Matthew, Carabelli, Alessandro M, Templeton, Kate E, de Silva, Thushan I, Wang, Dennis, Langford, Cordelia F, Gunson, Rory N, Cottrell, Simon, O’Grady, Justin, Kwiatkowski, Dominic, Lillie, Patrick J, Cortes, Nicholas, Moore, Nathan, Thomas, Claire, Burns, Phillipa J, Mahungu, Tabitha W, Liggett, Steven, Beckett, Angela H, Holden, Matthew TG, Levett, Lisa J, Osman, Husam, Hassan-Ibrahim, Mohammed O, Simpson, David A, Chand, Meera, Gupta, Ravi K, Darby, Alistair C, Paterson, Steve, Pybus, Oliver G, Volz, Erik, de Angelis, Daniela, Robertson, David L, Page, Andrew J, Bassett, Andrew R, Wong, Nick, Taha, Yusri, Erkiert, Michelle J, Spencer Chapman, Michael H, Dewar, Rebecca, McHugh, Martin P, Mookerjee, Siddharth, Aplin, Stephen, Harvey, Matthew, Sass, Thea, Umpleby, Helen, and Wheeler, Helen
Subjects: Genetics, Prevention, Emerging Infectious Diseases, Infectious Diseases, Lung, Good Health and Well Being, Amino Acid Substitution, COVID-19, England, Epidemiological Monitoring, Genome, Viral, Genomics, Humans, Molecular Epidemiology, Mutation, Quarantine, SARS-CoV-2, Spatio-Temporal Analysis, Spike Glycoprotein, Coronavirus, Wellcome Sanger Institute COVID-19 Surveillance Team, COVID-19 Genomics UK (COG-UK) Consortium*, General Science & Technology
Abstract: The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.
Published: 2021

3. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

Author: Meng, Bo, Kemp, Steven A, Papa, Guido, Datir, Rawlings, Ferreira, Isabella ATM, Marelli, Sara, Harvey, William T, Lytras, Spyros, Mohamed, Ahmed, Gallo, Giulia, Thakur, Nazia, Collier, Dami A, Mlcochova, Petra, Consortium, The COVID-19 Genomics UK, Robson, Samuel C, Loman, Nicholas J, Connor, Thomas R, Golubchik, Tanya, Nunez, Rocio T Martinez, Ludden, Catherine, Corden, Sally, Johnston, Ian, Bonsall, David, Smith, Colin P, Awan, Ali R, Bucca, Giselda, Torok, M Estee, Saeed, Kordo, Prieto, Jacqui A, Jackson, David K, Hamilton, William L, Snell, Luke B, Moore, Catherine, Harrison, Ewan M, Goncalves, Sonia, Fairley, Derek J, Loose, Matthew W, Watkins, Joanne, Livett, Rich, Moses, Samuel, Amato, Roberto, Nicholls, Sam, Bull, Matthew, Smith, Darren L, Barrett, Jeff, Aanensen, David M, Curran, Martin D, Parmar, Surendra, Aggarwal, Dinesh, Shepherd, James G, Parker, Matthew D, Glaysher, Sharon, Bashton, Matthew, Underwood, Anthony P, Pacchiarini, Nicole, Loveson, Katie F, Templeton, Kate E, Langford, Cordelia F, Sillitoe, John, de Silva, Thushan I, Wang, Dennis, Kwiatkowski, Dominic, Rambaut, Andrew, O’Grady, Justin, Cottrell, Simon, Holden, Matthew TG, Thomson, Emma C, Osman, Husam, Andersson, Monique, Chauhan, Anoop J, Hassan-Ibrahim, Mohammed O, Lawniczak, Mara, Alderton, Alex, Chand, Meera, Constantinidou, Chrystala, Unnikrishnan, Meera, Darby, Alistair C, Hiscox, Julian A, Paterson, Steve, Martincorena, Inigo, Volz, Erik M, Page, Andrew J, Pybus, Oliver G, Bassett, Andrew R, Ariani, Cristina V, Chapman, Michael H Spencer, Li, Kathy K, Shah, Rajiv N, Jesudason, Natasha G, Taha, Yusri, McHugh, Martin P, Dewar, Rebecca, Jahun, Aminu S, McMurray, Claire, Pandey, Sarojini, McKenna, James P, Nelson, Andrew, Young, Gregory R, McCann, Clare M, and Elliott, Scott
Subjects: Emerging Infectious Diseases, Infectious Diseases, Lung, Pneumonia, Good Health and Well Being, Animals, Antibodies, Neutralizing, Antibodies, Viral, COVID-19, Cell Line, Chlorocebus aethiops, HEK293 Cells, Humans, Immune Evasion, Mutation, Pandemics, Phylogeny, Protein Binding, Recurrence, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Vero Cells, COVID-19 Genomics UK (COG-UK) Consortium, Alpha variant, B.1.1.7, antibody escape, deletion, infectivity, neutralizing antibodies, resistance, spike mutation, Biochemistry and Cell Biology, Medical Physiology
Abstract: We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted.
Published: 2021

4. Medicine Maker: An Outreach Activity for Pharmaceutical Manufacturing and Health Literacy

Author: McHugh, Martin, Hayes, Sarah, Tajber, Lidia, and Ryan, Laurie
Abstract: Public engagement in medicine has become more important in promoting population health management and literacy. Medicine is a topic of great societal importance, and many public engagement activities have been developed to promote this area. However, they often narrowly focus on patient groups, diseases, a singular pharmaceutical drug or analytical technique. Despite the importance of these activities, general audiences are still heavily reliant on doctors and pharmacists for information about their medicine and lack basic knowledge around medication use and personal safety. Given this, a broader engagement approach is warranted to target health literacy among the wider public. "Medicine Maker" is a hands-on public engagement workshop that provides audiences with the opportunity to "manufacture" and inspect the quality of proxy or "dummy" medicine through guided inquiry. Here, we detail the development of the Medicine Maker workshop from its origins in the teaching of Irish third-level pharmacy students, to its initial application with a variety of lay audiences. Formal and informal feedback from participants indicates that the workshop can help foster a more critical understanding of medicine manufacturing, quality control, and personal health.
Published: 2022
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5. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

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

Author: Mackey Katrina, McHugh Martin, and McGlacken Gerard P.
Subjects: engagement, hooks, interest, organic chemistry, relevancy, Chemistry, QD1-999
Abstract: Organic chemistry often represents a key impasse for students during their third level science education. Both intrinsic and extrinsic factors contribute to perceived difficulties in learning the subject. Moreover, the teaching of multi-step organic synthesis at third level has well-documented challenges. At University College Cork (UCC), we have adopted a strategy to engage students at the mid to late degree stage using an innovative teaching hook, to inspire interest and engagement. The approach was taken to outline chronologically some of the seminal breakthroughs in synthesis, and organic chemistry more generally, from the 1950 s to a few of the current leaders of today. Importantly the focus is on the people, the circumstance and the stories surrounding them. As a relevance-based hooking strategy grounded in a storytelling pedagogy, the goal was to inform students of the potential in organic chemistry and thus spark their interest for the subsequent lectures. Over multiple interventions, feedback from students has been highly positive. We posit that the design framework behind the ‘The People and Personalities’ could be adapted to many disciplines in a similarly successful manner. Overall, this approach proved inspirational for students, and was a most timely intervention in their degree program.
Published: 2022
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7. Bacterial and fungal communities in tracheal aspirates of intubated COVID-19 patients: a pilot study

Author: Ruiz-Rodriguez, Alicia, Lusarreta-Parga, Paula, de Steenhuijsen Piters, Wouter A. A., Koppensteiner, Lilian, Balcazar-Lopez, Carlos E., Campbell, Robyn, Dewar, Rebecca, McHugh, Martin P., Dockrell, David, Templeton, Kate E., and Bogaert, Debby
Published: 2022
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8. Anchoring Ocean Literacy: Participatory iBook Design within Secondary Science Classrooms

Author: McHugh, Martin, McCauley, Veronica, Davison, Kevin, Raine, Robin, and Grehan, Anthony
Abstract: This article elucidates a participatory design process in which a prototype iBook was embedded within the context of secondary science classrooms through multiple interventions. The fundamental design intention of the iBook is to increase students' ocean literacy in a curriculum that lacks marine science. Two e-learning ecologies were identified across two schools; an iPad school and non-iPad school. Participants include two second-year science classes (14-15-year-olds) and their respective teachers. Science teachers were asked to implement the iBook, based on their appraisal, as an accompaniment to their lessons throughout three interventions. Qualitative data took the form of teacher interviews, teacher reflections and student exit cards. Findings illuminate emergent design principles of iBooks that enthuse students with content; mainly to draw upon their personal interest corresponding to interactive technologies. The benefits of participatory design research are highlighted with reference to augmenting student ocean literacy in the science classroom.
Published: 2020
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9. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

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

Author: Koshy, Cherian, Ash, Amy, Wise, Emma, Moore, Nathan, Mori, Matilde, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Fairley, Derek J, Curran, Tanya, McKenna, James P, Adams, Helen, Fraser, Christophe, Golubchik, Tanya, Bonsall, David, Hassan-Ibrahim, Mohammed O, Malone, Cassandra S, Cogger, Benjamin J, Wantoch, Michelle, Reynolds, Nicola, Warne, Ben, Maksimovic, Joshua, Spellman, Karla, McCluggage, Kathryn, John, Michaela, Beer, Robert, Afifi, Safiah, Morgan, Sian, Marchbank, Angela, Price, Anna, Kitchen, Christine, Gulliver, Huw, Merrick, Ian, Southgate, Joel, Guest, Martyn, Munn, Robert, Workman, Trudy, Connor, Thomas R, Fuller, William, Bresner, Catherine, Snell, Luke B, Patel, Amita, Charalampous, Themoula, Nebbia, Gaia, Batra, Rahul, Edgeworth, Jonathan, Robson, Samuel C, Beckett, Angela H, Aanensen, David M, Underwood, Anthony P, Yeats, Corin A, Abudahab, Khalil, Taylor, Ben EW, Menegazzo, Mirko, Clark, Gemma, Smith, Wendy, Khakh, Manjinder, Fleming, Vicki M, Lister, Michelle M, Howson-Wells, Hannah C, Berry, Louise, Boswell, Tim, Joseph, Amelia, Willingham, Iona, Jones, Carl, Holmes, Christopher, Bird, Paul, Helmer, Thomas, Fallon, Karlie, Tang, Julian, Raviprakash, Veena, Campbell, Sharon, Sheriff, Nicola, Blakey, Victoria, Williams, Lesley-Anne, Loose, Matthew W, Holmes, Nadine, Moore, Christopher, Carlile, Matthew, Wright, Victoria, Sang, Fei, Debebe, Johnny, Coll, Francesc, Signell, Adrian W, Betancor, Gilberto, Wilson, Harry D, Eldirdiri, Sahar, Kenyon, Anita, Davis, Thomas, Pybus, Oliver G, du Plessis, Louis, Zarebski, Alex E, Raghwani, Jayna, Kraemer, Moritz UG, Francois, Sarah, Attwood, Stephen W, Vasylyeva, Tetyana I, Escalera Zamudio, Marina, Gutierrez, Bernardo, Torok, M. Estee, Hamilton, William L, Goodfellow, Ian G, Hall, Grant, Jahun, Aminu S, Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte L, Georgana, Iliana, Moses, Samuel, Lowe, Hannah, Bedford, Luke, Moore, Jonathan, Stonehouse, Susanne, Fisher, Chloe L, Awan, Ali R, BoYes, John, Breuer, Judith, Harris, Kathryn Ann, Brown, Julianne Rose, Shah, Divya, Atkinson, Laura, Lee, Jack CD, Storey, Nathaniel, Flaviani, Flavia, Alcolea-Medina, Adela, Williams, Rebecca, Vernet, Gabrielle, Chapman, Michael R, Levett, Lisa J, Heaney, Judith, Chatterton, Wendy, Pusok, Monika, Xu-McCrae, Li, Smith, Darren L, Bashton, Matthew, Young, Gregory R, Holmes, Alison, Randell, Paul Anthony, Cox, Alison, Madona, Pinglawathee, Bolt, Frances, Price, James, Mookerjee, Siddharth, Ragonnet-Cronin, Manon, Nascimento, Fabricia F., Jorgensen, David, Siveroni, Igor, Johnson, Rob, Boyd, Olivia, Geidelberg, Lily, Volz, Erik M, Rowan, Aileen, Taylor, Graham P, Smollett, Katherine L, Loman, Nicholas J, Quick, Joshua, McMurray, Claire, Stockton, Joanne, Nicholls, Sam, Rowe, Will, Poplawski, Radoslaw, McNally, Alan, Martinez Nunez, Rocio T, Mason, Jenifer, Robinson, Trevor I, O'Toole, Elaine, Watts, Joanne, Breen, Cassie, Cowell, Angela, Sluga, Graciela, Machin, Nicholas W, Ahmad, Shazaad S Y, George, Ryan P, Halstead, Fenella, Sivaprakasam, Venkat, Hogsden, Wendy, Illingworth, Chris J, Jackson, Chris, Thomson, Emma C, Shepherd, James G, Asamaphan, Patawee, Niebel, Marc O, Li, Kathy K, Shah, Rajiv N, Jesudason, Natasha G, Tong, Lily, Broos, Alice, Mair, Daniel, Nichols, Jenna, Carmichael, Stephen N, Nomikou, Kyriaki, Aranday-Cortes, Elihu, Johnson, Natasha, Starinskij, Igor, da Silva Filipe, Ana, Robertson, David L, Orton, Richard J, Hughes, Joseph, Vattipally, Sreenu, Singer, Joshua B, Nickbakhsh, Seema, Hale, Antony D, Macfarlane-Smith, Louissa R, Harper, Katherine L, Carden, Holli, Taha, Yusri, Payne, Brendan AI, Burton-Fanning, Shirelle, Waugh, Sheila, Collins, Jennifer, Eltringham, Gary, Rushton, Steven, O'Brien, Sarah, Bradley, Amanda, Maclean, Alasdair, Mollett, Guy, Blacow, Rachel, Templeton, Kate E, McHugh, Martin P, Dewar, Rebecca, Wastenge, Elizabeth, Dervisevic, Samir, Stanley, Rachael, Meader, Emma J, Coupland, Lindsay, Smith, Louise, Graham, Clive, Barton, Edward, Padgett, Debra, Scott, Garren, Swindells, Emma, Greenaway, Jane, Nelson, Andrew, McCann, Clare M, Yew, Wen C, Andersson, Monique, Peto, Timothy, Justice, Anita, Eyre, David, Crook, Derrick, Sloan, Tim J, Duckworth, Nichola, Walsh, Sarah, Chauhan, Anoop J, Glaysher, Sharon, Bicknell, Kelly, Wyllie, Sarah, Elliott, Scott, Lloyd, Allyson, Impey, Robert, Levene, Nick, Monaghan, Lynn, Bradley, Declan T, Wyatt, Tim, Allara, Elias, Pearson, Clare, Osman, Husam, Bosworth, Andrew, Robinson, Esther, Muir, Peter, Vipond, Ian B, Hopes, Richard, Pymont, Hannah M, Hutchings, Stephanie, Curran, Martin D, Parmar, Surendra, Lackenby, Angie, Mbisa, Tamyo, Platt, Steven, Miah, Shahjahan, Bibby, David, Manso, Carmen, Hubb, Jonathan, Chand, Meera, Dabrera, Gavin, Ramsay, Mary, Bradshaw, Daniel, Thornton, Alicia, Myers, Richard, Schaefer, Ulf, Groves, Natalie, Gallagher, Eileen, Lee, David, Williams, David, Ellaby, Nicholas, Harrison, Ian, Hartman, Hassan, Manesis, Nikos, Patel, Vineet, Bishop, Chloe, Chalker, Vicki, Ledesma, Juan, Twohig, Katherine A, Holden, Matthew T.G., Shaaban, Sharif, Birchley, Alec, Adams, Alexander, Davies, Alisha, Gaskin, Amy, Plimmer, Amy, Gatica-Wilcox, Bree, McKerr, Caoimhe, Moore, Catherine, Williams, Chris, Heyburn, David, De Lacy, Elen, Hilvers, Ember, Downing, Fatima, Shankar, Giri, Jones, Hannah, Asad, Hibo, Coombes, Jason, Watkins, Joanne, Evans, Johnathan M, Fina, Laia, Gifford, Laura, Gilbert, Lauren, Graham, Lee, Perry, Malorie, Morgan, Mari, Bull, Matthew, Cronin, Michelle, Pacchiarini, Nicole, Craine, Noel, Jones, Rachel, Howe, Robin, Corden, Sally, Rey, Sara, Kumziene-SummerhaYes, Sara, Taylor, Sarah, Cottrell, Simon, Jones, Sophie, Edwards, Sue, O'Grady, Justin, Page, Andrew J, Mather, Alison E, Baker, David J, Rudder, Steven, Aydin, Alp, Kay, Gemma L, Trotter, Alexander J, Alikhan, Nabil-Fareed, de Oliveira Martins, Leonardo, Le-Viet, Thanh, Meadows, Lizzie, Casey, Anna, Ratcliffe, Liz, Simpson, David A, Molnar, Zoltan, Thompson, Thomas, Acheson, Erwan, Masoli, Jane AH, Knight, Bridget A, Ellard, Sian, Auckland, Cressida, Jones, Christopher R, Mahungu, Tabitha W, Irish-Tavares, Dianne, Haque, Tanzina, Hart, Jennifer, Witele, Eric, Fenton, Melisa Louise, Dadrah, Ashok, Symmonds, Amanda, Saluja, Tranprit, Bourgeois, Yann, Scarlett, Garry P, Loveson, Katie F, Goudarzi, Salman, Fearn, Christopher, Cook, Kate, Dent, Hannah, Paul, Hannah, Partridge, David G, Raza, Mohammad, Evans, Cariad, Johnson, Kate, Liggett, Steven, Baker, Paul, Bonner, Stephen, Essex, Sarah, Lyons, Ronan A, Saeed, Kordo, Mahanama, Adhyana I.K, Samaraweera, Buddhini, Silveira, Siona, Pelosi, Emanuela, Wilson-Davies, Eleri, Williams, Rachel J, Kristiansen, Mark, Roy, Sunando, Williams, Charlotte A, Cotic, Marius, Bayzid, Nadua, Westhorpe, Adam P, Hartley, John A, Jannoo, Riaz, Lowe, Helen L, Karamani, Angeliki, Ensell, Leah, Prieto, Jacqui A, Jeremiah, Sarah, Grammatopoulos, Dimitris, Pandey, Sarojini, Berry, Lisa, Jones, Katie, Richter, Alex, Beggs, Andrew, Best, Angus, Percival, Benita, Mirza, Jeremy, Megram, Oliver, Mayhew, Megan, Crawford, Liam, Ashcroft, Fiona, Moles-Garcia, Emma, Cumley, Nicola, Smith, Colin P, Bucca, Giselda, Hesketh, Andrew R, Blane, Beth, Girgis, Sophia T, Leek, Danielle, Sridhar, Sushmita, Forrest, Sally, Cormie, Claire, Gill, Harmeet K, Dias, Joana, Higginson, Ellen E, Maes, Mailis, Young, Jamie, Kermack, Leanne M, Gupta, Ravi Kumar, Ludden, Catherine, Peacock, Sharon J, Palmer, Sophie, Churcher, Carol M, Hadjirin, Nazreen F, Carabelli, Alessandro M, Brooks, Ellena, Smith, Kim S, Galai, Katerina, McManus, Georgina M, Ruis, Chris, Davidson, Rose K, Rambaut, Andrew, Williams, Thomas, Balcazar, Carlos E, Gallagher, Michael D, O'Toole, Áine, Rooke, Stefan, Hill, Verity, Williamson, Kathleen A, Stanton, Thomas D, Michell, Stephen L, Bewshea, Claire M, Temperton, Ben, Michelsen, Michelle L, Warwick-Dugdale, Joanna, Manley, Robin, Farbos, Audrey, Harrison, James W, Sambles, Christine M, Studholme, David J, Jeffries, Aaron R, Darby, Alistair C, Hiscox, Julian A, Paterson, Steve, Iturriza-Gomara, Miren, Jackson, Kathryn A, Lucaci, Anita O, Vamos, Edith E, Hughes, Margaret, Rainbow, Lucille, Eccles, Richard, Nelson, Charlotte, Whitehead, Mark, Turtle, Lance, Haldenby, Sam T, Gregory, Richard, Gemmell, Matthew, Wierzbicki, Claudia, Webster, Hermione J, de Silva, Thushan I, Smith, Nikki, Angyal, Adrienn, Lindsey, Benjamin B, Groves, Danielle C, Green, Luke R, Wang, Dennis, Freeman, Timothy M, Parker, Matthew D, Keeley, Alexander J, Parsons, Paul J, Tucker, Rachel M, Brown, Rebecca, Wyles, Matthew, Whiteley, Max, Zhang, Peijun, Gallis, Marta, Louka, Stavroula F, Constantinidou, Chrystala, Unnikrishnan, Meera, Ott, Sascha, Cheng, Jeffrey K.J., Bridgewater, Hannah E., Frost, Lucy R., Taylor-Joyce, Grace, Stark, Richard, Baxter, Laura, Alam, Mohammad T., Brown, Paul E, Aggarwal, Dinesh, Cerda, Alberto C, Merrill, Tammy V, Wilson, Rebekah E, McClure, Patrick C, Chappell, Joseph G, Tsoleridis, Theocharis, Ball, Jonathan, Buck, David, Todd, John A, Green, Angie, Trebes, Amy, MacIntyre-Cockett, George, de Cesare, Mariateresa, Alderton, Alex, Amato, Roberto, Ariani, Cristina V, Beale, Mathew A, Beaver, Charlotte, Bellis, Katherine L, Betteridge, Emma, Bonfield, James, Danesh, John, Dorman, Matthew J, Drury, Eleanor, Farr, Ben W, Foulser, Luke, Goncalves, Sonia, Goodwin, Scott, Gourtovaia, Marina, Harrison, Ewan M, Jackson, David K, Jamrozy, Dorota, Johnston, Ian, Kane, Leanne, Kay, Sally, Keatley, Jon-Paul, Kwiatkowski, Dominic, Langford, Cordelia F, Lawniczak, Mara, Letchford, Laura, Livett, Rich, Lo, Stephanie, Martincorena, Inigo, McGuigan, Samantha, Nelson, Rachel, Palmer, Steve, Park, Naomi R, Patel, Minal, Prestwood, Liam, Puethe, Christoph, Quail, Michael A, Rajatileka, Shavanthi, Scott, Carol, Shirley, Lesley, Sillitoe, John, Spencer Chapman, Michael H, Thurston, Scott AJ, Tonkin-Hill, Gerry, Weldon, Danni, Rajan, Diana, Bronner, Iraad F, Aigrain, Louise, Redshaw, Nicholas M, Lensing, Stefanie V, Davies, Robert, Whitwham, Andrew, Liddle, Jennifier, Lewis, Kevin, Tovar-Corona, Jaime M, Leonard, Steven, Durham, Jillian, Bassett, Andrew R, McCarthy, Shane, Moll, Robin J, James, Keith, Oliver, Karen, Makunin, Alex, Barrett, Jeff, Gunson, Rory N, Graham, Mark S, Sudre, Carole H, May, Anna, Antonelli, Michela, Murray, Benjamin, Varsavsky, Thomas, Kläser, Kerstin, Canas, Liane S, Molteni, Erika, Modat, Marc, Drew, David A, Nguyen, Long H, Polidori, Lorenzo, Selvachandran, Somesh, Hu, Christina, Capdevila, Joan, Hammers, Alexander, Chan, Andrew T, Wolf, Jonathan, Spector, Tim D, Steves, Claire J, and Ourselin, Sebastien
Published: 2021
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11. Evaluation of the molecular detection of ciprofloxacin resistance in Neisseria gonorrhoeae by the ResistancePlus GC assay (SpeeDx)

Author: Cotton, Seb, McHugh, Martin P, Etherson, Michelle, Shepherd, Jill, and Templeton, Kate E
Published: 2021
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12. Top Tips for Designing and Managing a Public Engagement Laboratory.

Author: McHugh, Martin, Eren, Ebru, Guralp, Genco, Hari, Krishna, Guerin, Sarah, Hayes, Sarah, O'Hehir, Colm, O'Sullivan, Eamonn, Zauers, Alida, and Tyndall, Caitriona
Published: 2024
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13. Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium.

Author: McHugh, Martin P, Pettigrew, Kerry A, Taori, Surabhi, Evans, Thomas J, Leanord, Alistair, Gillespie, Stephen H, Templeton, Kate E, and Holden, Matthew T G
Subjects: *ENTEROCOCCUS faecium, *DRUG resistance in microorganisms, *MOBILE genetic elements, *GENETIC variation, *GENES, *PLASMIDS
Abstract: Background WGS is increasingly being applied to healthcare-associated vancomycin-resistant Enterococcus faecium (VREfm) outbreaks. Within-patient diversity could complicate transmission resolution if single colonies are sequenced from identified cases. Objectives Determine the impact of within-patient diversity on transmission resolution of VREfm. Materials and methods Fourteen colonies were collected from VREfm positive rectal screens, single colonies were collected from clinical samples and Illumina WGS was performed. Two isolates were selected for Oxford Nanopore sequencing and hybrid genome assembly to generate lineage-specific reference genomes. Mapping to closely related references was used to identify genetic variations and closely related genomes. A transmission network was inferred for the entire genome set using Phyloscanner. Results and discussion In total, 229 isolates from 11 patients were sequenced. Carriage of two or three sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within genomes from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies. Conclusions Patients can carry multiple sequence types of VREfm, and even within related lineages the presence of mobile genetic elements and antimicrobial resistance genes can vary. VREfm within-patient diversity could be considered in future to aid accurate resolution of transmission networks. [ABSTRACT FROM AUTHOR]
Published: 2024
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14. Detection of Norovirus by BD MAX™, Xpert® Norovirus, and xTAG® Gastrointestinal Pathogen Panel in stool and vomit samples

Author: McHugh, Martin P., Guerendiain, Daniel, Hardie, Alison, Kenicer, Juliet, MacKenzie, Laura, and Templeton, Kate E.
Published: 2018
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15. Comparison of Unyvero P55 Pneumonia Cartridge, in-house PCR and culture for the identification of respiratory pathogens and antibiotic resistance in bronchoalveolar lavage fluids in the critical care setting

Author: Gadsby, Naomi J., McHugh, Martin P., Forbes, Callum, MacKenzie, Laura, Hamilton, Stephen K. D., Griffith, David M., and Templeton, Kate E.
Published: 2019
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16. Reply to Zelyas and Robinson

Author: Gadsby, Naomi J., Russell, Clark D., McHugh, Martin P., Mark, Harriet, Morris, Andrew Conway, Laurenson, Ian F., Hill, Adam T., and Templeton, Kate E.
Published: 2016

17. Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia

Author: Gadsby, Naomi J., Russell, Clark D., McHugh, Martin P., Mark, Harriet, Morris, Andrew Conway, Laurenson, Ian F., Hill, Adam T., and Templeton, Kate E.
Published: 2016

18. Discordance between semi-quantitative nucleic acid detection of bacteria and quantitative bacteriology in sputum from patients with pneumonia.

Author: Gadsby, Naomi J., Dunn, James J., Johnson, Coreen L., McQuillan, Taylor, McHugh, Martin P., Templeton, Kate E., Rodriguez-Barradas, Maria C., and Musher, Daniel M.
Published: 2023
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19. Effects of microwaves on fungal pathogens of wheat seed.

Author: Knox, Oliver G.G., McHugh, Martin J., Fountaine, James M., and Havis, Neil D.
Subjects: PATHOGENIC fungi, WHEAT seeds, PLANT DNA, MICROWAVES, DNA analysis, GERMINATION
Abstract: Abstract: An investigation into the effect of microwaves on the fungal pathogens of winter wheat was undertaken. This was achieved by microwaving seed at 0, 15, 30 and 45 s. Agar plate tests and DNA analysis were then used to assess pathogen loads and germination, emergence and tetrazolium tests used to investigate seed viability after treatment. Throughout all treatment times, microwaving significantly reduced levels of contamination on seed and was particularly effective at controlling Fusarium spp. and Microdochium nivale. Conventional seed survived microwave treatment better than organic seed. Subsequent analysis and experimentation revealed that seed moisture content was inherently linked to losses in seed vigour upon exposure to microwaves. Seed levels of fungal DNA did not decrease with the observed loss of culturable fungal propagules, thus fungal death was attributed to heat and desiccation rather than denaturing DNA. Microwave treatment of wheat seed may offer a method to significantly reduce fungal loads on both conventional and organic wheat seed. [Copyright &y& Elsevier]
Published: 2013
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20. Breandán S. Mac Aodha, 1934-2001.

Author: McHugh, Martin F.
Subjects: MAC Aodha, Breandan S.
Abstract: Presents an obituary for Breandán S. Mac Aodha, a member of the American Name Society.
Published: 2002
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21. Stochastic background search correlating ALLEGRO with LIGO engineering data.

Author: Whelan, John T., Daw, Edward, Heng, Ik Siong, McHugh, Martin P., and Lazzarini, Albert
Published: 2003
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22. Development of an amplicon-based sequencing approach in response to the global emergence of mpox.

Author: Chen NFG, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak CJ, Sevinsky J, Libuit K, Park DJ, Hemarajata P, Garrigues JM, Green NM, Sierra-Patev S, Carpenter-Azevedo K, Huard RC, Pearson C, Incekara K, Nishimura C, Huang JP, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes JP, Aquino C, Savino IM, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa HH, McHugh MP, Maloney DM, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton KE, Churchwell G, Lee PA, Pedrosa M, McGruder B, Schmedes S, Plumb MR, Wang X, Barcellos RB, Godinho FMS, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND, Gallagher GR, and Vogels CBF
Subjects: Humans, Pandemics, SARS-CoV-2 genetics, Genomics, COVID-19 epidemiology, Mpox (monkeypox), Zika Virus, Zika Virus Infection
Abstract: The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon-based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole-genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: NDG is a consultant for Tempus Labs and the National Basketball Association for work related to COVID-19. All other authors have declared that no competing interests exist., (Copyright: © 2023 Chen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Published: 2023
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23. Analysis of the ARTIC V4 and V4.1 SARS-CoV-2 primers and their impact on the detection of Omicron BA.1 and BA.2 lineage-defining mutations.

Author: Ulhuq FR, Barge M, Falconer K, Wild J, Fernandes G, Gallagher A, McGinley S, Sugadol A, Tariq M, Maloney D, Kenicer J, Dewar R, Templeton K, and McHugh MP
Subjects: Humans, SARS-CoV-2 genetics, Mutation, Binding Sites, COVID-19
Abstract: The ARTIC protocol uses a multiplexed PCR approach with two primer pools tiling the entire SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genome. Primer pool updates are necessary for accurate amplicon sequencing of evolving SARS-CoV-2 variants with novel mutations. The suitability of the ARTIC V4 and updated V4.1 primer scheme was assessed using whole genome sequencing of Omicron from clinical samples using Oxford Nanopore Technology. Analysis of Omicron BA.1 genomes revealed that 93.22 % of clinical samples generated improved genome coverage at 50× read depth with V4.1 primers when compared to V4 primers. Additionally, the V4.1 primers improved coverage of BA.1 across amplicons 76 and 88, which resulted in the detection of the variant-defining mutations G22898A, A26530G and C26577G. The Omicron BA.2 sub-variant (VUI-22JAN-01) replaced BA.1 as the dominant variant by March 2022, and analysis of 168 clinical samples showed reduced coverage across amplicons 15 and 75. Upon further interrogation of primer binding sites, a mutation at C4321T [present in 163/168 (97 %) of samples] was identified as a possible cause of complete dropout of amplicon 15. Furthermore, two mutations were identified within the primer binding regions for amplicon 75: A22786C (present in 90 % of samples) and C22792T (present in 12.5 % of samples). Together, these mutations may result in reduced coverage of amplicon 75, and further primer updates would allow the identification of the two BA.2-defining mutations present in amplicon 75: A22688G and T22679C. This work highlights the need for ongoing surveillance of primer matches as circulating variants evolve and change.
Published: 2023
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24. Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus.

Author: Chen NFG, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak CJ, Sevinsky J, Libuit K, Park DJ, Hemarajata P, Garrigues JM, Green NM, Sierra-Patev S, Carpenter-Azevedo K, Huard RC, Pearson C, Incekara K, Nishimura C, Huang JP, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes JP, Aquino C, Savino IM, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa HH, McHugh MP, Maloney DM, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton KE, Churchwell G, Lee PA, Pedrosa M, McGruder B, Schmedes S, Plumb MR, Wang X, Barcellos RB, Godinho FMS, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND, Gallagher GR, and Vogels CBF
Abstract: The 2022 multi-country monkeypox (mpox) outbreak concurrent with the ongoing COVID-19 pandemic has further highlighted the need for genomic surveillance and rapid pathogen whole genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for SARS-CoV-2. Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical samples that tested presumptive positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR cycle threshold below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.
Published: 2023
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25. Genomics-informed outbreak investigations of SARS-CoV-2 using civet.

Author: O'Toole Á, Hill V, Jackson B, Dewar R, Sahadeo N, Colquhoun R, Rooke S, McCrone JT, Duggan K, McHugh MP, Nicholls SM, Poplawski R, Aanensen D, Holden M, Connor T, Loman N, Goodfellow I, Carrington CVF, Templeton K, and Rambaut A
Abstract: The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different 'catchments' and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 O’Toole et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Published: 2022
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26. Presence of optrA- mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing.

Author: McHugh MP, Parcell BJ, Pettigrew KA, Toner G, Khatamzas E, El Sakka N, Karcher AM, Walker J, Weir R, Meunier D, Hopkins KL, Woodford N, Templeton KE, Gillespie SH, and Holden MTG
Subjects: Animals, Anti-Bacterial Agents pharmacology, Drug Resistance, Bacterial genetics, Enterococcus faecalis genetics, Linezolid pharmacology, Microbial Sensitivity Tests, Multilocus Sequence Typing, Plasmids genetics, Enterococcus faecium genetics, Gram-Positive Bacterial Infections
Abstract: Transferable linezolid resistance due to optrA , poxtA , cfr and cfr -like genes is increasingly detected in enterococci associated with animals and humans globally. We aimed to characterize the genetic environment of optrA in linezolid-resistant Enterococcus faecalis isolates from Scotland. Six linezolid-resistant E. faecalis isolated from urogenital samples were confirmed to carry the optrA gene by PCR. Short read (Illumina) sequencing showed the isolates were genetically distinct (>13900 core SNPs) and belonged to different MLST sequence types. Plasmid contents were examined using hybrid assembly of short and long read (Oxford Nanopore MinION) sequencing technologies. The optrA gene was located on distinct plasmids in each isolate, suggesting that transfer of a single plasmid did not contribute to optrA dissemination in this collection. pTM6294-2, BX5936-1 and pWE0438-1 were similar to optrA -positive plasmids from China and Japan, while the remaining three plasmids had limited similarity to other published examples. We identified the novel Tn 6993 transposon in pWE0254-1 carrying linezolid ( optrA ), macrolide ( ermB ) and spectinomycin [ANT(9)-Ia] resistance genes. OptrA amino acid sequences differed by 0-20 residues. We report multiple variants of optrA on distinct plasmids in diverse strains of E. faecalis . It is important to identify the selection pressures driving the emergence and maintenance of resistance against linezolid to retain the clinical utility of this antibiotic.
Published: 2022
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27. Author Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

Author: da Silva Filipe A, Shepherd JG, Williams T, Hughes J, Aranday-Cortes E, Asamaphan P, Ashraf S, Balcazar C, Brunker K, Campbell A, Carmichael S, Davis C, Dewar R, Gallagher MD, Gunson R, Hill V, Ho A, Jackson B, James E, Jesudason N, Johnson N, McWilliam Leitch EC, Li K, MacLean A, Mair D, McAllister DA, McCrone JT, McDonald SE, McHugh MP, Morris AK, Nichols J, Niebel M, Nomikou K, Orton RJ, O'Toole Á, Palmarini M, Parcell BJ, Parr YA, Rambaut A, Rooke S, Shaaban S, Shah R, Singer JB, Smollett K, Starinskij I, Tong L, Sreenu VB, Wastnedge E, Holden MTG, Robertson DL, Templeton K, and Thomson EC
Published: 2021
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28. Publisher Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

Author: da Silva Filipe A, Shepherd JG, Williams T, Hughes J, Aranday-Cortes E, Asamaphan P, Ashraf S, Balcazar C, Brunker K, Campbell A, Carmichael S, Davis C, Dewar R, Gallagher MD, Gunson R, Hill V, Ho A, Jackson B, James E, Jesudason N, Johnson N, McWilliam Leitch EC, Li K, MacLean A, Mair D, McAllister DA, McCrone JT, McDonald SE, McHugh MP, Morris AK, Nichols J, Niebel M, Nomikou K, Orton RJ, O'Toole Á, Palmarini M, Parcell BJ, Parr YA, Rambaut A, Rooke S, Shaaban S, Shah R, Singer JB, Smollett K, Starinskij I, Tong L, Sreenu VB, Wastnedge E, Holden MTG, Robertson DL, Templeton K, and Thomson EC
Published: 2021
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29. Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

Author: da Silva Filipe A, Shepherd JG, Williams T, Hughes J, Aranday-Cortes E, Asamaphan P, Ashraf S, Balcazar C, Brunker K, Campbell A, Carmichael S, Davis C, Dewar R, Gallagher MD, Gunson R, Hill V, Ho A, Jackson B, James E, Jesudason N, Johnson N, McWilliam Leitch EC, Li K, MacLean A, Mair D, McAllister DA, McCrone JT, McDonald SE, McHugh MP, Morris AK, Nichols J, Niebel M, Nomikou K, Orton RJ, O'Toole Á, Palmarini M, Parcell BJ, Parr YA, Rambaut A, Rooke S, Shaaban S, Shah R, Singer JB, Smollett K, Starinskij I, Tong L, Sreenu VB, Wastnedge E, Holden MTG, Robertson DL, Templeton K, and Thomson EC
Subjects: Adult, Aged, Europe epidemiology, Genome, Viral, High-Throughput Nucleotide Sequencing, Humans, Male, Middle Aged, Molecular Epidemiology, Phylogeny, SARS-CoV-2 isolation & purification, Spain epidemiology, Travel statistics & numerical data, COVID-19 epidemiology, COVID-19 virology, SARS-CoV-2 genetics
Abstract: Coronavirus disease 2019 (COVID-19) was first diagnosed in Scotland on 1 March 2020. During the first month of the outbreak, 2,641 cases of COVID-19 led to 1,832 hospital admissions, 207 intensive care admissions and 126 deaths. We aimed to identify the source and number of introductions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into Scotland using a combined phylogenetic and epidemiological approach. Sequencing of 1,314 SARS-CoV-2 viral genomes from available patient samples enabled us to estimate that SARS-CoV-2 was introduced to Scotland on at least 283 occasions during February and March 2020. Epidemiological analysis confirmed that early introductions of SARS-CoV-2 originated from mainland Europe (the majority from Italy and Spain). We identified subsequent early outbreaks in the community, within healthcare facilities and at an international conference. Community transmission occurred after 2 March, 3 weeks before control measures were introduced. Earlier travel restrictions or quarantine measures, both locally and internationally, would have reduced the number of COVID-19 cases in Scotland. The risk of multiple reintroduction events in future waves of infection remains high in the absence of population immunity.
Published: 2021
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30. Multicenter Evaluation of QIAstat-Dx Respiratory Panel V2 for Detection of Viral and Bacterial Respiratory Pathogens.

Author: Boers SA, Melchers WJG, Peters CJA, Toonen M, McHugh MP, Templeton KE, and Claas ECJ
Subjects: Bacteria genetics, Diagnostic Tests, Routine, Humans, Retrospective Studies, Molecular Diagnostic Techniques, Respiratory Tract Infections diagnosis
Abstract: QIAstat-Dx Respiratory Panel V2 (RP) is a novel molecular-method-based syndromic test for the simultaneous and rapid (∼70-min) detection of 18 viral and 3 bacterial pathogens causing respiratory infections. This report describes the first multicenter retrospective comparison of the performance of the QIAstat-Dx RP assay to the established ePlex Respiratory Pathogen Panel (RPP) assay, for which we used 287 respiratory samples from patients suspected with respiratory infections. The QIAstat-Dx RP assay detected 312 (92%) of the 338 respiratory targets that were detected by the ePlex RPP assay. Most of the discrepant results have been observed in the low-pathogen-load samples. In addition, the QIAstat-Dx RP assay detected 19 additional targets in 19 respiratory samples that were not detected by the ePlex RPP assay. Nine of these discordant targets were considered to represent true positives after discrepancy testing by a third method. The main advantage of the QIAstat-Dx system compared to other syndromic testing systems, including the ePlex RPP assay, is the ability to generate cycle threshold ( C T ) values, which could help with the interpretation of results. Taking the data together, this study showed good performance of the QIAstat-Dx RP assay in comparison to the ePlex RPP assay for the detection of respiratory pathogens. The QIAstat-Dx RP assay offers a new, rapid, and accurate sample-to-answer multiplex panel for the detection of the most common viral and bacterial respiratory pathogens and therefore has the potential to direct appropriate therapy and infection control precautions., (Copyright © 2020 Boers et al.)
Published: 2020
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31. Rapid molecular testing for Staphylococcus aureus bacteraemia improves clinical management.

Author: McHugh MP, Parcell BJ, MacKenzie FM, Templeton KE, and Scottish Microbiology And Virology Network Smvn Molecular Diagnostics Evaluation Group
Subjects: Bacteremia blood, Bacteremia microbiology, Blood microbiology, Humans, Prospective Studies, Staphylococcal Infections blood, Staphylococcal Infections microbiology, Staphylococcus aureus genetics, Bacteremia diagnosis, Blood Culture methods, Staphylococcal Infections diagnosis, Staphylococcus aureus isolation & purification
Abstract: Introduction. Staphylococcus aureus bacteraemia (SAB) causes significant morbidity and mortality. Standard diagnostic methods require 24-48 h to provide results, during which time management is guideline-based and may be suboptimal. Aim. Evaluate the impact of rapid molecular detection of S. aureus in positive blood culture bottle fluid on patient management. Methodology. Samples were tested prospectively at two clinical centres. Positive blood cultures with Gram-positive cocci in clusters on microscopy were tested with the Xpert MRSA/SA blood culture assay (Cepheid), as well as standard culture-based identification and antimicrobial sensitivity tests. Results were passed to clinical microbiologists in real time and used for patient management. Results. Of 264 blood cultures tested (184 and 80 from each centre), S. aureus was grown from 39 (14.8 %) with one identified as methicillin-resistant S. aureus ; all Xpert results agreed with culture results. Median turnaround time from culture flagging positive to result reporting for Xpert was 1.7 h, compared to 25.7 h for species identification by culture. Xpert results allowed early changes to management in 40 (16.8 %) patients, with Xpert positive patients starting specific therapy for SAB and Xpert negative patients stopping or avoiding empiric antimicrobials for SAB. Conclusion. Rapid and accurate detection of S. aureus with the Xpert MRSA/SA BC assay in positive blood culture bottles allowed earlier targeted patient management. Negative Xpert results are suggestive of coagulase negative staphylococci, allowing de-escalation of antimicrobial therapy if clinically appropriate.
Published: 2020
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32. Reduced turnaround time and improved diagnosis of invasive serogroup B Neisseria meningitidis and Streptococcus pneumoniae infections using a lyophilized quadruplex quantitative PCR.

Author: McHugh MP, Gray SJ, Kaczmarski EB, and Guiver M
Subjects: Bacterial Proteins genetics, Bacterial Proteins metabolism, Humans, Meningitis, Meningococcal microbiology, Neisseria meningitidis, Serogroup B classification, Neisseria meningitidis, Serogroup B genetics, Pneumococcal Infections microbiology, Streptococcus pneumoniae classification, Streptococcus pneumoniae genetics, Meningitis, Meningococcal diagnosis, Neisseria meningitidis, Serogroup B isolation & purification, Pneumococcal Infections diagnosis, Real-Time Polymerase Chain Reaction methods, Streptococcus pneumoniae isolation & purification
Abstract: Since 1996 the Meningococcal Reference Unit (MRU) in Manchester has provided a national service for PCR confirmation of meningococcal and pneumococcal disease. Neisseria meningitidis serogroup B is predominant in the UK, accounting for >60% of cases. In response to this, the MRU has developed a quadruplex quantitative PCR that detects N. meningitidis capsule transporter (ctrA), serogroup B sialyltransferase (siaDB), Streptococcus pneumoniae pneumolysin (ply) and an internal control. The assay was prepared in a ready-to-use lyophilized format by Applied Biosystems. Laboratory validation showed excellent performance in a specificity panel of 52 isolates and improved detection in comparison with the routine assay. Testing of 244 patient samples showed sensitivity of 93% [95% confidence interval (CI): 88-98%] for the ctrA assay, 95% (95% CI: 91-100%) for the siaDB assay and 100% (95% CI: 95-100%) for the ply assay. Specificity was 100% (95% CI: 98-100%) for both meningococcal targets and 95% (95% CI: 92-98%) for ply. The quadruplex also retained high performance in mixed samples and had acceptable reproducibility. After introduction of the quadruplex into routine use the turnaround time for N. meningitidis group B PCR confirmation reduced from 37 to 29 h and the internal control has proved useful for detecting inhibitory samples. The quadruplex assay provides rapid group B confirmation of meningococcal positive samples, enabling timely public health interventions for the most common disease-causing meningococcal serogroup in the UK.
Published: 2015
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32 results on '"McHugh, Martin P"'

1. An Observational Narrative of Student Reaction to Video Hooks

2. Genomic reconstruction of the SARS-CoV-2 epidemic in England

3. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

4. Medicine Maker: An Outreach Activity for Pharmaceutical Manufacturing and Health Literacy

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

6. Some people and personalities of organic chemistry: a teaching hook for mid-level university students

7. Bacterial and fungal communities in tracheal aspirates of intubated COVID-19 patients: a pilot study

8. Anchoring Ocean Literacy: Participatory iBook Design within Secondary Science Classrooms

9. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

10. Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

11. Evaluation of the molecular detection of ciprofloxacin resistance in Neisseria gonorrhoeae by the ResistancePlus GC assay (SpeeDx)

12. Top Tips for Designing and Managing a Public Engagement Laboratory.

13. Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium.

14. Detection of Norovirus by BD MAX™, Xpert® Norovirus, and xTAG® Gastrointestinal Pathogen Panel in stool and vomit samples

15. Comparison of Unyvero P55 Pneumonia Cartridge, in-house PCR and culture for the identification of respiratory pathogens and antibiotic resistance in bronchoalveolar lavage fluids in the critical care setting

16. Reply to Zelyas and Robinson

17. Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia

18. Discordance between semi-quantitative nucleic acid detection of bacteria and quantitative bacteriology in sputum from patients with pneumonia.

19. Effects of microwaves on fungal pathogens of wheat seed.

20. Breandán S. Mac Aodha, 1934-2001.

21. Stochastic background search correlating ALLEGRO with LIGO engineering data.

22. Development of an amplicon-based sequencing approach in response to the global emergence of mpox.

23. Analysis of the ARTIC V4 and V4.1 SARS-CoV-2 primers and their impact on the detection of Omicron BA.1 and BA.2 lineage-defining mutations.

24. Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus.

25. Genomics-informed outbreak investigations of SARS-CoV-2 using civet.

26. Presence of optrA- mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing.

27. Author Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

28. Publisher Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

29. Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

30. Multicenter Evaluation of QIAstat-Dx Respiratory Panel V2 for Detection of Viral and Bacterial Respiratory Pathogens.

31. Rapid molecular testing for Staphylococcus aureus bacteraemia improves clinical management.

32. Reduced turnaround time and improved diagnosis of invasive serogroup B Neisseria meningitidis and Streptococcus pneumoniae infections using a lyophilized quadruplex quantitative PCR.

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