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2. The Role of Fungi in Food Production and Processing

Author

John Pouris, Foteini Kolyva, Spyridoula Bratakou, Chrysovalantou Argyro Vogiatzi, Dimitrios Chaniotis, and Apostolos Beloukas

Subjects
fermentation, food processing, food safety, fungi, mycotoxin contamination, Technology, Engineering (General). Civil engineering (General), TA1-2040, Biology (General), QH301-705.5, Physics, QC1-999, Chemistry, QD1-999
Abstract

Fungi play an important and multifaceted role in the production and processing of food, influencing various stages from cultivation to consumption. This paper explores the complex relationship between fungi and food systems, highlighting their diverse contributions. Firstly, fungi serve as essential agents in food cultivation, aiding in the breakdown of organic matter and the recycling of nutrients, and promoting plant growth through symbiotic relationships. Moreover, fungi such as yeasts and molds are integral to fermentation processes, yielding a wide array of fermented foods and beverages with unique flavors and textures. Additionally, fungi are indispensable in the creation of enzymes and bioactive compounds utilized in food processing, enhancing the nutritional value, shelf life, and safety. However, certain fungal species pose significant challenges as food spoilage agents and mycotoxin producers, necessitating stringent quality control measures. Understanding the intricate interplay between fungi and food systems is essential for optimizing food production, ensuring food security, and mitigating the risks associated with fungal contamination. This paper synthesizes current research to elucidate the important role that fungus play in shaping the modern food industry and underscores the importance of ongoing scientific inquiry in harnessing their potential for sustainable and safe food production.

Published
2024
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4. Acclimation of the Grapevine Vitis vinifera L. cv. Assyrtiko to Water Deficit: Coordination of Structural and Functional Leaf Traits and the Dynamic of Calcium Oxalate Crystals

Author

Foteini Kolyva, Dimosthenis Nikolopoulos, Panagiota Bresta, Georgios Liakopoulos, George Karabourniotis, and Sophia Rhizopoulou

Subjects
alarm photosynthesis, chlorophyll fluorescence, grapevine, leaf gas exchange, water potential, water deficit, Botany, QK1-989
Abstract

Grapevine leaves contain abundant CaOx crystals located either within the mesophyll in the form of raphides, or in the bundle sheaths as druses. CaOx crystals function as internal carbon pools providing CO2 for a baseline level of photosynthesis, named “alarm photosynthesis”, despite closed stomata; thus, preventing the photoinhibition and the oxidative risk due to carbon starvation under adverse conditions. Structural and functional leaf traits of acclimated grapevine plants (Vitis vinifera L. cv. Assyrtiko) were investigated in response to water availability, in order to evaluate the dynamic functionality of CaOx. Leaf water potential, leaf area, leaf mass per area, stomatal properties, gas exchange parameters and performance index (PI) were decreased in leaves of vines acclimated to water deficit in comparison to the leaves of well-irrigated vines, although the chlorophyll fluorescence parameters showed that the operational efficiency of the photosystem II (PSII) photochemistry (Fv/Fm) did not change, indicating that the photosynthetic apparatus was not subjected to water stress. During the afternoon, more than half of the morning’s existing druses disappeared in the drought-acclimated leaves. Also, the raphides’ area of the drought-acclimated leaves was reduced more than that of the well-watered leaves. The substantial decomposition of druses under water deficit conditions compared to that of the raphides may have important implications for the maintenance of their different though overlapping roles. According to the results, it seems likely that, under water deficit conditions, a mechanism of “alarm photosynthesis” provides an additional tolerance trait in the leaves of Vitis vinifera cv. Assyrtiko; hence, leaf structure relates to function.

Published
2023
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6. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Author

Koshy, Cherian, Wise, Emma, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Mori, Matilde, Fairley, Derek J., Curran, Tanya, McKenna, James P., Adams, Helen, Fraser, Christophe, Golubchik, Tanya, Bonsall, David, Moore, Catrin, Caddy, Sarah L., Khokhar, Fahad A., 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., Charalampous, Themoula, Nebbia, Gaia, Batra, Rahul, Edgeworth, Jonathan, Robson, Samuel C., Beckett, Angela, Loveson, Katie F., Aanensen, David M., Underwood, Anthony P., Yeats, Corin A., Abudahab, Khalil, Taylor, Ben E.W., 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, Bird, Paul, Helmer, Thomas, Fallon, Karlie, Holmes, Christopher, Tang, Julian, Raviprakash, Veena, Campbell, Sharon, Sheriff, Nicola, 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., Feltwell, Theresa, Houldcroft, Charlotte J., Eldirdiri, Sahar, Kenyon, Anita, Davis, Thomas, Pybus, Oliver, du Plessis, Louis, Zarebski, Alex, Raghwani, Jayna, Kraemer, Moritz, Francois, Sarah, Attwood, Stephen, Vasylyeva, Tetyana, Torok, M. Estee, Hamilton, William L., Goodfellow, Ian G., Hall, Grant, Jahun, Aminu S., Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte L., Georgana, Iliana, Yakovleva, Anna, Meredith, Luke W., Moses, Samuel, Lowe, Hannah, Ryan, Felicity, Fisher, Chloe L., Awan, Ali R., Boyes, John, Breuer, Judith, Harris, Kathryn Ann, Brown, Julianne Rose, Shah, Divya, Atkinson, Laura, Lee, Jack C.D., Alcolea-Medina, Adela, Moore, Nathan, Cortes, Nicholas, Williams, Rebecca, Chapman, Michael R., Levett, Lisa J., Heaney, Judith, Smith, Darren L., Bashton, Matthew, Young, Gregory R., Allan, John, Loh, Joshua, Randell, Paul A., Cox, Alison, Madona, Pinglawathee, Holmes, Alison, Bolt, Frances, Price, James, Mookerjee, Siddharth, Rowan, Aileen, Taylor, Graham P., Ragonnet-Cronin, Manon, Nascimento, Fabricia F., Jorgensen, David, Siveroni, Igor, Johnson, Rob, Boyd, Olivia, Geidelberg, Lily, Volz, Erik M., Brunker, Kirstyn, Smollett, Katherine L., Loman, Nicholas J., Quick, Joshua, McMurray, Claire, Stockton, Joanne, Nicholls, Sam, Rowe, Will, Poplawski, Radoslaw, Martinez-Nunez, Rocio T., Mason, Jenifer, Robinson, Trevor I., O'Toole, Elaine, Watts, Joanne, Breen, Cassie, Cowell, Angela, Ludden, Catherine, Sluga, Graciela, Machin, Nicholas W., Ahmad, Shazaad S.Y., George, Ryan P., Halstead, Fenella, Sivaprakasam, Venkat, Thomson, Emma C., Shepherd, James G., Asamaphan, Patawee, Niebel, Marc O., Li, Kathy K., Shah, Rajiv N., Jesudason, Natasha G., Parr, Yasmin A., 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., Hale, Antony D., Macfarlane-Smith, Louissa R., Harper, Katherine L., Taha, Yusri, Payne, Brendan A.I., Burton-Fanning, Shirelle, Waugh, Sheila, Collins, Jennifer, Eltringham, Gary, Templeton, Kate E., McHugh, Martin P., Dewar, Rebecca, Wastenge, Elizabeth, Dervisevic, Samir, Stanley, Rachael, Prakash, Reenesh, Stuart, Claire, Elumogo, Ngozi, Sethi, Dheeraj K., Meader, Emma J., Coupland, Lindsay J., Potter, Will, Graham, Clive, Barton, Edward, Padgett, Debra, Scott, Garren, Swindells, Emma, Greenaway, Jane, Nelson, Andrew, Yew, Wen C., Resende Silva, Paola C., Andersson, Monique, Shaw, Robert, Peto, Timothy, Justice, Anita, Eyre, David, Crooke, Derrick, Hoosdally, Sarah, Sloan, Tim J., Duckworth, Nichola, Walsh, Sarah, Chauhan, Anoop J., Glaysher, Sharon, Bicknell, Kelly, Wyllie, Sarah, Butcher, Ethan, Elliott, Scott, Lloyd, Allyson, Impey, Robert, Levene, Nick, Monaghan, Lynn, Bradley, Declan T., Allara, Elias, Pearson, Clare, 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, Osman, Husam, Bosworth, Andrew, Robinson, Esther, 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., Wain, John, Webber, Mark A., Mather, Alison E., Baker, David J., Rudder, Steven, Yasir, Muhammad, Thomson, Nicholas M., Aydin, Alp, Tedim, Ana P., Kay, Gemma L., Trotter, Alexander J., Gilroy, Rachel A.J., Alikhan, Nabil-Fareed, de Oliveira Martins, Leonardo, Le-Viet, Thanh, Meadows, Lizzie, Kolyva, Anastasia, Diaz, Maria, Bell, Andrew, Gutierrez, Ana Victoria, Charles, Ian G., Adriaenssens, Evelien M., Kingsley, Robert A., Casey, Anna, Simpson, David A., Molnar, Zoltan, Thompson, Thomas, Acheson, Erwan, Masoli, Jane A.H., Knight, Bridget A., Hattersley, Andrew, Ellard, Sian, Auckland, Cressida, Mahungu, Tabitha W., Irish-Tavares, Dianne, Haque, Tanzina, Bourgeois, Yann, Scarlett, Garry P., Partridge, David G., Raza, Mohammad, Evans, Cariad, Johnson, Kate, Liggett, Steven, Baker, Paul, Essex, Sarah, Lyons, Ronan A., Caller, Laura G., Castellano, Sergi, Williams, Rachel J., Kristiansen, Mark, Roy, Sunando, Williams, Charlotte A., Dyal, Patricia L., Tutill, Helena J., Panchbhaya, Yasmin N., Forrest, Leysa M., Niola, Paola, Findlay, Jacqueline, Brooks, Tony T., Gavriil, Artemis, Mestek-Boukhibar, Lamia, Weeks, Sam, Pandey, Sarojini, Berry, Lisa, Jones, Katie, Richter, Alex, Beggs, Andrew, Smith, Colin P., Bucca, Giselda, Hesketh, Andrew R., Harrison, Ewan M., Peacock, Sharon J., Palmer, Sophie, Churcher, Carol M., Bellis, Katherine L., Girgis, Sophia T., Naydenova, Plamena, Blane, Beth, Sridhar, Sushmita, Ruis, Chris, Forrest, Sally, Cormie, Claire, Gill, Harmeet K., Dias, Joana, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Kermack, Leanne M., Hadjirin, Nazreen F., Aggarwal, Dinesh, Griffith, Luke, Swingler, Tracey, Davidson, Rose K., Rambaut, Andrew, Williams, Thomas, Balcazar, Carlos E., Gallagher, Michael D., O'Toole, Áine, Rooke, Stefan, Jackson, Ben, Colquhoun, Rachel, Ashworth, Jordan, Hill, Verity, McCrone, J.T., Scher, Emily, Yu, Xiaoyu, 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, Kwiatkowski, Dominic, 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, 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., McClure, Patrick C., Chappell, Joseph G., Tsoleridis, Theocharis, Ball, Jonathan, Grammatopoulos, Dimitris, Buck, David, Todd, John A., Green, Angie, Trebes, Amy, MacIntyre-Cockett, George, de Cesare, Mariateresa, Langford, Cordelia, Alderton, Alex, Amato, Roberto, Goncalves, Sonia, Jackson, David K., Johnston, Ian, Sillitoe, John, Palmer, Steve, Lawniczak, Mara, Berriman, Matt, Danesh, John, Livett, Rich, Shirley, Lesley, Farr, Ben, Quail, Mike, Thurston, Scott, Park, Naomi, Betteridge, Emma, Weldon, Danni, Goodwin, Scott, Nelson, Rachel, Beaver, Charlotte, Letchford, Laura, Jackson, David A., Foulser, Luke, McMinn, Liz, Prestwood, Liam, Kay, Sally, Kane, Leanne, Dorman, Matthew J., Martincorena, Inigo, Puethe, Christoph, Keatley, Jon-Paul, Tonkin-Hill, Gerry, Smith, Christen, Jamrozy, Dorota, Beale, Mathew A., Patel, Minal, Ariani, Cristina, Spencer-Chapman, Michael, Drury, Eleanor, Lo, Stephanie, Rajatileka, Shavanthi, Scott, Carol, James, Keith, Buddenborg, Sarah K., Berger, Duncan J., Patel, Gaurang, Garcia-Casado, Maria V., Dibling, Thomas, McGuigan, Samantha, Rogers, Hazel A., Hunter, Adam D., Souster, Emily, Neaverson, Alexandra S., Volz, Erik, McCrone, John T., O’Toole, Áine, Johnson, Robert, Rey, Sara M., Nicholls, Samuel M., Colquhoun, Rachel M., Shepherd, James, Pascall, David J., Shah, Rajiv, Jesudason, Natasha, Li, Kathy, Jarrett, Ruth, Goodfellow, Ian, and Pybus, Oliver G.

Published
2021
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7. Evaluation of treatment and long-term management of anaphylaxis in pediatric departments of Greece

Author

Chiampou, Evanthia, primary, Dourous, Konstantinos, additional, Moriki, Dafni, additional, Marina, Mitrogiorgou, additional, Anastasiou-Katsiardani, Anastasia, additional, Tanou, Kalliopi, additional, Grammeniatis, Vasilis, additional, Zisi, Anna, additional, Perikleous, Evanthia, additional, Galanakis, Emmanouil, additional, Lioudaki, Marilia, additional, Vrouvaki, Fonti, additional, Kolyva, Soultana, additional, Mavroudi, Antigoni, additional, Nivatsi, Maria, additional, Ntouma, Stirgianna, additional, Stefanaki, Evangelia, additional, Triga, Maria, additional, Kakava, Panagiota, additional, Lagiou, Olga, additional, Priftis, Kostas N, additional, Chaliasos, Nikolaous, additional, and Tsabouri, Sophia, additional

Published
2024
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8. CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes

Author

Dave J. Baker, Alp Aydin, Thanh Le-Viet, Gemma L. Kay, Steven Rudder, Leonardo de Oliveira Martins, Ana P. Tedim, Anastasia Kolyva, Maria Diaz, Nabil-Fareed Alikhan, Lizzie Meadows, Andrew Bell, Ana Victoria Gutierrez, Alexander J. Trotter, Nicholas M. Thomson, Rachel Gilroy, Luke Griffith, Evelien M. Adriaenssens, Rachael Stanley, Ian G. Charles, Ngozi Elumogo, John Wain, Reenesh Prakash, Emma Meader, Alison E. Mather, Mark A. Webber, Samir Dervisevic, Andrew J. Page, and Justin O’Grady

Subjects
SARS-CoV-2, Nanopore, Sequencing, NGS, Genome, Genetic, Medicine, Genetics, QH426-470
Abstract

Abstract We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by sequencing 2 plates containing 95 and 59 SARS-CoV-2 genomes on nanopore and Illumina platforms and comparing to the ARTIC LoCost nanopore method. Of the 154 samples sequenced using all 3 methods, ≥ 90% genome coverage was obtained for 64.3% using ARTIC LoCost, 71.4% using CoronaHiT-ONT and 76.6% using CoronaHiT-Illumina, with almost identical clustering on a maximum likelihood tree. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally.

Published
2021
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9. From Biodiversity to Musketry: Detection of Plant Diversity in Pre-Industrial Peloponnese during the Flora Graeca Expedition

Author

Chrysanthi Chimona, Sophia Papadopoulou, Foteini Kolyva, Maria Mina, and Sophia Rhizopoulou

Subjects
archives, botanical collection, Greece, landscape, pre-rebellion period, Science
Abstract

As the interest in natural, sustainable ecosystems arises in many fields, wild plant diversity is reconsidered. The present study is based on extant literature evidence from the journey of John Sibthorp (Professor of Botany, Oxford University) to Peloponnese (Greece) in pre-industrial time. In the year 1795, Peloponnese was a botanically unknown region, very dangerous for travellers and under civil unrest, in conjuncture with a pre-rebellion period. Our study reveals approximately 200 wild plant taxa that were collected from Peloponnese localities in 1795, transported to Oxford University (UK), and quoted in the magnificent edition Flora Graeca Sibthorpiana of the 19th century. Moreover, these plants currently constitute a living collection in Peloponnese, confirmed according to updated data on the vascular Flora of Greece. The presented lists constitute a source of information for plant biologists, linking the past to the present, shedding light on the study of adaptive traits of wild Mediterranean plants and revealing the temporal dimension of natural history. Nowadays, increasing and thorough understanding of the considered plants’ functionality to abiotic and biotic environmental stimuli provides a new framework of sustainability and management options.

Published
2022
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13. SURVEYING THE UNDERWATER ARCAHEOLOGICAL SITE OF CAPE GLAROS AT PAGASETIKOS GULF

Author

E. Diamanti, E. Spondylis, F. Vlachaki, and E. Kolyva

Subjects
Technology, Engineering (General). Civil engineering (General), TA1-2040, Applied optics. Photonics, TA1501-1820
Abstract

The Hellenic Institute of Marine Archaeology (H.I.M.A.)1 has been conducting an underwater archaeological research in the west coast of southern Pagasetikos Gulf, since 2000. Every year the underwater research focuses on specific archaeological targets that have been recovered during previous field campaigns. The current publication elaborates on the comprehensive documentation of the underwater archaeological site at Cape Glaros, during the 2015 field season, under the direction of the archaeologist Elias Spondylis. The 2015 research campaign was conducted within the framework of the ITACA- Innovation Technologies and Applications for Coastal Archaeological sites European Project (FP7/2007-2013, GA No 606805), at two archaeological sites, namely the Cape Glaros and Metohi. It was among the most important challenges of the project to successfully produce the detailed and accurate 3D mapping of the Cape Glaros site that covers an extended area. Four large concentrations of pottery finds and numerous anchors of different typology have been recorded, that can be dated from the late Hellenistic to the Byzantine periods. This challenge was tackled through the simultaneous implementation of three recording methods; photogrammetry, geodesy and conventional architectural mapping. The workflow of the documentation process, including data acquisition, processing and graphic visualization, along with the derived results are presented below. 1The Hellenic Institute of Marine Archaeology (H.I.M.A.) is a private, non-profit organization, founded in 1973, which undertakes maritime archaeological research under the supervision or in collaboration with the Greek Ministry of Culture. It has over 100 members, with diverse academic credentials, all of whom work, mainly, on a voluntary basis. 3D recording of underwater archaeological sites has been applied to numerous projects that have been carried out by the multidisciplinary team of H.I.M.A. in locations of utmost archaeological importance and interest, such as Modi island (Poros) and numerous wreck sites in Pagasetikos and South Euboean (Diamanti, Vlachaki, 2015) Gulfs and others.

Published
2017
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14. Dependence on NIRS Source-Detector Spacing of Cytochrome c Oxidase Response to Hypoxia and Hypercapnia in the Adult Brain

Author

Kolyva, Christina, Ghosh, Arnab, Tachtsidis, Ilias, Highton, David, Smith, Martin, Elwell, Clare E., Cohen, Irun R., Series Editor, Lajtha, Abel, Series Editor, Paoletti, Rodolfo, Series Editor, Lambris, John D., Series Editor, Van Huffel, Sabine, editor, Naulaers, Gunnar, editor, Caicedo, Alexander, editor, Bruley, Duane F., editor, and Harrison, David K., editor

Published
2013
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15. Reduction of Cytochrome c Oxidase During Vasovagal Hypoxia-Ischemia in Human Adult Brain: A Case Study

Author

Ghosh, Arnab, Kolyva, Christina, Tachtsidis, Ilias, Highton, David, Elwell, Clare E., Smith, Martin, Cohen, Irun R., Series Editor, Lajtha, Abel, Series Editor, Paoletti, Rodolfo, Series Editor, Lambris, John D., Series Editor, Van Huffel, Sabine, editor, Naulaers, Gunnar, editor, Caicedo, Alexander, editor, Bruley, Duane F., editor, and Harrison, David K., editor

Published
2013
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16. Oscillations in Cerebral Haemodynamics in Patients with Falciparum Malaria

Author

Kolyva, Christina, Kingston, Hugh, Tachtsidis, Ilias, Mohanty, Sanjib, Mishra, Saroj, Patnaik, Rajya, Maude, Richard J., Dondorp, Arjen M., Elwell, Clare E., Back, Nathan, Series Editor, Cohen, Irun R., Series Editor, Lajtha, Abel, Series Editor, Lambris, John D., Series Editor, Paoletti, Rodolfo, Series Editor, Welch, William J., editor, Palm, Fredrik, editor, Bruley, Duane F., editor, and Harrison, David K., editor

Published
2013
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17. Normobaric Hyperoxia Does Not Change Optical Scattering or Pathlength but Does Increase Oxidised Cytochrome c Oxidase Concentration in Patients with Brain Injury

Author

Ghosh, Arnab, Tachtsidis, Ilias, Kolyva, Christina, Highton, David, Elwell, Clare, Smith, Martin, Back, Nathan, Series Editor, Cohen, Irun R., Series Editor, Lajtha, Abel, Series Editor, Lambris, John D., Series Editor, Paoletti, Rodolfo, Series Editor, Welch, William J., editor, Palm, Fredrik, editor, Bruley, Duane F., editor, and Harrison, David K., editor

Published
2013
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19. Use of a Hybrid Optical Spectrometer for the Measurement of Changes in Oxidized Cytochrome c Oxidase Concentration and Tissue Scattering During Functional Activation

Author

Ghosh, Arnab, Tachtsidis, Ilias, Kolyva, Christina, Cooper, Chris E., Smith, Martin, Elwell, Clare E., Wolf, Martin, editor, Bucher, Hans Ulrich, editor, Rudin, Markus, editor, Van Huffel, Sabine, editor, Wolf, Ursula, editor, Bruley, Duane F., editor, and Harrison, David K, editor

Published
2012
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24. CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes

Author

Alexander J. Trotter, Emma Meader, Maria Diaz, Alp Aydin, Ana Victoria Gutierrez, Lizzie Meadows, Reenesh Prakash, Steven Rudder, Ana P. Tedim, Alison E. Mather, Anastasia Kolyva, Justin O'Grady, Andrew J. Page, Dave Baker, Thanh Le-Viet, Mark A. Webber, Ian G. Charles, Nicholas M. Thomson, Evelien M. Adriaenssens, Leonardo de Oliveira Martins, Rachel Gilroy, Rachael Stanley, Nabil-Fareed Alikhan, John Wain, Samir Dervisevic, Gemma L. Kay, Ngozi Elumogo, Andrew Bell, Luke Griffith, Page, Andrew J [0000-0001-6919-6062], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Nanopore, Scale (ratio), lcsh:QH426-470, Computer science, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030106 microbiology, Pcr cloning, Method, lcsh:Medicine, Computational biology, Genome, Viral, Biology, Multiplexing, Genome, DNA sequencing, 03 medical and health sciences, Genetic, Genetics, Humans, Sequencing, ARTIC, Molecular Biology, Pandemics, Genetics (clinical), Transposase, Whole genome sequencing, Whole Genome Sequencing, SARS-CoV-2, lcsh:R, COVID-19, High-Throughput Nucleotide Sequencing, lcsh:Genetics, 030104 developmental biology, Minion, NGS, Molecular Medicine, RNA, Viral, Nanopore sequencing
Abstract

The COVID-19 pandemic has spread to almost every country in the world since it started in China in late 2019. Controlling the pandemic requires a multifaceted approach including whole genome sequencing to support public health interventions at local and national levels. One of the most widely used methods for sequencing is the ARTIC protocol, a tiling PCR approach followed by Oxford Nanopore sequencing (ONT) of up to 96 samples at a time. There is a need, however, for a flexible, platform agnostic, method that can provide multiple throughput options depending on changing requirements as the pandemic peaks and troughs. Here we present CoronaHiT, a method capable of multiplexing up to 96 small genomes on a single MinION flowcell or >384 genomes on Illumina NextSeq, using transposase mediated addition of adapters and PCR based addition of barcodes to ARTIC PCR products. We demonstrate the method by sequencing 95 and 59 SARS-CoV-2 genomes for routine and rapid outbreak response runs, respectively, on Nanopore and Illumina platforms and compare to the standard ARTIC LoCost nanopore method. Of the 154 samples sequenced using the three approaches, genomes with ≥ 90% coverage (GISAID criteria) were generated for 64.3% of samples for ARTIC LoCost, 71.4% for CoronaHiT-ONT, and 76.6% for CoronaHiT-Illumina and have almost identical clustering on a maximum likelihood tree. In conclusion, we demonstrate that CoronaHiT can multiplex up to 96 SARS-CoV-2 genomes per MinION flowcell and that Illumina sequencing can be performed on the same libraries, which will allow significantly higher throughput. CoronaHiT provides increased coverage for higher Ct samples, thereby increasing the number of high quality genomes that pass the GISAID QC threshold. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally, to help control the pandemic.

Published
2021

27. 10.6 VARIATION OF THE ASYMPTOTIC DIASTOLIC PRESSURE WITH DIFFERENT FITTING TECHNIQUES IN HEALTHY HUMANS

Author

Nicola Pomella, Christina Kolyva, Ernst Rietzschel, Patrick Segers, Ashraf W. Khir, and Madalina Negoita

Subjects
Specialties of internal medicine, RC581-951, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background: Reservoir-wave model assumes the measured pressure (Pm) consists of two additive components: reservoir (Pr) and excess pressure (Pex)1–2. Calculation of Pr requires fitting the diastolic decay of Pm for calculating parameters P∞ (asymptotical value) and b (time constant)1. However, there is no consensus over the value of these parameters1–3–4. Although many investigators use free-fitting, different degrees of freedom (dof) could be used1–2–5. The aim of this study was to examine the effect of varying fitting method on P∞ ,b and calculate the peaks of Pr and Pex. Methods: Pressure data from common carotid artery of 505 middle-aged healthy subjects were selected from the Asklepios dataset. Free-fitting methods with 3 dof (dicrotic notch not fixed) and 2 dof (dicrotic notch fixed) were used to obtain P∞ , b and calculate Pr and Pex. Results: Mean value of P∞ change significantly between 3 dof and 2 dof (58 vs. 50 mmHg p0.05 Pex = 30 mmHg and 31 mmHg for 3 dof and 2 dof, respectively p>0.05). Conclusions: P∞ and b values are method-dependent with a large variation between methods. P∞ values in our study are higher than previously reported in literature, and variation in P∞ and b values don’t affect Pr- and Pex- peaks. Given the variability in the combination of P∞ ,b in different subjects, the use of free-fitting is more appropriate.

Published
2016
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32. P8.12 CAROTID ARTERY WAVE INTENSITY ANALYSIS IN HEALTHY HUMANS DURING EXERCISE

Author

Nicola Pomella, Eurico Wilhelm Neto, Christina Kolyva, Mark Rakobowchuk, Jose Gonzalez-Alonso, and Ashraf William Khir

Subjects
Specialties of internal medicine, RC581-951, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background: The study of wave reflections in the carotid artery may reveal the vasoactive response of the cerebral circulation to exercise, which is not yet fully characterised. Therefore, we aim to examine the effect of exercise on wave intensity parameters measured in the carotid artery of healthy humans, using non-invasive wave intensity analysis. Methods: Ultrasound measurements of right common carotid diameter and flow velocity were obtained from 8 healthy male athletes (27 ± 4 y). Two measurements were taken at rest, followed by measurements during 5-min incremental steps of cycling at 0%, 20%, 40%, 60% and 70% of the subjects’ peak workload, then eight measurements during post-exercise recovery. Wave speed (c) and the intensity peaks and energies of Forward Compression (FCW), Backward Compression (BCW) and Forward Expansion (FEW) waves were determined and compared between the three stages. The reflection index (RI) is calculated as RI=BCW/FCW. Results: All parameters increased, following the increase of workload. At end of recovery, all parameters returned to rest values. During exercise, c increased by 200%. The intensity of FCW, BCW and FEW increased by 600%, 1100% and 600% during exercise; likewise the energy increased by 450%, 500% and 800%, respectively. Also, RI increased during exercise by 170%. Conclusions: RI results indicate that cerebral resistance increases with increased workload. Also, the increase of FEW magnitude suggests that an increase in exercise workload is associated with a greater cardiac muscle speed of deceleration in late systole.

Published
2015
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45. Ο ρόλος της παχυσαρκίας στην ανοσολογική απάντηση ασθενών με σύνδρομο σήψης

Author

Anastasia Kolyva

Subjects
medicine.medical_specialty, education.field_of_study, business.industry, Adipose tissue macrophages, Population, Adipose tissue, medicine.disease, medicine.disease_cause, Proinflammatory cytokine, Sepsis, Endocrinology, Internal medicine, Immunology, medicine, TBARS, Tumor necrosis factor alpha, education, business, Oxidative stress
Abstract

Σκοπός: Η σήψη αποτελεί μια από τις σημαντικότερες αιτίες νοσηλείας και θνησιμότητας στον ανεπτυγμένο κόσμο, όπου σχεδόν τα δύο - τρίτα του πληθυσμού υποφέρουν από παχυσαρκία. Σαν αποτέλεσμα, η συνύπαρξη των δύο αυτών καταστάσεων έχει γίνει όλο και συχνότερη στην κλινική πράξη και ένας συνεχώς αυξανόμενος αριθμός κλινικών μελετών προσπαθεί να προσεγγίσει την πιθανή επίδραση της παχυσαρκίας στην νοσηρότητα και θνησιμότητα των ασθενών με σήψη, με έως τώρα αντιφατικά αποτελέσματα. Σκοπός της παρούσας μελέτης είναι να διερευνήσει τον τρόπο με τον οποίο η παχυσαρκία επηρεάζει την ανοσιακή απάντηση των σηπτικών ασθενών, εκτιμώντας τον αριθμό και την κατάσταση ενεργοποίησης των μακροφάγων του λιπώδους ιστού, τα επίπεδα του TNFα στον ορό και στον λιπώδη ιστό και δείκτες οξειδωτικού stress στο πλάσμα.Ασθενείς και Μέθοδοι: Μελετήθηκαν 106 ασθενείς, οι οποίοι χωρίστηκαν σε τέσσερις ομάδες (Ελέγχου n=26, Παχυσαρκίας n=27, Σήψης n=27, Σήψης & Παχυσαρκίας n=26). Ο αριθμός των μακροφάγων στο υποδόριο και ενδοκοιλιακό λίπος και οι υπότυποί τους (M1 και M2) αναγνωρίστηκαν με ανοσοϊστοχημική τεχνική υπό μικροσκόπηση. Τα επίπεδα του TNFα mRNA στο υποδόριο και ενδοκοιλιακό λίπος μετρήθηκαν με real-time reverse transcription-PCR. Στον ορό τα επίπεδα του TNFα μετρήθηκαν με sandwich enzyme-linked immunosorbent assay (ELISA). Το οξειδωτικό stress στο πλάσμα εκτιμήθηκε χρησιμοποιώντας επιλεγμένους βιοδείκτες [TBARS (thiobarbituric acid-reactive substances), Πρωτεϊνικά Καρβονύλια, TAC (total antioxidant capacity)].Αποτελέσματα: Παρατηρήθηκε ότι η σήψη αυξάνει τον ολικό αριθμό και τον Μ2 υπότυπο των μακροφάγων στο ενδοκοιλιακό λίπος, ενώ η παχυσαρκία δεν φάνηκε να επηρεάζει τη συγκέντρωση των μακροφάγων στο λίπος. Η παχυσαρκία βρέθηκε ότι αυξάνει τα επίπεδα του TNFα mRNA (P

Published
2021
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46. Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management

Author

Colin S Brown, Maria Diaz, Luke Bedford, Ana P. Tedim, Steven Rudder, Meera Chand, Muhammad Yasir, Luke Griffith, Will Potter, Rachel Gilroy, Nicholas M. Thomson, Rachael Stanley, Emma Meader, Robert A Kingsley, Ana Victoria Gutierrez, S. J. Louise Smith, Thanh Le-Viet, John Wain, Ian G. Charles, Alexander J. Trotter, Alp Aydin, Ngozi Elumogo, Justin O'Grady, Gemma L. Kay, Reenesh Prakash, Dheeraj K. Sethi, Rose K Davidson, Claire Stuart, Evelien M. Adriaenssens, Alison E Mather, Dinesh Aggarwal, Nabil-Fareed Alikhan, Andrew J. Page, Lizzie Meadows, Anastasia Kolyva, David Baker, Mark A. Webber, Lindsay Coupland, Leonardo de Oliveira Martins, Andrew Bell, Tracey E. Swingler, Samir Dervisevic, Aggarwal, Dinesh [0000-0002-5938-8172], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Genetic Linkage, 030106 microbiology, Population, Genomics, Context (language use), Genome, Viral, genomic epidemiology, Biology, Polymorphism, Single Nucleotide, DNA sequencing, Disease Outbreaks, 03 medical and health sciences, Pandemic, Cluster Analysis, Humans, Longitudinal Studies, ARTIC, education, genome, Pandemics, Phylogeny, Whole genome sequencing, education.field_of_study, Whole Genome Sequencing, SARS-CoV-2, COVID-19, Outbreak, sequencing, General Medicine, United Kingdom, 030104 developmental biology, Evolutionary biology, NGS, Spike Glycoprotein, Coronavirus, Large-Scale Sequencing
Abstract

The COVID-19 pandemic has spread rapidly throughout the world. In the UK, the initial peak was in April 2020; in the county of Norfolk (UK) and surrounding areas, which has a stable, low-density population, over 3200 cases were reported between March and August 2020. As part of the activities of the national COVID-19 Genomics Consortium (COG-UK) we undertook whole genome sequencing of the SARS-CoV-2 genomes present in positive clinical samples from the Norfolk region. These samples were collected by four major hospitals, multiple minor hospitals, care facilities and community organizations within Norfolk and surrounding areas. We combined clinical metadata with the sequencing data from regional SARS-CoV-2 genomes to understand the origins, genetic variation, transmission and expansion (spread) of the virus within the region and provide context nationally. Data were fed back into the national effort for pandemic management, whilst simultaneously being used to assist local outbreak analyses. Overall, 1565 positive samples (172 per 100 000 population) from 1376 cases were evaluated; for 140 cases between two and six samples were available providing longitudinal data. This represented 42.6 % of all positive samples identified by hospital testing in the region and encompassed those with clinical need, and health and care workers and their families. In total, 1035 cases had genome sequences of sufficient quality to provide phylogenetic lineages. These genomes belonged to 26 distinct global lineages, indicating that there were multiple separate introductions into the region. Furthermore, 100 genetically distinct UK lineages were detected demonstrating local evolution, at a rate of ~2 SNPs per month, and multiple co-occurring lineages as the pandemic progressed. Our analysis: identified a discrete sublineage associated with six care facilities; found no evidence of reinfection in longitudinal samples; ruled out a nosocomial outbreak; identified 16 lineages in key workers which were not in patients, indicating infection control measures were effective; and found the D614G spike protein mutation which is linked to increased transmissibility dominates the samples and rapidly confirmed relatedness of cases in an outbreak at a food processing facility. The large-scale genome sequencing of SARS-CoV-2-positive samples has provided valuable additional data for public health epidemiology in the Norfolk region, and will continue to help identify and untangle hidden transmission chains as the pandemic evolves.

Published
2021
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50. P5.21 EARLY IABP INFLATION SUPPRESSES LEFT VENTRICULAR FUNCTION AS INDICATED BY WAVE INTENSITY ANALYSIS

Author

C. Kolyva, G.M. Pantalos, J.R. Pepper, and A.W. Khir

Subjects
Specialties of internal medicine, RC581-951, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background: Timing errors during Intra-Aortic Balloon Pump (IABP) support can be detrimental when interfering with cardiac function. In vivo hemodynamics and left ventricular (LV) function were monitored during premature IAB inflation, and the associated mechanisms investigated with Wave Intensity Analysis. Methods: Six healthy, anaesthetised, open-chest sheep received IABP support with frequency 1:3 (n=3) and 1:1 (n=3). Aortic (Qao) and coronary (Qcor) flow, and aortic (Pao) and left ventricular (PLV) pressure were recorded simultaneously with and without IABP. Early inflation (EI) was triggered -91±9ms (1:3) and −105±36ms (1:1) before the incisura. Integrating systolic Qao and subsequent negative Qao yielded stroke volume (SV) and backflow, respectively. Forward expansion (FEW) and forward compression (FCW) wave energies, generated by the slowing of LV contraction preceding inflation and by early LV ejection following deflation, respectively, were obtained. Results are mean±standard deviation. Results: EI increased diastolic (d) Qcor in 1:3 but not in 1:1. EI appears to be detrimental for LV function, as indicated by substantial FEW reduction in both frequencies, concurring with increased backflow. Systolic (s) Pao and PLV did not corroborate suppressed LV function, but SV tended to decrease at 1:3 in the systole preceding EI. FCW reduction was also observed. IABP on IABP off 1:3 1:1 1:3 1:1 FEW (J/m2) 0.026±0.015* 0.031±0.017* 0.059±0.026 0.073±0.026 FCW (J/m2) 0.117±0.044* 0.086±0.051* 0.147±0.048 0.087±0.060 SV (ml) 67±16 78±28 71±17 77±32 Backflow (ml) 3.0±0.3* 4.410.9* 1.8±0.3 3.1±0.4 dQcor (ml/min) 182±17* 148±6* 150±17 149±36 sPLV (mmHg) 67±10 69±5* 67±13 76±7 sPao (mmHg) 71±11 73±8* 71±13 81±8 *P

Published
2013
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