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1,906 results on '"Sims, David"'

151. Complete genome sequence of Kytococcus sedentarius type strain (strain 541T)

Author

Sims, David

Subjects
Basic biological sciences, mesophile, free-living, marine, aerobic, opportunistic pathogenic, Dermacoccaceae
Abstract

Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of the species, and is of phylogenetic interest because of its location in the Dermacoccaceae, a poorly studied family within the actinobacterial suborder Micrococcineae. K. sedentarius is known for the production of oligoketide antibiotics as well as for its role as an opportunistic pathogen causing valve endocarditis, hemorrhagic pneumonia, and pitted keratolysis. It is strictly aerobic and can only grow when several amino acids are provided in the medium. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from a marine environment. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Dermacoccaceae and the 2,785,024 bp long single replicon genome with its 2639 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Published
2008

152. Spatio-temporal genetic tagging of a cosmopolitan planktivorous shark provides insight to gene flow, temporal variation and site-specific re-encounters

Author

Lieber, Lilian, Hall, Graham, Hall, Jackie, Berrow, Simon, Johnston, Emmett, Gubili, Chrysoula, Sarginson, Jane, Francis, Malcolm, Duffy, Clinton, Wintner, Sabine P., Doherty, Philip D., Godley, Brendan J., Hawkes, Lucy A., Witt, Matthew J., Henderson, Suzanne M., de Sabata, Eleonora, Shivji, Mahmood S., Dawson, Deborah A., Sims, David W., Jones, Catherine S., and Noble, Leslie R.

Published
2020
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156. Supplementary Figures and Table for Repapi et al. 2022

Author

Repapi, Emmanouela, Agarwal, Devika, Napolitani, Giorgio, Sims, David, and Taylor, Stephen

Subjects
mass cytometry, genetic processes, single cell proteomics, natural sciences, CyTOF, single cell transcriptomics, single cell integration, CD11c B cells
Abstract

This repository contains supplementary figures and table for Repapi et al (2022):Integration of single-cell RNA-Seq and CyTOF data characterises heterogeneity of rare cell subpopulations

Published
2023
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160. Data from Germline and Somatic Genetic Variants in the p53 Pathway Interact to Affect Cancer Risk, Progression, and Drug Response

Author

Zhang, Ping, primary, Kitchen-Smith, Isaac, primary, Xiong, Lingyun, primary, Stracquadanio, Giovanni, primary, Brown, Katherine, primary, Richter, Philipp H., primary, Wallace, Marsha D., primary, Bond, Elisabeth, primary, Sahgal, Natasha, primary, Moore, Samantha, primary, Nornes, Svanhild, primary, De Val, Sarah, primary, Surakhy, Mirvat, primary, Sims, David, primary, Wang, Xuting, primary, Bell, Douglas A., primary, Zeron-Medina, Jorge, primary, Jiang, Yanyan, primary, Ryan, Anderson J., primary, Selfe, Joanna L., primary, Shipley, Janet, primary, Kar, Siddhartha, primary, Pharoah, Paul D., primary, Loveday, Chey, primary, Jansen, Rick, primary, Grochola, Lukasz F., primary, Palles, Claire, primary, Protheroe, Andrew, primary, Millar, Val, primary, Ebner, Daniel V., primary, Pagadala, Meghana, primary, Blagden, Sarah P., primary, Maughan, Timothy S., primary, Domingo, Enric, primary, Tomlinson, Ian, primary, Turnbull, Clare, primary, Carter, Hannah, primary, and Bond, Gareth L., primary

Published
2023
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161. Supplementary Data from Germline and Somatic Genetic Variants in the p53 Pathway Interact to Affect Cancer Risk, Progression, and Drug Response

Author

Zhang, Ping, primary, Kitchen-Smith, Isaac, primary, Xiong, Lingyun, primary, Stracquadanio, Giovanni, primary, Brown, Katherine, primary, Richter, Philipp H., primary, Wallace, Marsha D., primary, Bond, Elisabeth, primary, Sahgal, Natasha, primary, Moore, Samantha, primary, Nornes, Svanhild, primary, De Val, Sarah, primary, Surakhy, Mirvat, primary, Sims, David, primary, Wang, Xuting, primary, Bell, Douglas A., primary, Zeron-Medina, Jorge, primary, Jiang, Yanyan, primary, Ryan, Anderson J., primary, Selfe, Joanna L., primary, Shipley, Janet, primary, Kar, Siddhartha, primary, Pharoah, Paul D., primary, Loveday, Chey, primary, Jansen, Rick, primary, Grochola, Lukasz F., primary, Palles, Claire, primary, Protheroe, Andrew, primary, Millar, Val, primary, Ebner, Daniel V., primary, Pagadala, Meghana, primary, Blagden, Sarah P., primary, Maughan, Timothy S., primary, Domingo, Enric, primary, Tomlinson, Ian, primary, Turnbull, Clare, primary, Carter, Hannah, primary, and Bond, Gareth L., primary

Published
2023
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162. Supplementary Table 2 from Genome-wide Profiling of Genetic Synthetic Lethality Identifies CDK12 as a Novel Determinant of PARP1/2 Inhibitor Sensitivity

Author

Bajrami, Ilirjana, primary, Frankum, Jessica R., primary, Konde, Asha, primary, Miller, Rowan E., primary, Rehman, Farah L., primary, Brough, Rachel, primary, Campbell, James, primary, Sims, David, primary, Rafiq, Rumana, primary, Hooper, Sean, primary, Chen, Lina, primary, Kozarewa, Iwanka, primary, Assiotis, Ioannis, primary, Fenwick, Kerry, primary, Natrajan, Rachael, primary, Lord, Christopher J., primary, and Ashworth, Alan, primary

Published
2023
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163. Supplementary Table 3 from Genome-wide Profiling of Genetic Synthetic Lethality Identifies CDK12 as a Novel Determinant of PARP1/2 Inhibitor Sensitivity

Author

Bajrami, Ilirjana, primary, Frankum, Jessica R., primary, Konde, Asha, primary, Miller, Rowan E., primary, Rehman, Farah L., primary, Brough, Rachel, primary, Campbell, James, primary, Sims, David, primary, Rafiq, Rumana, primary, Hooper, Sean, primary, Chen, Lina, primary, Kozarewa, Iwanka, primary, Assiotis, Ioannis, primary, Fenwick, Kerry, primary, Natrajan, Rachael, primary, Lord, Christopher J., primary, and Ashworth, Alan, primary

Published
2023
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165. Data from Genome-wide Profiling of Genetic Synthetic Lethality Identifies CDK12 as a Novel Determinant of PARP1/2 Inhibitor Sensitivity

Author

Bajrami, Ilirjana, primary, Frankum, Jessica R., primary, Konde, Asha, primary, Miller, Rowan E., primary, Rehman, Farah L., primary, Brough, Rachel, primary, Campbell, James, primary, Sims, David, primary, Rafiq, Rumana, primary, Hooper, Sean, primary, Chen, Lina, primary, Kozarewa, Iwanka, primary, Assiotis, Ioannis, primary, Fenwick, Kerry, primary, Natrajan, Rachael, primary, Lord, Christopher J., primary, and Ashworth, Alan, primary

Published
2023
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166. Supplementary Table 1 from Genome-wide Profiling of Genetic Synthetic Lethality Identifies CDK12 as a Novel Determinant of PARP1/2 Inhibitor Sensitivity

Author

Bajrami, Ilirjana, primary, Frankum, Jessica R., primary, Konde, Asha, primary, Miller, Rowan E., primary, Rehman, Farah L., primary, Brough, Rachel, primary, Campbell, James, primary, Sims, David, primary, Rafiq, Rumana, primary, Hooper, Sean, primary, Chen, Lina, primary, Kozarewa, Iwanka, primary, Assiotis, Ioannis, primary, Fenwick, Kerry, primary, Natrajan, Rachael, primary, Lord, Christopher J., primary, and Ashworth, Alan, primary

Published
2023
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167. Supplementary Information from Genome-wide Profiling of Genetic Synthetic Lethality Identifies CDK12 as a Novel Determinant of PARP1/2 Inhibitor Sensitivity

Author

Bajrami, Ilirjana, primary, Frankum, Jessica R., primary, Konde, Asha, primary, Miller, Rowan E., primary, Rehman, Farah L., primary, Brough, Rachel, primary, Campbell, James, primary, Sims, David, primary, Rafiq, Rumana, primary, Hooper, Sean, primary, Chen, Lina, primary, Kozarewa, Iwanka, primary, Assiotis, Ioannis, primary, Fenwick, Kerry, primary, Natrajan, Rachael, primary, Lord, Christopher J., primary, and Ashworth, Alan, primary

Published
2023
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168. Supplementary Figures from Genome-wide Profiling of Genetic Synthetic Lethality Identifies CDK12 as a Novel Determinant of PARP1/2 Inhibitor Sensitivity

Author

Bajrami, Ilirjana, primary, Frankum, Jessica R., primary, Konde, Asha, primary, Miller, Rowan E., primary, Rehman, Farah L., primary, Brough, Rachel, primary, Campbell, James, primary, Sims, David, primary, Rafiq, Rumana, primary, Hooper, Sean, primary, Chen, Lina, primary, Kozarewa, Iwanka, primary, Assiotis, Ioannis, primary, Fenwick, Kerry, primary, Natrajan, Rachael, primary, Lord, Christopher J., primary, and Ashworth, Alan, primary

Published
2023
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170. Supplementary Table 5 from Genome-wide Profiling of Genetic Synthetic Lethality Identifies CDK12 as a Novel Determinant of PARP1/2 Inhibitor Sensitivity

Author

Bajrami, Ilirjana, primary, Frankum, Jessica R., primary, Konde, Asha, primary, Miller, Rowan E., primary, Rehman, Farah L., primary, Brough, Rachel, primary, Campbell, James, primary, Sims, David, primary, Rafiq, Rumana, primary, Hooper, Sean, primary, Chen, Lina, primary, Kozarewa, Iwanka, primary, Assiotis, Ioannis, primary, Fenwick, Kerry, primary, Natrajan, Rachael, primary, Lord, Christopher J., primary, and Ashworth, Alan, primary

Published
2023
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171. Supplementary Table 4 from Genome-wide Profiling of Genetic Synthetic Lethality Identifies CDK12 as a Novel Determinant of PARP1/2 Inhibitor Sensitivity

Author

Bajrami, Ilirjana, primary, Frankum, Jessica R., primary, Konde, Asha, primary, Miller, Rowan E., primary, Rehman, Farah L., primary, Brough, Rachel, primary, Campbell, James, primary, Sims, David, primary, Rafiq, Rumana, primary, Hooper, Sean, primary, Chen, Lina, primary, Kozarewa, Iwanka, primary, Assiotis, Ioannis, primary, Fenwick, Kerry, primary, Natrajan, Rachael, primary, Lord, Christopher J., primary, and Ashworth, Alan, primary

Published
2023
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172. The impact of the pandemic on early career researchers' work‐life and scholarly communications: A quantitative aerial analysis

Author

Nicholas, David, primary, Herman, Eti, additional, Clark, David, additional, Boukacem‐Zeghmouri, Cherifa, additional, Rodríguez‐Bravo, Blanca, additional, Abrizah, Abdullah, additional, Watkinson, Anthony, additional, Sims, David, additional, ´Świgoń, Marzena, additional, Xu, Jie, additional, Serbina, Galina, additional, Jamali, Hamid R., additional, Tenopir, Carol, additional, and Allard, Suzie, additional

Published
2023
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173. ‘Cracks’ in the scholarly communications system: Insights from a longitudinal international study of early career researchers

Author

Nicholas, David, primary, Boukacem‐Zeghmouri, Cherifa, additional, Rodríguez‐Bravo, Blanca, additional, Herman, Eti, additional, Abrizah, Abdullah, additional, Clark, David, additional, Serbina, Galina, additional, Sims, David, additional, Świgoń, Marzena, additional, Xu, Jie, additional, Watkinson, Anthony, additional, Jamali, Hamid R., additional, Tenopir, Carol, additional, and Allard, Suzie, additional

Published
2023
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176. The pandemic and changes in early career researchers’ career prospects, research and publishing practices

Author

Jamali, Hamid R., primary, Nicholas, David, additional, Sims, David, additional, Watkinson, Anthony, additional, Herman, Eti, additional, Boukacem-Zeghmouri, Cherifa, additional, Rodríguez-Bravo, Blanca, additional, Świgoń, Marzena, additional, Abrizah, Abdullah, additional, Xu, Jie, additional, Tenopir, Carol, additional, and Allard, Suzie, additional

Published
2023
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177. Outside the library: Early career researchers and use of alternative information sources in pandemic times

Author

Herman, Eti, primary, Nicholas, David, additional, Clark, David, additional, Boukacem‐Zeghmouri, Chérifa, additional, Rodríguez‐Bravo, Blanca, additional, Abrizah, Abdullah, additional, Sims, David, additional, Watkinson, Anthony, additional, Xu, Jie, additional, Serbina, Galina, additional, Świgoń, Marzena, additional, Jamali, Hamid R., additional, Tenopir, Carol, additional, and Allard, Suzie, additional

Published
2023
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179. Key Questions in Marine Megafauna Movement Ecology

Author

Hays, Graeme C., Ferreira, Luciana C., Sequeira, Ana M.M., Meekan, Mark G., Duarte, Carlos M., Bailey, Helen, Bailleul, Fred, Bowen, W. Don, Caley, M. Julian, Costa, Daniel P., Eguíluz, Victor M., Fossette, Sabrina, Friedlaender, Ari S., Gales, Nick, Gleiss, Adrian C., Gunn, John, Harcourt, Rob, Hazen, Elliott L., Heithaus, Michael R., Heupel, Michelle, Holland, Kim, Horning, Markus, Jonsen, Ian, Kooyman, Gerald L., Lowe, Christopher G., Madsen, Peter T., Marsh, Helene, Phillips, Richard A., Righton, David, Ropert-Coudert, Yan, Sato, Katsufumi, Shaffer, Scott A., Simpfendorfer, Colin A., Sims, David W., Skomal, Gregory, Takahashi, Akinori, Trathan, Philip N., Wikelski, Martin, Womble, Jamie N., and Thums, Michele

Published
2016
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183. Juvenile survival and movements of two threatened oceanic sharks in the North Atlantic Ocean inferred from tag-recovery data

Author

Mucientes, Gonzalo, Fernández-Chacón, Albert, Queiroz, Nuno, Sims, David W., Villegas-Ríos, David, Xunta de Galicia, European Commission, and Consejo Superior de Investigaciones Científicas (España)

Subjects
Blue shark, Survival, Shortfin mako, North Atlantic, Tag-recovery data, Fishing mortality, Dispersal behavior
Abstract

15 pages, 4 tables, 3 figures.-- This is an open access article under the terms of the Creative Commons Attribution License, Understanding population dynamics, movements, and fishing mortality is critical to establish effective shark conservation measures across international boundaries in the ocean. There are few survival and dispersal estimates of juveniles of oceanic shark species in the North Atlantic despite it being one of the most fished regions in the world. Here we provide estimates of dispersal, survival, and proportion of fishing mortality in the North Atlantic for two threatened oceanic sharks: the blue shark (Prionace glauca) and the shortfin mako shark (Isurus oxyrinchus). Our results are based on multi-event models applied to tag-recovery data of 700 blue sharks and 132 shortfin makos tagged over a decade. A total of 60 blue sharks (8.57% of tagged) and 30 makos (22.73%) were recovered by the longline fishery between 2009 and 2017. Tag-reporting rate (percentage of returned information when a tagged shark was caught) was estimated to be high (0.794 ± 0.232 SE). Mean annual survival, as predicted from the models, was higher for blue shark (0.835 ± 0.040 SE) than for shortfin mako (0.618 ± 0.189 SE). Models predicted that fishing caused more than a half of total mortality in the study area for both species (0.576 ± 0.209), and more than a third of tagged individuals dispersed from the study area permanently (0.359 ± 0.073). Our findings, focused mainly on juveniles from oceanic areas, contribute to a better understanding of shark population dynamics in the North Atlantic and highlight the need for further conservation measures for both blue shark and shortfin mako, such as implementing efficient bycatch mitigation measures and static/dynamic time–area closures in the open ocean, GM was funded by Isabel Barreto program of Xunta de Galicia (Spain) and FCT grants PTDC/MAR-BIO/4458/2012; IF/01611/2013 and ICETA 2017-49. DVR has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 793627 (BEMAR) and from the program IF_ERC from the Spanish National Research Council. NQ was supported by FCT (CEECIND/02857/2018). DWS was supported by a Marine Biological Association Senior Research Fellowship

Published
2023

184. Physiological factors regulating appetite in the lesser spotted dogfish shark, Scyliorhinus canicula (L.)

Author

Sims, David William

Subjects
590, Zoology
Abstract

Some aspects of digestive and systemic function were investigated in relation to their role in the peripheral regulation of appetite in juvenile and adult, S. canicula. This study represents the first evaluation of the physiological factors that contribute to the control of shark appetite. Daily food intake trials on both juvenile and adult dogfish showed repeatable, self-regulated feeding rhythms indicating the existence of an endogenous component to food intake control. After dogfish consumed satiation meals of 7% wet body weight (wbw) the appetite return increased at constant rates as deprivation time increased. The relative rate of food processing was 50% faster in juveniles than adults. The pattern of gastric emptying of squid diet was exponential and dependent on the degree of stomach fullness, with meals of different size being emptied at different relative rates. It was also shown that dogfish were capable of shunting undigested food into the intestine soon after consumption of large meals. There was inverse proportionality between rate of gastric evacuation and appetite return rate indicating the importance of the physiological perception of relative stomach emptiness in the establishment of appetite. Gastric emptying rates were not influenced by changes in the digestible energy level of the diet, which suggests this shark exhibits a predominantly bulk dependent feeding pattern. Increases in post-prandial metabolism or specific dynamic action (SDA) did not seemingly alter the rate of appetite return in dogfish, though SDA and appetite return were shown to be closely linked metabolic processes. The SDA process in dogfish may have a saturation level determined by cellular metabolism rather than by the respiratory system. The levels of plasma glucose remained uniform after food consumption. The concentrations of triglycerides and protein in plasma were closely controlled post-prandially, suggesting a possible role for these metabolites as systemic signals of metabolic satiety. The results of this investigation are discussed with regard to the multifactorial control of appetite in sharks and the possible use of physiological studies of appetite in the further understanding of fish feeding strategies.

Published
1994

188. Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19

Author

Kotanidis, Christos P, primary, Xie, Cheng, additional, Alexander, Donna, additional, Rodrigues, Jonathan C L, additional, Burnham, Katie, additional, Mentzer, Alexander, additional, O’Connor, Daniel, additional, Knight, Julian, additional, Siddique, Muhammad, additional, Lockstone, Helen, additional, Thomas, Sheena, additional, Kotronias, Rafail, additional, Oikonomou, Evangelos K, additional, Badi, Ileana, additional, Lyasheva, Maria, additional, Shirodaria, Cheerag, additional, Lumley, Sheila F, additional, Constantinides, Bede, additional, Sanderson, Nicholas, additional, Rodger, Gillian, additional, Chau, Kevin K, additional, Lodge, Archie, additional, Tsakok, Maria, additional, Gleeson, Fergus, additional, Adlam, David, additional, Rao, Praveen, additional, Indrajeet, Das, additional, Deshpande, Aparna, additional, Bajaj, Amrita, additional, Hudson, Benjamin J, additional, Srivastava, Vivek, additional, Farid, Shakil, additional, Krasopoulos, George, additional, Sayeed, Rana, additional, Ho, Ling-Pei, additional, Neubauer, Stefan, additional, Newby, David E, additional, Channon, Keith M, additional, Deanfield, John, additional, Antoniades, Charalambos, additional, Ahern, David J, additional, Ai, Zhichao, additional, Ainsworth, Mark, additional, Allan, Chris, additional, Allcock, Alice, additional, Angus, Brian, additional, Ansari, M Azim, additional, Arancibia-Cárcamo, Carolina, additional, Aschenbrenner, Dominik, additional, Attar, Moustafa, additional, Baillie, J Kenneth, additional, Barnes, Eleanor, additional, Bashford-Rogers, Rachael, additional, Bashyal, Archana, additional, Beer, Sally, additional, Berridge, Georgina, additional, Beveridge, Amy, additional, Bibi, Sagida, additional, Bicanic, Tihana, additional, Blackwell, Luke, additional, Bowness, Paul, additional, Brent, Andrew, additional, Brown, Andrew, additional, Broxholme, John, additional, Buck, David, additional, Byrne, Helen, additional, Camara, Susana, additional, Ferreira, Ivan Candido, additional, Charles, Philip, additional, Chen, Wentao, additional, Chen, Yi-Ling, additional, Chong, Amanda, additional, Clutterbuck, Elizabeth, additional, Coles, Mark, additional, Conlon, Christopher, additional, Cornall, Richard, additional, Cribbs, Adam, additional, Curion, Fabiola, additional, Davenport, Emma, additional, Davidson, Neil, additional, Davis, Simon, additional, Dendrou, Calliope, additional, Dequaire, Julie, additional, Dib, Lea, additional, Docker, James, additional, Dold, Christina, additional, Dong, Tao, additional, Downes, Damien, additional, Drakesmith, Hal, additional, Dunachie, Susanna, additional, Duncan, David, additional, Eijsbouts, Chris, additional, Esnouf, Robert, additional, Espinosa, Alexis, additional, Etherington, Rachel, additional, Fairfax, Benjamin, additional, Fairhead, Rory, additional, Fang, Hai, additional, Fassih, Shayan, additional, Felle, Sally, additional, Fernandez Mendoza, Maria, additional, Ferreira, Ricardo, additional, Fischer, Roman, additional, Foord, Thomas, additional, Forrow, Aden, additional, Frater, John, additional, Fries, Anastasia, additional, Gallardo Sanchez, Veronica, additional, Garner, Lucy, additional, Geeves, Clementine, additional, Georgiou, Dominique, additional, Godfrey, Leila, additional, Golubchik, Tanya, additional, Gomez Vazquez, Maria, additional, Green, Angie, additional, Harper, Hong, additional, Harrington, Heather, additional, Heilig, Raphael, additional, Hester, Svenja, additional, Hill, Jennifer, additional, Hinds, Charles, additional, Hird, Clare, additional, Hoekzema, Renee, additional, Hollis, Benjamin, additional, Hughes, Jim, additional, Hutton, Paula, additional, Jackson-Wood, Matthew, additional, Jainarayanan, Ashwin, additional, James-Bott, Anna, additional, Jansen, Kathrin, additional, Jeffery, Katie, additional, Jones, Elizabeth, additional, Jostins, Luke, additional, Kerr, Georgina, additional, Kim, David, additional, Klenerman, Paul, additional, Kumar, Vinod, additional, Kumar Sharma, Piyush, additional, Kurupati, Prathiba, additional, Kwok, Andrew, additional, Lee, Angela, additional, Linder, Aline, additional, Lockett, Teresa, additional, Lonie, Lorne, additional, Lopopolo, Maria, additional, Lukoseviciute, Martyna, additional, Luo, Jian, additional, Marinou, Spyridoula, additional, Marsden, Brian, additional, Martinez, Jose, additional, Matthews, Philippa, additional, Mazurczyk, Michalina, additional, McGowan, Simon, additional, McKechnie, Stuart, additional, Mead, Adam, additional, Mi, Yuxin, additional, Monaco, Claudia, additional, Montadon, Ruddy, additional, Napolitani, Giorgio, additional, Nassiri, Isar, additional, Novak, Alex, additional, O'Brien, Darragh, additional, O'Connor, Daniel, additional, O'Donnell, Denise, additional, Ogg, Graham, additional, Overend, Lauren, additional, Park, Inhye, additional, Pavord, Ian, additional, Peng, Yanchun, additional, Penkava, Frank, additional, Pereira Pinho, Mariana, additional, Perez, Elena, additional, Pollard, Andrew, additional, Powrie, Fiona, additional, Psaila, Bethan, additional, Quan, T Phuong, additional, Repapi, Emmanouela, additional, Revale, Santiago, additional, Silva-Reyes, Laura, additional, Richard, Jean-Baptiste, additional, Rich-Griffin, Charlotte, additional, Ritter, Thomas, additional, Rollier, Christine, additional, Rowland, Matthew, additional, Ruehle, Fabian, additional, Salio, Mariolina, additional, Sansom, Stephen Nicholas, additional, Sanches Peres, Raphael, additional, Santos Delgado, Alberto, additional, Sauka-Spengler, Tatjana, additional, Schwessinger, Ron, additional, Scozzafava, Giuseppe, additional, Screaton, Gavin, additional, Seigal, Anna, additional, Semple, Malcolm, additional, Sergeant, Martin, additional, Simoglou Karali, Christina, additional, Sims, David, additional, Skelly, Donal, additional, Slawinski, Hubert, additional, Sobrinodiaz, Alberto, additional, Sousos, Nikolaos, additional, Stafford, Lizzie, additional, Stockdale, Lisa, additional, Strickland, Marie, additional, Sumray, Otto, additional, Sun, Bo, additional, Taylor, Chelsea, additional, Taylor, Stephen, additional, Taylor, Adan, additional, Thongjuea, Supat, additional, Thraves, Hannah, additional, Todd, John, additional, Tomic, Adriana, additional, Tong, Orion, additional, Trebes, Amy, additional, Trzupek, Dominik, additional, Tucci, Felicia Anna, additional, Turtle, Lance, additional, Udalova, Irina, additional, Uhlig, Holm, additional, van Grinsven, Erinke, additional, Vendrell, Iolanda, additional, Verheul, Marije, additional, Voda, Alexandru, additional, Wang, Guanlin, additional, Wang, Lihui, additional, Wang, Dapeng, additional, Watkinson, Peter, additional, Watson, Robert, additional, Weinberger, Michael, additional, Whalley, Justin, additional, Witty, Lorna, additional, Wray, Katherine, additional, Xue, Luzheng, additional, Yuen Yeung, Hing, additional, Yin, Zixi, additional, Young, Rebecca, additional, Youngs, Jonathan, additional, Zhang, Ping, additional, Zurke, Yasemin-Xiomara, additional, Banning, Adrian, additional, Antonopoulos, Alexios, additional, Kelion, Andrew, additional, Kardos, Attila, additional, Hudson, Benjamin, additional, Koo, Bon-Kwon, additional, Kotanidis, Christos, additional, Mahon, Ciara, additional, Berry, Colin, additional, Newby, David, additional, Connolly, Derek, additional, Scaletta, Diane, additional, Nicol, Ed, additional, McAlindon, Elisa, additional, Oikonomou, Evangelos, additional, Pugliese, Francesca, additional, Pontone, Gianluca, additional, Benedetti, Giulia, additional, He, Guo-Wei, additional, West, Henry, additional, Kondo, Hidekazu, additional, Benedek, Imre, additional, Das, Intrajeet, additional, Graby, John, additional, Greenwood, John, additional, Rodrigues, Jonathan, additional, Ge, Junbo, additional, Channon, Keith, additional, Fabritz, Larissa, additional, Fan, Li-Juan, additional, Kingham, Lucy, additional, Guglielmo, Marco, additional, Schmitt, Matthias, additional, Beer, Meinrad, additional, Anderson, Michelle, additional, Desai, Milind, additional, Marwan, Mohamed, additional, Takahashi, Naohiko, additional, Mehta, Nehal, additional, Dai, Neng, additional, Screaton, Nicholas, additional, Sabharwal, Nikant, additional, Maurovich-Horvat, Pál, additional, Kharbanda, Rajesh, additional, Preston, Rebecca, additional, Wood, Richard, additional, Blankstein, Ron, additional, Rajani, Ronak, additional, Mirsadraee, Saeed, additional, Munir, Shahzad, additional, Klömpken, Steffen, additional, Petersen, Steffen, additional, Achenbach, Stephan, additional, Anthony, Susan, additional, Mak, Sze, additional, Mittal, Tarun, additional, Benedek, Theodora, additional, Sharma, Vinoda, additional, and Lin, Wen-Hua, additional

Published
2022
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189. Unbiased single cell spatial analysis localises inflammatory clusters of immature neutrophils-CD8 T cells to alveolar progenitor cells in fatal COVID-19 lungs

Author

Weeratunga, Praveen, Denney, Laura, Bull, Joshua A., Repapi, Emmanouela, Sergeant, Martin, Etherington, Rachel, Chaitanya Vuppussetty, Turner, Gareth D.H., Clelland, Colin, Cross, Amy, Issa, Fadi, De Andrea, Carlos Eduardo, Bermejo, Ignacio Melero, Sims, David, McGowan, Simon, Yasemin-Xiomara Zurke, Ahern, David J., Gamez, Eddie C, Whalley, Justin, Richards, Duncan, Klenerman, Paul, Monaca, Claudia, Udalova, Irina A., Dong, Tao, Ogg, Graham, Knight, Julian C., Byrne, Helen M., Taylor, Stephen, and Ling-Pei Ho

Subjects
Organising pnemonia, Spatial proteomics, Immune-structural interactions, Multi-Dimensional Viewer (MDV) software, Spatial analysis, Inflammatory network, Severe COVID-19 disease, COVID-19 lung disease, Diffuse alveolar damage, Spatial Omics Oxford Pipeline (SpOOx)
Abstract

Single cell spatial interrogation of the immune-structural interactions in COVID -19 lungs is challenging, mainly because of the marked cellular infiltrate and architecturally distorted microstructure. To address this, we developed a suite of mathematical tools to search for statistically significant co-locations amongst immune and structural cells identified using 37-plex imaging mass cytometry. This unbiased method revealed a cellular map interleaved with an inflammatory network of immature neutrophils, cytotoxic CD8 T cells, megakaryocytes and monocytes co-located with regenerating alveolar progenitors and endothelium. Of note, a highly active cluster of immature neutrophils and cytotoxic CD8 T cells, was found spatially linked with alveolar progenitor cells, and temporally with the diffuse alveolar damage stage. These findings provide new insights into how immune cells interact in the lungs of severe COVID-19 disease. We provide our pipeline Spatial Omics Oxford Pipeline (SpOOx)and visual-analytical tool, Multi-Dimensional Viewer (MDV) software, as a resource for spatial analysis.

Published
2022
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190. Middle Eastern Cities in a Time of Climate Crisis

Author

Abosira, Mohammed, Alaeddine, Tala, Badir, Romani, Bonnefoi, Florian, Deboulet, Agnès, Díaz-Bone, León, Dorghamy, Ahmed El, El-Gerzawy, Ragia, Fanchette, Sylvie, Florin, Bénédicte, Garcia, Ibrahim, Ghodbane, Dalila, Hady, Nabeel El, Hassan, Iman, Huybrechts, Eric, Ibrahim, Kareem, Iskandar, Laila, Mansour, Waleed, Menoret, Pascal, Mousa, Heba Attia, Saksouk, Abir, Sayed, Sara, Seyam, Sara, Sims, David, Zaazaa, Ahmed, Deboulet, Agnès, and Mansour, Waleed

Subjects
anthropocene, Economics, sustainable mobility, air pollution, Environmental Studies, urban development challenges, climate change, urban governance, BUS072000, RNU, cities in transition, architecture and rehabilitation, waste, social and ecological justice, urban expansions, nature-based solutions
Abstract

The climate crisis is hitting around the world, including in the Middle East and its cities. Urban regions are exposed to increasingly frequent heat waves and floods that leave decision makers without immediate answers. In the context of this global crisis, this book addresses the need for a better understanding of the current model of urban expansion. Cities are major sources of greenhouse gas (GHG) emissions but they are also celebrated for their contribution to economic growth. The current moment is one of a large paradigm shift as climate change is now recognized as a legitimate public problem. This is especially true for city dwellers, who are increasingly exposed to climate change, the loss of biodiversity and heavy pollution while natural breathing spaces continue to shrink around them. The sixteen chapters of this book do not offer any off-the-rack or technical solutions, but they analyze the urban conundrum and the contribution of cities to the climate crisis. Some chapters focus on individual car ownership, land privatization, waste management and land use changes under the guise of development. Others explore local and contextual answers to urban governance issues. With the support of CEDEJ and the Friedrich-Ebert-Stiftung, researchers, experts and civil society actors explore the ongoing transformations of Middle Eastern urban environments and mobilities and question them in relation to the climate crisis. The contributions are based on empirical knowledge gathered in the Nile Delta, the Greater Cairo Region, Riyadh and Beirut. Without concessions to mainstream thinking, this book contributes to a better understanding of urban challenges, climate threats and policy responses in contexts marked by growing environmental inequalities.

Published
2022

191. Greater Cairo and Greenhouse Gas Emissions

Author

Sims, David

Subjects
anthropocene, fragmented built environments, Economics, desert land, New Administrative Capital, sustainable mobility, air pollution, Environmental Studies, urban development challenges, new towns, private vehicles, climate change, urban sprawl, urban governance, BUS072000, RNU, cities in transition, architecture and rehabilitation, Egypt, waste, social and ecological justice, urban expansions, low residential densities, nature-based solutions
Abstract

Egypt has taken the threats of global climate change seriously. It has adopted all of the United Nations Framework Convention on Climate Change’s (UNFCCC) protocols relating to global warming (in 1994, 2015, 2016 and 2017) and has incorporated global warming concerns in a range of national plans and visions, particularly Egypt’s Vision 2030, the Long-Term Low Emission Development Strategy 2050 and the National Climate Change Strategy 2050 (UNFCCC 2022, 3). It has also taken a number of very v...

Published
2022

198. Circles in the sea: annual courtship “torus” behaviour of basking sharks Cetorhinus maximus identified in the eastern North Atlantic Ocean

Author

Sims, David W., primary, Berrow, Simon D., additional, O'Sullivan, Ken M., additional, Pfeiffer, Nicholas J., additional, Collins, Richard, additional, Smith, Kev L., additional, Pfeiffer, Brianna M., additional, Connery, Paul, additional, Wasik, Shane, additional, Flounders, Lois, additional, Queiroz, Nuno, additional, Humphries, Nicolas E., additional, Womersley, Freya C., additional, and Southall, Emily J., additional

Published
2022
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200. Diving into the vertical dimension of elasmobranch movement ecology

Author

Andrzejaczek, Samantha, primary, Lucas, Tim C.D., additional, Goodman, Maurice C., additional, Hussey, Nigel E., additional, Armstrong, Amelia J., additional, Carlisle, Aaron, additional, Coffey, Daniel M., additional, Gleiss, Adrian C., additional, Huveneers, Charlie, additional, Jacoby, David M. P., additional, Meekan, Mark G., additional, Mourier, Johann, additional, Peel, Lauren R., additional, Abrantes, Kátya, additional, Afonso, André S., additional, Ajemian, Matthew J., additional, Anderson, Brooke N., additional, Anderson, Scot D., additional, Araujo, Gonzalo, additional, Armstrong, Asia O., additional, Bach, Pascal, additional, Barnett, Adam, additional, Bennett, Mike B., additional, Bezerra, Natalia A., additional, Bonfil, Ramon, additional, Boustany, Andre M., additional, Bowlby, Heather D., additional, Branco, Ilka, additional, Braun, Camrin D., additional, Brooks, Edward J., additional, Brown, Judith, additional, Burke, Patrick J., additional, Butcher, Paul, additional, Castleton, Michael, additional, Chapple, Taylor K., additional, Chateau, Olivier, additional, Clarke, Maurice, additional, Coelho, Rui, additional, Cortes, Enric, additional, Couturier, Lydie I. E., additional, Cowley, Paul D., additional, Croll, Donald A., additional, Cuevas, Juan M., additional, Curtis, Tobey H., additional, Dagorn, Laurent, additional, Dale, Jonathan J., additional, Daly, Ryan, additional, Dewar, Heidi, additional, Doherty, Philip D., additional, Domingo, Andrés, additional, Dove, Alistair D. M., additional, Drew, Michael, additional, Dudgeon, Christine L., additional, Duffy, Clinton A. J., additional, Elliott, Riley G., additional, Ellis, Jim R., additional, Erdmann, Mark V., additional, Farrugia, Thomas J., additional, Ferreira, Luciana C., additional, Ferretti, Francesco, additional, Filmalter, John D., additional, Finucci, Brittany, additional, Fischer, Chris, additional, Fitzpatrick, Richard, additional, Forget, Fabien, additional, Forsberg, Kerstin, additional, Francis, Malcolm P., additional, Franks, Bryan R., additional, Gallagher, Austin J., additional, Galvan-Magana, Felipe, additional, García, Mirta L., additional, Gaston, Troy F., additional, Gillanders, Bronwyn M., additional, Gollock, Matthew J., additional, Green, Jonathan R., additional, Green, Sofia, additional, Griffiths, Christopher A., additional, Hammerschlag, Neil, additional, Hasan, Abdi, additional, Hawkes, Lucy A., additional, Hazin, Fabio, additional, Heard, Matthew, additional, Hearn, Alex, additional, Hedges, Kevin J., additional, Henderson, Suzanne M., additional, Holdsworth, John, additional, Holland, Kim N., additional, Howey, Lucy A., additional, Hueter, Robert E., additional, Humphries, Nicholas E., additional, Hutchinson, Melanie, additional, Jaine, Fabrice R. A., additional, Jorgensen, Salvador J., additional, Kanive, Paul E., additional, Labaja, Jessica, additional, Lana, Fernanda O., additional, Lassauce, Hugo, additional, Lipscombe, Rebecca S., additional, Llewellyn, Fiona, additional, Macena, Bruno C. L., additional, Mambrasar, Ronald, additional, McAllister, Jaime D., additional, McCully Phillips, Sophy R., additional, McGregor, Frazer, additional, McMillan, Matthew N., additional, McNaughton, Lianne M., additional, Mendonça, Sibele A., additional, Meyer, Carl G., additional, Meyers, Megan, additional, Mohan, John A., additional, Montgomery, John C., additional, Mucientes, Gonzalo, additional, Musyl, Michael K., additional, Nasby-Lucas, Nicole, additional, Natanson, Lisa J., additional, O’Sullivan, John B., additional, Oliveira, Paulo, additional, Papastamtiou, Yannis P., additional, Patterson, Toby A., additional, Pierce, Simon J., additional, Queiroz, Nuno, additional, Radford, Craig A., additional, Richardson, Andy J., additional, Richardson, Anthony J., additional, Righton, David, additional, Rohner, Christoph A., additional, Royer, Mark A., additional, Saunders, Ryan A., additional, Schaber, Matthias, additional, Schallert, Robert J., additional, Scholl, Michael C., additional, Seitz, Andrew C., additional, Semmens, Jayson M., additional, Setyawan, Edy, additional, Shea, Brendan D., additional, Shidqi, Rafid A., additional, Shillinger, George L., additional, Shipley, Oliver N., additional, Shivji, Mahmood S., additional, Sianipar, Abraham B., additional, Silva, Joana F., additional, Sims, David W., additional, Skomal, Gregory B., additional, Sousa, Lara L., additional, Southall, Emily J., additional, Spaet, Julia L. Y., additional, Stehfest, Kilian M., additional, Stevens, Guy, additional, Stewart, Joshua D., additional, Sulikowski, James A., additional, Syakurachman, Ismail, additional, Thorrold, Simon R., additional, Thums, Michele, additional, Tickler, David, additional, Tolloti, Mariana T., additional, Townsend, Kathy A., additional, Travassos, Paulo, additional, Tyminski, John P., additional, Vaudo, Jeremy J., additional, Veras, Drausio, additional, Wantiez, Laurent, additional, Weber, Sam B., additional, Wells, R.J. David, additional, Weng, Kevin C., additional, Wetherbee, Bradley M., additional, Williamson, Jane E., additional, Witt, Matthew J., additional, Wright, Serena, additional, Zilliacus, Kelly, additional, Block, Barbara A., additional, and Curnick, David J., additional

Published
2022
Full Text
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