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Start Over Author "Cooper, J." Publication Year Range Last 10 years Publisher elsevier b.v.
43 results on '"Cooper, J."'

2. SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination

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Baillie, J. Kenneth, Openshaw, Peter J.M., Semple, Malcolm G., Alex, Beatrice, Andrikopoulos, Petros, Bach, Benjamin, Barclay, Wendy S., Bogaert, Debby, Chand, Meera, Chechi, Kanta, Cooke, Graham S., da Silva Filipe, Ana, de Silva, Thushan, Docherty, Annemarie B., dos Santos Correia, Gonçalo, Dumas, Marc-Emmanuel, Dunning, Jake, Fletcher, Tom, Green, Christopher A., Greenhalf, William, Griffin, Julian, Gupta, Rishi K., Harrison, Ewen M., Ho, Antonia Y.W., Holden, Karl, Horby, Peter W., Ijaz, Samreen, Khoo, Say, Klenerman, Paul, Law, Andrew, Lewis, Matthew, Liggi, Sonia, Lim, Wei Shen, Maslen, Lynn, Mentzer, Alexander J., Merson, Laura, Meynert, Alison M, Moore, Shona C., Noursadeghi, Mahdad, Olanipekun, Michael, Osagie, Anthonia, Palmarini, Massimo, Palmieri, Carlo, Paxton, William A., Pollakis, Georgios, Price, Nicholas, Rambaut, Andrew, Robertson, David L, Russell, Clark D., Sancho-Shimizu, Vanessa, Sands, Caroline, 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, Thomson, Emma C., Thwaites, Ryan S., Turtle, Lance C.W., Zambon, Maria, Drake, Thomas M., Fairfield, Cameron J., Knight, Stephen R., Mclean, Kenneth A., Murphy, Derek, Norman, Lisa, Pius, Riinu, Shaw, Catherine A., Connor, Marie, Dalton, Jo, Gamble, Carrol, Girvan, Michelle, Halpin, Sophie, Harrison, Janet, Jackson, Clare, Lee, James, Marsh, Laura, Plotkin, Daniel, Roberts, Stephanie, Saviciute, Egle, Clohisey, Sara, Hendry, Ross, Knight, Susan, Lahnsteiner, Eva, Leeming, Gary, Norris, Lucy, Scott-Brown, James, Tait, Sarah, Wham, Murray, Clark, Richard, Coutts, Audrey, Donelly, Lorna, Fawkes, Angie, Gilchrist, Tammy, Hafezi, Katarzyna, MacGillivray, Louise, Maclean, Alan, McCafferty, Sarah, Morrice, Kirstie, Murphy, Lee, Wrobel, Nicola, Carson, Gail, 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, Brittain-Long, Robin, Bulteel, Naomi, Burden, Tom, Burtenshaw, Andrew, Caruth, Vikki, Chadwick, David, Chambler, Duncan, Chee, Nigel, Child, Jenny, Chukkambotla, Srikanth, Clark, Tom, Collini, Paul, Cosgrove, Catherine, Cupitt, Jason, Cutino-Moguel, Maria-Teresa, Dark, Paul, Dawson, Chris, Dervisevic, Samir, Donnison, Phil, Douthwaite, Sam, Drummond, Andrew, DuRand, Ingrid, Dushianthan, Ahilanadan, Dyer, Tristan, Evans, Cariad, Eziefula, Chi, Fegan, Chrisopher, Finn, Adam, Fullerton, Duncan, Garg, Sanjeev, Garg, Atul, Gkrania-Klotsas, Effrossyni, Godden, Jo, Goldsmith, Arthur, Graham, Clive, Grammatikopoulos, Tassos, Hardy, Elaine, Hartshorn, Stuart, Harvey, Daniel, Havalda, Peter, Hawcutt, Daniel B., Hobrok, Maria, Hodgson, Luke, Hormis, Anil, Howard, Joanne, 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, Moses, Samuel, Mpenge, Mbiye, Mulla, Rohinton, Murphy, Michael, Nagarajan, Thapas, Nagel, Megan, Nelson, Mark, Norris, Lillian, O'Shea, Matthew K., Ostermann, Marlies, Otahal, Igor, Pais, Mark, Panchatsharam, Selva, Papakonstantinou, Danai, Papineni, Padmasayee, Paraiso, Hassan, Patel, Brij, Pattison, Natalie, Pepperell, Justin, Peters, Mark, Phull, Mandeep, Pintus, Stefania, 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, Sarah, Sarah, Schmid, Matthias, Shah, Aarti, Shankar-Hari, Manu, Shanmuga, Prad, Sharma, Anil, Shawcross, Anna, Singh Pooni, Jagtur, Sizer, Jeremy, 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, Rachel, Vincent-Smith, Lisa, Visuvanathan, Shico, Vuylsteke, Alan, Waddy, Sam, Wake, Rachel, Walden, Andrew, Welters, Ingeborg, Whitehouse, Tony, Whittaker, Paul, Whittington, Ashley, Wijesinghe, Meme, Williams, Martin, Wilson, Lawrence, Winchester, Stephen, Wiselka, Martin, Wolverson, Adam, Wootton, Daniel G, Workman, Andrew, Yates, Bryan, Young, Peter, McDonald, Sarah E., Shaw, 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Petousi, N., Petrie, J., Pfeffer, P., Phipps, J., Pimm, J., Piper Hanley, K., Pius, R., Plant, H., Plein, S., Plekhanova, T., Plowright, M., Poinasamy, K., Polgar, O., Poll, L., Porter, J.C., Porter, J., Portukhay, S., Powell, N., Prabhu, A., Pratt, J., Price, A., Price, C., Price, D., Price, L., Prickett, A., Propescu, J., Prosper, S., Pugmire, S., Quaid, S., Quigley, J., Quint, J., Qureshi, H., Qureshi, I.N., Radhakrishnan, K., Rahman, N.M., Ralser, M., Raman, B., Ramos, A., Ramos, H., Rangeley, J., Rangelov, B., Ratcliffe, L., Ravencroft, P., Reddington, A., Reddy, R., Redfearn, H., Redwood, D., Reed, A., Rees, M., Rees, T., Regan, K., Reynolds, W., Ribeiro, C., Richards, A., Richardson, E., Richardson, M., Rivera-Ortega, P., Roberts, K., Robertson, E., Robinson, E., Robinson, L., Roche, L., Roddis, C., Rodger, J., Ross, A., Ross, G., Rossdale, J., Rostron, A., Rowe, A., Rowland, A., Rowland, J., Rowland, M.J., Rowland-Jones, S.L., Roy, K., Roy, M., Rudan, I., Russell, R., Russell, 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N., Steiner, M., Stensel, D., Stephens, G., Stephenson, L., Stern, M., Stewart, I., Stimpson, R., Stockdale, S., Stockley, J., Stoker, W., Stone, R., Storrar, W., Storrie, A., Storton, K., Stringer, E., Strong-Sheldrake, S., Stroud, N., Subbe, C., Sudlow, C.L., Suleiman, Z., Summers, C., Summersgill, C., Sutherland, D., Sykes, D.L., Sykes, R., Talbot, N., Tan, A.L., Tarusan, L., Tavoukjian, V., Taylor, A., Taylor, C., Taylor, J., Te, A., Tedd, H., Tee, C.J., Teixeira, J., Tench, H., Terry, S., Thackray-Nocera, S., Thaivalappil, F., Thamu, B., Thickett, D., Thomas, C., Thomas, D.C., Thomas, S., Thomas, A.K., Thomas-Woods, T., Thompson, T., Thompson, A.A.R., Thornton, T., Thorpe, M., Thwaites, R.S., Tilley, J., Tinker, N., Tiongson, G.F., Tobin, M., Tomlinson, J., Tong, C., Toshner, M., Touyz, R., Tripp, K.A., Tunnicliffe, E., Turnbull, A., Turner, E., Turner, S., Turner, V., Turner, K., Turney, S., Turtle, L., Turton, H., Ugoji, J., Ugwuoke, R., Upthegrove, R., Valabhji, J., Ventura, M., Vere, J., Vickers, C., Vinson, B., Wade, E., Wade, P., Wain, L.V., Wainwright, T., Wajero, L.O., Walder, S., Walker, S., Wall, E., Wallis, T., Walmsley, S., Walsh, J.A., Walsh, S., Warburton, L., Ward, T.J.C., Warwick, K., Wassall, H., Waterson, S., Watson, E., Watson, L., Watson, J., Weir McCall, J., Welch, C., Welch, H., Welsh, B., Wessely, S., West, S., Weston, H., Wheeler, H., White, S., Whitehead, V., Whitney, J., Whittaker, S., Whittam, B., Whitworth, V., Wight, A., Wild, J., Wilkins, M., Wilkinson, D., Williams, B., Williams, N., Williams, J., Williams-Howard, S.A., Willicombe, M., Willis, G., Willoughby, J., Wilson, A., Wilson, D., Wilson, I., Window, N., Witham, M., Wolf-Roberts, R., Wood, C., Woodhead, F., Woods, J., Wootton, D.G., Wormleighton, J., Worsley, J., Wraith, D., Wrey Brown, C., Wright, C., Wright, L., Wright, S., Wyles, J., Wynter, I., Xu, M., Yasmin, N., Yasmin, S., Yates, T., Yip, K.P., Young, B., Young, S., Young, A., Yousuf, A.J., Zawia, A., Zeidan, L., Zhao, B., Zheng, B., Zongo, O., Liew, Felicity, Talwar, Shubha, Cross, Andy, Willett, Brian J., Scott, Sam, Logan, Nicola, Siggins, Matthew K., Swieboda, Dawid, Sidhu, Jasmin K., Efstathiou, Claudia, Davis, Chris, Mohamed, Noura, Nunag, Jose, King, Clara, Rowland-Jones, Sarah L., Chalmers, James D., Ho, Ling-Pei, Horsley, Alexander, Raman, Betty, Poinasamy, Krisnah, Marks, Michael, Kon, Onn Min, Howard, Luke, Wootton, Daniel G., Dunachie, Susanna, Quint, Jennifer K., Evans, Rachael A., Wain, Louise V., Fontanella, Sara, de Silva, Thushan I., Ho, Antonia, Harrison, Ewen, Brightling, Christopher, and Turtle, Lance

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2023
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6. The instrument suite of the European Spallation Source

Author

Andersen, K.H., Argyriou, D.N, Jackson, A.J., Houston, J., Henry, P.F., Deen, P.P., Toft-Petersen, R., Beran, P., Strobl, M., Arnold, T., Wacklin-Knecht, H., Tsapatsaris, N., Oksanen, E., Woracek, R., Schweika, W., Mannix, D., Hiess, A., Kennedy, S., Kirstein, O., Petersson Årsköld, S., Taylor, J., Hagen, M.E., Laszlo, G., Kanaki, K., Piscitelli, F., Khaplanov, A., Stefanescu, I., Kittelmann, Th., Pfeiffer, D., Hall-Wilton, R., Lopez, C.I., Aprigliano, G., Whitelegg, L., Moreira, F.Y., Olsson, M., Bordallo, H.N., Martín-Rodríguez, D., Schneider, H., Sharp, M., Hartl, M., Nagy, G., Ansell, S., Pullen, S., Vickery, A., Fedrigo, A., Mezei, F., Arai, M., Heenan, R.K., Halcrow, W., Turner, D., Raspino, D., Orszulik, A., Cooper, J., Webb, N., Galsworthy, P., Nightingale, J., Langridge, S., Elmer, J., Frielinghaus, H., Hanslik, R., Gussen, A., Jaksch, S., Engels, R., Kozielewski, T., Butterweck, S., Feygenson, M., Harbott, P., Poqué, A., Schwaab, A., Lieutenant, K., Violini, N., Voigt, J., Brückel, T., Koenen, M., Kämmerling, H., Babcock, E., Salhi, Z., Wischnewski, A., Heynen, A., Désert, S., Jestin, J., Porcher, F., Fabrèges, X., Fabrèges, G., Annighöfer, B., Klimko, S., Dupont, Th., Robillard, Th., Goukassov, A., Longeville, S., Alba-Simionesco, Ch., Bourges, Ph., Guyon Le Bouffy, J., Lavie, P., Rodrigues, S., Calzada, E., Lerche, M., Schillinger, B., Schmakat, Ph., Schulz, M., Seifert, M., Lohstroh, W., Petry, W., Neuhaus, J., Loaiza, L., Tartaglione, A., Glavic, A., Schütz, S., Stahn, J., Lehmann, E., Morgano, M., Schefer, J., Filges, U., Klauser, Ch., Niedermayer, Ch., Fenske, J., Nowak, G., Rouijaa, M., Siemers, D.J., Kiehn, R., Müller, M., Carlsen, H., Udby, L., Lefmann, K., Birk, J.O., Holm-Dahlin, S., Bertelsen, M., Hansen, U. Bengaard, Olsen, M.A., Christensen, M., Iversen, K., Christensen, N.B., Rønnow, H.M., Freeman, P.G., Hauback, B.C., Kolevatov, R., Llamas-Jansa, I., Orecchini, A., Sacchetti, F., Petrillo, C., Paciaroni, A., Tozzi, P., Zanatta, M., Luna, P., Herranz, I., del Moral, O.G., Huerta, M., Magán, M., Mosconi, M., Abad, E., Aguilar, J., Stepanyan, S., Bakedano, G., Vivanco, R., Bustinduy, I., Sordo, F., Martínez, J.L., Lechner, R.E., Villacorta, F.J., Šaroun, J., Lukáš, P., Markó, M., Zanetti, M., Bellissima, S., del Rosso, L., Masi, F., Bovo, C., Chowdhury, M., De Bonis, A., Di Fresco, L., Scatigno, C., Parker, S.F., Fernandez-Alonso, F., Colognesi, D., Senesi, R., Andreani, C., Gorini, G., Scionti, G., and Schreyer, A.

Published
2020
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11. Single-molecule dynamics of DNA gyrase in evolutionarily distant bacteria Mycobacterium tuberculosis and Escherichia coli.

Author

Galvin, Cooper J., Hobson, Matthew, Xianglong Meng, Jonathan, Ierokomos, Athena, Ivanov, Ivan E., Berger, James M., and Bryant, Zev

Subjects
*DNA topoisomerase II, *ESCHERICHIA coli, *MYCOBACTERIUM tuberculosis, *BACTERIA, *ANTIBIOTICS, *SPECIES
Abstract

DNA gyrase is an essential nucleoprotein motor present in all bacteria and is a major target for antibiotic treatment of Mycobacterium tuberculosis (MTB) infection. Gyrase hydrolyzes ATP to add negative supercoils to DNA using a strand passage mechanism that has been investigated using biophysical and biochemical approaches. To analyze the dynamics of substeps leading to strand passage, single-molecule rotor bead tracking (RBT) has been used previously to follow real-time supercoiling and conformational transitions in Escherichia coli (EC) gyrase. However, RBT has not yet been applied to gyrase from other pathogenically relevant bacteria, and it is not known whether substeps are conserved across evolutionarily distant species. Here, we compare gyrase supercoiling dynamics between two evolutionarily distant bacterial species, MTB and EC. We used RBT to measure supercoiling rates, processivities, and the geometries and transition kinetics of conformational states of purified gyrase proteins in complex with DNA. Our results show that E. coli and MTB gyrases are both processive, with the MTB enzyme displaying velocities ~5.5× slower than the EC enzyme. Compared with EC gyrase, MTB gyrase also more readily populates an intermediate state with DNA chirally wrapped around the enzyme, in both the presence and absence of ATP. Our substep measurements reveal common features in conformational states of EC and MTB gyrases interacting with DNA but also suggest differences in populations and transition rates that may reflect distinct cellular needs between these two species. [ABSTRACT FROM AUTHOR]

Published
2023
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12. Filtration performance of three models of N95 filtering facepiece respirators following clinical usage and vaporized hydrogen peroxide decontamination.

Author

Cooper, J., Csapó, A., Ranasinghe, R., Jeronimo, M., Brockington-Tyhy, T., Alawfi, S., and Wong, T.

Abstract

Background: N95 filtering facepiece respirators (FFRs) are essential personal protective equipment (PPE) for protecting healthcare workers from airborne pathogens.Aim: To perform the first large-scale evaluation of particulate filtration efficiency (PFE) of three models of N95 FFRs following clinical usage and vaporized hydrogen peroxide (VHP) decontamination.Methods: Three variables were assessed for effect on PFE following VHP decontamination: VHP sterilizer model, N95 respirator model, and prior N95 clinical usage.Findings: The VHP sterilizer model and N95 FFR model impacted PFE performance. Worn N95 FFRs had a 91% lower odds of exhibiting ≥95% PFE compared with the control.Conclusion: This work highlights the importance of validating any N95 FFR decontamination programme in its entirety, including prior clinical usage. [ABSTRACT FROM AUTHOR]

Published
2023
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13. Evaluation of a new sink design incorporating ozonated water.

Author

Cooper, J, Himaras, Y, Wong, T, and Bryce, E

Abstract

Background: Novel sink and U-trap designs have been developed to reduce contamination by users and diminish biofilm. Real-world experience with new sink designs and adjunctive measures such as ozone has been limited.Aims: To assess a new sink design for splashback and to evaluate the ozonated water feature for reduction of microbial bioburden.Methods: A portable sink unit was created that permitted the application of white absorbent paper to plexiglass shields beside and behind the sink. Participants, wearing painter coveralls and masks, spread 30 mL of tempera paint over their hands and washed for 20 s with neutral soap. Each participant repeated this five times sequentially, and cumulative results were recorded. Escherichia coli was exposed to ozonated water from the sink unit and to regular tap water and evaluated for microbial survival.Findings: Compared with a conventional sink, the SmartFLO3 sink had less environmental contamination within the sink, surrounding area and splashback on to the participant. Despite modifications to enhance ozone generation, readings of reactive oxygen species did not exceed 0.3 ppm, and no significant bactericidal effect was demonstrated.Conclusions: The SmartFLO3 sink reduces splashback and has the potential to reduce pathogen transmission from sinks. At the low levels of ozone generated in this study, no clear bacterial killing effect was observed compared with tap water alone. [ABSTRACT FROM AUTHOR]

Published
2020
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15. COVID-19 preventive measures showing an unintended decline in infectious diseases in Taiwan.

Author

Galvin, Cooper J., Li, Yu-Chuan (Jack), Malwade, Shwetambara, and Syed-Abdul, Shabbir

Subjects
*COMMUNICABLE diseases, *COVID-19, *COVID-19 pandemic, *SOCIAL distancing, *MEDICAL masks
Abstract

• A pandemic situation may increase public awareness to take necessary precautions. • The Taiwan government encouraged the use of face masks and sanitizer, as well as social distancing as a part of prevention during the COVID-19 outbreak. • This response may have contributed to a decline in other infectious diseases. Most of the communicable diseases have contact, airborne and/or droplet mode of transsmission. Following the outbreak of COVID-19, the Taiwan government implemented the use of masks and sanitizer, as well as other preventive measures like social distancing for prevention. This public response likely contributed significantly to the decline in the outbreak of other infectious diseases. [ABSTRACT FROM AUTHOR]

Published
2020
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16. Why coastal regulations fail.

Author

Neal, William J., Pilkey, Orrin H., Cooper, J. Andrew G., and Longo, Norma J.

Subjects
DECISION making, WETLAND mitigation, POLITICAL stability, COASTS
Abstract

This perspective examines case examples, primarily from the U. S. Carolinas and Alabama, that illustrate some of the flaws of four federal programs of the last 50 years (National Flood Insurance Program, U. S. Coastal Barrier Resources Act, Coastal Area Management Act, Stafford Disaster Relief Act), as well as general reasons for state and local regulation failures. The latter include: variances that undercut the regulatory intent by the tyranny of small decisions, emergency dispensations, and compensatory mitigation; allowances for ‘temporary’ shore-hardening structures that become permanent; establishing control lines that are not adjusted to shifting shorelines; over-simplifying (one-size-fits-all) and misapplying (importing inappropriate strategies) regulations; conflicting jurisdictional boundaries; and the political instability of regulatory laws. Political-legislative realm failures include: 1) generalized laws do not match the complexity of coasts; 2) legislators lack the foresight to provide funding for regulatory monitoring/enforcement/penalties; 3) legislative bodies lack continuity of visions or goals for the future (e.g., overturn or weaken prior regulatory legislation); and 4) politicians are subject to conflicts of interest (e.g., affluent coastal land owners; pro-development lobbies). The political-legislative disconnect from the reality of Nature, and failure to use longer-term projections of erosion rates, sediment supply, and effects of sea-level rise, are the most frequent culprits in regulatory failure. New starting points for sound regulatory coastal management are better-informed politicians with the will to enact laws based on science that reflect natural variability, and laws that are unflawed by variances or over simplification. Regulations need to have continuity, proper funding, and enforcement. [ABSTRACT FROM AUTHOR]

Published
2018
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20. Seismic architecture, stratigraphy and evolution of a subtropical marine embayment: Maputo Bay, Mozambique.

Author

Green, Andrew N., Cooper, J. Andrew G., Wiles, Errol A., and De Lecea, Ander M.

Subjects
*SUBMARINE geology, *STRATIGRAPHIC geology, *HURRICANES, *BEACHROCK, *GLACIAL melting
Abstract

The seismic stratigraphy, architecture and evolution of a large subtropical embayment, Maputo Bay, Southern Mozambique is described. Nine seismic units are documented; and show repeated phases of incised valley formation and transgressive infilling. Trangressive infilling alternates between the classic wave-dominated transgressive succession of fluvial and central estuarine bay deposits and the filling by intertidal flat and tidal bedforms developed during stages of inlet restriction and shallowing associated with barrier growth at stillstand intervals. Imprinted on the succession are several key facets of subtropical stratigraphy, hurricane-generated erosional surfaces and beachrock horizons. The upper stratigraphy comprises the highstand bayhead delta, a prograding feature constructed by several flood events. In comparison with literature from other similar systems such as lagoons, coastal lakes and estuaries, a generic three stage stratigraphic model of large marine embayments is proposed that includes incision during glaciations; transgressive infilling during deglaciations; and shallowing during the stillstand episodes of the recent deglaciation. [ABSTRACT FROM AUTHOR]

Published
2015
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23. Accelerating the global response against the exponentially growing COVID-19 outbreak through decent data sharing.

Author

Galvin, Cooper J, Fernandez-Luque, Luis, and Li, Yu-Chuan (Jack)

Subjects
*COVID-19 pandemic, *INFORMATION sharing, *SARS-CoV-2, *COVID-19, *SYNTHETIC fuels, *PREDICTION models
Abstract

The novel coronavirus disease 2019 (COVID-19) is a novel and exponentially growing disease, and consequently, the accelerated development of knowledge from good data is possible quickly and globally. In order to combat the global pandemic of COVID-19, all humans on earth need to make difficult strategic decisions on three very different scales, all fueled by Analytical and Artificial Intelligence-based predictive Models. [ABSTRACT FROM AUTHOR]

Published
2021
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25. Diverse lineages of multidrug resistant clinical Salmonella enterica and a cryptic outbreak in New Hampshire, USA revealed from a year-long genomic surveillance.

Author

Park, Cooper J., Li, Jinfeng, Zhang, Xinglu, Gao, Fengxiang, Benton, Christopher S., and Andam, Cheryl P.

Subjects
*SALMONELLA enterica, *TYPHOID fever, *SALMONELLA diseases, *GASTROINTESTINAL agents, *SINGLE nucleotide polymorphisms, *MULTIDRUG resistance
Abstract

Salmonella enterica , the causative agent of gastrointestinal diseases and typhoid fever, is a human and animal pathogen that causes significant mortality and morbidity worldwide. In this study, we examine the genomic diversity and phylogenetic relationships of 63 S. enterica isolates from human-derived clinical specimens submitted to the Department of Health and Human Services (DHHS) in the state of New Hampshire, USA in 2017. We found a remarkably large genomic, phylogenetic and serotype variation among the S. enterica isolates, dominated by serotypes Enteritidis (sequence type [ST] 11), Heidelberg (ST 15) and Typhimurium (ST 19). Analysis of the distribution of single nucleotide polymorphisms in the core genome suggests that the ST 15 cluster is likely a previously undetected or cryptic outbreak event that occurred in the south/southeastern part of New Hampshire in August–September. We found that nearly all of the clinical S. enterica isolates carried horizontally acquired genes that confer resistance to multiple classes of antimicrobials, most notably aminoglycosides, fluoroquinolones and macrolides. Majority of the isolates (76.2%) carry at least four resistance determinants per genome. We also detected the genes mdtK and mdsABC that encode multidrug efflux pumps and the gene sdiA that encodes a regulator for a third multidrug resistance pump. Our results indicate rapid microevolution and geographical dissemination of multidrug resistant lineages over a short time span. These findings are critical to aid the DHHS and similar public health laboratories in the development of effective disease control measures, epidemiological studies and treatment options for serious Salmonella infections. • Large genomic, phylogenetic and serotype variation in S. enterica. • Genetic determinants that confer resistance to multiple classes of antimicrobials. • Genes that encode or regulate multidrug efflux pumps. • A previously undetected or cryptic outbreak event in August–September. • Microevolution and geographical dissemination of multidrug resistance in one year. [ABSTRACT FROM AUTHOR]

Published
2021
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30. Late Quaternary evolution and sea-level history of a glaciated marine embayment, Bantry Bay, SW Ireland.

Author

Plets, Ruth M.K., Callard, S. Louise, Cooper, J. Andrew G., Long, Antony J., Quinn, Rory J., Belknap, Daniel F., Edwards, Robin J., Jackson, Derek W.T., Kelley, Joseph T., Long, David, Milne, Glenn A., and Monteys, Xavier

Subjects
*SEA level, *SHORELINES, *GLACIATION, *RADIOCARBON dating, *GEOPHYSICS
Abstract

Ireland experienced a spatially complex pattern of relative sea-level (RSL) changes and shoreline development caused by the interplay of isostatic and eustatic (ice equivalent sea level) processes since the Last Glacial Maximum (LGM). Using a combination of high-resolution marine geophysical data, vibrocores, foraminiferal analysis and 10 AMS radiocarbon dates, we reconstruct the Late Quaternary evolution and RSL history of Bantry Bay, a large (40 km long, 5–10 km wide) embayment in SW Ireland. The data indicate two infill phases: one before and one after the LGM, separated by glacial and lowstand sediments. The pre-LGM history is not dated and the depositional history is inferred. A large sediment lobe formed at the outer edge of Bantry Bay as a lowstand ice-proximal glacimarine outwash system as the ice retreated after the LGM, at a sea level ca. 80 m lower than present. Iceberg scour immediately west of this location likely relate to the break-up of the local Kerry–Cork Ice Cap. Long curvilinear ridges, seen both offshore and on top of the sediment lobe, probably formed as shoreface ridges under stronger-than-present tidal currents during a period of RSL stability (pre-14.6 ka cal BP). A subsequent infill phase is characterised by a basin-wide erosional (ravinement) surface and the deposition of inter- and sub-tidal estuarine sediments. Although our data support the general trends, our stratigraphic and radiocarbon data suggest a higher sea level between 11 and 13.5 ka cal BP than predicted by existing glacial isostatic adjustment models. [ABSTRACT FROM AUTHOR]

Published
2015
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31. Comparison of Holstein-Friesian and Norwegian Red dairy cattle for estrus length and estrous signs.

Author

Sveberg, G., Rogers, G. W., Cooper, J., Refsdal, A. O., Erhard, H. W., Kommisrud, E., Buckley, F., Waldmann, A., and Ropstad, E.

Subjects
*ESTRUS, *CATTLE fertility, *HOLSTEIN-Friesian cattle, *MAMMAL fertility, *REPRODUCTION
Abstract

This study addressed the effect of breed on estrus length and estrous behavior by observing 20 Holstein-Friesian (HF) and 20 Norwegian Red (NRF) cows on an outdoor wood-chip pad through 1 estrous cycle (22 d). Detailed behavioral data were collected by continuous (24 h) video monitoring of all cows. Accurate estimation of duration of estrous periods, behavioral signs (sum per period and counts per hour), and duration and number of sexually active groups were reported through all stages of mount estrus (prestand, standing estrus, and poststand). These dependent variables were analyzed with a basic statistical model that included fixed effects for breed and lactation group. Other independent variables (milk yield, body condition score, and number of cows in standing estrus) were added to the basic model one by one and included in an expanded model if they had an effect on the respective dependent variables. Estrus duration was considerably shorter in HF compared with NRF cows for all the major periods: mount estrus (11.2 ± 3.0 vs 21.3 ± 2.7 h), standing estrus (7.1 ± 1.4 vs 11.7 ± 1.3 h), mounting period (6.9 ± 2.7 vs 18.2 ± 2.4 h), and mounted period (9.2 ± 2.8 vs 17.5 ± 2.6 h). Additionally, the NRF cows spent more time in sexually active groups (36.1 ± 4.0 vs 17.6 ± 4.8%) during standing estrus compared with HF cows. The NRF cows participated in a greater number of sexually active groups (9.6 ± 1.3 vs 5.5 ± 1.3) with longer average duration (0.42 ± 0.04 vs 0.20 ± 0.04 h) and continued to be more active in these groups through late stages of estrus (poststand) compared with the HF breed. Mounting activity differed between breeds as NRF mounted more times in total (46.3 ± 6.2 vs 18.1 ± 6.3) and per hour (2.6 ± 0.4 vs 1.5 ± 0.5) during mount estrus. In addition, NRF tended to express the primary estrous sign, standing when mounted, more often during standing estrus (32.4 ± 5.0 vs 18.5 ± 5.2). The HF initiated more unsuccessful mounts (1.6 ± 0.3 vs 0.6 ± 0.3) per hour than did NRF during mount estrus. A significant effect of milk yield was demonstrated only on this behavior. For other estrous signs, HF cows initiated chase-up (2.0 ± 0.5 vs 0.5 ± 0.4) and anogenital sniff (3.7 ± 0.6 vs 2.0 ± 0.5) more frequently (counts per hour), whereas NRF expressed more total head butt behavior (32.3 ± 4.7 vs 14.2 ± 4.8) during mount estrus. Body condition score had a significant effect on receptive behavior. Measures of estrus duration, sexually active group activity, and behavior related to estrus should be subjected to larger studies for improved heat detection and possible implementation in breeding programs. [ABSTRACT FROM AUTHOR]

Published
2015
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32. COMPARISON OF IN-HOSPITAL CARDIOVASCULAR OUTCOMES BETWEEN PATIENTS UNDERGOING ALLOGENEIC VERSUS AUTOLOGOUS HEMATOPOIETIC STEM CELL TRANSPLANTATION.

Author

Krishan, Satyam, Asad, Zain Ul Abideen, Quiroga, Dionisia, ghazi, sanam, Quartermaine, Cooper J., Braunstein, Zachary, Kola-Kehinde, Onaopepo O., Shaaban, Adnan, Habib, Alma, Khan, Sarah, Cheng, Richard Kar-Hang, Brammer, Jonathan, and Addison, Daniel

Subjects
*STEM cell transplantation, *HEMATOPOIETIC stem cell transplantation
Published
2024
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33. Glial activation precedes alpha-synuclein pathology in a mouse model of Parkinson's disease.

Author

Izco, Maria, Blesa, Javier, Verona, Guglielmo, Cooper, J Mark, and Alvarez-Erviti, Lydia

Subjects
*LABORATORY mice, *PARKINSON'S disease, *ALPHA-synuclein, *ANIMAL disease models, *SUBSTANTIA nigra
Abstract

[Display omitted] • Microglial cell activation in SNpc precedes alpha-synuclein inclusion formation. • In striatum a significant astrogliosis was observed 90 dpi. • Alpha-synuclein monomer did not result in long-term glia activation. • Neuroinflammation is an early event in PD pathogenesis. Neuroinflammation is increasingly recognized as an important feature in the pathogenesis of Parkinson's disease (PD). However, it remains unclear whether neuroinflammation contributes to nigral degeneration in PD or is merely a secondary marker of neurodegeneration. We aimed to investigate the temporal relationship between synucleopathy, neuroinflammation and nigrostriatal degeneration in a mouse model of PD. Mice received unilateral intrastriatal injection of alpha-synuclein pre-formed fibrils, alpha-synuclein monomer or vehicle and were sacrificed at 15, 30 and 90 days post-injection. Intrastriatal inoculation of alpha-synuclein fibrils led to significant alpha-synuclein aggregation in the substantia nigra peaking at 30 days after injection while the significant increase in Iba-1 cells, GFAP cells and IL-1β expression peaked earlier at 15 days. At 90 days, the striatal dopaminergic denervation was associated with astroglial activation. Alpha-synuclein monomer did not result in long-term glia activation or increase in inflammatory markers. The spread of alpha-synuclein aggregates into the cortex was not associated with any changes to neuroinflammatory markers. Our results demonstrate that in the substantia nigra glial activation is an early event that precedes alpha-synuclein inclusion formation, suggesting neuroinflammation could play an important early role in the pathogenesis of PD. [ABSTRACT FROM AUTHOR]

Published
2021
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34. Whole-island wind bifurcation and localized topographic steering: Impacts on aeolian dune dynamics.

Author

Smith, Alex, Jackson, Derek W.T., Cooper, J. Andrew G., Beyers, Meiring, and Breen, Colin

Abstract

Topographic steering has been observed around Gran Canaria, a high-profile circular island located in the Canary Island Archipelago, Spain, culminating in a complex lee-side wind regime at the Maspalomas dunefield. Maspalomas has experienced rapid environmental changes since the 1960s, coincident with a boom in the tourism industry in the region and requires further examination on the linkages between meso-scale airflow patterns and aeolian processes modifying the landscape. The aim of this work is to simulate mean and turbulent airflow conditions at Maspalomas due to incremental changes in the regional wind direction and to compare these results to the predicted and observed aeolian dynamics taken from meteorological records, a global wind retro-analysis model, and remote sensing data. A Smagorinsky Large Eddy Simulation (S-LES) model was used to identify meso-scale airflow perturbations and turbulence at different locations around the island. Variability in meteorological data was also identified, with sites recording accelerated or retarded velocities and directional distributions ranging between unimodal to bimodal. Using a global retro-analysis model, relatively consistent up-wind conditions were predicted over a period coinciding with three aerial LiDAR surveys (i.e., 2006, 2008, and 2011) at the Maspalomas dunefield. Despite the consistent predicted airflow conditions, dune migration rates dropped from 7.26 m y−1 to 2.80 m y−1 and 28% of dunes experienced crest reversal towards the east, or opposite of the primary westerly migration direction during the second time period. Our results indicate that meso-scale airflow steering alters local wind conditions that can modify sediment transport gradients at Maspalomas. Given the rapidity of environmental changes and anthropogenic impacts at Maspalomas, these findings improve our understanding on the aeolian dynamics at Maspalomas and can be used to inform future management strategies. Lastly, the approach used in this study could be applied to other high-profile island settings or similarly complex aeolian environments. Unlabelled Image • Whole-island airflow bifurcation and topographic steering occurs around a dunefield. • Inconsistency in regional wind patterns and dune migrations rates were observed. • Meteorological observations, wind modelling, and remote sensing data were compared. • Incident winds are perturbed, modifying aeolian transport patterns at the dunefield. • Down-scaling winds may better predict dominate drivers in aeolian environments. [ABSTRACT FROM AUTHOR]

Published
2021
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35. PSY13 PANCREATIC STONE PROTEIN AS AN ALTERNATIVE TO STANDARD OF CARE DIAGNOSTICS FOR SEPSIS: A PRELIMINARY ECONOMIC MODEL.

Author

Schneider, J., Dick, K., and Cooper, J.

Subjects
*ECONOMIC models, *NEONATAL sepsis, *DRUG resistance in bacteria, *CLOSTRIDIOIDES difficile, *SEPSIS
Abstract

Sepsis is a life-threatening organ dysfunction in response to infection. Results A rapid near patient PSP test was found to reduce costs by $5,379 per patient in the ED and $16,796 per patient in the ICU compared to standard of care. [Extracted from the article]

Published
2020
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36. Structural characterization of (Sm,Tb)PO4 solid solutions and pressure-induced phase transitions.

Author

Heuser, J.M., Schlenz, H., Bosbach, D., Neumeier, S., Deissmann, G., Palomares, R.I., Cooper, J., Lang, M., Bauer, J.D., Winkler, B., Rodriguez, M.J. Lozano, and Scheinost, A.C.

Subjects
*SAMARIUM compounds, *CRYSTAL structure, *SOLID solutions, *PHASE transitions, *PRESSURE, *MONAZITE, *XENOTIME
Abstract

Sm 1- x Tb x PO 4 solid solutions were synthesized and extensively characterized by powder X-ray diffraction, vibrational spectroscopy, and X-ray absorption spectroscopy. At ambient conditions solid solutions up to x  = 0.75 crystallize in the monazite structure, whereas TbPO 4 is isostructural to xenotime. For x  = 0.8 a mixture of both polymorphs was obtained. Moreover, a phase with anhydrite structure was observed coexisting with xenotime, which was formed due to mechanical stress. Selected solid solutions were investigated at pressures up to ∼40 GPa using in situ high pressure synchrotron X-ray diffraction and in situ high pressure Raman spectroscopy. SmPO 4 and Sm 0.5 Tb 0.5 PO 4 monazites are (meta)stable up to the highest pressures studied here. TbPO 4 xenotime was found to transform into the monazite structure at a pressure of about 10 GPa. The transformation of Sm 0.2 Tb 0.8 PO 4 xenotime into the monazite polymorph commences already at about 3 GPa. This study describes the reversibility of the pressure-induced (Sm,Tb)PO 4 xenotime-monazite transformation. [ABSTRACT FROM AUTHOR]

Published
2018
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39. Acute bilateral leg amputation following combat injury in UK servicemen.

Author

Penn-Barwell, J.G., Bennett, P.M., Kay, A., Sargeant, I.D., Fries, C.A., Cooper, J., Kendrew, J.M., Midwinter, M., Rickard, R.F., Porter, K., Rowlands, T., Mountain, A., Jeffrey, S., Evirviades, D., and Cubison, T.

Subjects
*LEG amputation, *MILITARY personnel's injuries, *LEG injuries, *MEDICAL rehabilitation, *COLOSTOMY, *BLOOD transfusion, *THERAPEUTICS
Abstract

Abstract: Background: This study aims to characterise the injuries and surgical management of British servicemen sustaining bilateral lower limb amputations. Methods: The UK Military Trauma Registry was searched for all cases of primary bilateral lower limb amputation sustained between March 2004 and March 2010. Amputations were excluded if they occurred more than 7 days after injury or if they were at the ankle or more distal. Results: There were 1694 UK military patients injured or killed during this six-year study period. Forty-three of these (2.8%) were casualties with bilateral lower limb amputations. All casualties were men with a mean age of 25.1 years (SD 4.3): all were injured in Afghanistan by Improvised Explosive Devices (IEDs). Six casualties were in vehicles when they were injured with the remaining 37 (80%) patrolling on foot. The mean New Injury Severity Score (NISS) was 48.2 (SD 13.2): four patients had a maximum score of 75. The mean TRISS probability of survival was 60% (SD 39.4), with 18 having a survival probability of less than 50% i.e. unexpected survivors. The most common amputation pattern was bilateral trans-femoral (TF) amputations, which was seen in 25 patients (58%). Nine patients also lost an upper limb (triple amputation): no patients survived loss of all four limbs. In retained upper limbs extensive injuries to the hands and forearms were common, including loss of digits. Six patients (14%) sustained an open pelvic fracture. Perineal/genital injury was a feature in 19 (44%) patients, ranging from unilateral orchidectomy to loss of genitalia and permanent requirement for colostomy and urostomy. The mean requirement for blood products was 66 units (SD 41.7). The maximum transfusion was 12 units of platelets, 94 packed red cells, 8 cryoprecipitate, 76 units of fresh frozen plasma and 3 units of fresh whole blood, a total of 193 units of blood products. Conclusions: Our findings detail the severe nature of these injuries together with the massive surgical and resuscitative efforts required to firstly keep patients alive and secondly reconstruct and prepare them for rehabilitation. [Copyright &y& Elsevier]

Published
2014
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40. Oral subchronic exposure to the mycotoxin ochratoxin A induces key pathological features of Parkinson's disease in mice six months after the end of the treatment.

Author

Izco, María, Vettorazzi, Ariane, Forcen, Raquel, Blesa, Javier, de Toro, Maria, Alvarez-Herrera, Natalia, Cooper, J Mark, Gonzalez-Peñas, Elena, Lopez de Cerain, Adela, and Alvarez-Erviti, Lydia

Subjects
*PARKINSON'S disease, *OCHRATOXINS, *PATHOLOGICAL physiology, *MOUSE diseases, *METABOLITES, *ALPHA-synuclein, *WESTERN diet
Abstract

Some epidemiological studies with different levels of evidence have pointed to a higher risk of Parkinson's disease (PD) after exposure to environmental toxicants. A practically unexplored potential etiological factor is a group of naturally-occurring fungal secondary metabolites called mycotoxins. The mycotoxin ochratoxin A (OTA) has been reported to be neurotoxic in mice. To further identify if OTA exposure could have a role in PD pathology, Balb/c mice were orally treated with OTA (0.21, 0.5 mg/kg bw) four weeks and left for six months under normal diet. Effects of OTA on the onset, progression of alpha-synuclein pathology and development of motor deficits were evaluated. Immunohistochemical and biochemical analyses showed that oral subchronic OTA treatment induced loss of striatal dopaminergic innervation and dopaminergic cell dysfunction responsible for motor impairments. Phosphorylated alpha-synuclein levels were increased in gut and brain. LAMP-2A protein was decreased in tissues showing alpha-synuclein pathology. Cell cultures exposed to OTA exhibited decreased LAMP-2A protein, impairment of chaperone-mediated autophagy and decreased alpha-synuclein turnover which was linked to miRNAs deregulation, all reminiscent of PD. These results support the hypothesis that oral exposure to low OTA doses in mice can lead to biochemical and pathological changes reported in PD. • Ochratoxin A altered motor function and dopaminergic system 6 months after exposure. • Phosphorylated alpha-synuclein levels were increased in gut and brain of mice. • LAMP-2A protein was decreased in tissues showing alpha-synuclein pathology. • LAMP-2A and alpha-synuclein turnover decreased in vitro due to miRNA dysregulation. • All these features have been previously described in Parkinson's Disease. [ABSTRACT FROM AUTHOR]

Published
2021
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41. Assessing the use of NMR chemical shifts for prediction of VLE in non-ideal binary liquid mixtures.

Author

Zhu, Q., Moggridge, G.D., Dalton, T., Cooper, J., Mantle, M.D., Gladden, L.F., and D׳Agostino, C.

Subjects
*CHEMICAL shift (Nuclear magnetic resonance), *PREDICTION models, *VAPOR-liquid equilibrium, *BINARY mixtures, *HYDROCARBONS, *THERMODYNAMICS
Abstract

A method of estimating vapour liquid equilibrium (VLE) using NMR chemical shift data has been proposed by Xu et al. (2012) . This method is based on the concept that the average local composition around each species is determined by the thermodynamics of the system, and also determines the screening of the NMR active groups within that molecule, and so their NMR chemical shifts. Xu et al. (2012) ׳s method has been replicated and verified; results are confirmed to be accurate for alcohol+hydrocarbon mixtures, giving VLE predictions of comparable accuracy to the UNIFAC, generally considered the best predictive activity coefficient model available. However, for more strongly non-ideal mixtures, the method becomes less reliable, giving significantly less accurate predictions of total pressure than UNIFAC. Several causes for this are identified. The model proposed by Xu et al. (2012) is unable to fit minima or maxima in chemical shifts, which are observed experimentally in some binary mixtures. Different NMR resonances within the same molecule lead to different predictions of VLE, clearly an un-physical result. The thermodynamics of strongly non-ideal mixtures are determined by more complex interactions than a simple description of average local composition around each component in the mixtures, for example strong and directional hydrogen bonds. Different groups within the same molecule may have different local compositions in their immediate vicinity; for example in the case of alcohol+water mixtures, one would expect a clustering of water molecules around the hydroxyl group but not the aliphatic group. Hence, the concept of a simple local composition model is not valid for these more complex cases, and it is therefore not surprising that a model based on this simple concept is often not effective in predicting VLE. [ABSTRACT FROM AUTHOR]

Published
2014
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