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2. Effects of Langmuir Turbulence on Upper Ocean Carbonate Chemistry

Author

Smith, Katherine M., Hamlington, Peter E., Niemeyer, Kyle E., Fox-Kemper, Baylor, and Lovenduski, Nicole S.

Subjects
Physics - Atmospheric and Oceanic Physics
Abstract

Effects of wave-driven Langmuir turbulence on the air-sea flux of carbon dioxide (CO$_2$) are examined using large eddy simulations featuring actively reacting carbonate chemistry in the ocean mixed layer at small scales. Four strengths of Langmuir turbulence are examined with three types of carbonate chemistry: time-dependent, instantaneous equilibrium chemistry, and no reactions. The time-dependent model is obtained by reducing a detailed eight-species chemical mechanism using computational singular perturbation analysis, resulting in a quasi-steady-state approximation for hydrogen ion (H$^+$), i.e., fixed pH. The reduced mechanism is then integrated in two half-time steps before and after the advection solve using a Runge--Kutta--Chebyshev scheme that is robust for stiff systems of differential equations. The simulations show that, as the strength of Langmuir turbulence increases, CO$_2$ fluxes are enhanced by rapid overturning of the near-surface layer, which rivals the removal rate of CO$_2$ by time-dependent reactions. Equilibrium chemistry and non-reactive models are found to bring more and less carbon, respectively, into the ocean as compared to the more realistic time-dependent model. These results have implications for Earth system models that either neglect Langmuir turbulence or use equilibrium, instead of time-dependent, chemical mechanisms., Comment: 25 pages, 9 figures

Published
2018
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5. IL-17–high asthma with features of a psoriasis immunophenotype

Author

Adcock, I.M., Ahmed, H., Auffray, C., Bakke, P., Bansal, A.T., Baribaud, F., Bates, S., Bel, E.H., Bigler, J., Bisgaard, H., Boedigheimer, M.J., Bønnelykke, K., Brandsma, J., Brinkman, P., Bucchioni, E., Burg, D., Bush, A., Caruso, M., Chaiboonchoe, A., Chanez, P., Chung, K.F., Compton, C.H., Corfield, J., D'Amico, A., Dahlen, S.E., De Meulder, B., Djukanovic, R., Erpenbeck, V.J., Erzen, D., Fichtner, K., Fitch, N., Fleming, L.J., Formaggio, E., Fowler, S.J., Frey, U., Gahlemann, M., Geiser, T., Guo, Y., Hashimoto, S., Haughney, J., Hedlin, G., Hekking, P.W., Higenbottam, T., Hohlfeld, J.M., Holweg, C., Horváth, I., Howarth, P., James, A.J., Knowles, R., Knox, A.J., Krug, N., Lefaudeux, D., Loza, M.J., Lutter, R., Manta, A., Masefield, S., Mazein, A., Meiser, A., Middelveld, R.J.M., Miralpeix, M., Montuschi, P., Mores, N., Murray, C.S., Musial, J., Myles, D., Pahus, L., Pandis, I., Pavlidis, S., Powell, P., Praticò, G., Rao, M. Puig N., Riley, J., Roberts, A., Roberts, G., Rowe, A., Sandström, T., Seibold, W., Selby, A., Shaw, D.E., Sigmund, R., Singer, F., Skipp, P.J., Sousa, A.R., Sterk, P.J., Sun, K., Thornton, B., van Aalderen, W.M., van Geest, M., Vestbo, J., Vissing, N.H., Wagener, A.H., Wagers, S.S., Weiszhart, Z., Wheelock, C.E., Wilson, S.J., Aliprantis, Antonios, Allen, David, Alving, Kjell, Badorrek, P., Balgoma, David, Ballereau, S., Barber, Clair, Batuwitage, Manohara Kanangana, Bautmans, A., Bedding, A., Behndig, A.F., Beleta, Jorge, Berglind, A., Berton, A., Bochenek, Grazyna, Braun, Armin, Campagna, D., Carayannopoulos, Leon, Casaulta, C., Chaleckis, Romanas, Dahlén, B., Davison, imothy, De Alba, Jorge, De Lepeleire, Inge, Dekker, Tamara, Delin, Ingrid, Dennison, P., Dijkhuis, Annemiek, Dodson, Paul, Draper, Aleksandra, Dyson, K., Edwards, Jessica, El Hadjam, L., Emma, Rosalia, Ericsson, Magnus, Faulenbach, C., Flood, Breda, Galffy, G., Gallart, Hector, Garissi, D., Gent, J., Gerhardsson de Verdier, M., Gibeon, D., Gomez, Cristina, Gove, Kerry, Gozzard, Neil, Guillmant-Farry, E., Henriksson, E., Hewitt, Lorraine, Hoda, U., Hu, Richard, Hu, Sile, Hu, X., Jeyasingham, E., Johnson, K., Jullian, N., Kamphuis, Juliette, Kennington, Erika J., Kerry, Dyson, Kerry, G., Klüglich, M., Knobel, Hugo, Kolmert, Johan, Konradsen, J.R., Kots, Maxim, Kretsos, Kosmas, Krueger, L., Kuo, Scott, Kupczyk, Maciej, Lambrecht, Bart, Lantz, A.-S., Larminie, Christopher, Larsson, L.X., Latzin, P., Lazarinis, N., Lemonnier, N., Lone-Latif, Saeeda, Lowe, L.A., Manta, Alexander, Marouzet, Lisa, Martin, Jane, Mathon, Caroline, McEvoy, L., Meah, Sally, Menzies-Gow, A., Metcalf, Leanne, Mikus, Maria, Monk, Philip, Naz, Shama, Nething, K., Nicholas, Ben, Nihlén, U., Nilsson, Peter, Niven, R., Nordlund, B., Nsubuga, S., Pacino, Antonio, Palkonen, Susanna, Pellet, J., Pennazza, Giorgio, Petrén, Anne, Pink, Sandy, Pison, C., Postle, Anthony, Rahman-Amin, Malayka, Ravanetti, Lara, Ray, Emma, Reinke, Stacey, Reynolds, Leanne, Riemann, K., Robberechts, Martine, Rocha, J.P., Rossios, C., Russell, Kirsty, Rutgers, Michael, Santini, G., Santoninco, Marco, Saqi, M., Schoelch, Corinna, Schofield, James P.R., Scott, S., Sehgal, N., Sjödin, Marcus, Smids, Barbara, Smith, Caroline, Smith, Jessica, Smith, Katherine M., Söderman, P., Sogbessan, A., Spycher, F., Staykova, Doroteya, Stephan, S., Stokholm, J., Strandberg, K., Sunther, M., Szentkereszty, M., Tamasi, L., Tariq, K., Thörngren, John-Olof, Thorsen, Jonathan, Valente, S., van de Pol, Marianne, van Drunen, C.M., Van Eyll, Jonathan, Versnel, Jenny, Vink, Anton, von Garnier, C., Vyas, A., Wald, Frans, Walker, Samantha, Ward, Jonathan, Wetzel, Kristiane, Wiegman, Coen, Williams, Siân, Yang, Xian, Yeyasingham, Elizabeth, Amgen, W. Yu, Zetterquist, W., Zolkipli, Z., Zwinderman, A.H., Östling, Jörgen, van Geest, Marleen, Jevnikar, Zala, Wilson, Susan, Lutter, Rene, Shaw, Dominick E., Bakke, Per S., Caruso, Massimo, Dahlen, Sven-Erik, Fowler, Stephen J., Horváth, Ildikó, Krug, Norbert, Montuschi, Paolo, Sanak, Marek, Sandström, Thomas, Sun, Kai, Pandis, Ioannis, Auffray, Charles, Sousa, Ana R., Guo, Yike, Adcock, Ian M., Howarth, Peter, Chung, Kian Fan, Bigler, Jeanette, Sterk, Peter J., Skipp, Paul J., Djukanović, Ratko, and Vaarala, Outi

Published
2019
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8. Computationally efficient parameter estimation for high-dimensional ocean biogeochemical models.

Author

Kern, Skyler, McGuinn, Mary E., Smith, Katherine M., Pinardi, Nadia, Niemeyer, Kyle E., Lovenduski, Nicole S., and Hamlington, Peter E.

Subjects
MATHEMATICAL optimization, GLOBAL optimization, COST functions, TEST methods
Abstract

Biogeochemical (BGC) models are widely used in ocean simulations for a range of applications but typically include parameters that are determined based on a combination of empiricism and convention. Here, we describe and demonstrate an optimization-based parameter estimation method for high-dimensional (in parameter space) BGC ocean models. Our computationally efficient method combines the respective benefits of global and local optimization techniques and enables simultaneous parameter estimation at multiple ocean locations using multiple state variables. We demonstrate the method for a 17-state-variable BGC model with 51 uncertain parameters, where a one-dimensional (in space) physical model is used to represent vertical mixing. We perform a twin-simulation experiment to test the accuracy of the method in recovering known parameters. We then use the method to simultaneously match multi-variable observational data collected at sites in the subtropical North Atlantic and Pacific. We examine the effects of different objective functions, sometimes referred to as cost functions, which quantify the disagreement between model and observational data. We further examine increasing levels of data sparsity and the choice of state variables used during the optimization. We end with a discussion of how the method can be applied to other BGC models, ocean locations, and mixing representations. [ABSTRACT FROM AUTHOR]

Published
2024
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9. Computationally efficient parameter estimation for high-dimensional ocean biogeochemical models

Author

Kern, Skyler, McGuinn, Mary E., Smith, Katherine M., Pinardi, Nadia, Niemeyer, Kyle E., Lovenduski, Nicole S., and Hamlington, Peter E.

Abstract

Biogeochemical (BGC) models are widely used in ocean simulations for a range of applications, but typically include parameters that are determined based on a combination of empiricism and convention. Here, we describe and demonstrate an optimization-based parameter estimation method for ocean BGC models with large numbers of uncertain parameters. Our computationally efficient method combines the respective benefits of global and local optimization techniques and enables simultaneous parameter estimation at multiple ocean locations using multiple state variables. We demonstrate the method for a 17-state-variable BGC model with 51 uncertain parameters, where a one-dimensional physical model is used to represent vertical mixing. We perform a twin-simulation experiment to test the accuracy of the method in recovering known parameters. We then use the method to simultaneously match multi-variable observational data collected at sites in the subtropical North Atlantic and Pacific. We examine the effects of different objective functions, increasing levels of data sparsity, and the choice of state variables used during the optimization. We end with a discussion of how the method can be applied to other BGC models, ocean locations, and mixing representations.

Published
2023

10. Parameterizing Eddy Transport of Biogeochemical Tracers

Author

Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Prend, Channing J, Flierl, Glenn R, Smith, Katherine M, Kaminski, Alexis K, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Prend, Channing J, Flierl, Glenn R, Smith, Katherine M, and Kaminski, Alexis K

Published
2023

27. Stratification of asthma phenotypes by airway proteomic signatures

Author

Schofield, James P. R., Burg, Dominic, Nicholas, Ben, Strazzeri, Fabio, Brandsma, Joost, Staykova, Doroteya, Folisi, Caterina, Bansal, Aruna T., Xian, Yang, Guo, Yike, Rowe, Anthony, Corfield, Julie, Wilson, Susan, Ward, Jonathan, Lutter, Rene, Shaw, Dominick E., Bakke, Per S., Caruso, Massimo, Dahlen, Sven-Erik, Fowler, Stephen J., Horvath, Ildiko, Howarth, Peter, Krug, Norbert, Montuschi, Paolo, Sanak, Marek, Sandstrom, Thomas, Sun, Kai, Pandis, Ioannis, Riley, John, Auffray, Charles, De Meulder, Bertrand, Lefaudeux, Diane, Sousa, Ana R., Adcock, Ian M., Chung, Kian Fan, Sterk, Peter J., Skipp, Paul J., Djukanovic, Ratko, Ahmed, H., Allen, D., Badorrek, P., Ballereau, S., Baribaud, F., Batuwitage, M. K., Bedding, A., Behndig, A. F., Berglind, A., Berton, A., Bigler, J., Boedigheimer, M. J., Bonnelykke, K., Brinkman, P., Bush, A., Campagna, D., Casaulta, C., Chaiboonchoe, A., Davison, T., De Meulder, B., Delin, I., Dennison, P., Dodson, P., El Hadjam, L., Erzen, D., Faulenbach, C., Fichtner, K., Fitch, N., Formaggio, E., Gahlemann, M., Galffy, G., Garissi, D., Garret, T., Gent, J., Guillmant-Farry, E., Henriksson, E., Hoda, U., Hohlfeld, J. M., Hu, X., James, A., Johnson, K., Jullian, N., Kerry, G., Klueglich, M., Knowles, R., Konradsen, J. R., Kretsos, K., Krueger, L., Lantz, A. -S, Larminie, C., Latzin, P., Lefaudeux, D., Lemonnier, N., Lowe, L. A., Lutter, R., Manta, A., Mazein, A., McEvoy, L., Menzies-Gow, A., Mores, N., Murray, C. S., Nething, K., Nihlen, U., Niven, R., Nordlund, B., Nsubuga, S., Pellet, J., Pison, C., Pratico, G., Puig Valls, M., Riemann, K., Rocha, J. P., Rossios, C., Santini, G., Saqi, M., Scott, S., Sehgal, N., Selby, A., Soderman, P., Sogbesan, A., Spycher, F., Stephan, S., Stokholm, J., Sunther, M., Szentkereszty, M., Tamasi, L., Tariq, K., Valente, S., van Aalderen, W. M., van Drunen, C. M., Van Eyll, J., Vyas, A., Yu, W., Zetterquist, W., Zolkipli, Z., Zwinderman, A. H., Adriaens, Nora, Aliprantis, Antonios, Alving, Kjell, Bakke, Per, Balgoma, David, Barber, Clair, Baribaud, Frederic, Bates, Stewart, Bautmans, An, Beleta, Jorge, Bochenek, Grazyna, Braun, Armin, Carayannopoulos, Leon, Rocha, Joao Pedro Carvalho da Purificacao, Chaleckis, Romanas, D'Amico, Arnaldo, De Alba, Jorge, De Lepeleire, Inge, Dekker, Tamara, Dijkhuis, Annemiek, Draper, Aleksandra, Edwards, Jessica, Emma, Rosalia, Ericsson, Magnus, Flood, Breda, Gallart, Hector, Gomez, Cristina, Gove, Kerry, Gozzard, Neil, Haughney, John, Hewitt, Lorraine, Hohlfeld, Jens, Holweg, Cecile, Hu, Richard, Hu, Sile, Kamphuis, Juliette, Kennington, Erika J., Kerry, Dyson, Knobel, Hugo, Kolmert, Johan, Kots, Maxim, Kuo, Scott, Kupczyk, Maciej, Lambrecht, Bart, Lone-Latif, Saeeda, Loza, Matthew J., Marouzet, Lisa, Martin, Jane, Masefield, Sarah, Mathon, Caroline, Meah, Sally, Meiser, Andrea, Metcalf, Leanne, Mikus, Maria, Miralpeix, Montse, Monk, Philip, Naz, Shama, Nilsson, Peter, Ostling, Jorgen, Pacino, Antonio, Palkonen, Susanna, Pavlidis, Stelios, Pennazza, Giorgio, Petren, Anne, Pink, Sandy, Postle, Anthony, Powell, Pippa, Rahman-Amin, Malayka, Rao, Navin, Ravanetti, Lara, Ray, Emma, Reinke, Stacey, Reynolds, Leanne, Robberechts, Martine, Roberts, Amanda, Russell, Kirsty, Rutgers, Michael, Santoninco, Marco, Schoelch, Corinna, Sjodin, Marcus, Smids, Barbara, Smith, Caroline, Smith, Jessica, Smith, Katherine M., Thorngren, John-Olof, Thornton, Bob, Thorsen, Jonathan, van de Pol, Marianne, van Geest, Marleen, Versnel, Jenny, Vink, Anton, Wald, Frans, Walker, Samantha, Weiszhart, Zsoka, Wetzel, Kristiane, Wheelock, Craig E., Wiegman, Coen, Williams, Sian, Wilson, Susan J., Woodcock, Ashley, Yang, Xian, Yeyasingham, Elizabeth, Prins, Jan-Bas, Gahlemann, Martina, Visintin, Luigi, Evans, Hazel, Puhl, Martine, Buzermaniene, Lina, Hudson, Val, Bond, Laura, de Boer, Pim, Widdershoven, Guy, Sigmund, Ralf, Supple, David, Hamerlijnck, Dominique, Negus, Jenny, Kamphuis, Julitte, Sergison, Lehanne, Onstein, Susanne, MacNee, William, Bernardini, Renato, Bont, Louis, Wecksell, Per-Ake, Graduate School, AII - Inflammatory diseases, Pulmonology, Ear, Nose and Throat, Epidemiology and Data Science, APH - Methodology, Publica, and Commission of the European Communities

Subjects
0301 basic medicine, Male, Proteomics, Allergy, Proteome, Neutrophils, Respiratory Medicine and Allergy, Transcriptome, 0302 clinical medicine, neutrophils, Forced Expiratory Volume, Immunology and Allergy, CD44, 610 Medicine & health, Lungmedicin och allergi, phenotypes, Middle Aged, medicine.anatomical_structure, Phenotype, 1107 Immunology, Female, eosinophils, medicine.symptom, Life Sciences & Biomedicine, Adult, Settore BIO/14 - FARMACOLOGIA, Immunology, Computational biology, 03 medical and health sciences, Young Adult, proteomics, Eosinophilia, medicine, Humans, U-BIOPRED Study Group, Asthma, Aged, Science & Technology, Microarray analysis techniques, business.industry, Sputum, biomarkers, DEGRADATION, Eosinophil, medicine.disease, Eosinophils, EXACERBATIONS, 030104 developmental biology, 030228 respiratory system, business
Abstract

Background: Stratification by eosinophil and neutrophil counts increases our understanding of asthma and helps target therapy, but there is room for improvement in our accuracy in prediction of treatment responses and a need for better understanding of the underlying mechanisms. Objective: We sought to identify molecular subphenotypes of asthma defined by proteomic signatures for improved stratification. Methods: Unbiased label-free quantitative mass spectrometry and topological data analysis were used to analyze the proteomes of sputum supernatants from 246 participants (206 asthmatic patients) as a novel means of asthma stratification. Microarray analysis of sputum cells provided transcriptomics data additionally to inform on underlying mechanisms. Results: Analysis of the sputum proteome resulted in 10 clusters (ie, proteotypes) based on similarity in proteomic features, representing discrete molecular subphenotypes of asthma. Overlaying granulocyte counts onto the 10 clusters as metadata further defined 3 of these as highly eosinophilic, 3 as highly neutrophilic, and 2 as highly atopic with relatively low granulocytic inflammation. For each of these 3 phenotypes, logistic regression analysis identified candidate protein biomarkers, and matched transcriptomic data pointed to differentially activated underlying mechanisms. Conclusion: This study provides further stratification of asthma currently classified based on quantification of granulocytic inflammation and provided additional insight into their underlying mechanisms, which could become targets for novel therapies. asthma proteomics biomarkers eosinophils neutrophils

Published
2019

28. IL-17–high asthma with features of a psoriasis immunophenotype

Author

Östling, Jörgen, primary, van Geest, Marleen, additional, Schofield, James P.R., additional, Jevnikar, Zala, additional, Wilson, Susan, additional, Ward, Jonathan, additional, Lutter, Rene, additional, Shaw, Dominick E., additional, Bakke, Per S., additional, Caruso, Massimo, additional, Dahlen, Sven-Erik, additional, Fowler, Stephen J., additional, Horváth, Ildikó, additional, Krug, Norbert, additional, Montuschi, Paolo, additional, Sanak, Marek, additional, Sandström, Thomas, additional, Sun, Kai, additional, Pandis, Ioannis, additional, Auffray, Charles, additional, Sousa, Ana R., additional, Guo, Yike, additional, Adcock, Ian M., additional, Howarth, Peter, additional, Chung, Kian Fan, additional, Bigler, Jeanette, additional, Sterk, Peter J., additional, Skipp, Paul J., additional, Djukanović, Ratko, additional, Vaarala, Outi, additional, Adcock, I.M., additional, Ahmed, H., additional, Auffray, C., additional, Bakke, P., additional, Bansal, A.T., additional, Baribaud, F., additional, Bates, S., additional, Bel, E.H., additional, Bigler, J., additional, Bisgaard, H., additional, Boedigheimer, M.J., additional, Bønnelykke, K., additional, Brandsma, J., additional, Brinkman, P., additional, Bucchioni, E., additional, Burg, D., additional, Bush, A., additional, Caruso, M., additional, Chaiboonchoe, A., additional, Chanez, P., additional, Chung, K.F., additional, Compton, C.H., additional, Corfield, J., additional, D'Amico, A., additional, Dahlen, S.E., additional, De Meulder, B., additional, Djukanovic, R., additional, Erpenbeck, V.J., additional, Erzen, D., additional, Fichtner, K., additional, Fitch, N., additional, Fleming, L.J., additional, Formaggio, E., additional, Fowler, S.J., additional, Frey, U., additional, Gahlemann, M., additional, Geiser, T., additional, Guo, Y., additional, Hashimoto, S., additional, Haughney, J., additional, Hedlin, G., additional, Hekking, P.W., additional, Higenbottam, T., additional, Hohlfeld, J.M., additional, Holweg, C., additional, Horváth, I., additional, Howarth, P., additional, James, A.J., additional, Knowles, R., additional, Knox, A.J., additional, Krug, N., additional, Lefaudeux, D., additional, Loza, M.J., additional, Lutter, R., additional, Manta, A., additional, Masefield, S., additional, Mazein, A., additional, Meiser, A., additional, Middelveld, R.J.M., additional, Miralpeix, M., additional, Montuschi, P., additional, Mores, N., additional, Murray, C.S., additional, Musial, J., additional, Myles, D., additional, Pahus, L., additional, Pandis, I., additional, Pavlidis, S., additional, Powell, P., additional, Praticò, G., additional, Rao, M. Puig N., additional, Riley, J., additional, Roberts, A., additional, Roberts, G., additional, Rowe, A., additional, Sandström, T., additional, Seibold, W., additional, Selby, A., additional, Shaw, D.E., additional, Sigmund, R., additional, Singer, F., additional, Skipp, P.J., additional, Sousa, A.R., additional, Sterk, P.J., additional, Sun, K., additional, Thornton, B., additional, van Aalderen, W.M., additional, van Geest, M., additional, Vestbo, J., additional, Vissing, N.H., additional, Wagener, A.H., additional, Wagers, S.S., additional, Weiszhart, Z., additional, Wheelock, C.E., additional, Wilson, S.J., additional, Aliprantis, Antonios, additional, Allen, David, additional, Alving, Kjell, additional, Badorrek, P., additional, Balgoma, David, additional, Ballereau, S., additional, Barber, Clair, additional, Batuwitage, Manohara Kanangana, additional, Bautmans, A., additional, Bedding, A., additional, Behndig, A.F., additional, Beleta, Jorge, additional, Berglind, A., additional, Berton, A., additional, Bochenek, Grazyna, additional, Braun, Armin, additional, Campagna, D., additional, Carayannopoulos, Leon, additional, Casaulta, C., additional, Chaleckis, Romanas, additional, Dahlén, B., additional, Davison, imothy, additional, De Alba, Jorge, additional, De Lepeleire, Inge, additional, Dekker, Tamara, additional, Delin, Ingrid, additional, Dennison, P., additional, Dijkhuis, Annemiek, additional, Dodson, Paul, additional, Draper, Aleksandra, additional, Dyson, K., additional, Edwards, Jessica, additional, El Hadjam, L., additional, Emma, Rosalia, additional, Ericsson, Magnus, additional, Faulenbach, C., additional, Flood, Breda, additional, Galffy, G., additional, Gallart, Hector, additional, Garissi, D., additional, Gent, J., additional, Gerhardsson de Verdier, M., additional, Gibeon, D., additional, Gomez, Cristina, additional, Gove, Kerry, additional, Gozzard, Neil, additional, Guillmant-Farry, E., additional, Henriksson, E., additional, Hewitt, Lorraine, additional, Hoda, U., additional, Hu, Richard, additional, Hu, Sile, additional, Hu, X., additional, Jeyasingham, E., additional, Johnson, K., additional, Jullian, N., additional, Kamphuis, Juliette, additional, Kennington, Erika J., additional, Kerry, Dyson, additional, Kerry, G., additional, Klüglich, M., additional, Knobel, Hugo, additional, Kolmert, Johan, additional, Konradsen, J.R., additional, Kots, Maxim, additional, Kretsos, Kosmas, additional, Krueger, L., additional, Kuo, Scott, additional, Kupczyk, Maciej, additional, Lambrecht, Bart, additional, Lantz, A.-S., additional, Larminie, Christopher, additional, Larsson, L.X., additional, Latzin, P., additional, Lazarinis, N., additional, Lemonnier, N., additional, Lone-Latif, Saeeda, additional, Lowe, L.A., additional, Manta, Alexander, additional, Marouzet, Lisa, additional, Martin, Jane, additional, Mathon, Caroline, additional, McEvoy, L., additional, Meah, Sally, additional, Menzies-Gow, A., additional, Metcalf, Leanne, additional, Mikus, Maria, additional, Monk, Philip, additional, Naz, Shama, additional, Nething, K., additional, Nicholas, Ben, additional, Nihlén, U., additional, Nilsson, Peter, additional, Niven, R., additional, Nordlund, B., additional, Nsubuga, S., additional, Pacino, Antonio, additional, Palkonen, Susanna, additional, Pellet, J., additional, Pennazza, Giorgio, additional, Petrén, Anne, additional, Pink, Sandy, additional, Pison, C., additional, Postle, Anthony, additional, Rahman-Amin, Malayka, additional, Ravanetti, Lara, additional, Ray, Emma, additional, Reinke, Stacey, additional, Reynolds, Leanne, additional, Riemann, K., additional, Robberechts, Martine, additional, Rocha, J.P., additional, Rossios, C., additional, Russell, Kirsty, additional, Rutgers, Michael, additional, Santini, G., additional, Santoninco, Marco, additional, Saqi, M., additional, Schoelch, Corinna, additional, Scott, S., additional, Sehgal, N., additional, Sjödin, Marcus, additional, Smids, Barbara, additional, Smith, Caroline, additional, Smith, Jessica, additional, Smith, Katherine M., additional, Söderman, P., additional, Sogbessan, A., additional, Spycher, F., additional, Staykova, Doroteya, additional, Stephan, S., additional, Stokholm, J., additional, Strandberg, K., additional, Sunther, M., additional, Szentkereszty, M., additional, Tamasi, L., additional, Tariq, K., additional, Thörngren, John-Olof, additional, Thorsen, Jonathan, additional, Valente, S., additional, van de Pol, Marianne, additional, van Drunen, C.M., additional, Van Eyll, Jonathan, additional, Versnel, Jenny, additional, Vink, Anton, additional, von Garnier, C., additional, Vyas, A., additional, Wald, Frans, additional, Walker, Samantha, additional, Wetzel, Kristiane, additional, Wiegman, Coen, additional, Williams, Siân, additional, Yang, Xian, additional, Yeyasingham, Elizabeth, additional, Amgen, W. Yu, additional, Zetterquist, W., additional, Zolkipli, Z., additional, and Zwinderman, A.H., additional

Published
2019
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30. Structural mutants of dengue virus 2 transmembrane domains exhibit host-range phenotype

Author

Thomas Gwynneth S, Piper Amanda, Vancini Ricardo, Ribeiro Mariana, Spears Carla J, Nanda Kavita, Smith Katherine M, Thomas Malcolm E, Brown Dennis T, and Hernandez Raquel

Subjects
Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background There are over 700 known arboviruses and at least 80 immunologically distinct types that cause disease in humans. Arboviruses are transmitted among vertebrates by biting insects, chiefly mosquitoes and ticks. These viruses are widely distributed throughout the world, depending on the presence of appropriate hosts (birds, horses, domestic animals, humans) and vectors. Mosquito-borne arboviruses present some of the most important examples of emerging and resurgent diseases of global significance. Methods A strategy has been developed by which host-range mutants of Dengue virus can be constructed by generating deletions in the transmembrane domain (TMD) of the E glycoprotein. The host-range mutants produced and selected favored growth in the insect hosts. Mouse trials were conducted to determine if these mutants could initiate an immune response in an in vivo system. Results The DV2 E protein TMD defined as amino acids 452SWTMKILIGVIITWIG467 was found to contain specific residues which were required for the production of this host-range phenotype. Deletion mutants were found to be stable in vitro for 4 sequential passages in both host cell lines. The host-range mutants elicited neutralizing antibody above that seen for wild-type virus in mice and warrant further testing in primates as potential vaccine candidates. Conclusions Novel host-range mutants of DV2 were created that have preferential growth in insect cells and impaired infectivity in mammalian cells. This method for creating live, attenuated viral mutants that generate safe and effective immunity may be applied to many other insect-borne viral diseases for which no current effective therapies exist.

Published
2011
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32. BFM17 v1.0: Reduced-Order Biogeochemical Flux Model for Upper Ocean Biophysical Simulations.

Author

Smith, Katherine M., Kern, Skyler, Hamlington, Peter E., Zavatarelli, Marco, Pinardi, Nadia, Klee, Emily F., and Niemeyer, Kyle E.

Subjects
*REDUCED-order models, *FLUX (Energy), *ECOSYSTEM dynamics, *OCEAN, *ORGANIC compounds, *CHLOROPHYLL
Abstract

We present a newly developed reduced-order biogeochemical flux model that is complex and flexible enough to capture open-ocean ecosystem dynamics, but reduced enough to incorporate into highly resolved numerical simulations with limited additional computational cost. The reduced-order model, which is derived from the full 56 state variable Biogeochemical Flux Model (BFM56; Vichi et al. (2007)), follows a biological and chemical functional group approach and allows for the development of critical non-Redfield nutrient ratios. Matter is expressed in units of carbon, nitrogen, and phosphate, following techniques used in more complex models. To reduce the overall computational cost and to focus on open-ocean conditions, the reduced model eliminates certain processes, such as benthic, silicate, and iron influences, and parameterizes others, such as the bacterial loop. The model explicitly tracks 17 state variables, divided into phytoplankton, zooplankton, dissolved organic matter, particulate organic matter, and nutrient groups. It is correspondingly called the Biogeochemical Flux Model 17 (BFM17). After providing a detailed description of BFM17, we couple it with the one-dimensional Princeton Ocean Model (POM) for validation using observational data from the Sargasso Sea. Results show good agreement with the observational data and with corresponding results from BFM56, including the ability to capture the subsurface chlorophyll maximum and bloom intensity. In comparison to previous reduced-order models of similar size, BFM17 provides improved correlations between model output and field data, indicating that significant improvements in the reproduction of in situ data can be achieved with a low number of variables, while maintaining the functional group approach. [ABSTRACT FROM AUTHOR]

Published
2020
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35. Validated and longitudinally stable asthma phenotypes based on cluster analysis of the ADEPT study

Author

Loza, M. J., Djukanovic, R., Chung, K. F., Horowitz, D., Ma, K., Branigan, P., Barnathan, E. S., Susulic, V. S., Silkoff, P. E., Sterk, P. J., Baribaud, F., Strambu, I., Laviolette, M., Singh, D., Fitzgerald, J. M., Lam, S., Kelsen, S., Eich, A., Ludwig-Sengpiel, A., Hupp, G. C., Backer, V., Porsbjerg, C., Girodet, P. O., Berger, P., Leigh, R., Kline, J., Dransfield, M., Calhoun, W., Hussaini, A., Khatri, S., Chanez, P., Ian, A., Fleming Louis, J., David, G., Sile, H., Scott, K., Sally, M., Andrea, M., Stelios, P., Christos, R., Kirsty, R., Kai, S., Coen, W., Xian, Y., Nora, A., Ariane, W., Kees, v. D., Marianne, v. d. P., Wim, v. A., Sterk Peter, J., Barbara, S., Lara, R., Rene, L., Paul, B., Elisabeth, B., Koos, Z., Tamara, D., Simone, H., Annemiek, D., Pieter-Paul, H., Saeeda, L. -L., Hassan, A., Betrand, D. M., Diane, L., Antonios, A., Kjell, A., Charles, A., Philipp, B., Per, B., David, B., Sven-Erik, D., Ingrid, D., Cristina, G., James Anna, J., Roelinde, M., Shama, N., Anne, P., Stacey, R., Wheelock Craig, E., Hector, G., Maciej, K., Johan, K., Marcus, S., Bansal Aruna, T., Frederic, B., Navin, R., An, B., Inge, D. L., Martine, R., Behndig Annelie, F., Thomas, S., Jorge, B., De Jorge, A., Ann, B., Gunilla, H., Nordlund, Bjorn, Jon, K., Wilhelm, Z., Alix, B., Jorgen, O., van Marleen, G., de Maria, G. V., Lars, L., Ulf, N., Jeannette, B., Boedigheimer Michel, J., Richard, H., Xugang, H., Wen, Y., Hans, B., Klaus, B., Jonathan, T., Nadja, V., Grazyna, B., Jacek, M., Joost, B., Ben, N., Anthony, P., Doroteya, S., Armin, B., Jens, H., Norbert, K., Dominic, B., Schofield James, P. R., Skipp Paul, J., Leon, C., Bob, T., Caruso, Massimo, Rocha Joao Pedro, C. P., Julaiha, G., Andrew, M. -G., Adesimbo, S., Amphun, C., Romanas, C., Caroline, M., Pascal, C., Courtney, C., Jessica, E., Val, H., Kennington Erika, J., Leanne, M., Malayka, R. -A., Leanne, R., Jessica, S., Jenny, V., Samantha, W., Breda, F., Amanda, R., David, S., Chris, C., David, M., John, R., Sousa Ana, R., Julie, C., D'Amico, Arnaldo, Giorgio, P., Marco, S., Barbro, D., Ann-Sofie, L., Pim, B., Patrick, D., Kamran, T., Clair, B., Kerry, G., Aleksandra, D., Neil, F., Trevor, G., Scott, W., Rosalia, E., Davide, C., Magnus, E., Veit, E., Damijan, E., Klaus, F., Katja, N., Corinna, S., Frans, W., Kathrin, R., Kluglich, Matthias, Fowler Stephen, J., Murray Clare, S., Jorgen, V., Ashley, W., Urs, F., Martina, G., Gabriella, G., Ildiko, H., Marton, S., Lilla, T., Zsoka, W., Thomas, G., Neil, G., Yi-ke, G., John, H., Sian, W., Elisabeth, H., Nikos, L., Karin, S., Lorraine, H., Lisa, M., Jane, M., Sandy, P., Emma, R., Caroline, S., Tim, H., Uruj, H., Cecile, H., Matthews John, G., Peter, H., Graham, R., Juliette, K., Dyson, K., Hugo, K., Anton, V., Richard, K., Alan, K., Shaw Dominick, E., Maxim, K., Linn, K., Bart, L., Sarah, M., Pippa, P., Alexander, M., Maria, M., Peter, N., Montse, M., Philip, M., Paolo, M., Nadia, M., Giuseppe, S., Salvatore, V., Antonio, P., Laurie, P., Susanna, P., Ioannis, P., Anthony, R., Wolfgang, S., Kristiane, W., Florian, S., Smith Katherine, M., Paivi, S., John-Olof, T., von Christophe, G., Jonathan, W., Wilson Susan, J., Elizabeth, Y., AII - Amsterdam institute for Infection and Immunity, Pulmonology, Graduate School, Experimental Immunology, APH - Amsterdam Public Health, Epidemiology and Data Science, Medical Research Council (MRC), Commission of the European Communities, and National Institute for Health Research

Subjects
Oncology, Time Factors, AIRWAY INFLAMMATION, Respiratory System, Vital Capacity, Disease, Severity of Illness Index, 0302 clinical medicine, RESEARCH-PROGRAM, Forced Expiratory Volume, Observational study, Eosinophilic, Medicine and Health Sciences, 030212 general & internal medicine, Longitudinal Studies, Lung, SEVERE EOSINOPHILIC ASTHMA, INDUCED SPUTUM, Interleukin-13, Biological markers, Adept, Prognosis, ADEPT (Airways Disease Endotyping for Personalized Therapeutics) and U-BIOPRED (Unbiased Biomarkers for the Prediction of Respiratory Disease Outcome Consortium) investigators, Phenotype, 3. Good health, Cohort, Biomarker (medicine), Inflammation Mediators, Life Sciences & Biomedicine, medicine.drug, Pulmonary and Respiratory Medicine, medicine.medical_specialty, Genotype, QUESTIONNAIRE, 610 Medicine & health, 1102 Cardiovascular Medicine And Haematology, 03 medical and health sciences, Th2 Cells, Cluster analysis, Fuzzy Logic, Predictive Value of Tests, Internal medicine, medicine, Humans, Asthma, Science & Technology, IDENTIFICATION, business.industry, MEPOLIZUMAB, Research, Biology and Life Sciences, Reproducibility of Results, 1103 Clinical Sciences, medicine.disease, Cross-Sectional Studies, 030228 respiratory system, Gene Expression Regulation, Immunology, Interleukin-4, business, Mepolizumab
Abstract

Background Asthma is a disease of varying severity and differing disease mechanisms. To date, studies aimed at stratifying asthma into clinically useful phenotypes have produced a number of phenotypes that have yet to be assessed for stability and to be validated in independent cohorts. The aim of this study was to define and validate, for the first time ever, clinically driven asthma phenotypes using two independent, severe asthma cohorts: ADEPT and U-BIOPRED. Methods Fuzzy partition-around-medoid clustering was performed on pre-specified data from the ADEPT participants (n = 156) and independently on data from a subset of U-BIOPRED asthma participants (n = 82) for whom the same variables were available. Models for cluster classification probabilities were derived and applied to the 12-month longitudinal ADEPT data and to a larger subset of the U-BIOPRED asthma dataset (n = 397). High and low type-2 inflammation phenotypes were defined as high or low Th2 activity, indicated by endobronchial biopsies gene expression changes downstream of IL-4 or IL-13. Results Four phenotypes were identified in the ADEPT (training) cohort, with distinct clinical and biomarker profiles. Phenotype 1 was “mild, good lung function, early onset”, with a low-inflammatory, predominantly Type-2, phenotype. Phenotype 2 had a “moderate, hyper-responsive, eosinophilic” phenotype, with moderate asthma control, mild airflow obstruction and predominant Type-2 inflammation. Phenotype 3 had a “mixed severity, predominantly fixed obstructive, non-eosinophilic and neutrophilic” phenotype, with moderate asthma control and low Type-2 inflammation. Phenotype 4 had a “severe uncontrolled, severe reversible obstruction, mixed granulocytic” phenotype, with moderate Type-2 inflammation. These phenotypes had good longitudinal stability in the ADEPT cohort. They were reproduced and demonstrated high classification probability in two subsets of the U-BIOPRED asthma cohort. Conclusions Focusing on the biology of the four clinical independently-validated easy-to-assess ADEPT asthma phenotypes will help understanding the unmet need and will aid in developing tailored therapies. Trial registration NCT01274507 (ADEPT), registered October 28, 2010 and NCT01982162 (U-BIOPRED), registered October 30, 2013. Electronic supplementary material The online version of this article (doi:10.1186/s12931-016-0482-9) contains supplementary material, which is available to authorized users.

Published
2016

36. U-BIOPRED clinical adult asthma clusters linked to a subset of sputum omics

Author

Lefaudeux, Diane, primary, De Meulder, Bertrand, additional, Loza, Matthew J., additional, Peffer, Nancy, additional, Rowe, Anthony, additional, Baribaud, Frédéric, additional, Bansal, Aruna T., additional, Lutter, Rene, additional, Sousa, Ana R., additional, Corfield, Julie, additional, Pandis, Ioannis, additional, Bakke, Per S., additional, Caruso, Massimo, additional, Chanez, Pascal, additional, Dahlén, Sven-Erik, additional, Fleming, Louise J., additional, Fowler, Stephen J., additional, Horvath, Ildiko, additional, Krug, Norbert, additional, Montuschi, Paolo, additional, Sanak, Marek, additional, Sandstrom, Thomas, additional, Shaw, Dominic E., additional, Singer, Florian, additional, Sterk, Peter J., additional, Roberts, Graham, additional, Adcock, Ian M., additional, Djukanovic, Ratko, additional, Auffray, Charles, additional, Chung, Kian Fan, additional, Adriaens, Nora, additional, Ahmed, Hassan, additional, Aliprantis, Antonios, additional, Alving, Kjell, additional, Badorek, Philipp, additional, Balgoma, David, additional, Barber, Clair, additional, Bautmans, An, additional, Behndig, Annelie F., additional, Bel, Elisabeth, additional, Beleta, Jorge, additional, Berglind, Ann, additional, Berton, Alix, additional, Bigler, Jeanette, additional, Bisgaard, Hans, additional, Bochenek, Grazyna, additional, Boedigheimer, Michael J., additional, Bøonnelykke, Klaus, additional, Brandsma, Joost, additional, Braun, Armin, additional, Brinkman, Paul, additional, Burg, Dominic, additional, Campagna, Davide, additional, Carayannopoulos, Leon, additional, Carvalho da Purfição Rocha, João P., additional, Chaiboonchoe, Amphun, additional, Chaleckis, Romanas, additional, Coleman, Courtney, additional, Compton, Chris, additional, D'Amico, Arnaldo, additional, Dahlén, Barbro, additional, De Alba, Jorge, additional, de Boer, Pim, additional, De Lepeleire, Inge, additional, Dekker, Tamara, additional, Delin, Ingrid, additional, Dennison, Patrick, additional, Dijkhuis, Annemiek, additional, Draper, Aleksandra, additional, Edwards, Jessica, additional, Emma, Rosalia, additional, Ericsson, Magnus, additional, Erpenbeck, Veit, additional, Erzen, Damijan, additional, Faulenbach, Cornelia, additional, Fichtner, Klaus, additional, Fitch, Neil, additional, Flood, Breda, additional, Frey, Urs, additional, Gahlemann, Martina, additional, Galffy, Gabriella, additional, Gallart, Hector, additional, Garret, Trevor, additional, Geiser, Thomas, additional, Gent, Jilaiha, additional, Gerhardsson de Verdier, Maria, additional, Gibeon, David, additional, Gomez, Cristina, additional, Gove, Kerry, additional, Gozzard, Neil, additional, Guo, Yi-Ke, additional, Hashimoto, Simone, additional, Haughney, John, additional, Hedlin, Gunilla, additional, Hekking, Pieter-Paul, additional, Henriksson, Elisabeth, additional, Hewitt, Lorraine, additional, Higgenbottam, Tim, additional, Hoda, Uruj, additional, Hohlfeld, Jans, additional, Holweg, Cecile, additional, Howarth, Peter, additional, Hu, Richard, additional, Hu, Sile, additional, Hu, Xugang, additional, Hudson, Val, additional, James, Anna J., additional, Kamphuis, Juliette, additional, Kennington, Erika J., additional, Kerry, Dyson, additional, Klüglich, Matthias, additional, Knobel, Hugo, additional, Knowles, Richard, additional, Knox, Alan, additional, Kolmert, Johan, additional, Konradsen, Jon, additional, Kots, Maxim, additional, Krueger, Linn, additional, Kuo, Scott, additional, Kupczyk, Maciej, additional, Lambrecht, Bart, additional, Lantz, Ann-Sofie, additional, Larsson, Lars, additional, Lazarinis, Nikos, additional, Lone-Satif, Saeeda, additional, Marouzet, Lisa, additional, Martin, Jane, additional, Masefield, Sarah, additional, Mathon, Caroline, additional, Matthews, John G., additional, Mazein, Alexander, additional, Meah, Sally, additional, Maiser, Andrea, additional, Menzies-Gow, Andrew, additional, Metcalf, Leanne, additional, Middelveld, Roelinde, additional, Mikus, Maria, additional, Miralpeix, Montse, additional, Monk, Philips, additional, Mores, Nadia, additional, Murray, Clare S., additional, Musial, Jacek, additional, Myles, David, additional, Naz, Shama, additional, Nething, Katja, additional, Nicholas, Ben, additional, Nihlen, Ulf, additional, Nilsson, Peter, additional, Nordlund, Björn, additional, Östling, Jörgen, additional, Pacino, Antonio, additional, Pahus, Laurie, additional, Palkonnen, Susanna, additional, Pavlidis, Stelios, additional, Pennazza, Giorgio, additional, Petrén, Anne, additional, Pink, Sandy, additional, Postle, Anthony, additional, Powel, Pippa, additional, Rahman-Amin, Malayka, additional, Rao, Navin, additional, Ravanetti, Lara, additional, Ray, Emma, additional, Reinke, Stacey, additional, Reynolds, Leanne, additional, Riemann, Kathrin, additional, Riley, John, additional, Robberechts, Martine, additional, Roberts, Amanda, additional, Rossios, Christos, additional, Russell, Kirsty, additional, Rutgers, Michael, additional, Santini, Giuseppe, additional, Sentoninco, Marco, additional, Schoelch, Corinna, additional, Schofield, James P.R., additional, Seibold, Wolfgang, additional, Sigmund, Ralf, additional, Sjödin, Marcus, additional, Skipp, Paul J., additional, Smids, Barbara, additional, Smith, Caroline, additional, Smith, Jessica, additional, Smith, Katherine M., additional, Söderman, Päivi, additional, Sogbesan, Adesimbo, additional, Staykova, Doroteya, additional, Strandberg, Karin, additional, Sun, Kai, additional, Supple, David, additional, Szentkereszty, Marton, additional, Tamasi, Lilla, additional, Tariq, Kamran, additional, Thörngren, John-Olof, additional, Thornton, Bob, additional, Thorsen, Jonathan, additional, Valente, Salvatore, additional, van Aalderenm, Wim, additional, van de Pol, Marianne, additional, van Drunen, Kees, additional, van Geest, Marleen, additional, Versnel, Jenny, additional, Vestbo, Jorgen, additional, Vink, Anton, additional, Vissing, Nadja, additional, von Garnier, Christophe, additional, Wagerner, Arianne, additional, Wagers, Scott, additional, Wald, Frans, additional, Walker, Samantha, additional, Ward, Jonathan, additional, Weiszhart, Zsoka, additional, Wetzel, Kristiane, additional, Wheelock, Craig E., additional, Wiegman, Coen, additional, Williams, Siân, additional, Wilson, Susan J., additional, Woosdcock, Ashley, additional, Yang, Xian, additional, Yeyashingham, Elizabeth, additional, Yu, Wen, additional, Zetterquist, Wilhelm, additional, and Zwinderman, Koos, additional

Published
2017
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37. Children At-Risk For Hearing Impairment: A Retrospective Study Of The Ontario Infant Hearing Program Population

Author

Smith, Katherine M.

Subjects
Neonatal Screening, Surveillance, Risk Factors, Health Policy, otorhinolaryngologic diseases, Health Services Research, Public Health, Referral Route, Public Affairs, Public Policy and Public Administration, Hearing Loss
Abstract

There is widespread agreement that infant hearing screening programs are effective but such programs may fail to detect all hearing impairment and children can develop subsequent hearing loss after passing the initial screen. This is the core rationale for surveillance programs that are analyzed in this thesis. Infants with hearing risk factors are followed using surveillance programs that include monitoring by audiological assessment. The study population in this thesis consists of 2,390 children with normal hearing and 248 children with hearing impairment from different referral routes. The Infant Hearing Program Surveillance group is 1.48% of the number of hearing-impaired children. The thesis methodology identifies children with at least one risk factor and then analyzes the different referral routes and hearing loss features. It concludes that there is a need for further evaluation and improvements in surveillance programs, as well as all parts of screening and habilitation.

Published
2013

39. RISK OF CIN2+ AMONG WOMEN WITH A HISTORY OF PREVIOUS TREATMENT FOR CERVICAL INTRAEPITHELIAL NEOPLASIA: ASCUS and LSIL Pap smears post-treatment

Author

Burks, Heather R., Smith, Katherine M., Wentzensen, Nicolas, Tenney, Meaghan, Dunn, S. Terrence, Wang, Sophia S., and Gold, Michael A.

Subjects
Adult, Vaginal Smears, Young Adult, Adolescent, Humans, Female, Middle Aged, Medical History Taking, Uterine Cervical Dysplasia, Risk Assessment, Article, Aged, Papanicolaou Test
Abstract

The objective of the current study was to describe outcomes among women with low-grade abnormalities on cervical cytology screening in the setting of previous excisional or ablative treatment for cervical intraepithelial neoplasia (CIN).Study participants were recruited into the Study to Understand Cervical Cancer Early Endpoints and Determinants. At enrollment, the patient's previous cytology results, previous colposcopic biopsy results, and previous cervical procedures were recorded. Study procedures included collection of biospecimens followed by colposcopy and biopsy. From clinical records, additional information regarding previous treatment for CIN was collected.Two hundred seventy-four women had an atypical squamous cells of uncertain significance (ASCUS) referral Pap and 532 women had a low-grade squamous intraepithelial lesion (LSIL) referral Pap. For patients with an ASCUS referral Pap, previous treatment was associated with an odds ratio for CIN 2+ (45.0% vs 28.2% of untreated patients) of 2.08 (95% confidence interval = 1.05-4.13, p = .04). For patients with an LSIL referral Pap, 33.3% of those women with previous treatment had CIN 2+ compared with 16.7% of those patients enrolled with no previous treatment (odds ratio = 2.49, 95% confidence interval = 1.12-5.51, p = .03).Patients with a history of previous treatment for CIN have a 2-fold risk of CIN 2+ at the time of colposcopy referral for ASCUS or LSIL cervical cytology.

Published
2011

43. Clinical Evaluation of the Cartridge-Based GeneXpert Human Papillomavirus Assay in Women Referred for Colposcopy

Author

Einstein, Mark H., primary, Smith, Katherine M., additional, Davis, Thomas E., additional, Schmeler, Kathleen M., additional, Ferris, Daron G., additional, Savage, Ashlyn H., additional, Gray, Jermaine E., additional, Stoler, Mark H., additional, Wright, Thomas C., additional, Ferenczy, Alex, additional, and Castle, Philip E., additional

Published
2014
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47. Chikungunya Virus Host Range E2 Transmembrane Deletion Mutants Induce Protective Immunity against Challenge in C57BL/6J Mice

Author

Piper, Amanda, primary, Ribeiro, Mariana, additional, Smith, Katherine M., additional, Briggs, Caitlin M., additional, Huitt, Emerson, additional, Nanda, Kavita, additional, Spears, Carla J., additional, Quiles, Michelle, additional, Cullen, John, additional, Thomas, Malcolm E., additional, Brown, Dennis T., additional, and Hernandez, Raquel, additional

Published
2013
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49. Testing of Novel Dengue Virus 2 Vaccines in African Green Monkeys: Safety, Immunogenicity, and Efficacy

Author

Smith, Katherine M., primary, Nanda, Kavita, additional, Spears, Carla J., additional, Piper, Amanda, additional, Ribeiro, Mariana, additional, Quiles, Michelle, additional, Briggs, Caitlin M., additional, Thomas, Gwynneth S., additional, Thomas, Malcolm E., additional, Brown, Dennis T., additional, Hernandez, Raquel, additional, and McCarl, Victoria, additional

Published
2012
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