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11. Simultaneous Hot and Dry Extreme‐Events Increase Wetland Methane Emissions: An Assessment of Compound Extreme‐Event Impacts Using Ameriflux and FLUXNET‐CH4 Site Data Sets.

Author

Lippmann, T. J. R., van der Velde, Y., Naudts, K., Hensgens, G., Vonk, J. E., and Dolman, H.

Abstract

Wetlands are the largest natural source of global atmospheric methane (CH4). Despite advances to our understanding of changes in temperature and precipitation extremes, their impacts on carbon‐rich ecosystems such as wetlands, remain significantly understudied. Here, we quantify the impacts of extreme temperature, precipitation, and dry events on wetland CH4 dynamics by investigating the effects of both compound and discrete extreme‐events. We use long‐term climate data to identify extreme‐events and 45 eddy covariance sites data sets sourced from the FLUXNET‐CH4 database and Ameriflux project to assess impacts on wetland CH4 emissions. These findings reveal that compound hot + dry extreme‐events lead to large increases in daily CH4 emissions. However, per event, discrete dry‐only extreme‐events cause the largest total decrease in CH4 emissions, due to their long duration. Despite dry‐only extreme‐events leading to an overall reduction in CH4 emissions, enhanced fluxes are often observed for the first days of dry‐only extreme‐events. These effects differ depending on wetland type, where marsh sites tend to be sensitive to most types of extreme‐events. Lagged impacts are significant for at least the 12 months following several types of extreme‐events. These findings have implications for understanding how extreme‐event impacts may evolve in the context of climate change, where changes in the frequency and intensity of temperature and precipitation extreme‐events are already observed. With increasing occurrences of enhanced CH4 fluxes in response to hot‐only extreme‐events and hot + wet extreme‐events and fewer occurrences of reduced CH4 fluxes during cold‐only extreme‐events, the impact of wetland CH4 emissions on climate warming may be increasing. Key Points: Compound extreme‐events (e.g., hot + dry extreme‐events) cause large impacts on daily CH4 emissions relative to discrete extreme‐eventsDry‐only extreme‐events show large total decreases in CH4 emissions due to the long duration of events, despite initial flux increasesLagged impacts are significant for at least the 12 months following most types of extreme‐events [ABSTRACT FROM AUTHOR]

Published
2024
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12. Traveling Light: Arctic Coastal Erosion Releases Mostly Matrix Free, Unprotected Organic Carbon.

Author

van Crimpen, F. C. J., Madaj, L., Whalen, D., Tesi, T., van Genuchten, J. M., Bröder, L., Eglinton, T. I., Haghipour, N., and Vonk, J. E.

Subjects
PERMAFROST, BEACH erosion, SEA ice, CHEMICAL properties, GRAIN size
Abstract

The Arctic rapidly warms and sea ice retreats, a large fraction of organic carbon (OC), currently stored in coastal permafrost will be released into the marine system. Once reintroduced into the active carbon cycle, this material will either be decomposed or buried on the shelf depending on its hydrodynamic and chemical properties. Currently, carbon estimates are based on bulk measurements, which does not take the hydrodynamic pathway of different fractions into account. Therefore, eight coastal permafrost locations have been sampled along the Canadian Beaufort Sea Coast, hydrodynamically fractionated and analyzed for their C, N, 13C and 14C content. We found that the matrix‐free fraction (low density <1.8 g/cm3, and high‐density >1.8 g/cm3; <38 μm) account for 77%–98% of the OC. By using a coastal classification combined with field data, our results showed that short coastal segments can become key players in delivering matrix‐free, easily degradable OC to the marine system. Plain Language Summary: Arctic coastlines consisting out of permafrost, permanently frozen ground, experience accelerated erosion due to rising global temperatures. This erosion poses a threat to local communities and releases thawed permafrost material into the Arctic Ocean. Permafrost coasts store significant amounts of organic carbon (OC), and as they thaw and erode, this carbon is released, impacting the climate through the potential release of CO2. Current estimates rely on bulk measurements, but the behavior of released OC in the ocean remains poorly understood. To address this, we used hydrodynamic fractionation on eight sampled coastal permafrost sites along the Canadian Beaufort Sea. By doing so we separate the material based on density and grain size. The results show that a significant portion of OC (77%–98%) falls into the low‐density and the high‐density fine (<38 μm) fraction, containing easily degradable plant‐rich material. Due to these two fractions short coastal segments can become key players for the delivery of degradable OC into the ocean. Key Points: Coastal types vary in size and density distribution, high‐density prevailing in weight and low‐density dominating organic carbon contentBetween 77% and 98% of eroded organic carbon resides in the matrix‐free fraction, prone to degradation and CO2 releaseHydrodynamic fractionation and site‐specific properties contribute to integration of results into land‐ocean flux models [ABSTRACT FROM AUTHOR]

Published
2024
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13. Two Recent p-adic Approaches Towards the (Effective) Mordell Conjecture

Author

Balakrishnan, J. S., Best, A. J., Bianchi, F., Lawrence, B., Müller, J. S., Triantafillou, N., Vonk, J., Chambert-Loir, Antoine, Series Editor, Lu, Jiang-Hua, Series Editor, Ruzhansky, Michael, Series Editor, Tschinkel, Yuri, Series Editor, Charollois, Pierre, editor, Freixas i Montplet, Gerard, editor, and Maillot, Vincent, editor

Published
2021
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15. Childhood-onset Asthma Is Characterized by Airway Epithelial Hillock-to-Squamous Differentiation in Early Life

Author

Koppelman, G.H., primary, Kersten, E.T.G., additional, Pett, J.P., additional, Malmström, K., additional, Chun, Y., additional, Jonker, M., additional, Wilbrey-Clark, A., additional, Worlock, K.B., additional, Van den Berge, M., additional, Vermeulen, R., additional, Vonk, J., additional, Sebire, N., additional, Louhi, J., additional, Timens, W., additional, Teichmann, S., additional, Bunyavanich, S., additional, Nikolic, M., additional, Nawijn, M.C., additional, Mäkelä, M., additional, and Meyer, K., additional

Published
2024
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20. Emissies uit zeer verse mest

Author

Boxmeer, E. van, Verdoes, N., Vonk, J., Huis in 't Veld, J., Workel, L., Boxmeer, E. van, Verdoes, N., Vonk, J., Huis in 't Veld, J., and Workel, L.

Abstract

Presentatie gegeven op 24 mei tijdens een webinar over de invloeden van nieuwe stalsystemen op de eigenschappen, emissies en waarde van mest. Deze slides gaan over het effect van snelle mestverwijdering uit stallen op broeikasgas- en ammoniakemissie en organische stofafbraak in mest. Het onderzoek richt zich op de emissies uit mest die vrijkomen in de eerste 70 uur na uitscheiding.

Published
2024

21. Differential linguistic features of verbal fluency in behavioral variant frontotemporal dementia and primary progressive aphasia.

Author

van den Berg, E., Dijkzeul, J. C. M., Poos, J. M., Eikelboom, W. S., van Hemmen, J., Franzen, S., de Jong, F. J., Dopper, E. G. P., Vonk, J. M. J., Papma, J. M., Satoer, D., Jiskoot, L. C., and Seelaar, H.

Subjects
EXECUTIVE function, SEMANTIC memory, FRONTOTEMPORAL dementia, LANGUAGE ability, REGRESSION analysis, FRONTOTEMPORAL lobar degeneration
Abstract

Frontotemporal dementia (FTD) is an early-onset neurodegenerative disorder with a heterogeneous clinical presentation. Verbal fluency is regularly used as a sensitive measure of language ability, semantic memory, and executive functioning, but qualitative changes in verbal fluency in FTD are currently overlooked. This retrospective study examined qualitative, linguistic features of verbal fluency in 137 patients with behavioral variant (bv)FTD (n = 50), or primary progressive aphasia (PPA) [25 non-fluent variant (nfvPPA), 27 semantic variant (svPPA), and 34 logopenic variant (lvPPA)] and 25 control participants. Between-group differences in clustering, switching, lexical frequency (LF), age of acquisition (AoA), neighborhood density (ND), and word length (WL) were examined in the category and letter fluency with analysis of variance adjusted for age, sex, and the total number of words. Associations with other cognitive functions were explored with linear regression analysis. The results showed that the verbal fluency performance of patients with svPPA could be distinguished from controls and other patient groups by fewer and smaller clusters, more switches, higher LF, and lower AoA (all p < 0.05). Patients with lvPPA specifically produced words with higher ND than the other patient groups (p < 0.05). Patients with bvFTD produced longer words than the PPA groups (p < 0.05). Clustering, switching, LF, AoA, and ND—but not WL—were differentially predicted by measures of language, memory, and executive functioning (range standardized regression coefficient 0.25–0.41). In addition to the total number of words, qualitative linguistic features differ between subtypes of FTD. These features provide additional information on lexical processing and semantic memory that may aid the differential diagnosis of FTD. [ABSTRACT FROM AUTHOR]

Published
2024
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27. Conceptualizing the Mentoring of Beginning Teachers.

Author

Vonk, J. H. C.

Abstract

This paper reports on an element of a long term research project on the development of a conceptual framework for the training of mentors of beginning teachers. Three aspects are being investigated: (1) mentors' perceptions about mentoring; (2) the relation between mentors' perceptions and their actions in practice; and (3) the effect of mentoring as perceived by beginning teachers and other interested parties. This paper reports on a case study of the first aspect, with a focus on qualities mentors perceive as important for adequate mentoring and how mentors perceive their own mentoring style. An inventory was completed by 36 participants in two 1995-96 mentor training courses. It was found that the collaborative nondirective approach dominated, that mentors expected a development plan from their protegees, and that mentors supported protegees only on request. The result was too little direction and guidance for beginning teachers. It is concluded that, especially in the beginning of the induction process, mentors need to take up their role of instructor more explicitly and work out strategies that will guide the beginning teachers in the process of planning and monitoring their own learning. The appendix contains the inventory instrument. (Contains 26 references.) (JLS)

Published
1996

28. Conceptualizing Novice Teachers' Professional Development: A Base for Supervisory Interventions.

Author

Vonk, J. H. C.

Abstract

In this paper a conceptual framework is presented which describes the various dimensions and factors that constitute the processes of a beginning teacher's professional development during preservice and the induction period. The frame in question is based on data resulting from earlier research and on a broad study of recent literature. The model contains three dimensions: the personal dimension, which comprises issues that relate to a teacher's development as a person; the knowledge and skills dimension, which comprises issues that relate to the development of a teacher's content knowledge and professional knowledge and skills; and the ecological dimension, which comprises issues that relate to the environment in which teacher development is taking place. The personal dimension covers issues such as becoming mature, emotions, the development of knowledge about self, and the use of oneself as an instrument. The knowledge and skills dimension covers elements such as the development of academic and pedagogical content knowledge, the development of classroom management skills, and the development of pedagogical and teaching skills. The ecological dimension comprises all the issues that are related to the socialization of teachers in a certain school context, e.g., adaptation to a certain school culture, meeting the demands of colleagues, school administrators, parents and the like. The content of each of the issues is illustrated with data gained from research. The last section briefly discusses some implications for supervisory interventions. (Contains 40 references.) (Author/ND)

Published
1995

29. Mentoring Beginning Teachers: Development of a Knowledge Base for Mentors.

Author

Vonk, J. H. C.

Abstract

The mentoring model described in this paper assumes teachers to be self-directing professionals, and adopts the formalized mentor-protege relationship as the starting point and the individual teacher's professional development as the organizing principle for the induction of teachers into the profession. The essential elements of a mentor's knowledge base are described as: the dimensions in the process of beginning teachers' professional development, which include the personal dimension, environmental dimension, and knowledge and skills dimension; a framework witin which to analyze their classroom teaching and guide them in solving problems; and a teacher's professional learning process model which aims at meaningful learning from experience. One recommendation is that it is best to ensure a strict division between people who are responsible for mentoring and those who are responsible for the final assessment of the teacher concerned. (Contains 46 references.) (JDD)

Published
1993

32. Whole-genome sequencing reveals host factors underlying critical COVID-19

Author

Kousathanas, A, Pairo-Castineira, E, Rawlik, K, Stuckey, A, Odhams, C, Walker, S, Russell, C, Malinauskas, T, Wu, Y, Millar, J, Shen, X, Elliott, K, Griffiths, F, Oosthuyzen, W, Morrice, K, Keating, S, Wang, B, Rhodes, D, Klaric, L, Zechner, M, Parkinson, N, Siddiq, A, Goddard, P, Donovan, S, Maslove, D, Nichol, A, Semple, M, Zainy, T, Maleady-Crowe, F, Todd, L, Salehi, S, Knight, J, Elgar, G, Chan, G, Arumugam, P, Patch, C, Rendon, A, Bentley, D, Kingsley, C, Kosmicki, J, Horowitz, J, Baras, A, Abecasis, G, Ferreira, M, Justice, A, Mirshahi, T, Oetjens, M, Rader, D, Ritchie, M, Verma, A, Fowler, T, Shankar-Hari, M, Summers, C, Hinds, C, Horby, P, Ling, L, Mcauley, D, Montgomery, H, Openshaw, P, Elliott, P, Walsh, T, Tenesa, A, Shelton, J, Shastri, A, Ye, C, Weldon, C, Filshtein-Sonmez, T, Coker, D, Symons, A, Esparza-Gordillo, J, Aslibekyan, S, Auton, A, Pathak, G, Karjalainen, J, Stevens, C, Andrews, S, Kanai, M, Cordioli, M, Polimanti, R, Pirinen, M, Harerimana, N, Veerapen, K, Wolford, B, Nguyen, H, Solomonson, M, Liao, R, Chwialkowska, K, Trankiem, A, Balaconis, M, Hayward, C, Richmond, A, Campbell, A, Morris, M, Fawns-Ritchie, C, Glessner, J, Shaw, D, Chang, X, Polikowski, H, Petty, L, Chen, H, Wanying, Z, Hakonarson, H, Porteous, D, Below, J, North, K, Mccormick, J, Timmers, P, Wilson, J, D'Mellow, K, Kerr, S, Niemi, M, Nkambul, L, von Hohenstaufen, K, Sobh, A, Eltoukhy, M, Yassen, A, Hegazy, M, Okasha, K, Eid, M, Moahmed, H, Shahin, D, El-Sherbiny, Y, Elhadidy, T, Abd Elghafar, M, El-Jawhari, J, Mohamed, A, Elnagdy, M, Samir, A, Abdel-Aziz, M, Khafaga, W, El-Lawaty, W, Torky, M, El-shanshory, M, Batini, C, Lee, P, Shrine, N, Williams, A, Tobin, M, Guyatt, A, John, C, Packer, R, Ali, A, Free, R, Wang, X, Wain, L, Hollox, E, Venn, L, Bee, C, Adams, E, Niavarani, A, Sharififard, B, Aliannejad, R, Amirsavadkouhi, A, Naderpour, Z, Tadi, H, Aleagha, A, Ahmadi, S, Moghaddam, S, Adamsara, A, Saeedi, M, Abdollahi, H, Hosseini, A, Chariyavilaskul, P, Chamnanphon, M, Suttichet, T, Shotelersuk, V, Pongpanich, M, Phokaew, C, Chetruengchai, W, Jantarabenjakul, W, Putchareon, O, Torvorapanit, P, Puthanakit, T, Suchartlikitwong, P, Hirankarn, N, Nilaratanakul, V, Sodsai, P, Brumpton, B, Hveem, K, Willer, C, Zhou, W, Rogne, T, Solligard, E, Asvold, B, Abedalthagafi, M, Alaamery, M, Alqahtani, S, Barakeh, D, Al Harthi, F, Alsolm, E, Safieh, L, Alowayn, A, Alqubaishi, F, Al Mutairi, A, Mangul, S, Alshareef, A, Sawaji, M, Almutairi, M, Aljawini, N, Albesher, N, Arabi, Y, Mahmoud, E, Khattab, A, Halawani, R, Alahmadey, Z, Albakri, J, Felemban, W, Suliman, B, Hasanato, R, Al-Awdah, L, Alghamdi, J, Alzahrani, D, Aljohani, S, Al-Afghani, H, Alrashed, M, Aldhawi, N, Albardis, H, Alkwai, S, Alswailm, M, Almalki, F, Albeladi, M, Almohammed, I, Barhoush, E, Albader, A, Massadeh, S, Almalik, A, Alotaibi, S, Alghamdi, B, Jung, J, Fawzy, M, Lee, Y, Magnus, P, Trogstad, L, Helgeland, O, Harris, J, Mangino, M, Spector, T, Duncan, E, Smieszek, S, Przychodzen, B, Polymeropoulos, C, Polymeropoulos, V, Polymeropoulos, M, Fernandez-Cadenas, I, Perez-Tur, J, Llucia-Carol, L, Cullell, N, Muino, E, Carcel-Marquez, J, Dediego, M, Iglesias, L, Planas, A, Soriano, A, Rico, V, Aguero, D, Bedini, J, Lozano, F, Domingo, C, Robles, V, Ruiz-Jaen, F, Marquez, L, Gomez, J, Coto, E, Albaiceta, G, Garcia-Clemente, M, Dalmau, D, Arranz, M, Dietl, B, Serra-Llovich, A, Soler, P, Colobran, R, Martin-Nalda, A, Martinez, A, Bernardo, D, Rojo, S, Fiz-Lopez, A, Arribas, E, de la Cal-Sabater, P, Segura, T, Gonzalez-Villa, E, Serrano-Heras, G, Marti-Fabregas, J, Jimenez-Xarrie, E, de Felipe Mimbrera, A, Masjuan, J, Garcia-Madrona, S, Dominguez-Mayoral, A, Villalonga, J, Menendez-Valladares, P, Chasman, D, Buring, J, Ridker, P, Franco, G, Sesso, H, Manson, J, Medina-Gomez, C, Uitterlinden, A, Ikram, M, Kristiansson, K, Koskelainen, S, Perola, M, Donner, K, Kivinen, K, Palotie, A, Ripatti, S, Ruotsalainen, S, Kaunisto, M, Nakanishi, T, Butler-Laporte, G, Forgetta, V, Morrison, D, Ghosh, B, Laurent, L, Belisle, A, Henry, D, Abdullah, T, Adeleye, O, Mamlouk, N, Kimchi, N, Afrasiabi, Z, Rezk, N, Vulesevic, B, Bouab, M, Guzman, C, Petitjean, L, Tselios, C, Xue, X, Schurr, E, Afilalo, J, Afilalo, M, Oliveira, M, Brenner, B, Lepage, P, Ragoussis, J, Auld, D, Brassard, N, Durand, M, Chasse, M, Kaufmann, D, Lathrop, G, Mooser, V, Richards, J, Li, R, Adra, D, Rahmouni, S, Georges, M, Moutschen, M, Misset, B, Darcis, G, Guiot, J, Guntz, J, Azarzar, S, Gofflot, S, Beguin, Y, Claassen, S, Malaise, O, Huynen, P, Meuris, C, Thys, M, Jacques, J, Leonard, P, Frippiat, F, Giot, J, Sauvage, A, von Frenckell, C, Belhaj, Y, Lambermont, B, Pigazzini, S, Nkambule, L, Daya, M, Shortt, J, Rafaels, N, Wicks, S, Crooks, K, Barnes, K, Gignoux, C, Chavan, S, Laisk, T, Lall, K, Lepamets, M, Magi, R, Esko, T, Reimann, E, Milani, L, Alavere, H, Metsalu, K, Puusepp, M, Metspalu, A, Naaber, P, Laane, E, Pesukova, J, Peterson, P, Kisand, K, Tabri, J, Allos, R, Hensen, K, Starkopf, J, Ringmets, I, Tamm, A, Kallaste, A, Bochud, P, Rivolta, C, Bibert, S, Quinodoz, M, Kamdar, D, Boillat, N, Nussle, S, Albrich, W, Suh, N, Neofytos, D, Erard, V, Voide, C, de Cid, R, Galvan-Femenia, I, Blay, N, Carreras, A, Cortes, B, Farre, X, Sumoy, L, Moreno, V, Mercader, J, Guindo-Martinez, M, Torrents, D, Kogevinas, M, Garcia-Aymerich, J, Castano-Vinyals, G, Dobano, C, Renieri, A, Mari, F, Fallerini, C, Daga, S, Benetti, E, Baldassarri, M, Fava, F, Frullanti, E, Valentino, F, Doddato, G, Giliberti, A, Tita, R, Amitrano, S, Bruttini, M, Croci, S, Meloni, I, Mencarelli, M, Rizzo, C, Pinto, A, Beligni, G, Tommasi, A, Di Sarno, L, Palmieri, M, Carriero, M, Alaverdian, D, Busani, S, Bruno, R, Vecchia, M, Belli, M, Picchiotti, N, Sanarico, M, Gori, M, Furini, S, Mantovani, S, Ludovisi, S, Mondelli, M, Castelli, F, Quiros-Roldan, E, Antoni, M, Zanella, I, Vaghi, M, Rusconi, S, Siano, M, Montagnani, F, Emiliozzi, A, Fabbiani, M, Rossetti, B, Bargagli, E, Bergantini, L, D'Alessandro, M, Cameli, P, Bennett, D, Anedda, F, Marcantonio, S, Scolletta, S, Franchi, F, Mazzei, M, Guerrini, S, Conticini, E, Cantarini, L, Frediani, B, Tacconi, D, Spertilli, C, Feri, M, Donati, A, Scala, R, Guidelli, L, Spargi, G, Corridi, M, Nencioni, C, Croci, L, Bandini, M, Caldarelli, G, Piacentini, P, Desanctis, E, Cappelli, S, Canaccini, A, Verzuri, A, Anemoli, V, Ognibene, A, Pancrazzi, A, Lorubbio, M, D'Arminio Monforte, A, Miraglia, F, Girardis, M, Venturelli, S, Cossarizza, A, Antinori, A, Vergori, A, Gabrieli, A, Riva, A, Francisci, D, Schiaroli, E, Paciosi, F, Scotton, P, Andretta, F, Panese, S, Scaggiante, R, Gatti, F, Parisi, S, Baratti, S, Della Monica, M, Piscopo, C, Capasso, M, Russo, R, Andolfo, I, Iolascon, A, Fiorentino, G, Carella, M, Castori, M, Merla, G, Squeo, G, Aucella, F, Raggi, P, Marciano, C, Perna, R, Bassetti, M, Di Biagio, A, Sanguinetti, M, Masucci, L, Valente, S, Mandala, M, Giorli, A, Salerni, L, Zucchi, P, Parravicini, P, Menatti, E, Trotta, T, Giannattasio, F, Coiro, G, Lena, F, Coviello, D, Mussini, C, Martinelli, E, Mancarella, S, Tavecchia, L, Crotti, L, Gabbi, C, Rizzi, M, Maggiolo, F, Ripamonti, D, Bachetti, T, La Rovere, M, Sarzi-Braga, S, Bussotti, M, Ceri, S, Pinoli, P, Raimondi, F, Biscarini, F, Stella, A, Zguro, K, Capitani, K, Suardi, C, Dei, S, Parati, G, Ravaglia, S, Artuso, R, Botta, G, Di Domenico, P, Rancan, I, Perrella, A, Bianchi, F, Romani, D, Bergomi, P, Catena, E, Colombo, R, Tanfoni, M, Vincenti, A, Ferri, C, Grassi, D, Pessina, G, Tumbarello, M, Di Pietro, M, Sabrina, R, Luchi, S, Barbieri, C, Acquilini, D, Andreucci, E, Segala, F, Tiseo, G, Falcone, M, Lista, M, Poscente, M, De Vivo, O, Petrocelli, P, Guarnaccia, A, Baroni, S, Smith, A, Boughton, A, Li, K, Lefaive, J, Annis, A, Chittoor, G, Josyula, N, Leader, J, Carey, D, Gass, M, Cantor, M, Yadav, A, van Heel, D, Hunt, K, Mason, D, Huang, Q, Finer, S, Trivedi, B, Griffiths, C, Martin, H, Wright, J, Trembath, R, Soranzo, N, Zhao, J, Butterworth, A, Danesh, J, Di Angelantonio, E, Franke, L, Boezen, M, Deelen, P, Claringbould, A, Lopera, E, Warmerdam, R, Vonk, J, van Blokland, I, Lanting, P, Ori, A, Zollner, S, Wang, J, Beck, A, Peloso, G, Ho, Y, Sun, Y, Huffman, J, O'Donnell, C, Cho, K, Tsao, P, Gaziano, J, Nivard, M, de Geus, E, Bartels, M, Jan Hottenga, J, Weiss, S, Karlson, E, Smoller, J, Green, R, Feng, Y, Murphy, S, Meigs, J, Woolley, A, Perez, E, Li, B, Verma, S, Lucas, A, Bradford, Y, Zeberg, H, Frithiof, R, Hultstrom, M, Lipcsey, M, Tardif, N, Rooyackers, O, Grip, J, Maricic, T, Karczewski, K, Atkinson, E, Tsuo, K, Baya, N, Turley, P, Gupta, R, Callier, S, Walters, R, Palmer, D, Sarma, G, Cheng, N, Lu, W, Bryant, S, Churchhouse, C, Cusick, C, Goldstein, J, King, D, Seed, C, Finucane, H, Martin, A, Satterstrom, F, Wilson, D, Armstrong, J, Rudkin, J, Band, G, Earle, S, Lin, S, Arning, N, Crook, D, Wyllie, D, O'Connell, A, Spencer, C, Koelling, N, Caulfield, M, Scott, R, Moutsianas, L, Pasko, D, Ball, C, Hong, E, Rand, K, Girshick, A, Guturu, H, Baltzell, A, Roberts, G, Park, D, Coignet, M, Mccurdy, S, Knight, S, Partha, R, Rhead, B, Zhang, M, Berkowitz, N, Gaddis, M, Noto, K, Ruiz, L, Pavlovic, M, Sloofman, L, Charney, A, Beckmann, N, Schadt, E, Jordan, D, Thompson, R, Gettler, K, Abul-Husn, N, Ascolillo, S, Buxbaum, J, Chaudhary, K, Cho, J, Itan, Y, Kenny, E, Belbin, G, Sealfon, S, Sebra, R, Salib, I, Collins, B, Levy, T, Britvan, B, Keller, K, Tang, L, Peruggia, M, Hiester, L, Niblo, K, Aksentijevich, A, Labkowsky, A, Karp, A, Zlatopolsky, M, Preuss, M, Loos, R, Nadkarni, G, Do, R, Hoggart, C, Choi, S, Underwood, S, O'Reilly, P, Huckins, L, Zyndorf, M, Daly, M, Neale, B, Ganna, A, Fawkes, A, Murphy, L, Rowan, K, Ponting, C, Vitart, V, Yang, J, Bretherick, A, Hendry, S, Law, A, Baillie, J, Kousathanas A., Pairo-Castineira E., Rawlik K., Stuckey A., Odhams C. 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P., Vitart V., Yang J., Bretherick A. D., Hendry S. C., Law A., and Baillie J. K.

Abstract

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.

Published
2022

33. Inventarisatie van methaansensoren en validatie van de Axetris LGD Compact-A CH4 ten behoeve van continue emissiemonitoring in de melkveehouderij

Author

Schep, C.A., Vonk, J., Rikkers, T., van Dooren, H.J.C., Ogink, N.W.M., Schep, C.A., Vonk, J., Rikkers, T., van Dooren, H.J.C., and Ogink, N.W.M.

Abstract

Sensors for measurement of methane concentration in the range typical for dairy housing are not available yet. This project developed criteria for continuous monitoring of methane emissions from dairy housing and explored the market availability. Eventually the Axetris LGD Compact-A CH4 sensor was chosen for extensive lab and field validation tests. Four identical sensors of this type were subjected to the study. Based on the results it can be concluded that this type of sensor performs equally to the reference method and can be used for measurement of methane concentration in dairy housing without further restrictions or corrections whenever the concentration within the concentration limits of 0-100 ppm. It is recommended to follow up on this research by comparing the sensor results with reference measurements to check on possible drift as a result of sensor aging. In the meantime, it is recommended to calibrate the sensor in a laboratory yearly according to the available test and validation protocol., Het aantonen van de effectiviteit van technische maatregelen die de methaanemissie uit melkveestallen reduceren vereist dat deze op praktijkniveau worden doorgemeten. Momenteel ontbreekt het echter aan sensoren die de concentratie van methaan in melkveestallen continu kunnen meten. In het project ‘Ontwikkelen van een methaansensor ten behoeve van continue bedrijfsmonitoring’ zijn eisen opgesteld waaraan een dergelijke sensor moet voldoen en is de beschikbaarheid daarvan bij marktpartijen geïnventariseerd. Hieruit kwam een drietal opties naar voren die middels verkennende metingen in laboratorium en praktijk met elkaar vergeleken zijn. Van deze drie is de Axetris LGD Compact-A CH4 gevalideerd volgens het ontwikkel- en validatieprotocol (Vonk et al. 2021). Uit dit onderzoek wordt geconcludeerd dat de Axetris LGD Compact-A CH4 sensor gelijkwaardig is aan de referentiemethode en daarmee zonder correctie kan worden toegepast binnen een concentratiebereik van 0-100 ppm. Aanbevolen wordt om deze sensoren de komende jaren met referentiemetingen te blijven volgen om drift als gevolg van veroudering op langere termijn te kunnen vaststellen. Tot die tijd wordt geadviseerd jaarlijks laboratoriummetingen uit te voeren.

Published
2023

34. Raming van luchtemissies uit de landbouw tot 2030, met doorkijk naar 2040 : Achtergronddocument veehouderij en akkerbouw bij de Klimaat- en Energieverkenning 2022

Author

Vonk, J., van Bruggen, C., Lagerwerf, L.A., Huijsmans, J.F.M., Luesink, H.H., van der Zee, T., Velthof, G.L., Vonk, J., van Bruggen, C., Lagerwerf, L.A., Huijsmans, J.F.M., Luesink, H.H., van der Zee, T., and Velthof, G.L.

Abstract

In the context of the Climate and Energy Outlook 2022 (KEV2022), projections for process emissions of greenhouse gases and air polluting compounds from agriculture (animal husbandry and arable farming) were made with the National Emission Model for Agriculture (NEMA). Based on expected developments, emissions to air from enteric fermentation, manure management and agricultural soils were calculated. Respective emissions of methane, nitrous oxide, carbon dioxide from calcareous fertilizers and urea, ammonia, nitrogen oxide, particulate matter and non-methane volatile organic compounds are determined for 2025 and 2030, with a look through towards 2035 and 2040., In het kader van de Klimaat- en Energieverkenning 2022 (KEV2022) zijn met het National Emission Model for Agriculture (NEMA) ramingen voor procesemissies van broeikasgassen en luchtverontreinigende stoffen vanuit de landbouw (veehouderij en akkerbouw) opgesteld. Hiertoe zijn op basis van de verwachte ontwikkelingen luchtemissies door pens- en darmfermentatie, mestmanagement en landbouwbodems berekend. De betreffende emissies van methaan, lachgas, koolstofdioxide door kalkmeststoffen en ureum, ammoniak, stikstofoxide, fijnstof en niet-methaan vluchtige organische stoffen zijn bepaald voor 2025 en 2030, met een doorkijk naar 2035 en 2040.

Published
2023

36. Sedimentary Organic Matter Composition and Transport Across the Beaufort Shelf (Canadian Arctic)

Author

Bröder, L., primary, Bigler, L., additional, O’Regan, M., additional, Fritz, M., additional, Tesi, T., additional, Juhls, B., additional, Eulenburg, A., additional, Priest, T., additional, Matsuoka, A., additional, Pellerin, A., additional, Bossé-Demers, T., additional, Rudbäck, D., additional, Haghipour, N., additional, Eglinton, T., additional, Overduin, P., additional, Vonk, J., additional, and Lattaud, J., additional

Published
2023
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38. Nasal airway epithelium differentiates between asthma and healthy subjects and identifies clinically relevant asthma endotypes

Author

Karp, T, primary, Faiz, A, additional, Kerstjens, H A M, additional, Boudewijn, I M, additional, Kraft, M, additional, Vonk, J M, additional, Nawijn, M C, additional, Heijink, I H, additional, Fabbri, L M, additional, Rabe, K F, additional, Nicolini, G, additional, Papi, A, additional, Brightling, C, additional, Singh, D, additional, Van Der Molen, T, additional, Siddiqui, S, additional, Christenson, S, additional, Guryev, V, additional, and Van Den Berge, M, additional

Published
2022
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39. COPD-associated changes in lung extracellular matrix

Author

Joglekar, M M, primary, Koloko Ngassie, M L, additional, Bekker, N J, additional, Reinders-Luinge, M A, additional, Borghuis, T, additional, Vonk, J M, additional, Pouwels, S D, additional, Melgert, B N, additional, Timens, W, additional, Brandsma, C, additional, and Burgess, J K, additional

Published
2022
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40. Maintenance and reliever therapy with budesonide/formoterol versus fixed dose fluticasone/salmeterol in patients with COPD

Author

Muiser, S, primary, Imkamp, K, additional, Seigers, D, additional, Halbersma, N, additional, Vonk, J, additional, Luijk, B, additional, Braunstahl, G, additional, Van Den Berg, J W, additional, Kroesen, B, additional, Kocks, J, additional, Heijink, I, additional, Reddel, H, additional, Kerstjens, H, additional, and Van Den Berge, M, additional

Published
2022
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43. Whole genome sequencing reveals host factors underlying critical Covid-19

Author

Kousathanas, A., Pairo-Castineira, E., Rawlik, K., Stuckey, A., Odhams, C. A., Walker, S., Russell, C. D., Malinauskas, T., Wu, Y., Millar, J., Shen, X., Elliott, K. S., Griffiths, F., Oosthuyzen, W., Morrice, K., Keating, S., Wang, B., Rhodes, D., Klaric, L., Zechner, M., Parkinson, N., Siddiq, A., Goddard, P., Donovan, S., Maslove, D., Nichol, A., Semple, M. G., Zainy, T., Maleady-Crowe, F., Todd, L., Salehi, S., Knight, J., Elgar, G., Chan, G., Arumugam, P., Patch, C., Rendon, A., Bentley, D., Kingsley, C., Kosmicki, J. A., Horowitz, J. E., Baras, A., Abecasis, G. R., Ferreira, M. A. R., Justice, A., Mirshahi, T., Oetjens, M., Rader, D. J., Ritchie, M. D., Verma, A., Fowler, T. A., Shankar-Hari, M., Summers, C., Hinds, C., Horby, P., Mcauley, D., Montgomery, H., Openshaw, P. J. M., Elliott, P., Walsh, T., Tenesa, A., Fawkes, A., Murphy, L., Rowan, K., Ponting, C. P., Vitart, V., Wilson, J. F., Yang, J., Bretherick, A. D., Scott, R. H., Hendry, S. C., Moutsianas, L., Law, A., Caulfield, M. J., Baillie, J. K., Begg, C., Ling, L., Pereira, A. C., Aravindan, L., Armstrong, R., Biggs, H., Boz, C., Brown, A., Clark, R., Coutts, A., Coyle, J., Cullum, L., Das, S., Day, N., Donnelly, L., Duncan, E., Finernan, P., Fourman, M. H., Furlong, A., Furniss, J., Gallagher, B., Gilchrist, T., Golightly, A., Hafezi, K., Hamilton, D., Hendry, R., Law, D., Law, R., Law, S., Lidstone-Scott, R., Macgillivray, L., Maclean, A., Mal, H., Mccafferty, S., Mcmaster, E., Meikle, J., Moore, S. C., Murphy, S., Hellen, M., Zheng, C., Chen, J., Paterson, T., Schon, K., Stenhouse, A., Das, M., Swets, M., Szoor-McElhinney, H., Taneski, F., Turtle, L., Wackett, T., Ward, M., Weaver, J., Wrobel, N., Arbane, G., Bociek, A., Campos, S., Grau, N., Jones, T. O., Lim, R., Marotti, M., Ostermann, M., Whitton, C., Alldis, Z., Astin-Chamberlain, R., Bibi, F., Biddle, J., Blow, S., Bolton, M., Borra, C., Bowles, R., Burton, M., Choudhury, Y., Collier, D., Cox, A., Easthope, A., Ebano, P., Fotiadis, S., Gurasashvili, J., Halls, R., Hartridge, P., Kallon, D., Kassam, J., Lancoma-Malcolm, I., Matharu, M., May, P., Mitchelmore, O., Newman, T., Patel, M., Pheby, J., Pinzuti, I., Prime, Z., Prysyazhna, O., Shiel, J., Taylor, M., Tierney, C., Wood, S., Zak, A., Zongo, O., Bonner, S., Hugill, K., Jones, J., Liggett, S., Headlam, E., Bandla, N., Gellamucho, M., Davies, M., Thompson, C., Abdelrazik, M., Bakthavatsalam, D., Elhassan, M., Ganesan, A., Haldeos, A., Moreno-Cuesta, J., Purohit, D., Vincent, R., Xavier, K., Kumar, R., Frater, Alessia, Saleem, M., Carter, D., Jenkins, S., Lamond, Z., Wall, A., Fernandez-Roman, J., Hamilton, D. O., Johnson, E., Johnston, B., Martinez Guzman, Maria Loreto, Mulla, S., Shaw, D., Waite, A. A. C., Waugh, V., Welters, I. D., Williams, K., Cavazza, A., Cockrell, M., Corcoran, E., Depante, M., Finney, C., Jerome, E., Mcphail, M., Nayak, M., Noble, H., O'Reilly, K., Pappa, E., Saha, R., Saha, S., Smith, Jenovia Amisti, Knighton, A., Antcliffe, D., Banach, D., Brett, S., Coghlan, P., Fernandez, Z., Gordon, A., Rojo, R., Arias, S. S., Templeton, M., Meredith, M., Morris, L., Ryan, L., Clark, A., Sampson, J., Peters, C., Dent, M., Langley, M., Ashraf, Sana, Wei, S., Andrew, A., Bashyal, A., Davidson, N., Hutton, P., Mckechnie, S., Wilson, J., Baptista, D., Crowe, R., Fernandes, R., Herdman-Grant, R., Joseph, A., O'Connor, D., Allen, M., Loveridge, A., Mckenley, I., Morino, E., Naranjo, A., Simms, R., Sollesta, K., Swain, A., Venkatesh, H., Khera, J., Fox, J., Andrew, G., Barclay, L., Callaghan, M., Campbell, R., Clark, S., Hope, D., Marshall, L., Mcculloch, C., Briton, K., Singleton, J., Birch, S., Brimfield, L., Daly, Z., Pogson, D., Rose, S., Nown, A., Battle, C., Brinkworth, E., Harford, R., Murphy, C., Newey, L., Rees, T., Williams, M., Arnold, S., Polgarova, P., Stroud, K., Meaney, E., Jones, M., Ng, A., Agrawal, S., Pathan, N., White, D., Daubney, E., Elston, K., Grauslyte, L., Hussain, M., Phull, M., Pogreban, T., Rosaroso, L., Salciute, E., Franke, G., Wong, J., George, A., de Gordoa, L. O. -R., Peasgood, E., Phillips, C., Bates, M., Dasgin, J., Gill, J., Nilsson, A., Scriven, J., Collins, A., Khaliq, W., Gude, E. T., Delgado, C. C., Dawson, D., Ding, L., Durrant, G., Ezeobu, O., Farnell-Ward, S., Harrison, A., Kanu, R., Leaver, S., Maccacari, E., Manna, S., Saluzzio, R. P., Queiroz, J., Samakomva, T., Sicat, C., Texeira, J., Da Gloria, E. F., Lisboa, A., Rawlins, J., Mathew, J., Kinch, A., Hurt, W. J., Shah, N., Clark, V., Thanasi, M., Yun, N., Patel, K., Bennett, S., Goodwin, E., Jackson, M., Kent, A., Tibke, C., Woodyatt, W., Zaki, A., Abraheem, A., Bamford, P., Cawley, K., Dunmore, C., Faulkner, M., Girach, R., Jeffrey, H., Jones, R., London, E., Nagra, I., Nasir, F., Sainsbury, H., Smedley, C., Patel, T., Smith, M., Chukkambotla, S., Kazi, A., Hartley, J., Dykes, J., Hijazi, M., Keith, S., Khan, M., Ryan-Smith, J., Springle, P., Thomas, J., Truman, N., Saad, S., Coleman, D., Fine, C., Matt, R., Gay, B., Dalziel, J., Ali, S., Goodchild, D., Harling, R., Bhatterjee, R., Goddard, W., Davison, C., Duberly, S., Hargreaves, J., Bolton, R., Davey, M., Golden, D., Seaman, R., Cherian, S., Cutler, S., Heron, A. E., Roynon-Reed, A., Szakmany, T., Williams, G., Richards, O., Cheema, Y., Brooke, H., Buckley, S., Suarez, J. C., Charlesworth, R., Hansson, K., Norris, J., Poole, A., Rose, A., Sandhu, R., Sloan, B., Smithson, E., Thirumaran, M., Wagstaff, V., Metcalfe, A., Brunton, M., Caterson, J., Coles, H., Frise, M., Rai, S. G., Jacques, N., Keating, L., Tilney, E., Bartley, S., Bhuie, P., Gibson, S., Lyle, A., Mcneela, F., Radhakrishnan, J., Hughes, A., Yates, B., Reynolds, J., Campbell, H., Thompsom, M., Dodds, S., Duffy, S., Greer, S., Shuker, K., Tridente, A., Khade, R., Sundar, A., Tsinaslanidis, G., Birkinshaw, I., Carter, J., Howard, K., Ingham, J., Joy, R., Pearson, H., Roche, S., Scott, Z., Bancroft, H., Bellamy, M., Carmody, M., Daglish, J., Moore, F., Rhodes, J., Sangombe, M., Kadiri, S., Croft, M., White, I., Frost, V., Aquino, M., Jha, R., Krishnamurthy, V., Lim, L., Combes, E., Joefield, T., Monnery, S., Beech, V., Trotman, S., Christine, Almaden-Boyle, Austin, P., Cabrelli, L., Cole, S., Casey, M., Chapman, S., Whyte, C., Baird, Y., Butler, A., Chadbourn, I., Folkes, L., Fox, H., Gardner, A., Gomez, R., Hobden, G., Hodgson, L., King, K., Margarson, M., Martindale, T., Meadows, E., Raynard, D., Thirlwall, Y., Helm, D., Margalef, J., Criste, K., Cusack, R., Golder, K., Golding, H., Jones, O., Leggett, S., Male, M., Marani, M., Prager, K., Williams, T., Roberts, B., Salmon, K., Anderson, P., Archer, K., Austin, K., Davis, C., Durie, A., Kelsall, O., Thrush, J., Vigurs, C., Wild, L., Wood, H. -L., Tranter, H., Cowley, N., Mcalindon, M., Burtenshaw, A., Digby, S., Low, E., Morgan, A., Cother, N., Rankin, T., Clayton, S., Mccurdy, A., Ahmed, C., Baines, B., Clamp, S., Colley, J., Haq, R., Hayes, A., Hulme, J., Hussain, S., Joseph, S., Maqsood, Z., Purewal, M., Benham, L., Bradshaw, Z., Brown, J., Caswell, M., Cupitt, J., Melling, S., Preston, S., Slawson, N., Stoddard, E., Warden, S., Deacon, B., Lynch, C., Pothecary, C., Roche, L., Howe, G. S., Singh, Jaywant, Turner, K., Ellis, H., Stroud, N., Hunt, J., Dearden, J., Dobson, E., Drummond, A., Mulcahy, M., Munt, S., O'Connor, G., Philbin, J., Rishton, C., Tully, R., Winnard, S., Cathcart, S., Duffy, K., Puxty, A., Puxty, K., Turner, L., Ireland, J., Semple, G., Long, K., Whiteley, S., Wilby, E., Ogg, B., Cowton, A., Kay, Abigail, Kent, M., Potts, K., Wilkinson, A., Campbell, S., Brown, E., Melville, J., Naisbitt, J., Joseph, R., Lazo, M., Walton, O., Neal, A., Alexander, P., Allen, S., Bradley-Potts, J., Brantwood, C., Egan, J., Felton, T., Padden, G., Ward, L., Moss, S., Glasgow, S., Abel, L., Brett, M., Digby, B., Gemmell, L., Hornsby, J., Macgoey, P., O'Neil, P., Price, R., Rodden, N., Rooney, K., Sundaram, R., Thomson, N., Hopkins, B., Thrasyvoulou, L., Willis, H., Clark, M., Coulding, M., Jude, E., Mccormick, J., Mercer, O., Potla, D., Rehman, H., Savill, H., Turner, V., Downes, C., Holding, K., Riches, K., Hilton, M., Hayman, M., Subramanian, D., Daniel, P., Adanini, O., Bhatia, N., Msiska, M., Collins, R., Clement, I., Patel, B., Gulati, A., Hays, C., Webster, K., Hudson, A., Webster, A., Stephenson, E., Mccormack, L., Slater, V., Nixon, R., Hanson, H., Fearby, M., Kelly, S., Bridgett, V., Robinson, P., Camsooksai, J., Humphrey, C., Reschreiter, H., Wadams, B., Death, Y., Bastion, V., Clarke, D., David, B., Kent, H., Lorusso, Riccardo, Lubimbi, G., Murdoch, S., Penacerrada, M., Thomas, A., Valentine, J., Vochin, A., Wulandari, R., Djeugam, B., Bell, G., English, K., Katary, A., Wilcox, L., Bruce, M., Connolly, K., Duncan, T., Michael, H. T., Lindergard, G., Hey, S., Fox, C., Alfonso, J., Durrans, L. J., Guerin, J., Blackledge, B., Harris, J., Hruska, M., Eltayeb, A., Lamb, T., Hodgkiss, T., Cooper, L., Rothwell, J., Allan, A., Anderson, F., Kaye, C., Liew, J., Medhora, J., Scott, T., Trumper, E., Botello, A., Lankester, L., Nikitas, N., Wells, C., Stowe, B., Spencer, K., Brandwood, C., Smith, L., Birchall, K., Kolakaluri, L., Baines, D., Sukumaran, A., Apetri, E., Basikolo, C., Catlow, L., Charles, B., Dark, P., Doonan, R., Harvey, A., Horner, D., Knowles, K., Lee, S., Lomas, D., Lyons, C., Marsden, T., Mclaughlan, D., Mcmorrow, L., Pendlebury, J., Perez, J., Poulaka, M., Proudfoot, N., Slaughter, M., Slevin, K., Thomas, V., Walker, D., Michael, A., Collis, M., Cosier, T., Millen, G., Richardson, N., Schumacher, N., Weston, H., Rand, J., Baxter, N., Henderson, S., Kennedy-Hay, S., Mcparland, C., Rooney, L., Sim, M., Mccreath, G., Akeroyd, L., Bano, S., Bromley, M., Gurr, L., Lawton, T., Morgan, J., Sellick, K., Warren, D., Wilkinson, B., Mcgowan, J., Ledgard, C., Stacey, A., Pye, K., Bellwood, R., Bentley, M., Bewley, J., Garland, Z., Grimmer, L., Gumbrill, B., Johnson, R., Sweet, K., Webster, D., Efford, G., Convery, K., Fottrell-Gould, D., Hudig, L., Keshet-Price, J., Randell, G., Stammers, K., Bokhari, M., Linnett, V., Lucas, R., Mccormick, W., Ritzema, J., Sanderson, A., Wild, H., Rostron, A., Roy, A., Woods, L., Cornell, S., Wakinshaw, F., Rogerson, K., Jarmain, J., Parker, R., Reddy, A., Turner-Bone, I., Harding, P., Abernathy, C., Foster, L., Gratrix, A., Martinson, V., Parkinson, P., Stones, E., Carbral-Ortega, L., Bercades, G., Brealey, D., Hass, I., Maccallum, N., Martir, G., Raith, E., Reyes, A., Smyth, D., Zitter, L., Benyon, S., Marriott, S., Park, L., Keenan, S., Gordon, E., Quinn, H., Baines, K., Cagova, L., Fofano, A., Garner, L., Holcombe, H., Mepham, S., Mitchell, A. M., Mwaura, L., Praman, K., Vuylsteke, A., Zamikula, J., Purewal, B., Rivers, V., Bell, S., Blakemore, H., Borislavova, B., Faulkner, B., Gendall, E., Goff, E., Hayes, K., Thomas, M., Worner, R., Smith, K., Stephens, D., Mew, L., Mwaura, E., Stewart, R., Williams, F., Wren, L., Sutherland, S. -B., Bevan, E., Martin, J., Trodd, D., Watson, G., Brown, C. W., Akinkugbe, O., Bamford, A., Beech, E., Belfield, H., Bell, M., Davies, C., Jones, G. A. L., Mchugh, T., Meghari, H., O'Neill, L., Peters, M. J., Ray, S., Tomas, A. L., Burn, I., Hambrook, G., Manso, K., Penn, R., Shanmugasundaram, P., Tebbutt, J., Thornton, D., Cole, J., Davies, R., Duffin, D., Hill, H., Player, B., Thomas, E., Williams, A., Griffin, D., Muchenje, N., Mupudzi, M., Partridge, R., Conyngham, J. -A., Thomas, R., Wright, M., Corral, M. A., Jacob, R., Jones, C., Denmade, C., Beavis, S., Dale, K., Gascoyne, R., Hawes, J., Pritchard, K., Stevenson, L., Whileman, A., Doble, P., Hutter, J., Pawley, C., Shovelton, C., Vaida, M., Butcher, D., O'Sullivan, S., Butterworth-Cowin, N., Ahmad, N., Barker, J., Bauchmuller, K., Bird, S., Cawthron, K., Harrington, K., Jackson, Y., Kibutu, F., Lenagh, B., Masuko, S., Mills, G. H., Raithatha, A., Wiles, M., Willson, J., Newell, H., Lye, A., Nwafor, L., Jarman, C., Rowland-Jones, S., Foote, D., Thompson, R., Watson, J., Hesseldon, L., Macharia, I., Chetam, L., Ford, A., Anderson, S., Housley, K., Milner, L., Hanratty, H., Trower, H., Phillips, P., Oxspring, S., Donne, B., Jardine, C., Williams, D., Hay, A., Flanagan, R., Hughes, G., Latham, S., Mckenna, E., Anderson, J., Hull, R., Rhead, K., Cruz, C., Pattison, N., Charnock, R., Mcfarland, D., Cosgrove, D., Ahmed, A., Morris, A., Jakkula, S., Nune, A., Ali, Amjad, Brady, M., Dale, S., Dance, A., Gledhill, L., Greig, J., Hanson, K., Holdroyd, K., Home, M., Kelly, D., Kitson, R., Matapure, L., Melia, D., Mellor, S., Nortcliffe, T., Pinnell, J., Robinson, M., Shaw, L., Shaw, R., Thomis, L., Wilson, A., Wood, T., Bayo, L. -A., Merwaha, E., Ishaq, T., Hanley, S., Hibbert, M., Tetla, D., Woodford, C., Durga, L., Kennard-Holden, G., Branney, D., Frankham, J., Pitts, S., White, N., Laha, S., Verlander, M., Altabaibeh, A., Alvaro, A., Gilbert, K., Ma, L., Mostoles, L., Parmar, C., Simpson, K., Jetha, C., Booker, L., Pratley, A., Adams, C., Agasou, A., Arden, T., Bowes, A., Boyle, P., Beekes, M., Button, H., Capps, N., Carnahan, M., Carter, A., Childs, D., Donaldson, D., Hard, K., Hurford, F., Hussain, Y., Javaid, A., Jose, S., Leigh, M., Martin, T., Millward, H., Motherwell, N., Rikunenko, R., Stickley, J., Summers, J., Ting, L., Tivenan, H., Tonks, L., Wilcox, R., Skinner, D., Gaylard, J., Mullan, D., Newman, J., Holland, M., Keenan, N., Lyons, M., Wassall, H., Marsh, C., Mahenthran, M., Carter, E., Kong, T., Blackman, H., Creagh-Brown, B., Donlon, S., Michalak-Glinska, N., Mtuwa, S., Pristopan, V., Salberg, A., Smith, E., Stone, S., Piercy, C., Verula, J., Burda, D., Montaser, R., Harden, L., Mayangao, I., Marriott, C., Bradley, P., Harris, C., Andrews, E., Birch, J., Collins, E., Hammerton, K., O'Leary, R., Purvis, S., Barber, R., Hewitt, C., Hilldrith, A., Jackson-Lawrence, K., Shepardson, S., Wills, M., Butler, S., Tavares, S., Cunningham, A., Hindale, J., Arif, S., Bean, S., Burt, K., Spivey, M., Demetriou, C., Eckbad, C., Hierons, S., Howie, L., Mitchard, S., Ramos, L., Serrano-Ruiz, A., White, K., Kelly, F., Cristiano, D., Dormand, N., Farzad, Z., Gummadi, M., Liyanage, K., Salmi, S., Sloane, G., Thwaites, V., Varghese, M., Zborowski, A. 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Forgetta, V, Morrison, D, Ghosh, B, Laurent, L, Belisle, A, Henry, D, Abdullah, T, Adeleye, O, Mamlouk, N, Kimchi, N, Afrasiabi, Z, Rezk, N, Vulesevic, B, Bouab, M, Guzman, C, Petitjean, L, Tselios, C, Xue, X, Schurr, E, Afilalo, J, Afilalo, M, Oliveira, M, Brenner, B, Lepage, P, Ragoussis, J, Auld, D, Brassard, N, Durand, M, Chasse, M, Kaufmann, D, Lathrop, G, Mooser, V, Richards, J, Li, R, Adra, D, Rahmouni, S, Georges, M, Moutschen, M, Misset, B, Darcis, G, Guiot, J, Guntz, J, Azarzar, S, Gofflot, S, Beguin, Y, Claassen, S, Malaise, O, Huynen, P, Meuris, C, Thys, M, Jacques, J, Leonard, P, Frippiat, F, Giot, J, Sauvage, A, von Frenckell, C, Belhaj, Y, Lambermont, B, Pigazzini, S, Nkambule, L, Daya, M, Shortt, J, Rafaels, N, Wicks, S, Crooks, K, Barnes, K, Gignoux, C, Chavan, S, Laisk, T, Lall, K, Lepamets, M, Magi, R, Esko, T, Reimann, E, Milani, L, Alavere, H, Metsalu, K, Puusepp, M, Metspalu, A, Naaber, P, Laane, E, Pesukova, J, Peterson, P, Kisand, K, Tabri, J, Allos, R, Hensen, K, Starkopf, J, Ringmets, I, Tamm, A, Kallaste, A, Bochud, P, Rivolta, C, Bibert, S, Quinodoz, M, Kamdar, D, Boillat, N, Nussle, S, Albrich, W, Suh, N, Neofytos, D, Erard, V, Voide, C, de Cid, R, Galvan-Femenia, I, Blay, N, Carreras, A, Cortes, B, Farre, X, Sumoy, L, Moreno, V, Mercader, J, Guindo-Martinez, M, Torrents, D, Kogevinas, M, Garcia-Aymerich, J, Castano-Vinyals, G, Dobano, C, Renieri, A, Mari, F, Fallerini, C, Daga, S, Benetti, E, Baldassarri, M, Fava, F, Frullanti, E, Valentino, F, Doddato, G, Giliberti, A, Tita, R, Amitrano, S, Bruttini, M, Croci, S, Meloni, I, Mencarelli, M, Rizzo, C, Pinto, A, Beligni, G, Tommasi, A, Di Sarno, L, Palmieri, M, Carriero, M, Alaverdian, D, Busani, S, Bruno, R, Vecchia, M, Belli, M, Picchiotti, N, Sanarico, M, Gori, M, Furini, S, Mantovani, S, Ludovisi, S, Mondelli, M, Castelli, F, Quiros-Roldan, E, Antoni, M, Zanella, I, Vaghi, M, Rusconi, S, Siano, M, Montagnani, F, Emiliozzi, A, Fabbiani, M, Rossetti, B, Bargagli, E, Bergantini, L, D'Alessandro, M, Cameli, P, Bennett, D, Anedda, F, Marcantonio, S, Scolletta, S, Franchi, F, Mazzei, M, Guerrini, S, Conticini, E, Cantarini, L, Frediani, B, Tacconi, D, Spertilli, C, Feri, M, Donati, A, Scala, R, Guidelli, L, Spargi, G, Corridi, M, Nencioni, C, Croci, L, Bandini, M, Caldarelli, G, Piacentini, P, Desanctis, E, Cappelli, S, Canaccini, A, Verzuri, A, Anemoli, V, Ognibene, A, Pancrazzi, A, Lorubbio, M, D'Arminio Monforte, A, Miraglia, F, Girardis, M, Venturelli, S, Cossarizza, A, Antinori, A, Vergori, A, Gabrieli, A, Riva, A, Francisci, D, Schiaroli, E, Paciosi, F, Scotton, P, Andretta, F, Panese, S, Scaggiante, R, Gatti, F, Parisi, S, Baratti, S, Della Monica, M, Piscopo, C, Capasso, M, Russo, R, Andolfo, I, Iolascon, A, Fiorentino, G, Carella, M, Castori, M, Merla, G, Squeo, G, Aucella, F, Raggi, P, Marciano, C, Perna, R, Bassetti, M, Di Biagio, A, Sanguinetti, M, Masucci, L, Valente, S, Mandala, M, Giorli, A, Salerni, L, Zucchi, P, Parravicini, P, Menatti, E, Trotta, T, Giannattasio, F, Coiro, G, Lena, F, Coviello, D, Mussini, C, Martinelli, E, Mancarella, S, Tavecchia, L, Crotti, L, Gabbi, C, Rizzi, M, Maggiolo, F, Ripamonti, D, Bachetti, T, La Rovere, M, Sarzi-Braga, S, Bussotti, M, Ceri, S, Pinoli, P, Raimondi, F, Biscarini, F, Stella, A, Zguro, K, Capitani, K, Suardi, C, Dei, S, Parati, G, Ravaglia, S, Artuso, R, Botta, G, Di Domenico, P, Rancan, I, Perrella, A, Bianchi, F, Romani, D, Bergomi, P, Catena, E, Colombo, R, Tanfoni, M, Vincenti, A, Ferri, C, Grassi, D, Pessina, G, Tumbarello, M, Di Pietro, M, Sabrina, R, Luchi, S, Barbieri, C, Acquilini, D, Andreucci, E, Segala, F, Tiseo, G, Falcone, M, Lista, M, Poscente, M, De Vivo, O, Petrocelli, P, Guarnaccia, A, Baroni, S, Smith, A, Boughton, A, Li, K, Lefaive, J, Annis, A, Chittoor, G, Josyula, N, Leader, J, Carey, D, Gass, M, Cantor, M, Yadav, A, van Heel, D, Hunt, K, Mason, D, Huang, Q, Finer, S, Trivedi, B, Griffiths, C, Martin, H, Wright, J, Trembath, R, Soranzo, N, Zhao, J, Butterworth, A, Danesh, J, Di Angelantonio, E, Franke, L, Boezen, M, Deelen, P, Claringbould, A, Lopera, E, Warmerdam, R, Vonk, J, van Blokland, I, Lanting, P, Ori, A, Zollner, S, Wang, J, Beck, A, Peloso, G, Ho, Y, Sun, Y, Huffman, J, O'Donnell, C, Cho, K, Tsao, P, Gaziano, J, Nivard, M, de Geus, E, Bartels, M, Jan Hottenga, J, Weiss, S, Karlson, E, Smoller, J, Green, R, Feng, Y, Murphy, S, Meigs, J, Woolley, A, Perez, E, Li, B, Verma, S, Lucas, A, Bradford, Y, Zeberg, H, Frithiof, R, Hultstrom, M, Lipcsey, M, Tardif, N, Rooyackers, O, Grip, J, Maricic, T, Karczewski, K, Atkinson, E, Tsuo, K, Baya, N, Turley, P, Gupta, R, Callier, S, Walters, R, Palmer, D, Sarma, G, Cheng, N, Lu, W, Bryant, S, Churchhouse, C, Cusick, C, Goldstein, J, King, D, Seed, C, Finucane, H, Martin, A, Satterstrom, F, Wilson, D, Armstrong, J, Rudkin, J, Band, G, Earle, S, Lin, S, Arning, N, Crook, D, Wyllie, D, O'Connell, A, Spencer, C, Koelling, N, Caulfield, M, Scott, R, Moutsianas, L, Pasko, D, Ball, C, Hong, E, Rand, K, Girshick, A, Guturu, H, Baltzell, A, Roberts, G, Park, D, Coignet, M, Mccurdy, S, Knight, S, Partha, R, Rhead, B, Zhang, M, Berkowitz, N, Gaddis, M, Noto, K, Ruiz, L, Pavlovic, M, Sloofman, L, Charney, A, Beckmann, N, Schadt, E, Jordan, D, Thompson, R, Gettler, K, Abul-Husn, N, Ascolillo, S, Buxbaum, J, Chaudhary, K, Cho, J, Itan, Y, Kenny, E, Belbin, G, Sealfon, S, Sebra, R, Salib, I, Collins, B, Levy, T, Britvan, B, Keller, K, Tang, L, Peruggia, M, Hiester, L, Niblo, K, Aksentijevich, A, Labkowsky, A, Karp, A, Zlatopolsky, M, Preuss, M, Loos, R, Nadkarni, G, Do, R, Hoggart, C, Choi, S, Underwood, S, O'Reilly, P, Huckins, L, Zyndorf, M, Daly, M, Neale, B, Ganna, A, Fawkes, A, Murphy, L, Rowan, K, Ponting, C, Vitart, V, Yang, J, Bretherick, A, Hendry, S, Law, A, Baillie, J, Kousathanas, Athanasios [0000-0001-6265-6521], Pairo-Castineira, Erola [0000-0002-2423-3090], Rawlik, Konrad [0000-0002-0010-370X], Walker, Susan [0000-0002-5016-6426], Malinauskas, Tomas [0000-0002-4847-5529], Wu, Yang [0000-0002-0128-7280], Shen, Xia [0000-0003-4390-1979], Elliott, Katherine S [0000-0002-8125-797X], Keating, Sean [0000-0001-8552-5604], Wang, Bo [0000-0002-1580-797X], Klaric, Lucija [0000-0003-3105-8929], Parkinson, Nick [0000-0001-6336-5654], Nichol, Alistair [0000-0002-4689-1238], Semple, Malcolm G [0000-0001-9700-0418], Salehi, Shahla [0000-0002-5058-7706], Knight, Julian [0000-0002-0377-5536], Elgar, Greg [0000-0001-7323-1596], Patch, Christine [0000-0002-4191-0663], Baras, Aris [0000-0002-6830-3396], Abecasis, Goncalo R [0000-0003-1509-1825], Ferreira, Manuel AR [0000-0001-9059-1825], Rader, Daniel J [0000-0002-9245-9876], Ritchie, Marylyn D [0000-0002-1208-1720], Shankar-Hari, Manu [0000-0002-5338-2538], Summers, Charlotte [0000-0002-7269-2873], Hinds, Charles [0000-0001-5094-8324], McAuley, Danny [0000-0002-3283-1947], Montgomery, Hugh [0000-0001-8797-5019], Elliott, Paul [0000-0002-7511-5684], Tenesa, Albert [0000-0003-4884-4475], Murphy, Lee [0000-0001-6467-7449], Rowan, Kathy [0000-0001-8217-5602], Ponting, Chris P [0000-0003-0202-7816], Vitart, Veronique [0000-0002-4991-3797], Wilson, James F [0000-0001-5751-9178], Yang, Jian [0000-0003-2001-2474], Bretherick, Andrew D [0000-0001-9258-3140], Hendry, Sara Clohisey [0000-0001-7489-9846], Moutsianas, Loukas [0000-0001-5453-345X], Law, Andy [0000-0003-1868-2364], Caulfield, Mark J [0000-0001-9295-3594], Baillie, J Kenneth [0000-0001-5258-793X], Apollo - University of Cambridge Repository, National Institute for Health Research, UKRI MRC COVID-19 Rapid Response Call, UK Research and Innovation, Internal Medicine, Epidemiology, Center of Experimental and Molecular Medicine, AII - Infectious diseases, Amsterdam Neuroscience - Neuroinfection & -inflammation, Neurology, Stem Cell Aging Leukemia and Lymphoma (SALL), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Life Course Epidemiology (LCE), Groningen Research Institute for Asthma and COPD (GRIAC), APH - Methodology, APH - Mental Health, Biological Psychology, AMS - Ageing & Vitality, AMS - Sports, APH - Personalized Medicine, APH - Health Behaviors & Chronic Diseases, Department of Health & Social Care (UK), Medical Research Council (UK), Roslin Institute, Pérez-Tur, Jordi, Institute for Molecular Medicine Finland, Doctoral Programme in Population Health, Centre of Excellence in Complex Disease Genetics, Aarno Palotie / Principal Investigator, Genomics of Neurological and Neuropsychiatric Disorders, Department of Public Health, Samuli Olli Ripatti / Principal Investigator, Complex Disease Genetics, Faculty Common Matters (Faculty of Social Sciences), Data Science Genetic Epidemiology Lab, CAMM - Research Program for Clinical and Molecular Metabolism, investigators, GenOMICC, investigators, 23andMe, and Initiative, COVID-19 Human Genetics

Subjects
Genome-wide association studies, PATHWAY, Fucosyltransferase, Lectins, Receptors, Genetics research, TOOL, Phospholipid Transfer Proteins, Genome, Multidisciplinary, C-Type, ATP-Binding Cassette Transporters, Cell Adhesion Molecules, Critical Care, E-Selectin, Factor VIII, Fucosyltransferases, Genome-Wide Association Study, Humans, Interleukin-10 Receptor beta Subunit, Lectins, C-Type, Mucin-1, Nerve Tissue Proteins, Receptors, Cell Surface, Repressor Proteins, SARS-CoV-2, COVID-19, Critical Illness, Genome, Human, Host-Pathogen Interactions, Whole Genome Sequencing, 1184 Genetics, developmental biology, physiology, ASSOCIATION, GenOMICC investigators, COVID-19/genetics, Host-Pathogen Interactions/genetics, Multidisciplinary Sciences, Host-Pathogen Interaction, Cell Surface, Science & Technology - Other Topics, Infectious diseases, Critical Illne, Human, Respiratory distress syndrome, General Science & Technology, ATP-Binding Cassette Transporter, DENDRITIC CELLS, 23andMe investigators, Settore MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA, Phospholipid Transfer Protein, SDG 3 - Good Health and Well-being, LINKAGE, Science & Technology, SARS-CoV-2/pathogenicity, Repressor Protein, SIGNAL, ONTOLOGY, COVID-19 Human Genetics Initiative, Critical Illness/mortality, Cell Adhesion Molecule, Nerve Tissue Protein, Genome, Human/genetics
Abstract

34 páginas, 3 figuras, 1 tabla., Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2-4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease., GenOMICC was funded by the Department of Health and Social Care (DHSC), Illumina, LifeArc, the Medical Research Council (MRC), UKRI, Sepsis Research (the Fiona Elizabeth Agnew Trust), the Intensive Care Society, a Wellcome Trust Senior Research Fellowship (J.K.B., 223164/Z/21/Z) a BBSRC Institute Program Support Grant to the Roslin Institute (BBS/E/D/20002172, BBS/E/D/10002070 and BBS/E/D/30002275) and UKRI grants MC_ PC_20004, MC_PC_19025, MC_PC_1905 and MRNO2995X/1. WGS was performed by Illumina Article at Illumina Laboratory Services and was overseen by Genomics England. We would like to thank all at Genomics England who have contributed to the sequencing, clinical and genomic data analysis. This research is supported in part by the Data and Connectivity National Core Study, led by Health Data Research UK in partnership with the Office for National Statistics and funded by UK Research and Innovation (grant ref. MC_PC_20029). A.D.B. would like to acknowledge funding from the Wellcome PhD training fellowship for clinicians (204979/Z/16/Z) and the Edinburgh Clinical Academic Track (ECAT) programme. We thank the research participants and employees of 23andMe for making this work possible. Genomics England and the 100,000 Genomes Project were funded by the National Institute for Health Research, the Wellcome Trust, the MRC, Cancer Research UK, the DHSC and NHS England. We are grateful for the support from S. Hill and the team in NHS England and the 13 Genomic Medicine Centres that delivered the 100,000 Genomes Project, which provided most of the control genome sequences for this study. We thank the participants in the 100,000 Genomes Project, who made this study possible, and the Genomics England Participant Panel for their strategic advice, involvement and engagement. We acknowledge NHS Digital, Public Health England and the Intensive Care National Audit and Research Centre, who provided life-course longitudinal clinical data on the participants. This work forms part of the portfolio of research of the National Institute for Health Research Barts Biomedical Research Centre. Mark Caulfield is an NIHR Senior Investigator. This study owes a great deal to the National Institute for Healthcare Research Clinical Research Network (NIHR CRN) and the Chief Scientist’s Office (Scotland), who facilitate recruitment into research studies in NHS hospitals, and to the global ISARIC and InFACT consortia. Additional replication was conducted using the UK Biobank Resource (project 26041). The Penn Medicine BioBank is funded by a gift from the Smilow family; the National Center for Advancing Translational Sciences of the National Institutes of Health under CTSA award number UL1TR001878; and the Perelman School of Medicine at the University of Pennsylvania. We thank the AncestryDNA customers who voluntarily contributed information in the COVID-19 survey. HRS (dbGaP accession: phs000428.v1.p1): HRS was supported by the National Institute on Aging (NIA U01AG009740). The genotyping was funded separately by the National Institute on Aging (RC2 AG036495, RC4 AG039029). Genotyping was conducted by the NIH Center for Inherited Disease Research (CIDR) at Johns Hopkins University. Genotyping quality control and final preparation of the data were performed by the Genetics Coordinating Center at the University of Washington. The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by the NCI, NHGRI, NHLBI, NIDA, NIMH and NINDS. The data used for the analyses described in this manuscript were obtained from the GTEx Portal on 22 August 2021 (GTEx Analysis Release v.8 (dbGaP Accession phs000424.v8.p2). We thank the research participants and employees of 23andMe for making this work possible. A full list of contributors who have provided data that were collated in the HGI project, including previous iterations, is available at https://www.covid19hg.org/acknowledgements. The views expressed are those of the authors and not necessarily those of the DHSC, NHS, Department for International Development (DID), NIHR, MRC, Wellcome Trust or Public Health England.

Published
2022

44. Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility

Author

van Blokland, I, Lanting, P, Ori, A, Vonk, J, Warmerdam, R, Herkert, J, Boulogne, F, Claringbould, A, Lopera-Maya, E, Bartels, M, Hottenga, J, Ganna, A, Karjalainen, J, Hayward, C, Fawns-Ritchie, C, Campbell, A, Porteous, D, Cirulli, E, Barrett, K, Riffle, S, Bolze, A, White, S, Tanudjaja, F, Wang, X, Ramirez, J, Lim, Y, Lu, J, Washington, N, de Geus, E, Deelen, P, Boezen, H, Franke, L, Mierau, J, Dekens, J, Nolte, I, Dijkema, M, Wiersma, H, Jankipersadsing, S, Cho, J, Loos, R, Moscati, A, Chang, Y, Choe, P, Chung, J, Ham, S, Joo, E, Jung, J, Kang, C, Kim, H, Kim, E, Lee, H, Park, S, Park, K, Park, J, Ryu, S, Song, K, Paik, N, Albillos, A, Asselta, R, Bujanda, L, Buti, M, Duga, S, Fernandez, J, Gomez, M, Invernizzi, P, Prati, D, Banales, J, Folseraas, T, Franke, A, Hov, J, Karlsen, T, Valenti, L, Degenhardt, F, Ellighaus, D, Eythorsson, E, Haraldsson, A, Helgason, D, Holm, H, Ingvarsson, R, Jonsdottir, I, Norddahl, G, Palsson, R, Saemundsdottir, J, Stefansson, K, Thorsteinsdottir, U, Gudbjartsson, D, Jonsson, H, Melsted, P, Sulem, P, Sveinbjornsson, G, Alarcon-Riquelme, M, Bernardo, D, Rello, S, Martinez-Bueno, M, Amtrano, S, Bruttini, M, Floriana, V, Giliberti, A, Benetti, E, Fallerini, C, Furini, S, Pinto, A, Baldassarri, M, Fava, F, Mari, F, Renieri, A, Croci, S, Tita, R, Frullanti, E, Altshul, D, Huang, Q, Hunt, K, Martin, H, Mason, D, Trembath, R, Trivedi, B, Wright, J, Finer, S, Griffiths, C, van Heel, D, Jannes, C, Krieger, J, Pereira, A, Marques, E, Dalton, K, Deboever, C, Jimenez-Morales, D, Palomera, A, Pinsky, B, Smith, E, Szalma, S, Tralau-Stewart, C, Wong, E, Gorzynski, J, de Jong, H, Amar, D, Delaneau, O, Hughes, C, Ioannidis, A, Raja, A, Rubinacci, S, Tanigawa, Y, Ashley, E, Bustamante, C, Parikh, V, Rivas, M, Wheeler, M, Busson, A, Goffard, J, Migeotte, I, Peyrassol, X, Smits, G, Vandernoot, I, Wilkin, F, Bouysran, Y, Pichon, B, Tiembe, N, Green, R, Karlson, B, Meigs, J, Mercader, J, Murphy, S, Perez, E, Slaugenhaupt, S, Smoller, J, Weiss, S, Woolley, A, Feng, Y, Nivard, M, Brusco, A, Bulik, C, Franchimont, D, Landen, M, Louis, E, Pedersen, N, Rahmouni, S, Striano, P, Vermeire, S, Zara, F, Al-Muftah, W, Badji, R, Ismail, S, Al-Sarraj, Y, Mbarek, H, Arumugam, P, Caulfield, M, Need, A, Oscroft, T, Rendon, A, Scott, R, Chan, G, Kousathanas, A, Moutsianas, L, Odhams, C, Pasko, D, Rhodes, D, Stuckey, A, Atkinson, E, Baya, N, Butler-Laporte, G, Finucane, H, Forgetta, V, Kanai, M, Karczewski, K, Koelling, N, Martin, A, Nakanishi, T, Palmer, D, Richards, J, Spencer, C, Turley, P, Walters, R, Wilson, D, Armstrong, J, O'Connell, A, Wyllie, D, Bryant, S, Churchhouse, C, Di Angelantonio, E, Chapman, M, Danesh, J, Ouwehand, W, Roberts, D, Watkins, N, Butterworth, A, Zhao, J, Biesecker, L, Davis, L, Kerchberger, E, Lee, S, Priest, J, Richards, B, Sankaran, V, Chwialkowska, K, Francescatto, M, Stevens, C, Trankiem, A, Balaconis, K, Liao, R, Daly, M, Neale, B, Bernasconi, A, Ceri, S, Cordioli, M, Niemi, M, Zhou, W, Nguyen, H, Solomonson, M, Gopalan, S, Hou, K, Jansen, P, de Leeuw, C, Lu, Z, Mancuso, N, Marouli, E, Papadopoulou, A, Pasaniuc, B, Pathak, G, Polimanti, R, Posthuma, D, Savage, J, Uffelmann, E, Visscher, P, Wendt, F, Wray, N, Yengo, L, van Blokland I. V., Lanting P., Ori A. P. S., Vonk J. M., Warmerdam R. C. A., Herkert J. C., Boulogne F., Claringbould A., Lopera-Maya E. A., Bartels M., Hottenga J. -J., Ganna A., Karjalainen J., Hayward C., Fawns-Ritchie C., Campbell A., Porteous D., Cirulli E. T., Barrett K. M. S., Riffle S., Bolze A., White S., Tanudjaja F., Wang X., Ramirez J. M., Lim Y. W., Lu J. T., Washington N. L., de Geus E. J. C., Deelen P., Boezen H. M., Franke L. H., Mierau J. O., Dekens J., Nolte I., Dijkema M. X. L., Wiersma H. H., Jankipersadsing S. A., Cho J. H., Loos R. J. F., Moscati A., Chang Y., Choe P. G., Chung J., Ham S., Joo E. -J., Jung J., Kang C. K., Kim H. -L., Kim H. B., Kim E. S., Lee H. -J., Park S., Park K. -U., Park J. S., Ryu S., Song K. -H., Kim H. -N., Paik N. -J., Albillos A., Asselta R., Bujanda L., Buti M., Duga S., Fernandez J., Gomez M. R., Invernizzi P., Prati D., Banales J. M., Folseraas T., Franke A., Hov J. R., Karlsen T. H., Valenti L., Degenhardt F., Ellighaus D., Eythorsson E. S., Haraldsson A., Helgason D., Holm H., Ingvarsson R. F., Jonsdottir I., Norddahl G. L., Palsson R., Saemundsdottir J., Stefansson K., Thorsteinsdottir U., Gudbjartsson D. F., Jonsson H., Melsted P., Sulem P., Sveinbjornsson G., Alarcon-Riquelme M. E., Bernardo D., Rello S. R., Martinez-Bueno M., Amtrano S., Bruttini M., Floriana V., Giliberti A. R., Benetti E., Fallerini C., Furini S., Pinto A. M., Baldassarri M., Fava F., Mari F., Renieri A., Croci S., Tita R., Frullanti E., Altshul D., Huang Q., Hunt K. A., Martin H. C., Mason D., Trembath R. C., Trivedi B., Wright J., Finer S., Griffiths C., van Heel D. A., Jannes C. E., Krieger J. E., Pereira A. C., Marques E., Dalton K., DeBoever C., Jimenez-Morales D., Palomera A. C., Pinsky B., Smith E., Szalma S., Tralau-Stewart C., Wong E., Gorzynski J., de Jong H., Amar D., Delaneau O., Hughes C., Ioannidis A., Raja A., Rubinacci S., Tanigawa Y., Ashley E., Bustamante C., Parikh V., Rivas M., Wheeler M., Busson A., Goffard J. -C., Migeotte I., Peyrassol X., Smits G., Vandernoot I., Wilkin F., Bouysran Y., Pichon B., Tiembe N., Green R., Karlson B., Meigs J., Mercader J., Murphy S., Perez E., Slaugenhaupt S., Smoller J., Weiss S., Woolley A., Feng Y. -C. A., Nivard M. G., Brusco A., Bulik C. M., Franchimont D., Landen M., Louis E., Pedersen N., Rahmouni S., Striano P., Vermeire S., Zara F., Al-Muftah W., Badji R., Ismail S., Al-Sarraj Y., Mbarek H., Arumugam P., Caulfield M., Need A. C., Oscroft T., Rendon A., Scott R. H., Chan G., Kousathanas A., Moutsianas L., Odhams C. A., Pasko D., Rhodes D., Stuckey A., Atkinson E. G., Baya N., Butler-Laporte G., Finucane H., Forgetta V., Kanai M., Karczewski K. J., Koelling N., Martin A. R., Nakanishi T., Palmer D. S., Richards J. B., Spencer C. C. A., Turley P., Walters R. K., Wilson D. J., Armstrong J., O'Connell A. M., Wyllie D. H., Bryant S., Churchhouse C., Di Angelantonio E., Chapman M., Danesh J., Ouwehand W., Roberts D., Watkins N., Butterworth A., Zhao J. H., Biesecker L., Davis L., van Heel D., Kerchberger E., Lee S., Priest J., Richards B., Sankaran V., Chwialkowska K., Francescatto M., Stevens C., Trankiem A., Balaconis K., Liao R., Daly M., Neale B., Bernasconi A., Ceri S., Cordioli M., Niemi M., Zhou W., Nguyen H., Solomonson M., Gopalan S., Hou K., Jansen P., de Leeuw C., Lu Z., Mancuso N., Marouli E., Papadopoulou A., Pasaniuc B., Pathak G., Polimanti R., Posthuma D., Savage J., Uffelmann E., Visscher P., Wendt F. R., Wray N., Yengo L., van Blokland, I, Lanting, P, Ori, A, Vonk, J, Warmerdam, R, Herkert, J, Boulogne, F, Claringbould, A, Lopera-Maya, E, Bartels, M, Hottenga, J, Ganna, A, Karjalainen, J, Hayward, C, Fawns-Ritchie, C, Campbell, A, Porteous, D, Cirulli, E, Barrett, K, Riffle, S, Bolze, A, White, S, Tanudjaja, F, Wang, X, Ramirez, J, Lim, Y, Lu, J, Washington, N, de Geus, E, Deelen, P, Boezen, H, Franke, L, Mierau, J, Dekens, J, Nolte, I, Dijkema, M, Wiersma, H, Jankipersadsing, S, Cho, J, Loos, R, Moscati, A, Chang, Y, Choe, P, Chung, J, Ham, S, Joo, E, Jung, J, Kang, C, Kim, H, Kim, E, Lee, H, Park, S, Park, K, Park, J, Ryu, S, Song, K, Paik, N, Albillos, A, Asselta, R, Bujanda, L, Buti, M, Duga, S, Fernandez, J, Gomez, M, Invernizzi, P, Prati, D, Banales, J, Folseraas, T, Franke, A, Hov, J, Karlsen, T, Valenti, L, Degenhardt, F, Ellighaus, D, Eythorsson, E, Haraldsson, A, Helgason, D, Holm, H, Ingvarsson, R, Jonsdottir, I, Norddahl, G, Palsson, R, Saemundsdottir, J, Stefansson, K, Thorsteinsdottir, U, Gudbjartsson, D, Jonsson, H, Melsted, P, Sulem, P, Sveinbjornsson, G, Alarcon-Riquelme, M, Bernardo, D, Rello, S, Martinez-Bueno, M, Amtrano, S, Bruttini, M, Floriana, V, Giliberti, A, Benetti, E, Fallerini, C, Furini, S, Pinto, A, Baldassarri, M, Fava, F, Mari, F, Renieri, A, Croci, S, Tita, R, Frullanti, E, Altshul, D, Huang, Q, Hunt, K, Martin, H, Mason, D, Trembath, R, Trivedi, B, Wright, J, Finer, S, Griffiths, C, van Heel, D, Jannes, C, Krieger, J, Pereira, A, Marques, E, Dalton, K, Deboever, C, Jimenez-Morales, D, Palomera, A, Pinsky, B, Smith, E, Szalma, S, Tralau-Stewart, C, Wong, E, Gorzynski, J, de Jong, H, Amar, D, Delaneau, O, Hughes, C, Ioannidis, A, Raja, A, Rubinacci, S, Tanigawa, Y, Ashley, E, Bustamante, C, Parikh, V, Rivas, M, Wheeler, M, Busson, A, Goffard, J, Migeotte, I, Peyrassol, X, Smits, G, Vandernoot, I, Wilkin, F, Bouysran, Y, Pichon, B, Tiembe, N, Green, R, Karlson, B, Meigs, J, Mercader, J, Murphy, S, Perez, E, Slaugenhaupt, S, Smoller, J, Weiss, S, Woolley, A, Feng, Y, Nivard, M, Brusco, A, Bulik, C, Franchimont, D, Landen, M, Louis, E, Pedersen, N, Rahmouni, S, Striano, P, Vermeire, S, Zara, F, Al-Muftah, W, Badji, R, Ismail, S, Al-Sarraj, Y, Mbarek, H, Arumugam, P, Caulfield, M, Need, A, Oscroft, T, Rendon, A, Scott, R, Chan, G, Kousathanas, A, Moutsianas, L, Odhams, C, Pasko, D, Rhodes, D, Stuckey, A, Atkinson, E, Baya, N, Butler-Laporte, G, Finucane, H, Forgetta, V, Kanai, M, Karczewski, K, Koelling, N, Martin, A, Nakanishi, T, Palmer, D, Richards, J, Spencer, C, Turley, P, Walters, R, Wilson, D, Armstrong, J, O'Connell, A, Wyllie, D, Bryant, S, Churchhouse, C, Di Angelantonio, E, Chapman, M, Danesh, J, Ouwehand, W, Roberts, D, Watkins, N, Butterworth, A, Zhao, J, Biesecker, L, Davis, L, Kerchberger, E, Lee, S, Priest, J, Richards, B, Sankaran, V, Chwialkowska, K, Francescatto, M, Stevens, C, Trankiem, A, Balaconis, K, Liao, R, Daly, M, Neale, B, Bernasconi, A, Ceri, S, Cordioli, M, Niemi, M, Zhou, W, Nguyen, H, Solomonson, M, Gopalan, S, Hou, K, Jansen, P, de Leeuw, C, Lu, Z, Mancuso, N, Marouli, E, Papadopoulou, A, Pasaniuc, B, Pathak, G, Polimanti, R, Posthuma, D, Savage, J, Uffelmann, E, Visscher, P, Wendt, F, Wray, N, Yengo, L, van Blokland I. V., Lanting P., Ori A. P. S., Vonk J. M., Warmerdam R. C. A., Herkert J. C., Boulogne F., Claringbould A., Lopera-Maya E. A., Bartels M., Hottenga J. -J., Ganna A., Karjalainen J., Hayward C., Fawns-Ritchie C., Campbell A., Porteous D., Cirulli E. T., Barrett K. M. S., Riffle S., Bolze A., White S., Tanudjaja F., Wang X., Ramirez J. M., Lim Y. W., Lu J. T., Washington N. L., de Geus E. J. C., Deelen P., Boezen H. M., Franke L. H., Mierau J. O., Dekens J., Nolte I., Dijkema M. X. L., Wiersma H. H., Jankipersadsing S. A., Cho J. H., Loos R. J. F., Moscati A., Chang Y., Choe P. G., Chung J., Ham S., Joo E. -J., Jung J., Kang C. K., Kim H. -L., Kim H. B., Kim E. S., Lee H. -J., Park S., Park K. -U., Park J. S., Ryu S., Song K. -H., Kim H. -N., Paik N. -J., Albillos A., Asselta R., Bujanda L., Buti M., Duga S., Fernandez J., Gomez M. R., Invernizzi P., Prati D., Banales J. M., Folseraas T., Franke A., Hov J. R., Karlsen T. H., Valenti L., Degenhardt F., Ellighaus D., Eythorsson E. S., Haraldsson A., Helgason D., Holm H., Ingvarsson R. F., Jonsdottir I., Norddahl G. L., Palsson R., Saemundsdottir J., Stefansson K., Thorsteinsdottir U., Gudbjartsson D. F., Jonsson H., Melsted P., Sulem P., Sveinbjornsson G., Alarcon-Riquelme M. E., Bernardo D., Rello S. R., Martinez-Bueno M., Amtrano S., Bruttini M., Floriana V., Giliberti A. R., Benetti E., Fallerini C., Furini S., Pinto A. M., Baldassarri M., Fava F., Mari F., Renieri A., Croci S., Tita R., Frullanti E., Altshul D., Huang Q., Hunt K. A., Martin H. C., Mason D., Trembath R. C., Trivedi B., Wright J., Finer S., Griffiths C., van Heel D. A., Jannes C. E., Krieger J. E., Pereira A. C., Marques E., Dalton K., DeBoever C., Jimenez-Morales D., Palomera A. C., Pinsky B., Smith E., Szalma S., Tralau-Stewart C., Wong E., Gorzynski J., de Jong H., Amar D., Delaneau O., Hughes C., Ioannidis A., Raja A., Rubinacci S., Tanigawa Y., Ashley E., Bustamante C., Parikh V., Rivas M., Wheeler M., Busson A., Goffard J. -C., Migeotte I., Peyrassol X., Smits G., Vandernoot I., Wilkin F., Bouysran Y., Pichon B., Tiembe N., Green R., Karlson B., Meigs J., Mercader J., Murphy S., Perez E., Slaugenhaupt S., Smoller J., Weiss S., Woolley A., Feng Y. -C. A., Nivard M. G., Brusco A., Bulik C. M., Franchimont D., Landen M., Louis E., Pedersen N., Rahmouni S., Striano P., Vermeire S., Zara F., Al-Muftah W., Badji R., Ismail S., Al-Sarraj Y., Mbarek H., Arumugam P., Caulfield M., Need A. C., Oscroft T., Rendon A., Scott R. H., Chan G., Kousathanas A., Moutsianas L., Odhams C. A., Pasko D., Rhodes D., Stuckey A., Atkinson E. G., Baya N., Butler-Laporte G., Finucane H., Forgetta V., Kanai M., Karczewski K. J., Koelling N., Martin A. R., Nakanishi T., Palmer D. S., Richards J. B., Spencer C. C. A., Turley P., Walters R. K., Wilson D. J., Armstrong J., O'Connell A. M., Wyllie D. H., Bryant S., Churchhouse C., Di Angelantonio E., Chapman M., Danesh J., Ouwehand W., Roberts D., Watkins N., Butterworth A., Zhao J. H., Biesecker L., Davis L., van Heel D., Kerchberger E., Lee S., Priest J., Richards B., Sankaran V., Chwialkowska K., Francescatto M., Stevens C., Trankiem A., Balaconis K., Liao R., Daly M., Neale B., Bernasconi A., Ceri S., Cordioli M., Niemi M., Zhou W., Nguyen H., Solomonson M., Gopalan S., Hou K., Jansen P., de Leeuw C., Lu Z., Mancuso N., Marouli E., Papadopoulou A., Pasaniuc B., Pathak G., Polimanti R., Posthuma D., Savage J., Uffelmann E., Visscher P., Wendt F. R., Wray N., and Yengo L.

Abstract

Epidemiological and genetic studies on COVID-19 are currently hindered by inconsistent and limited testing policies to confirm SARS-CoV-2 infection. Recently, it was shown that it is possible to predict COVID-19 cases using cross-sectional self-reported disease-related symptoms. Here, we demonstrate that this COVID-19 prediction model has reasonable and consistent performance across multiple independent cohorts and that our attempt to improve upon this model did not result in improved predictions. Using the existing COVID- 19 prediction model, we then conducted a GWAS on the predicted phenotype using a total of 1,865 predicted cases and 29,174 controls. While we did not find any common, largeeffect variants that reached genome-wide significance, we do observe suggestive genetic associations at two SNPs (rs11844522, p = 1.9x10-7; rs5798227, p = 2.2x10-7). Explorative analyses furthermore suggest that genetic variants associated with other viral infectious diseases do not overlap with COVID-19 susceptibility and that severity of COVID-19 may have a different genetic architecture compared to COVID-19 susceptibility. This study represents a first effort that uses a symptom-based predicted phenotype as a proxy for COVID-19 in our pursuit of understanding the genetic susceptibility of the disease. We conclude that the inclusion of symptom-based predicted cases could be a useful strategy in a scenario of limited testing, either during the current COVID-19 pandemic or any future viral outbreak.

Published
2021

49. Fish grazing enhanced by nutrient enrichment may limit invasive seagrass expansion

Author

Smulders, Fee O.H., Becker, S. Tatiana, Campbell, Justin E., Bakker, Elisabeth S., Boässon, Mickey J., Bouwmeester, Mark M., Vonk, J. Arie, Christianen, Marjolijn J.A., Smulders, Fee O.H., Becker, S. Tatiana, Campbell, Justin E., Bakker, Elisabeth S., Boässon, Mickey J., Bouwmeester, Mark M., Vonk, J. Arie, and Christianen, Marjolijn J.A.

Abstract

The success of invasive macrophytes can depend on local nutrient availability and consumer pressure, which may interact. We therefore experimentally investigated the interacting effects of nutrient (nitrogen and phosphorus) addition, the exclusion of large herbivorous fishes and mimicked grazing on the expansion rates of the invasive seagrass Halophila stipulacea. The experiments were established on Bonaire and Aruba, two islands in the southern Caribbean, which differ in fish community structure. We observed that multiple Caribbean fish species feed on H. stipulacea. At both study sites, nutrient enrichment decreased invasive leaf carbon:nitrogen ratios. However only on Bonaire, where herbivore fish abundance was 7 times higher and diversity was 4.5 times higher, did nutrient enrichment result in a significant reduction of H. stipulacea expansion into native Thalassia testudinum meadows. This effect was likely due to increased herbivory on nutrient enriched seagrass leaves, as we found that excluding large herbivorous fish (e.g. parrotfish) doubled invasive expansion rates in bare patches on Bonaire. On Aruba, H. stipulacea expansion rates were higher overall, which coincided with lower abundances and diversity of native fishes, and were limited by mimicked fish grazing. We suggest that top-down control by the native fish community may counteract eutrophication effects by increased grazing pressure on nutrient-rich invasive seagrass leaves. We conclude that diverse and abundant herbivore communities likely play an important role in limiting invasion success and their conservation and restoration may serve as a tool to slow down seagrass invasions.

Published
2022

50. Contrasting Export of Particulate Organic Carbon From Greenlandic Glacial and Nonglacial Streams

Author

Swiss Federal Institute of Technology (ETH) - Geological Institute, Department of Earth Sciences, UCL - SST/ELI/ELIE - Environmental Sciences, Bröder, Lisa, Hirst, Catherine, Opfergelt, Sophie, Thomas, Maxime, Vonk, J. E., Haghipour, N., Eglinton, T. I., Fouché, J., Swiss Federal Institute of Technology (ETH) - Geological Institute, Department of Earth Sciences, UCL - SST/ELI/ELIE - Environmental Sciences, Bröder, Lisa, Hirst, Catherine, Opfergelt, Sophie, Thomas, Maxime, Vonk, J. E., Haghipour, N., Eglinton, T. I., and Fouché, J.

Abstract

On-going shrinkage of Greenland's icecap, permafrost thaw, and changes in precipitation are exposing its landscapes to erosion and remobilization of ancient organic carbon (OC) held in soils and sedimentary rocks. The fate of this OC and potential feedbacks to climate are still unclear. Here, we show that the glacial Zackenberg river (Northeastern Greenland) exports aged particulate OC (POC, uncalibrated radiocarbon ages of ∼4,000 years). Many of the smaller periglacial streams affected by abrupt permafrost thaw transport substantially older POC (up to 32,000 years), especially with enhanced discharge following intense precipitation. Mineralogical analysis, and density and size fractionation of soils and both glacial and nonglacial river sediments reveal that OC is largely associated with phyllosilicate minerals, suggesting stabilization against microbial processing. Enhanced export of ancient, mineral-associated OC as a consequence of summer rainfall may accelerate translocation of OC from terrestrial to marine environments, but could have limited consequences for climate.

Published
2022

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