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1,718 results on '"Mansfield, J"'

51. Language vs. individuals in cross-linguistic corpus typology

Author

Haig, G., Schnell, S., Barth, D., Evans, N., Arka, I. W., Bergqvist, H., Forker, D., Gipper, S., Hodge, G., Kashima, E., Kasuga, Y., Kawakami, C., Kimoto, Y., Knuchel, D., Kogura, N., Kurabe, K., Mansfield, J., Narrog, H., Pratiwi, D. P. E., Putten, S. van, Senge, C., Tykhostup, O., Haig, G., Schnell, S., Barth, D., Evans, N., Arka, I. W., Bergqvist, H., Forker, D., Gipper, S., Hodge, G., Kashima, E., Kasuga, Y., Kawakami, C., Kimoto, Y., Knuchel, D., Kogura, N., Kurabe, K., Mansfield, J., Narrog, H., Pratiwi, D. P. E., Putten, S. van, Senge, C., and Tykhostup, O.

Abstract

Contains fulltext : 286116.pdf (Publisher’s version ) (Open Access)

Published
2021

52. Whither magnetic hyperthermia? A tentative roadmap

Author

Rubia-Rodríguez I., Santana-Otero A., Spassov S., Tombácz E., Johansson C., De La Presa P., Terán, Francisco, Morales M.P., Veintemillas-Verdaguer S., Thanh N.T.K., Besenhard M.O., Wilhelm C., Gazeau F., Harmer Q., Mayes E., Manshian B.B., Soenen S.J., Gu Y., Millán Á., Efthimiadou E.K., Gaudet J., Goodwill P., Mansfield J., Steinhoff U., Wells J., Wiekhorst F., Ortega D., Rubia-Rodríguez I., Santana-Otero A., Spassov S., Tombácz E., Johansson C., De La Presa P., Terán, Francisco, Morales M.P., Veintemillas-Verdaguer S., Thanh N.T.K., Besenhard M.O., Wilhelm C., Gazeau F., Harmer Q., Mayes E., Manshian B.B., Soenen S.J., Gu Y., Millán Á., Efthimiadou E.K., Gaudet J., Goodwill P., Mansfield J., Steinhoff U., Wells J., Wiekhorst F., and Ortega D.

Published
2021

53. Diets containing inulin but not lupins help to prevent swine dysentery in experimentally challenged pigs

Author

Hansen, C.F., Phillips, N.D., La, T., Hernandez, A., Mansfield, J., Kim, J.C., Mullan, B.P., Hampson, D.J., and Pluske, J.R.

Subjects
Inulin -- Research, Lupines -- Research, Dysentery -- Research, Swine -- Food and nutrition, Swine -- Physiological aspects, Swine -- Research, Zoology and wildlife conservation
Abstract

Swine dysentery is a contagious mucohemorrhagic diarrheal disease caused by the intestinal spirochete Brachyspira hyodysenteriae that colonizes and induces inflammation of the cecum and colon. It has been reported that a diet containing chicory root and sweet lupin can prevent swine dysentery. This experiment was conducted to test the hypothesis that inulin in the chicory root rather than galactans in lupins was responsible for protective effects. An experiment with a 2 x 2 factorial arrangement of treatments was undertaken using pigs fed barley- and triticale-based diets, with the main effects being protein source [185 g/kg of canola meal (decreased galactans) or 220 g/kg of lupins (greater galactans)] and inulin supplementation (0 or 80 g/kg). Forty Large White x Landrace pigs weighing 21 [+ or -] 3 kg, with 10 pigs per diet, were allowed to adapt to the diets for 2 wk, and then each pig was challenged orally 4 times with a broth culture containing B. hyodysenteriae on consecutive days. Pigs were killed when they showed clinical signs of dysentery or 6 wk postchallenge. Pigs fed diets without inulin had 8.3 times greater risk (P = 0.017) of developing swine dysentery and were 16 times more likely (P = 0.004) to have colon contents that were culture-positive for B. hyodysenteriae, compared with the pigs fed a diet with 80 g/kg of inulin. Diets containing lupins did not prevent pigs from developing clinical swine dysentery; however, inclusion of lupins or inulin or both in the diets delayed the onset of disease compared with the diet based mainly on canola meal (P < 0.05). Diet did not influence the total concentration of organic acids in the ileum, cecum, or upper and lower colon; however, the molar proportions of the organic acids were influenced (P < 0.05). Consequently the pH values in the cecum, and upper and lower colon were not influenced (P > 0.05) by diet. However the pH values of the ileal digesta were decreased in pigs fed the diet with both lupins and inulin compared with the diet containing only lupins (P < 0.05). In conclusion, this study shows that diets supplemented with highly fermentable carbohydrates from inulin protected pigs against developing swine dysentery. Key words: Brachyspira hyodysenteriae, fermentable carbohydrate, inulin, lupin, pig, swine dysentery doi: 10.2527/jas.2009-2719

Published
2010

54. OC-001 anti-TNF Withdrawal in IBD: Initial Results from a Pan-UK Study

Author

Kennedy, NA, Warner, B, Johnston, E, Basquill, C, Harris, R, Lamb, CA, Singh, A, Fadra, AS, Cameron, F, Basavaraju, U, Mason, J, Lithgo, K, Penez, L, Stansfield, C, Lal, S, Cummings, F, Hart, A, Johnson, M, Russell, R, Wilson, D, Gooding, I, Thomson, J, Gaya, D, Lindsay, J, Ahmad, T, Mansfield, J, Gordon, J, Satsangi, J, Irving, P, and Lees, CW

Published
2014
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56. Category clustering: A probabilistic bias in the morphology of verbal agreement marking

Author

Mansfield, J, Stoll, S, Bickel, B, Mansfield, J, Stoll, S, and Bickel, B

Abstract

Recent research has revealed several languages (e.g. Chintang, Rarámuri, Tagalog, Murrinhpatha) that challenge the general expectation of strict sequential ordering in morphological structure. However, it has remained unclear whether these languages exhibit random placement of affixes or whether there are some underlying probabilistic principles that predict their placement. Here we address this question for verbal agreement markers and hypothesize a probabilistic universal of category clustering, with two effects: (i) markers in paradigmatic opposition tend to be placed in the same morphological position (‘paradigmatic alignment’; Crysmann & Bonami 2016); (ii) morphological positions tend to be categorically uniform (‘featural coherence’; Stump 2001). We first show in a corpus study that category clustering drives the distribution of agreement prefixes in speakers’ production of Chintang, a language where prefix placement is not constrained by any categorical rules of sequential ordering. We then show in a typological study that the same principle also shapes the evolution of morphological structure: although exceptions are attested, paradigms are much more likely to obey rather than to violate the principle. Category clustering is therefore a good candidate for a universal force shaping the structure and use of language, potentially due to benefits in processing and learning.

Published
2020

57. Dementia prevention, intervention, and care: 2020 report of the Lancet Commission

Author

Livingston, G, Huntley, J, Sommerlad, A, Ames, D, Ballard, C, Banerjee, S, Brayne, C, Burns, A, Cohen-Mansfield, J, Cooper, C, Costafreda, SG, Dias, A, Fox, N, Gitlin, LN, Howard, R, Kales, HC, Kivimaki, M, Larson, EB, Ogunniyi, A, Orgeta, V, Ritchie, K, Rockwood, K, Sampson, EL, Samus, Q, Schneider, LS, Selbaek, G, Teri, L, Mukadam, N, Livingston, G, Huntley, J, Sommerlad, A, Ames, D, Ballard, C, Banerjee, S, Brayne, C, Burns, A, Cohen-Mansfield, J, Cooper, C, Costafreda, SG, Dias, A, Fox, N, Gitlin, LN, Howard, R, Kales, HC, Kivimaki, M, Larson, EB, Ogunniyi, A, Orgeta, V, Ritchie, K, Rockwood, K, Sampson, EL, Samus, Q, Schneider, LS, Selbaek, G, Teri, L, and Mukadam, N

Published
2020

58. Demorphologization and deepening complexity in Murrinhpatha.

Author

Arkadiev, P, Gardani, F, Mansfield, J, Nordlinger, R, Arkadiev, P, Gardani, F, Mansfield, J, and Nordlinger, R

Abstract

This volume explores the multiple aspects of morphological complexity, offering typological, acquisitional, sociolinguistic, and diachronic perspectives.

Published
2020

59. UniMorph 3.0: Universal morphology

Author

Calzolari, N, McCarthy, AD, Kirov, C, Grella, M, Nidhi, A, Xia, P, Gorman, K, Vylomova, E, Mielke, SJ, Nicolai, G, Silfverberg, M, Arkhangelskij, T, Krizhanovsky, N, Krizhanovsky, A, Klyachko, E, Sorokin, A, Mansfield, J, Ernštreits, V, Pinter, Y, Jacobs, CL, Cotterell, R, Hulden, M, Yarowsky, D, Calzolari, N, McCarthy, AD, Kirov, C, Grella, M, Nidhi, A, Xia, P, Gorman, K, Vylomova, E, Mielke, SJ, Nicolai, G, Silfverberg, M, Arkhangelskij, T, Krizhanovsky, N, Krizhanovsky, A, Klyachko, E, Sorokin, A, Mansfield, J, Ernštreits, V, Pinter, Y, Jacobs, CL, Cotterell, R, Hulden, M, and Yarowsky, D

Abstract

The Universal Morphology (UniMorph) project is a collaborative effort providing broad-coverage instantiated normalized morphological paradigms for hundreds of diverse world languages. The project comprises two major thrusts: a language-independent feature schema for rich morphological annotation and a type-level resource of annotated data in diverse languages realizing that schema. We have implemented several improvements to the extraction pipeline which creates most of our data, so that it is both more complete and more correct. We have added 66 new languages, as well as new parts of speech for 12 languages. We have also amended the schema in several ways. Finally, we present three new community tools: two to validate data for resource creators, and one to make morphological data available from the command line. UniMorph is based at the Center for Language and Speech Processing (CLSP) at Johns Hopkins University in Baltimore, Maryland. This paper details advances made to the schema, tooling, and dissemination of project resources since the UniMorph 2.0 release described at LREC 2018.

Published
2020

61. P88 The impact of NOD2 deficiency on the gut mycobiota in crohn’s disease patients in remission

Author

Bridge, S, primary, Nelson, A, additional, Kennedy, N, additional, Lodge, J, additional, Morgan, H, additional, Berry, S, additional, Simpkins, R, additional, Tremelling, M, additional, Nutland, S, additional, Probert, C, additional, Parkes, M, additional, Mansfield, J, additional, Smith, D, additional, Hold, G, additional, Lees, C, additional, Stewart, C, additional, and Lamb, C, additional

Published
2021
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63. 1568O Quality of life in cancer patients treated with immune checkpoint inhibitors: A meta-analysis

Author

Gonzalez, B.D., primary, Eisel, S.L., additional, Bowles, K.E., additional, Hoogland, A.I., additional, James, B.W., additional, Small, B.J., additional, Sharpe, S., additional, Hyland, K.A., additional, Bulls, H.W., additional, Christy, S.M., additional, Mansfield, J., additional, Nelson, A.M., additional, Alla, R., additional, Maharaj, K., additional, Kennedy, B., additional, Lafranchise, E., additional, Williams, N.L., additional, Postow, M.A., additional, Dicker, A.P., additional, and Jim, H.S.L., additional

Published
2020
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64. P579 Randomised open-label controlled trial of ciprofloxacin/doxycycline/hydroxychloroquine combination compared with standard budesonide in active Crohn’s disease (APRICOT)

Author

Rhodes, J M, primary, Subramanian, S, additional, Flanagan, P, additional, Horgan, G, additional, Martin, K, additional, Mansfield, J, additional, Parkes, M, additional, Hart, A, additional, Dallal, H, additional, Iqbal, T, additional, Butterworth, J, additional, Culshaw, K, additional, and Probert, C, additional

Published
2020
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68. NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease

Author

Schwerd, T., Bryant, R. V., Pandey, S., Capitani, M., Meran, L., Cazier, J. -B., Jung, J., Mondal, K., Parkes, M., Mathew, C. G., Fiedler, K., McCarthy, D. J., Sullivan, P. B., Rodrigues, A., Travis, S. P. L., Moore, C., Sambrook, J., Ouwehand, W. H., Roberts, D. J., Danesh, J., Russell, R. K., Wilson, D. C., Kelsen, J. R., Cornall, R., Denson, L. A., Kugathasan, S., Knaus, U. G., Serra, E. G., Anderson, C. A., Duerr, R. H., McGovern, D. P. B., Cho, J., Powrie, Fiona, Li, V. S. W., Muise, A. M., Uhlig, H. H., Donnelly, P., Bell, J., Bentley, D., McVean, G., Ratcliffe, P., Taylor, J., Wilkie, A. O. M., Broxholme, J., Buck, D., Gregory, L., Gregory, J., Lunter, G., Tomlinson, I., Allan, C., Attar, M., Green, A., Humphray, S., Kingsbury, Z., Lamble, S., Lonie, L., Pagnamenta, A., Piazza, P., Polanco, G., Trebes, A., Copley, R., Fiddy, S., Grocock, R., Hatton, E., Holmes, C., Hughes, L., Humburg, P., Kanapin, A., Lise, S., Martin, H., Murray, L., McCarthy, D., Rimmer, A., Sahgal, N., Wright, B., Yau, C., Arancibia, Carolina, Bailey, Adam, Barnes, Ellie, Bird-Lieberman, Beth, Brain, Oliver, Braden, Barbara, Collier, Jane, East, James, Geremia, Alessandra, Howarth, Lucy, Keshav, Satish, Klenerman, Paul, Leedham, Simon, Palmer, Rebecca, Rodrigues, Astor, Simmons, Alison, Sullivan, Peter B, Travis, Simon P L, Uhlig, Holm H, Heuschkel, Rob, Zilbauer, Matthias, Auth, Marcus K. H., Shah, Neil, Kammermeier, Jochen, Croft, Nick, Barakat, Farah, Russell, Richard K., Wilson, David C., Henderson, Paul, Braegger, Christian P., Posovszky, Carsten, Fyderek, Krzysztof, Wedrychowicz, Andrzej, Zurek, Marlen, Strisciuglio, Caterina, Elawad, Mamoun, Lo, Bernice, Parkes, Miles, Satsangi, Jack, Anderson, Carl A., Jostins, L., Kennedy, N. A., Lamb, C. A., Ahmad, T., Edwards, C., Hart, A., Hawkey, C., Mansfield, J. C., Mowat, C., Newman, W. G., Satsangi, J., Simmons, A., Tremelling, M., Lee, J. C., Prescott, N. J., Lees, C. W., Barrett, J. C., UK IBD Genetics Consortium, COLORS in IBD, Oxford IBD cohort study investigators, WGS500 Consortium, INTERVAL Study, Schwerd, T., Bryant, R. V., Pandey, S., Capitani, M., Meran, L., Cazier, J. -B., Jung, J., Mondal, K., Parkes, M., Mathew, C. G., Fiedler, K., Mccarthy, D. J., Sullivan, P. B., Rodrigues, A., Travis, S. P. L., Moore, C., Sambrook, J., Ouwehand, W. H., Roberts, D. J., Danesh, J., Russell, R. K., Wilson, D. C., Kelsen, J. R., Cornall, R., Denson, L. A., Kugathasan, S., Knaus, U. G., Serra, E. G., Anderson, C. A., Duerr, R. H., Mcgovern, D. P. B., Cho, J., Powrie, Fiona, Li, V. S. W., Muise, A. M., Uhlig, H. H., Donnelly, P., Bell, J., Bentley, D., Mcvean, G., Ratcliffe, P., Taylor, J., Wilkie, A. O. M., Broxholme, J., Buck, D., Gregory, L., Gregory, J., Lunter, G., Tomlinson, I., Allan, C., Attar, M., Green, A., Humphray, S., Kingsbury, Z., Lamble, S., Lonie, L., Pagnamenta, A., Piazza, P., Polanco, G., Trebes, A., Copley, R., Fiddy, S., Grocock, R., Hatton, E., Holmes, C., Hughes, L., Humburg, P., Kanapin, A., Lise, S., Martin, H., Murray, L., Mccarthy, D., Rimmer, A., Sahgal, N., Wright, B., Yau, C., Arancibia, Carolina, Bailey, Adam, Barnes, Ellie, Bird-Lieberman, Beth, Brain, Oliver, Braden, Barbara, Collier, Jane, East, Jame, Geremia, Alessandra, Howarth, Lucy, Keshav, Satish, Klenerman, Paul, Leedham, Simon, Palmer, Rebecca, Rodrigues, Astor, Simmons, Alison, Sullivan, Peter B, Travis, Simon P L, Uhlig, Holm H, Heuschkel, Rob, Zilbauer, Matthia, Auth, Marcus K. H., Shah, Neil, Kammermeier, Jochen, Croft, Nick, Barakat, Farah, Russell, Richard K., Wilson, David C., Henderson, Paul, Braegger, Christian P., Posovszky, Carsten, Fyderek, Krzysztof, Wedrychowicz, Andrzej, Zurek, Marlen, Strisciuglio, Caterina, Elawad, Mamoun, Lo, Bernice, Parkes, Mile, Satsangi, Jack, Anderson, Carl A., Jostins, L., Kennedy, N. A., Lamb, C. A., Ahmad, T., Edwards, C., Hart, A., Hawkey, C., Mansfield, J. C., Mowat, C., Newman, W. G., Satsangi, J., Simmons, A., Tremelling, M., Lee, J. C., Prescott, N. J., Lees, C. W., Barrett, J. C., UK IBD Genetics, Consortium, COLORS in, Ibd, Oxford IBD cohort study, Investigator, Wgs500, Consortium, and Interval, Study

Subjects
Male, Genotype, Colon, Immunology, Mutation, Missense, Genetic Association Studie, Polymorphism, Single Nucleotide, Article, Mice, Animals, Humans, Immunology and Allergy, Genetic Predisposition to Disease, Child, Genetic Association Studies, Genes, Modifier, Genome, Animal, Inflammatory Bowel Disease, High-Throughput Nucleotide Sequencing, Inflammatory Bowel Diseases, digestive system diseases, Host-Pathogen Interaction, Mice, Inbred C57BL, Child, Preschool, Host-Pathogen Interactions, NADPH Oxidase 1, Reactive Oxygen Species, Reactive Oxygen Specie, Human
Abstract

Genetic defects that affect intestinal epithelial barrier function can present with very early-onset inflammatory bowel disease (VEOIBD). Using whole-genome sequencing, a novel hemizygous defect in NOX1 encoding NAPDH oxidase 1 was identified in a patient with ulcerative colitis-like VEOIBD. Exome screening of 1,878 pediatric patients identified further seven male inflammatory bowel disease (IBD) patients with rare NOX1 mutations. Loss-of-function was validated in p.N122H and p.T497A, and to a lesser degree in p.Y470H, p.R287Q, p.I67M, p.Q293R as well as the previously described p.P330S, and the common NOX1 SNP p.D360N (rs34688635) variant. The missense mutation p.N122H abrogated reactive oxygen species (ROS) production in cell lines, ex vivo colonic explants, and patient-derived colonic organoid cultures. Within colonic crypts, NOX1 constitutively generates a high level of ROS in the crypt lumen. Analysis of 9,513 controls and 11,140 IBD patients of non-Jewish European ancestry did not reveal an association between p.D360N and IBD. Our data suggest that loss-of-function variants in NOX1 do not cause a Mendelian disorder of high penetrance but are a context-specific modifier. Our results implicate that variants in NOX1 change brush border ROS within colonic crypts at the interface between the epithelium and luminal microbes.

Published
2018

69. IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes

Author

Momozawa, Y, Dmitrieva, J, Theatre, E, Deffontaine, V, Rahmouni, S, Charloteaux, B, Crins, F, Docampo, E, Elansary, M, Gori, AS, Lecut, C, Mariman, R, Mni, M, Oury, C, Altukhov, I, Alexeev, D, Aulchenko, Y, Amininejad, L, Bouma, G, Hoentjen, F, Lowenberg, M, Oldenburg, B, Pierik, MJ, de Jong, AE, van der Woude, C.J., Visschedijk, MC, Lathrop, M, Hugot, JP, Weersma, RK, Vos, M, Franchimont, D, Vermeire, S, Kubo, M, Louis, E, Georges, M, Abraham, C, Achkar, JP, Ahmad, T, Ananthakrishnan, AN, Andersen, V, Anderson, CA, Andrews, JM, Annese, V, Aumais, G, Baidoo, L, Baldassano, RN, Bampton, PA, Barclay, M, Barrett, JC, Bayless, TM, Bethge, J, Bitton, A, Boucher, G, Brand, S, Brandt, B, Brant, SR, Buning, C, Chew, A, Cho, JH, Cleynen, I, Cohain, A, Croft, A, Daly, MJ, D'Amato, M, Danese, S, Jong, D, Denapiene, G, Denson, LA, Devaney, KL, Dewit, O, D'Inca, R, Dubinsky, M, Duerr, RH, Edwards, C, Ellinghaus, D, Essers, J, Ferguson, LR, Festen, EA, Fleshner, P, Florin, T, Franke, A, Fransen, K, Gearry, R, Gieger, C, Glas, J, Goyette, P, Green, T, Griffiths, AM, Guthery, SL, Hakonarson, H, Halfvarson, J, Hanigan, K, Haritunians, T, de Hart, A, Hawkey, C, Hayward, NK, Hedl, M, Henderson, P, Hu, XH, Huang, HL, Hui, KY, Imielinski, M, Ippoliti, A, Jonaitis, L, Jostins, L, Karlsen, TH, Kennedy, NA, Khan, MA, Kiudelis, G, Krishnaprasad, K, Kugathasan, S, Kupcinskas, L, Latiano, A, Laukens, D, Lawrance, IC, Lee, JC, Lees, CW, Leja, M, van Limbergen, J, Lionetti, P, Liu, JZ, Mahy, G, Mansfield, J, Massey, D, Mathew, CG, McGovern, DPB, Milgrom, R, Mitrovic, M, Montgomery, GW, Mowat, C, Newman, W, Ng, A, Ng, SC, Ng, SME, Nikolaus, S, Ning, K, Nothen, M, Oikonomou, I, Palmieri, O, Parkes, M, Phillips, A, Ponsioen, CY, Potocnik, U, Prescott, NJ, Proctor, DD, Radford-Smith, G, Rahier, JF, Raychaudhuri, S, Regueiro, M, Rieder, F, Rioux, JD, Ripke, S, Roberts, R, Russell, RK, Sanderson, JD, Sans, M, Satsangi, J, Schadt, EE, Schreiber, S, Schulte, D, Schumm, LP, Scott, R, Seielstad, M, Sharma, Y, Silverberg, MS, Simms, LA, Skieceviciene, J, Spain, SL, Steinhart, AH, Stempak, JM, Stronati, L, Sventoraityte, J, Targan, SR, Taylor, KM, Velde, A, Torkvist, L, Tremelling, M, van Sommeren, S, Vasiliauskas, E, Verspaget, HW, Walters, T, Wang, K, Wang, MH, Wei, Z, Whiteman, D, Wijmenga, C, Wilson, DC, Winkelmann, J, Xavier, RJ, Zhang, B, Zhang, CK, Zhang, H, Zhang, W, Zhao, HY, Zhao, ZZ, Momozawa, Y, Dmitrieva, J, Theatre, E, Deffontaine, V, Rahmouni, S, Charloteaux, B, Crins, F, Docampo, E, Elansary, M, Gori, A, Lecut, C, Mariman, R, Mni, M, Oury, C, Altukhov, I, Alexeev, D, Aulchenko, Y, Amininejad, L, Bouma, G, Hoentjen, F, Lowenberg, M, Oldenburg, B, Pierik, Mj, vander Meulen-de Jong, Ae, van der Woude, Cj, Visschedijk, Mc, Lathrop, M, Hugot, Jp, Weersma, Rk, De Vos, M, Franchimont, D, Vermeire, S, Kubo, M, Louis, E, Georges, M, Abraham, C, Achkar, Jp, Ahmad, T, Ananthakrishnan, An, Andersen, V, Anderson, Ca, Andrews, Jm, Annese, V, Aumais, G, Baidoo, L, Baldassano, Rn, Bampton, Pa, Barclay, M, Barrett, Jc, Bayless, Tm, Bethge, J, Bitton, A, Boucher, G, Brand, S, Brandt, B, Brant, Sr, Buning, C, Chew, A, Cho, Jh, Cleynen, I, Cohain, A, Croft, A, Daly, Mj, D'Amato, M, Danese, S, De Jong, D, Denapiene, G, Denson, La, Devaney, Kl, Dewit, O, D'Inca, R, Dubinsky, M, Duerr, Rh, Edwards, C, Ellinghaus, D, Essers, J, Ferguson, Lr, Festen, Ea, Fleshner, P, Florin, T, Franke, A, Fransen, K, Gearry, R, Gieger, C, Glas, J, Goyette, P, Green, T, Griffiths, Am, Guthery, Sl, Hakonarson, H, Halfvarson, J, Hanigan, K, Haritunians, T, Hart, A, Hawkey, C, Hayward, Nk, Hedl, M, Henderson, P, Hu, Xh, Huang, Hl, Hui, Ky, Imielinski, M, Ippoliti, A, Jonaitis, L, Jostins, L, Karlsen, Th, Kennedy, Na, Khan, Ma, Kiudelis, G, Krishnaprasad, K, Kugathasan, S, Kupcinskas, L, Latiano, A, Laukens, D, Lawrance, Ic, Lee, Jc, Lees, Cw, Leja, M, Van Limbergen, J, Lionetti, P, Liu, Jz, Mahy, G, Mansfield, J, Massey, D, Mathew, Cg, Mcgovern, Dpb, Milgrom, R, Mitrovic, M, Montgomery, Gw, Mowat, C, Newman, W, Ng, A, Ng, Sc, Ng, Sme, Nikolaus, S, Ning, K, Nothen, M, Oikonomou, I, Palmieri, O, Parkes, M, Phillips, A, Ponsioen, Cy, Potocnik, U, Prescott, Nj, Proctor, Dd, Radford-Smith, G, Rahier, Jf, Raychaudhuri, S, Regueiro, M, Rieder, F, Rioux, Jd, Ripke, S, Roberts, R, Russell, Rk, Sanderson, Jd, Sans, M, Satsangi, J, Schadt, Ee, Schreiber, S, Schulte, D, Schumm, Lp, Scott, R, Seielstad, M, Sharma, Y, Silverberg, M, Simms, La, Skieceviciene, J, Spain, Sl, Steinhart, Ah, Stempak, Jm, Stronati, L, Sventoraityte, J, Targan, Sr, Taylor, Km, ter Velde, A, Torkvist, L, Tremelling, M, van Sommeren, S, Vasiliauskas, E, Verspaget, Hw, Walters, T, Wang, K, Wang, Mh, Wei, Z, Whiteman, D, Wijmenga, C, Wilson, Dc, Winkelmann, J, Xavier, Rj, Zhang, B, Zhang, Ck, Zhang, H, Zhang, W, Zhao, Hy, Zhao, Zz, Gastroenterology & Hepatology, UCL - SSS/IREC/GAEN - Pôle d'Hépato-gastro-entérologie, and UCL - (MGD) Service de gastro-entérologie

Subjects
Adult, Male, Multifactorial Inheritance, QUANTITATIVE TRAIT LOCUS, Genotype, SEQUENCING DATA, Quantitative Trait Loci, SUSCEPTIBILITY, Polymorphism, Single Nucleotide, Article, Cohort Studies, CODING VARIANTS, Crohn Disease, 80 and over, Journal Article, Medicine and Health Sciences, LOCUS, Humans, Genetic Predisposition to Disease, Polymorphism, GENOME-WIDE ASSOCIATION, Genetic Association Studies, Aged, Aged, 80 and over, Science & Technology, Female, Gene Expression Profiling, Inflammatory Bowel Diseases, Middle Aged, Sequence Analysis, DNA, COMPLEX TRAITS, Biology and Life Sciences, Single Nucleotide, DNA, CROHNS-DISEASE, Multidisciplinary Sciences, QUANTITATIVE TRAIT, RARE VARIANTS, Science & Technology - Other Topics, LOW-FREQUENCY, Sequence Analysis, INFLAMMATORY-BOWEL-DISEASE
Abstract

GWAS have identified >200 risk loci for Inflammatory Bowel Disease (IBD). The majority of disease associations are known to be driven by regulatory variants. To identify the putative causative genes that are perturbed by these variants, we generate a large transcriptome data set (nine disease-relevant cell types) and identify 23,650 cis-eQTL. We show that these are determined by ∼9720 regulatory modules, of which ∼3000 operate in multiple tissues and ∼970 on multiple genes. We identify regulatory modules that drive the disease association for 63 of the 200 risk loci, and show that these are enriched in multigenic modules. Based on these analyses, we resequence 45 of the corresponding 100 candidate genes in 6600 Crohn disease (CD) cases and 5500 controls, and show with burden tests that they include likely causative genes. Our analyses indicate that ≥10-fold larger sample sizes will be required to demonstrate the causality of individual genes using this approach., Most of the more than 200 known genetic risk loci for inflammatory bowel disease (IBD) reside in regulatory regions. Here, the authors provide eQTL datasets for six circulating immune cell types and ileal, colonic and rectal biopsies to map regulatory modules and identify potential causative genes for IBD.

Published
2018

78. Session 19 Plant-microbe interaction

Author

Ádám, A. L., Bestwick, C. S., Galal, A. A., Ladyzhenskaya, E., Barna, B., Mansfield, J. W., Király, Z., Andrianova, T. V., Vasjuk, V. A., Barna, B., Bratek, Z., Király, I., Vértessy, J., Balla, I., Cordovilla, M. P., Ocaña, A., Zuñiga, D., Soussi, M., Lluch, C., Didonet, A. D., Magalhāes, Ac., Dmitriev, A. P., Perkovskaya, G. Y., Grodzinsky, D. M., Dunaevsky, Y. E., Pavlukova, E. B., Beliakova, G. A., Belozersky, M. A., Gartland, J. S., Gartland, K. M. A., Main, G. D., Brasier, C. M., Fenning, T. M., Gonzalez, E. M., Gordon, A. J., James, C., Arrese-Igor, C., HŘib, J., Janisch, R., Vooková, B., Kaush, M. V., Seniciak, V. I., Lungu, V. I., Toma, S. I., Király, I., Bóka, Z., Bratek, Z., Kirichenko, E. V., Malichenko, S. M., Kislin, E. N., Semichyeva, T. V., Maklolepsza, U., Urbanek, H., Martín, R., Matínez-Murillo, R., Bentura, M. L., Rodrigo, J., Golvano, M. P., Mattsson, U., Sellstedt, A., Milieva, E., Stancheva, Y., Rodeva, V., Poveda, J. L., Caba, J. M., Sanchez-Guerrero, I., Ligero, F., Rusterucci, C., Ricci, P., Milat, M-L., Blein, J-P, Šantrůčková, H., Elhottová, D., Šantrůček, J., Scala, A., Tegli, S., Sellstedt, A., Reddell, P., Serezhkina, G. V., Tamás, L., FriČ, F., Tavares, F., Sellstedt, A., Parente, A., and Salema, R.

Published
1994
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83. Scoring reading parameters : An inter-rater reliability study using the MNREAD chart

Author

Baskaran, Karthikeyan, Macedo, António Filipe, He, Yingchen, Hernandez-Moreno, Laura, Queirós, Tatiana, Mansfield, J. Stephen, Calabrèse, Aurélie, Baskaran, Karthikeyan, Macedo, António Filipe, He, Yingchen, Hernandez-Moreno, Laura, Queirós, Tatiana, Mansfield, J. Stephen, and Calabrèse, Aurélie

Abstract

Purpose First, to evaluate inter-rater reliability when human raters estimate the reading performance of visually impaired individuals using the MNREAD acuity chart. Second, to evaluate the agreement between computer-based scoring algorithms and compare them with human rating. Methods Reading performance was measured for 101 individuals with low vision, using the Portuguese version of the MNREAD test. Seven raters estimated the maximum reading speed (MRS) and critical print size (CPS) of each individual MNREAD curve. MRS and CPS were also calculated automatically for each curve using two different algorithms: the original standard deviation method (SDev) and a non-linear mixed effects (NLME) modeling. Intra-class correlation coefficients (ICC) were used to estimate absolute agreement between raters and/or algorithms. Results Absolute agreement between raters was ‘excellent’ for MRS (ICC = 0.97; 95%CI [0.96, 0.98]) and ‘moderate’ to ‘good’ for CPS (ICC = 0.77; 95%CI [0.69, 0.83]). For CPS, inter-rater reliability was poorer among less experienced raters (ICC = 0.70; 95%CI [0.57, 0.80]) when compared to experienced ones (ICC = 0.82; 95%CI [0.76, 0.88]). Absolute agreement between the two algorithms was ‘excellent’ for MRS (ICC = 0.96; 95%CI [0.91, 0.98]). For CPS, the best possible agreement was found for CPS defined as the print size sustaining 80% of MRS (ICC = 0.77; 95%CI [0.68, 0.84]). Absolute agreement between raters and automated methods was ‘excellent’ for MRS (ICC = 0.96; 95% CI [0.88, 0.98] for SDev; ICC = 0.97; 95% CI [0.95, 0.98] for NLME). For CPS, absolute agreement between raters and SDev ranged from ‘poor’ to ‘good’ (ICC = 0.66; 95% CI [0.3, 0.80]), while agreement between raters and NLME was ‘good’ (ICC = 0.83; 95% CI [0.76, 0.88]). Conclusion For MRS, inter-rater reliability is excellent, even considering the possibility of noisy and/or incomplete data collected in low-vision individuals. For CPS, inter-rater reliability is lower. This may be problem

Published
2019
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84. Epistemic authority and sociolinguistic stance in an Australian Aboriginal language

Author

Mansfield, J and Mansfield, J

Abstract

Murrinhpatha, an Aboriginal language of northern Australia, has an initialk-alternation in verbs that has hitherto been resistant to grammatical analysis. I argue thatk-does not encode any feature of event structure, but rather signals the speaker’s epistemic primacy over the addressee. This authority may relate to concrete perceptual factors in the field of discourse, or to socially normative authority, where it asserts the speaker’s epistemic rights. These rights are most salient in the domains of kin, country and totems, as opposed to other topics in which speakers are habitually circumspect and co-construct knowledge. My analysis of thek-alternation thus brings together the typology of epistemic grammar (Evans, Bergqvist, & San Roque, 2018a, 2018b), and a sociolinguistic perspective on stance (Jaffe, 2009).

Published
2019

96. IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes

Author

Momozawa, Y., Dmitrieva, J., Theatre, E., Deffontaine, V., Rahmouni, S., Charloteaux, B., Crins, F., Docampo, E., Elansary, M., Gori, A.S., Lecut, C., Mariman, R., Mni, M., Oury, C., Altukhov, I., Alexeev, D., Aulchenko, Y., Amininejad, L., Bouma, G., Hoentjen, F., Lowenberg, M., Oldenburg, B., Pierik, M.J., vander Meulen-de Jong, A.E., Woude, C.J. van der, Visschedijk, M.C., Lathrop, M., Hugot, J.P., Weersma, R.K., Vos, M. de, Franchimont, D., Vermeire, S., Kubo, M., Louis, E., Georges, M., Abraham, C., Achkar, J.P., Ahmad, T., Ananthakrishnan, A.N., Andersen, V., Anderson, C.A., Andrews, J.M., Annese, V., Aumais, G., Baidoo, L., Baldassano, R.N., Bampton, P.A., Barclay, M., Barrett, J.C., Bayless, T.M., Bethge, J., Bitton, A., Boucher, G., Brand, S., Brandt, B., Brant, S.R., Buning, C., Chew, A., Cho, J.H., Cleynen, I., Cohain, A., Croft, A., Daly, M.J., D'Amato, M., Danese, S., Jong, D. de, Denapiene, G., Denson, L.A., Devaney, K.L., Dewit, O., D'Inca, R., Dubinsky, M., Duerr, R.H., Edwards, C., Ellinghaus, D., Essers, J., Ferguson, L.R., Festen, E.A., Fleshner, P., Florin, T., Franke, A., Fransen, K., Gearry, R., Gieger, C., Glas, J., Goyette, P., Green, T., Griffiths, A.M., Guthery, S.L., Hakonarson, H., Halfvarson, J., Hanigan, K., Haritunians, T., Hart, A., Hawkey, C., Hayward, N.K., Hedl, M., Henderson, P., Hu, X.H., Huang, H.L., Hui, K.Y., Imielinski, M., Ippoliti, A., Jonaitis, L., Jostins, L., Karlsen, T.H., Kennedy, N.A., Khan, M.A., Kiudelis, G., Krishnaprasad, K., Kugathasan, S., Kupcinskas, L., Latiano, A., Laukens, D., Lawrance, I.C., Lee, J.C., Lees, C.W., Leja, M., Limbergen, J. van, Lionetti, P., Liu, J.Z., Mahy, G., Mansfield, J., Massey, D., Mathew, C.G., McGovern, D.P.B., Milgrom, R., Mitrovic, M., Montgomery, G.W., Mowat, C., Newman, W., Ng, A., Ng, S.C., Ng, S.M.E., Nikolaus, S., Ning, K., Nothen, M., Oikonomou, I., Palmieri, O., Parkes, M., Phillips, A., Ponsioen, C.Y., Potocnik, U., Prescott, N.J., Proctor, D.D., Radford-Smith, G., Rahier, J.F., Raychaudhuri, S., Regueiro, M., Rieder, F., Rioux, J.D., Ripke, S., Roberts, R., Russell, R.K., Sanderson, J.D., Sans, M., Satsangi, J., Schadt, E.E., Schreiber, S., Schulte, D., Schumm, L.P., Scott, R., Seielstad, M., Sharma, Y., Silverberg, M.S., Simms, L.A., Skieceviciene, J., Spain, S.L., Steinhart, A.H., Stempak, J.M., Stronati, L., Sventoraityte, J., Targan, S.R., Taylor, K.M., Velde, A. ter, Torkvist, L., Tremelling, M., Sommeren, S. van, Vasiliauskas, E., Verspaget, H.W., Walters, T., Wang, K., Wang, M.H., Wei, Z., Whiteman, D., Wijmenga, C., Wilson, D.C., Winkelmann, J., Xavier, R.J., Zhang, B., Zhang, C.K., Zhang, H., Zhang, W., Zhao, H.Y., Zhao, Z.Z., and Int IBD Genetics Consortium

Published
2018

97. The impact of NOD2 variants on fecal microbiota in Crohn's Disease and controls without gastrointestinal disease

Author

Kennedy, N, Lamb, C, Berry, S, Walker, A, Mansfield, J, Parkes, M, Simpkins, R, Tremelling, M, Nutland, S, Simmons, A, Consortium, Uk Ibd Genetics, Parkhill, J, Probert, C, Hold, G, and Lees, C

Subjects
Crohn’s disease, Adult, Male, genotype, Nod2 Signaling Adaptor Protein, Middle Aged, NOD2, digestive system diseases, Gastrointestinal Microbiome, Feces, Crohn Disease, Case-Control Studies, RNA, Ribosomal, 16S, Mutation, microbiota, Humans, Female, Genetic Predisposition to Disease, Original Research Articles–Basic Science, Aged
Abstract

Background/Aims Current models of Crohn’s disease (CD) describe an inappropriate immune response to gut microbiota in genetically susceptible individuals. NOD2 variants are strongly associated with development of CD, and NOD2 is part of the innate immune response to bacteria. This study aimed to identify differences in fecal microbiota in CD patients and non-IBD controls stratified by NOD2 genotype. Methods Patients with CD and non-IBD controls of known NOD2 genotype were identified from patients in previous UK IBD genetics studies and the Cambridge bioresource (genotyped/phenotyped volunteers). Individuals with known CD-associated NOD2 mutations were matched to those with wild-type genotype. We obtained fecal samples from patients in clinical remission with low fecal calprotectin (Results Ninety-one individuals were in the primary analysis (37 CD, 30 bioresource controls, and 24 household controls). Comparing CD with nonIBD controls, there were reductions in bacterial diversity, Ruminococcaceae, Rikenellaceae, and Christensenellaceae and an increase in Enterobacteriaceae. No significant differences could be identified in microbiota by NOD2 genotype, but fecal butanoic acid was higher in Crohn’s patients carrying NOD2 mutations. Conclusions In this well-controlled study of NOD2 genotype and fecal microbiota, we identified no significant genotype-microbiota associations. This suggests that the changes associated with NOD2 genotype might only be seen at the mucosal level, or that environmental factors and prior inflammation are the predominant determinant of the observed dysbiosis in gut microbiota.

Published
2018

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