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1. Gradual pressure-induced change in the magnetic structure of the non-collinear antiferromagnet Mn$_3$Ge

Author

Sukhanov, A. S., Singh, Sanjay, Caron, L., Hansen, Th., Hoser, A., Kumar, V., Borrmann, H., Fitch, A., Devi, P., Manna, K., Felser, C., and Inosov, D. S.

Subjects
Condensed Matter - Strongly Correlated Electrons
Abstract

By means of powder neutron diffraction we investigate changes in the magnetic structure of the coplanar non-collinear antiferromagnet Mn$_3$Ge caused by an application of hydrostatic pressure up to 5\phantom{ }GPa. At ambient conditions the kagom\'e layers of Mn atoms in Mn$_3$Ge order in a triangular 120$^{\circ}$ spin structure. Under high pressure the spins acquire a uniform out-of-plane canting, gradually transforming the magnetic texture to a non-coplanar configuration. With increasing pressure the canted structure fully transforms into the collinear ferromagnetic one. We observed that magnetic order is accompanied by a noticeable magnetoelastic effect, namely, spontaneous magnetostriction. The latter induces an in-plane magnetostrain of the hexagonal unit cell at ambient pressure and flips to an out-of-plane strain at high pressures in accordance with the change of the magnetic structure.

Published
2018
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3. Four groups of type 2 diabetes contribute to the etiological and clinical heterogeneity in newly diagnosed individuals: An IMI DIRECT study

Author

Wesolowska-Andersen A, Brorsson CA, Bizzotto R, Mari A, Tura A, Koivula R, Mahajan A, Vinuela A, Tajes JF, Sharma S, Haid M, Prehn C, Artati A, Hong MG, Musholt PB, Kurbasic A, De Masi F, Tsirigos K, Pedersen HK, Gudmundsdottir V, Thomas CE, Banasik K, Jennison C, Jones A, Kennedy G, Bell J, Thomas L, Frost G, Thomsen H, Allin K, Hansen TH, Vestergaard H, Hansen T, Rutters F, Elders P, t'Hart L, Bonnefond A, Canouil M, Brage S, Kokkola T, Heggie A, McEvoy D, Hattersley A, McDonald T, Teare H, Ridderstrale M, Walker M, Forgie I, Giordano GN, Froguel P, Pavo I, Ruetten H, Pedersen O, Dermitzakis E, Franks PW, Schwenk JM, Adamski J, Pearson E, McCarthy MI, Brunak S, and ID Consortium

Subjects
General Economics, Econometrics and Finance
Published
2022
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4. Combinatorial, additive and dose-dependent drug-microbiome associations

Author

Forslund, SK, Chakaroun, R, Zimmermann-Kogadeeva, M, Markó, L, Aron-Wisnewsky, J, Nielsen, T, Moitinho-Silva, L, Schmidt, TSB, Falony, G, Vieira-Silva, S, Adriouch, S, Alves, RJ, Assmann, K, Bastard, J-P, Birkner, T, Caesar, R, Chilloux, J, Coelho, LP, Fezeu, L, Galleron, N, Helft, G, Isnard, R, Ji, B, Kuhn, M, Le Chatelier, E, Myridakis, A, Olsson, L, Pons, N, Prifti, E, Quinquis, B, Roume, H, Salem, J-E, Sokolovska, N, Tremaroli, V, Valles-Colomer, M, Lewinter, C, Søndertoft, NB, Pedersen, HK, Hansen, TH, Amouyal, C, Andersson Galijatovic, EA, Andreelli, F, Barthelemy, O, Batisse, J-P, Belda, E, Berland, M, Bittar, R, Blottière, H, Bosquet, F, Boubrit, R, Bourron, O, Camus, M, Cassuto, D, Ciangura, C, Collet, J-P, Dao, M-C, Djebbar, M, Doré, A, Engelbrechtsen, L, Fellahi, S, Fromentin, S, Galan, P, Gauguier, D, Giral, P, Hartemann, A, Hartmann, B, Holst, JJ, Hornbak, M, Hoyles, L, Hulot, J-S, Jaqueminet, S, Jørgensen, NR, Julienne, H, Justesen, J, Kammer, J, Krarup, N, Kerneis, M, Khemis, J, Kozlowski, R, Lejard, V, Levenez, F, Lucas-Martini, L, Massey, R, Martinez-Gili, L, Maziers, N, Medina-Stamminger, J, Montalescot, G, Moute, S, Neves, AL, Olanipekun, M, Le Pavin, LP, Poitou, C, Pousset, F, Pouzoulet, L, Rodriguez-Martinez, A, Rouault, C, Silvain, J, Svendstrup, M, Swartz, T, Vanduyvenboden, T, Vatier, C, Walther, S, Gøtze, JP, Køber, L, Vestergaard, H, Hansen, T, Zucker, J-D, Hercberg, S, Oppert, J-M, Letunic, I, Nielsen, J, Bäckhed, F, Ehrlich, SD, Dumas, M-E, Raes, J, Pedersen, O, Clément, K, Stumvoll, M, Bork, P, The MetaCardis Consortium (Hoyles, L.), European Molecular Biology Laboratory [Heidelberg] (EMBL), Max Delbrück Center for Molecular Medicine [Berlin] (MDC), Helmholtz-Gemeinschaft = Helmholtz Association, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Berlin Institute of Health (BIH), German Center for Cardiovascular Research (DZHK), Universität Leipzig, Nutrition et obésités: approches systémiques (UMR-S 1269) (Nutriomics), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), University of Copenhagen = Københavns Universitet (UCPH), University of New South Wales [Sydney] (UNSW), Paul Scherrer Institute (PSI), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Heidelberg University, Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle (CRESS - U1153), Université Sorbonne Paris Nord-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Recherche Saint-Antoine (CRSA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), CHU Henri Mondor [Créteil], Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], University of Gothenburg (GU), Imperial College London, MetaGenoPolis (MGP (US 1367)), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay, Institut de cardiologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Chalmers University of Technology [Gothenburg, Sweden], Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Sorbonne Université (SU)-Institut de Recherche pour le Développement (IRD [France-Nord]), Centre d'investigation clinique Paris Est [CHU Pitié Salpêtrière] (CIC Paris-Est), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Biobyte Solutions [Heidelberg, Germany] (BS), IT University of Copenhagen (ITU), Sahlgrenska University Hospital [Gothenburg], Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), National Heart and Lung Institute [London] (NHLI), Imperial College London-Royal Brompton and Harefield NHS Foundation Trust, McGill University and Genome Quebec Innovation Centre, Helmholtz Institute Ulm (HIU), Helmholtz Zentrum München = German Research Center for Environmental Health, University of Würzburg = Universität Würzburg, Yonsei University, MetaCardis Consortium*: Chloe Amouyal, Ehm Astrid Andersson Galijatovic, Fabrizio Andreelli, Olivier Barthelemy, Jean-Paul Batisse, Eugeni Belda, Magalie Berland, Randa Bittar, Hervé Blottière, Frederic Bosquet, Rachid Boubrit, Olivier Bourron, Mickael Camus, Dominique Cassuto, Cecile Ciangura, Jean-Philippe Collet, Maria-Carlota Dao, Morad Djebbar, Angélique Doré, Line Engelbrechtsen, Soraya Fellahi, Sebastien Fromentin, Pilar Galan, Dominique Gauguier, Philippe Giral, Agnes Hartemann, Bolette Hartmann, Jens Juul Holst, Malene Hornbak, Lesley Hoyles, Jean-Sebastien Hulot, Sophie Jaqueminet, Niklas Rye Jørgensen, Hanna Julienne, Johanne Justesen, Judith Kammer, Nikolaj Krarup, Mathieu Kerneis, Jean Khemis, Ruby Kozlowski, Véronique Lejard, Florence Levenez, Lea Lucas-Martini, Robin Massey, Laura Martinez-Gili, Nicolas Maziers, Jonathan Medina-Stamminger, Gilles Montalescot, Sandrine Moute, Ana Luisa Neves, Michael Olanipekun, Laetitia Pasero Le Pavin, Christine Poitou, Francoise Pousset, Laurence Pouzoulet, Andrea Rodriguez-Martinez, Christine Rouault, Johanne Silvain, Mathilde Svendstrup, Timothy Swartz, Thierry Vanduyvenboden, Camille Vatier, Stefanie Walther., ANR-16-IDEX-0004,ULNE,ULNE(2016), ANR-18-IBHU-0001,PreciDIAB,PreciDIAB Institute, the holistic approach of personal diabets care(2018), Dumas, Marc-Emmanuel, Universität Leipzig [Leipzig], Service de Nutrition [CHU Pitié-Salpétrière], Institut E3M [CHU Pitié-Salpêtrière], CHU Henri Mondor, Centre d'investigation clinique pluridisciplinaire [CHU Pitié Salpêtrière] (CIC-1901(ex CIC-1421)), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Imperial College London - National Heart and Lung Institute, and Division of Computational and Systems Medicine, Imperial College London, London, SW7 2AZ, UK

Subjects
Clostridiales, Science & Technology, Multidisciplinary, ANTIBIOTIC USE, IMPACT, Microbiota, [SDV]Life Sciences [q-bio], HUMAN GUT MICROBIOME, Atherosclerosis, Gastrointestinal Microbiome, [SDV] Life Sciences [q-bio], Multidisciplinary Sciences, PROTON PUMP INHIBITORS, Cardiovascular and Metabolic Diseases, GUIDELINE, Metabolome, MANAGEMENT, Humans, Science & Technology - Other Topics, ALTERS
Abstract

During the transition from a healthy state to cardiometabolic disease, patients become heavily medicated, which leads to an increasingly aberrant gut microbiome and serum metabolome, and complicates biomarker discovery1-5. Here, through integrated multi-omics analyses of 2,173 European residents from the MetaCardis cohort, we show that the explanatory power of drugs for the variability in both host and gut microbiome features exceeds that of disease. We quantify inferred effects of single medications, their combinations as well as additive effects, and show that the latter shift the metabolome and microbiome towards a healthier state, exemplified in synergistic reduction in serum atherogenic lipoproteins by statins combined with aspirin, or enrichment of intestinal Roseburia by diuretic agents combined with beta-blockers. Several antibiotics exhibit a quantitative relationship between the number of courses prescribed and progression towards a microbiome state that is associated with the severity of cardiometabolic disease. We also report a relationship between cardiometabolic drug dosage, improvement in clinical markers and microbiome composition, supporting direct drug effects. Taken together, our computational framework and resulting resources enable the disentanglement of the effects of drugs and disease on host and microbiome features in multimedicated individuals. Furthermore, the robust signatures identified using our framework provide new hypotheses for drug-host-microbiome interactions in cardiometabolic disease. ispartof: NATURE vol:600 issue:7889 pages:500-+ ispartof: location:England status: published

Published
2021
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5. Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology (vol 11, 5881, 2020)

Author

Molinaro, A, Lassen, PB, Henricsson, M, Wu, H, Adriouch, S, Belda, E, Chakaroun, R, Nielsen, T, Bergh, P-O, Rouault, C, Andre, S, Marquet, F, Andreelli, F, Salem, J-E, Assmann, K, Bastard, J-P, Forslund, S, Le Chatelier, E, Falony, G, Pons, N, Prifti, E, Quinquis, B, Roume, H, Vieira-Silva, S, Hansen, TH, Pedersen, HK, Lewinter, C, Sonderskov, NB, Kober, L, Vestergaard, H, Hansen, T, Zucker, J-D, Galan, P, Dumas, M-E, Raes, J, Oppert, J-M, Letunic, I, Nielsen, J, Bork, P, Ehrlich, SD, Stumvoll, M, Pedersen, O, Aron-Wisnewsky, J, Clement, K, Backhed, F, and Commission of the European Communities

Subjects
Multidisciplinary Sciences, MetaCardis Consortium, Science & Technology, Science & Technology - Other Topics
Published
2020

6. Predicting and elucidating the etiology of fatty liver disease: A machine learning modeling and validation study in the IMI DIRECT cohorts

Author

Atabaki-Pasdar, N, Ohlsson, M, Vinuela, A, Frau, F, Pomares-Millan, H, Haid, M, Jones, AG, Thomas, EL, Koivula, RW, Kurbasic, A, Mutie, PM, Fitipaldi, H, Fernandez, J, Dawed, AY, Giordano, GN, Forgie, IM, McDonald, TJ, Rutters, F, Cederberg, H, Chabanova, E, Dale, M, Masi, FD, Thomas, CE, Allin, KH, Hansen, TH, Heggie, A, Hong, M-G, Elders, PJM, Kennedy, G, Kokkola, T, Pedersen, HK, Mahajan, A, McEvoy, D, Pattou, F, Raverdy, V, Haussler, RS, Sharma, S, Thomsen, HS, Vangipurapu, J, Vestergaard, H, 't Hart, LM, Adamski, J, Musholt, PB, Brage, S, Brunak, S, Dermitzakis, E, Frost, G, Hansen, T, Laakso, M, Pedersen, O, Ridderstrale, M, Ruetten, H, Hattersley, AT, Walker, M, Beulens, JWJ, Mari, A, Schwenk, JM, Gupta, R, McCarthy, MI, Pearson, ER, Bell, JD, Pavo, I, Franks, PW, Epidemiology and Data Science, General practice, APH - Health Behaviors & Chronic Diseases, Amsterdam Reproduction & Development (AR&D), ACS - Diabetes & metabolism, ACS - Heart failure & arrhythmias, APH - Aging & Later Life, Atabaki-Pasdar, Naeimeh [0000-0001-7229-1888], Ohlsson, Mattias [0000-0003-1145-4297], Viñuela, Ana [0000-0003-3771-8537], Pomares-Millan, Hugo [0000-0001-9245-4576], Haid, Mark [0000-0001-6118-1333], Jones, Angus G. [0000-0002-0883-7599], Thomas, E. Louise [0000-0003-4235-4694], Koivula, Robert W. [0000-0002-1646-4163], Kurbasic, Azra [0000-0002-1910-2619], Fitipaldi, Hugo [0000-0001-5352-2134], Dawed, Adem Y. [0000-0003-0224-2428], Forgie, Ian M. [0000-0002-8800-6145], Cederberg, Henna [0000-0003-2901-9373], Dale, Matilda [0000-0002-5788-7744], Masi, Federico De [0000-0003-4859-4170], Thomas, Cecilia Engel [0000-0001-6201-6380], Allin, Kristine H. [0000-0002-6880-5759], Hansen, Tue H. [0000-0001-5948-8993], Elders, Petra J. M. [0000-0002-5907-7219], Kennedy, Gwen [0000-0002-9856-3236], Kokkola, Tarja [0000-0002-3303-3912], Pedersen, Helle Krogh [0000-0001-9609-7377], Mahajan, Anubha [0000-0001-5585-3420], McEvoy, Donna [0000-0003-1546-5567], Häussler, Ragna S. [0000-0003-1664-8875], Vangipurapu, Jagadish [0000-0001-6657-2659], Vestergaard, Henrik [0000-0003-3090-269X], ‘t Hart, Leen M. [0000-0003-4401-2938], Brage, Soren [0000-0002-1265-7355], Frost, Gary [0000-0003-0529-6325], Hansen, Torben [0000-0001-8748-3831], Hattersley, Andrew T. [0000-0001-5620-473X], Mari, Andrea [0000-0002-1436-5591], Schwenk, Jochen M. [0000-0001-8141-8449], Gupta, Ramneek [0000-0001-6841-6676], McCarthy, Mark I. [0000-0002-4393-0510], Pearson, Ewan R. [0000-0001-9237-8585], Bell, Jimmy D. [0000-0003-3804-1281], Franks, Paul W. [0000-0002-0520-7604], Apollo - University of Cambridge Repository, HUS Abdominal Center, Clinicum, Department of Medicine, Endokrinologian yksikkö, Jones, Angus G [0000-0002-0883-7599], Thomas, E Louise [0000-0003-4235-4694], Koivula, Robert W [0000-0002-1646-4163], Dawed, Adem Y [0000-0003-0224-2428], Forgie, Ian M [0000-0002-8800-6145], Allin, Kristine H [0000-0002-6880-5759], Hansen, Tue H [0000-0001-5948-8993], Elders, Petra JM [0000-0002-5907-7219], Häussler, Ragna S [0000-0003-1664-8875], 't Hart, Leen M [0000-0003-4401-2938], Hattersley, Andrew T [0000-0001-5620-473X], Schwenk, Jochen M [0000-0001-8141-8449], McCarthy, Mark I [0000-0002-4393-0510], Pearson, Ewan R [0000-0001-9237-8585], Bell, Jimmy D [0000-0003-3804-1281], Franks, Paul W [0000-0002-0520-7604], and IMI

Subjects
Male, Proteomics, Oral Glucose Suppression Test, Biochemistry, Machine Learning, Fats, Database and Informatics Methods, Endocrinology, Medicine and Health Sciences, Insulin, Prospective Studies, 11 Medical and Health Sciences, GLOBAL EPIDEMIOLOGY, INSULIN SENSITIVITY, Proteomic Databases, Liver Diseases, Middle Aged, Lipids, Medicine, Female, Life Sciences & Biomedicine, Research Article, Computer and Information Sciences, Endocrine Disorders, BIOMARKERS, Gastroenterology and Hepatology, Research and Analysis Methods, Risk Assessment, Diabetes Complications, Medicine, General & Internal, SDG 3 - Good Health and Well-being, Artificial Intelligence, General & Internal Medicine, NAFLD, Diabetes Mellitus, Humans, Metabolomics, Diabetic Endocrinology, Pharmacology, Science & Technology, Models, Statistical, Reproducibility of Results, Biology and Life Sciences, ALCOHOLIC STEATOHEPATITIS, Hormones, Pharmacologic-Based Diagnostics, Fatty Liver, Metabolism, Biological Databases, 3121 General medicine, internal medicine and other clinical medicine, Metabolic Disorders
Abstract

Background Non-alcoholic fatty liver disease (NAFLD) is highly prevalent and causes serious health complications in individuals with and without type 2 diabetes (T2D). Early diagnosis of NAFLD is important, as this can help prevent irreversible damage to the liver and, ultimately, hepatocellular carcinomas. We sought to expand etiological understanding and develop a diagnostic tool for NAFLD using machine learning. Methods and findings We utilized the baseline data from IMI DIRECT, a multicenter prospective cohort study of 3,029 European-ancestry adults recently diagnosed with T2D (n = 795) or at high risk of developing the disease (n = 2,234). Multi-omics (genetic, transcriptomic, proteomic, and metabolomic) and clinical (liver enzymes and other serological biomarkers, anthropometry, measures of beta-cell function, insulin sensitivity, and lifestyle) data comprised the key input variables. The models were trained on MRI-image-derived liver fat content (, In a modelling study, Naeimeh Atabaki-Pasdar and colleagues apply machine learning techniques to develop models to predict non-alcoholic fatty liver disease diagnosis using multi-omic and clinical data from individuals with and without type 2 diabetes in the IMI DIRECT cohorts., Author summary Why was this study done? Globally, about 1 in 4 adults have non-alcoholic fatty liver disease (NAFLD), which adversely affects energy homeostasis (in particular blood glucose concentrations), blood detoxification, drug metabolism, and food digestion. Although numerous noninvasive tests to detect NAFLD exist, these typically include inaccurate blood-marker tests or expensive imaging methods. The purpose of this work was to develop accurate noninvasive methods to aid in the clinical prediction of NAFLD. What did the researchers do and find? The analyses applied machine learning methods to data from the deep-phenotyped IMI DIRECT cohorts (n = 1,514) to identify sets of highly informative variables for the prediction of NAFLD. The criterion measure was liver fat quantified from MRI. We developed a total of 18 prediction models that ranged from very inexpensive models of modest accuracy to more expensive biochemistry- and/or omics-based models with high accuracy. We found that models using measures commonly collected in either clinical settings or research studies proved adequate for the prediction of NAFLD. The addition of detailed omics data significantly improved the predictive utility of these models. We also found that of all omics markers, proteomic markers yielded the highest predictive accuracy when appropriately combined. What do these findings mean? We envisage that these new approaches to predicting fatty liver may be of clinical value when screening at-risk populations for NAFLD. The identification of specific molecular features that underlie the development of NAFLD provides novel insights into the disease’s etiology, which may lead to the development of new treatments.

Published
2020
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10. Discovery of Biomarkers for Glycaemic Deterioration before and after the Onset of Type 2 Diabetes: Descriptive Characteristics of the Epidemiological Studies within the IMI DIRECT Consortium

Author

Koivula, RW, Forgie, IM, Kurbasic, A, Vinuela, A, Heggie, A, Giordano, GN, Hansen, TH, Hudson, M, Koopman, ADM, Rutters, F, Siloaho, M, Allin, KH, Brage, S, Brorsson, CA, Dawed, AY, De Masi, F, Groves, CJ, Kokkola, T, Mahajan, A, Perry, MH, Rauh, SP, Ridderstrale, M, Teare, HJA, Thomas, EL, Tura, A, Vestergaard, H, White, T, Adamski, J, Bell, JD, Beulens, JW, Brunak, S, Dermitzakis, ET, Froguel, P, Frost, G, Gupta, R, Hansen, T, Hattersley, A, Jablonka, B, Kaye, J, Laakso, M, McDonald, TJ, Pedersen, O, Schwenk, JM, Pavo, I, Mari, A, McCarthy, MI, Ruetten, H, Walker, M, Pearson, E, Franks, PW, Koivula, RW, Forgie, IM, Kurbasic, A, Vinuela, A, Heggie, A, Giordano, GN, Hansen, TH, Hudson, M, Koopman, ADM, Rutters, F, Siloaho, M, Allin, KH, Brage, S, Brorsson, CA, Dawed, AY, De Masi, F, Groves, CJ, Kokkola, T, Mahajan, A, Perry, MH, Rauh, SP, Ridderstrale, M, Teare, HJA, Thomas, EL, Tura, A, Vestergaard, H, White, T, Adamski, J, Bell, JD, Beulens, JW, Brunak, S, Dermitzakis, ET, Froguel, P, Frost, G, Gupta, R, Hansen, T, Hattersley, A, Jablonka, B, Kaye, J, Laakso, M, McDonald, TJ, Pedersen, O, Schwenk, JM, Pavo, I, Mari, A, McCarthy, MI, Ruetten, H, Walker, M, Pearson, E, and Franks, PW

Abstract

Here, we describe the characteristics of the Innovative Medicines Initiative (IMI) Diabetes Research on Patient Stratification (DIRECT) epidemiological cohorts at baseline and follow-up examinations (18, 36 and 48 months of follow-up).

Published
2019

11. The GPR experiment on NETLANDER

Author

Berthelier, J.J., Ney, R., Costard, F., Hamelin, M., Meyer, A., Martinat, B., Reineix, A., Hansen, Th., Bano, M., Kofman, W., Lefeuvre, F., and Paillou, P.

Published
2000
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13. Objective assessment of dietary patterns using metabolic phenotyping: a randomized, controlled, crossover trial

Author

Garcia Perez, I, Posma, JM, Gibson, R, Chambers, ES, Hansen, TH, Vestergaard, H, Hansen, T, Beckmann, M, Pedersen, O, Elliott, P, Stamler, J, Nicholson, JK, Draper, J, Mathers, JC, Holmes, E, Frost, G, Van Epps, H, National Institutes of Health, National Institute for Health Research, Imperial College Healthcare NHS Trust- BRC Funding, and Medical Research Council (MRC)

Abstract

Background: The burden of non-communicable diseases, such as obesity, diabetes, coronary heart disease and cancer, can be reduced by the consumption of healthy diets. Accurate monitoring of changes in dietary patterns in response to food policy implementation is challenging. Metabolic profiling allows simultaneous measurement of hundreds of metabolites in urine, many of them influenced by food intake. We aim to classify people according to dietary behaviour and enhance dietary reporting using metabolic profiling of urine. Methods: To develop metabolite models from 19 healthy volunteers who attended a clinical research unit for four day periods on four occasions. We used the World Health Organisation’s healthy eating guidelines (increase fruits, vegetables, wholegrains, dietary fibre and decrease fats, sugars, and salt) to develop four dietary interventions lasting for four days each that ranged from a diet associated with a low to high risk of developing non-communicable disease. Urine samples were measured by 1H-NMR spectroscopy. This study is registered as an International Standard Randomized Controlled Trial, number ISRCTN 43087333. INTERMAP U.K. (n=225) and a healthy-eating Danish cohort (n=66) were used as free-living validation datasets. Findings: There was clear separation between the urinary metabolite profiles of the four diets. We also demonstrated significant stepwise differences in metabolite levels between the lowest and highest metabolic risk diets and developed metabolite models for each diet. Application of the derived metabolite models to independent cohorts confirmed the association between urinary metabolic and dietary profiles in INTERMAP (P

Published
2016

14. Advances in the use of Paris-Edinburgh presses for high pressure neutron scattering.

Author

Klotz, S., Hansen, Th., Lelièvre-Berna, E., Amand, L., Maurice, J., and Payre, C.

Subjects
*NEUTRON scattering, *PRESSURE, *GASKETS, *PRESS
Abstract

Paris-Edinburgh (PE) presses are nowadays the dominant high pressure devices for neutron scattering in the 10 GPa range and above. Here, we present developments of gasket-anvil assemblies with 30% improved pressure performance and considerably increased lifetime compared to the currently used "single-toroidal" anvils, and giving nevertheless a similar signal-to-background ratio. We also present an improved Bridgman seal package which makes the low-temperature operation of the PE press significantly more reliable. A systematic investigation of background sources in the "equatorial" scattering geometry is reported. [ABSTRACT FROM AUTHOR]

Published
2019
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17. Investigating solar degradation mechanisms of the Ta3N5 photoelectrode by in-situ transmission electron microscopy

Author

Thøgersen Annett, Dahl Øystein, Kadkhodazadeh Shima, Seifner Michael, Sunding Martin Fleissner, Svenum Ingeborg-Helene, Grandcolas Mathieu, Hansen Thomas Willum, Jensen Ingvild Julie Thue, and Chatzitakis Athanasios

Subjects
degradation, tem, operando, ta3n5, hydrogen, Microbiology, QR1-502, Physiology, QP1-981, Zoology, QL1-991
Published
2024
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18. Beam damage and dynamics modelled with equivariant neural networks

Author

Valencia Cuauhtémoc Nuñez, Nissen Mathias Stokkebye, Giese Patrick, Helveg Stig, Hansen Thomas Willum, and Schiøtz Jakob

Subjects
equivariant neural network potentials, hr-tem, image simulation, molecular dynamics, nanoparticles, Microbiology, QR1-502, Physiology, QP1-981, Zoology, QL1-991
Published
2024
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19. Effect of composition and pressure on phase transitions in FexO at low temperature.

Author

Glazyrin, K., Dubrovinsky, L., Klotz, S., Uhlarz, M., Wosnitza, J., Hansen, Th., and Dubrovinskaia, N.

Subjects
PHASE transitions, NEUTRONS, IRON oxides, LOW temperature engineering, OPTICAL diffraction
Abstract

We report the results of high-resolution neutron powder diffraction studies of FexO (x = 0.925, 0.94) in the vicinity of the low-temperature antiferromagnetic transition and at pressures up to 8 GPa. Our analysis shows that the P-T phase diagram of FexO is strongly affected by the composition and defect structure of the material. We observe the divergence of critical temperatures of magnetic and structural transitions. In contrast to the stoichiometric antiferromagnet MnO, we find no correlation between the magnitude of the magnetic moment of iron and the degree of the rhombohedral distortion in FexO. We suggest that the defect structure of antiferromagnetic FexO significantly influences the temperature of the structural transition. [ABSTRACT FROM AUTHOR]

Published
2011
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23. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages

Author

Gautiar, EL, Shay, T, Miller, J, Greter, M, Jakubzick, C, Ivanov, S, Helft, J, Chow, A, Elpek, KG, Gordonov, S, Mazloom, AR, Ma'Ayan, A, Chua, WJ, Hansen, TH, Turley, SJ, Merad, M, Randolph, GJ, Best, AJ, Knell, J, Goldrath, A, Brown, B, Jojic, V, Koller, D, Cohen, N, Brenner, M, Regev, A, Fletcher, A, Bellemare-Pelletier, A, Malhotra, D, Jianu, R, Laidlaw, D, Collins, J, Narayan, K, Sylvia, K, Kang, J, Gazit, R, Garrison, BS, Rossi, DJ, Kim, F, Rao, TN, Wagers, A, Shinton, SA, Hardy, RR, Monach, P, Bezman, NA, Sun, JC, Kim, CC, Lanier, LL, Heng, T, Kreslavsky, T, Painter, M, Ericson, J, Davis, S, Mathis, D, and Benoist, C

Abstract

We assessed gene expression in tissue macrophages from various mouse organs. The diversity in gene expression among different populations of macrophages was considerable. Only a few hundred mRNA transcripts were selectively expressed by macrophages rather than dendritic cells, and many of these were not present in all macrophages. Nonetheless, well-characterized surface markers, including MerTK and FcγR1 (CD64), along with a cluster of previously unidentified transcripts, were distinctly and universally associated with mature tissue macrophages. TCEF3, C/EBP-α, Bach1 and CREG-1 were among the transcriptional regulators predicted to regulate these core macrophage-associated genes. The mRNA encoding other transcription factors, such as Gata6, was associated with single macrophage populations. We further identified how these transcripts and the proteins they encode facilitated distinguishing macrophages from dendritic cells. © 2012 Nature America, Inc. All rights reserved.

Published
2012
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26. Megapixel imaging of (micro)nutrients in mature barley grains

Author

Lombi, E, Smith, E, Hansen, TH, Paterson, D, de Jonge, MD, Howard, DL, Persson, DP, Husted, S, Ryan, C, Schjoerring, JK, Lombi, E, Smith, E, Hansen, TH, Paterson, D, de Jonge, MD, Howard, DL, Persson, DP, Husted, S, Ryan, C, and Schjoerring, JK

Abstract

Understanding the accumulation and distribution of essential nutrients in cereals is of primary importance for improving the nutritional quality of this staple food. While recent studies have improved the understanding of micronutrient loading into the barley grain, a detailed characterization of the distribution of micronutrients within the grain is still lacking. High-definition synchrotron X-ray fluorescence was used to investigate the distribution and association of essential elements in barley grain at the micro scale. Micronutrient distribution within the scutellum and the embryo was shown to be highly variable between elements in relation to various morphological features. In the rest of the grain, the distribution of some elements such as Cu and Zn was not limited to the aleurone layer but extended into the endosperm. This pattern of distribution was less marked in the case of Fe and, in particular, Mn. A significant difference in element distribution was also found between the ventral and dorsal part of the grains. The correlation between the elements was not consistent between and within tissues, indicating that the transport and storage of elements is highly regulated. The complexity of the spatial distribution and associations has important implications for improving the nutritional content of cereal crops such as barley.

Published
2011

27. In fear of abandonment : slum life, community leaders and politics in Recife, Brazil

Author

Blom Hansen, Th., Nuijten, Monique, de Vries, Pieter, Koster, M., Blom Hansen, Th., Nuijten, Monique, de Vries, Pieter, and Koster, M.

Abstract

This book sets out to contribute to the pursuit of ‘making nonpersons full human beings’ (Boff & Boff:1987:8). It provides insights in the lives of residents of the slum of “Chão de Estrelas” in Recife, Brazil. I argue that slum dwellers should not be mystified and misrecognised as “the other”, as different from “normal” citizens, because of their marginalised position. I show that the slum is, in fact, an eminently knowable world. This book presents how slum dwellers, directed by local lideres comunitarios, community leaders, strive for material and intangible resources and engage in utopian projects. I argue that the needs and aspirations of these people, who are at constant risk of being ignored, disconnected, and abandoned, emerge from their yearnings for recognition and connectivity, and a fear of abandonment. To understand this life in the slum, I focus on the ways slum dwellers attempt to realise their needs and aspirations, modes of operating which I call “slum politics”. Chapter 1 defines slum politics as grounded in the needs and aspirations of those who live in the margins. Drawing on the work of Oscar Lewis (1959, 1965), it analyses how life in the slum, through stigmatisation and a long history of marginalisation, is reproduced in ways that are fundamentally different from middle- and upper-class people. This difference, expressed in particular needs and aspirations, is not generated because slum dwellers are a different kind of people, but because have they been structurally segregated in the dominant political and economic order. This chapter documents how these particular needs and aspirations, although not solely held by slum dwellers, are more emphatically and urgently present in their lives in the margins of the political and economic order, and have material, intangible and utopian dimensions. Material needs exist, for instance, for money, food, and employment. Intangible, or social, needs can be viewed in attempts to establish connections to all

Published
2009

28. Deuterated Clathrate Hydrates as a Novel Moderator Material for Very Cold Neutrons. Project Aperçu and First Results

Author

Czamler Valentin, Hansen Thomas C., Koza Michael Marek, Wagner Richard, and Zimmer Oliver

Subjects
Physics, QC1-999
Abstract

Clathrate hydrates are water-based solids with large crystallographic unit cells that show promise as potential moderators for use in new, more intense sources of very cold neutrons (VCN), which would enhance neutron scattering techniques and increase sensitivity of particle physics experiments. These so-called inclusion compounds seem particularly suitable for this application due to the low-energy modes of guest molecules encaged in nano-voids formed by a crystalline network of hydrogen bonded water molecules. In this article we present first results of an ongoing, extensive experimental campaign with the aim of characterizing the scattering properties of deuterated clathrate hydrates relevant for moderator applications. Experiments include neutron diffraction (carried out at Institut Laue-Langevin (ILL) using the instrument D20), as well as measurements of the temperature-dependent dynamical structure factor S (q, ω) in absolute units (carried out on ILL’s Panther and IN5). These measurements will serve as a benchmark for development of new scattering kernels.

Published
2023
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42. Pressure dependence of Morin transition in α-Fe2O3 hematite.

Author

Klotz, S., Strässle, Th., and Hansen, Th.

Abstract

We report high-pressure neutron diffraction data on the Morin-transition TM in α-Fe2O3 hematite, up to 8 GPa and under hydrostatic conditions. We find a strictly linear pressure coefficient of with no evidence for intermediate magnetic states as indicated by all previous non-hydrostatic measurements. The behaviour of TM is highly regular and can well be explained within the framework of Artman et al.'s single-ion model if a change of the single-ion anisotropy energy by +1%/GPa is assumed. Such a value seems not to be unusual for iron oxides. [ABSTRACT FROM AUTHOR]

Published
2013
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