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51. Research and Innovation for Climate Services Report on the synergy and mismatch analysis EXECUTIVE SUMMARY

Author: Petra Manderscheid (BELSPO / JPI Climate) Roger Street (UKCIP, Ines Alterio (ANR, Lisa Bettington (NERC, Margaret Desmond (EPA/University College Cork, Marc Kierans (EPA, Harilaos Loukos (The Climate Data Factory, Andrea Sharpe (NERC, Tara Shine (Independent Consultant On Climate Justice, Environment, and Sustainable Development
Published: 2017
Full Text: View/download PDF

52. Portable neonatal EEG monitoring and sonification on an Android Device

Author: Universitat Politècnica de Catalunya. Departament de Teoria del Senyal i Comunicacions, University College Cork, Nadeu Camprubí, Climent, Popovici, Emanuel, Poveda Pena, Jonatan, Universitat Politècnica de Catalunya. Departament de Teoria del Senyal i Comunicacions, University College Cork, Nadeu Camprubí, Climent, Popovici, Emanuel, and Poveda Pena, Jonatan
Abstract: Automatic analysis and description of the sounds present in a neonatal intensive care unit in order to study their effect on the babies., In this work a real-time and portable software to check the brain status of preterm babies is implemented using an EEG sonification algorithm based on a Phase Vocoder, faster, cheaper and easier to use than the current working systems in medical facilities. A multi-threaded and real-time version of a Phase Vocoder built on an Android smartphone is proposed to achieve portability and an instantaneous brain check. The sonification of the neonatal EEG, instead of its visualisation, allows healthcare professionals to fast check with a very short training, unloading work of the few neonatologist in the health centre, in case there are available, and to provision an alternative system when a constant monitoring is not affordable for every patient. The results and our surveys on clinical personnel demonstrate that this system is completely feasible and it provides a base to develop and launch into the market a new tool for the analysis of the brain activity., En este trabajo se ha desarrollado un software para comprobar el estado de actividad cerebral de niños prematuros que implementa un algoritmo de sonificación, en tiempo real y de forma portable, y más rápido, barato y fácil de utilizar que los sistemas actuales. Se trata de una versión multi-hilo I en tiempo real del vocoder de fase implementada en un teléfono inteligente con Android, para conseguir portabilidad y una comprobación instantánea de la actividad cerebral. La sonificación del EEG prenatal és una alternativa a su visualización que permite a los profesionales de la sanidad una comprobación rápida de la actividad cerebral y que requiere un entrenamiento corto. Así se ve reducida la carga de trabajo de los pocos neonatólogos que hay en el centro de salud, si es que hay alguno, y proporciona una alternativa cuando el monitoreo continuo no es una opción viable para todos los pacientes. Los resultados y las encuestas hechas a personal clínico demuestran que este sistema es totalmente viable y proporciona una base para desarrollar y lanzar al mercado una nueva herramienta de análisis de actividad cerebral., En aquest treball s'ha desenvolupat un programari per comprovar l'estat d'activitat cerebral de nens prematurs que implementa un algoritme de sonificació, en temps real i de forma portable, i és més ràpid, barat i fàcil d'utilitzar que els sistemes actuals. Es tracta d'una versió multifil i en temps real del vocoder de fase implementada en un telèfon intel·ligent amb Android, per aconseguir portabilitat i una comprovació instantània de l'activitat cerebral. La sonificació de l'EEG prenatal és una alternativa a la seva visualització que permet als professionals sanitaris una comprovació ràpida de l' activitat cerebral i requereix un entrenament breu. Així es redueix la càrrega de feina dels pocs neonatòlegs que hi ha en el centre de salut, si és que n'hi ha algun, i proporciona una alternativa quan el monitoratge continu no es una opció viable per a tots els pacients. Els resultats i les enquestes fetes amb personal clínic demostren que aquest sistema es totalment viable i proporciona una base per desenvolupar i llençar al mercat una nova eina d'anàlisis d'activat cerebral.
Published: 2017

53. The forces that shaped the Irish Regional Technical College buildings

Author: Ó Riain, Marc (Cork Centre for Architectural Education, University College Cork & Cork Institute of Technology), McCarthney, Kevin, Harrison, Jim (Cork Centre for Architectural Education), and Gomes Correia, Larissa (Cork Institute of Technology)
Subjects: modernism, architecture, environmental thinking
Abstract: peer-reviewed The paper charts the early development of environmental thinking in Architecture up to the radical paradigm shift of modernism and brutalism. The resulting emphasis on proportional grammar over the technical performance of the interior environment would be common threads in Educational architecture leading up to the design of the Regional Technical Colleges (RTCs) in 1967. Changes in technology, materials and skills shortages led to the development of post war steel frame Hertfordshire Schools which greatly influenced the future direction of Technological School and College design. Financial rationalisation saw a movement away from the steel frame CLASP models to concrete frame Intergrid systems, which would directly influence a key precedent of the RTC design, the M&M building at the University of Birmingham. The intelligence of the building design by ARUP would be compromised by the Modernist emphasis on plastic over glazed facades, which lacked shading suffered from great heat loss. The movement away from quality materiality and exposed grid structure, resulted in a loss of delight and a greater level of brutalism.
Published: 2015

54. Memoria e accidente in “Case Sparse: Visioni di Case che Crollano”

Author: Gianni Celati. Translation, Tradition, Rewriting (23-24 September 2016: University College Cork, Dep. of Italian, Cork, Ireland), Tenzon, Michele, Gianni Celati. Translation, Tradition, Rewriting (23-24 September 2016: University College Cork, Dep. of Italian, Cork, Ireland), and Tenzon, Michele
Abstract: info:eu-repo/semantics/nonPublished
Published: 2016

55. What are reasons for the large gender differences in the lethality of suicidal acts?: an epidemiological analysis in four European countries

Author: Universitätsklinikum Leipzig, Semmelweis University Budapest, University Medical Center, Universidade Nova de Lisboa, University College Cork, University of Stirling, Tallinn University, University of Leuven, London School of Economics, University of Molise, National Institute for Health, Migration and Poverty, University “Gabriele d’Annunzio” Foundation, Universitätsklinikum Würzburg, Universitätsklinikum Magdeburg, University of Porto, PLoS, Mergl, Roland, Koburger, Nicole, Heinrichs, Katharina, Székely, András, Tóth, Mónika Ditta, Coyne, James, Quintão, Sónia, Arensman, Ella, Coffey, Claire, Maxwell, Margaret, Värnik, Airi, von Audenhove, Chantalle, Daid, David Mc, Sarchiapone, Marco, Schmidtke, Armin, Genz, Axel, Gusmão, Ricardo, Hegerl, Ulrich, Universitätsklinikum Leipzig, Semmelweis University Budapest, University Medical Center, Universidade Nova de Lisboa, University College Cork, University of Stirling, Tallinn University, University of Leuven, London School of Economics, University of Molise, National Institute for Health, Migration and Poverty, University “Gabriele d’Annunzio” Foundation, Universitätsklinikum Würzburg, Universitätsklinikum Magdeburg, University of Porto, PLoS, Mergl, Roland, Koburger, Nicole, Heinrichs, Katharina, Székely, András, Tóth, Mónika Ditta, Coyne, James, Quintão, Sónia, Arensman, Ella, Coffey, Claire, Maxwell, Margaret, Värnik, Airi, von Audenhove, Chantalle, Daid, David Mc, Sarchiapone, Marco, Schmidtke, Armin, Genz, Axel, Gusmão, Ricardo, and Hegerl, Ulrich
Abstract: Background: In Europe, men have lower rates of attempted suicide compared to women and at the same time a higher rate of completed suicides, indicating major gender differences in lethality of suicidal behaviour. The aim of this study was to analyse the extent to which these gender differences in lethality can be explained by factors such as choice of more lethal methods or lethality differences within the same suicide method or age. In addition, we explored gender differences in the intentionality of suicide attempts.
Published: 2015

56. Analysing variations in health expectancy - seminar presentations

Author: Centre for Ageing Research and Development in Ireland (CARDI) and Institute of Public Health in Ireland (IPH) and University College Cork
Subjects: Healthy life expectancy, Ageing, Policy, Inequalities
Abstract: A recent report by the Centre for Ageing Research and Development in Ireland (CARDI) entitled Illustrating Ageing in Ireland, North and South found that since the 1920s the number of years males can expect to live rose by about 20 years while the number of years females can expect to live rose by about 24-25 years. It is not clear, however, if these years of life gained are lived in good health.While there is considerable policy focus on reducing inequalities in life expectancy, much less is known about the variation in health expectancy that exists across the island of Ireland. The debate hinges on our understanding of what is driving the changes in life expectancy, healthy life expectancy and the gap between the two.IPH in association with CARDI, hosted a Health Analysts' Special Interest Group (HASIG) seminar discussing the policy implications of this debate. The seminar introduced the range of health expectancy measures and compared them to life expectancy. Initial findings from the all-island study of life expectancy and healthy life expectancy were also presented.
Published: 2010
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57. Identity at the EU Border

Author: UACES Conference (University College Cork, Irlande), Danero Iglesias, Julien, UACES Conference (University College Cork, Irlande), and Danero Iglesias, Julien
Abstract: info:eu-repo/semantics/nonPublished
Published: 2014

58. Ordered 2D colloidal photonic crystals on gold substrates by surfactant-assisted fast-rate dip coating

Author: Irish Research Council for Science, Engineering and Technology, Ministerio de Ciencia e Innovación (España), European Commission, Science Foundation Ireland, University College Cork, Khunsin, W., Sotomayor Torres, C. M., O'Dwyer, Colm, Irish Research Council for Science, Engineering and Technology, Ministerio de Ciencia e Innovación (España), European Commission, Science Foundation Ireland, University College Cork, Khunsin, W., Sotomayor Torres, C. M., and O'Dwyer, Colm
Abstract: Surfactant induced ordering of 2D and 3D colloidal crystal photonic crystals is possible on metallic substrates by dip-coating at fast rates (≈1 mm/min). Ordered monolayer opals on conductive gold-coated silicon substrates behave as a 2D diffraction grating. The method allows high throughput, ordered colloidal crystal formation useful as nanomaterials templates for energy storage or functional materials.
Published: 2014

59. Italia e Francia: il caso di Ugo Foscolo

Author: Graduate Conference in Italian Studies (04.02.2012: University College Cork (UCC)), Bearelle, Sarah, Graduate Conference in Italian Studies (04.02.2012: University College Cork (UCC)), and Bearelle, Sarah
Abstract: info:eu-repo/semantics/nonPublished
Published: 2012

60. Diversity of Bifidobacteria within the Infant Gut Microbiota

Author: Cariparma Bank Foundation, Regione Emilia Romagna, Federation of European Microbiological Societies, Irish Research Council for Science, Engineering and Technology, University College Cork, Science Foundation Ireland, Turroni, Francesca, Gueimonde Fernández, Miguel, Margolles Barros, Abelardo, Ventura, Marco, Cariparma Bank Foundation, Regione Emilia Romagna, Federation of European Microbiological Societies, Irish Research Council for Science, Engineering and Technology, University College Cork, Science Foundation Ireland, Turroni, Francesca, Gueimonde Fernández, Miguel, Margolles Barros, Abelardo, and Ventura, Marco
Abstract: [Background] The human gastrointestinal tract (GIT) represents one of the most densely populated microbial ecosystems studied to date. Although this microbial consortium has been recognized to have a crucial impact on human health, its precise composition is still subject to intense investigation. Among the GIT microbiota, bifidobacteria represent an important commensal group, being among the first microbial colonizers of the gut. However, the prevalence and diversity of members of the genus Bifidobacterium in the infant intestinal microbiota has not yet been fully characterized, while some inconsistencies exist in literature regarding the abundance of this genus., [Methods/Principal Findings] In the current report, we assessed the complexity of the infant intestinal bifidobacterial population by analysis of pyrosequencing data of PCR amplicons derived from two hypervariable regions of the 16 S rRNA gene. Eleven faecal samples were collected from healthy infants of different geographical origins (Italy, Spain or Ireland), feeding type (breast milk or formula) and mode of delivery (vaginal or caesarean delivery), while in four cases, faecal samples of corresponding mothers were also analyzed., [Conclusions] In contrast to several previously published culture-independent studies, our analysis revealed a predominance of bifidobacteria in the infant gut as well as a profile of co-occurrence of bifidobacterial species in the infant’s intestine.
Published: 2012

61. Collaborative Tagging as a User-Generated Tool for the Organisation of Online Healthcare Resources: Research Proposals

Author: ASIS&T European Workshop 2011 (AEW 2011) (1-2 Juin 2011: University College Cork, Irlande), Durieux, Valérie, ASIS&T European Workshop 2011 (AEW 2011) (1-2 Juin 2011: University College Cork, Irlande), and Durieux, Valérie
Abstract: This paper examines the potential of collaborative tagging to organise online healthcare resources. First, users‘ tags are compared to librarians‘ descriptors. The comparison shows that the majority of tags are relevant and useful for the information retrieval process. Moreover, numerous tags provide the tagged resources with additional access points compared with descriptors. Second, an analysis of end-users‘ seeking practices is envisioned in order to find out if collaborative tagging could help them in their information retrieval process. To collect the relevant data, three successive steps are considered: ethnographical observations, in-depth interviews and focus groups., info:eu-repo/semantics/nonPublished
Published: 2011

62. New species of Medicorophium Bousfield, M. longisetosum n. sp. from the western Mediterranean, coast of Spain

Author: Universidad de Alicante. Departamento de Ciencias del Mar y Biología Aplicada, University College (Cork, Ireland). Department of Biological, Environmental and Earth Sciences, Université de Lille 1. Station Marine de Wimereux, Myers, Alan A., de-la-Ossa-Carretero, Jose Antonio, Dauvin, Jean-Claude, Universidad de Alicante. Departamento de Ciencias del Mar y Biología Aplicada, University College (Cork, Ireland). Department of Biological, Environmental and Earth Sciences, Université de Lille 1. Station Marine de Wimereux, Myers, Alan A., de-la-Ossa-Carretero, Jose Antonio, and Dauvin, Jean-Claude
Abstract: The Mediterranean Amphipoda fauna has been widely studied and can be considered one of the best known in the world (Conradi & López-González 1999); however knowledge of the fauna is not uniform throughout the entire Mediterranean, being still fragmentary on the coasts of the Iberian Peninsula (Jimeno & Turón 1995; Bellan-Santini & Ruffo 1998). Studying benthos communities along Comunidad Valenciana coast (East Spanish coast), a new species of the genus Medicorophium was found in areas characterised by medium-tofine sand community of Spisula subtruncata. Despite the fact that this community is commonly found in the shallow soft-bottom non-vegetated areas of the western Mediterranean Sea (Cardell et al. 1999), this species was not previously reported. A key to the species of Corophium, Apocorophium, Monocorophium and Medicorophium (tribe Corophiini) found on the Mediterranean coast of Spain is provided.
Published: 2010

63. Simulations of time-resolved x-ray diffraction in Laue geometry

Author: FOCUS Center and Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA, Physics Department and NMRC, University College, Cork, Republic of Ireland, Department of Physics, Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, UK, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Ann Arbor, Fahy, S., Lings, B., Wark, J. S., DeCamp, M. F., Reis, D. A., FOCUS Center and Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA, Physics Department and NMRC, University College, Cork, Republic of Ireland, Department of Physics, Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, UK, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Ann Arbor, Fahy, S., Lings, B., Wark, J. S., DeCamp, M. F., and Reis, D. A.
Abstract: A method for computer simulation of time-resolved x-ray diffraction (TRXD) in asymmetric Laue (transmission) geometry with an arbitrary propagating strain perpendicular to the crystal surface is presented. We present two case studies for possible strain generation by short-pulse laser irradiation: (i) a thermoelastic-like analytical model; (ii) a numerical model including the effects of electron–hole diffusion, Auger recombination, deformation potential and thermal diffusion. A comparison with recent experimental results is also presented.
Published: 2006

64. Narrating the Female Body Space in Carlo Cassola’s Paura e tristezza

Author: Department of Italian Research Seminar Series, 2004-05 (7 Dec. 2004: University College Cork, Ireland), Best, David Albert, Department of Italian Research Seminar Series, 2004-05 (7 Dec. 2004: University College Cork, Ireland), and Best, David Albert
Abstract: info:eu-repo/semantics/nonPublished
Published: 2004

65. Paolo Volponi’s Psychological Landscapes: From Rural Topography to Mental Space in La macchina mondiale

Author: Hemispheres: Cross-Currents Interdisciplinary International Conference (3 May 2002: School of Languages and Literatures, University College Cork, Ireland), Best, David Albert, Hemispheres: Cross-Currents Interdisciplinary International Conference (3 May 2002: School of Languages and Literatures, University College Cork, Ireland), and Best, David Albert
Abstract: info:eu-repo/semantics/nonPublished
Published: 2002

66. Study on Street Children in Four Selected Towns in Ethiopia

Author: Lalor, Kevin, Veale, Angela, Adefrisew, Azeb, UNICEF, and University College Cork
Subjects: African Studies, Race and Ethnicity, Social Work, Sociology of Culture, street children, Regional Sociology, Rural Sociology, Ethiopia
Abstract: The child is the most precious asset and the focal point of development for any country. However, unless children are brought up in a stimulating and conducive environment getting the best possible care and protection, their physical, mental, emotional and social development is susceptible to permanent damage. Ethiopia, being one of the least developed countries of the world due to interrelated and complex socio-economic factors including man-made and natural calamities, a large portion of our population - especially children - are victimized by social evils like famine, disease, poverty, mass displacement, lack of education and family instability. Owing to the fact that children are the most vulnerable group among the whole society and also because they constitute half of the population it is evident that a considerable number of Ethiopian children are living under difficult circumstances. Therefore, as in a number of other third world countries there are many poor, displaced, unaccompanied and orphaned children in our country. A considerable proportion of these children work on the street with some even totally living on the street without any adult care and protection. These children are forced to the streets in their tight for survival. They supplement their parents meagre income or support themselves with the small incomes they earn doing menial jobs. In doing this, street children face the danger of getting into accidents and violence, they get exploited and abused, many are forced to drop out of school or never get the chance to be enroled at all and some drift into begging or petty crime. This study is undertaken mainly for updating the findings of previous studies, monitoring changing trends, examining new facts of the problem and getting a better understanding of the phenomenon in the country by covering at least some of the major centres where the problem is acute. Thus, the outcome of this research can be useful in the formation of tne social welfare programme of the country. Finally, in recognition of the urgency of the problem and the limited resources available, the Ministry of Labour and Social Affairs expresses appreciation to all agencies engaged in the rehabilitation of street children and prevention of the problem. The Ministry also calls for more co-operation and support between concerned governmental and non-governmental organizations in their efforts for improving the situation of street children and in curbing the overwhelming nature of the problem.
Published: 1992

67. Study on Street Children in Four Selected Towns in Ethiopia

Author: Adefrisew, Azeb, Lalor, Kevin, Veale, Angela, and UNICEF And University College Cork
Published: 1992
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68. Studies of a European shellfish disease: Bonamia ostreae parasite of the flat oyster Ostrea edulis ; control and treatment. Final Report

Author: Bachere, Evelyne, Ifremer, Unité de Pathologie, Immunologie et Génétique Moléculaire des Invertébrés Marins, F-17390 La Tremblade, France, CEV, Centro Experimental de Vilaxoan, Conselleria de Pesca, Villagarcia de Arosa, Spain, CSIC, Consejo Superior Investigaciones Cientificas, Peira de Bouzas S/N, Avda E. Cabello 636208, Vigo, Spain, UCC, University College Cork, Dept of Zoology Cork, Ireland, FCR, Fisheries Research Center, Abbotstown, Castleknock, Dublin 15, Ireland, and US, University of Southampton, Dept of Oceanography Southampton S09 5NH, United Kingdom
Subjects: Ostrea edulis, Oyster, Epidemiology, Bonamia ostreae, Disease, Parasitology
Abstract: Bonamia ostreae, an intrahemocytic protozoan parasite infecting the oyster Ostrea edulis, is responsible for an endemic disease affecting all intensive breeding areas of European countries. Epidemiological studies showed variable prevalences, 43% in Galicia (Spain), from 6% to 32% in France and 45% in the most important area of Ireland. The impact of oyster transfers, handlings, high densities have been implicated in the disease development but environmental stressors could be more involved than zootechnical methods. The effect of water temperature, salinity and tidal exposure were particulary examined to assess stress induced changes and determine physiological, biochemical and immunological state indices of oyster populations, which will contribute to progress in the establishment of prophylactic measures. With Bonamia purification protocol, experimental infections have permitted to study bonamiosis development kinetics, confirming a latent period with unknown location of the parasite within the animal tissues. Concerning hemocyte-parasite interactions studies, using in vitro hemocyte infections and chemiluminescence technique, it has been shown that Bonamia counteracts the oxidative defence system in both O. edulis and C. gigas. The question of specificity barrier and elimination of B. ostreae in Japanese oyster remains unresolved. Finally, experimental infections allowed to undertake a selection program for Bonamia resistant oysters. This could be the most effective strategy to ensure uninterupted production of flat oysters.
Published: 1990

69. Incident adverse drug reactions in geriatric inpatients: a multicentred observational study

Author: [ 1 ] Univ Coll Cork, Dept Med, Cork, Ireland Show more [ 2 ] Cork Univ Hosp, Dept Geriatr Med, Cork, Ireland Show more [ 3 ] Natl Univ Ireland, Dept Med, Univ Coll Cork, Cork, Ireland Show more [ 4 ] Natl Univ Ireland, Univ Coll Cork, Dept Epidemiol, Cork, Ireland Show more [ 5 ] Clin Res Facil, Hlth Res Board, Cork, Ireland Show more [ 6 ] Natl Univ Ireland, Univ Coll Cork, Dept Pharm, Cork, Ireland Show more [ 7 ] Univ Ghent, Dept Internal Med, Sect Geriatr, Ghent, Belgium Show more [ 8 ] Univ Ghent, Ghent, Belgium Show more [ 9 ] Landspitali Univ Hosp, Dept Geriatr Med, Reykjavik, Iceland Show more [ 10 ] IRCCS INRCA, Geriatria & Accettaz Geriatr Urgenza, Ancona, Italy Show more [ 11 ] Hosp Univ Ramon & Cajal IRYCIS, Madrid, Spain Show more [ 12 ] Hosp Univ Ramon & Cajal, Madrid, Spain [ 13 ] NHS Grampian, Aberdeen, Scotland Show more [ 14 ] Univ Aberdeen, Sch Med & Dent, Aberdeen, Scotland, Department of Medicine, University College Cork National University of Ireland, Cork, Ireland, Department of Epidemiology, University College Cork National University of Ireland, Cork, Ireland, Health Research Board Clinical Research Facility, Ireland, Department of Pharmacy, University College Cork National University of Ireland, Cork, Ireland, Department of Internal Medicine, Section of Geriatrics, Universiteit Gent, Gent, Belgium, Universiteit Gent, Gent, Belgium, Department of Geriatric Medicine, Landspitali University Hospital, Reykjavik, Iceland, Geriatria ed Accettazione Geriatrica d’urgenza, IRCCS-INRCA, Ancona, Italy, Hospital Universitario Ramón y Cajal (IRYCIS), Spain, Hospital Universitario Ramón y Cajal, Madrid, Spain, NHS Grampian, Aberdeen, UK, University of Aberdeen School of Medicine and Dentistry, Aberdeen, UK, Department of Medicine, University College Cork & Department of Geriatric Medicine, Cork University Hospital, Wilton, Cork, Ireland, Lavan, Amanda, Eustace, Joseph, Dahly, Darren, Flanagan, Evelyn, Gallagher, Paul, Cullinane, Shane, Petrovic, Mirko, Perehudoff, Katrina, Gudmondsson, Adalsteinn, Samuelsson, Ólafur, Sverrisdóttir, Ástrós, Cherubin, Antonio, Dimitri, Frederica, Rimland, Joe, Cruz-Jentoft, Alfonso, Vélez-Díaz-Pallarés, Manuel, Lozano Montoya, Isabel, Soiza, Roy L., Subbarayan, Selvarani, O’Mahony, Denis, [ 1 ] Univ Coll Cork, Dept Med, Cork, Ireland Show more [ 2 ] Cork Univ Hosp, Dept Geriatr Med, Cork, Ireland Show more [ 3 ] Natl Univ Ireland, Dept Med, Univ Coll Cork, Cork, Ireland Show more [ 4 ] Natl Univ Ireland, Univ Coll Cork, Dept Epidemiol, Cork, Ireland Show more [ 5 ] Clin Res Facil, Hlth Res Board, Cork, Ireland Show more [ 6 ] Natl Univ Ireland, Univ Coll Cork, Dept Pharm, Cork, Ireland Show more [ 7 ] Univ Ghent, Dept Internal Med, Sect Geriatr, Ghent, Belgium Show more [ 8 ] Univ Ghent, Ghent, Belgium Show more [ 9 ] Landspitali Univ Hosp, Dept Geriatr Med, Reykjavik, Iceland Show more [ 10 ] IRCCS INRCA, Geriatria & Accettaz Geriatr Urgenza, Ancona, Italy Show more [ 11 ] Hosp Univ Ramon & Cajal IRYCIS, Madrid, Spain Show more [ 12 ] Hosp Univ Ramon & Cajal, Madrid, Spain [ 13 ] NHS Grampian, Aberdeen, Scotland Show more [ 14 ] Univ Aberdeen, Sch Med & Dent, Aberdeen, Scotland, Department of Medicine, University College Cork National University of Ireland, Cork, Ireland, Department of Epidemiology, University College Cork National University of Ireland, Cork, Ireland, Health Research Board Clinical Research Facility, Ireland, Department of Pharmacy, University College Cork National University of Ireland, Cork, Ireland, Department of Internal Medicine, Section of Geriatrics, Universiteit Gent, Gent, Belgium, Universiteit Gent, Gent, Belgium, Department of Geriatric Medicine, Landspitali University Hospital, Reykjavik, Iceland, Geriatria ed Accettazione Geriatrica d’urgenza, IRCCS-INRCA, Ancona, Italy, Hospital Universitario Ramón y Cajal (IRYCIS), Spain, Hospital Universitario Ramón y Cajal, Madrid, Spain, NHS Grampian, Aberdeen, UK, University of Aberdeen School of Medicine and Dentistry, Aberdeen, UK, Department of Medicine, University College Cork & Department of Geriatric Medicine, Cork University Hospital, Wilton, Cork, Ireland, Lavan, Amanda, Eustace, Joseph, Dahly, Darren, Flanagan, Evelyn, Gallagher, Paul, Cullinane, Shane, Petrovic, Mirko, Perehudoff, Katrina, Gudmondsson, Adalsteinn, Samuelsson, Ólafur, Sverrisdóttir, Ástrós, Cherubin, Antonio, Dimitri, Frederica, Rimland, Joe, Cruz-Jentoft, Alfonso, Vélez-Díaz-Pallarés, Manuel, Lozano Montoya, Isabel, Soiza, Roy L., Subbarayan, Selvarani, and O’Mahony, Denis
Abstract: To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files, BACKGROUND: Adverse drug reactions (ADRs) are common in older adults and frequently have serious clinical and economic consequences. This study was conducted as a feasibility study for a randomized control trial (RCT) that will investigate the efficacy of a software engine to optimize medications and reduce incident (in-hospital) ADRs. This study's objectives were to (i) establish current incident ADR rates across the six sites participating in the forthcoming RCT and (ii) assess whether incident ADRs are predictable. METHODS: This was a multicentre, prospective observational study involving six European hospitals. Adults aged ⩾ 65 years, hospitalized with an acute illness and on pharmacological treatment for three or more conditions were eligible for inclusion. Adverse events (AEs) were captured using a trigger list of 12 common ADRs. An AE was deemed an ADR when its association with an administered drug was adjudicated as being probable/certain, according to the World Health Organization Uppsala Monitoring Centre causality assessment. The proportion of patients experiencing at least one, probable/certain, incident ADR within 14 days of enrolment/discharge was recorded. RESULTS: A total of 644 patients were recruited, evenly split by sex and overwhelmingly of White ethnicity. Over 80% of admissions were medical. The median number of chronic conditions was five (interquartile range 4-6), with eight or more conditions present in approximately 10%. The mean number of prescribed medications was 9.9 (standard deviation 3.8), which correlated strongly with the number of conditions (r = 0.54, p < 0.0001). A total of 732 AEs were recorded in 382 patients, of which 363 were incident. The majority of events were classified as probably or possibly drug related, with heterogeneity across sites (χ2 = 88.567, df = 20, p value < 0.001). Out of 644 patients, 139 (21.6%; 95% confidence interval 18.5-25.0%) experienced an ADR. Serum electrolyte abnormalities were the most common ADR

70. Physician's appraisal vs documented signs and symptoms in the interpretation of food challenge tests: The EuroPrevall birth cohort

Author: [ 1 ] Robert Koch Inst, Dept Infect Dis Epidemiol, Berlin, Germany Show more [ 2 ] Charite Univ Med Berlin, Dept Dermatol Venerol & Allergol, Berlin, Germany Show more [ 3 ] German Rheumatism Res Ctr, Berlin, Germany [ 4 ] RTI Int, HTA Hlth Econ Strategy & Res, Manchester, Lancs, England Show more [ 5 ] Univ Groningen, Univ Med Ctr Groningen, Dept Pediat Pulmonol & Pediat Allergol, Groningen, Netherlands Show more [ 6 ] Univ Southampton, Univ Child Hlth, Southampton, Hants, England Show more [ 7 ] Univ Southampton, Clin Expt Sci, Southampton, Hants, England Show more [ 8 ] Paediat Hosp Bambino Gesu, Dept Paediat, Rome, Italy Show more [ 9 ] Univ Athens, Dept Allergy & Clin Immunol, Pediat Clin 2, Athens, Greece Show more [ 10 ] Univ Manchester, Div Infect Immun & Resp Med, Manchester, Lancs, England Show more [ 11 ] Hosp Univ La Paz, Alergia Infantil, Madrid, Spain [ 12 ] Med Univ, Dept Immunol Rheumatol & Allergy, Lodz, Poland [ 13 ] Landspitali, Dept Immunol, Reykjavik, Iceland Show more [ 14 ] Vilnius Univ, Fac Med, Vilnius, Lithuania Show more [ 15 ] Univ Coll, Paediat & Child Hlth, Cork, Ireland Show more [ 16 ] Charite Univ Med Berlin, Dept Paediat Pneumol & Immunol, Berlin, Germany Show more [ 17 ] Charite Univ Med Berlin, Inst Social Med Epidemiol & Hlth Econ, Berlin, Germany, Department for Infectious Disease Epidemiology; Robert Koch Institute; Berlin Germany, German Rheumatism Research Center; Berlin Germany, HTA Health Economics Strategy and Research; RTI International; Manchester UK, Department of Pediatric Pulmonology & Pediatric Allergology; University of Groningen, University Medical Center Groningen; Groningen The Netherlands, University Child Health; University of Southampton; Southampton Hampshire UK, Clinical Experimental Sciences; University of Southampton; Southampton Hampshire UK, Department of Paediatrics; Paediatric Hospital Bambino Gesù; Rome Italy, Department of Allergy and Clinical Immunology; 2nd Pediatric Clinic; National & Kapodistrian University of Athens; Athens Greece, Division of Infection Immunity & Respiratory Medicine; University of Manchester; Manchester UK, Alergia Infantil; Hospital Universitario La Paz; Madrid Spain, Department of Immunology, Rheumatology and Allergy; Medical University; Lodz Poland, Department of Immunology; Landspitali - The National University Hospital of Iceland; Reykjavik Iceland, Faculty of Medicine; Vilnius University; Vilnius Lithuania, Paediatrics and Child Health; University College; Cork Ireland, Department of Paediatric Pneumology and Immunology; Charité - Universitätsmedizin Berlin; Berlin Germany, Institute for Social Medicine, Epidemiology and Health Economics; Charité - Universitätsmedizin Berlin; Berlin Germany, Grabenhenrich, Linus B., Reich, Andreas, McBride, Doreen, Sprikkelman, Aline, Roberts, Graham, Grimshaw, Kate E. C., Fiocchi, Alessandro G., Saxoni-Papageorgiou, Photini, Papadopoulos, Nikolaos G., Fiandor, Ana, Quirce, Santiago, Kowalski, Marek L., Sigurdardottir, Sigurveig T., Dubakiene, Ruta, Hourihane, Jonathan O. B., Rosenfeld, Leonard, Niggemann, Bodo, Keil, Thomas, Beyer, Kirsten, [ 1 ] Robert Koch Inst, Dept Infect Dis Epidemiol, Berlin, Germany Show more [ 2 ] Charite Univ Med Berlin, Dept Dermatol Venerol & Allergol, Berlin, Germany Show more [ 3 ] German Rheumatism Res Ctr, Berlin, Germany [ 4 ] RTI Int, HTA Hlth Econ Strategy & Res, Manchester, Lancs, England Show more [ 5 ] Univ Groningen, Univ Med Ctr Groningen, Dept Pediat Pulmonol & Pediat Allergol, Groningen, Netherlands Show more [ 6 ] Univ Southampton, Univ Child Hlth, Southampton, Hants, England Show more [ 7 ] Univ Southampton, Clin Expt Sci, Southampton, Hants, England Show more [ 8 ] Paediat Hosp Bambino Gesu, Dept Paediat, Rome, Italy Show more [ 9 ] Univ Athens, Dept Allergy & Clin Immunol, Pediat Clin 2, Athens, Greece Show more [ 10 ] Univ Manchester, Div Infect Immun & Resp Med, Manchester, Lancs, England Show more [ 11 ] Hosp Univ La Paz, Alergia Infantil, Madrid, Spain [ 12 ] Med Univ, Dept Immunol Rheumatol & Allergy, Lodz, Poland [ 13 ] Landspitali, Dept Immunol, Reykjavik, Iceland Show more [ 14 ] Vilnius Univ, Fac Med, Vilnius, Lithuania Show more [ 15 ] Univ Coll, Paediat & Child Hlth, Cork, Ireland Show more [ 16 ] Charite Univ Med Berlin, Dept Paediat Pneumol & Immunol, Berlin, Germany Show more [ 17 ] Charite Univ Med Berlin, Inst Social Med Epidemiol & Hlth Econ, Berlin, Germany, Department for Infectious Disease Epidemiology; Robert Koch Institute; Berlin Germany, German Rheumatism Research Center; Berlin Germany, HTA Health Economics Strategy and Research; RTI International; Manchester UK, Department of Pediatric Pulmonology & Pediatric Allergology; University of Groningen, University Medical Center Groningen; Groningen The Netherlands, University Child Health; University of Southampton; Southampton Hampshire UK, Clinical Experimental Sciences; University of Southampton; Southampton Hampshire UK, Department of Paediatrics; Paediatric Hospital Bambino Gesù; Rome Italy, Department of Allergy and Clinical Immunology; 2nd Pediatric Clinic; National & Kapodistrian University of Athens; Athens Greece, Division of Infection Immunity & Respiratory Medicine; University of Manchester; Manchester UK, Alergia Infantil; Hospital Universitario La Paz; Madrid Spain, Department of Immunology, Rheumatology and Allergy; Medical University; Lodz Poland, Department of Immunology; Landspitali - The National University Hospital of Iceland; Reykjavik Iceland, Faculty of Medicine; Vilnius University; Vilnius Lithuania, Paediatrics and Child Health; University College; Cork Ireland, Department of Paediatric Pneumology and Immunology; Charité - Universitätsmedizin Berlin; Berlin Germany, Institute for Social Medicine, Epidemiology and Health Economics; Charité - Universitätsmedizin Berlin; Berlin Germany, Grabenhenrich, Linus B., Reich, Andreas, McBride, Doreen, Sprikkelman, Aline, Roberts, Graham, Grimshaw, Kate E. C., Fiocchi, Alessandro G., Saxoni-Papageorgiou, Photini, Papadopoulos, Nikolaos G., Fiandor, Ana, Quirce, Santiago, Kowalski, Marek L., Sigurdardottir, Sigurveig T., Dubakiene, Ruta, Hourihane, Jonathan O. B., Rosenfeld, Leonard, Niggemann, Bodo, Keil, Thomas, and Beyer, Kirsten
Abstract: To access publisher's full text version of this article click on the hyperlink below, BACKGROUND: Blinded food challenges are considered the current gold standard for the diagnosis of food allergies. We used data from a pan-European multicenter project to assess differences between study centers, aiming to identify the impact of subjective aspects for the interpretation of oral food challenges. METHODS: Nine study centers of the EuroPrevall birth cohort study about food allergy recruited 12 049 newborns and followed them for up to 30 months in regular intervals. Intensive training was conducted and every center visited to ensure similar handling of the protocols. Suspected food allergy was clinically evaluated by double-blind, placebo-controlled food challenges using a nine dose escalation protocol. The primary challenge outcomes based on physician's appraisal were compared to documented signs and symptoms. RESULTS: Of 839 challenges conducted, study centers confirmed food allergy in 15.6% to 53.6% of locally conducted challenges. Centers reported 0 to 16 positive placebo challenges. Worsening of eczema was the most common sign when challenged with placebo. Agreement between documented objective signs and the challenge outcome assigned by the physician was heterogeneous, with Cohen's kappa spanning from 0.42 to 0.84. CONCLUSIONS: These differences suggest that the comparison of food challenge outcomes between centers is difficult despite common protocols and training. We recommend detailed symptom assessment and documentation as well as objective sign-based challenge outcome algorithms to assure accuracy and comparability of blinded food challenges. Training and supervision of staff conducting food challenges is a mandatory component of reliable outcome data.

71. Using the Global Constraint Seeker for Learning Structured Constraint Models: A First Attempt

Author: TASC ; École nationale supérieure des Mines de Nantes (EM NANTES) ; École Nationale Supérieure des Mines - Nantes - École Nationale Supérieure des Mines - Nantes - Laboratoire d'Informatique de Nantes Atlantique (LINA) ; CNRS - Université de Nantes - École Nationale Supérieure des Mines - Nantes - CNRS - Université de Nantes, Cork Constraint Computation Centre (4C UCC) ; University College Cork, Beldiceanu, Nicolas, Simonis, Helmut, TASC ; École nationale supérieure des Mines de Nantes (EM NANTES) ; École Nationale Supérieure des Mines - Nantes - École Nationale Supérieure des Mines - Nantes - Laboratoire d'Informatique de Nantes Atlantique (LINA) ; CNRS - Université de Nantes - École Nationale Supérieure des Mines - Nantes - CNRS - Université de Nantes, Cork Constraint Computation Centre (4C UCC) ; University College Cork, Beldiceanu, Nicolas, and Simonis, Helmut
Abstract: International audience, Considering problems that have a strong internal structure, this paper shows how to generate constraint models from a set of positive, flat samples (i.e., solutions) without knowing a priori neither the constraint candidates, nor the way variables are shared within constraints. We describe two key contributions to building such a model generator: (1) First, learning is modeled as a bicriteria optimization problem over ranked constraint candidates returned by the Constraint Seeker, where we optimize both the compactness of the model, and the rank (or appropriateness) of the selected constraints. (2) Second, filtering out irrelevant candidate models is achieved by using meta data of the global constraint catalog that describe links between constraints. Some initial experiments on a proof-of-concept implementation show promising results.

72. A Constraint Seeker: Finding and Ranking Global Constraints from Examples

Author: TASC ; École nationale supérieure des Mines de Nantes (EM NANTES) ; École Nationale Supérieure des Mines - Nantes - École Nationale Supérieure des Mines - Nantes - Laboratoire d'Informatique de Nantes Atlantique (LINA) ; CNRS - Université de Nantes - École Nationale Supérieure des Mines - Nantes - CNRS - Université de Nantes, TASC (INRIA - LINA) ; CNRS - INRIA - Université de Nantes - École Nationale Supérieure des Mines - Nantes, Cork Constraint Computation Centre (4C UCC) ; University College Cork, Springer-Verlag, Beldiceanu, Nicolas, Simonis, Helmut, TASC ; École nationale supérieure des Mines de Nantes (EM NANTES) ; École Nationale Supérieure des Mines - Nantes - École Nationale Supérieure des Mines - Nantes - Laboratoire d'Informatique de Nantes Atlantique (LINA) ; CNRS - Université de Nantes - École Nationale Supérieure des Mines - Nantes - CNRS - Université de Nantes, TASC (INRIA - LINA) ; CNRS - INRIA - Université de Nantes - École Nationale Supérieure des Mines - Nantes, Cork Constraint Computation Centre (4C UCC) ; University College Cork, Springer-Verlag, Beldiceanu, Nicolas, and Simonis, Helmut
Abstract: International audience, In this paper we describe a Constraint Seeker application which provides a web interface to search for global constraints in the global constraint catalog, given positive and negative, fully instantiated (ground) examples. Based on the given instances the tool returns a ranked list of matching constraints, the rank indicating whether the constraint is likely to be the intended constraint of the user. We give some examples of use cases and generated output, describe the different elements of the search and ranking process, discuss the role of constraint programming in the different tools used, and provide evaluation results over the complete global constraint catalog. The Constraint Seeker is an example for the use of generic meta-data provided in the catalog to solve a specific problem.

73. A Model Seeker: Extracting Global Constraint Models from Positive Examples

Author: TASC ; École nationale supérieure des Mines de Nantes (EM NANTES) ; École Nationale Supérieure des Mines - Nantes - École Nationale Supérieure des Mines - Nantes - Laboratoire d'Informatique de Nantes Atlantique (LINA) ; CNRS - Université de Nantes - École Nationale Supérieure des Mines - Nantes - CNRS - Université de Nantes, TASC (INRIA - LINA) ; CNRS - INRIA - Université de Nantes - École Nationale Supérieure des Mines - Nantes, Cork Constraint Computation Centre (4C UCC) ; University College Cork, Springer-Verlag, Beldiceanu, Nicolas, Simonis, Helmut, TASC ; École nationale supérieure des Mines de Nantes (EM NANTES) ; École Nationale Supérieure des Mines - Nantes - École Nationale Supérieure des Mines - Nantes - Laboratoire d'Informatique de Nantes Atlantique (LINA) ; CNRS - Université de Nantes - École Nationale Supérieure des Mines - Nantes - CNRS - Université de Nantes, TASC (INRIA - LINA) ; CNRS - INRIA - Université de Nantes - École Nationale Supérieure des Mines - Nantes, Cork Constraint Computation Centre (4C UCC) ; University College Cork, Springer-Verlag, Beldiceanu, Nicolas, and Simonis, Helmut
Abstract: International audience, We describe a system which generates finite domain constraint models from positive example solutions, for highly structured problems. The system is based on the global constraint catalog, providing the library of constraints that can be used in modeling, and the Constraint Seeker tool, which finds a ranked list of matching constraints given one or more sample call patterns. We have tested the modeler with 230 examples, ranging from 4 to 6,500 variables, using between 1 and 7,000 samples. These examples come from a variety of domains, including puzzles, sports-scheduling, packing & placement, and design theory. When comparing against manually specified "canonical" models for the examples, we achieve a hit rate of 50\%, processing the complete benchmark set in less than one hour on a laptop. Surprisingly, in many cases the system finds usable candidate lists even when working with a single, positive example.

74. University College Cork

Author: University College Cork, UCC, University College Cork, and UCC
Abstract: Educational, Cork, Cork, NIVAL holds a file on this collegeSee also: 'Boole Library', Cork

75. Evidence of a range expansion in sunfish from 47 years of coastal sightings

Author: Lyashevska, Olga, Brophy, Deirdre, Wing, Steve, Johns, David G., Haberlin, Damien, Doyle, Thomas K., Marine and Freshwater Research Centre, Galway Mayo Institute of Technology, Galway, Ireland, Cape Clear Bird Observatory, Birdwatch Ireland, Wicklow, Ireland, The Marine Biological Association of the UK, Plymouth, UK, Science Foundation Ireland Research Centre for Energy, Climate and Marine, Environmental Research Centre, University College Cork, Cork, Ireland, School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland, and Open Access funding provided by the IReL Consortium. This research was supported by a grant from the Irish Environmental Protection Agency (Ecosystem tipping points: learning from the past to manage for the future, project code 2015-NC-MS-3).
Subjects: Ecology, Marine and Freshwater Research Centre, Jellyfish, Citizen science, Hurdle model, Aquatic Science, Dermochelys coriacea, Ecology, Evolution, Behavior and Systematics, Mola mola, Muggiaea atlantica
Abstract: Almost nothing is known about the historical abundance of the ocean sunfish. Yet as an ecologically and functionally important taxa, understanding changes in abundance may be a useful indicator of how our seas are responding to anthropogenic changes including overfishing and climate change. Within this context, sightings from a coastal bird observatory (51.26$$^\circ$$ ∘ N, 9.30$$^\circ$$ ∘ W) over a 47 year period (from April to October 1971–2017) provided the first long-term index of sunfish abundance. Using a general linear mixed effect model with a hurdle to deal with imperfect detectability and to model trends, a higher probability of detecting sunfish was found in the 1990s and 2000s. Continuous Plankton Recorder (CPR) phytoplankton color indices and the annual mean position of the 13 $$^{\circ }$$ ∘ C sea surface isotherm were significantly correlated with the probability of detecting sunfish. An increase in siphonophore abundance (as measured by the CPR) was also documented. However, this increase occurred 10–15 years after the sunfish increase and was not significantly correlated with sunfish abundance. Our results suggest that the observed increase in sunfish sightings is evidence of a range expansion because it was significantly correlated with the mean position of the 13 $$^{\circ }$$ ∘ C isotherm which moved northwards by over 200 km. Furthermore, the observed increase in sunfish occured 10 years before sunfish sightings are documented in Icelandic and Norwegian waters, and was concurrent with well-known range expansions for other fish species during the 1990s. This study demonstrates how sustained citizen science projects can provide unique insights on the historical abundance of this enigmatic species.
Published: 2022
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76. A Uniformly Convergent Galerkin Method on a Shishkin Mesh for a Convection-Diffusion Problem

Author: Stynes, Martin and O'Riordan, Eugene
Published: 1997
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77. Archaea, specific genetic traits, and development of improved bacterial live biotherapeutic products: another face of next-generation probiotics

Author: Matthieu Martineau, Paul W. O'Toole, Marie-Edith Arnal, Khaled Fadhlaoui, Paméla Camponova, Jean-François Brugère, Bernard Ollivier, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Chimie Interface Biologie pour l’Environnement, la Santé et la Toxicologie (CIBEST ), SYstèmes Moléculaires et nanoMatériaux pour l’Energie et la Santé (SYMMES), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Alimentary Pharmabiotic Centre (APC), Biosciences Institute (BSI), University College Cork (UCC)-University College Cork (UCC), and ANR-16-IDEX-0001,CAP 20-25,CAP 20-25(2016)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Genetic traits, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Gut flora, urologic and male genital diseases, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Applied Microbiology and Biotechnology, law.invention, chemistry.chemical_compound, Probiotic, Mice, law, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, 0303 health sciences, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], General Medicine, 3. Good health, Amino acid, Biological Therapy, Biochemistry, Cardiovascular Diseases, Biotechnology, Methanogenesis, Pyrrolysine, digestive system, 03 medical and health sciences, Methylamines, Human gut, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Humans, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], 030304 developmental biology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 030306 microbiology, Probiotics, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, biology.organism_classification, Archaea, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Diet, Gastrointestinal Microbiome, chemistry, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Metabolism, Inborn Errors, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Trimethylamine (TMA) and its oxide TMAO are important biomolecules involved in disease-associated processes in humans (e.g., trimethylaminuria and cardiovascular diseases). TMAO in plasma (pTMAO) stems from intestinal TMA, which is formed from various components of the diet in a complex interplay between diet, gut microbiota, and the human host. Most approaches to prevent the occurrence of such deleterious molecules focus on actions to interfere with gut microbiota metabolism to limit the synthesis of TMA. Some human gut archaea however use TMA as terminal electron acceptor for producing methane, thus indicating that intestinal TMA does not accumulate in some human subjects. Therefore, a rational alternative approach is to eliminate neo-synthesized intestinal TMA. This can be achieved through bioremediation of TMA by these peculiar methanogenic archaea, either by stimulating or providing them, leading to a novel kind of next-generation probiotics referred to as archaebiotics. Finally, specific components which are involved in this archaeal metabolism could also be used as intestinal TMA sequesters, facilitating TMA excretion along with stool. Referring to a standard pharmacological approach, these TMA traps could be synthesized ex vivo and then delivered into the human gut. Another approach is the engineering of known probiotic strain in order to metabolize TMA, i.e., live engineered biotherapeutic products. These alternatives would require, however, to take into account the necessity of synthesizing the 22nd amino acid pyrrolysine, i.e., some specificities of the genetics of TMA-consuming archaea. Here, we present an overview of these different strategies and recent advances in the field that will sustain such biotechnological developments. KEY POINTS: • Some autochthonous human archaea can use TMA for their essential metabolism, a methyl-dependent hydrogenotrophic methanogenesis. • They could therefore be used as next-generation probiotics for preventing some human diseases, especially cardiovascular diseases and trimethylaminuria. • Their genetic capacities can also be used to design live recombinant biotherapeutic products. • Encoding of the 22nd amino acid pyrrolysine is necessary for such alternative developments.
Published: 2020
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78. Sub-chronic toxicity of low concentrations of industrial volatile organic pollutants in vitro

Author: Heffron, James [Environmental Research Institute, University College Cork, Cork (Ireland) and Department of Biochemistry, University College Cork, Cork (Ireland)]
Published: 2007
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79. Impact of fluidized bed granulation on structure and functional properties of the agglomerates based on the durum wheat semolina

Author: Thierry Ruiz, Agnès Duri, Denis Ring, Bettina Bellocq, Kevin Cronin, Bernard Cuq, Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Department of Process & Chemical Engineering, University College Cork, ANR ALID 2013, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Bellocq, Bettina, Cronin, Kevin, Ring, Denis, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University College Cork (UCC), and ANR-13-ALID-0002,Dur-Dur,Innovations agronomiques, techniques et organisationnelles au service de la DURabilité de la filière blé DUR(2013)
Subjects: Yield (engineering), Materials science, Ingénierie des aliments, agglomération humide, Condensed Matter, 02 engineering and technology, Industrial and Manufacturing Engineering, Hydrotextural diagramm, Fluidized bed, fluidized bed, Granulation, 020401 chemical engineering, [SDV.IDA]Life Sciences [q-bio]/Food engineering, analyse de texture, Hydrotextural diagram, Food engineering, Agglomeration, Couscous grains structure, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], 0204 chemical engineering, Water content, couscous, Matière Condensée, 2. Zero hunger, Economies of agglomeration, General Chemistry, 021001 nanoscience & nanotechnology, Shear (sheet metal), Chemical engineering, blé dur, Agglomerate, hard wheat, lit fluidisé, 0210 nano-technology, Fluidized bed granulation, Food Science
Abstract: The granulation step determines the production yield and the final characteristics of the agglomerated couscous grains of durum wheat. The objective of the present work was to explore the capability of the fluidised bed technology to produce agglomerates of durum wheat semolina. The impacts of different processing conditions have been investigated on the structure and functional properties of the agglomerates. The size, shape, water content, compactness, and mechanical strength of the granules were measured. The fluidized bed agglomeration process has been found to produce agglomerates of durum wheat with different attributes compared to those produced by granulation using the low shear mixers. The results were discussed in regard to the hydro-textural approach, in order to get a better understanding of the mechanisms and relationships between process, structure, and properties. Two major agglomeration mechanisms contribute to the growth of the wet agglomerates: a fractal-structuring process followed by a phenomenon of densification. By studying the evolution of the compactness, diameter and water content, it was demonstrated that inter granular arrangements led to an expansion followed by a densification of the wet agglomerates. A relationship was proposed to describe the growth using a fluidized bed of the wet agglomerates of durum wheat semolina.
Published: 2018
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80. Development of a core outcome set for medication review in older patients with multimorbidity and polypharmacy: a study protocol

Author: Anne Spinewine, Jean-Baptiste Beuscart, Olivia Dalleur, Wilma Knol, Shane Cullinan, Stefanie Thevelin, Claudio Schneider, Benoît Boland, Nicolas Rodondi, Denis O'Mahony, Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Université Catholique de Louvain = Catholic University of Louvain (UCL), Cliniques Universitaires Saint-Luc [Bruxelles], University Medical Center [Utrecht], Royal College of Surgeons in Ireland (RCSI), Bern University Hospital [Berne] (Inselspital), University College Cork (UCC), University of Bern, Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille, CHU Lille, Université de Lille, Université Catholique de Louvain = Catholic University of Louvain [UCL], METRICS : Evaluation des technologies de santé et des pratiques médicales - ULR 2694, Evaluation des technologies de santé et des pratiques médicales - ULR 2694 [METRICS], Royal College of Surgeons in Ireland [RCSI], Bern University Hospital [Berne] [Inselspital], University College Cork [UCC], UCL - SSS/LDRI - Louvain Drug Research Institute, UCL - SSS/IRSS - Institut de recherche santé et société, UCL - (MGD) Département de pharmacie, UCL - (SLuc) Département de pharmacie, and UCL - (SLuc) Service de gériatrie
Subjects: Research design, Delphi Technique, [SDV]Life Sciences [q-bio], Delphi method, 030204 cardiovascular system & hematology, 0302 clinical medicine, Surveys and Questionnaires, Health care, 030212 general & internal medicine, 610 Medicine & health, Mesh:Aged, Clinical Trials as Topic, General Medicine, Mesh:Delphi Technique, 3. Good health, Systematic review, Research Design, 360 Social problems & social services, Mesh:Surveys and Questionnaires, medicine.medical_specialty, multimorbidity, Medication Therapy Management, Mesh:Clinical Trials as Topic/standards, Mesh:Research Design, 03 medical and health sciences, Study protocol, Medication therapy management, Mesh:Polypharmacy, medicine, Humans, polypharmacy, Aged, Mesh:Multimorbidity, Protocol (science), Polypharmacy, business.industry, RC952-954.6, Multimorbidity, Core outcome set, core outcome set, study protocol, Mesh:Medication Therapy Management/standards, Clinical trial, Mesh:Humans, Geriatrics, Clinical Interventions in Aging, Family medicine, Geriatrics and Gerontology, business
Abstract: Jean-Baptiste Beuscart,1 Olivia Dalleur,1 Benoit Boland,2 Stefanie Thevelin,1 Wilma Knol,3 Shane Cullinan,4 Claudio Schneider,5 Denis O’Mahony,6 Nicolas Rodondi,4,7 Anne Spinewine1,8 1Université catholique de Louvain, Louvain Drug Research Institute, Clinical Pharmacy Research Group, Brussels, Belgium; 2Geriatric Medicine, Cliniques universitaires Saint-Luc, Brussels, Université catholique de Louvain, Belgium; 3Department of Geriatric Medicine and Expertise Centre Pharmacotherapy in Old Persons (EPHOR), University Medical Centre Utrecht, Netherlands; 4School of Pharmacy, Royal College of Surgeons in Ireland, Dublin, Ireland; 5Department of General Internal Medicine, Bern University Hospital, Bern, Switzerland; 6Department of Medicine (Geriatrics), University College Cork, Cork, Ireland; 7Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerland; 8Université catholique de Louvain, CHU UCL Namur, Pharmacy Department, Yvoir, Belgium Background: Medication review has been advocated to address the challenge of polypharmacy in older patients, yet there is no consensus on how best to evaluate its efficacy. Heterogeneity of outcomes reported in clinical trials can hinder the comparison of clinical trial findings in systematic reviews. Moreover, the outcomes that matter most to older patients might be under-reported or disregarded altogether. A core outcome set can address this issue as it defines a minimum set of outcomes that should be reported in all clinical trials in any particular field of research. As part of the European Commission-funded project, called OPtimising thERapy to prevent Avoidable hospital admissions in the Multimorbid elderly, this paper describes the methods used to develop a core outcome set for clinical trials of medication review in older patients with multimorbidity. Methods/design: The study was designed in several steps. First, a systematic review established which outcomes were measured in published and ongoing clinical trials of medication review in older patients. Second, we undertook semistructured interviews with older patients and carers aimed at identifying additional relevant outcomes. Then, a multilanguage European Delphi survey adapted to older patients was designed. The international Delphi survey was conducted with older patients, health care professionals, researchers, and clinical experts in geriatric pharmacotherapy to validate outcomes to be included in the core outcome set. Consensus meetings were conducted to validate the results. Discussion: We present the method for developing a core outcome set for medication review in older patients with multimorbidity. This study protocol could be used as a basis to develop core outcome sets in other fields of geriatric research. Keywords: core outcome set, study protocol, polypharmacy, multimorbidity
Published: 2017
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81. Functional carbohydrate binding modules identified in evolved dits from siphophages infecting various Gram-positive bacteria

Author: Hayes, Stephen, Vincentelli, Renaud, Mahony, Jennifer, Nauta, Arjen, Ramond, Laurie, Lugli, Gabriele, Ventura, Marco, Van Sinderen, Douwe, Cambillau, Christian, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), School of Microbiology, University College Cork (UCC), FrieslandCampina, Università degli studi di Parma = University of Parma (UNIPR), Alimentary Pharmabiot Ctr, Biosci Inst, Dept Microbiol, Università degli studi di Parma [Parme, Italie], University College Cork, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), and University of Parma = Università degli studi di Parma [Parme, Italie]
Subjects: Models, Molecular, Phage-host interactions, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Protein Conformation, Carbohydrates, Virion, Distal tail protein, Viral Tail Proteins, Siphoviridae, Lactococcus lactis, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Carbohydrate binding module, Receptor-binding protein, Bacteriophage, Protein Binding
Abstract: International audience; With increasing numbers of 3D structures of bacteriophage components, combined with powerful in silico predictive tools, it has become possible to decipher the structural assembly and associated functionality of phage adhesion devices. Recently, decorations have been reported in the tail and neck passage structures of members of the so-called 936 group of lactococcal siphophages. In the current report, using bioinformatic analysis we identified a conserved carbohydrate binding module (CBM) among many of the virion baseplate Dit components, in addition to the CBM present in the 'classical' receptor binding proteins (RBPs). We observed that, within these so-called 'evolved' Dit proteins, the identified CBMs have structurally conserved folds, yet can be grouped into four distinct classes. We expressed such modules in fusion with GFP, and demonstrated their binding capability to their specific host using fluorescent binding assays with confocal microscopy. We detected evolved Dits in several phages infecting various Gram-positive bacterial species, including mycobacteria. The omnipresence of CBM domains in siphophages indicates their auxiliary role in infection, as they can assist in the specific recognition of and attachment to their host, thus ensuring a highly efficient and specific phage-host adhesion process as a prelude to DNA injection.
Published: 2018
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82. A Cross-Sectional Analysis of Body Composition Among Healthy Elderly From the European NU-AGE Study: Sex and Country Specific Features

Author: Aurelia Santoro, Alberto Bazzocchi, Giulia Guidarelli, Rita Ostan, Enrico Giampieri, Daniele Mercatelli, Maria Scurti, Agnes Berendsen, Olga Surala, Amy Jennings, Nathalie Meunier, Elodie Caumon, Rachel Gillings, Fawzi Kadi, Frederic Capel, Kevin D. Cashman, Barbara Pietruszka, Edith J. M. Feskens, Lisette C. P. G. M. De Groot, Giuseppe Battista, Stefano Salvioli, Claudio Franceschi, Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Alma Mater Studiorum, University of Bologna, Centro Interdipartimentale « L. Galvani» (CIG), Istituto Ortopedico Rizzoli di Bologna, Department of Experimental, Diagnostic and Specialty Medicine, Institute of Neurological Sciences of Bologna IRCCS, Division of Human Nutrition and Health, Wageningen University and Research Center (WUR), Department of Human Nutrition, Faculty of Life Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Norwich Medical School, University of East Anglia, Centre Hospitalier Universitaire de Clermont-Ferrand, Örebro University Hospital [Örebro, Sweden], Örebro University, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Cork Centre for Vitamin D and Nutrition Research, University College Cork, European Union's Seventh Framework Program 266486, Santoro, A., Santoro A, Bazzocchi A, Guidarelli G, Ostan R, Giampieri E, Mercatelli D, Scurti M, Berendsen A, Surala O, Jennings A, Meunier N, Caumon E, Gillings R, Kadi F, Capel F, Cashman KD, Pietruszka B, Feskens EJM, De Groot LCPGM, Battista G, Salvioli S, Franceschi C., Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Wageningen University and Research [Wageningen] (WUR), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of East Anglia [Norwich] (UEA), CHU Clermont-Ferrand, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), University College Cork (UCC), and European Project: 266486,EC:FP7:KBBE,FP7-KBBE-2010-4,NU-AGE(2011)
Subjects: 0301 basic medicine, Fysiologi, Cross-sectional study, Physiology, Disease cluster, Body composition, elderly, lcsh:Physiology, 03 medical and health sciences, 0302 clinical medicine, Elderly, Physiology (medical), Diabetes mellitus, fat, medicine, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], sex, Mass index, Physiologie, Original Research, VLAG, Bone mineral, Global Nutrition, DXA, Wereldvoeding, body composition, Fat mass, lcsh:QP1-981, business.industry, DXA (Dual-energy X-ray Absorptiometry), Lean mass, Healthy elderly, medicine.disease, Obesity, body composition, DXA, elderly, sex, Europe, fat, lean and bone mass, 3. Good health, Bone mass, Europe, 030104 developmental biology, Fat, Lean body mass, lean and bone mass, Sex, Lean, business, 030217 neurology & neurosurgery, Demography
Abstract: Body composition (BC) is an emerging important factor for the characterization of metabolic status. The assessment of BC has been studied in various populations and diseases such as obesity, diabetes, endocrine diseases as well as physiological and paraphysiological conditions such as growth and aging processes, and physical training. A gold standard technique for the assessment of human BC at molecular level is represented by dual-energy X-ray absorptiometry (DXA), which is able to precisely assess the body mass (and areal bone mineral density-aBMD) on a regional and whole-body basis. For the first time, within the framework of the NU-AGE project, BC has been assessed by means of a whole-body DXA scan in 1121 sex-balanced free-living, apparently healthy older adults aged 65-79 years enrolled in 5 European countries (Italy, France, United Kingdom, Netherlands, and Poland). The aim of this analysis is to provide a complete profile of BC in healthy elderly participants from five European countries and to investigate country- and sex-related differences by state-of-the-art DXA technology. To compare BC data collected in different centers, specific indexes and ratios have been used. Non-parametric statistical tests showed sex-specific significant differences in certain BC parameters. In particular, women have higher fat mass (FM) (Fat/Lean mass ratio: by 67%, p < 2.2e-16) and lower lean mass (Lean Mass index: by -18%, p < 2.2e-16) than men. On the other hand, men have higher android FM than women (Android/gynoid FM ratio: by 56%, p < 2.2e-16). Interesting differences also emerged among countries. Polish elderly have higher FM (Fat/Lean mass ratio: by 52%, p < 2.2e-16) and lower lean mass (Skeletal Mass index: by -23%, p < 2.2e-16) than elderly from the other four countries. At variance, French elderly show lower FM (Fat/Lean mass ratio: by -34%, p < 2.2e-16) and higher lean mass (Skeletal Mass index: by 18%, p < 2.2e-16). Moreover, five BC profiles in women and six in men have been identified by a cluster analysis based on BC parameters. Finally, these data can serve as reference for normative average and variability of BC in the elderly populations across Europe.
Published: 2018
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83. Multiscale in modelling and validation for solar photovoltaics

Author: Witold Jacak, Emmanuel Stratakis, J. C. Rimada, Hele Savin, Efrat Lifshitz, Mimoza Ristova, Mateja Hočevar, Radovan Kopecek, Blas Garrido, M. J. M. Gomes, Mircea Guina, Konstantinos Petridis, Alessio Gagliardi, David Fuertes Marrón, Ivana Capan, Jacky Even, Jaroslav Zadny, Pavel Tománek, V. Donchev, Stefan Birner, Janne Halme, Zoe Amin-Akhlaghi, Fatma Yuksel, Frederic Cortes Juan, Ahmed Neijm, Lejo k. Joseph, Søren Madsen, Abdurrahman Şengül, Marija Drev, Kristian Berland, Jose G. F. Coutinho, Knut Deppert, Diego Alonso-Álvarez, José Silva, Lucjan Jacak, Georg Pucker, Marco Califano, Violetta Gianneta, Nicholas J. Ekins-Daukes, Nikola Bednar, Urs Aeberhard, Shuxia Tao, Spyridon Kassavetis, Rasit Turan, Jelena Radovanović, Katarzyna Kluczyk, Ullrich Steiner, Ivana Savic, Maria E. Messing, Victor Neto, Stanko Tomić, Neil Beattie, Shengda Wang, Androula G. Nassiopoulou, Antonio Martí Vega, Denis Mencaraglia, M. Sendova-Vassileva, Ákos Nemcsics, Felipe Murphy Armando, Boukje Ehlen, Jean-François Guillemoles, Matthias Auf der Maur, James P. Connolly, Laurent Pedesseau, Clas Persson, Christin David, Lacramioara Popescu, Bostjan Cerne, N. Adamovic, Jean-Louis Lazzari, JM José Maria Ulloa, Urša Opara Krašovec, Irinela Chilibon, Jan Storch, Zoran Jakšić, Antti Tukiainen, Tareq Abu Hamed, Martin Loncaric, Laurentiu Fara, V. Kazukauskas, Jean-Paul Kleider, Javad Zarbakhsh, Dead Sea-Arava Science Center (DSASC), Institut für Energie- und Klimaforschung - Photovoltaik (IEK-5), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, Imperial College London, ZAMSTEC − Science, Technology and Engineering Consulting, Università degli Studi di Roma Tor Vergata [Roma], University of Northumbria at Newcastle [United Kingdom], University of Leeds, Rudjer Boskovic Institute [Zagreb], Laboratoire Génie électrique et électronique de Paris (GeePs), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Universitat Politècnica de València (UPV), Lund University [Lund], Institut des Fonctions Optiques pour les Technologies de l'informatiON (Institut FOTON), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École Nationale Supérieure des Sciences Appliquées et de Technologie (ENSSAT)-Centre National de la Recherche Scientifique (CNRS), University Politehnica of Bucharest [Romania] (UPB), Universidad Politécnica de Madrid (UPM), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), National Center for Scientific Research 'Demokritos' (NCSR), Centre of Physics of the University of Minho (CFUM), Institut de Recherche et Développement sur l'Energie Photovoltaïque (IRDEP), Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-EDF R&D (EDF R&D), EDF (EDF)-EDF (EDF), Tampere University of Technology [Tampere] (TUT), Aalto University, University of Ljubljana, Wroclaw University of Science and Technology, University of Belgrade [Belgrade], Aristotle University of Thessaloniki, Vilnius University [Vilnius], Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Aarhus University [Aarhus], University College Cork (UCC), Óbuda University [Budapest], Universidade de Aveiro, University of Oslo (UiO), Technological Educational Institute of Crete, Fondazione Bruno Kessler [Trento, Italy] (FBK), University of Havana (Universidad de la Habana) (UH), Ss. Cyril and Methodius University in Skopje (UKIM), Tyndall National Institute [Cork], Zonguldak Bülent Ecevit University (BEU), Universidade de Taubaté (UNITAU), Cavendish Laboratory, University of Cambridge [UK] (CAM), Institute of Chemical Process Fundamentals of the ASCR, Czech Republic, Foundation for Research and Technology - Hellas (FORTH), Eindhoven University of Technology [Eindhoven] (TU/e), Brno University of Technology [Brno] (BUT), University of Salford, Middle East Technical University [Ankara] (METU), Gebze Technical University, Czech Academy of Sciences [Prague] (CAS), Carinthia University of Applied Sciences, MP1406, European Cooperation in Science and Technology, Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École Nationale Supérieure des Sciences Appliquées et de Technologie (ENSSAT)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), EDF R&D (EDF R&D), EDF (EDF)-EDF (EDF)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Ss. Cyril and Methodius University in Skopje, Universidade do Minho, Dead Sea and Arava Science Center, Vienna University of Technology, Forschungszentrum Jülich, University of Rome Tor Vergata, Northumbria University, University of Oslo, nextnano GmbH, Rudjer Boskovic Institute, ZEL-EN d.o.o., National Institute of Research and Development for Optoelectronics, Université Paris-Saclay, Polytechnic University of Valencia, University of Aveiro, Madrid Institute for Advanced Studies in Nanoscience, Lund University, Sofia University St. Kliment Ohridski, Trimo Grp, Boukje.com Consulting, Centre National de la Recherche Scientifique (CNRS), University Politehnica of Bucharest, Technical University of Munich, University of Barcelona, Institute of Nanoscience and Nanotechnology, The University of Tokyo, Tampere University of Technology, Department of Applied Physics, Wrocław University of Science and Technology, University of Belgrade, ISC Konstanz eV, Vilnius University, Aix-Marseille Université, Technion-Israel Institute of Technology, Aarhus University, Polytechnic University of Madrid, University College Cork, Demokritos National Centre for Scientific Research, Silvaco Europe Ltd, Óbuda University, Hellenic Mediterranean University, Fondazione Bruno Kessler, University of Havana, SS Cyril and Methodius University in Skopje, Department of Electronics and Nanoengineering, Bulgarian Academy of Sciences, Bulent Ecevit University, Adolphe Merkle Institute, Czech Academy of Sciences, Foundation for Research and Technology - Hellas, Eindhoven University of Technology, Brno University of Technology, Middle East Technical University, Aalto-yliopisto, Zonguldak Bülent Ecevit Üniversitesi, Center for Computational Energy Research, and Computational Materials Physics
Subjects: Nano structures, lcsh:TJ807-830, Modelling and validation, 02 engineering and technology, semiconductors, 01 natural sciences, 7. Clean energy, Settore ING-INF/01 - Elettronica, Environmental footprints, law.invention, [SPI.MAT]Engineering Sciences [physics]/Materials, Semiconductor materials, WAVE BASIS-SET, law, Photovoltaics, CARRIER MULTIPLICATION, Multi-scale simulation, multi-scale modelling, Telecomunicaciones, COLLOIDAL QUANTUM DOTS, device simulation, NANOMETER-SCALE, Photovoltaic cells, Physics, Photovoltaic system, Nanostructured materials, Renewable energy resources, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Multiscale modeling, Electronic, Optical and Magnetic Materials, Characterization (materials science), Renewable energy, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, ELECTRONIC-STRUCTURE, SDG 12 – Verantwoordelijke consumptie en productie, Energías Renovables, Physical Sciences, TIGHT-BINDING, Systems engineering, Electrónica, 0210 nano-technology, NEAR-FIELD, solar cells, third generation photovoltaics, nano structures, Solar cells, J500, Ciências Naturais::Ciências Físicas, F300, H600, Third generation photovoltaics, ta221, Renewable energy source, Ciências Físicas [Ciências Naturais], lcsh:Renewable energy sources, GREENS-FUNCTION, Solar power generation, Different length scale, Physics, Applied, OPTICAL-RESPONSE, 0103 physical sciences, Solar cell, SDG 7 - Affordable and Clean Energy, Electrical and Electronic Engineering, 010306 general physics, Device simulations, Ecological footprint, Science & Technology, ta114, Renewable Energy, Sustainability and the Environment, business.industry, TOTAL-ENERGY CALCULATIONS, [SPI.NRJ]Engineering Sciences [physics]/Electric power, Environmental technology, Nanostructures, Multiple exciton generation, 13. Climate action, Conversion efficiency, business, SDG 12 - Responsible Consumption and Production, SDG 7 – Betaalbare en schone energie
Abstract: Photovoltaics is amongst the most important technologies for renewable energy sources, and plays a key role in the development of a society with a smaller environmental footprint. Key parameters for solar cells are their energy conversion efficiency, their operating lifetime, and the cost of the energy obtained from a photovoltaic system compared to other sources. The optimization of these aspects involves the exploitation of new materials and development of novel solar cell concepts and designs. Both theoretical modeling and characterization of such devices require a comprehensive view including all scales from the atomic to the macroscopic and industrial scale. The different length scales of the electronic and optical degrees of freedoms specifically lead to an intrinsic need for multiscale simulation, which is accentuated in many advanced photovoltaics concepts including nanostructured regions. Therefore, multiscale modeling has found particular interest in the photovoltaics community, as a tool to advance the field beyond its current limits. In this article, we review the field of multiscale techniques applied to photovoltaics, and we discuss opportunities and remaining challenges. © T. Abu Hamed et al., published by EDP Sciences, 2018., European Cooperation in Science and Technology: MP1406, The authors are grateful for the financial support by the COST Action MP1406 “MultiscaleSolar.”
Published: 2018
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84. A Decade of Streptococcus thermophilus Phage Evolution in an Irish Dairy Plant

Author: Lavelle, Katherine, Murphy, James, Fitzgerald, Brian, Lugli, Gabriele Andrea, Zomer, Aldert, Neve, Horst, Ventura, Marco, Franz, Charles M, Cambillau, Christian, van Sinderen, Douwe, Mahony, Jennifer, LS Klinisch Onderzoek Wagenaar, dI&I I&I-4, University College Cork (UCC), University of Melbourne, University of Limerick (UL), Max Rubner-Institute, Dept Microbiol & Biotechnol, Max Rubner Inst, Università degli studi di Parma [Parme, Italie], Department of Safety and Quality of Fruit and Vegetables, Federal Research Institute for Nutrition and Food, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Alimentary Pharmabiot Ctr, Biosci Inst, Dept Microbiol, University College Cork, School of Microbiology, University of Parma = Università degli studi di Parma [Parme, Italie], Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Università degli studi di Parma = University of Parma (UNIPR), LS Klinisch Onderzoek Wagenaar, and dI&I I&I-4
Subjects: 0301 basic medicine, Streptococcus thermophilus, Streptococcus Phages, Genotype, Cultured Milk Products, viruses, 030106 microbiology, Lysin, Genomics, receptor binding protein, Applied Microbiology and Biotechnology, Carbohydrate receptor, Host Specificity, Bacteriophage, Viral Proteins, 03 medical and health sciences, bacteriophage, Lysogenic cycle, genomics, Evolutionary and Genomic Microbiology, Dairy industry, Lysogeny, Phylogeny, 2. Zero hunger, Genetics, Receptor binding protein, Ecology, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Streptococcus, biology.organism_classification, Biological Evolution, Dairying, dairy industry, Fermentation, Bacterial virus, Ireland, Bacteria, Food Science, Biotechnology
Abstract: Phages of Streptococcus thermophilus present a major threat to the production of many fermented dairy products. To date, only a few studies have assessed the biodiversity of S. thermophilus phages in dairy fermentations. In order to develop strategies to limit phage predation in this important industrial environment, it is imperative that such studies are undertaken and that phage-host interactions of this species are better defined. The present study investigated the biodiversity and evolution of phages within an Irish dairy fermentation facility over an 11-year period. This resulted in the isolation of 17 genetically distinct phages, all of which belong to the so-called cos group. The evolution of phages within the factory appears to be influenced by phages from other dairy plants introduced into the factory for whey protein powder production. Modular exchange, primarily within the regions encoding lysogeny and replication functions, was the major observation among the phages isolated between 2006 and 2016. Furthermore, the genotype of the first isolate in 2006 was observed continuously across the following decade, highlighting the ability of these phages to prevail in the factory setting for extended periods of time. The proteins responsible for host recognition were analyzed, and carbohydrate-binding domains (CBDs) were identified in the distal tail (Dit), the baseplate proteins, and the Tail-associated lysin (Tal) variable regions (VR1 and VR2) of many isolates. This supports the notion that S. thermophilus phages recognize a carbohydrate receptor on the cell surface of their host. IMPORTANCE Dairy fermentations are consistently threatened by the presence of bacterial viruses (bacteriophages or phages), which may lead to a reduction in acidification rates or even complete loss of the fermentate. These phages may persist in factories for long periods of time. The objective of the current study was to monitor the progression of phages infecting the dairy bacterium Streptococcus thermophilus over a period of 11 years in an Irish dairy plant so as to understand how these phages evolve. A focused analysis of the genomic region that encodes host recognition functions highlighted that the associated proteins harbor a variety of carbohydrate-binding domains, which corroborates the notion that phages of S. thermophilus recognize carbohydrate receptors at the initial stages of the phage cycle.
Published: 2018
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85. Viromes of one year old infants reveal the impact of birth mode on microbiome diversity

Author: Feargal J. Ryan, Angela McCann, Paul Ross, Colin Hill, Susan Mills, Catherine Stanton, Tony Blake, Stephen R. Stockdale, C. Anthony Ryan, Marion Dalmasso, University College Cork (UCC), Aliments Bioprocédés Toxicologie Environnements (ABTE), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Alimentary Pharmabiotic Centre (APC), Biosciences Institute (BSI), and University College Cork (UCC)-University College Cork (UCC)
Subjects: 0301 basic medicine, medicine.medical_treatment, Physiology, lcsh:Medicine, Gut flora, Microbiology, Pediatrics, General Biochemistry, Genetics and Molecular Biology, Birth mode, 03 medical and health sciences, Virology, medicine, Human virome, Caesarean section, Microbiome, Bacteriophage, biology, Transmission (medicine), Virome, General Neuroscience, lcsh:R, Infant, General Medicine, crAssphage, biology.organism_classification, 030104 developmental biology, Metagenomics, Cohort, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, General Agricultural and Biological Sciences
Abstract: International audience; Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssphage is acquired early in life, both in this cohort and two others, although no difference in birth mode is detected. A previous study has shown that bacterial OTU's (operational taxonomic units) identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results indicate that vertical transmission of viral communities from mother to child may play a role in shaping the early life microbiome, and that birth mode should be considered when studying the early life gut virome.
Published: 2018
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86. Impact of functional properties and release kinetics on antioxidant activity of biopolymer active films and coatings

Author: Cadhla Tanner, Thomas Karbowiak, Frédéric Debeaufort, Philippe Cayot, Nasreddine Benbettaïeb, Procédés Alimentaires et Microbiologiques [Dijon] ( PAM ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Département Génie biologique [IUT de Dijon/Auxerre - université de Bourgogne], Institut Universitaire de Technologie - IUT Dijon/Auxerre, Université de Bourgogne ( UB ) -Université de Bourgogne ( UB ), Department of Microbiology and Environmental Research Institute (Cork, Ireland), University College Cork ( UCC ), Procédés Alimentaires et Microbiologiques [Dijon] (PAM), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut Universitaire de Technologie - Dijon/Auxerre (IUT Dijon), Université de Bourgogne (UB)-Université de Bourgogne (UB), and University College Cork (UCC)
Subjects: Antioxidant, food.ingredient, Coumaric Acids, DPPH, [SDV]Life Sciences [q-bio], medicine.medical_treatment, Kinetics, Chitosan-fish gelatin film, engineering.material, Gelatin, Antioxidants, Permeability, Analytical Chemistry, Ferulic acid, chemistry.chemical_compound, Functional and structural properties, Biopolymers, Caffeic Acids, 0404 agricultural biotechnology, food, Tensile Strength, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Fish Products, Caffeic acid, medicine, Organic chemistry, Chitosan, Free radical scavenging activity, [ SDV ] Life Sciences [q-bio], Release properties, [ SDV.IDA ] Life Sciences [q-bio]/Food engineering, 04 agricultural and veterinary sciences, General Medicine, Phenylethyl Alcohol, 040401 food science, Tyrosol, chemistry, engineering, Active packaging, Biopolymer, Food Science, Nuclear chemistry
Abstract: International audience; This work deals with the study of the release kinetics of some natural antioxidants (ferulic acid, caffeic acid and tyrosol) from chitosan-fish gelatin edible films immersed ethanol at 96%, as well as the kinetics of their antioxidant activity using the DPPH assay. The aim was to determine how film functional properties influence the release kinetic and antioxidant activity. The addition of antioxidants to chitosan-fish gelatin matrix decreased the water vapour permeability by more than 30%. The tensile strength (TS) increased up to 50% after the incorporation of antioxidants. Some molecular interactions between polymer chains and antioxidants were confirmed by FTIR where spectra displayed a shift of the amide-III peak. Films containing caffeic acid or a caffeic-ferulic acid mixture exhibited the highest radical scavenging activity, leading to a 90% antioxidant activity at equilibrium but the release rate controlled the efficacy of the system.
Published: 2018
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87. Minimum Information about a Biosynthetic Gene cluster

Author: Patrick Caffrey, Renzo Kottmann, Eriko Takano, Sean Doyle, Axel A. Brakhage, Matthew Cummings, Juan Pablo Gomez-Escribano, Yvonne Mast, Ryan F. Seipke, Rob Lavigne, Markus Nett, Hans-Wilhelm Nützmann, Jan Claesen, David H. Sherman, Daniel Petras, Pablo Cruz-Morales, Carl J. Balibar, Anne Osbourn, Oscar P. Kuipers, Leonilde M. Moreira, Xinyu Liu, Marcia S. Osburne, Bohdan Ostash, David P. Fewer, Changsheng Zhang, Pelin Yilmaz, Mohamed S. Donia, Anja Greule, Hyun Uk Kim, Nicholas J. Tobias, Frank Oliver Glöckner, Christoph Geiger, Chia Y. Lee, William H. Gerwick, Philipp Wiemann, Bertolt Gust, Susan E. Jensen, Wilfred A. van der Donk, Jan Kormanec, Ben Shen, Christopher M. Thomas, Jason Micklefield, Srikanth Duddela, R. Cameron Coates, René De Mot, Anthony S. Haines, Neha Garg, Guohui Pan, Roderich D. Süssmuth, Hyung Jin Kwon, Jonathan D. Walton, Lena Gerwick, Jörn Piel, Monika Ehling-Schulz, Zhenhua Tian, Jonathan L. Klassen, Xiaohui Yan, Emily A. Monroe, Yunchang Xie, Russell J. Cox, Keishi Ishida, Grace Yim, Stefano Donadio, Nadine Ziemert, Yuta Tsunematsu, Matthew L. Hillwig, Miroslav Petricek, Sylvie Lautru, Tilmann Weber, Andrew W. Truman, Rainer Breitling, Peter Kötter, Nikos C. Kyrpides, Stephanie Düsterhus, Christian Hertweck, Hideaki Oikawa, Sean F. Brady, Christopher T. Walsh, Adam C. Jones, Marcus A. Moore, Bradley S. Moore, Barrie Wilkinson, Simone M. Mantovani, Nathan A. Moss, Elizabeth E. Wyckoff, Emily P. Balskus, Kapil Tahlan, Fengan Yu, Monica Höfte, Jos M. Raaijmakers, Taifo Mahmud, Yit-Heng Chooi, Yi Tang, Andreas Bechthold, Douglas A. Mitchell, Joanne M. Willey, Helge B. Bode, John B. Biggins, Margherita Sosio, Yi-Qiang Cheng, Carmen Méndez, Leonard Kaysser, Joleen Masschelein, Daniel Krug, Federico Rosconi, Marnix H. Medema, Kaarina Sivonen, Tomohisa Kuzuyama, Mikko Metsä-Ketelä, Esther K. Schmitt, Carsten Kegler, Andriy Luzhetskyy, Gilles P. van Wezel, Bai Linquan, Kai Blin, Jens Nielsen, Bertrand Aigle, Amrita Pati, Harald Gross, Muriel Viaud, Pieter C. Dorrestein, Carla S. Jones, Michael A. Fischbach, Shelley M. Payne, Zhe Rui, Gerard D. Wright, Wen Liu, Alexey V. Melnik, Barry Scott, Brett A. Neilan, Nancy P. Keller, Rainer Borriss, Katrin Jungmann, Michalis Hadjithomas, Evi Stegmann, Daniel J. Edwards, F. Jerry Reen, Alexander Kristian Apel, Wolfgang Wohlleben, Michael J. Smanski, Leonard Katz, Fergal O'Gara, Eric J. N. Helfrich, Sergey B. Zotchev, Olivier Ploux, Arnold J. M. Driessen, Rolf Müller, Jean-Luc Pernodet, K. D. Entian, José A. Salas, Irene de Bruijn, Francisco Barona-Gómez, Jianhua Ju, Jon Clardy, Molecular Microbiology, Molecular Genetics, Jacobs University [Bremen], Microbial genomics and bioinformatics research group, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Max-Planck-Gesellschaft, Atmospheric Chemistry Observations and Modeling Laboratory (ACOML), National Center for Atmospheric Research [Boulder] (NCAR), Department of Food and Environmental Sciences, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Collaborative Mass Spectrometry Innovation Center, University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Heilongjiang Institute of Science and Technology, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Merck Stiftungsprofessur fûr Molekulare Biotechnologie Fachbereich Biowissenscharten, Goethe-University Frankfurt am Main, Department of Opto-Mechatronics Engineering and Cogno-Mechatronics Engineering, Pusan National University, University of Liverpool, College of Computer Science and Technology [Zhejiang] (Zhejiang University), University of Florida [Gainesville] (UF), School of Management, University of Science and Technology of China [Hefei] (USTC), State Key Laboratory of Nuclear Physics and Technology (SKL-NPT), Peking University [Beijing], Massachusetts Institute of Technology (MIT), Memorial Sloane Kettering Cancer Center [New York], South China Sea Institute of Oceanology, Chinese Academy of Sciences [Beijing] (CAS), Dynamique des Génomes et Adaptation Microbienne (DynAMic), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Institut für Biologie [Berlin] (IFB), Humboldt University Of Berlin, School of Biomolecular and Biomedical Science and Centre for Synthesis and Chemical Biology, University College Dublin [Dublin] (UCD), Parallélisme, Réseaux, Systèmes, Modélisation (PRISM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego], Grenoble Institut des Neurosciences (GIN), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Pixyl Medical [Grenoble], Integrated Optical MicroSystems (IOMS), University of Twente-MESA+ Institute for Nanotechnology, 7Lehrstuhl für Mikrobielle Ökologie, Department für Grundlagen der Biowissenschaften, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Service Néphrologie Pédiatrique, CHU Strasbourg-Hôpital de Hautepierre [Strasbourg], Advanced Resources and Risk Technology, Laboratory of Phytopathology (K.C., H.S., B.A., M.H.), Universiteit Gent = Ghent University (UGENT), Trifork Aarhus C, Aalborg University [Denmark] (AAU), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Groupe d'Etude de la Matière Condensée (GEMAC), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen [Groningen], DOE Joint Genome Institute [Walnut Creek], Microbiologie Moléculaire des Actinomycètes (ACTINO), Département Microbiologie (Dpt Microbio), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Gene Technology, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Joint Center for Structural Genomics (JCSG), Stanford University, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches et d'Applications Pédagogiques en Langues (CRAPEL), Université Nancy 2, Space Sciences Laboratory [Berkeley] (SSL), University of California [Berkeley] (UC Berkeley), Polytechnic Institute of Leiria, NMR Laboratory, Université de Mons, Université de Mons (UMons), School of Biomedical Science, Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), BIOMERIT Research Centre, School of Microbiology, University College Cork (UCC), Department of Engineering Science, University of Oxford, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire Charles Friedel, Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Phytopathology, Wageningen University and Research [Wageningen] (WUR), Department of Microbial Ecology, Netherlands Institute of Ecology, Department of Animal Production, Universidad de Córdoba = University of Córdoba [Córdoba], IMV Technologies, Gulliver (UMR 7083), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Institut für Chemie, Technical University of Berlin / Technische Universität Berlin (TU), Lipides - Nutrition - Cancer (U866) (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA), Centre de Recherche Paul Pascal (CRPP), Université de Bordeaux (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), DEPARTMENT OF CHEMISTRY, Durham University, Molekulare Ökologie, Joint Attosecond Science Laboratory, University of Ottawa and National Research Council, Department of Mechanical and Aerospace Engineering [Univ California Davis] (MAE - UC Davis), University of California [Davis] (UC Davis), University of Helsinki, University of California-University of California, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Humboldt-Universität zu Berlin, University of Twente [Netherlands]-MESA+ Institute for Nanotechnology, Technische Universität München [München] (TUM), Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Biosystems, KU Leuven, Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), University of California [Berkeley], NMR and Molecular Imaging Laboratory [Mons], University of Mons [Belgium] (UMONS), University of Oxford [Oxford], Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC), Universidad de Córdoba [Cordoba], Technische Universität Berlin (TU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Department of Mechanical and Aerospace Engineering [Davis], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), University of Florida [Gainesville], Institut für Biologie, Humboldt Universität zu Berlin, Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF), Ghent University [Belgium] (UGENT), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Stanford University [Stanford], Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), NMR and Molecular Imaging Laboratory, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS), Wageningen University and Research Centre [Wageningen] (WUR), Gulliver, ESPCI ParisTech-Centre National de la Recherche Scientifique (CNRS), Technische Universität Berlin (TUB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Max Planck Society (GERMANY), Max Planck Society (GERMANY)-Max Planck Society (GERMANY), Laboratoire Leprince-Ringuet ( LLR ), Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), Atmospheric Chemistry Observations and Modeling Laboratory ( ACOML ), National Center for Atmospheric Research [Boulder] ( NCAR ), University of California [San Diego] ( UC San Diego ), Eidgenössische Technische Hochschule [Zürich] ( ETH Zürich ), University of Science and Technology of China [Hefei] ( USTC ), State Key Laboratory of Nuclear Physics and Technology ( SKL-NPT ), Massachusetts Institute of Technology ( MIT ), Memorial Sloan Kettering Cancer Center ( MSKCC ), Shanghai Ocean University, Dynamique des Génomes et Adaptation Microbienne ( DynAMic ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), University College Dublin [Dublin] ( UCD ), Parallélisme, Réseaux, Systèmes, Modélisation ( PRISM ), Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ) -Centre National de la Recherche Scientifique ( CNRS ), Grenoble Institut des Neurosciences ( GIN ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -CHU Grenoble-Université Joseph Fourier - Grenoble 1 ( UJF ), Integrated Optical MicroSystems ( IOMS ), Technische Universität München [München] ( TUM ), Ghent University [Belgium] ( UGENT ), Aalborg University [Denmark] ( AAU ), Centers for Disease Control and Prevention [Atlanta] ( CDC ), Groupe d'Etude de la Matière Condensée ( GEMAC ), Groningen Biomolecular Sciences and Biotechnology Institute ( GBB ), Microbiologie Moléculaire des Actinomycètes ( ACTINO ), Département Microbiologie ( Dpt Microbio ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de génétique et microbiologie [Orsay] ( IGM ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Joint Center for Structural Genomics ( JCSG ), Centre européen de recherche et d'enseignement de géosciences de l'environnement ( CEREGE ), Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Collège de France ( CdF ) -Institut National de la Recherche Agronomique ( INRA ) -Institut national des sciences de l'Univers ( INSU - CNRS ), Centre de Recherches et d'Applications Pédagogiques en Langues ( CRAPEL ), Space Sciences Laboratory [Berkeley] ( SSL ), Université de Mons ( UMons ), Planning and Transport Research Centre ( PATREC ) -Planning and Transport Research Centre ( PATREC ), University College Cork ( UCC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL ( ENSCP ) -Centre National de la Recherche Scientifique ( CNRS ), Wageningen University and Research Centre [Wageningen] ( WUR ), ESPCI ParisTech, Technische Universität Berlin ( TUB ), Lipides - Nutrition - Cancer (U866) ( LNC ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon ( ENSBANA ), Centre de recherche Paul Pascal, CNRS, Université de Bordeaux ( UPR8641 ), Centre de Recherche Paul Pascal, CNRS, Université de Bordeaux, University Durham, University of California [Davis] ( UC Davis ), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), [GIN] Grenoble Institut des Neurosciences (GIN), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), and Saarland University, Building A4.1, 66123 Saarbruecken, Germany.
Subjects: MESH : Protein Biosynthesis, protein synthesis, Operon, MESH : Polysaccharides, International Cooperation, MESH: Plants, plant, Review, MESH: Terpenes, gene cluster, polyketide, data base, genetic database, Gene cluster, acyltransferase, Databases, Genetic, MESH : Metagenome, MESH : Genetic Markers, genetics, terpene, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), ComputingMilieux_MISCELLANEOUS, MESH : Peptides, MESH: Peptides, biology, fungus, nonribosomal peptide synthesis, Plants, bacterium, peptide, priority journal, MESH: Protein Biosynthesis, Multigene Family, MESH : Terpenes, MESH: Computational Biology, Genetic Markers, MESH: Terminology as Topic, Bioinformatics, MESH : Multigene Family, biological activity, Article, metagenome, Alkaloids, Manchester Institute of Biotechnology, Terminology as Topic, Bioinformatica, MESH : Bacteria, Peptide Biosynthesis, MESH : Databases, Genetic, Molecular Biology, MESH : Fungi, MESH: Polyketides, standardization, secondary metabolism, [ SDV ] Life Sciences [q-bio], Bacteria, ta1182, Computational Biology, MESH : Terminology as Topic, operon, Laboratorium voor Phytopathologie, MESH: International Cooperation, gene function, Metagenomics, polysaccharide, Laboratory of Phytopathology, chemical structure, Metagenome, MESH: Multigene Family, EPS, biosynthesis, Peptides, MESH : Computational Biology, MESH : International Cooperation, [SDV]Life Sciences [q-bio], MESH: Genetic Markers, information, MESH : Alkaloids, Synthetic biology, MESH: Peptide Biosynthesis, Nucleic Acid-Independent, database, MESH: Databases, Genetic, Genetics, MESH : Polyketides, MESH : Peptide Biosynthesis, Nucleic Acid-Independent, ddc:540, standards, Peptide Biosynthesis, Nucleic Acid-Independent, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, nomenclature, genetic marker, alkaloid derivative, MESH: Fungi, Biology, MESH : Plants, peptide derivative, Polyketide, MESH: Alkaloids, Polysaccharides, ddc:570, Life Science, 14. Life underwater, Secondary metabolism, enzyme specificity, Gene, nonhuman, Terpenes, Fungi, nucleotide sequence, Cell Biology, MESH: Metagenome, ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology, alkaloid, MESH: Bacteria, MESH: Polysaccharides, 13. Climate action, Polyketides, Protein Biosynthesis, synthetic biology, metabolism
Abstract: M.H.M. was supported by a Rubicon fellowship of the Netherlands Organization for Scientific Research (NWO;Rubicon 825.13.001). The work of R.K. was supported by the European Union’s Seventh Framework Programme(Joint Call OCEAN.2011–2: Marine microbial diversity—new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no.287589 (Micro B3). M.C. was supported by a Biotechnology and Biological Sciences Research Council (BBSRC)studentship (BB/J014478/1). The GSC is supported by funding from the Natural Environment Research Council(UK), the National Institute for Energy Ethics and Society(NIEeS; UK), the Gordon and Betty Moore Foundation,the National Science Foundation (NSF; US) and the US Department of Energy. The Manchester Synthetic Biology Research Centre, SYNBIOCHEM, is supported by BBSRC/Engineering and Physical Sciences Research Council(EPSRC) grant BB/M017702/1, Medema, M.H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J.B., Blin, K., De Bruijn, I., Chooi, Y.H., Claesen, J., Coates, R.C., Cruz-Morales, P., Duddela, S., Düsterhus, S., Edwards, D.J., Fewer, D.P., Garg, N., Geiger, C., Gomez-Escribano, J.P., Greule, A., Hadjithomas, M., Haines, A.S., Helfrich, E.J.N., Hillwig, M.L., Ishida, K., Jones, A.C., Jones, C.S., Jungmann, K., Kegler, C., Kim, H.U., Kötter, P., Krug, D., Masschelein, J., Melnik, A.V., Mantovani, S.M., Monroe, E.A., Moore, M., Moss, N., Nützmann, H.-W., Pan, G., Pati, A., Petras, D., Reen, F.J., Rosconi, F., Rui, Z., Tian, Z., Tobias, N.J., Tsunematsu, Y., Wiemann, P., Wyckoff, E., Yan, X., Yim, G., Yu, F., Xie, Y., Aigle, B., Apel, A.K., Balibar, C.J., Balskus, E.P., Barona-Gómez, F., Bechthold, A., Bode, H.B., Borriss, R., Brady, S.F., Brakhage, A.A., Caffrey, P., Cheng, Y.Q., Clardy, J., Cox, R.J., De Mot, R., Donadio, S., Donia, M.S., Van Der Donk, W.A., Dorrestein, P.C., Doyle, S., Driessen, A.J.M., Ehling-Schulz, M., Entian, K.-D., Fischbach, M.A., Gerwick, L., Gerwick, W.H., Gross, H., Gust, B., Hertweck, C., Höfte, M., Jensen, S.E., Ju, J., Katz, L., Kaysser, L., Klassen, J.L., Keller, N.P., Kormanec, J., Kuipers, O.P., Kuzuyama, T., Kyrpides, N.C., Kwon, H.-J., Lautru, S., Lavigne, R., Lee, C.Y., Linquan, B., Liu, X., Liu, W., Luzhetskyy, A., Mahmud, T., Mast, Y., Méndez, C., Metsä-Ketelä, M., Micklefield, J., Mitchell, D.A., Moore, B.S., Moreira, L.M., Müller, R., Neilan, B.A., Nett, M., Nielsen, J., O'Gara, F., Oikawa, H., Osbourn, A., Osburne, M.S., Ostash, B., Payne, S.M., Pernodet, J.-L., Petricek, M., Piel, J., Ploux, O., Raaijmakers, J.M., Salas, J.A., Schmitt, E.K., Scott, B., Seipke, R.F., Shen, B., Sherman, D.H., Sivonen, K., Smanski, M.J., Sosio, M., Stegmann, E., Süssmuth, R.D., Tahlan, K., Thomas, C.M., Tang, Y., Truman, A.W., Viaud, M., Walton, J.D., Walsh, C.T., Weber, T., Van Wezel, G.P., Wilkinson, B., Willey, J.M., Wohlleben, W., Wright, G.D., Ziemert, N., Zhang, C., Zotchev, S.B., Breitling, R., Takano, E., Glöckner, F.O.
Published: 2015
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88. A Trial to Determine the Effects of Exercise in Inflammatory Bowel Disease and Rheumatoid Arthritis (ExMET-IBD)

Author: Professor Fergus Shanahan, Professor and Chair Department of Medicine and Director Alimentary Pharmabiotic Centre, University College Cork
Published: 2015

89. Faecal Microbiota Transplantation in Irritable Bowel Syndrome

Author: Professor Fergus Shanahan, Professor and Chair Department of Medicine and Director Alimentary Pharmabiotic Centre, University College Cork
Published: 2015

90. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems

Author: Tari Haahtela, Hubert Plovier, Lucette Flandroy, Eeva Furman, Graham A. W. Rook, Gerard Clarke, Gabriele Berg, Ellen Decaestecker, Yolanda Sanz, Maria Carlota Dao, Sébastien Massart, Theofilos Poutahidis, Science Foundation Ireland, European Commission, Technische Universität Graz ( TU Graz ), University College Cork ( UCC ), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition ( ICAN ), CHU Pitié-Salpêtrière [APHP]-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Assistance publique - Hôpitaux de Paris (AP-HP)-Université Pierre et Marie Curie - Paris 6 ( UPMC ), Katholieke Universiteit Leuven ( KU Leuven ), Finnish Environment Institute ( SYKE ), University of Helsinki [Helsinki], Université de Liège, Instituto de Agroquímica y Tecnología de Alimentos - Institute of Agrochemistry and Food Technology [Valencia] ( IATA-CSIC ), University College of London [London] ( UCL ), Department of Dermatology, Allergology and Venereology, Clinicum, University of Helsinki, HUS Inflammation Center, UCL - SSS/LDRI - Louvain Drug Research Institute, SPF Santé publique, sécurité de la chaîne alimentaire et environnement [Saint-Gilles, Belgique], Laboratory of Pathology [Thessaloniki, Greece] (Faculty of Health Sciences), Aristotle University of Thessaloniki-School of Veterinary Medicine [Thessaloniki, Greece], Technische Universität Graz (TU Graz), University College Cork (UCC), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Université Pierre et Marie Curie - Paris 6 (UPMC)-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], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Finnish Environment Institute (SYKE), Instituto de Agroquímica y Tecnología de Alimentos - Institute of Agrochemistry and Food Technology [Valencia] (IATA-CSIC), University College of London [London] (UCL), 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)-Sorbonne Université (SU)-Sorbonne Université (SU), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and HAL UPMC, Gestionnaire
Subjects: 0301 basic medicine, Biodiversity, EcoHealth, Soil, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Environmental Microbiology, Human Activities, Waste Management and Disposal, Natural environment, 1183 Plant biology, microbiology, virology, Ecology, Microbiota, [ SDV.SPEE ] Life Sciences [q-bio]/Santé publique et épidémiologie, ENVIRONMENTAL CHEMICALS, Plants, RUSSIAN KARELIA, AKKERMANSIA-MUCINIPHILA, Pollution, 3. Good health, Microbes, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, One Health, Health, BACTERIAL COMMUNITIES, Environmental Monitoring, Environmental Engineering, 030106 microbiology, HUMAN GUT MICROBIOME, CANCER-RISK, Context (language use), Biology, 03 medical and health sciences, Microbial ecology, INTESTINAL MICROBIOTA, COMMENSAL BACTERIA, Environmental Chemistry, Animals, Humans, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Life Style, Ecosystem, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, business.industry, fungi, Immunoregulation, ALLERGIC SENSITIZATION, Commensalism, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, 13. Climate action, Agriculture, SEA SPRAY AEROSOL, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Adaptation, business
Abstract: Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems. These include immune system development and regulation, metabolic and endocrine pathways, brain function and epigenetic modification of the genome. Importantly, parental microbiotas have transgenerational impacts on the health of progeny. Humans, animals and plants share similar relationships with microbes. Research paradigms from humans and other mammals, amphibians, insects, planktonic crustaceans and plants demonstrate the influence of environmental microbial ecosystems on the microbiota and health of organisms, and indicate links between environmental and internal microbial diversity and good health. Therefore, overlapping compositions, and interconnected roles of microbes in human, animal and plant health should be considered within the broader context of terrestrial and aquatic microbial ecosystems that are challenged by the human lifestyle and by agricultural and industrial activities. Here, we propose research priorities and organizational, educational and administrative measures that will help to identify safe microbe-associated health-promoting modalities and practices. In the spirit of an expanding version of “One health” that includes environmental health and its relation to human cultures and habits (EcoHealth), we urge that the lifestyle-microbiota-human health nexus be taken into account in societal decision making., GC's attendance at the workshop was supported by the APC Microbiome Institute via Science Foundation Ireland funding (Grant number SFI/12/RC/2273). ED was supported by FWO grant G.0643.13. GB was funded by the European Union (BIOCOMES; 612713) and by the Austrian and Styrian Science Fund (FWF; P29285-BBL). M-CD received funding from the Programme for Research, Technological Development and Demonstration under grant agreement HEALTH-F4-2012-305312 (METACARDIS) and Horizon 2020 Framework Programme (EPoS, grant #634413) as well as Assistance Publique Hôpitaux de Paris. HP is a research fellow at FRS-FNRS, Belgium. The contribution of YS is supported by the European Union's Seventh Framework Program under the grant agreement no 613979 (MyNewGut).
Published: 2018
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91. Archaea microbial candidates in next-generation probiotics development

Author: Paul W. O'Toole, Nathalie Ballet, Céline Ribière, Pascal Vandeckerkove, Wajdi Ben Hania, Jean-François Brugère, Marie-Edith Arnal, Bernard Ollivier, Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Aix Marseille Université (AMU), University College Cork (UCC), Lesaffre International, Science Foundation Ireland through a Centre award SFI/12/RC/2273, Lesaffre International for research development on some aspects of Methanomassiliicoccales biology, Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Alimentary Pharmabiotic Centre (APC), Biosciences Institute (BSI), University College Cork (UCC)-University College Cork (UCC), Société Industrielle Lesaffre, INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
Subjects: 0301 basic medicine, trimethylamine oxide, archaea, [SDV]Life Sciences [q-bio], 030106 microbiology, TMAO, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 03 medical and health sciences, Human gut, cardiovascular disease, Three-domain system, Medicine, Microbiome, développement, Genetics, biology, business.industry, Gastrointestinal Microbiome, Gastroenterology, probiotique, biology.organism_classification, 030104 developmental biology, Metabolic phenotype, atherosclerosis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, methanomassiliicoccales, Bacteria, Archaea
Abstract: International audience; Pharmabiotics and probiotics in current use or under development belong to 2 of 3 domains of life, Eukarya (eg, yeasts) and Bacteria (eg, lactobacilli). Archaea constitute a third domain of life, and are currently not used as probiotics, despite several interesting features. This includes the absence of known pathogens in humans, animals, or plants and the existence of some archaea closely associated to humans in various microbiomes. We promote the concept that some specific archaea that naturally thrive in the human gut are potential next-generation probiotics that can be rationally selected on the basis of their metabolic phenotype not being encountered in other human gut microbes, neither Bacteria nor Eukarya. The example of the possible bioremediation of the proatherogenic compound trimethylamine into methane by archaeal microbes is described.
Published: 2017
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92. Potentially Modifiable Determinants of Malnutrition in Older Adults: A Systematic Review

Author: O’keeffe, M., Kelly, M., O’herlihy, E., O’toole, P., Kearney, P., Timmons, S., Stanton, C., Rolland, Y., Sulmont-Rossé, Claire, Maitre, I., Boeing, H., Stelmach, M., Nagel, G., Wolters, M., Hebestreit, A., De GROOT, L., Teh, R., Peyron, Marie-Agnès, Dardevet, Dominique, Papet, Isabelle, Streicher, M., Torbahn, G., Kiesswetter, E., Visser, M., Volkert, D., O’connor, E., Department of Biological Sciences, Dartmouth College, University College Cork (UCC), Gérontopôle, Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Ecole supérieure d'Agricultures d'Angers (ESA), Deutsches Institut für Ernährungsforschung Potsdam-Rehbrücke (DifE), Leibniz Association, Universität Ulm - Ulm University [Ulm, Allemagne], Leibniz Institute for Prevention Research and Epidemiology - BIPS, Wageningen University and Research Center (WUR), University of Auckland [Auckland], Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), VU University Amsterdam, University of Limerick, University College Cork ( UCC ), CHU Toulouse [Toulouse], Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Ecole Supérieure d'Agricultures d'Angers ( ESA d'Angers ), Institute of Human Nutrition Potsdam-Rehbruecke, University of Ulm, Leibniz Institute for Prevention Research and Epidemiology - BIPS GmbH, Wageningen University and Research Center ( WUR ), University of Auckland, Unité de Nutrition Humaine - Clermont Auvergne ( UNH ), Université Clermont Auvergne ( UCA ) -Institut national de la recherche agronomique [Auvergne/Rhône-Alpes] ( INRA Auvergne/Rhône-Alpes ), Friedrich-Alexander-Universität Erlangen-Nürnberg, Dartmouth College [Hanover], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse], Centre National de la Recherche Scientifique (CNRS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Wageningen University and Research [Wageningen] (WUR), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), University of Limerick (UL), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Vrije Universiteit Amsterdam [Amsterdam] (VU), and Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU)
Subjects: personne âgée, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, méthode de prévention, nutritional deficiency, malnutrition, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, senior citizens
Abstract: Part of special issue: Abstracts of the 39th ESPEN CongressPart of special issue:Abstracts of the 39th ESPEN Congress; Potentially Modifiable Determinants of Malnutrition in Older Adults: A Systematic Review. 39. ESPEN Congress
Published: 2017
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93. Another Brick in the Wall: a Rhamnan Polysaccharide Trapped inside Peptidoglycan of Lactococcus lactis

Author: Irina Sadovskaya, Evgeny Vinogradov, Pascal Courtin, Julija Armalyte, Mickael Meyrand, Efstathios Giaouris, Simon Palussière, Sylviane Furlan, Christine Pèéchoux, Stuart Ainsworth, Jennifer Mahony, Douwe van Sinderen, Saulius Kulakauskas, Yann Guèéérardel, Marie-Pierre Chapot-Chartier, Mark S. Turner, Indranil Biswas, Université du Littoral Côte d'Opale (ULCO), Institut Charles Viollette (ICV) - EA 7394 (ICV), Université d'Artois (UA)-Institut National de la Recherche Agronomique (INRA)-Université du Littoral Côte d'Opale (ULCO)-Institut Supérieur d'Agriculture-Université de Lille, Institute for Biological Sciences, National Research Council of Canada (NRC), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Génétique Animale et Biologie Intégrative (GABI), School of Microbiology, University College Cork (UCC), APC Microbiome Institute [Cork], Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Région Ile-de-France, French ANR project 'Lactophages' [ANR-11-BSV8-004-01], Science Foundation Ireland (SFI) [14/TIDA/2287, 15/SIRG/3430], SFI [13/IA/1953], Chapot-Chartier, Marie-Pierre, CNRS, INRA, ISA, Univ. Artois, Univ. Littoral Côte d’Opale, Université de Lille, Institut Charles Viollette (ICV) - EA 7394 [ICV], Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576, Université du Littoral Côte d'Opale [ULCO], National Research Council of Canada [NRC], MICrobiologie de l'ALImentation au Service de la Santé [MICALIS], Génétique Animale et Biologie Intégrative [GABI], University College Cork [UCC], Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 [UGSF], Turner, Mark S., Biswas, Indranil, and Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Magnetic Resonance Spectroscopy, Lactococcus, 030106 microbiology, Mutant, polysaccharides, Peptidoglycan, rhamnan, Polysaccharide, Microbiology, Bacterial cell structure, Cell wall, Mannans, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Polysaccharides, Virology, Glycosyltransferase, Deoxy Sugars, chemistry.chemical_classification, Cell Wall, HR-MAS NMR, Rhamnan, biology, Lactococcus lactis, Cell Membrane, Microbiology and Parasitology, biology.organism_classification, Microbiologie et Parasitologie, eye diseases, QR1-502, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Biochemistry, cell wall, Mutation, biology.protein, ATP-Binding Cassette Transporters, Research Article
Abstract: Polysaccharides are ubiquitous components of the Gram-positive bacterial cell wall. In Lactococcus lactis, a polysaccharide pellicle (PSP) forms a layer at the cell surface. The PSP structure varies among lactococcal strains; in L. lactis MG1363, the PSP is composed of repeating hexasaccharide phosphate units. Here, we report the presence of an additional neutral polysaccharide in L. lactis MG1363 that is a rhamnan composed of α-l-Rha trisaccharide repeating units. This rhamnan is still present in mutants devoid of the PSP, indicating that its synthesis can occur independently of PSP synthesis. High-resolution magic-angle spinning nuclear magnetic resonance (HR-MAS NMR) analysis of whole bacterial cells identified a PSP at the surface of wild-type cells. In contrast, rhamnan was detected only at the surface of PSP-negative mutant cells, indicating that rhamnan is located underneath the surface-exposed PSP and is trapped inside peptidoglycan. The genetic determinants of rhamnan biosynthesis appear to be within the same genetic locus that encodes the PSP biosynthetic machinery, except the gene tagO encoding the initiating glycosyltransferase. We present a model of rhamnan biosynthesis based on an ABC transporter-dependent pathway. Conditional mutants producing reduced amounts of rhamnan exhibit strong morphological defects and impaired division, indicating that rhamnan is essential for normal growth and division. Finally, a mutation leading to reduced expression of lcpA, encoding a protein of the LytR-CpsA-Psr (LCP) family, was shown to severely affect cell wall structure. In lcpA mutant cells, in contrast to wild-type cells, rhamnan was detected by HR-MAS NMR, suggesting that LcpA participates in the attachment of rhamnan to peptidoglycan., IMPORTANCE In the cell wall of Gram-positive bacteria, the peptidoglycan sacculus is considered the major structural component, maintaining cell shape and integrity. It is decorated with other glycopolymers, including polysaccharides, the roles of which are not fully elucidated. In the ovococcus Lactococcus lactis, a polysaccharide with a different structure between strains forms a layer at the bacterial surface and acts as the receptor for various bacteriophages that typically exhibit a narrow host range. The present report describes the identification of a novel polysaccharide in the L. lactis cell wall, a rhamnan that is trapped inside the peptidoglycan and covalently bound to it. We propose a model of rhamnan synthesis based on an ABC transporter-dependent pathway. Rhamnan appears as a conserved component of the lactococcal cell wall playing an essential role in growth and division, thus highlighting the importance of polysaccharides in the cell wall integrity of Gram-positive ovococci.
Published: 2017
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94. Randomised controlled trial demonstrates that fermented infant formula with short-chain galacto-oligosaccharides and long-chain fructo-oligosaccharides reduces the incidence of infantile colic

Author: Derek Forde, Frédéric Huet, Thomas Ludwig, Jonathan O'b Hourihane, Philippe Alliet, Hetty Bouritius, Yvan Vandenplas, Stefaan Peeters, Growth and Development, Clinical sciences, Units of Pediatric Gastroenterology, Universitair Ziekenhuis Brussel, Nutricia Research, Kinderartsenpraktijk, Slaney Medical Centre, Algemeen Stedelijk Ziekenhuis Aalst, Génétique des Anomalies du Développement (GAD), Université de Bourgogne (UB)-IFR100 - Structure fédérative de recherche Santé-STIC, Paediatric & Child Hlth, University College Cork (UCC), Nutricia Research, the Netherlands, Génétique des Anomalies du Développement ( GAD ), Université de Bourgogne ( UB ) -IFR100 - Structure fédérative de recherche Santé-STIC, University College Cork ( UCC ), and IFR100 - Structure fédérative de recherche Santé-STIC-Université de Bourgogne (UB)
Subjects: Colic, Cultured Milk Products, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, Breastfeeding, Oligosaccharides, Prebiotic, Gastrointestinal tolerance, Gastroenterology, law.invention, 0302 clinical medicine, birth, Randomized controlled trial, law, Prospective Studies, functional gastrointestinal disorders, Prospective cohort study, Crying, Incidence (epidemiology), Regular Article, health, infant formula, General Medicine, Infantile colic, 3. Good health, mixture, prebiotic, Infant formula, 030211 gastroenterology & hepatology, medicine.symptom, Long chain, infantile colic, medicine.medical_specialty, life, 03 medical and health sciences, Double-Blind Method, children, 030225 pediatrics, Internal medicine, medicine, Humans, Pediatrics, Perinatology, and Child Health, childhood, business.industry, Infant, Newborn, Infant, constipation, medicine.disease, Surgery, Prebiotics, age, gastrointestinal tolerance, Pediatrics, Perinatology and Child Health, symptoms, Fermented formula, fermented formula, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Regular Articles
Abstract: Aim: We examined the effects on gastrointestinal (GI) tolerance of a novel infant formula that combined specific fermented formula (FERM) with short-chain galacto-oligosaccharides and long-chain fructo-oligosaccharides (scGOS/lcFOS), with a 9: 1 ratio and concentration of 0.8 g/100 mL. Methods: This prospective, double-blind, randomised, controlled trial comprised 432 healthy, term infants aged 0-28 days whose parents decided to not start, or discontinued, breastfeeding. Infant formula with scGOS/lcFOS+50%FERM, scGOS/lcFOS+15%FERM, 50%FERM and scGOS/lcFOS were tested. Parents completed standardised seven-day diaries on GI symptoms, crying, sleeping and stool characteristics each month until the infants were 17 weeks. Results: All the formulas were well tolerated. At four weeks, the overall incidence of infantile colic was significantly lower (8%) with scGOS/lcFOS+50%FERM than scGOS/lcFOS (20%, p = 0.034) or 50% FERM (20%, p = 0.036). Longitudinal modelling showed that scGOS/lcFOS+ 50%FERM-fed infants also displayed a persistently lower daily crying duration and showed a consistent stool-softening effect than infants who received formula without scGOS/lcFOS. Conclusion: The combination of fermented formula with scGOS/lcFOS was well tolerated and showed a lower overall crying time, a lower incidence of infantile colic and a stool-softening effect in healthy term infants. These findings suggest for the first time that a specific infant formula has a preventive effect on infantile colic in formula-fed infants. Nutricia Research, the Netherlands, provided the funding to conduct the study. The funder contributed to the design of the study, interpretation of the findings and writing of the manuscript.
Published: 2017
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95. Stable isotope analysis reveals biases in the performance of a morphological method to distinguish the migratory behaviour of European robins Erithacus rubecula

Author: Iván de la Hera, José Luis Tellería, Antón Pérez-Rodríguez, Guillermo Fandos, Javier Pérez-Tris, Alejandro Onrubia, Javier Fernández-López, Departamento de Zoología y Antropología Física, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), School of Biological, Earth and Environmental Sciences [Cork] (BEES), University College Cork (UCC), Real Jardín Botánico de Madrid, Spanish National Research Council (CSIC), Fundación Migres, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Research funded by the Spanish Ministry of Economy and Competitiveness (Project CGL2011- 22953/BOS, CGL2007-62937/BOS and CGL2013-41642-P/BOS, and PhD grants)., Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Universidad Complutense de Madrid [Madrid] ( UCM ), School of Biological, Earth and Environmental Sciences, University College Cork ( UCC ), Spanish National Research Council ( CSIC ), Biogéosciences [Dijon] ( BGS ), and Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS )
Subjects: 0106 biological sciences, Species complex, funciones discriminantes, Erithacus, Plumas rectrices, deuterio, Biology, 010603 evolutionary biology, 01 natural sciences, 010605 ornithology, Rectrix feathers, Deuterio, sympatric interactions, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Ecology, Evolution, Behavior and Systematics, Overwintering, deuterium, plumas rectrices, Isotope analysis, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Discriminant functions, Ecology, Hydrogen isotope, Campo de Gibraltar, Deuterium, biology.organism_classification, Sympatric interactions, Discriminant functions, Rectrix feathers, Sympatric interactions, Campo de Gibraltar, Interacciones simpátricas, Funciones discriminantes, Sympatric speciation, [ SDV.BA.ZV ] Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, rectrix feathers, Habitat distribution, Animal Science and Zoology, interacciones simpátricas, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, discriminant functions
Abstract: Morphological methods to distinguish between avian groups of research interest (e.g. different sexes, populations or cryptic species) need to be externally validated to ensure reliable performance across situations. In this study, we used stable hydrogen isotope ratios of feathers (δHf) to test the validity of morphological classification functions (MCFs) previously designed to assess the migratory behaviour of European Robins Erithacus rubecula wintering in southern Iberia. Our results show that a great number of migrants (mostly females and juveniles) were erroneously assigned as sedentary, which could compromise the reliability of previous ecological studies that made use of these MCFs. The development of improved MCFs or the use of alternative differentiation methods (δHf) could help us to gain a more realistic insight into the habitat distribution and ecological interactions of sympatric migratory and sedentary robins overwintering in southern Iberia., Los métodos morfológicos para distinguir grupos de aves con interés de investigación (e.g. distinción de sexos, poblaciones o especies crípticas) requieren de validación independiente para asegurar su funcionamiento adecuado de forma consistente. En este estudio, usamos la relación de isó- topos estables del hidrógeno en las plumas (δ2 Hf ) para comprobar la validez de las funciones de clasificación morfológicas (MCFs) diseñadas con anterioridad para identificar el comportamiento migratorio de los petirrojos Erithacus rubecula invernantes en el sur ibérico. Los resultados revelaron que un gran número de migrantes (sobre todo hembras y jóvenes) fueron clasificados erróneamente como sedentarios, lo que podría comprometer la fiabilidad de los estudios ecológicos previos que han hecho uso de estas MCFs. El desarrollo de MCFs mejoradas o el uso de métodos de diferenciación alternativos (δ2 Hf ) podrían ayudarnos a obtener una idea más realista acerca de la distribución entre hábitats e interacciones ecológicas de los petirrojos migratorios y sedentarios que invernan en simpatría en el sur ibérico
Published: 2017
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96. Host recognition by lactic acid bacterial phages

Author: Jennifer Mahony, Christian Cambillau, Douwe van Sinderen, School of Microbiology, University College Cork (UCC), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Department of Microbiology, University College Cork, and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Streptococcus thermophilus, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Lactococcus, receptor, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, Bacteriophage, chemistry.chemical_compound, bacteriophage, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Lactobacillus, Bacteriophages, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Lactic acid, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Lactococcus lactis, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Infectious Diseases, Host-Pathogen Interactions, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Receptors, Virus, MESH: Virus Attachment, 030106 microbiology, Virus Attachment, Computational biology, Microbiology, MESH: Fermentation, MESH: Streptococcus thermophilus, 03 medical and health sciences, MESH: Cell Wall, MESH: Leuconostoc, Leuconostoc, MESH: Bacteriophages, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], MESH: Host-Pathogen Interactions, biology.organism_classification, MESH: Receptors, Virus, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, chemistry, carbohydrate, MESH: Lactococcus lactis, Fermentation, dairy, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, cell wall, protein, MESH: Lactobacillus, Bacteria
Abstract: International audience; Bacteriophage infection of lactic acid bacteria (LAB) is one of the most significant causes of inconsistencies in the manufacture of fermented foods, affecting production schedules and organoleptic properties of the final product. Consequently, LAB phages, and particularly those infecting Lactococcus lactis, have been the focus of intensive research efforts. During the past decade, multidisciplinary scientific approaches have uncovered molecular details on the exquisite process of how a lactococcal phage recognises and binds to its host. Such approaches have incorporated genomic/molecular analyses and their partnership with phage structural analysis and host cell wall biochemical studies are discussed in this review, which will also provide our views on future directions of this research field.
Published: 2017
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97. Investigation of the production of wet agglomerates of couscous grains using a fluidized bed granulator

Author: Bellocq, Bettina, Cuq, Bernard, Ruiz, Thierry, Duri-Bechemilh, Agnès, Cronin, Kevin, Ring, Denis, Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Department of Process & Chemical Engineering, University College Cork, ANR ALID Dur-Dur, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University College Cork (UCC), ANR-13-ALID-0002,Dur-Dur,Innovations agronomiques, techniques et organisationnelles au service de la DURabilité de la filière blé DUR(2013), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)
Subjects: semolina, fluidized bed, blé dur, hard wheat, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Couscous grains, Fluidized bed granulator, food and beverages, agglomération humide, Wet agglomerates, lit fluidisé, semoule
Abstract: Mastering the industrial processes in which wheat powders are used to produce couscous is still partly based on practical industrial experience and empirical knowledge. Wet agglomeration, rolling, cooking, drying and screening are the main unit operations which are sequentially involved in the couscous grain production. Granulation is the main step that determines the production yield and the final size and shape of the couscous grain. Control of granule size distribution after the wet granulation stage is a very important quality constraint. The objective of this work is to explore whether the novel technique of fluidised bed granulation can produce agglomerates of durum wheat semolina and to investigate if this method could prove a successful alternative to the conventional method using low shear mixer technology to produce the couscous grains.The couscous agglomerates were produced in a batch fluidised bed granulator with water as the binding medium (top spray). The size, shape, hydrotextural properties (moisture content and compactness) and strength of the granules were measured. Fluidised bed granulation provided a more controlled size distribution than is achievable with the corresponding low shear granulation approach. The agglomerates have specific hydrotextural properties, with different values of their functional attributes that allow us to think to a new ways of texturing durum wheat semolina agglomerates. The final grains size, shape and moisture content were similar to the values measured for commercially available samples. Nevertheless granule compactness was lower. The strength of the granules increased with an increase in the size and the compactness of the final couscous grain.
Published: 2017

98. Structural studies of the deacylated glycolipids and lipoteichoic acid of Lactococcus cremoris 3107

Author: Ruiz-Cruz, Sofía, Sadovskaya, Irina, Mahony, Jennifer, Grard, Thierry, Chapot-Chartier, Marie-Pierre, van Sinderen, Douwe, Vinogradov, Evguenii, Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Biochimie des Produits Aquatiques (BPA), Université du Littoral Côte d'Opale (ULCO)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), University College Cork (UCC), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute for Biological Science, and National Research Council of Canada (NRC)
Subjects: Lactococcus cremoris 3107, [SDV]Life Sciences [q-bio], Lactic acid bacteria, Glycolipids, Lipoteichoic acid, Cell walls, NMR
Abstract: International audience; Lactococcus cremoris and Lactococcus lactis are among the most extensively exploited species of lactic acid bacteria in dairy fermentations. The cell wall of lactococci, like other Gram-positive bacteria, possesses a thick peptidoglycan layer, which may incorporate cell wall polysaccharides (CWPS), wall teichoic acids (WTA), and/or lipoteichoic acids (LTA).In this study, we report the isolation, purification and structural analysis of the carbohydrate moieties of glycolipids (GL) and LTA of the L. cremoris model strain 3107. Chemical structures of these compounds were studied by chemical methods, NMR spectroscopy and positive and negative mode ESI MS. We found that the LTA of strain 3107 is composed of short chains of 1,3-polyglycerol phosphate (PGP), attached to O-6 of the non-reducing glucose of the kojibiose-Gro backbone of the glycolipid anchor. Extraction of cells with cold TCA afforded the detection of 1,3-glycerol phosphate chains randomly substituted at O-2 of glycerol by D-Ala. Unlike the LTA of L. lactis strains studied to date, the PGP backbone of the LTA of L. cremoris 3107 did not carry any glycosyl substitution. The deacylated glycolipid fraction contained the free kojibiose-Gro oligosaccharide, identical to the backbone of the GL anchor of LTA, and its shorter fragment α-Glc-1-Gro. These OS may have originated from the GL precursors of LTA biosynthesis.
Published: 2023
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99. Effect of a grazing period prior to finishing on a high concentrate diet on meat quality from bulls and steers

Author: Maurice G. O'Sullivan, Edward G. O'Riordan, Brigitte Picard, Aidan P. Moloney, Joseph P. Kerry, Mark McGee, Lara Morán, Food Research Ctentre, Teagasc Food Research Centre [Fermoy, County Cork, Ireland], School Food and Nutrition Science, University College Cork, Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Animal and Grassland Research an Innovation Centre, Irish Department of Agriculture, Food and the Marine's competitive research programmes 11/SF/322, Teagasc Food Research Centre, Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Teagasc Food Research Centre [Fermoy, Ireland], University College Cork (UCC), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: Male, fibre musculaire, [SDV]Life Sciences [q-bio], Muscle Fibers, Skeletal, Muscle Proteins, Grazing period, Sarcomere, Muscle fibre profile, chemistry.chemical_compound, Myosin, Grazing, Cooking, 2. Zero hunger, muscle fibre profile, food and beverages, 04 agricultural and veterinary sciences, Anatomy, Hydrogen-Ion Concentration, 040401 food science, Tenderness, tenderness, Adipose Tissue, Taste, Body Composition, période de pâturage, Intramuscular fat, Dietary Proteins, medicine.symptom, Increased intramuscular fat, skeletal myocytes, Longissimus Thoracis, Color, Biology, gelding, tendrete de la viande, 0404 agricultural biotechnology, Animal science, grazing period, medicine, Food Quality, Animals, Humans, Herbivory, Castration, Muscle, Skeletal, [ SDV ] Life Sciences [q-bio], 0402 animal and dairy science, Consumer Behavior, castration, 040201 dairy & animal science, Animal Feed, Dietary Fats, Diet, Red Meat, chemistry, Cattle, Orchiectomy, texture, Food Science
Abstract: Bulls and steers (n = 60) were assigned to a pre-finishing grazing period and subsequently finished on concentrates or offered concentrates without grazing until slaughter (19 months). Colour and pH of longissimus thoracis were measured (48 h post-slaughter), and samples collected for proximate composition, collagen, sarcomere length, muscle fibre and enzymatic profile analysis. Steaks for texture, cook loss and sensory were aged (14 days). Castration increased intramuscular fat content, cook loss and myosin isoforms IIa and I proportions, and decreased IIx proportion (P < 0.05). Steer meat was positively correlated to overall tenderness, texture and acceptability (P < 0.05). The presence of a pre-finishing grazing period decreased intramuscular fat and increased the proportion of IIa compared with animals on concentrates, while no differences were found in sensory. Muscle colour, collagen, sarcomere length and instrumental texture were not modified by diet or castration. In conclusion, beef sensory characteristics were unaffected by diet, whereas castration resulted in a small improvement; however all the treatments produced an acceptable product.
Published: 2017
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100. Lipolysis and Metabolism of Fatty Acids in Cheese

Author: Anne Thierry, Henry-Eric Spinnler, Martin G. Wilkinson, Paul L.H. McSweeney, Yvonne F. Collins, M.C. Abeijón Mukdsi, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Teagasc Food Research Centre [Fermoy, Ireland], Centro de Referencia para Lactobacilos [Tucumán] (CERELA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), School of Food and Nutritional Sciences, University College Cork (UCC), University of Limerick (UL), Génie et Microbiologie des Procédés Alimentaires (GMPA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Paul McSweeney, Teagasc Food Research Centre [Fermoy, County Cork, Ireland], University College Cork, McSweeney, Paul LH., Fox, Patrick F., Cotter, Paul D., and Everett, David W.
Subjects: 0106 biological sciences, 0301 basic medicine, esterase, FREE FATTY ACIDS, fromage, ESTER, 01 natural sciences, matière grasse laitière, [SDV.IDA]Life Sciences [q-bio]/Food engineering, lipase, Food science, méthylkétone, Flavor, 2. Zero hunger, chemistry.chemical_classification, Lipoprotein lipase, biology, acide gras, food and beverages, Biochemistry, lactone, Swiss cheese, ESTERASE, Otras Producción Animal y Lechería, Glyceride, 03 medical and health sciences, 010608 biotechnology, Lipolysis, LACTONE, flaveur, Lipase, CHEESE, Fatty acid, lipolyse, Producción Animal y Lechería, flavour, 030104 developmental biology, chemistry, FAT, CIENCIAS AGRÍCOLAS, biology.protein, lipolysis, LIPASE, Rennet, ester, fatty acid, METHYLKETONE, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, LIPOLYSIS, FLAVOR
Abstract: Enzymatic hydrolysis (lipolysis) of milk glycerides to free fatty acids is essential for flavor development in cheese. The principal lipolytic agents in cheese include lipoprotein lipase from raw milk, pregastric esterase in cheeses made using rennet paste, and enzymes from the starter and nonstarter microbiota. Lactic acid bacteria are weakly lipolytic and mainly possess nonlipolytic esterases located intracellularly. Lipolysis level is, thus, low in many internal bacterially ripened cheeses. It is higher in certain varieties, such as Swiss cheese, smear-ripened, and particularly mold-ripened cheeses, in which specific lipolytic secondary microbiota develops. Exogenous lipases are occasionally used to develop flavor. Short-chain fatty acids directly contribute to flavor, but fatty acids can also act as precursors for the production of a wide range of other flavor compounds, such as esters, lactones, and methylketones that are associated with diverse flavors. Methods for determining levels of fatty acids are also discussed. Fil: Thierry, Anne. Institut National de la Recherche Agronomique; Francia Fil: Collins, Yvonne F.. Teagasc Food Research Centre; Irlanda Fil: Abeijon Mukdsi, Maria Claudia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina. Universidad del Norte Santo Tomás de Aquino; Argentina Fil: McSweeney, Paul LH.. University College. School of Food and Nutritional Sciences; Irlanda Fil: Wilkinson, Martin G.. University of Limerick; Irlanda Fil: Spinnler, Henri E.. Institut National de la Recherche Agronomique; Francia
Published: 2017
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