Design and implementation of the AMIGA embedded system for data acquisition

The successful installation, commissioning, and operation of the Pierre Auger Observatory would not have been possible without the strong commitment and effort from the technical and admin-istrative staff in Malargtie. We are very grateful to the following agencies and organizations for financial support: Comision Nacional de Energla Atomica, Agencia Nacional de Promocion Cientffica y Tec-nologica (ANPCyT) , Consejo Nacional de Investigaciones Cientfficas y Tecnicas (CONICET) , Gobierno de la Provincia de Mendoza, Municipalidad de Malargtie, NDM Holdings and Valle Las Leilas, in gratitude for their continuing cooperation over land access, Argentina; the Australian Research Council; Conselho Nacional de Desenvolvimento Cientffico e Tecnologico (CNPq) , Fi-nanciadora de Estudos e Projetos (FINEP) , FundagAo de Amparo a Pesquisa do Estado de Rio de Janeiro (FAPERJ) , SAo Paulo Research Foundation (FAPESP) Grants No. 2010/07359-6 and No. 1999/05404-3, Ministerio de Ciencia e Tecnologia (MCT) , Brazil; Grant No.MSMT CR LG15014, LO1305 and LM2015038 and the Czech Science Foundation Grant No. 14-17501S, Czech Republic; Centre de Calcul IN2P3/CNRS, Centre National de la Recherche Scientifique (CNRS) , Conseil Regional Ile-de-France, Departement Physique Nucleaire et Corpusculaire (PNC-IN2P3/CNRS) , Departement Sciences de l'Univers (SDU-INSU/CNRS) , Institut Lagrange de Paris (ILP) Grant No. LABEX ANR-10-LABX-63, within the Investissements d'Avenir Programme Grant No. ANR-11-IDEX-0004-02, France; Bundesministerium fur Bildung und Forschung (BMBF) , Deutsche Forschungsgemeinschaft (DFG) , Finanzministerium Baden-Wurttemberg, Helmholtz Al-liance for Astroparticle Physics (HAP) , Helmholtz-Gemeinschaft Deutscher Forschungszentren (HGF) , Ministerium fur Wissenschaft und Forschung, Nordrhein Westfalen, Ministerium fur Wis-senschaft, Forschung und Kunst, Baden-Wurttemberg, Germany; Istituto Nazionale di Fisica Nu-cleare (INFN) ,Istituto Nazionale di Astrofisica (INAF) , Ministero dell'Istruzione, dell'Universita e della Ricerca (MIUR) , Gran Sasso Center for Astroparticle Physics (CFA) , CETEMPS Cen-ter of Excellence, Ministero degli Affari Esteri (MAE) , Italy; Consejo Nacional de Ciencia y Tecnologia (CONACYT) No. 167733, Mexico; Universidad Nacional Autonoma de Mexico (UNAM) , PAPIIT DGAPA-UNAM, Mexico; Ministerie van Onderwijs, Cultuur en Wetenschap, Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) , Stichting voor Fundamenteel Onderzoek der Materie (FOM) , Netherlands; National Centre for Research and Development, Grants No. ERA-NET-ASPERA/01/11 and No. ERA-NET-ASPERA/02/11, National Science Cen-tre, Grants No. 2013/08/M/ST9/00322, No. 2013/08/M/ST9/00728 and No. HARMONIA 5 - 2013/10/M/ST9/00062, Poland; Portuguese national funds and FEDER funds within Programa Operacional Factores de Competitividade through Fundagdo para a Ciencia e a Tecnologia (COM-PETE) , Portugal; Romanian Authority for Scientific Research ANCS, CNDI-UEFISCDI partner-ship projects Grants No. 20/2012 and No.194/2012 and PN 16 42 01 02; Slovenian Research Agency, Slovenia; Comunidad de Madrid, Fondo Europeo de Desarrollo Regional (FEDER) funds, Ministerio de Economia y Competitividad, Xunta de Galicia, European Community 7th Frame-work Program, Grant No. FP7-PEOPLE-2012-IEF-328826, Spain; Science and Technology Fa-cilities Council, United Kingdom; Department of Energy, Contracts No. DE-AC02-07CH11359, No. DE-FR02-04ER41300, No. DE-FG02-99ER41107 and No. DE-SC0011689, National Science Foundation, Grant No. 0450696, The Grainger Foundation, U.S.A. ; NAFOSTED, Vietnam; Marie Curie-IRSES/EPLANET, European Particle Physics Latin American Network, European Union 7th Framework Program, Grant No. PIRSES-2009-GA-246806; and UNESCO.The Auger Muon Infill Ground Array (AMIGA) is part of the AugerPrime upgrade of the Pierre Auger Observatory. It consists of particle counters buried 2.3m underground next to the water-Cherenkov stations that form the 23.5 km2 large infilled array. The reduced distance between detectors in this denser area allows the lowering of the energy threshold for primary cosmic ray reconstruction down to about 1017 eV. At the depth of 2.3m the electromagnetic component of cosmic ray showers is almost entirely absorbed so that the buried scintillators provide an independent and direct measurement of the air showers muon content. This work describes the design and implementation of the AMIGA embedded system, which provides centralized control, data acquisition and environment monitoring to its detectors. The presented system was firstly tested in the engineering array phase ended in 2017, and lately selected as the final design to be installed in all new detectors of the production phase. The system was proven to be robust and reliable and has worked in a stable manner since its first deployment.Comision Nacional de Energla AtomicaANPCyTConsejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET)Gobierno de la Provincia de MendozaMunicipalidad de MalargtieNDM HoldingsAustralian Research CouncilConselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ)Financiadora de Inovacao e Pesquisa (Finep)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) 2010/07359-6 1999/05404-3Ministerio de Ciencia e Tecnologia (MCT) , BrazilGrant Agency of the Czech Republic Czech Republic Government 14-17501SCentre de Calcul IN2P3/CNRSCentre National de la Recherche Scientifique (CNRS) Region Ile-de-France Departement Physique Nucleaire et Corpusculaire PNC-IN2P3/CNRS Departement Sciences de l'Univers (SDU-INSU/CNRS) French National Research Agency (ANR) LABEX ANR-10-LABX-63 ANR-11-IDEX-0004-02Federal Ministry of Education & Research (BMBF)German Research Foundation (DFG) Finanzministerium Baden-Wurttemberg, Helmholtz Al-liance for Astroparticle Physics (HAP) Helmholtz Association Ministerium fur Wissenschaft und Forschung, Nordrhein Westfalen Ministerium fur Wis-senschaft, Forschung und Kunst, Baden-Wurttemberg, GermanyIstituto Nazionale di Fisica Nucleare (INFN) Istituto Nazionale Astrofisica (INAF)Ministry of Education, Universities and Research (MIUR)Gran Sasso Center for Astroparticle Physics (CFA)CETEMPS Cen-ter of ExcellenceMinistry of Foreign Affairs and International Cooperation (Italy)Consejo Nacional de Ciencia y Tecnologia (CONACyT) 167733Mexico; Universidad Nacional Autonoma de Mexico (UNAM)Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)Universidad Nacional Autonoma de MexicoMinisterie van Onderwijs, Cultuur en Wetenschap Netherlands Organization for Scientific Research (NWO) FOM (The Netherlands) Netherlands GovernmentNational Centre for Research & Development, Poland ERA-NET-ASPERA/01/11 ERA-NET-ASPERA/02/11National Science Centre, Poland 2013/08/M/ST9/00322 2013/08/M/ST9/00728 HARMONIA 5 - 2013/10/M/ST9/00062Portuguese national fundsFEDER funds within Programa Operacional Factores de Competitividade through Fundagdo para a Ciencia e a Tecnologia (COM-PETE) , PortugalRomanian Authority for Scientific Research ANCSConsiliul National al Cercetarii Stiintifice (CNCS) Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii (UEFISCDI) 20/2012 194/2012 PN 16 42 01 02Slovenian Research Agency - SloveniaComunidad de MadridFondo Europeo de Desarrollo Regional (FEDER) funds, Ministerio de Economia y Competitividad,Xunta de Galicia ,European Community 7th Frame-work Program FP7-PEOPLE-2012-IEF-328826UK Research & Innovation (UKRI)Science & Technology Facilities Council (STFC)United States Department of Energy (DOE) DE-FG02-99ER41107 DE-SC0011689National Science Foundation (NSF) 0450696Grainger Foundation, U.S.ANational Foundation for Science & Technology Development (NAFOSTED)Marie Curie-IRSES/EPLANETEuropean Particle Physics Latin American Network European Commission PIRSES-2009-GA-246806UNESCOMSMT CR LG15014 LO1305 LM201503

Design, upgrade and characterization of the silicon photomultiplier front-end for the AMIGA detector at the Pierre Auger Observatory

The successful installation, commissioning, and operation of the Pierre Auger Observatory would not have been possible without the strong commitment and effort from the technical and administrative staff in Malargue. We are very grateful to the following agencies and organizations for financial support: Argentina -Comision Nacional de Energia Atomica; Agencia Nacional de Promocion Cientifica y Tecnologica (ANPCyT); Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET); Gobierno de la Provincia de Mendoza; Municipalidad de Malargue; NDM Holdings and Valle Las Lenas; in gratitude for their continuing cooperation over land access; Australia -the Australian Research Council; Brazil -Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq); Financiadora de Estudos e Projetos (FINEP); Fundacao de Amparo a Pesquisa do Estado de Rio de Janeiro (FAPERJ); Sao Paulo Research Foundation (FAPESP) Grants No. 2019/10151-2, No. 2010/07359-6 and No. 1999/05404-3; Ministerio da Ciencia, Tecnologia, Inovacoes e Comunicacoes (MCTIC); Czech Republic Grant No. MSMT CR LTT18004, LM2015038, LM2018102, CZ.02.1.01/0.0/0.0/16_013/0001402, CZ.02.1.01/0.0/0.0/18_046/0016010 and CZ.02.1.01/0.0/0.0/17_049/0008422; France -Centre de Calcul IN2P3/CNRS; Centre National de la Recherche Scientifique (CNRS); Conseil Regional Ile-de-France; Departement Physique Nucleaire et Corpusculaire (PNC-IN2P3/CNRS); Departement Sciences de l'Univers (SDU-INSU/CNRS); Institut Lagrange de Paris (ILP) Grant No. LABEX ANR-10-LABX-63 within the Investissements d'Avenir Programme Grant No. ANR-11-IDEX-0004-02; Germany-Bundesministerium fur Bildung und Forschung (BMBF); Deutsche Forschungsgemeinschaft (DFG); Finanzministerium Baden-Wurttemberg; Helmholtz Alliance for Astroparticle Physics (HAP); Helmholtz-Gemeinschaft Deutscher Forschungszentren (HGF); Ministerium fur Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen; Ministerium fur Wissenschaft, Forschung und Kunst des Landes Baden-Wurttemberg; Italy-Istituto Nazionale di Fisica Nucleare (INFN); Istituto Nazionale di Astrofisica (INAF); Ministero dell'Istruzione, dell'Universita e della Ricerca (MIUR); CETEMPS Center of Excellence; Ministero degli Affari Esteri (MAE); Mexico-Consejo Nacional de Ciencia y Tecnologia (CONACYT) No. 167733; Universidad Nacional Autonoma de Mexico (UNAM); PAPIIT DGAPA-UNAM; The Netherlands -Ministry of Education, Culture and Science; Netherlands Organisation for Scientific Research (NWO); Dutch national e-infrastructure with the support of SURF Cooperative; Poland-Ministry of Science and Higher Education, grant No. DIR/WK/2018/11; National Science Centre, Grants No. 2013/08/M/ST9/00322, No. 2016/23/B/ST9/01635 and No. HARMONIA 5-2013/10/M/ST9/00062, UMO-2016/22/M/ST9/00198; Portugal -Portuguese national funds and FEDER funds within Programa Operacional Factores de Competitividade through Fundacao para a Ciencia e a Tecnologia (COMPETE); Romania-Romanian Ministry of Education and Research, the Program Nucleu within MCI(PN19150201/16N/2019 and PN19060102) and project PN-III-P1-1.2-PCCDI-2017-0839/19PCCDI/2018 within PNCDI III; Slovenia -Slovenian Research Agency, grants P1-0031, P1-0385, I0-0033, N1-0111; Spain-Ministerio de Economia, Industria y Competitividad (FPA2017-85114-P and FPA2017-85197-P), Xunta de Galicia (ED431C 2017/07), Junta de Andalucia (SOMM17/6104/UGR), Feder Funds, RENATA Red Nacional Tematica de Astroparticulas (FPA2015-68783-REDT) and Maria de Maeztu Unit of Excellence (MDM-2016-0692); U.S.A. -Department of Energy, Contracts No. DE-AC02-07CH11359, No. DE-FR02-04ER41300, No. DE-FG02-99ER41107 and No. DE-SC0011689; National Science Foundation, Grant No. 0450696; The Grainger Foundation; Marie Curie-IRSES/EPLANET; European Particle Physics Latin American Network; and UNESCO.AMIGA (Auger Muons and Infill for the Ground Array) is an upgrade of the Pierre Auger Observatory to complement the study of ultra-high-energy cosmic rays (UHECR) by measuring the muon content of extensive air showers (EAS). It consists of an array of 61 water Cherenkov detectors on a denser spacing in combination with underground scintillation detectors used for muon density measurement. Each detector is composed of three scintillation modules, with 10 m(2) detection area per module, buried at 2.3 m depth, resulting in a total detection area of 30 m(2). Silicon photomultiplier sensors (SiPM) measure the amount of scintillation light generated by charged particles traversing the modules. In this paper, the design of the front-end electronics to process the signals of those SiPMs and test results from the laboratory and from the Pierre Auger Observatory are described. Compared to our previous prototype, the new electronics shows a higher performance, higher efficiency and lower power consumption, and it has a new acquisition system with increased dynamic range that allows measurements closer to the shower core. The new acquisition system is based on the measurement of the total charge signal that the muonic component of the cosmic ray shower generates in the detector.Argentina - Comision Nacional de Energia AtomicaArgentina - Agencia Nacional de Promocion Cientifica y Tecnologica (ANPCyT)Argentina - Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET)Argentina - Gobierno de la Provincia de MendozaArgentina - Municipalidad de MalargueArgentina - NDM HoldingsArgentina - Valle Las LenasAustralian Research CouncilConselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ) Fundacao de Apoio a Pesquisa do Distrito Federal (FAPDF) Brazil - Financiadora de Estudos e Projetos (FINEP)Fundacao Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio De Janeiro (FAPERJ)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) 2019/10151-2 2010/07359-6 1999/05404-3Brazil - Ministerio da Ciencia, Tecnologia, Inovacoes e Comunicacoes (MCTIC)Brazil - Czech Republic Grant MSMT CR LTT18004 LM2015038 LM2018102 CZ.02.1.01/0.0/0.0/16_013/0001402 CZ.02.1.01/0.0/0.0/18_046/0016010 CZ.02.1.01/0.0/0.0/17_049/0008422France - Centre de Calcul IN2P3/CNRSCentre National de la Recherche Scientifique (CNRS)France - Conseil Regional Ile-de-FranceFrance - Departement Physique Nucleaire et Corpusculaire (PNC-IN2P3/CNRS)France - Departement Sciences de l'Univers (SDU-INSU/CNRS)French National Research Agency (ANR) LABEX ANR-10-LABX-63Institut Lagrange de Paris (ILP) within the Investissements d'Avenir Programme ANR-11-IDEX-0004-02Federal Ministry of Education & Research (BMBF)Bundesministerium fur Bildung und Forschung (BMBF)German Research Foundation (DFG)Germany - Finanzministerium Baden-WurttembergGermany - Helmholtz Alliance for Astroparticle Physics (HAP)Germany - Helmholtz-Gemeinschaft Deutscher Forschungszentren (HGF)Germany - Ministerium fur Innovation, Wissenschaft und Forschung des Landes Nordrhein-WestfalenGermany - Ministerium fur Wissenschaft, Forschung und Kunst des Landes Baden-WurttembergItaly - Istituto Nazionale di Fisica Nucleare (INFN)Italy - Istituto Nazionale di Astrofisica (INAF)Italy - Ministero dell'Istruzione, dell'Universita e della Ricerca (MIUR)Italy - CETEMPS Center of ExcellenceConsejo Nacional de Ciencia y Tecnologia (CONACyT) 167733Mexico - Universidad Nacional Autonoma de Mexico (UNAM)Mexico - PAPIIT DGAPA-UNAMNetherlands - Ministry of Education, Culture and ScienceNetherlands Organization for Scientific Research (NWO)Netherlands Organisation for Scientific Research (NWO)The Netherlands - SURF CooperativePoland - Ministry of Science and Higher Education DIR/WK/2018/11 Poland - National Science Centre 2013/08/M/ST9/00322 2016/23/B/ST9/01635 HARMONIA 5-2013/10/M/ST9/00062 UMO-2016/22/M/ST9/00198Portugal - Portuguese national funds Portugal - FEDER funds within Programa Operacional Factores de Competitividade through Fundacao para a Ciencia e a Tecnologia (COMPETE)Romania - Romanian Ministry of Education and Research Romania - Program Nucleu within MCI PN19150201/16N/2019 PN19060102 Romania - PNCDI III PN-III-P1-1.2-PCCDI-2017-0839/19PCCDI/2018Slovenian Research Agency - Slovenia P1-0031 P1-0385 I0-0033 N1-0111Spain - Ministerio de Economia, Industria y Competitividad FPA2017-85114-P FPA2017-85197-PSpain - Xunta de Galicia ED431C 2017/07Junta de Andalucia SOMM17/6104/UGRSpain - Feder FundsSpain - RENATA Red Nacional Tematica de Astroparticulas FPA2015-68783-REDTSpain - Maria de Maeztu Unit of Excellence MDM-2016-0692United States Department of Energy (DOE) DE-AC02-07CH11359National Science Foundation (NSF) 0450696U.S.A. - Grainger Foundation U.S.A. - Marie Curie-IRSES/EPLANET U.S.A. - European Particle Physics Latin American Network U.S.A. - UNESCOItaly - Ministero degli Affari Esteri (MAE)The Netherlands - Dutch national e-infrastructur

Deep-learning based reconstruction of the shower maximum Xmax using the water-Cherenkov detectors of the Pierre Auger Observatory

The successful installation, commissioning, and operation of the Pierre Auger Observatory would not have been possible without the strong commitment and effort from the technical and administrative staff in Malargue. We are very grateful to the following agencies and organizations for financial support. Argentina - Comision Nacional de Energia Atomica; Agencia Nacional de Promocion Cientifica y Tecnologica (ANPCyT); Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET); Gobierno de la Provincia de Mendoza; Municipalidad de Malargue; NDM Holdings and Valle Las Lenas; in gratitude for their continuing cooperation over land access; Australia -the Australian Research Council; Brazil - Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq); Financiadora de Estudos e Projetos (FINEP); Fundacao de Amparo a Pesquisa do Estado de Rio de Janeiro (FAPERJ); Sao Paulo Research Foundation (FAPESP) Grants No. 2019/10151-2, No. 2010/07359-6 and No. 1999/05404-3; Ministerio da Ciencia, Tecnologia, Inovacoes e Comunicacoes (MCTIC); Czech Republic Grant No. MSMT CR LTT18004, LM2015038, LM2018102, CZ.02.1.01/0.0/0.0/16_013/0001402, CZ.02.1.01/0.0/0.0/18_046/0016010 and CZ.02.1.01/0.0/0.0/17_049/0008422; France -Centre de Calcul IN2P3/CNRS; Centre National de la Recherche Scientifique (CNRS); Conseil Regional Ile-de-France; Departement Physique Nucleaire et Corpusculaire (PNC-IN2P3/CNRS); Departement Sciences de l'Univers (SDU-INSU/CNRS); Institut Lagrange de Paris (ILP) Grant No. LABEX ANR-10-LABX-63 within the Investissements d'Avenir Programme Grant No. ANR-11-IDEX-0004-02; Germany-Bundesministerium fur Bildung und Forschung (BMBF); Deutsche Forschungsgemeinschaft (DFG); Finanzministerium Baden-Wurttemberg; Helmholtz Alliance for Astroparticle Physics (HAP); Helmholtz-Gemeinschaft Deutscher Forschungszentren (HGF); Ministerium fur Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen; Ministerium fur Wissenschaft, Forschung und Kunst des Landes Baden-Wurttemberg; Italy - Istituto Nazionale di Fisica Nucleare (INFN); Istituto Nazionale di Astrofisica (INAF); Ministero dell'Istruzione, dell'Universita e della Ricerca (MIUR); CETEMPS Center of Excellence; Ministero degli Affari Esteri (MAE); Mexico-Consejo Nacional de Ciencia y Tecnologia (CONACYT) No. 167733; Universidad Nacional Autonoma de Mexico (UNAM); PAPIIT DGAPA-UNAM; The Netherlands - Ministry of Education, Culture and Science; Netherlands Organisation for Scientific Research (NWO); Dutch national e-infrastructure with the support of SURF Cooperative; Poland - Ministry of Science and Higher Education, grant No. DIR/WK/2018/11; National Science Centre, Grants No. 2013/08/M/ST9/00322, No. 2016/23/B/ST9/01635 and No. HARMONIA 5-2013/10/M/ST9/00062, UMO-2016/22/M/ST9/00198; Portugal - Portuguese national funds and FEDER funds within Programa Operacional Factores de Competitividade through Fundacao para a Ciencia e a Tecnologia (COMPETE); Romania-Romanian Ministry of Education and Research, the Program Nucleu within MCI (PN19150201/16N/2019 and PN-19060102) and project PNIII-P1-1.2-PCCDI-2017-0839/19PCCDI/2018 within PNCDI III; Slovenia - Slovenian Research Agency, grants P1-0031, P1-0385, I0-0033, N1-0111; Spain - Ministerio de Economia, Industria y Competitividad (FPA2017-85114-P and PID2019-104676GB-C32, Xunta de Galicia (ED431C 2017/07), Junta de Andalucia (SOMM17/6104/UGR, P18-FR-4314) Feder Funds, RENATA Red Nacional Tematica de Astroparticulas (FPA2015-68783-REDT) and Maria de Maeztu Unit of Excellence (MDM-2016-0692); USA -Department of Energy, Contracts No. DE-AC02-07CH11359, No. DE-FR02-04ER41300, No. DE-FG02-99ER41107 and No. DE-SC0011689; National Science Foundation, Grant No. 0450696; The Grainger Foundation; Marie Curie-IRSES/EPLANET; European Particle Physics Latin American Network; and UNESCO.The atmospheric depth of the air shower maximum X-max is an observable commonly used for the determination of the nuclear mass composition of ultra-high energy cosmic rays. Direct measurements of X-max are performed using observations of the longitudinal shower development with fluorescence telescopes. At the same time, several methods have been proposed for an indirect estimation of X-max from the characteristics of the shower particles registered with surface detector arrays. In this paper, we present a deep neural network (DNN) for the estimation of X-max The reconstruction relies on the signals induced by shower particles in the ground based water-Cherenkov detectors of the Pierre Auger Observatory. The network architecture features recurrent long short-term memory layers to process the temporal structure of signals and hexagonal convolutions to exploit the symmetry of the surface detector array. We evaluate the performance of the network using air showers simulated with three different hadronic interaction models. Thereafter, we account for long-term detector effects and calibrate the reconstructed X-max using fluorescence measurements. Finally, we show that the event-by-event resolution in the reconstruction of the shower maximum improves with increasing shower energy and reaches less than 25 g/cm(2) at energies above 2x10(19) eV.United States Department of Energy (DOE) DE-AC02-07CH11359 - DE-FR02-04ER41300 - DE- FG02-99ER41107 - DE-SC0011689Argentina - Comision Nacional de Energia AtomicaArgentina - Agencia Nacional de Promocion Cientifica y Tecnologica (ANPCyT)Argentina - Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET)Argentina - Gobierno de la Provincia de MendozaArgentina - Municipalidad de MalargueAustralian Research CouncilConselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ) Fundacao de Apoio a Pesquisa do Distrito Federal (FAPDF)Brazil - Financiadora de Estudos e Projetos (FINEP)Fundacao Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio De Janeiro (FAPERJ)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) 2019/10151-2-2010/07359-6-1999/05404-3Brazil - Ministerio da Ciencia, Tecnologia, Inovacoes e Comunicacoes (MCTIC)Czech Republic Grant MSMT CR LTT18004 - LM2015038 - LM2018102 - CZ.02.1.01/0.0/0.0/16_013/0001402 - CZ.02.1.01/0.0/0.0/18_046/0016010 - CZ.02.1.01/0.0/0.0/17_049/0008422France - Centre de Calcul IN2P3/CNRSCentre National de la Recherche Scientifique (CNRS)France - Conseil Regional Ile-de-FranceFrance - Departement Physique Nucleaire et Corpusculaire (PNC-IN2P3/CNRS)France - Departement Sciences de l'Univers (SDU-INSU/CNRS)French National Research Agency (ANR) LABEX ANR-10-LABX-63 - ANR-11-IDEX-0004-02Federal Ministry of Education & Research (BMBF)German Research Foundation (DFG)Germany-Finanzministerium Baden-WurttembergGermany-Helmholtz Alliance for Astroparticle Physics (HAP)Germany-Helmholtz-Gemeinschaft Deutscher Forschungszentren (HGF)Germany-Ministerium fur Innovation, Wissenschaft und Forschung des Landes Nordrhein-WestfalenGermany-Ministerium fur Wissenschaft, Forschung und Kunst des Landes Baden-WurttembergItaly - Istituto Nazionale di Fisica Nucleare (INFN)Italy - Istituto Nazionale di Astrofisica (INAF)Italy - Ministero dell'Istruzione, dell'Universita e della Ricerca (MIUR)Italy - CETEMPS Center of ExcellenceItaly - Ministero degli Affari Esteri (MAE)Consejo Nacional de Ciencia y Tecnologia (CONACyT) 167733Mexico-Universidad Nacional Autonoma de Mexico (UNAM)Mexico-PAPIIT DGAPA-UNAMThe Netherlands - Ministry of Education, Culture and ScienceNetherlands Organization for Scientific Research (NWO)The Netherlands - SURF CooperativePoland - Ministry of Science and Higher Education DIR/WK/2018/11Poland - National Science Centre 2013/08/M/ST9/00322 - 2016/23/B/ST9/01635 -HARMONIA 5-2013/10/M/ST9/00062 - UMO-2016/22/M/ST9/00198Portugal - Portuguese national fundsPortugal - FEDER funds within Programa Operacional Factores de Competitividade through Fundacao para a Ciencia e a Tecnologia (COMPETE)Romania-Romanian Ministry of Education and ResearchRomania-Program Nucleu within MCI PN19150201/16N/2019 - PN-19060102Romania-PNCDI III PNIII-P1-1.2-PCCDI-2017-0839/19PCCDI/2018Slovenian Research Agency - Slovenia P1-0031 - P1-0385 - I0-0033 - N1-0111Spain - Ministerio de Economia, Industria y Competitividad FPA2017-85114-P - PID2019-104676GB-C32Spain - Xunta de Galicia ED431C 2017/07Junta de Andalucia SOMM17/6104/UGR - P18-FR-4314Spain - RENATA Red Nacional Tematica de Astroparticulas FPA2015-68783-REDTSpain - Maria de Maeztu Unit of Excellence MDM-2016-0692National Science Foundation (NSF) 0450696USA - Grainger FoundationUSA - Marie Curie-IRSES/EPLANETUSA - European Particle Physics Latin American NetworkUSA - UNESCOArgentina - NDM Holdings and Valle Las LenasThe Netherlands - Dutch national e-infrastructureSpain - Feder Fund

How good are rodent models of carcinogenesis in predicting efficacy in humans? A systematic review and meta-analysis of colon chemoprevention in rats, mice and men

Tumours in rodent and human colon share many histological and genetic features. To know if rodent models of colon carcinogenesis are good predictors of chemopreventive efficacy in humans, we made a meta-analysis of aspirin, beta-carotene, calcium, and wheat bran studies. Controlled intervention studies of adenoma recurrence in human volunteers were compared with chemoprevention studies of carcinogen-induced tumours in rats, and of polyps in Min (Apc(+/-)) mice: 6714 volunteers, 3911 rats and 458 mice were included in the meta-analyses. Difference between models was small since most global relative risks were between 0.76 and 1.00. A closer look showed that carcinogen-induced rat studies matched human trials for aspirin, calcium, carotene, and were compatible for wheat bran. Min mice results were compatible with human results for aspirin, but discordant for calcium and wheat bran (no carotene study). These few results suggest that rodent models roughly predict effect in humans, but the prediction is not accurate for all agents. Based on three cases only, the carcinogen-induced rat model seems better than the Min mouse model. However, rodent studies are useful to screen potential chemopreventive agents, and to study mechanisms of carcinogenesis and chemoprevention

BrAPI-an application programming interface for plant breeding applications

Motivation: Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. Results: To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases