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Aaij R, Albrecht J, Belous M, Billoir P, Boettcher T, Brea Rodríguez A, Vom Bruch D, Cámpora Pérez DH, Casais Vidal A, Craik DC, Fernandez Declara P, Funke L, Gligorov VV, Jashal B, Kazeev N, Martínez Santos D, Pisani F, Pliushchenko D, Popov S, Quagliani R, Rangel M, Reiss F, Sánchez Mayordomo C, Schwemmer R, Sokoloff M, Stevens H, Ustyuzhanin A, Vilasís Cardona X, Williams M. Allen: A High-Level Trigger on GPUs for LHCb. ACTA ACUST UNITED AC 2021; 4:7. [PMID: 33385105 PMCID: PMC7769791 DOI: 10.1007/s41781-020-00039-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/03/2020] [Indexed: 11/28/2022]
Abstract
We describe a fully GPU-based implementation of the first level trigger for the upgrade of the LHCb detector, due to start data taking in 2021. We demonstrate that our implementation, named Allen, can process the 40 Tbit/s data rate of the upgraded LHCb detector and perform a wide variety of pattern recognition tasks. These include finding the trajectories of charged particles, finding proton-proton collision points, identifying particles as hadrons or muons, and finding the displaced decay vertices of long-lived particles. We further demonstrate that Allen can be implemented in around 500 scientific or consumer GPU cards, that it is not I/O bound, and can be operated at the full LHC collision rate of 30 MHz. Allen is the first complete high-throughput GPU trigger proposed for a HEP experiment.
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Affiliation(s)
- R Aaij
- Nikhef National Institute for Subatomic Physics, Amsterdam, The Netherlands
| | - J Albrecht
- Fakultät Physik, Technische Universität Dortmund, Dortmund, Germany
| | - M Belous
- National Research University Higher School of Economics, Moscow, Russia.,Yandex School of Data Analysis, Moscow, Russia
| | - P Billoir
- LPNHE, Sorbonne Université, Paris Diderot Sorbonne Paris Cité, CNRS/IN2P3, Paris, France
| | - T Boettcher
- Massachusetts Institute of Technology, Cambridge, USA
| | - A Brea Rodríguez
- Instituto Galego de Física de Altas Enerxías (IGFAE), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - D Vom Bruch
- LPNHE, Sorbonne Université, Paris Diderot Sorbonne Paris Cité, CNRS/IN2P3, Paris, France
| | - D H Cámpora Pérez
- Nikhef National Institute for Subatomic Physics, Amsterdam, The Netherlands.,Faculty of Science and Engineering, Maastricht University, Maastricht, The Netherlands
| | - A Casais Vidal
- Instituto Galego de Física de Altas Enerxías (IGFAE), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - D C Craik
- Massachusetts Institute of Technology, Cambridge, USA
| | - P Fernandez Declara
- European Organization for Nuclear Research (CERN), Geneva, Switzerland.,Department of Computer Science and Engineering, University Carlos III of Madrid, Madrid, Spain
| | - L Funke
- Fakultät Physik, Technische Universität Dortmund, Dortmund, Germany
| | - V V Gligorov
- LPNHE, Sorbonne Université, Paris Diderot Sorbonne Paris Cité, CNRS/IN2P3, Paris, France
| | - B Jashal
- Instituto de Física Corpuscular, Centro Mixto Universidad de Valencia, CSIC, Valencia, Spain
| | - N Kazeev
- National Research University Higher School of Economics, Moscow, Russia.,Yandex School of Data Analysis, Moscow, Russia
| | - D Martínez Santos
- Instituto Galego de Física de Altas Enerxías (IGFAE), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - F Pisani
- European Organization for Nuclear Research (CERN), Geneva, Switzerland.,INFN Sezione di Bologna, Bologna, Italy.,Università di Bologna, Bologna, Italy
| | - D Pliushchenko
- Yandex School of Data Analysis, Moscow, Russia.,National Research University Higher School of Economics, Saint Petersburg, Russia
| | - S Popov
- National Research University Higher School of Economics, Moscow, Russia.,Yandex School of Data Analysis, Moscow, Russia.,National University of Science and Technology MISIS, Moscow, Russia
| | - R Quagliani
- LPNHE, Sorbonne Université, Paris Diderot Sorbonne Paris Cité, CNRS/IN2P3, Paris, France
| | - M Rangel
- Instituto de Física, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - F Reiss
- LPNHE, Sorbonne Université, Paris Diderot Sorbonne Paris Cité, CNRS/IN2P3, Paris, France
| | - C Sánchez Mayordomo
- Instituto de Física Corpuscular, Centro Mixto Universidad de Valencia, CSIC, Valencia, Spain
| | - R Schwemmer
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - M Sokoloff
- University of Cincinnati, Cincinnati, OH USA
| | - H Stevens
- Fakultät Physik, Technische Universität Dortmund, Dortmund, Germany
| | - A Ustyuzhanin
- National Research University Higher School of Economics, Moscow, Russia.,Yandex School of Data Analysis, Moscow, Russia.,National University of Science and Technology MISIS, Moscow, Russia
| | | | - M Williams
- Massachusetts Institute of Technology, Cambridge, USA
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Heinrich T, Funke L, Köhler M, Schkade UK, Ullrich F, Löbner W, Höpner J, Weiß D. Optimization of the selection of analysis methods for the determination of naturally occurring radionuclides. KERNTECHNIK 2013. [DOI: 10.3139/124.100547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The determination of naturally occurring radionuclides in the environment is a complex problem. Particularly the optimization of the analysis methods is very important, while the choice of the method influences the financial and personnel resources, as well as the quality of the results. This work is prepared from a working group within the working group(suggest instead use Research Group) “natural radioactivity” of the German-Swiss radiation protection association (FS). It is a recommendation for clients of existing laboratories, as well as new or renovated laboratories, which order measurements. This article shows some excerpts of the full work.
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Affiliation(s)
- T. Heinrich
- (E-Mail: ), Staatliche Umweltbetriebsgesellschaft; Geschäftsbereich Umweltradioaktivität; Altwahnsdorf 12; 01445 Radebeul; Germany
| | - L. Funke
- IAF – Radioökologie GmbH; Karpatenstr. 20; 01326 Dresden; Germany
| | - M. Köhler
- Verein für Kernverfahrenstechnik und Analytik e. V.; Fachbereich Analytik; Postfach 51 01 19, 01314 Dresden; Germany
| | - U.-K. Schkade
- Bundesamt für Strahlenschutz; Köpenicker Allee 120 – 130; 10318 Berlin; Germany
| | - F. Ullrich
- Thüringer Landesanstalt für Umwelt und Geologie; Hermann-Drechsler-Str. 1; 07548 Gera; Germany
| | - W. Löbner
- Wismut GmbH, Jagdschänkenstr. 29, 09117 Chemnitz, Germany
| | - J. Höpner
- Wismut GmbH, Jagdschänkenstr. 29, 09117 Chemnitz, Germany
| | - D. Weiß
- Gesellschaft für Anlagen- und Reaktorsicherheit (GRS) mbH; Kurfürstendamm 200; 10719 Berlin
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Olsen O, Funke L, Long JF, Fukata M, Kazuta T, Trinidad JC, Moore KA, Misawa H, Welling PA, Burlingame AL, Zhang M, Bredt DS. Renal defects associated with improper polarization of the CRB and DLG polarity complexes in MALS-3 knockout mice. ACTA ACUST UNITED AC 2008; 179:151-64. [PMID: 17923534 PMCID: PMC2064744 DOI: 10.1083/jcb.200702054] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Kidney development and physiology require polarization of epithelia that line renal tubules. Genetic studies show that polarization of invertebrate epithelia requires the crumbs, partition-defective-3, and discs large complexes. These evolutionarily conserved protein complexes occur in mammalian kidney; however, their role in renal development remains poorly defined. Here, we find that mice lacking the small PDZ protein mammalian LIN-7c (MALS-3) have hypomorphic, cystic, and fibrotic kidneys. Proteomic analysis defines MALS-3 as the only known core component of both the crumbs and discs large cell polarity complexes. MALS-3 mediates stable assembly of the crumbs tight junction complex and the discs large basolateral complex, and these complexes are disrupted in renal epithelia from MALS-3 knockout mice. Interestingly, MALS-3 controls apico-basal polarity preferentially in epithelia derived from metanephric mesenchyme, and defects in kidney architecture owe solely to MALS expression in these epithelia. These studies demonstrate that defects in epithelial cell polarization can cause cystic and fibrotic renal disease.
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Affiliation(s)
- Olav Olsen
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA.
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Olsen O, Funke L, Long J, Fukata M, Nicoll RA, Zhang M, Bredt DS. Renal cysts and fibrosis caused by epithelial cell polarity defects in mice lacking mammalian Lin‐7c (MALS‐3). FASEB J 2007. [DOI: 10.1096/fasebj.21.5.a544-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Olav Olsen
- PhysiologyUniversity of CaliforniaSan Francisco, 600 16th Street Box 2140, Genentech Hall Rm N274San FranciscoCA94143
| | - Lars Funke
- PhysiologyUniversity of CaliforniaSan Francisco, 600 16th Street Box 2140, Genentech Hall Rm N274San FranciscoCA94143
| | - Jia‐fu Long
- Hong Kong University of Science and TechnologyClear Water BayKowloonHong Kong
| | - Masaki Fukata
- PhysiologyUniversity of CaliforniaSan Francisco, 600 16th Street Box 2140, Genentech Hall Rm N274San FranciscoCA94143
| | - Roger A Nicoll
- Cellular and Molecular PharmacologyUniversity of CaliforniaSan Francisco, 600 16th Street, Genentech HallSan FranciscoCA94143
| | - Mingjie Zhang
- Hong Kong University of Science and TechnologyClear Water BayKowloonHong Kong
| | - David S Bredt
- Integrative BiologyEli Lilly and CompanyDepartment of Integrative BiologyEli Lilly and CompanyIndianapolisIN46285
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Elias GM, Funke L, Stein V, Grant SG, Bredt DS, Nicoll RA. Synapse-Specific and Developmentally Regulated Targeting of AMPA Receptors by a Family of MAGUK Scaffolding Proteins. Neuron 2007. [DOI: 10.1016/j.neuron.2007.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Elias GM, Funke L, Stein V, Grant SG, Bredt DS, Nicoll RA. Synapse-specific and developmentally regulated targeting of AMPA receptors by a family of MAGUK scaffolding proteins. Neuron 2007; 52:307-20. [PMID: 17046693 DOI: 10.1016/j.neuron.2006.09.012] [Citation(s) in RCA: 306] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2006] [Revised: 08/07/2006] [Accepted: 09/05/2006] [Indexed: 11/15/2022]
Abstract
Trafficking of AMPA receptors (AMPA-Rs) to and from synapses controls the strength of excitatory synaptic transmission. However, proteins that cluster AMPA-Rs at synapses remain poorly understood. Here we show that PSD-95-like membrane-associated guanylate kinases (PSD-MAGUKs) mediate this synaptic targeting, and we uncover a remarkable functional redundancy within this protein family. By manipulating endogenous neuronal PSD-MAGUK levels, we find that both PSD-95 and PSD-93 independently mediate AMPA-R targeting at mature synapses. We also reveal unanticipated synapse heterogeneity as loss of either PSD-95 or PSD-93 silences largely nonoverlapping populations of excitatory synapses. In adult PSD-95 and PSD-93 double knockout animals, SAP-102 is upregulated and compensates for the loss of synaptic AMPA-Rs. At immature synapses, PSD-95 and PSD-93 play little role in synaptic AMPA-R clustering; instead, SAP-102 dominates. These studies establish a PSD-MAGUK-specific regulation of AMPA-R synaptic expression that establishes and maintains glutamatergic synaptic transmission in the mammalian central nervous system.
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Affiliation(s)
- Guillermo M Elias
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94143, USA
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Abstract
RNA editing by A-to-I modification has been recognized as an important molecular mechanism for generating RNA and protein diversity. In mammals, it is mediated by a family of adenosine deaminases that act on RNAs (ADARs). The large version of the editing enzyme ADAR1 (ADAR1-L), expressed from an interferon-responsible promoter, has a Z-DNA/Z-RNA binding domain at its N-terminus. We have tested the in vitro ability of the enzyme to act on a 50 bp segment of dsRNA with or without a Z-RNA forming nucleotide sequence. A-to-I editing efficiency is markedly enhanced in presence of the sequence favoring Z-RNA. In addition, an alteration in the pattern of modification along the RNA duplex becomes evident as reaction times decrease. These results suggest that the local conformation of dsRNA molecules might be an important feature for target selectivity by ADAR1 and other proteins with Z-RNA binding domains.
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Affiliation(s)
- Michael Koeris
- Department of Biology, Massachusetts Institute of TechnologyCambridge, MA 02142, USA
- Institut für Biochemie, Freie Universität BerlinGermany
| | - Lars Funke
- Department of Biology, Massachusetts Institute of TechnologyCambridge, MA 02142, USA
| | - Jay Shrestha
- Department of Biology, Massachusetts Institute of TechnologyCambridge, MA 02142, USA
| | - Alexander Rich
- Department of Biology, Massachusetts Institute of TechnologyCambridge, MA 02142, USA
| | - Stefan Maas
- Department of Biological Sciences, Lehigh UniversityBethlehem, PA 18015, USA
- To whom correspondence should be addressed. Tel: +1 610 758 6276; Fax: +1 610 758 4004;
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Abstract
Tissue development, differentiation, and physiology require specialized cellular adhesion and signal transduction at sites of cell-cell contact. Scaffolding proteins that tether adhesion molecules, receptors, and intracellular signaling enzymes organize macromolecular protein complexes at cellular junctions to integrate these functions. One family of such scaffolding proteins is the large group of membrane-associated guanylate kinases (MAGUKs). Genetic studies have highlighted critical roles for MAGUK proteins in the development and physiology of numerous tissues from a variety of metazoan organisms. Mutation of Drosophila discs large (dlg) disrupts epithelial septate junctions and causes overgrowth of imaginal discs. Similarly, mutation of lin-2, a related MAGUK in Caenorhabditis elegans, blocks vulval development, and mutation of the postsynaptic density protein PSD-95 impairs synaptic plasticity in mammalian brain. These diverse roles are explained by recent biochemical and structural analyses of MAGUKs, which demonstrate their capacity to assemble well--efined--yet adaptable--protein complexes at cellular junctions.
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Affiliation(s)
- Lars Funke
- Department of Physiology, University of California at San Francisco, California 94143, USA.
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Schulz H, Funke L, Schellenberger A. Study of long term radon transport by measuring the difference of the 210Pb and 226Ra activity in soil as a function of the depth. Health Phys 2003; 84:236-244. [PMID: 12553654 DOI: 10.1097/00004032-200302000-00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Long term radon transport has been studied by measuring the activity difference of 210Pb and 226Ra in soil as a function of the depth. The results are from test pits of 1-2 m depth made at a dam of a tailings pond and at the plateau of a waste rock pile. Soil samples of about 1 kg were taken at a successive distances of 5 cm and analyzed by means of gamma-ray spectroscopy using low background germanium n-type detectors. It is shown that by this method nearly model independent information about the radon transport over a period of several decades can be inferred from the data.
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Affiliation(s)
- H Schulz
- Radioökologie GmbH Dresden, Karpatenstr. 20, 01326 Dresden, Germany.
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Döring J, Schwengner R, Funke L, Rotter H, Winter G, Cederwall B, Lidén F, Johnson A, Atac A, Nyberg J, Sletten G. High-lying three-quasiparticle bands and signature splitting in 81Rb. Phys Rev C Nucl Phys 1994; 50:1845-1850. [PMID: 9969859 DOI: 10.1103/physrevc.50.1845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Winter G, Schwengner R, Reif J, Prade H, Funke L, Wirowski R, Nicolay N, Dewald A, Grawe H, Schubart R. Study of excited states in 85Kr and 86Kr: Evidence for neutron-core excitations in the N=50 nucleus 86Kr. Phys Rev C Nucl Phys 1993; 48:1010-1019. [PMID: 9968931 DOI: 10.1103/physrevc.48.1010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Döring J, Winter G, Funke L, Cederwall B, Lidén F, Johnson A, Atac A, Nyberg J, Sletten G, Sugawara M. Evidence for new isomers and band structures in 80Rb. Phys Rev C Nucl Phys 1992; 46:R2127-R2131. [PMID: 9968400 DOI: 10.1103/physrevc.46.r2127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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