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Amaducci S, Colonna N, Cosentino L, Cristallo S, Finocchiaro P, Krtička M, Massimi C, Mastromarco M, Mazzone A, Maugeri EA, Mengoni A, Roederer IU, Straniero O, Valenta S, Vescovi D, Aberle O, Alcayne V, Andrzejewski J, Audouin L, Babiano-Suarez V, Bacak M, Barbagallo M, Bennett S, Berthoumieux E, Billowes J, Bosnar D, Brown A, Busso M, Caamaño M, Caballero-Ontanaya L, Calviño F, Calviani M, Cano-Ott D, Casanovas A, Cerutti F, Chiaveri E, Cortés G, Cortés-Giraldo MA, Damone LA, Davies PJ, Diakaki M, Dietz M, Domingo-Pardo C, Dressler R, Ducasse Q, Dupont E, Durán I, Eleme Z, Fernández-Domínguez B, Ferrari A, Furman V, Göbel K, Garg R, Gawlik-Ramięga A, Gilardoni S, Gonçalves IF, González-Romero E, Guerrero C, Gunsing F, Harada H, Heinitz S, Heyse J, Jenkins DG, Junghans A, Käppeler F, Kadi Y, Kimura A, Knapová I, Kokkoris M, Kopatch Y, Kurtulgil D, Ladarescu I, Lederer-Woods C, Leeb H, Lerendegui-Marco J, Lonsdale SJ, Macina D, Manna A, Martínez T, Masi A, Mastinu P, Mendoza E, Michalopoulou V, Milazzo PM, Mingrone F, Moreno-Soto J, Musumarra A, Negret A, Nolte R, Ogállar F, Oprea A, Patronis N, Pavlik A, Perkowski J, Petrone C, Piersanti L, Pirovano E, Porras I, Praena J, Quesada JM, Ramos-Doval D, Rauscher T, Reifarth R, Rochman D, Rubbia C, Sabaté-Gilarte M, Saxena A, Schillebeeckx P, Schumann D, Sekhar A, Smith AG, Sosnin NV, Sprung P, Stamatopoulos A, Tagliente G, Tain JL, Tarifeño-Saldivia A, Tassan-Got L, Thomas T, Torres-Sánchez P, Tsinganis A, Ulrich J, Urlass S, Vannini G, Variale V, Vaz P, Ventura A, Vlachoudis V, Vlastou R, Wallner A, Woods PJ, Wright T, Žugec P. Measurement of the ^{140}Ce(n,γ) Cross Section at n_TOF and Its Astrophysical Implications for the Chemical Evolution of the Universe. Phys Rev Lett 2024; 132:122701. [PMID: 38579210 DOI: 10.1103/physrevlett.132.122701] [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] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/09/2023] [Accepted: 01/31/2024] [Indexed: 04/07/2024]
Abstract
^{140}Ce(n,γ) is a key reaction for slow neutron-capture (s-process) nucleosynthesis due to being a bottleneck in the reaction flow. For this reason, it was measured with high accuracy (uncertainty ≈5%) at the n_TOF facility, with an unprecedented combination of a high purity sample and low neutron-sensitivity detectors. The measured Maxwellian averaged cross section is up to 40% higher than previously accepted values. Stellar model calculations indicate a reduction around 20% of the s-process contribution to the Galactic cerium abundance and smaller sizeable differences for most of the heavier elements. No variations are found in the nucleosynthesis from massive stars.
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Affiliation(s)
- S Amaducci
- INFN Laboratori Nazionali del Sud, Catania, Italy
| | - N Colonna
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Italy
| | - L Cosentino
- INFN Laboratori Nazionali del Sud, Catania, Italy
| | - S Cristallo
- Istituto Nazionale di Astrofisica - Osservatorio Astronomico d'Abruzzo, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Perugia, Italy
| | | | - M Krtička
- Charles University, Prague, Czech Republic
| | - C Massimi
- Istituto Nazionale di Fisica Nucleare, Sezione di Bologna, Italy
- Dipartimento di Fisica e Astronomia, Università di Bologna, Italy
| | - M Mastromarco
- European Organization for Nuclear Research (CERN), Switzerland
| | - A Mazzone
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Italy
- Consiglio Nazionale delle Ricerche, Bari, Italy
| | - E A Maugeri
- Paul Scherrer Institut (PSI), Villigen, Switzerland
| | - A Mengoni
- Istituto Nazionale di Fisica Nucleare, Sezione di Bologna, Italy
- Agenzia nazionale per le nuove tecnologie, l'energia e lo sviluppo economico sostenibile (ENEA), Italy
| | - I U Roederer
- Department of Physics, North Carolina State University, Raleigh, Norh Carolina 27695, USA
- Department of Astronomy, University of Michigan, Ann Arbor, Michigan 48109, USA
- Joint Institute for Nuclear Astrophysics-Center for the Evolution of the Elements (JINA-CEE), USA
| | - O Straniero
- Istituto Nazionale di Astrofisica - Osservatorio Astronomico d'Abruzzo, Italy
- INFN Sezione Napoli, Napoli, Italy
| | - S Valenta
- Charles University, Prague, Czech Republic
| | - D Vescovi
- Istituto Nazionale di Astrofisica - Osservatorio Astronomico d'Abruzzo, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Perugia, Italy
| | - O Aberle
- European Organization for Nuclear Research (CERN), Switzerland
| | - V Alcayne
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Spain
| | | | - L Audouin
- Institut de Physique Nucléaire, CNRS-IN2P3, Univ. Paris-Sud, Université Paris-Saclay, F-91406 Orsay Cedex, France
| | - V Babiano-Suarez
- Instituto de Física Corpuscular, CSIC - Universidad de Valencia, Spain
| | - M Bacak
- European Organization for Nuclear Research (CERN), Switzerland
- TU Wien, Atominstitut, Stadionallee 2, 1020 Wien, Austria
- CEA Irfu, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - M Barbagallo
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Italy
- European Organization for Nuclear Research (CERN), Switzerland
| | - S Bennett
- University of Manchester, United Kingdom
| | - E Berthoumieux
- CEA Irfu, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - J Billowes
- University of Manchester, United Kingdom
| | - D Bosnar
- Department of Physics, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - A Brown
- University of York, United Kingdom
| | - M Busso
- Istituto Nazionale di Fisica Nucleare, Sezione di Perugia, Italy
- Dipartimento di Fisica e Geologia, Università di Perugia, Italy
| | - M Caamaño
- IGFAE-Universidade de Santiago de Compostela, Spain
| | | | - F Calviño
- Universitat Politècnica de Catalunya, Spain
| | - M Calviani
- European Organization for Nuclear Research (CERN), Switzerland
| | - D Cano-Ott
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Spain
| | | | - F Cerutti
- European Organization for Nuclear Research (CERN), Switzerland
| | - E Chiaveri
- European Organization for Nuclear Research (CERN), Switzerland
- University of Manchester, United Kingdom
| | - G Cortés
- Universitat Politècnica de Catalunya, Spain
| | | | - L A Damone
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Italy
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari, Italy
| | - P J Davies
- University of Manchester, United Kingdom
| | - M Diakaki
- European Organization for Nuclear Research (CERN), Switzerland
- National Technical University of Athens, Greece
| | - M Dietz
- School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - C Domingo-Pardo
- Instituto de Física Corpuscular, CSIC - Universidad de Valencia, Spain
| | - R Dressler
- Paul Scherrer Institut (PSI), Villigen, Switzerland
| | - Q Ducasse
- Physikalisch-Technische Bundesanstalt (PTB), Bundesallee 100, 38116 Braunschweig, Germany
| | - E Dupont
- CEA Irfu, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - I Durán
- IGFAE-Universidade de Santiago de Compostela, Spain
| | - Z Eleme
- University of Ioannina, Greece
| | | | - A Ferrari
- European Organization for Nuclear Research (CERN), Switzerland
| | - V Furman
- Affiliated with an institute or an international laboratory covered by a cooperation agreement with CERN
| | - K Göbel
- Goethe University Frankfurt, Germany
| | - R Garg
- School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | | | - S Gilardoni
- European Organization for Nuclear Research (CERN), Switzerland
| | | | - E González-Romero
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Spain
| | | | - F Gunsing
- CEA Irfu, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - H Harada
- Japan Atomic Energy Agency (JAEA), Tokai-Mura, Japan
| | - S Heinitz
- Paul Scherrer Institut (PSI), Villigen, Switzerland
| | - J Heyse
- European Commission, Joint Research Centre (JRC), Geel, Belgium
| | | | - A Junghans
- Helmholtz-Zentrum Dresden-Rossendorf, Germany
| | - F Käppeler
- Karlsruhe Institute of Technology, Campus North, IKP, 76021 Karlsruhe, Germany
| | - Y Kadi
- European Organization for Nuclear Research (CERN), Switzerland
| | - A Kimura
- Japan Atomic Energy Agency (JAEA), Tokai-Mura, Japan
| | - I Knapová
- Charles University, Prague, Czech Republic
| | - M Kokkoris
- National Technical University of Athens, Greece
| | - Y Kopatch
- Affiliated with an institute or an international laboratory covered by a cooperation agreement with CERN
| | | | - I Ladarescu
- Instituto de Física Corpuscular, CSIC - Universidad de Valencia, Spain
| | - C Lederer-Woods
- School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - H Leeb
- TU Wien, Atominstitut, Stadionallee 2, 1020 Wien, Austria
| | | | - S J Lonsdale
- School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - D Macina
- European Organization for Nuclear Research (CERN), Switzerland
| | - A Manna
- Istituto Nazionale di Fisica Nucleare, Sezione di Bologna, Italy
- Dipartimento di Fisica e Astronomia, Università di Bologna, Italy
| | - T Martínez
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Spain
| | - A Masi
- European Organization for Nuclear Research (CERN), Switzerland
| | - P Mastinu
- INFN Laboratori Nazionali di Legnaro, Italy
| | - E Mendoza
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Spain
| | - V Michalopoulou
- European Organization for Nuclear Research (CERN), Switzerland
- National Technical University of Athens, Greece
| | - P M Milazzo
- Istituto Nazionale di Fisica Nucleare, Sezione di Trieste, Italy
| | - F Mingrone
- European Organization for Nuclear Research (CERN), Switzerland
| | - J Moreno-Soto
- CEA Irfu, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - A Musumarra
- Istituto Nazionale di Fisica Nucleare, Sezione di Catania, Italy
- Department of Physics and Astronomy, University of Catania, Italy
| | - A Negret
- Horia Hulubei National Institute of Physics and Nuclear Engineering, Romania
| | - R Nolte
- Physikalisch-Technische Bundesanstalt (PTB), Bundesallee 100, 38116 Braunschweig, Germany
| | | | - A Oprea
- Horia Hulubei National Institute of Physics and Nuclear Engineering, Romania
| | | | - A Pavlik
- University of Vienna, Faculty of Physics, Vienna, Austria
| | | | - C Petrone
- Horia Hulubei National Institute of Physics and Nuclear Engineering, Romania
| | - L Piersanti
- Istituto Nazionale di Astrofisica - Osservatorio Astronomico d'Abruzzo, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Perugia, Italy
| | - E Pirovano
- Physikalisch-Technische Bundesanstalt (PTB), Bundesallee 100, 38116 Braunschweig, Germany
| | | | | | | | - D Ramos-Doval
- Institut de Physique Nucléaire, CNRS-IN2P3, Univ. Paris-Sud, Université Paris-Saclay, F-91406 Orsay Cedex, France
| | - T Rauscher
- Department of Physics, University of Basel, Switzerland
- Centre for Astrophysics Research, University of Hertfordshire, United Kingdom
| | | | - D Rochman
- Paul Scherrer Institut (PSI), Villigen, Switzerland
| | - C Rubbia
- European Organization for Nuclear Research (CERN), Switzerland
| | - M Sabaté-Gilarte
- European Organization for Nuclear Research (CERN), Switzerland
- Universidad de Sevilla, Spain
| | - A Saxena
- Bhabha Atomic Research Centre (BARC), India
| | - P Schillebeeckx
- European Commission, Joint Research Centre (JRC), Geel, Belgium
| | - D Schumann
- Paul Scherrer Institut (PSI), Villigen, Switzerland
| | - A Sekhar
- University of Manchester, United Kingdom
| | - A G Smith
- University of Manchester, United Kingdom
| | - N V Sosnin
- University of Manchester, United Kingdom
| | - P Sprung
- Paul Scherrer Institut (PSI), Villigen, Switzerland
| | | | - G Tagliente
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Italy
| | - J L Tain
- Instituto de Física Corpuscular, CSIC - Universidad de Valencia, Spain
| | | | - L Tassan-Got
- European Organization for Nuclear Research (CERN), Switzerland
- Institut de Physique Nucléaire, CNRS-IN2P3, Univ. Paris-Sud, Université Paris-Saclay, F-91406 Orsay Cedex, France
- National Technical University of Athens, Greece
| | - Th Thomas
- Goethe University Frankfurt, Germany
| | | | - A Tsinganis
- European Organization for Nuclear Research (CERN), Switzerland
| | - J Ulrich
- Paul Scherrer Institut (PSI), Villigen, Switzerland
| | - S Urlass
- European Organization for Nuclear Research (CERN), Switzerland
- Helmholtz-Zentrum Dresden-Rossendorf, Germany
| | - G Vannini
- Istituto Nazionale di Fisica Nucleare, Sezione di Bologna, Italy
- Dipartimento di Fisica e Astronomia, Università di Bologna, Italy
| | - V Variale
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Italy
| | - P Vaz
- Instituto Superior Técnico, Lisbon, Portugal
| | - A Ventura
- Istituto Nazionale di Fisica Nucleare, Sezione di Bologna, Italy
| | - V Vlachoudis
- European Organization for Nuclear Research (CERN), Switzerland
| | - R Vlastou
- National Technical University of Athens, Greece
| | - A Wallner
- Australian National University, Canberra, Australia
| | - P J Woods
- School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - T Wright
- University of Manchester, United Kingdom
| | - P Žugec
- Department of Physics, Faculty of Science, University of Zagreb, Zagreb, Croatia
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Baykalov P, Bussmann B, Nair R, Smith AG, Bodner G, Hadar O, Lazarovitch N, Rewald B. Semantic segmentation of plant roots from RGB (mini-) rhizotron images-generalisation potential and false positives of established methods and advanced deep-learning models. Plant Methods 2023; 19:122. [PMID: 37932745 PMCID: PMC10629126 DOI: 10.1186/s13007-023-01101-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/27/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Manual analysis of (mini-)rhizotron (MR) images is tedious. Several methods have been proposed for semantic root segmentation based on homogeneous, single-source MR datasets. Recent advances in deep learning (DL) have enabled automated feature extraction, but comparisons of segmentation accuracy, false positives and transferability are virtually lacking. Here we compare six state-of-the-art methods and propose two improved DL models for semantic root segmentation using a large MR dataset with and without augmented data. We determine the performance of the methods on a homogeneous maize dataset, and a mixed dataset of > 8 species (mixtures), 6 soil types and 4 imaging systems. The generalisation potential of the derived DL models is determined on a distinct, unseen dataset. RESULTS The best performance was achieved by the U-Net models; the more complex the encoder the better the accuracy and generalisation of the model. The heterogeneous mixed MR dataset was a particularly challenging for the non-U-Net techniques. Data augmentation enhanced model performance. We demonstrated the improved performance of deep meta-architectures and feature extractors, and a reduction in the number of false positives. CONCLUSIONS Although correction factors are still required to match human labelled root lengths, neural network architectures greatly reduce the time required to compute the root length. The more complex architectures illustrate how future improvements in root segmentation within MR images can be achieved, particularly reaching higher segmentation accuracies and model generalisation when analysing real-world datasets with artefacts-limiting the need for model retraining.
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Affiliation(s)
- Pavel Baykalov
- Institute of Forest Ecology, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
- Vienna Scientific Instruments GmbH, Alland, Austria
| | - Bart Bussmann
- IDLab, Department of Computer Science, University of Antwerp - Imec, Antwerp, Belgium
| | - Richard Nair
- Dept. Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Jena, Germany
- Discipline of Botany, School of Natural Sciences, Trinity College, Dublin, Ireland
| | | | - Gernot Bodner
- Institute of Agronomy, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Ofer Hadar
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Naftali Lazarovitch
- Wyler Department for Dryland Agriculture, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Beersheba, Israel
| | - Boris Rewald
- Institute of Forest Ecology, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria.
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic.
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Terrones-Campos C, Ledergerber B, Forbes N, Smith AG, Petersen J, Helleberg M, Lundgren J, Specht L, Vogelius IR. Prediction of Radiation-induced Lymphopenia following Exposure of the Thoracic Region and Associated Risk of Infections and Mortality. Clin Oncol (R Coll Radiol) 2023; 35:e434-e444. [PMID: 37149425 DOI: 10.1016/j.clon.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/08/2023] [Accepted: 04/11/2023] [Indexed: 05/08/2023]
Abstract
AIMS Large blood volumes are irradiated when the heart is exposed to radiation. The mean heart dose (MHD) may be a good surrogate for circulating lymphocytes exposure. We investigated the association between MHD and radiation-induced lymphopenia and explored the impact of the end-of-radiation-therapy (EoRT) lymphocyte count on clinical outcomes. MATERIALS AND METHODS In total, 915 patients were analysed: 303 patients with breast cancer and 612 with intrathoracic tumours: oesophageal cancer (291), non-small cell lung cancer (265) and small cell lung cancer (56). Heart contours were generated using an interactive deep learning delineation process and an individual dose volume histogram for each heart was obtained. A dose volume histogram for the body was extracted from the clinical systems. We compared different models analysing the effect of heart dosimetry on the EoRT lymphocyte count using multivariable linear regression and assessed goodness of fit. We published interactive nomograms for the best models. The association of the degree of EoRT lymphopenia with clinical outcomes (overall survival, cancer treatment failure and infection) was investigated. RESULTS An increasing low dose bath to the body and MHD were associated with a low EoRT lymphocyte count. The best models for intrathoracic tumours included dosimetric parameters, age, gender, number of fractions, concomitant chemotherapy and pre-treatment lymphocyte count. Models for patients with breast cancer showed no improvement when adding dosimetric variables to the clinical predictors. EoRT lymphopenia grade ≥3 was associated with decreased survival and increased risk of infections among patients with intrathoracic tumours. CONCLUSION Among patients with intrathoracic tumours, radiation exposure to the heart contributes to lymphopenia and low levels of peripheral lymphocytes after radiotherapy are associated with worse clinical outcomes.
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Affiliation(s)
- C Terrones-Campos
- Centre of Excellence for Health, Immunity and Infections (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
| | - B Ledergerber
- Centre of Excellence for Health, Immunity and Infections (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - N Forbes
- Centre of Excellence for Health, Immunity and Infections (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - A G Smith
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - J Petersen
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - M Helleberg
- Centre of Excellence for Health, Immunity and Infections (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - J Lundgren
- Centre of Excellence for Health, Immunity and Infections (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - L Specht
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - I R Vogelius
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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Bennett SA, Garrett K, Sharp DK, Freeman SJ, Smith AG, Wright TJ, Kay BP, Tang TL, Tolstukhin IA, Ayyad Y, Chen J, Davies PJ, Dolan A, Gaffney LP, Heinz A, Hoffman CR, Müller-Gatermann C, Page RD, Wilson GL. Direct Determination of Fission-Barrier Heights Using Light-Ion Transfer in Inverse Kinematics. Phys Rev Lett 2023; 130:202501. [PMID: 37267578 DOI: 10.1103/physrevlett.130.202501] [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] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/28/2023] [Accepted: 03/27/2023] [Indexed: 06/04/2023]
Abstract
We demonstrate a new technique for obtaining fission data for nuclei away from β stability. These types of data are pertinent to the astrophysical r process, crucial to a complete understanding of the origin of the heavy elements, and for developing a predictive model of fission. These data are also important considerations for terrestrial applications related to power generation and safeguarding. Experimentally, such data are scarce due to the difficulties in producing the actinide targets of interest. The solenoidal-spectrometer technique, commonly used to study nucleon-transfer reactions in inverse kinematics, has been applied to the case of transfer-induced fission as a means to deduce the fission-barrier height, among other variables. The fission-barrier height of ^{239}U has been determined via the ^{238}U(d,pf) reaction in inverse kinematics, the results of which are consistent with existing neutron-induced fission data indicating the validity of the technique.
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Affiliation(s)
- S A Bennett
- Department of Physics and Astronomy, University of Manchester, Manchester M13 9PL, United Kingdom
| | - K Garrett
- Department of Physics and Astronomy, University of Manchester, Manchester M13 9PL, United Kingdom
| | - D K Sharp
- Department of Physics and Astronomy, University of Manchester, Manchester M13 9PL, United Kingdom
| | - S J Freeman
- Department of Physics and Astronomy, University of Manchester, Manchester M13 9PL, United Kingdom
- CERN, CH-1211 Geneva 23, Switzerland
| | - A G Smith
- Department of Physics and Astronomy, University of Manchester, Manchester M13 9PL, United Kingdom
| | - T J Wright
- Department of Physics and Astronomy, University of Manchester, Manchester M13 9PL, United Kingdom
| | - B P Kay
- Physics Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - T L Tang
- Physics Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - I A Tolstukhin
- Physics Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Y Ayyad
- IGFAE, Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - J Chen
- Physics Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - P J Davies
- School of Physics, Engineering and Technology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - A Dolan
- Oliver Lodge Laboratory, University of Liverpool, Liverpool L69 7ZE, United Kingdom
| | - L P Gaffney
- Oliver Lodge Laboratory, University of Liverpool, Liverpool L69 7ZE, United Kingdom
| | - A Heinz
- Chalmers University of Technology, SE-41296 Göteborg, Sweden
| | - C R Hoffman
- Physics Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - C Müller-Gatermann
- Physics Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - R D Page
- Oliver Lodge Laboratory, University of Liverpool, Liverpool L69 7ZE, United Kingdom
| | - G L Wilson
- Physics Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
- Louisiana State University, Baton Rouge, Louisiana 70803, USA
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Wahlstedt I, George Smith A, Andersen CE, Behrens CP, Nørring Bekke S, Boye K, van Overeem Felter M, Josipovic M, Petersen J, Risumlund SL, Tascón-Vidarte JD, van Timmeren JE, Vogelius IR. Interfractional dose accumulation for MR-guided liver SBRT: Variation among algorithms is highly patient- and fraction-dependent. Radiother Oncol 2022; 182:109448. [PMID: 36566988 DOI: 10.1016/j.radonc.2022.109448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/22/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND PURPOSE Daily plan adaptations could take the dose delivered in previous fractions into account. Due to high dose delivered per fraction, low number of fractions, steep dose gradients, and large interfractional organ deformations, this might be particularly important for liver SBRT. This study investigates inter-algorithm variation of interfractional dose accumulation for MR-guided liver SBRT. MATERIALS AND METHODS We assessed 27 consecutive MR-guided liver SBRT treatments of 67.5 Gy in three (n = 15) or 50 Gy in five fractions (n = 12), both prescribed to the GTV. We calculated fraction doses on daily patient anatomy, warped these doses to the simulation MRI using seven different algorithms, and accumulated the warped doses. Thus, we obtained differences in planned doses and warped or accumulated doses for each algorithm. This enabled us to calculate the inter-algorithm variations in warped doses per fraction and in accumulated doses per treatment course. RESULTS The four intensity-based algorithms were more consistent with planned PTV dose than affine or contour-based algorithms. The mean (range) variation of the dose difference for PTV D95% due to dose warping by these intensity-based algorithms was 10.4 percentage points (0.3 to 43.7) between fractions and 8.6 (0.3 to 24.9) between accumulated treatment doses. As seen by these ranges, the variation was very dependent on the patient and the fraction being analyzed. Nevertheless, no correlations between patient or plan characteristics on the one hand and inter-algorithm dose warping variation on the other hand was found. CONCLUSION Inter-algorithm dose accumulation variation is highly patient- and fraction-dependent for MR-guided liver SBRT. We advise against trusting a single algorithm for dose accumulation in liver SBRT.
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Affiliation(s)
- Isak Wahlstedt
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 1, Bygning 101A, 2800 Kongens Lyngby, Denmark; Department of Oncology, Centre for Cancer and Organ Diseases, Copenhagen University Hospital - Rigshospitalet (RH), Blegdamsvej 9, 2100 Copenhagen, Denmark; Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte (HGH), Borgmester Ib Juuls Vej 7, 2730 Herlev, Denmark.
| | - Abraham George Smith
- Department of Oncology, Centre for Cancer and Organ Diseases, Copenhagen University Hospital - Rigshospitalet (RH), Blegdamsvej 9, 2100 Copenhagen, Denmark; Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen, Denmark
| | - Claus Erik Andersen
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 1, Bygning 101A, 2800 Kongens Lyngby, Denmark
| | - Claus Preibisch Behrens
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 1, Bygning 101A, 2800 Kongens Lyngby, Denmark; Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte (HGH), Borgmester Ib Juuls Vej 7, 2730 Herlev, Denmark
| | - Susanne Nørring Bekke
- Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte (HGH), Borgmester Ib Juuls Vej 7, 2730 Herlev, Denmark
| | - Kristian Boye
- Department of Oncology, Centre for Cancer and Organ Diseases, Copenhagen University Hospital - Rigshospitalet (RH), Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Mette van Overeem Felter
- Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte (HGH), Borgmester Ib Juuls Vej 7, 2730 Herlev, Denmark
| | - Mirjana Josipovic
- Department of Oncology, Centre for Cancer and Organ Diseases, Copenhagen University Hospital - Rigshospitalet (RH), Blegdamsvej 9, 2100 Copenhagen, Denmark; Department of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jens Petersen
- Department of Oncology, Centre for Cancer and Organ Diseases, Copenhagen University Hospital - Rigshospitalet (RH), Blegdamsvej 9, 2100 Copenhagen, Denmark; Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen, Denmark
| | - Signe Lenora Risumlund
- Department of Oncology, Centre for Cancer and Organ Diseases, Copenhagen University Hospital - Rigshospitalet (RH), Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - José David Tascón-Vidarte
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen, Denmark
| | | | - Ivan Richter Vogelius
- Department of Oncology, Centre for Cancer and Organ Diseases, Copenhagen University Hospital - Rigshospitalet (RH), Blegdamsvej 9, 2100 Copenhagen, Denmark; Department of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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6
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Malinowska M, Ruud AK, Jensen J, Svane SF, Smith AG, Bellucci A, Lenk I, Nagy I, Fois M, Didion T, Thorup-Kristensen K, Jensen CS, Asp T. Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass. Plant Genome 2022; 15:e20253. [PMID: 35975565 DOI: 10.1002/tpg2.20253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
The growing demand for food and feed crops in the world because of growing population and more extreme weather events requires high-yielding and resilient crops. Many agriculturally important traits are polygenic, controlled by multiple regulatory layers, and with a strong interaction with the environment. In this study, 120 F2 families of perennial ryegrass (Lolium perenne L.) were grown across a water gradient in a semifield facility with subsoil irrigation. Genomic (single-nucleotide polymorphism [SNP]), transcriptomic (gene expression [GE]), and DNA methylomic (MET) data were integrated with feed quality trait data collected from control and drought sections in the semifield facility, providing a treatment effect. Deep root length (DRL) below 110 cm was assessed with convolutional neural network image analysis. Bayesian prediction models were used to partition phenotypic variance into its components and evaluated the proportion of phenotypic variance in all traits captured by different regulatory layers (SNP, GE, and MET). The spatial effects and effects of SNP, GE, MET, the interaction between GE and MET (GE × MET) and GE × treatment (GEControl and GEDrought ) interaction were investigated. Gene expression explained a substantial part of the genetic and spatial variance for all the investigated phenotypes, whereas MET explained residual variance not accounted for by SNPs or GE. For DRL, MET also contributed to explaining spatial variance. The study provides a statistically elegant analytical paradigm that integrates genomic, transcriptomic, and MET information to understand the regulatory mechanisms of polygenic effects for complex traits.
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Affiliation(s)
- Marta Malinowska
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Anja Karine Ruud
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Just Jensen
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Simon Fiil Svane
- Dep. of Plant and Environmental Sciences, Univ. of Copenhagen, Taastrup, Denmark
| | | | - Andrea Bellucci
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Ingo Lenk
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Mattia Fois
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Thomas Didion
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | | | | | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
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7
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Smith AG, Han E, Petersen J, Olsen NAF, Giese C, Athmann M, Dresbøll DB, Thorup‐Kristensen K. RootPainter: deep learning segmentation of biological images with corrective annotation. New Phytol 2022; 236:774-791. [PMID: 35851958 PMCID: PMC9804377 DOI: 10.1111/nph.18387] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/30/2022] [Indexed: 05/27/2023]
Abstract
Convolutional neural networks (CNNs) are a powerful tool for plant image analysis, but challenges remain in making them more accessible to researchers without a machine-learning background. We present RootPainter, an open-source graphical user interface based software tool for the rapid training of deep neural networks for use in biological image analysis. We evaluate RootPainter by training models for root length extraction from chicory (Cichorium intybus L.) roots in soil, biopore counting, and root nodule counting. We also compare dense annotations with corrective ones that are added during the training process based on the weaknesses of the current model. Five out of six times the models trained using RootPainter with corrective annotations created within 2 h produced measurements strongly correlating with manual measurements. Model accuracy had a significant correlation with annotation duration, indicating further improvements could be obtained with extended annotation. Our results show that a deep-learning model can be trained to a high accuracy for the three respective datasets of varying target objects, background, and image quality with < 2 h of annotation time. They indicate that, when using RootPainter, for many datasets it is possible to annotate, train, and complete data processing within 1 d.
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Affiliation(s)
- Abraham George Smith
- Department of Plant and Environmental ScienceUniversity of CopenhagenHøjbakkegårds Alle 13Tåstrup2630Denmark
- Department of Computer ScienceUniversity of CopenhagenUniversitetsparken 12100CopenhagenDenmark
| | - Eusun Han
- Department of Plant and Environmental ScienceUniversity of CopenhagenHøjbakkegårds Alle 13Tåstrup2630Denmark
- CSIRO Agriculture and FoodPO Box 1700CanberraACT2601Australia
| | - Jens Petersen
- Department of Computer ScienceUniversity of CopenhagenUniversitetsparken 12100CopenhagenDenmark
| | - Niels Alvin Faircloth Olsen
- Department of Plant and Environmental ScienceUniversity of CopenhagenHøjbakkegårds Alle 13Tåstrup2630Denmark
| | - Christian Giese
- Department of Agroecology and Organic FarmingUniversity of BonnRegina‐Pacis‐Weg 353113BonnGermany
| | - Miriam Athmann
- Department of Organic Farming and Plant ProductionUniversity of KasselNordbahnhofstr. 1aD‐37213WitzenhausenGermany
| | - Dorte Bodin Dresbøll
- Department of Plant and Environmental ScienceUniversity of CopenhagenHøjbakkegårds Alle 13Tåstrup2630Denmark
| | - Kristian Thorup‐Kristensen
- Department of Plant and Environmental ScienceUniversity of CopenhagenHøjbakkegårds Alle 13Tåstrup2630Denmark
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8
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Chen G, Rasmussen CR, Dresbøll DB, Smith AG, Thorup-Kristensen K. Dynamics of Deep Water and N Uptake of Oilseed Rape ( Brassica napus L.) Under Varied N and Water Supply. Front Plant Sci 2022; 13:866288. [PMID: 35574102 PMCID: PMC9100933 DOI: 10.3389/fpls.2022.866288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Enhanced nitrogen (N) and water uptake from deep soil layers may increase resource use efficiency while maintaining yield under stressed conditions. Winter oilseed rape (Brassica napus L.) can develop deep roots and access deep-stored resources such as N and water to sustain its growth and productivity. Less is known of the performance of deep roots under varying water and N availability. In this study, we aimed to evaluate the effects of reduced N and water supply on deep N and water uptake for oilseed rape. Oilseed rape plants grown in outdoor rhizotrons were supplied with 240 and 80 kg N ha-1, respectively, in 2019 whereas a well-watered and a water-deficit treatment were established in 2020. To track deep water and N uptake, a mixture of 2H2O and Ca(15NO3)2 was injected into the soil column at 0.5- and 1.7-m depths. δ2H in transpiration water and δ15N in leaves were measured after injection. δ15N values in biomass samples were also measured. Differences in N or water supply had less effect on root growth. The low N treatment reduced water uptake throughout the soil profile and altered water uptake distribution. The low N supply doubled the 15N uptake efficiency at both 0.5 and 1.7 m. Similarly, water deficit in the upper soil layers led to compensatory deep water uptake. Our findings highlight the increasing importance of deep roots for water uptake, which is essential for maintaining an adequate water supply in the late growing stage. Our results further indicate the benefit of reducing N supply for mitigating N leaching and altering water uptake from deep soil layers, yet at a potential cost of biomass reduction.
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Affiliation(s)
- Guanying Chen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Ruø Rasmussen
- Earth and Life Institute, Université Catholique de Louvain, Ottignies-Louvain-la-Neuve, Belgium
| | - Dorte Bodin Dresbøll
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
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9
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Wahlstedt I, Andratschke N, Behrens CP, Ehrbar S, Gabryś HS, Schüler HG, Guckenberger M, Smith AG, Tanadini-Lang S, Tascón-Vidarte JD, Vogelius IR, van Timmeren JE. Gating has a negligible impact on dose delivered in MRI-guided online adaptive radiotherapy of prostate cancer. Radiother Oncol 2022; 170:205-212. [DOI: 10.1016/j.radonc.2022.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 12/24/2022]
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10
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Smith AG, Petersen J, Terrones-Campos C, Berthelsen AK, Forbes NJ, Darkner S, Specht L, Vogelius IR. RootPainter3D: Interactive-machine-learning enables rapid and accurate contouring for radiotherapy. Med Phys 2021; 49:461-473. [PMID: 34783028 DOI: 10.1002/mp.15353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 09/22/2021] [Accepted: 10/28/2021] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Organ-at-risk contouring is still a bottleneck in radiotherapy, with many deep learning methods falling short of promised results when evaluated on clinical data. We investigate the accuracy and time-savings resulting from the use of an interactive-machine-learning method for an organ-at-risk contouring task. METHODS We implement an open-source interactive-machine-learning software application that facilitates corrective-annotation for deep-learning generated contours on X-ray CT images. A trained-physician contoured 933 hearts using our software by delineating the first image, starting model training, and then correcting the model predictions for all subsequent images. These corrections were added into the training data, which was used for continuously training the assisting model. From the 933 hearts, the same physician also contoured the first 10 and last 10 in Eclipse (Varian) to enable comparison in terms of accuracy and duration. RESULTS We find strong agreement with manual delineations, with a dice score of 0.95. The annotations created using corrective-annotation also take less time to create as more images are annotated, resulting in substantial time savings compared to manual methods. After 923 images had been delineated, hearts took 2 min and 2 s to delineate on average, which includes time to evaluate the initial model prediction and assign the needed corrections, compared to 7 min and 1 s when delineating manually. CONCLUSIONS Our experiment demonstrates that interactive-machine-learning with corrective-annotation provides a fast and accessible way for non computer-scientists to train deep-learning models to segment their own structures of interest as part of routine clinical workflows.
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Affiliation(s)
- Abraham George Smith
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.,Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jens Petersen
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.,Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Cynthia Terrones-Campos
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Anne Kiil Berthelsen
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Physiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Nora Jarrett Forbes
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.,Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sune Darkner
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Lena Specht
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Ivan Richter Vogelius
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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11
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Han E, Smith AG, Kemper R, White R, Kirkegaard JA, Thorup-Kristensen K, Athmann M. Digging roots is easier with AI. J Exp Bot 2021; 72:4680-4690. [PMID: 33884416 DOI: 10.1093/jxb/erab174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
The scale of root quantification in research is often limited by the time required for sampling, measurement, and processing samples. Recent developments in convolutional neural networks (CNNs) have made faster and more accurate plant image analysis possible, which may significantly reduce the time required for root measurement, but challenges remain in making these methods accessible to researchers without an in-depth knowledge of machine learning. We analyzed root images acquired from three destructive root samplings using the RootPainter CNN software that features an interface for corrective annotation for easier use. Root scans with and without non-root debris were used to test if training a model (i.e. learning from labeled examples) can effectively exclude the debris by comparing the end results with measurements from clean images. Root images acquired from soil profile walls and the cross-section of soil cores were also used for training, and the derived measurements were compared with manual measurements. After 200 min of training on each dataset, significant relationships between manual measurements and RootPainter-derived data were noted for monolith (R2=0.99), profile wall (R2=0.76), and core-break (R2=0.57). The rooting density derived from images with debris was not significantly different from that derived from clean images after processing with RootPainter. Rooting density was also successfully calculated from both profile wall and soil core images, and in each case the gradient of root density with depth was not significantly different from manual counts. Differences in root-length density (RLD) between crops with contrasting root systems were captured using automatic segmentation at soil profiles with high RLD (1-5 cm cm-3) as well with low RLD (0.1-0.3 cm cm-3). Our results demonstrate that the proposed approach using CNN can lead to substantial reductions in root sample processing workloads, increasing the potential scale of future root investigations.
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Affiliation(s)
- Eusun Han
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 13, 2630 Taastrup, Denmark
| | - Abraham George Smith
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Roman Kemper
- Department of Agroecology and Organic Farming, Faculty of Agriculture, University of Bonn, Auf dem Hügel 6, 53121 Bonn, Germany
| | - Rosemary White
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT 2601, Australia
| | - John A Kirkegaard
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT 2601, Australia
| | - Kristian Thorup-Kristensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 13, 2630 Taastrup, Denmark
| | - Miriam Athmann
- Department of Organic Farming and Cropping Systems, University of Kassel, Nordbahnhofstr. 1a, 37213 Witzenhausen, Germany
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Jimenez-Solem E, Petersen TS, Hansen C, Hansen C, Lioma C, Igel C, Boomsma W, Krause O, Lorenzen S, Selvan R, Petersen J, Nyeland ME, Ankarfeldt MZ, Virenfeldt GM, Winther-Jensen M, Linneberg A, Ghazi MM, Detlefsen N, Lauritzen AD, Smith AG, de Bruijne M, Ibragimov B, Petersen J, Lillholm M, Middleton J, Mogensen SH, Thorsen-Meyer HC, Perner A, Helleberg M, Kaas-Hansen BS, Bonde M, Bonde A, Pai A, Nielsen M, Sillesen M. Developing and validating COVID-19 adverse outcome risk prediction models from a bi-national European cohort of 5594 patients. Sci Rep 2021; 11:3246. [PMID: 33547335 PMCID: PMC7864944 DOI: 10.1038/s41598-021-81844-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [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] [Received: 10/07/2020] [Accepted: 01/12/2021] [Indexed: 12/15/2022] Open
Abstract
Patients with severe COVID-19 have overwhelmed healthcare systems worldwide. We hypothesized that machine learning (ML) models could be used to predict risks at different stages of management and thereby provide insights into drivers and prognostic markers of disease progression and death. From a cohort of approx. 2.6 million citizens in Denmark, SARS-CoV-2 PCR tests were performed on subjects suspected for COVID-19 disease; 3944 cases had at least one positive test and were subjected to further analysis. SARS-CoV-2 positive cases from the United Kingdom Biobank was used for external validation. The ML models predicted the risk of death (Receiver Operation Characteristics—Area Under the Curve, ROC-AUC) of 0.906 at diagnosis, 0.818, at hospital admission and 0.721 at Intensive Care Unit (ICU) admission. Similar metrics were achieved for predicted risks of hospital and ICU admission and use of mechanical ventilation. Common risk factors, included age, body mass index and hypertension, although the top risk features shifted towards markers of shock and organ dysfunction in ICU patients. The external validation indicated fair predictive performance for mortality prediction, but suboptimal performance for predicting ICU admission. ML may be used to identify drivers of progression to more severe disease and for prognostication patients in patients with COVID-19. We provide access to an online risk calculator based on these findings.
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Affiliation(s)
- Espen Jimenez-Solem
- Department of Clinical Pharmacology, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Copenhagen Phase IV Unit (Phase4CPH), Department of Clinical Pharmacology and Center for Clinical Research and Prevention, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Tonny S Petersen
- Department of Clinical Pharmacology, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Casper Hansen
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Christian Hansen
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Christina Lioma
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Christian Igel
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Oswin Krause
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Stephan Lorenzen
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Raghavendra Selvan
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Janne Petersen
- Center for Clinical Research and Prevention, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Section of Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.,Copenhagen Phase IV Unit (Phase4CPH), Department of Clinical Pharmacology and Center for Clinical Research and Prevention, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Martin Erik Nyeland
- Department of Clinical Pharmacology, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Mikkel Zöllner Ankarfeldt
- Center for Clinical Research and Prevention, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Copenhagen Phase IV Unit (Phase4CPH), Department of Clinical Pharmacology and Center for Clinical Research and Prevention, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Gert Mehl Virenfeldt
- Center for Clinical Research and Prevention, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Matilde Winther-Jensen
- Center for Clinical Research and Prevention, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | | | - Nicki Detlefsen
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.,DTU Compute, Denmarks Technical University, Lyngby, Denmark
| | | | | | - Marleen de Bruijne
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.,Department of Radiology and Nuclear Medicine, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Bulat Ibragimov
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Jens Petersen
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Martin Lillholm
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Jon Middleton
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Anders Perner
- Department of Intensive Care Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Marie Helleberg
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Mikkel Bonde
- Center for Surgical Translational and Artificial Intelligence Research (CSTAR), Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Alexander Bonde
- Department of Surgical Gastroenterology, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen Ø, Denmark.,Center for Surgical Translational and Artificial Intelligence Research (CSTAR), Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Akshay Pai
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.,Cerebriu A/S, Copenhagen, Denmark
| | - Mads Nielsen
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Martin Sillesen
- Department of Surgical Gastroenterology, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen Ø, Denmark. .,Center for Surgical Translational and Artificial Intelligence Research (CSTAR), Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark. .,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
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13
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Guerrero C, Lerendegui-Marco J, Paul M, Tessler M, Heinitz S, Domingo-Pardo C, Cristallo S, Dressler R, Halfon S, Kivel N, Köster U, Maugeri EA, Palchan-Hazan T, Quesada JM, Rochman D, Schumann D, Weissman L, Aberle O, Amaducci S, Andrzejewski J, Audouin L, Bécares V, Bacak M, Balibrea J, Barak A, Barbagallo M, Barros S, Bečvář F, Beinrucker C, Berkovits D, Berthoumieux E, Billowes J, Bosnar D, Brugger M, Buzaglo Y, Caamaño M, Calviño F, Calviani M, Cano-Ott D, Cardella R, Casanovas A, Castelluccio DM, Cerutti F, Chen YH, Chiaveri E, Colonna N, Cortés G, Cortés-Giraldo MA, Cosentino L, Dafna H, Damone A, Diakaki M, Dietz M, Dupont E, Durán I, Eisen Y, Fernández-Domínguez B, Ferrari A, Ferreira P, Finocchiaro P, Furman V, Göbel K, García AR, Gawlik A, Glodariu T, Gonçalves IF, González-Romero E, Goverdovski A, Griesmayer E, Gunsing F, Harada H, Heftrich T, Heyse J, Hirsh T, Jenkins DG, Jericha E, Käppeler F, Kadi Y, Kaizer B, Katabuchi T, Kavrigin P, Ketlerov V, Khryachkov V, Kijel D, Kimura A, Kokkoris M, Kriesel A, Krtička M, Leal-Cidoncha E, Lederer-Woods C, Leeb H, Lo Meo S, Lonsdale SJ, Losito R, Macina D, Manna A, Marganiec J, Martínez T, Massimi C, Mastinu P, Mastromarco M, Matteucci F, Mendoza E, Mengoni A, Milazzo PM, Millán-Callado MA, Mingrone F, Mirea M, Montesano S, Musumarra A, Nolte R, Oprea A, Patronis N, Pavlik A, Perkowski J, Piersanti L, Porras I, Praena J, Rajeev K, Rauscher T, Reifarth R, Rodríguez-González T, Rout PC, Rubbia C, Ryan JA, Sabaté-Gilarte M, Saxena A, Schillebeeckx P, Schmidt S, Shor A, Sedyshev P, Smith AG, Stamatopoulos A, Tagliente G, Tain JL, Tarifeño-Saldivia A, Tassan-Got L, Tsinganis A, Valenta S, Vannini G, Variale V, Vaz P, Ventura A, Vlachoudis V, Vlastou R, Wallner A, Warren S, Weigand M, Weiss C, Wolf C, Woods PJ, Wright T, Žugec P. Neutron Capture on the s-Process Branching Point ^{171}Tm via Time-of-Flight and Activation. Phys Rev Lett 2020; 125:142701. [PMID: 33064503 DOI: 10.1103/physrevlett.125.142701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/02/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
The neutron capture cross sections of several unstable nuclides acting as branching points in the s process are crucial for stellar nucleosynthesis studies. The unstable ^{171}Tm (t_{1/2}=1.92 yr) is part of the branching around mass A∼170 but its neutron capture cross section as a function of the neutron energy is not known to date. In this work, following the production for the first time of more than 5 mg of ^{171}Tm at the high-flux reactor Institut Laue-Langevin in France, a sample was produced at the Paul Scherrer Institute in Switzerland. Two complementary experiments were carried out at the neutron time-of-flight facility (n_TOF) at CERN in Switzerland and at the SARAF liquid lithium target facility at Soreq Nuclear Research Center in Israel by time of flight and activation, respectively. The result of the time-of-flight experiment consists of the first ever set of resonance parameters and the corresponding average resonance parameters, allowing us to make an estimation of the Maxwellian-averaged cross sections (MACS) by extrapolation. The activation measurement provides a direct and more precise measurement of the MACS at 30 keV: 384(40) mb, with which the estimation from the n_TOF data agree at the limit of 1 standard deviation. This value is 2.6 times lower than the JEFF-3.3 and ENDF/B-VIII evaluations, 25% lower than that of the Bao et al. compilation, and 1.6 times larger than the value recommended in the KADoNiS (v1) database, based on the only previous experiment. Our result affects the nucleosynthesis at the A∼170 branching, namely, the ^{171}Yb abundance increases in the material lost by asymptotic giant branch stars, providing a better match to the available pre-solar SiC grain measurements compared to the calculations based on the current JEFF-3.3 model-based evaluation.
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Affiliation(s)
- C Guerrero
- Universidad de Sevilla, Seville, Spain
- Centro Nacional de Aceleradores (CNA) (Universidad de Sevilla-Junta de Andalucía-CSIC), Seville, Spain
| | | | - M Paul
- Hebrew University, Jerusalem, Israel
| | - M Tessler
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | - S Heinitz
- Paul Scherrer Institut (PSI), Villigen, Switzerland
| | - C Domingo-Pardo
- Instituto de Física Corpuscular (CSIC-University of Valencia), Valencia, Spain
| | - S Cristallo
- INAF-Osservatorio Astronomico d'Abruzzo, Teramo, Italy
- INFN Sezione Perugia, Perugia, Italy
| | - R Dressler
- Paul Scherrer Institut (PSI), Villigen, Switzerland
| | - S Halfon
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | - N Kivel
- Paul Scherrer Institut (PSI), Villigen, Switzerland
| | - U Köster
- Institut Laue-Langevin ILL, Grenoble, France
| | - E A Maugeri
- Paul Scherrer Institut (PSI), Villigen, Switzerland
| | | | | | - D Rochman
- Paul Scherrer Institut (PSI), Villigen, Switzerland
| | - D Schumann
- Paul Scherrer Institut (PSI), Villigen, Switzerland
| | - L Weissman
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | - O Aberle
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - S Amaducci
- INFN Laboratori Nazionali del Sud, Catania, Italy
| | | | - L Audouin
- Institut de Physique Nucléaire, CNRS-IN2P3, Univ. Paris-Sud, Université Paris-Saclay, Orsay Cedex, France
| | - V Bécares
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - M Bacak
- Technische Universität Wien, Vienna, Austria
| | - J Balibrea
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - A Barak
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | - M Barbagallo
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Italy
| | - S Barros
- Instituto Superior Técnico, Lisbon, Portugal
| | - F Bečvář
- Charles University, Prague, Czech Republic
| | | | - D Berkovits
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | - E Berthoumieux
- CEA Irfu, Université Paris-Saclay, Gif-sur-Yvette, France
| | - J Billowes
- University of Manchester, Manchester, United Kingdom
| | - D Bosnar
- Department of Physics, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - M Brugger
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - Y Buzaglo
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | - M Caamaño
- University of Santiago de Compostela, Santiago de Conpostela, Spain
| | - F Calviño
- Universitat Politècnica de Catalunya, Barcelona, Spain
| | - M Calviani
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - D Cano-Ott
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - R Cardella
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - A Casanovas
- Universitat Politècnica de Catalunya, Barcelona, Spain
| | - D M Castelluccio
- Agenzia nazionale per le nuove tecnologie (ENEA), Bologna, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Bologna, Italy
| | - F Cerutti
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - Y H Chen
- Institut de Physique Nucléaire, CNRS-IN2P3, Univ. Paris-Sud, Université Paris-Saclay, Orsay Cedex, France
| | - E Chiaveri
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - N Colonna
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Italy
| | - G Cortés
- Universitat Politècnica de Catalunya, Barcelona, Spain
| | | | - L Cosentino
- INFN Laboratori Nazionali del Sud, Catania, Italy
| | - H Dafna
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | - A Damone
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Italy
- Dipartimento di Fisica, Università degli Studi di Bari, Bari, Italy
| | - M Diakaki
- CEA Irfu, Université Paris-Saclay, Gif-sur-Yvette, France
| | - M Dietz
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - E Dupont
- CEA Irfu, Université Paris-Saclay, Gif-sur-Yvette, France
| | - I Durán
- University of Santiago de Compostela, Santiago de Conpostela, Spain
| | - Y Eisen
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | | | - A Ferrari
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - P Ferreira
- Instituto Superior Técnico, Lisbon, Portugal
| | | | - V Furman
- Joint Institute for Nuclear Research (JINR), Dubna, Russia
| | - K Göbel
- Goethe University Frankfurt, Seville, Germany
| | - A R García
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - A Gawlik
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | - T Glodariu
- Horia Hulubei National Institute of Physics and Nuclear Engineering, Jerusalem, Romania
| | | | - E González-Romero
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - A Goverdovski
- Institute of Physics and Power Engineering (IPPE), Obninsk, Russia
| | | | - F Gunsing
- Institut Laue-Langevin ILL, Grenoble, France
- CEA Irfu, Université Paris-Saclay, Gif-sur-Yvette, France
| | - H Harada
- Japan Atomic Energy Agency (JAEA), Tokai-mura, Japan
| | - T Heftrich
- Goethe University Frankfurt, Seville, Germany
| | - J Heyse
- Universitat Politècnica de Catalunya, Barcelona, Spain
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig, Germany
| | - T Hirsh
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | | | - E Jericha
- Technische Universität Wien, Vienna, Austria
| | - F Käppeler
- Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Y Kadi
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - B Kaizer
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | | | - P Kavrigin
- Technische Universität Wien, Vienna, Austria
| | - V Ketlerov
- Institute of Physics and Power Engineering (IPPE), Obninsk, Russia
| | - V Khryachkov
- Institute of Physics and Power Engineering (IPPE), Obninsk, Russia
| | - D Kijel
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | - A Kimura
- Japan Atomic Energy Agency (JAEA), Tokai-mura, Japan
| | - M Kokkoris
- National Technical University of Athens, Athens, Greece
| | - A Kriesel
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | - M Krtička
- Charles University, Prague, Czech Republic
| | - E Leal-Cidoncha
- University of Santiago de Compostela, Santiago de Conpostela, Spain
| | - C Lederer-Woods
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - H Leeb
- Technische Universität Wien, Vienna, Austria
| | - S Lo Meo
- Agenzia nazionale per le nuove tecnologie (ENEA), Bologna, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Bologna, Italy
| | - S J Lonsdale
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - R Losito
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - D Macina
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - A Manna
- Istituto Nazionale di Fisica Nucleare, Sezione di Bologna, Italy
- Dipartimento di Fisica e Astronomia, Università di Bologna, Bologna, Italy
| | | | - T Martínez
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - C Massimi
- Istituto Nazionale di Fisica Nucleare, Sezione di Bologna, Italy
- Dipartimento di Fisica e Astronomia, Università di Bologna, Bologna, Italy
| | - P Mastinu
- Istituto Nazionale di Fisica Nucleare, Sezione di Legnaro, Italy
| | - M Mastromarco
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Italy
| | - F Matteucci
- Istituto Nazionale di Fisica Nucleare, Sezione di Trieste, Italy
- Dipartimento di Astronomia, Università di Trieste, Trieste, Italy
| | - E Mendoza
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - A Mengoni
- Agenzia nazionale per le nuove tecnologie (ENEA), Bologna, Italy
| | - P M Milazzo
- Istituto Nazionale di Fisica Nucleare, Sezione di Trieste, Italy
| | - M A Millán-Callado
- Institut de Physique Nucléaire, CNRS-IN2P3, Univ. Paris-Sud, Université Paris-Saclay, Orsay Cedex, France
| | - F Mingrone
- Istituto Nazionale di Fisica Nucleare, Sezione di Bologna, Italy
| | - M Mirea
- Horia Hulubei National Institute of Physics and Nuclear Engineering, Jerusalem, Romania
| | - S Montesano
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - A Musumarra
- INFN Laboratori Nazionali del Sud, Catania, Italy
- Dipartimento di Fisica e Astronomia, Università di Catania, Catania, Italy
| | - R Nolte
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig, Germany
| | - A Oprea
- Horia Hulubei National Institute of Physics and Nuclear Engineering, Jerusalem, Romania
| | - N Patronis
- University of Ioannina, Ioannina, Greece
| | - A Pavlik
- University of Vienna, Faculty of Physics, Vienna, Austria
| | | | - L Piersanti
- INAF-Osservatorio Astronomico d'Abruzzo, Teramo, Italy
| | - I Porras
- University of Granada, Granada, Spain
| | - J Praena
- Universidad de Sevilla, Seville, Spain
- University of Granada, Granada, Spain
| | - K Rajeev
- Bhabha Atomic Research Centre (BARC), Mumbai, India
| | - T Rauscher
- Centre for Astrophysics Research, University of Hertfordshire, Hatfield, United Kingdom
- Department of Physics, University of Basel, Basel, Switzerland
| | - R Reifarth
- Goethe University Frankfurt, Seville, Germany
| | - T Rodríguez-González
- Universidad de Sevilla, Seville, Spain
- Centro Nacional de Aceleradores (CNA) (Universidad de Sevilla-Junta de Andalucía-CSIC), Seville, Spain
| | - P C Rout
- Bhabha Atomic Research Centre (BARC), Mumbai, India
| | - C Rubbia
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - J A Ryan
- University of Manchester, Manchester, United Kingdom
| | - M Sabaté-Gilarte
- Universidad de Sevilla, Seville, Spain
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - A Saxena
- Bhabha Atomic Research Centre (BARC), Mumbai, India
| | | | - S Schmidt
- Goethe University Frankfurt, Seville, Germany
| | - A Shor
- Soreq Nuclear Research Center (SNRC), Yavne, Israel
| | - P Sedyshev
- Joint Institute for Nuclear Research (JINR), Dubna, Russia
| | - A G Smith
- University of Manchester, Manchester, United Kingdom
| | | | - G Tagliente
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Italy
| | - J L Tain
- Instituto de Física Corpuscular (CSIC-University of Valencia), Valencia, Spain
| | | | - L Tassan-Got
- Institut de Physique Nucléaire, CNRS-IN2P3, Univ. Paris-Sud, Université Paris-Saclay, Orsay Cedex, France
| | - A Tsinganis
- National Technical University of Athens, Athens, Greece
| | - S Valenta
- Charles University, Prague, Czech Republic
| | - G Vannini
- Istituto Nazionale di Fisica Nucleare, Sezione di Bologna, Italy
- Dipartimento di Fisica e Astronomia, Università di Bologna, Bologna, Italy
| | - V Variale
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Italy
| | - P Vaz
- Instituto Superior Técnico, Lisbon, Portugal
| | - A Ventura
- Istituto Nazionale di Fisica Nucleare, Sezione di Bologna, Italy
| | - V Vlachoudis
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
| | - R Vlastou
- National Technical University of Athens, Athens, Greece
| | - A Wallner
- Australian National University, Canberra, Australia
| | - S Warren
- University of Manchester, Manchester, United Kingdom
| | - M Weigand
- Goethe University Frankfurt, Seville, Germany
| | - C Weiss
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
- Technische Universität Wien, Vienna, Austria
| | - C Wolf
- Goethe University Frankfurt, Seville, Germany
| | - P J Woods
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - T Wright
- University of Manchester, Manchester, United Kingdom
| | - P Žugec
- European Organization for Nuclear Research (CERN), Geneva, Switzerland
- Department of Physics, Faculty of Science, University of Zagreb, Zagreb, Croatia
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Abstract
BACKGROUND Plant root research can provide a way to attain stress-tolerant crops that produce greater yield in a diverse array of conditions. Phenotyping roots in soil is often challenging due to the roots being difficult to access and the use of time consuming manual methods. Rhizotrons allow visual inspection of root growth through transparent surfaces. Agronomists currently manually label photographs of roots obtained from rhizotrons using a line-intersect method to obtain root length density and rooting depth measurements which are essential for their experiments. We investigate the effectiveness of an automated image segmentation method based on the U-Net Convolutional Neural Network (CNN) architecture to enable such measurements. We design a data-set of 50 annotated chicory (Cichorium intybus L.) root images which we use to train, validate and test the system and compare against a baseline built using the Frangi vesselness filter. We obtain metrics using manual annotations and line-intersect counts. RESULTS Our results on the held out data show our proposed automated segmentation system to be a viable solution for detecting and quantifying roots. We evaluate our system using 867 images for which we have obtained line-intersect counts, attaining a Spearman rank correlation of 0.9748 and an r 2 of 0.9217. We also achieve an F 1 of 0.7 when comparing the automated segmentation to the manual annotations, with our automated segmentation system producing segmentations with higher quality than the manual annotations for large portions of the image. CONCLUSION We have demonstrated the feasibility of a U-Net based CNN system for segmenting images of roots in soil and for replacing the manual line-intersect method. The success of our approach is also a demonstration of the feasibility of deep learning in practice for small research groups needing to create their own custom labelled dataset from scratch.
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Affiliation(s)
- Abraham George Smith
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegaard Allé 13, 2630 Taastrup, Denmark
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - Jens Petersen
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - Raghavendra Selvan
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - Camilla Ruø Rasmussen
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegaard Allé 13, 2630 Taastrup, Denmark
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15
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Damone L, Barbagallo M, Mastromarco M, Mengoni A, Cosentino L, Maugeri E, Heinitz S, Schumann D, Dressler R, Käppeler F, Colonna N, Finocchiaro P, Andrzejewski J, Perkowski J, Gawlik A, Aberle O, Altstadt S, Ayranov M, Audouin L, Bacak M, Balibrea-Correa J, Ballof J, Bécares V, Bečvář F, Beinrucker C, Bellia G, Bernardes AP, Berthoumieux E, Billowes J, Borge MJG, Bosnar D, Brown A, Brugger M, Busso M, Caamaño M, Calviño F, Calviani M, Cano-Ott D, Cardella R, Casanovas A, Castelluccio DM, Catherall R, Cerutti F, Chen YH, Chiaveri E, Correia JGM, Cortés G, Cortés-Giraldo MA, Cristallo S, Diakaki M, Dietz M, Domingo-Pardo C, Dorsival A, Dupont E, Duran I, Fernandez-Dominguez B, Ferrari A, Ferreira P, Furman W, Ganesan S, García-Rios A, Gilardoni S, Glodariu T, Göbel K, Gonçalves IF, González-Romero E, Goodacre TD, Griesmayer E, Guerrero C, Gunsing F, Harada H, Heftrich T, Heyse J, Jenkins DG, Jericha E, Johnston K, Kadi Y, Kalamara A, Katabuchi T, Kavrigin P, Kimura A, Kivel N, Köster U, Kokkoris M, Krtička M, Kurtulgil D, Leal-Cidoncha E, Lederer-Woods C, Leeb H, Lerendegui-Marco J, Lo Meo S, Lonsdale SJ, Losito R, Macina D, Marganiec J, Marsh B, Martínez T, Masi A, Massimi C, Mastinu P, Matteucci F, Mazzone A, Mendoza E, Milazzo PM, Mingrone F, Mirea M, Musumarra A, Negret A, Nolte R, Oprea A, Patronis N, Pavlik A, Piersanti L, Piscopo M, Plompen A, Porras I, Praena J, Quesada JM, Radeck D, Rajeev K, Rauscher T, Reifarth R, Riego-Perez A, Rothe S, Rout P, Rubbia C, Ryan J, Sabaté-Gilarte M, Saxena A, Schell J, Schillebeeckx P, Schmidt S, Sedyshev P, Seiffert C, Smith AG, Sosnin NV, Stamatopoulos A, Stora T, Tagliente G, Tain JL, Tarifeño-Saldivia A, Tassan-Got L, Tsinganis A, Valenta S, Vannini G, Variale V, Vaz P, Ventura A, Vlachoudis V, Vlastou R, Wallner A, Warren S, Weigand M, Weiß C, Wolf C, Woods PJ, Wright T, Žugec P. ^{7}Be(n,p)^{7}Li Reaction and the Cosmological Lithium Problem: Measurement of the Cross Section in a Wide Energy Range at n_TOF at CERN. Phys Rev Lett 2018; 121:042701. [PMID: 30095928 DOI: 10.1103/physrevlett.121.042701] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/09/2018] [Indexed: 06/08/2023]
Abstract
We report on the measurement of the ^{7}Be(n,p)^{7}Li cross section from thermal to approximately 325 keV neutron energy, performed in the high-flux experimental area (EAR2) of the n_TOF facility at CERN. This reaction plays a key role in the lithium yield of the big bang nucleosynthesis (BBN) for standard cosmology. The only two previous time-of-flight measurements performed on this reaction did not cover the energy window of interest for BBN, and they showed a large discrepancy between each other. The measurement was performed with a Si telescope and a high-purity sample produced by implantation of a ^{7}Be ion beam at the ISOLDE facility at CERN. While a significantly higher cross section is found at low energy, relative to current evaluations, in the region of BBN interest, the present results are consistent with the values inferred from the time-reversal ^{7}Li(p,n)^{7}Be reaction, thus yielding only a relatively minor improvement on the so-called cosmological lithium problem. The relevance of these results on the near-threshold neutron production in the p+^{7}Li reaction is also discussed.
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Affiliation(s)
- L Damone
- INFN, Sezione di Bari, Italy
- Dipartimento di Fisica, Università degli Studi di Bari, Italy
| | - M Barbagallo
- INFN, Sezione di Bari, Italy
- European Organization for Nuclear Research (CERN), Switzerland
| | - M Mastromarco
- INFN, Sezione di Bari, Italy
- European Organization for Nuclear Research (CERN), Switzerland
| | - A Mengoni
- ENEA, Bologna, Italy
- INFN, Sezione di Bologna, Italy
| | - L Cosentino
- INFN, Laboratori Nazionali del Sud, Catania, Italy
| | - E Maugeri
- Paul Scherrer Institut, Villigen PSI, Switzerland
| | - S Heinitz
- Paul Scherrer Institut, Villigen PSI, Switzerland
| | - D Schumann
- Paul Scherrer Institut, Villigen PSI, Switzerland
| | - R Dressler
- Paul Scherrer Institut, Villigen PSI, Switzerland
| | - F Käppeler
- Karlsruhe Institute of Technology (KIT), Institut für Kernphysik, Karlsruhe, Germany
| | | | | | | | | | - A Gawlik
- Uniwersytet Łódzki, Lodz, Poland
| | - O Aberle
- European Organization for Nuclear Research (CERN), Switzerland
| | - S Altstadt
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - M Ayranov
- European Commission, DG-Energy, Luxembourg
| | - L Audouin
- Centre National de la Recherche Scientifique/IN2P3, IPN, Orsay, France
| | - M Bacak
- European Organization for Nuclear Research (CERN), Switzerland
- Atominstitut der Österreichischen Universitäten, Technische Universität Wien, Austria
| | - J Balibrea-Correa
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - J Ballof
- European Organization for Nuclear Research (CERN), Switzerland
| | - V Bécares
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - F Bečvář
- Charles University, Prague, Czech Republic
| | - C Beinrucker
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - G Bellia
- INFN, Laboratori Nazionali del Sud, Catania, Italy
- Dipartimento di Fisica e Astronomia, Università di Catania, Italy
| | - A P Bernardes
- European Organization for Nuclear Research (CERN), Switzerland
| | | | - J Billowes
- University of Manchester, Oxford Road, Manchester, United Kingdom
| | - M J G Borge
- European Organization for Nuclear Research (CERN), Switzerland
| | - D Bosnar
- Department of Physics, Faculty of Science, University of Zagreb, Croatia
| | - A Brown
- University of York, Heslington, York, United Kingdom
| | - M Brugger
- European Organization for Nuclear Research (CERN), Switzerland
| | - M Busso
- INFN, Sezione di Perugia, Italy
- Dipartimento di Fisica e Geologia, Università di Perugia, Italy
| | - M Caamaño
- Universidade de Santiago de Compostela, Spain
| | - F Calviño
- Universitat Politecnica de Catalunya, Barcelona, Spain
| | - M Calviani
- European Organization for Nuclear Research (CERN), Switzerland
| | - D Cano-Ott
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - R Cardella
- European Organization for Nuclear Research (CERN), Switzerland
- INFN, Laboratori Nazionali del Sud, Catania, Italy
| | - A Casanovas
- Universitat Politecnica de Catalunya, Barcelona, Spain
| | | | - R Catherall
- European Organization for Nuclear Research (CERN), Switzerland
| | - F Cerutti
- European Organization for Nuclear Research (CERN), Switzerland
| | - Y H Chen
- Centre National de la Recherche Scientifique/IN2P3, IPN, Orsay, France
| | - E Chiaveri
- European Organization for Nuclear Research (CERN), Switzerland
| | - J G M Correia
- European Organization for Nuclear Research (CERN), Switzerland
- C2TN, Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - G Cortés
- Universitat Politecnica de Catalunya, Barcelona, Spain
| | | | - S Cristallo
- INFN, Sezione di Perugia, Italy
- Istituto Nazionale di Astrofisica, Osservatorio Astronomico d'Abruzzo, Italy
| | - M Diakaki
- National Technical University of Athens (NTUA), Greece
| | - M Dietz
- School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - C Domingo-Pardo
- Instituto de Física Corpuscular, CSIC, Universidad de Valencia, Spain
| | - A Dorsival
- European Organization for Nuclear Research (CERN), Switzerland
| | - E Dupont
- CEA/Saclay, IRFU, Gif-sur-Yvette, France
| | - I Duran
- Universidade de Santiago de Compostela, Spain
| | | | - A Ferrari
- European Organization for Nuclear Research (CERN), Switzerland
| | - P Ferreira
- C2TN, Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - W Furman
- Joint Institute of Nuclear Research, Dubna, Russia
| | - S Ganesan
- Bhabha Atomic Research Centre (BARC), Mumbai, India
| | - A García-Rios
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - S Gilardoni
- European Organization for Nuclear Research (CERN), Switzerland
| | - T Glodariu
- Horia Hulubei National Institute for Physics and Nuclear Engineering (IFIN-HH), Bucharest-Magurele, Romania
| | - K Göbel
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - I F Gonçalves
- C2TN, Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - E González-Romero
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - T D Goodacre
- European Organization for Nuclear Research (CERN), Switzerland
| | - E Griesmayer
- Atominstitut der Österreichischen Universitäten, Technische Universität Wien, Austria
| | | | - F Gunsing
- CEA/Saclay, IRFU, Gif-sur-Yvette, France
| | - H Harada
- Japan Atomic Energy Agency (JAEA), Tokai-mura, Japan
| | - T Heftrich
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - J Heyse
- European Commission JRC, Institute for Reference Materials and Measurements, Geel, Belgium
| | - D G Jenkins
- University of York, Heslington, York, United Kingdom
| | - E Jericha
- Atominstitut der Österreichischen Universitäten, Technische Universität Wien, Austria
| | - K Johnston
- European Organization for Nuclear Research (CERN), Switzerland
| | - Y Kadi
- European Organization for Nuclear Research (CERN), Switzerland
| | - A Kalamara
- National Technical University of Athens (NTUA), Greece
| | | | - P Kavrigin
- Atominstitut der Österreichischen Universitäten, Technische Universität Wien, Austria
| | - A Kimura
- Japan Atomic Energy Agency (JAEA), Tokai-mura, Japan
| | - N Kivel
- Paul Scherrer Institut, Villigen PSI, Switzerland
| | - U Köster
- Institut Laue-Langevin (ILL), Grenoble, France
| | - M Kokkoris
- National Technical University of Athens (NTUA), Greece
| | - M Krtička
- Charles University, Prague, Czech Republic
| | - D Kurtulgil
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | | | - C Lederer-Woods
- School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - H Leeb
- Atominstitut der Österreichischen Universitäten, Technische Universität Wien, Austria
| | | | - S Lo Meo
- ENEA, Bologna, Italy
- INFN, Sezione di Bologna, Italy
| | - S J Lonsdale
- School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - R Losito
- European Organization for Nuclear Research (CERN), Switzerland
| | - D Macina
- European Organization for Nuclear Research (CERN), Switzerland
| | | | - B Marsh
- European Organization for Nuclear Research (CERN), Switzerland
| | - T Martínez
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - A Masi
- European Organization for Nuclear Research (CERN), Switzerland
| | - C Massimi
- INFN, Sezione di Bologna, Italy
- Dipartimento di Fisica e Astronomia, Università di Bologna, Italy
| | - P Mastinu
- INFN, Laboratori Nazionali di Legnaro, Italy
| | - F Matteucci
- INFN, Sezione di Trieste, Italy
- Dipartimento di Astronomia, Università di Trieste, Italy
| | - A Mazzone
- INFN, Sezione di Bari, Italy
- CNR, IC, Bari, Italy
| | - E Mendoza
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | | | - F Mingrone
- European Organization for Nuclear Research (CERN), Switzerland
| | - M Mirea
- Horia Hulubei National Institute for Physics and Nuclear Engineering (IFIN-HH), Bucharest-Magurele, Romania
| | - A Musumarra
- INFN, Laboratori Nazionali del Sud, Catania, Italy
- Dipartimento di Fisica e Astronomia, Università di Catania, Italy
| | - A Negret
- Horia Hulubei National Institute for Physics and Nuclear Engineering (IFIN-HH), Bucharest-Magurele, Romania
| | - R Nolte
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig, Germany
| | - A Oprea
- Horia Hulubei National Institute for Physics and Nuclear Engineering (IFIN-HH), Bucharest-Magurele, Romania
| | | | - A Pavlik
- University of Vienna, Faculty of Physics, Austria
| | - L Piersanti
- INFN, Sezione di Perugia, Italy
- Istituto Nazionale di Astrofisica, Osservatorio Astronomico d'Abruzzo, Italy
| | - M Piscopo
- INFN, Laboratori Nazionali del Sud, Catania, Italy
| | - A Plompen
- European Commission JRC, Institute for Reference Materials and Measurements, Geel, Belgium
| | | | - J Praena
- Universidad de Sevilla, Spain
- Universidad de Granada, Spain
| | | | - D Radeck
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig, Germany
| | - K Rajeev
- Bhabha Atomic Research Centre (BARC), Mumbai, India
| | - T Rauscher
- Centre for Astrophysics Research, School of Physics, Astronomy and Mathematics, University of Hertfordshire, Hatfield, United Kingdom
| | - R Reifarth
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - A Riego-Perez
- Universitat Politecnica de Catalunya, Barcelona, Spain
| | - S Rothe
- University of Manchester, Oxford Road, Manchester, United Kingdom
| | - P Rout
- Bhabha Atomic Research Centre (BARC), Mumbai, India
| | - C Rubbia
- European Organization for Nuclear Research (CERN), Switzerland
| | - J Ryan
- University of Manchester, Oxford Road, Manchester, United Kingdom
| | - M Sabaté-Gilarte
- European Organization for Nuclear Research (CERN), Switzerland
- Universidad de Sevilla, Spain
| | - A Saxena
- Bhabha Atomic Research Centre (BARC), Mumbai, India
| | - J Schell
- European Organization for Nuclear Research (CERN), Switzerland
- Institute for Materials Science and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Essen, Germany
| | - P Schillebeeckx
- European Commission JRC, Institute for Reference Materials and Measurements, Geel, Belgium
| | - S Schmidt
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - P Sedyshev
- Joint Institute of Nuclear Research, Dubna, Russia
| | - C Seiffert
- European Organization for Nuclear Research (CERN), Switzerland
| | - A G Smith
- University of Manchester, Oxford Road, Manchester, United Kingdom
| | - N V Sosnin
- University of Manchester, Oxford Road, Manchester, United Kingdom
| | | | - T Stora
- European Organization for Nuclear Research (CERN), Switzerland
| | | | - J L Tain
- Instituto de Física Corpuscular, CSIC, Universidad de Valencia, Spain
| | - A Tarifeño-Saldivia
- Universitat Politecnica de Catalunya, Barcelona, Spain
- Instituto de Física Corpuscular, CSIC, Universidad de Valencia, Spain
| | - L Tassan-Got
- Centre National de la Recherche Scientifique/IN2P3, IPN, Orsay, France
| | - A Tsinganis
- European Organization for Nuclear Research (CERN), Switzerland
| | - S Valenta
- Charles University, Prague, Czech Republic
| | - G Vannini
- INFN, Sezione di Bologna, Italy
- Dipartimento di Fisica e Astronomia, Università di Bologna, Italy
| | | | - P Vaz
- C2TN, Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | | | - V Vlachoudis
- European Organization for Nuclear Research (CERN), Switzerland
| | - R Vlastou
- National Technical University of Athens (NTUA), Greece
| | - A Wallner
- University of Vienna, Faculty of Physics, Austria
- Research School of Physics and Engineering, Australian National University, Canberra, Australia
| | - S Warren
- University of Manchester, Oxford Road, Manchester, United Kingdom
| | - M Weigand
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - C Weiß
- European Organization for Nuclear Research (CERN), Switzerland
| | - C Wolf
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - P J Woods
- School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - T Wright
- University of Manchester, Oxford Road, Manchester, United Kingdom
| | - P Žugec
- Department of Physics, Faculty of Science, University of Zagreb, Croatia
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16
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Chhabra Y, Wong HY, Nikolajsen LF, Steinocher H, Papadopulos A, Tunny KA, Meunier FA, Smith AG, Kragelund BB, Brooks AJ, Waters MJ. A growth hormone receptor SNP promotes lung cancer by impairment of SOCS2-mediated degradation. Oncogene 2018; 37:489-501. [PMID: 28967904 PMCID: PMC5799715 DOI: 10.1038/onc.2017.352] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 08/13/2017] [Accepted: 08/16/2017] [Indexed: 02/07/2023]
Abstract
Both humans and mice lacking functional growth hormone (GH) receptors are known to be resistant to cancer. Further, autocrine GH has been reported to act as a cancer promoter. Here we present the first example of a variant of the GH receptor (GHR) associated with cancer promotion, in this case lung cancer. We show that the GHRP495T variant located in the receptor intracellular domain is able to prolong the GH signal in vitro using stably expressing mouse pro-B-cell and human lung cell lines. This is relevant because GH secretion is pulsatile, and extending the signal duration makes it resemble autocrine GH action. Signal duration for the activated GHR is primarily controlled by suppressor of cytokine signalling 2 (SOCS2), the substrate recognition component of the E3 protein ligase responsible for ubiquitinylation and degradation of the GHR. SOCS2 is induced by a GH pulse and we show that SOCS2 binding to the GHR is impaired by a threonine substitution at Pro 495. This results in decreased internalisation and degradation of the receptor evident in TIRF microscopy and by measurement of mature (surface) receptor expression. Mutational analysis showed that the residue at position 495 impairs SOCS2 binding only when a threonine is present, consistent with interference with the adjacent Thr494. The latter is key for SOCS2 binding, together with nearby Tyr487, which must be phosphorylated for SOCS2 binding. We also undertook nuclear magnetic resonance spectroscopy approach for structural comparison of the SOCS2 binding scaffold Ile455-Ser588, and concluded that this single substitution has altered the structure of the SOCS2 binding site. Importantly, we find that lung BEAS-2B cells expressing GHRP495T display increased expression of transcripts associated with tumour proliferation, epithelial-mesenchymal transition and metastases (TWIST1, SNAI2, EGFR, MYC and CCND1) at 2 h after a GH pulse. This is consistent with prolonged GH signalling acting to promote cancer progression in lung cancer.
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Affiliation(s)
- Y Chhabra
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - H Y Wong
- University of Queensland Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | - L F Nikolajsen
- Structural Biology and NMR Laboratory (SBiNLab), Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - H Steinocher
- Structural Biology and NMR Laboratory (SBiNLab), Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - A Papadopulos
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - K A Tunny
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - F A Meunier
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - A G Smith
- School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - B B Kragelund
- Structural Biology and NMR Laboratory (SBiNLab), Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - A J Brooks
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - M J Waters
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
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17
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Garelius HKG, Johnston WT, Smith AG, Park S, de Swart L, Fenaux P, Symeonidis A, Sanz G, Čermák J, Stauder R, Malcovati L, Mittelman M, van de Loosdrecht AA, van Marrewijk CJ, Bowen D, Crouch S, de Witte TJM, Hellström-Lindberg E. Erythropoiesis-stimulating agents significantly delay the onset of a regular transfusion need in nontransfused patients with lower-risk myelodysplastic syndrome. J Intern Med 2017; 281:284-299. [PMID: 27926979 PMCID: PMC5596334 DOI: 10.1111/joim.12579] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND The EUMDS registry is an unique prospective, longitudinal observational registry enrolling newly diagnosed patients with lower-risk myelodysplastic syndrome (MDS) from 17 European countries from both university hospitals and smaller regional hospitals. OBJECTIVE The aim of this study was to describe the usage and clinical impact of erythropoiesis-stimulating agents (ESAs) in 1696 patients enrolled between 2008 and 2014. METHODS The effects of ESAs on outcomes were assessed using proportional hazards models weighting observations by propensity to receive ESA treatment within a subset of anaemic patients with or without a regular transfusion need. RESULTS ESA treatment (median duration of 27.5 months, range 0-77 months) was administered to 773 patients (45.6%). Outcomes were assessed in 897 patients (484 ESA treated and 413 untreated). ESA treatment was associated with a nonsignificant survival benefit (HR 0.82, 95% CI: 0.65-1.04, P = 0.09); this benefit was larger amongst patients without prior transfusions (P = 0.07). Amongst 539 patients for whom response to ESA treatment could be defined, median time to first post-ESA treatment transfusion was 6.1 months (IQR: 4.3-15.9 months) in those transfused before ESA treatment compared to 23.3 months (IQR: 7.0-47.8 months) in patients without prior transfusions (HR 2.4, 95% CI: 1.7-3.3, P < 0.0001). Responding patients had a better prognosis in terms of a lower risk of death (HR 0.65, 95% CI: 0.45-0.893, P = 0.018), whereas there was no significant effect on the risk of progression to acute myeloid leukaemia (HR 0.71, 95% CI: 0.39-1.29, P = 0.27). CONCLUSION Appropriate use of ESAs can significantly delay the onset of a regular transfusion need in patients with lower-risk MDS.
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Affiliation(s)
- H K G Garelius
- Department of Medicine, Section of Hematology and Coagulation, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - W T Johnston
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - A G Smith
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - S Park
- Clinique Universitaire d'hématologie, CHU de Grenoble, Université Grenoble, Grenoble, France
| | - L de Swart
- Department of Hematology, Radboud university medical center, Nijmegen, the Netherlands
| | - P Fenaux
- Service d'Hématologie, Hôpital Saint-Louis, Assistance Publique des Hôpitaux de Paris (AP-HP) and Université Paris 7, Paris, France
| | - A Symeonidis
- Department of Medicine, Division of Hematology, University of Patras Medical School, Patras, Greece
| | - G Sanz
- Department of Hematology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - J Čermák
- Department of Clinical Hematology, Institute of Hematology & Blood Transfusion, Praha, Czech Republic
| | - R Stauder
- Department of Internal Medicine V (Hematology and Oncology), Innsbruck Medical University, Innsbruck, Austria
| | - L Malcovati
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - M Mittelman
- Department of Medicine A, Tel Aviv Sourasky (Ichilov) Medical Center, Tel Aviv, Israel
| | - A A van de Loosdrecht
- Department of Hematology, VU Institute of Cancer and Immunology, VU University Medical Center, Amsterdam, the Netherlands
| | - C J van Marrewijk
- Department of Hematology, Radboud university medical center, Nijmegen, the Netherlands
| | - D Bowen
- St. James's Institute of Oncology, Leeds Teaching Hospitals, Leeds, UK
| | - S Crouch
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - T J M de Witte
- Department of Tumor Immunology, Nijmegen Center for Molecular Life Sciences, Radboud university medical center, Nijmegen, the Netherlands
| | - E Hellström-Lindberg
- Department of Medicine, Division of Hematology, Karolinska Institutet, Stockholm, Sweden
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18
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Barbagallo M, Musumarra A, Cosentino L, Maugeri E, Heinitz S, Mengoni A, Dressler R, Schumann D, Käppeler F, Colonna N, Finocchiaro P, Ayranov M, Damone L, Kivel N, Aberle O, Altstadt S, Andrzejewski J, Audouin L, Bacak M, Balibrea-Correa J, Barros S, Bécares V, Bečvář F, Beinrucker C, Berthoumieux E, Billowes J, Bosnar D, Brugger M, Caamaño M, Calviani M, Calviño F, Cano-Ott D, Cardella R, Casanovas A, Castelluccio DM, Cerutti F, Chen YH, Chiaveri E, Cortés G, Cortés-Giraldo MA, Cristallo S, Diakaki M, Domingo-Pardo C, Dupont E, Duran I, Fernandez-Dominguez B, Ferrari A, Ferreira P, Furman W, Ganesan S, García-Rios A, Gawlik A, Glodariu T, Göbel K, Gonçalves IF, González-Romero E, Griesmayer E, Guerrero C, Gunsing F, Harada H, Heftrich T, Heyse J, Jenkins DG, Jericha E, Katabuchi T, Kavrigin P, Kimura A, Kokkoris M, Krtička M, Leal-Cidoncha E, Lerendegui J, Lederer C, Leeb H, Lo Meo S, Lonsdale SJ, Losito R, Macina D, Marganiec J, Martínez T, Massimi C, Mastinu P, Mastromarco M, Mazzone A, Mendoza E, Milazzo PM, Mingrone F, Mirea M, Montesano S, Nolte R, Oprea A, Pappalardo A, Patronis N, Pavlik A, Perkowski J, Piscopo M, Plompen A, Porras I, Praena J, Quesada J, Rajeev K, Rauscher T, Reifarth R, Riego-Perez A, Rout P, Rubbia C, Ryan J, Sabate-Gilarte M, Saxena A, Schillebeeckx P, Schmidt S, Sedyshev P, Smith AG, Stamatopoulos A, Tagliente G, Tain JL, Tarifeño-Saldivia A, Tassan-Got L, Tsinganis A, Valenta S, Vannini G, Variale V, Vaz P, Ventura A, Vlachoudis V, Vlastou R, Vollaire J, Wallner A, Warren S, Weigand M, Weiß C, Wolf C, Woods PJ, Wright T, Žugec P. ^{7}Be(n,α)^{4}He Reaction and the Cosmological Lithium Problem: Measurement of the Cross Section in a Wide Energy Range at n_TOF at CERN. Phys Rev Lett 2016; 117:152701. [PMID: 27768364 DOI: 10.1103/physrevlett.117.152701] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Indexed: 06/06/2023]
Abstract
The energy-dependent cross section of the ^{7}Be(n,α)^{4}He reaction, of interest for the so-called cosmological lithium problem in big bang nucleosynthesis, has been measured for the first time from 10 meV to 10 keV neutron energy. The challenges posed by the short half-life of ^{7}Be and by the low reaction cross section have been overcome at n_TOF thanks to an unprecedented combination of the extremely high luminosity and good resolution of the neutron beam in the new experimental area (EAR2) of the n_TOF facility at CERN, the availability of a sufficient amount of chemically pure ^{7}Be, and a specifically designed experimental setup. Coincidences between the two alpha particles have been recorded in two Si-^{7}Be-Si arrays placed directly in the neutron beam. The present results are consistent, at thermal neutron energy, with the only previous measurement performed in the 1960s at a nuclear reactor. The energy dependence reported here clearly indicates the inadequacy of the cross section estimates currently used in BBN calculations. Although new measurements at higher neutron energy may still be needed, the n_TOF results hint at a minor role of this reaction in BBN, leaving the long-standing cosmological lithium problem unsolved.
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Affiliation(s)
| | - A Musumarra
- Dipartimento di Fisica e Astronomia DFA, Università di Catania, Italy
- INFN-Laboratori Nazionali del Sud, Catania, Italy
| | - L Cosentino
- INFN-Laboratori Nazionali del Sud, Catania, Italy
| | - E Maugeri
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - S Heinitz
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | | | - R Dressler
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - D Schumann
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - F Käppeler
- Karlsruhe Institute of Technology (KIT), Institut für Kernphysik, Karlsruhe, Germany
| | | | | | - M Ayranov
- European Commission, DG-Energy, Luxembourg
| | | | - N Kivel
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | | | - S Altstadt
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | | | - L Audouin
- Centre National de la Recherche Scientifique/IN2P3-IPN, Orsay, France
| | - M Bacak
- Atominstitut der Österreichischen Universitäten, Technische Universität Wien, Austria
| | - J Balibrea-Correa
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - S Barros
- C2TN-Instituto Superior Tecníco, Universidade de Lisboa, Portugal
| | - V Bécares
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - F Bečvář
- Charles University, Prague, Czech Republic
| | - C Beinrucker
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | | | - J Billowes
- University of Manchester, Oxford Road, Manchester, United Kingdom
| | - D Bosnar
- Department of Physics, Faculty of Science, University of Zagreb, Croatia
| | | | - M Caamaño
- Universidade de Santiago de Compostela, Spain
| | | | - F Calviño
- Universitat Politecnica de Catalunya, Barcelona, Spain
| | - D Cano-Ott
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - R Cardella
- INFN-Laboratori Nazionali del Sud, Catania, Italy
- CERN, Geneva, Switzerland
| | - A Casanovas
- Universitat Politecnica de Catalunya, Barcelona, Spain
| | | | | | - Y H Chen
- Centre National de la Recherche Scientifique/IN2P3-IPN, Orsay, France
| | | | - G Cortés
- Universitat Politecnica de Catalunya, Barcelona, Spain
| | | | - S Cristallo
- INAF-Osservatorio Astronomico di Collurania, Teramo, Italy
| | - M Diakaki
- National Technical University of Athens (NTUA), Greece
| | - C Domingo-Pardo
- Instituto de Física Corpuscular, CSIC-Universidad de Valencia, Spain
| | - E Dupont
- CEA/Saclay-IRFU, Gif-sur-Yvette, France
| | - I Duran
- Universidade de Santiago de Compostela, Spain
| | | | | | - P Ferreira
- C2TN-Instituto Superior Tecníco, Universidade de Lisboa, Portugal
| | - W Furman
- Joint Institute of Nuclear Research, Dubna, Russia
| | - S Ganesan
- Bhabha Atomic Research Centre (BARC), Mumbai, India
| | - A García-Rios
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - A Gawlik
- Uniwersytet Łódzki, Lodz, Poland
| | - T Glodariu
- Horia Hulubei National Institute of Physics and Nuclear Engineering-IFIN HH, Bucharest-Magurele, Romania
| | - K Göbel
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - I F Gonçalves
- C2TN-Instituto Superior Tecníco, Universidade de Lisboa, Portugal
| | - E González-Romero
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - E Griesmayer
- Atominstitut der Österreichischen Universitäten, Technische Universität Wien, Austria
| | | | - F Gunsing
- CEA/Saclay-IRFU, Gif-sur-Yvette, France
| | - H Harada
- Japan Atomic Energy Agency (JAEA), Tokai-mura, Japan
| | - T Heftrich
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - J Heyse
- European Commission JRC, Institute for Reference Materials and Measurements, Retieseweg 111, B-2440 Geel, Belgium
| | - D G Jenkins
- University of York, Heslington, York, United Kingdom
| | - E Jericha
- Atominstitut der Österreichischen Universitäten, Technische Universität Wien, Austria
| | | | - P Kavrigin
- Atominstitut der Österreichischen Universitäten, Technische Universität Wien, Austria
| | - A Kimura
- Japan Atomic Energy Agency (JAEA), Tokai-mura, Japan
| | - M Kokkoris
- National Technical University of Athens (NTUA), Greece
| | - M Krtička
- Charles University, Prague, Czech Republic
| | | | | | - C Lederer
- School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - H Leeb
- Atominstitut der Österreichischen Universitäten, Technis che Universität Wien, Austria
| | - S Lo Meo
- ENEA, Bologna, Italy
- INFN, Sezione di Bologna, Italy
| | - S J Lonsdale
- School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | | | | | | | - T Martínez
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - C Massimi
- INFN, Sezione di Bologna, Italy
- Dipartimento di Fisica e Astronomia, Università di Bologna
| | - P Mastinu
- INFN-Laboratori Nazionali di Legnaro, Italy
| | | | - A Mazzone
- INFN, Sezione di Bari, Italy
- CNR-IC, Bari, Italy
| | - E Mendoza
- Centro de Investigaciones Energeticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | | | - F Mingrone
- INFN, Sezione di Bologna, Italy
- Dipartimento di Fisica e Astronomia, Università di Bologna
| | - M Mirea
- Horia Hulubei National Institute of Physics and Nuclear Engineering-IFIN HH, Bucharest-Magurele, Romania
| | | | - R Nolte
- Physikalisch Technische Bundesanstalt (PTB), Braunschweig, Germany
| | - A Oprea
- Horia Hulubei National Institute of Physics and Nuclear Engineering-IFIN HH, Bucharest-Magurele, Romania
| | - A Pappalardo
- INFN-Laboratori Nazionali del Sud, Catania, Italy
| | | | - A Pavlik
- University of Vienna, Faculty of Physics, Austria
| | | | - M Piscopo
- INFN-Laboratori Nazionali del Sud, Catania, Italy
| | - A Plompen
- European Commission JRC, Institute for Reference Materials and Measurements, Retieseweg 111, B-2440 Geel, Belgium
| | | | - J Praena
- Universidad de Sevilla, Spain
- Universidad de Granada, Spain
| | | | - K Rajeev
- Bhabha Atomic Research Centre (BARC), Mumbai, India
| | - T Rauscher
- Centre for Astrophysics Research, School of Physics, Astronomy and Mathematics, University of Hertfordshire, Hatfield, United Kingdom
- Department of Physics, University of Basel, Basel, Switzerland
| | - R Reifarth
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - A Riego-Perez
- Universitat Politecnica de Catalunya, Barcelona, Spain
| | - P Rout
- Bhabha Atomic Research Centre (BARC), Mumbai, India
| | | | - J Ryan
- University of Manchester, Oxford Road, Manchester, United Kingdom
| | | | - A Saxena
- Bhabha Atomic Research Centre (BARC), Mumbai, India
| | - P Schillebeeckx
- European Commission JRC, Institute for Reference Materials and Measurements, Retieseweg 111, B-2440 Geel, Belgium
| | - S Schmidt
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - P Sedyshev
- Joint Institute of Nuclear Research, Dubna, Russia
| | - A G Smith
- University of Manchester, Oxford Road, Manchester, United Kingdom
| | | | | | - J L Tain
- Instituto de Física Corpuscular, CSIC-Universidad de Valencia, Spain
| | | | - L Tassan-Got
- Centre National de la Recherche Scientifique/IN2P3-IPN, Orsay, France
| | | | - S Valenta
- Charles University, Prague, Czech Republic
| | - G Vannini
- INFN, Sezione di Bologna, Italy
- Dipartimento di Fisica e Astronomia, Università di Bologna
| | | | - P Vaz
- C2TN-Instituto Superior Tecníco, Universidade de Lisboa, Portugal
| | | | | | - R Vlastou
- National Technical University of Athens (NTUA), Greece
| | | | - A Wallner
- University of Vienna, Faculty of Physics, Austria
- Research School of Physics and Engineering, Australian National University, ACT 0200, Australia
| | - S Warren
- University of Manchester, Oxford Road, Manchester, United Kingdom
| | - M Weigand
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - C Weiß
- CERN, Geneva, Switzerland
| | - C Wolf
- Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - P J Woods
- School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - T Wright
- University of Manchester, Oxford Road, Manchester, United Kingdom
| | - P Žugec
- Department of Physics, Faculty of Science, University of Zagreb, Croatia
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Kane EV, Smith AG, Howell D, Crouch S, Roman E. OP08 Emergency presentation in aggressive lymphoma and impact on survival: a report from the Haematological Malignancy Research Network. Br J Soc Med 2016. [DOI: 10.1136/jech-2016-208064.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Howell DA, Turner AK, Smith AG, Roman E. P80 Preferred and actual place of death in patients with blood cancers: Findings from a UK population-based study. Br J Soc Med 2016. [DOI: 10.1136/jech-2016-208064.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Howell DA, Appleton S, Smith AG, Roman E. P79 Routes to diagnosis of myeloma: findings from a UK population-based study. Br J Soc Med 2016. [DOI: 10.1136/jech-2016-208064.178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Howell DA, Wang HI, Roman E, Smith AG, Patmore R, Johnson MJ, Garry A, Howard M. Preferred and actual place of death in haematological malignancy. BMJ Support Palliat Care 2015; 7:150-157. [PMID: 26156005 PMCID: PMC5502252 DOI: 10.1136/bmjspcare-2014-000793] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 01/19/2015] [Accepted: 06/21/2015] [Indexed: 11/11/2022]
Abstract
Objectives Home is considered the preferred place of death for many, but patients with haematological malignancies (leukaemias, lymphomas and myeloma) die in hospital more often than those with other cancers and the reasons for this are not wholly understood. We examined preferred and actual place of death among people with these diseases. Methods The study is embedded within an established population-based cohort of patients with haematological malignancies. All patients diagnosed at two of the largest hospitals in the study area between May 2005 and April 2008 with acute myeloid leukaemia, diffuse large B-cell lymphoma or myeloma, who died before May 2010 were included. Data were obtained from medical records and routine linkage to national death records. Results 323 deceased patients were included. A total of 142 (44%) had discussed their preferred place of death; 45.8% wanted to die at home, 28.2% in hospital, 16.9% in a hospice, 5.6% in a nursing home and 3.5% were undecided; 63.4% of these died in their preferred place. Compared to patients with evidence of a discussion, those without were twice as likely to have died within a month of diagnosis (14.8% vs 29.8%). Overall, 240 patients died in hospital; those without a discussion were significantly more likely to die in hospital than those who had (p≤0.0001). Of those dying in hospital, 90% and 75.8% received haematology clinical input in the 30 and 7 days before death, respectively, and 40.8% died in haematology areas. Conclusions Many patients discussed their preferred place of death, but a substantial proportion did not and hospital deaths were common in this latter group. There is scope to improve practice, particularly among those dying soon after diagnosis. We found evidence that some people opted to die in hospital; the extent to which this compares with other cancers is of interest.
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Affiliation(s)
- D A Howell
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - H I Wang
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - E Roman
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - A G Smith
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - R Patmore
- Queen's Centre for Oncology and Haematology, Castle Hill Hospital, Hull, UK
| | - M J Johnson
- Hull York Medical School, University of Hull, Hull, UK
| | - A Garry
- York Teaching Hospital NHS Foundation Trust, York, UK
| | - M Howard
- York Teaching Hospital NHS Foundation Trust, York, UK
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Abstract
The gene regulatory circuitry through which pluripotent embryonic stem (ES) cells choose between self-renewal and differentiation appears vast and has yet to be distilled into an executive molecular program. We developed a data-constrained, computational approach to reduce complexity and to derive a set of functionally validated components and interaction combinations sufficient to explain observed ES cell behavior. This minimal set, the simplest version of which comprises only 16 interactions, 12 components, and three inputs, satisfies all prior specifications for self-renewal and furthermore predicts unknown and nonintuitive responses to compound genetic perturbations with an overall accuracy of 70%. We propose that propagation of ES cell identity is not determined by a vast interactome but rather can be explained by a relatively simple process of molecular computation.
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Affiliation(s)
- S-J Dunn
- Computational Science Laboratory, Microsoft Research, Cambridge, CB1 2FB, UK
| | - G Martello
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - B Yordanov
- Computational Science Laboratory, Microsoft Research, Cambridge, CB1 2FB, UK
| | - S Emmott
- Computational Science Laboratory, Microsoft Research, Cambridge, CB1 2FB, UK
| | - AG Smith
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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Howell DA, Wang HI, Roman E, Smith AG, Patmore R, Johnson MJ, Garry AC, Howard MR. Variations in specialist palliative care referrals: findings from a population-based patient cohort of acute myeloid leukaemia, diffuse large B-cell lymphoma and myeloma. BMJ Support Palliat Care 2014; 5:496-502. [PMID: 24644210 PMCID: PMC4717425 DOI: 10.1136/bmjspcare-2013-000578] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [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] [Received: 08/08/2013] [Accepted: 01/19/2014] [Indexed: 11/06/2022]
Abstract
Objective To develop and implement a methodology for capturing complete haematological malignancy pathway data and use it to identify variations in specialist palliative care (SPC) referrals. Methods In our established UK population-based patient cohort, 323 patients were diagnosed with acute myeloid leukaemia, diffuse large B-cell lymphoma or myeloma between May 2005 and April 2008, and died before April 2010. A day-by-day calendar approach was devised to collect pathway data, including SPC referrals, to supplement routinely collected information on clinical presentation, diagnosis, treatment, response, and date and place of death. Results 155 (47.9%) of the 323 patients had at least one SPC referral. The likelihood of referral increased with survival (OR 6.58, 95% CIs 3.32 to 13.03 for patients surviving ≥1 year compared to ≤1 month from diagnosis), and varied with diagnosis (OR 1.96, CIs 1.15 to 3.35 for myeloma compared to acute myeloid leukaemia). Compared to patients dying in hospital, those who died at home or in a hospice were also more likely to have had an SPC referral (OR 3.07, CIs 1.59 to 5.93 and 4.74, CIs 1.51 to 14.81, respectively). No associations were found for age and sex. Conclusions Our novel approach efficiently captured pathway data and SPC referrals, revealing evidence of greater integration between haematology and SPC services than previously reported. The likelihood of referral was much higher among those dying outside hospital, and variations in practice were observed by diagnosis, emphasising the importance of examining diseases individually.
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Affiliation(s)
- D A Howell
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, North Yorkshire, UK
| | - H-I Wang
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, North Yorkshire, UK
| | - E Roman
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, North Yorkshire, UK
| | - A G Smith
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, North Yorkshire, UK
| | - R Patmore
- Queens Centre for Oncology, Castle Hill Hospital, Hull, East Yorkshire, UK
| | - M J Johnson
- Hull York Medical School, The University of Hull, Hull, East Yorkshire, UK
| | - A C Garry
- York Teaching Hospital NHS Foundation Trust, York, North Yorkshire, UK
| | - M R Howard
- York Teaching Hospital NHS Foundation Trust, York, North Yorkshire, UK
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Smith AG, Painter D, Howell DA, Evans P, Smith G, Patmore R, Jack A, Roman E. Determinants of survival in patients with chronic myeloid leukaemia treated in the new era of oral therapy: findings from a UK population-based patient cohort. BMJ Open 2014; 4:e004266. [PMID: 24435897 PMCID: PMC3902525 DOI: 10.1136/bmjopen-2013-004266] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 12/03/2013] [Accepted: 12/05/2013] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVES To examine contemporary survival patterns in the general population of patients diagnosed with chronic myeloid leukaemia (CML), and to identify patient groups with less than optimal outcomes. DESIGN Prospective population-based cohort. SETTING The UK's Haematological Malignancy Research Network (catchment population 3.6 million, with >2000 new haematological malignancies diagnosed annually). PARTICIPANTS All patients newly diagnosed with CML, from September 2004 to August 2011 and followed up to 31 March 2013. MAIN OUTCOME MEASURE Incidence and survival. RESULTS With a median diagnostic age of 59 years, the CML age standardised (European) incidence was 0.9/100 000 (95% CIs 0.8 to 0.9), 5-year overall survival was 78.9% (72.3 to 84.0) and 5-year relative survival 88.6% (81.0 to 93.3). The efficacy of treatment across all ages was clearly demonstrated; the relative survival curves for those under 60 and over 60 years being closely aligned. Survival findings were similar for men and women, but varied with deprivation; the age and sex adjusted HR being 3.43 (1.89 to 6.22) for deprivation categories 4-5 (less affluent) versus 1-3 (more affluent). None of these differences were attributable to the biological features of the disease. CONCLUSIONS When therapy is freely provided, population-based survival for CML is similar to that reported in clinical trials, and age loses its prognostic significance. However, although most of the patients with CML now experience close to normal lifespans, those living in more deprived areas tend to have poorer outcomes, despite receiving the same clinical care. A significant improvement in overall population outcomes could be achieved if these socioeconomic differences, which may reflect the treatment compliance, could be eliminated.
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Affiliation(s)
- A G Smith
- Department of Health Sciences, University of York, York, UK
| | - D Painter
- Department of Health Sciences, University of York, York, UK
| | - D A Howell
- Department of Health Sciences, University of York, York, UK
| | - P Evans
- Haematological Malignancy Diagnostic Service, St James University Hospital, Leeds, UK
| | - G Smith
- St. James's Institute of Oncology, St James's University Hospital, Leeds, UK
| | - R Patmore
- Queens Centre for Oncology, Castle Hill Hospital, Hull, UK
| | - A Jack
- Haematological Malignancy Diagnostic Service, St James University Hospital, Leeds, UK
| | - E Roman
- Department of Health Sciences, University of York, York, UK
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Mack SJ, Cano P, Hollenbach JA, He J, Hurley CK, Middleton D, Moraes ME, Pereira SE, Kempenich JH, Reed EF, Setterholm M, Smith AG, Tilanus MG, Torres M, Varney MD, Voorter CEM, Fischer GF, Fleischhauer K, Goodridge D, Klitz W, Little AM, Maiers M, Marsh SGE, Müller CR, Noreen H, Rozemuller EH, Sanchez-Mazas A, Senitzer D, Trachtenberg E, Fernandez-Vina M. Common and well-documented HLA alleles: 2012 update to the CWD catalogue. ACTA ACUST UNITED AC 2013; 81:194-203. [PMID: 23510415 DOI: 10.1111/tan.12093] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 02/14/2013] [Accepted: 02/15/2013] [Indexed: 11/26/2022]
Abstract
We have updated the catalogue of common and well-documented (CWD) human leukocyte antigen (HLA) alleles to reflect current understanding of the prevalence of specific allele sequences. The original CWD catalogue designated 721 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, and -DPB1 loci in IMGT (IMmunoGeneTics)/HLA Database release 2.15.0 as being CWD. The updated CWD catalogue designates 1122 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1 and -DPB1 loci as being CWD, and represents 14.3% of the HLA alleles in IMGT/HLA Database release 3.9.0. In particular, we identified 415 of these alleles as being 'common' (having known frequencies) and 707 as being 'well-documented' on the basis of ~140,000 sequence-based typing observations and available HLA haplotype data. Using these allele prevalence data, we have also assigned CWD status to specific G and P designations. We identified 147/151 G groups and 290/415 P groups as being CWD. The CWD catalogue will be updated on a regular basis moving forward, and will incorporate changes to the IMGT/HLA Database as well as empirical data from the histocompatibility and immunogenetics community. This version 2.0.0 of the CWD catalogue is available online at cwd.immunogenomics.org, and will be integrated into the Allele Frequencies Net Database, the IMGT/HLA Database and National Marrow Donor Program's bioinformatics web pages.
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Affiliation(s)
- S J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
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Boger MS, Hulgan T, Haas DW, Mitchell V, Smith AG, Singleton JR, Peltier AC. Measures of small-fiber neuropathy in HIV infection. Auton Neurosci 2012; 169:56-61. [PMID: 22542355 DOI: 10.1016/j.autneu.2012.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 03/28/2012] [Accepted: 04/03/2012] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Noninvasive methods are needed to detect distal sensory polyneuropathy in HIV-infected persons on antiretroviral therapy (ART). METHODS Quantitative sudomotor axon reflex test (QSART) and Utah Early Neuropathy Scale (UENS), small-fiber sensitive measures, were assessed in subjects with and without clinical neuropathy. Pain was assessed by visual analog scale (VAS). RESULTS Twenty-two subjects had symptoms and signs of neuropathy, 19 had neither, and all were receiving ART. Median sweat volume (μL) was lower at all testing sites in those with neuropathy compared to those without (p<0.01 for all). UENS and VAS (mm) were higher in neuropathy subjects (p<0.05 for each). Lower sweat volume at all sites correlated with higher pin UENS subscore, total UENS, and VAS (p<0.05 for all). In multivariable analyses adjusting for age, CD4⁺ T cells, sex, and use of "d-drug" ART, QSART and UENS remained associated (p=0.003). CONCLUSION QSART and UENS have not been previously studied in this patient population and may identify small-fiber neuropathy in HIV-infected, ART-treated persons.
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Affiliation(s)
- M S Boger
- Department of Medicine, Division of Infectious Diseases, Medical University of South Carolina, Charleston, SC 29412, United States.
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Smith AG, Fan W, Regen L, Warnock S, Sprague M, Williams R, Nisperos B, Zhao LP, Loken MR, Hansen JA, Pereira S. Somatic mutations in the HLA genes of patients with hematological malignancy. ACTA ACUST UNITED AC 2012; 79:359-66. [PMID: 22489945 DOI: 10.1111/j.1399-0039.2012.01868.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- A G Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Zilliox L, Peltier AC, Wren PA, Anderson A, Smith AG, Singleton JR, Feldman EL, Alexander NB, Russell JW. Assessing autonomic dysfunction in early diabetic neuropathy: the Survey of Autonomic Symptoms. Neurology 2011; 76:1099-105. [PMID: 21422460 DOI: 10.1212/wnl.0b013e3182120147] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE Autonomic symptoms may occur frequently in diabetic and other neuropathies. There is a need to develop a simple instrument to measure autonomic symptoms in subjects with neuropathy and to test the validity of the instrument. METHODS The Survey of Autonomic Symptoms (SAS) consists of 11 items in women and 12 in men. Each item is rated by an impact score ranging from 1 (least severe) to 5 (most severe). The SAS was tested in observational studies and compared to a previously validated autonomic scale, the Autonomic Symptom Profile (ASP), and to a series of autonomic tests. RESULTS The SAS was tested in 30 healthy controls and 62 subjects with neuropathy and impaired glucose tolerance or newly diagnosed diabetes. An increased SAS score was associated with the previously validated ASP (rank order correlation=0.68; p<0.0001) and with quantitative measures of autonomic function: a reduced quantitative sudomotor axon reflex test sweat volume (0.31; p<0.05) and an abnormal 30:15 ratio (0.53; p<0.01). The SAS shows a high sensitivity and specificity (area under the receiver operating characteristic curve 0.828) that compares favorably with the ASP. The SAS scale domains had a good internal consistency and reliability (Cronbach α=0.76). The SAS symptom score was increased in neuropathy (95% confidence interval [CI] 2.99-4.14) compared to control (95% CI 0.58-1.69; p<0.0001) subjects. CONCLUSIONS The SAS is a new, valid, easily administered instrument to measure autonomic symptoms in early diabetic neuropathy and would be of value in assessing neuropathic autonomic symptoms in clinical trials and epidemiologic studies.
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Affiliation(s)
- L Zilliox
- Department of Neurology, University of Maryland and Maryland VA Healthcare System, Baltimore, MD, USA
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Lauria G, Hsieh ST, Johansson O, Kennedy WR, Leger JM, Mellgren SI, Nolano M, Merkies ISJ, Polydefkis M, Smith AG, Sommer C, Valls-Solé J. European Federation of Neurological Societies/Peripheral Nerve Society Guideline on the use of skin biopsy in the diagnosis of small fiber neuropathy. Report of a joint task force of the European Federation of Neurological Societies and the Peripheral Nerve Society. Eur J Neurol 2011; 17:903-12, e44-9. [PMID: 20642627 DOI: 10.1111/j.1468-1331.2010.03023.x] [Citation(s) in RCA: 525] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Revision of the guidelines on the use of skin biopsy in the diagnosis of peripheral neuropathy, published in 2005, has become appropriate owing to publication of more relevant articles. Most of the new studies focused on small fiber neuropathy (SFN), a subtype of neuropathy for which the diagnosis was first developed through skin biopsy examination. This revision focuses on the use of this technique to diagnose SFN. METHODS Task force members searched the Medline database from 2005, the year of the publication of the first EFNS guideline, to June 30th, 2009. All pertinent articles were rated according to the EFNS and PNS guidance. After a consensus meeting, the task force members created a manuscript that was subsequently revised by two experts (JML and JVS) in the field of peripheral neuropathy and clinical neurophysiology, who were not previously involved in the use of skin biopsy. RESULTS AND CONCLUSIONS Distal leg skin biopsy with quantification of the linear density of intraepidermal nerve fibers (IENF), using generally agreed upon counting rules, is a reliable and efficient technique to assess the diagnosis of SFN (Recommendation Level A). Normative reference values are available for bright-field immunohistochemistry (Recommendation Level A) but not yet for confocal immunofluorescence or the blister technique. The morphometric analysis of IENF density, either performed with bright-field or immunofluorescence microscopy, should always refer to normative values matched for age (Recommendation Level A). Newly established laboratories should undergo adequate training in a well-established skin biopsy laboratory and provide their own stratified for age and gender normative values, intra- and interobserver reliability, and interlaboratory agreement. Quality control of the procedure at all levels is mandatory (Good Practice Point). Procedures to quantify subepidermal nerve fibers and autonomic innervated structures, including erector pili muscles, and skin vessels, are under development but need to be confirmed by further studies. Sweat gland innervation can be examined using an unbiased stereologic technique recently proposed (Recommendation Level B). A reduced IENF density is associated with the risk of developing neuropathic pain (Recommendation Level B), but it does not correlate with its intensity. Serial skin biopsies might be useful for detecting early changes of IENF density, which predict the progression of neuropathy, and to assess degeneration and regeneration of IENF (Recommendation Level C). However, further studies are warranted to confirm its potential usefulness as an outcome measure in clinical practice and research. Skin biopsy has not so far been useful for identifying the etiology of SFN. Finally, we emphasize that 3-mm skin biopsy at the ankle is a safe procedure based on the experience of 10 laboratories reporting absence of serious side effects in approximately 35,000 biopsies and a mere 0.19% incidence of non-serious side effects in about 15 years of practice (Good Practice Point).
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Affiliation(s)
- G Lauria
- Neuromuscular Diseases Unit, IRCCS Foundation, 'Carlo Besta' Neurological Institute, Milan, Italy.
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Smith AG, O'Doherty JV, Reilly P, Ryan MT, Bahar B, Sweeney T. The effects of laminarin derived from Laminaria digitata on measurements of gut health: selected bacterial populations, intestinal fermentation, mucin gene expression and cytokine gene expression in the pig. Br J Nutr 2011; 105:669-77. [PMID: 21251335 DOI: 10.1017/s0007114510004277] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The aim of the present study was to establish the optimum inclusion level of laminarin derived from Laminaria digitata on selected microbial populations, intestinal fermentation, cytokine and mucin gene expression in the porcine ileum and colon. A total of twenty-one pigs (mean body weight 17·9 kg) were randomly assigned to one of three dietary treatments: T1 - basal (control) diet, T2 and T3 - basal diets supplemented with laminarin included at 300 and 600 parts per million (ppm), respectively. Selected intestinal bacterial populations and volatile fatty acid (VFA) concentrations were measured in the ileum and colon. Relative gene expression levels for specific cytokine and mucin genes were investigated in ileal and colonic tissue in the absence and presence of a lipopolysaccharide (LPS) challenge. There was an up-regulation of MUC2 gene expression at the 300 ppm inclusion level in the ileum. In the colon, there was a significant reduction in the enterobacteriaceae population at the 300 ppm inclusion level (P = 0·0421). Dietary supplementation of 600 ppm laminarin led to a significant increase in MUC2 (P = 0·0365) and MUC4 (P = 0·0401) expression in the colon, and in the total VFA concentration in the caecum (P = 0·0489). A significant increase was also recorded in IL-6 (P = 0·0289) and IL-8 gene expression (P = 0·0245) in LPS-challenged colonic tissue at both laminarin inclusion levels. In conclusion, dietary inclusion of 300 ppm laminarin appears to be the optimum dose in the present study due to the reduction in the enterobacteriaceae populations and enhanced IL-6 and IL-8 cytokine expression in response to an ex vivo LPS challenge.
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Affiliation(s)
- A G Smith
- School of Agriculture, Food Science and Veterinary Medicine, University College, Dublin, Republic of Ireland
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Halpern J, Harris S, Suarez V, Jeyaratnam R, Smith AG. Epithelioma cuniculatum: A case report. Foot Ankle Surg 2009; 15:114-6. [PMID: 19410181 DOI: 10.1016/j.fas.2008.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 08/11/2008] [Accepted: 08/13/2008] [Indexed: 02/04/2023]
Abstract
Epithelioma cuniculatum (carcinoma cuniculatum) is a rare, low-grade verrucous carcinoma of the foot first described in 1954. We present a case report of a 55-year-old man with an enlarging lesion on the sole of his right foot. Despite initial benign pathology the lesion continued to grow, soften in consistency and develop a foul odour. Repeat biopsy showed a well-differentiated squamous cell carcinoma and below-the-knee amputation was required. Epithelioma cuniculatum presents as a slow growing mass on the plantar aspect of the foot. Diagnosis is often delayed and may require multiple biopsies. Lesions rarely metastasise but more commonly invade locally requiring wide surgical excision.
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Affiliation(s)
- J Halpern
- Department of Dermatology, COPD, University Hospital of North Staffordshire, Hartshill Road, Stoke-on-Trent, England ST4 7PA, United Kingdom.
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Abstract
Reducing cancer mortality is a priority for the UK Government and emphasis has been placed on introducing targets to ensure prompt diagnosis. Help seeking is the first step on the pathway to diagnosis and should occur promptly; however, patients with lymphoma take longer to seek help for symptoms than those with many other cancers. Despite this, the help seeking behaviour of these patients has not been investigated. This qualitative study examined the beliefs and actions about help seeking among 32 patients, aged 65 and over and newly diagnosed with lymphoma in West Yorkshire during 2000. Patients reported an extremely wide range of symptoms which were not always interpreted as serious or potentially caused by cancer. This, in association with a clear lack of knowledge about lymphoma, often led to help seeking being deferred. The range and characteristics of symptoms can largely be explained in terms of variations in the type, site and size of the lymphoma. The UK Government targets focus on the time after help seeking, yet for lymphoma it is also crucial to reduce the time taken to seek help. More education about the potential symptoms of this disease is needed among the general public.
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Affiliation(s)
- D A Howell
- Epidemiology & Genetics Unit, Department of Health Sciences, University of York, York, UK.
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Abstract
To gain survival advantages potentially associated with prompt diagnosis, the UK government introduced identical waiting-time targets for all cancers, and guidelines to ensure that general practitioners make appropriate hospital referrals. For lymphoma, the evidence guiding these actions is limited. This study examined referral pathways in patients with lymphoma and variations in time to diagnosis by discipline of first referral. A case series study was conducted including all patients aged over 25 years, newly diagnosed with lymphoma in the UK county of West Yorkshire, during 2000. Data were extracted from primary care and hospital records of 189 patients. Referral pathways were described, and the number of days between first referral and diagnosis calculated. A distinct referral pathway did not exist; patients were initially referred to many disciplines. Surgical referrals predominated, and only 12% of patients were sent directly to haematology. Time to diagnosis varied by discipline and was shorter for patients sent to haematology than for most other common disciplines. UK government actions to ensure the prompt diagnosis of patients with lymphoma are not evidence-based. The complexity of the referral pathway in patients with lymphoma, which affects time to diagnosis, has been underestimated. Further government actions should be evidence-based, ensuring prompt diagnosis of lymphoma from whatever discipline patients originate.
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Affiliation(s)
- D A Howell
- Department of Health Sciences, University of York, York, UK.
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35
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Biswas A, van Pittius DG, Stephens M, Smith AG. Recurrent primary cutaneous lymphoma with florid pseudoepitheliomatous hyperplasia masquerading as squamous cell carcinoma. Histopathology 2008; 52:755-8. [DOI: 10.1111/j.1365-2559.2008.03013.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Worrillow LJ, Smith AG, Scott K, Andersson M, Ashcroft AJ, Dores GM, Glimelius B, Holowaty E, Jackson GH, Jones GL, Lynch CF, Morgan G, Pukkala E, Scott D, Storm HH, Taylor PR, Vyberg M, Willett E, Travis LB, Allan JM. Polymorphic MLH1 and risk of cancer after methylating chemotherapy for Hodgkin lymphoma. J Med Genet 2007; 45:142-6. [PMID: 17959715 DOI: 10.1136/jmg.2007.053850] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND AND OBJECTIVE Methylating agents are effective chemotherapy agents for Hodgkin lymphoma, but are associated with the development of second primary cancers. Cytotoxicity of methylating agents is mediated primarily by the DNA mismatch repair (MMR) system. Loss of MLH1, a major component of DNA MMR, results in tolerance to the cytotoxic effects of methylating agents and persistence of mutagenised cells at high risk of malignant transformation. We hypothesised that a common substitution in the basal promoter of MLH1 (position -93, rs1800734) modifies the risk of cancer after methylating chemotherapy. METHODS 133 patients who developed cancer following chemotherapy and/or radiotherapy (n = 133), 420 patients diagnosed with de novo myeloid leukaemia, 242 patients diagnosed with primary Hodgkin lymphoma, and 1177 healthy controls were genotyped for the MLH1 -93 polymorphism by allelic discrimination polymerase chain reaction (PCR) and restriction fragment length polymorphism assay. Odds ratios and 95% confidence intervals for cancer risk by MLH1 -93 polymorphism status, and stratified by previous exposure to methylating chemotherapy, were calculated using unconditional logistic regression. RESULTS Carrier frequency of the MLH1 -93 variant was higher in patients who developed therapy related acute myeloid leukaemia (t-AML) (75.0%, n = 12) or breast cancer (53.3%. n = 15) after methylating chemotherapy for Hodgkin lymphoma compared to patients without previous methylating exposure (t-AML, 30.4%, n = 69; breast cancer patients, 27.2%, n = 22). The MLH1 -93 variant allele was also over-represented in t-AML cases when compared to de novo AML cases (36.9%, n = 420) and healthy controls (36.3%, n = 952), and was associated with a significantly increased risk of developing t-AML (odds ratio 5.31, 95% confidence interval 1.40 to 20.15), but only in patients previously treated with a methylating agent. CONCLUSIONS These data support the hypothesis that the common polymorphism at position -93 in the core promoter of MLH1 defines a risk allele for the development of cancer after methylating chemotherapy for Hodgkin lymphoma. However, replication of this finding in larger studies is suggested.
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Affiliation(s)
- L J Worrillow
- Department of Biology, University of York, Heslington, York, UK
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37
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Mensah FK, Willett EV, Simpson J, Smith AG, Roman E. Birth order and sibship size: evaluation of the role of selection bias in a case-control study of non-Hodgkin's lymphoma. Am J Epidemiol 2007; 166:717-23. [PMID: 17591593 DOI: 10.1093/aje/kwm131] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Substantial heterogeneity has been observed among case-control studies investigating associations between non-Hodgkin's lymphoma and familial characteristics, such as birth order and sibship size. The potential role of selection bias in explaining such heterogeneity is considered within this study. Selection bias according to familial characteristics and socioeconomic status is investigated within a United Kingdom-based case-control study of non-Hodgkin's lymphoma diagnosed during 1998-2001. Reported distributions of birth order and maternal age are each compared with expected reference distributions derived using national birth statistics from the United Kingdom. A method is detailed in which yearly data are used to derive expected distributions, taking account of variability in birth statistics over time. Census data are used to reweight both the case and control study populations such that they are comparable with the general population with regard to socioeconomic status. The authors found little support for an association between non-Hodgkin's lymphoma and birth order or family size and little evidence for an influence of selection bias. However, the findings suggest that between-study heterogeneity could be explained by selection biases that influence the demographic characteristics of participants.
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Affiliation(s)
- F K Mensah
- Epidemiology and Genetics Unit, Department of Health Sciences, University of York, York, United Kingdom
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38
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Affiliation(s)
- H T Orme
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
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39
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Catovsky D, Richards S, Matutes E, Oscier D, Dyer M, Bezares RF, Pettitt AR, Hamblin T, Milligan DW, Child JA, Hamilton MS, Dearden CE, Smith AG, Bosanquet AG, Davis Z, Brito-Babapulle V, Else M, Wade R, Hillmen P. Assessment of fludarabine plus cyclophosphamide for patients with chronic lymphocytic leukaemia (the LRF CLL4 Trial): a randomised controlled trial. Lancet 2007; 370:230-239. [PMID: 17658394 DOI: 10.1016/s0140-6736(07)61125-8] [Citation(s) in RCA: 600] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Previous studies of patients with chronic lymphocytic leukaemia reported high response rates to fludarabine combined with cyclophosphamide. We aimed to establish whether this treatment combination provided greater survival benefit than did chlorambucil or fludarabine. METHODS 777 patients with chronic lymphocytic leukaemia requiring treatment were randomly assigned to fludarabine (n=194) or fludarabine plus cyclophosphamide (196) for six courses, or chlorambucil (387) for 12 courses. The primary endpoint was overall survival, with secondary endpoints of response rates, progression-free survival, toxic effects, and quality of life. Analysis was by intention to treat. This study is registered as an International Standard Randomised Controlled Trial, number NCT 58585610. FINDINGS There was no significant difference in overall survival between patients given fludarabine plus cyclophosphamide, fludarabine, or chlorambucil. Complete and overall response rates were better with fludarabine plus cyclophosphamide than with fludarabine (complete response rate 38%vs 15%, respectively; overall response rate 94%vs 80%, respectively; p<0.0001 for both comparisons), which were in turn better than with chlorambucil (complete response rate 7%, overall response rate 72%; p=0.006 and 0.04, respectively). Progression-free survival at 5 years was significantly better with fludarabine plus cyclophosphamide (36%) than with fludarabine (10%) or chlorambucil (10%; p<0.00005). Fludarabine plus cyclophosphamide was the best combination for all ages, including patients older than 70 years, and in prognostic groups defined by immunoglobulin heavy chain gene (V(H)) mutation status and cytogenetics, which were tested in 533 and 579 cases, respectively. Patients had more neutropenia and days in hospital with fludarabine plus cyclophosphamide, or fludarabine, than with chlorambucil. There was less haemolytic anaemia with fludarabine plus cyclophosphamide (5%) than with fludarabine (11%) or chlorambucil (12%). Quality of life was better for responders, but preliminary analyses showed no significant difference between treatments. A meta-analysis of these data and those of two published phase III trials showed a consistent benefit for the fludarabine plus cyclophosphamide regimen in terms of progression-free survival. INTERPRETATION Fludarabine plus cyclophosphamide should now become the standard treatment for chronic lymphocytic leukaemia and the basis for new protocols that incorporate monoclonal antibodies.
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Affiliation(s)
- D Catovsky
- Section of Haemato-Oncology, Institute of Cancer Research, Sutton, UK.
| | | | - E Matutes
- Section of Haemato-Oncology, Institute of Cancer Research, Sutton, UK
| | - D Oscier
- Royal Bournemouth Hospital, Bournemouth, UK
| | - Mjs Dyer
- Leicester Royal Infirmary, Leicester, UK
| | | | | | - T Hamblin
- Royal Bournemouth Hospital, Bournemouth, UK
| | | | | | | | - C E Dearden
- Section of Haemato-Oncology, Institute of Cancer Research, Sutton, UK
| | - A G Smith
- Southampton General Hospital, Southampton, UK
| | | | - Z Davis
- Royal Bournemouth Hospital, Bournemouth, UK
| | - V Brito-Babapulle
- Section of Haemato-Oncology, Institute of Cancer Research, Sutton, UK
| | - M Else
- Section of Haemato-Oncology, Institute of Cancer Research, Sutton, UK
| | - R Wade
- Clinical Trial Service Unit, Oxford, UK
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40
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Sampson JB, Smith SM, Smith AG, Singleton JR, Chin S, Pestronk A, Flanigan KM. Paraneoplastic myopathy: response to intravenous immunoglobulin. Neuromuscul Disord 2007; 17:404-8. [PMID: 17336069 DOI: 10.1016/j.nmd.2007.01.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [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: 09/01/2006] [Revised: 12/21/2006] [Accepted: 01/09/2007] [Indexed: 11/30/2022]
Abstract
Necrotizing myopathy is an unusual and severe form of paraneoplastic myopathy in which inflammation is minimal or absent. We report two cases of necrotizing myopathy which demonstrated significant response to intravenous immunoglobulin (IVIG) (one in spite of tumor progression). A third case represents the first association of anti-signal recognition particle (anti-SRP) syndrome with large-cell lung cancer. These cases highlight the role of histopathologic diagnosis in directing the treatment of paraneoplastic myopathy, and the role for IVIG in treatment of the syndrome.
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Affiliation(s)
- J B Sampson
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
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41
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Abstract
This study examines illness trajectories of patients with lymphoma and assesses whether UK government targets to reduce waiting time for diagnosis and treatment are achievable and appropriate. One hundred and ninety-four patients, residents in West Yorkshire, aged more than 25 years and newly diagnosed with lymphoma during 2000 were included. Data collected from interviews, primary care and hospital records were used to examine time between critical events on the illness trajectory and characteristics of patients not meeting proposed targets. Forty-two per cent of patients did not receive a hospital appointment within 2 weeks of general practitioner referral, 26% were not treated within 1 month of diagnosis and 64% were not treated within 2 months of referral. Target achievement differed by diagnostic group, and trends were seen by age and deprivation. The interval from onset of symptoms to treatment averaged more than 1 year and approximately half of this occurred before first medical contact. Results suggest that significant improvements are needed to achieve targets. Although existing targets particularly address referral and treatment intervals, these were the shortest intervals on the trajectory. Generalized targets may be inappropriate and unachievable for lymphoma as they do not consider individual disease characteristics or allow for variations in the urgency with which treatment is needed.
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Affiliation(s)
- D A Howell
- Epidemiology & Genetics Unit, Department of Heath Sciences, Seebohm Rowntree Building, University of York, York, UK.
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42
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Affiliation(s)
- J Hillier
- The RCA Laboratories, Princeton, New Jersey
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43
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Chen RD, Zimmermann E, Xu SX, Liu GS, Smith AG. Characterization of an anther- and tapetum-specific gene and its highly specific promoter isolated from tomato. Plant Cell Rep 2006; 25:231-40. [PMID: 16491381 DOI: 10.1007/s00299-005-0056-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Revised: 08/15/2005] [Accepted: 08/25/2005] [Indexed: 05/06/2023]
Abstract
A full-length genomic clone of 2,233 bp long containing an anther- and tapetum-specific gene TomA108 was isolated and characterized from tomato. The gene was present in one copy per haploid genome. The isolated clone contained 5' and 3' untranslated regions of 810 and 170 nucleotides, respectively and a single intron with highly repetitive sequences. The cDNA encoded the protein with an apparent mass of 10.6 kDa and a pI (isoelectric point) of 5.3. It was cysteine-rich and had an N-terminal hydrophobic domain with characteristics of a secretory signal. Amino acid sequence comparisons demonstrated that the protein was closely related to a family of cereal seed storage proteins and protease inhibitors. The fusion of beta-glucuronidase to the TomA108 promoter demonstrated that the promoter was highly active from early-meiosis to free microspores production in tapetum of tobacco. This strong and highly specific promoter can be potentially used to generate male sterility for efficient production of plant hybrids.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Cysteine/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- Enzyme Inhibitors/chemistry
- Flowers/genetics
- Gene Expression Regulation, Plant
- Genes, Plant/genetics
- Genome, Plant/genetics
- Glucuronidase/metabolism
- Solanum lycopersicum/genetics
- Molecular Sequence Data
- Open Reading Frames/genetics
- Organ Specificity
- Plant Proteins/chemistry
- Plants, Genetically Modified
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Regulatory Sequences, Nucleic Acid/genetics
- Sequence Alignment
- Sequence Homology, Amino Acid
- Nicotiana/cytology
- Nicotiana/enzymology
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Affiliation(s)
- R D Chen
- Department of Biochemistry, University of Saskatc Hewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada. [corrected]
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44
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Abstract
Plant tetrapyrroles are the most abundant biomolecules on the earth and are cofactors of many apoproteins essential for plant function. The four end-products sirohaem, chlorophyll, haem and phytochromobilin are synthesized by a common branched pathway, which is tightly regulated to ensure a continuous supply to the cognate apoproteins. This may induce strong competition between different branches of the pathway for common substrates. In addition, the intermediates, which are phototoxic, must not be allowed to accumulate in the cell. The major control points are during the synthesis of the initial precursor, ALA (5-aminolaevulinic acid), and at the branch points for the insertion of metal ions into the porphyrin macrocycle. A recent study has also suggested that tetrapyrroles are involved in the communication between the chloroplast and the nucleus, strengthening the necessity for tight regulation. However, intermediates remain difficult to quantify mainly due to their low content and the different properties of the intermediates. In this paper, we summarize the regulation of this pathway and we detail why it is important to have an accurate method for the determination of tetrapyrroles in plants.
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Affiliation(s)
- M Moulin
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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45
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Abstract
Pantothenate (vitamin B5) is a water-soluble vitamin essential for the synthesis of CoA and ACP (acyl-carrier protein, cofactors in energy yielding reactions including carbohydrate metabolism and fatty acid synthesis. Pantothenate is synthesized de novo by plants and micro-organisms; however, animals obtain the vitamin through their diet. Utilizing our knowledge of the pathway in Escherichia coli, we have discovered and cloned genes encoding the first and last enzymes of the pathway from Arabidopsis, panB1, panB2 and panC. It is unlikely that there is a homologue of the E. coli panD gene, therefore plants must make β-alanine by an alternative route. Possible candidates for the remaining gene, panE, are being investigated. GFP (green fluorescent protein) fusions of the three identified plant enzymes have been generated and the subcellular localization of the enzymes studied. Work is now being performed to elucidate expression patterns of the transcripts and characterize the proteins encoded by these genes.
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Affiliation(s)
- K M Coxon
- Department of Plant Sciences, Downing Street, Cambridge CB2 3EA, UK
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46
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Abstract
We report a 36-year-old man with atopic eczema who developed lymphomatoid papulosis while taking ciclosporin. Latent membrane protein 1 and in situ hybridization for Epstein-Barr virus were negative. There are only two reports in the literature of patients taking ciclosporin to control atopic eczema who developed primary cutaneous CD30+ T-cell lymphoproliferative disorders. The development of T-cell lymphoproliferative disorders including lymphomas is well described in patients with solid organ transplants who are taking ciclosporin. Also, it has been noted in patients taking ciclosporin for rheumatological conditions or psoriasis.
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Affiliation(s)
- S Laube
- Department of Dermatology, University Hospital of North Staffordshire, Stoke-on-Trent ST4 7PA, UK.
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47
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Strange RC, El-Genidy N, Ramachandran S, Lovatt TJ, Fryer AA, Smith AG, Lear JT, Wong C, Jones PW, Ichii-Jones F, Hoban PR. Susceptibility to basal cell carcinoma: associations with PTCH polymorphisms. Ann Hum Genet 2005; 68:536-45. [PMID: 15598212 DOI: 10.1046/j.1529-8817.2004.00132.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Loss of function of the human patched gene (PTCH) is common and critical in basal cell carcinoma (BCC) development. Indirect evidence suggests polymorphism in PTCH mediates BCC risk. We studied 659 BCC cases and 300 controls to determine if exon 2(318), 3(429), 11(1552), 12(1665), 12(1686), 14(2199) and 23(3944) and intron 9(1336-135) and 15(2560+9)PTCH variants were sufficiently common for use in case-control studies, and if selected markers were associated with risk. Intron 15(2560+9) and exon 23(3944) variants were studied further. Their genotype frequencies were not significantly different in controls and cases, though frequency of the G(2560+9)-C(3944) haplotype was lower in all cases (odds ratio=0.44, p=0.009) and those stratified by BCC site and rate of development of further tumours. This association was not mediated by the extent of UVR exposure. We confirmed the robustness of these findings by showing these associations demonstrated similar odds ratios in two groups of randomly selected cases and controls, and using the false positive report probability (FPRP) approach described by Wacholder et al. (2004). The FPRP value (0.168) was in the noteworthy category. These data, showing for the first time that PTCH polymorphism mediates susceptibility, are compatible with reports showing that PTCH haploinsufficiency influences development of BCC precursor lesions.
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Affiliation(s)
- R C Strange
- Human Genomics Research Group, Institute for Science and Technology in Medicine, Keele University School of Medicine, University Hospital of North Staffordshire, Hartshill, Stoke-on-Trent ST4 7QB Staffordshire, England
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48
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Sherwin JRA, Freeman TC, Stephens RJ, Kimber S, Smith AG, Chambers I, Smith SK, Sharkey AM. Identification of Genes Regulated by Leukemia-Inhibitory Factor in the Mouse Uterus at the Time of Implantation. Mol Endocrinol 2004; 18:2185-95. [PMID: 15178747 DOI: 10.1210/me.2004-0110] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The endometrium is prepared for implantation by the actions of estradiol (E2) and progesterone (P4). In mice the luminal epithelium (LE) only becomes fully receptive to the attaching blastocyst in response to the nidatory estrogen surge on d 4 of pregnancy. The cytokine leukemia-inhibitory factor (LIF) is rapidly induced by nidatory estrogen and has been shown to be the primary mediator of its action. Implantation fails in the absence of LIF, and injection of LIF on d 4 of pregnancy can substitute for the nidatory estrogen. In this study, we sought to identify genes regulated by LIF in the uterine epithelium. We used oligonucleotide microarrays to compare the transcript profiles of paired uterine horns from LIF-deficient MF1 mice after intraluminal injection of LIF or PBS on d 4 of pseudopregnancy. IGF-binding protein 3 was identified as a gene up-regulated by LIF; this was confirmed by RT-PCR. In situ hybridization showed that the primary site of IGF-binding protein 3 expression is the luminal epithelium (LE), the known site of LIF action in the uterus. We identified two other genes: amphiregulin and immune response gene-1, the expression of which were also up-regulated by LIF. Immune response gene 1 has recently been shown to be essential for implantation. Expression of all three of these genes in the LE is known to be regulated by P4. The expression of osteoblast-specific factor 2 and leukocyte 12/15 lipoxygenase, which are also expressed in LE under the control of P4, were not increased by LIF. This suggests that one of the actions of LIF on LE may be to enhance the expression of a subset of P4-regulated genes.
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Affiliation(s)
- J R A Sherwin
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.
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49
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Affiliation(s)
- A G Smith
- Epidemiology and Genetics Unit, University of Leeds, Leeds LS2 9LN.
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50
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Pinto C, Smith AG, Larsen CE, Fernández-Viña M, Husain Z, Clavijo OP, Wang ZC, Nisperos B, Hansen JA, Alper CA, Yunis EJ. HLA-Cw*0409N is associated with HLA-A*2301 and HLA-B*4403-carrying haplotypes. Hum Immunol 2004; 65:181-7. [PMID: 14969773 DOI: 10.1016/j.humimm.2003.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2003] [Accepted: 11/21/2003] [Indexed: 10/26/2022]
Abstract
The associations of HLA-B*4402 and HLA-B*4403 with alleles of HLA-A and HLA-Cw were investigated in panels of HLA-B*4403 and HLA-B*4402 homozygous individuals and in selected individuals carrying HLA-Cw*04 and HLA-B*4403. Some of these individuals were genotyped and also carried (HLA-DRB1*0701, DQB1*02). Among the latter, we studied individuals carrying the conserved extended haplotype (CEH) [HLA-Cw*04, B*4403, FC31, DRB1*0701, DQB1*02]. Four different common (HLA-Cw*, B*44) haplotypes were identified that extended to the HLA-A locus: HLA-A*0201, Cw*0501, B*4402; HLA-A*2902, Cw*1601, B*4403; HLA-A*2301, Cw*0401, B*4403; and HLA-A*2301, Cw*0409N, B*4403. We identified eight unrelated examples of the allele HLA-Cw*0409N. HLA-A*2301 was associated with both HLA-Cw*0401 and HLA-Cw*0409N, suggesting that HLA-Cw*0409N may have arisen from a mutation in a CEH. We estimate that approximately 2 to 5 in 1000 Caucasian individuals carry the allele HLA-Cw*0409N, making it one of the most frequent null HLA alleles known to date. Our findings demonstrate the first example of three different HLA-Cw-determined subtypes of a common or CEH carrying a shared HLA-B allele, in this case HLA-B*4403.
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Affiliation(s)
- C Pinto
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
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