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McCluskey AR, Caruana AJ, Kinane CJ, Armstrong AJ, Arnold T, Cooper JFK, Cortie DL, Hughes AV, Moulin JF, Nelson ARJ, Potrzebowski W, Starostin V. Advice on describing Bayesian analysis of neutron and X-ray reflectometry. J Appl Crystallogr 2023; 56:12-17. [PMID: 36777146 PMCID: PMC9901928 DOI: 10.1107/s1600576722011426] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/28/2022] [Indexed: 01/18/2023] Open
Abstract
As a result of the availability of modern software and hardware, Bayesian analysis is becoming more popular in neutron and X-ray reflectometry analysis. The understandability and replicability of these analyses may be harmed by inconsistencies in how the probability distributions central to Bayesian methods are represented in the literature. Herein advice is provided on how to report the results of Bayesian analysis as applied to neutron and X-ray reflectometry. This includes the clear reporting of initial starting conditions, the prior probabilities, the results of any analysis and the posterior probabilities that are the Bayesian equivalent of the error bar, to enable replicability and improve understanding. It is believed that this advice, grounded in the authors' experience working in the field, will enable greater analytical reproducibility in the work of the reflectometry community, and improve the quality and usability of results.
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Affiliation(s)
- Andrew R. McCluskey
- European Spallation Source ERIC, PO Box 176, Lund, SE-22100, Sweden,Correspondence e-mail: ,
| | - Andrew J. Caruana
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0QX, United Kingdom,Correspondence e-mail: ,
| | - Christy J. Kinane
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Alexander J. Armstrong
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Thomas Arnold
- European Spallation Source ERIC, PO Box 176, Lund, SE-22100, Sweden
| | - Joshaniel F. K. Cooper
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - David L. Cortie
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales, Australia
| | - Arwel V. Hughes
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Jean-Francois Moulin
- German Engineering Material Science at Heinz Maier-Leibnitz Zentrum, Helmholtz-Zentrum Hereon, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Andrew R. J. Nelson
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales, Australia
| | | | - Vladimir Starostin
- Institute of Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
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Rodrigues AM, Miguel C, Chaves I, António C. Mass spectrometry-based forest tree metabolomics. Mass Spectrom Rev 2021; 40:126-157. [PMID: 31498921 DOI: 10.1002/mas.21603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/24/2023]
Abstract
Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.
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Affiliation(s)
- Ana Margarida Rodrigues
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
| | - Célia Miguel
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Inês Chaves
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
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