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      Creating longitudinal datasets and cleaning existing data identifiers in a cystic fibrosis registry using a novel Bayesian probabilistic approach from astronomy

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          Abstract

          Patient registry data are commonly collected as annual snapshots that need to be amalgamated to understand the longitudinal progress of each patient. However, patient identifiers can either change or may not be available for legal reasons when longitudinal data are collated from patients living in different countries. Here, we apply astronomical statistical matching techniques to link individual patient records that can be used where identifiers are absent or to validate uncertain identifiers. We adopt a Bayesian model framework used for probabilistically linking records in astronomy. We adapt this and validate it across blinded, annually collected data. This is a high-quality (Danish) sub-set of data held in the European Cystic Fibrosis Society Patient Registry (ECFSPR). Our initial experiments achieved a precision of 0.990 at a recall value of 0.987. However, detailed investigation of the discrepancies uncovered typing errors in 27 of the identifiers in the original Danish sub-set. After fixing these errors to create a new gold standard our algorithm correctly linked individual records across years achieving a precision of 0.997 at a recall value of 0.987 without recourse to identifiers. Our Bayesian framework provides the probability of whether a pair of records belong to the same patient. Unlike other record linkage approaches, our algorithm can also use physical models, such as body mass index curves, as prior information for record linkage. We have shown our framework can create longitudinal samples where none existed and validate pre-existing patient identifiers. We have demonstrated that in this specific case this automated approach is better than the existing identifiers.

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          Most cited references26

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          The Spitzer Space Telescope Mission

          The Spitzer Space Telescope, NASA's Great Observatory for infrared astronomy, was launched 2003 August 25 and is returning excellent scientific data from its Earth-trailing solar orbit. Spitzer combines the intrinsic sensitivity achievable with a cryogenic telescope in space with the great imaging and spectroscopic power of modern detector arrays to provide the user community with huge gains in capability for exploration of the cosmos in the infrared. The observatory systems are largely performing as expected and the projected cryogenic lifetime is in excess of 5 years. This paper summarizes the on-orbit scientific, technical and operational performance of Spitzer. Subsequent papers in this special issue describe the Spitzer instruments in detail and highlight many of the exciting scientific results obtained during the first six months of the Spitzer mission.
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            Herschel Space Observatory - An ESA facility for far-infrared and submillimetre astronomy

            Herschel was launched on 14 May 2009, and is now an operational ESA space observatory offering unprecedented observational capabilities in the far-infrared and submillimetre spectral range 55-671 {\mu}m. Herschel carries a 3.5 metre diameter passively cooled Cassegrain telescope, which is the largest of its kind and utilises a novel silicon carbide technology. The science payload comprises three instruments: two direct detection cameras/medium resolution spectrometers, PACS and SPIRE, and a very high-resolution heterodyne spectrometer, HIFI, whose focal plane units are housed inside a superfluid helium cryostat. Herschel is an observatory facility operated in partnership among ESA, the instrument consortia, and NASA. The mission lifetime is determined by the cryostat hold time. Nominally approximately 20,000 hours will be available for astronomy, 32% is guaranteed time and the remainder is open to the worldwide general astronomical community through a standard competitive proposal procedure.
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              The Herschel-SPIRE instrument and its in-flight performance

              The Spectral and Photometric Imaging Receiver (SPIRE), is the Herschel Space Observatory`s submillimetre camera and spectrometer. It contains a three-band imaging photometer operating at 250, 350 and 500 microns, and an imaging Fourier Transform Spectrometer (FTS) which covers simultaneously its whole operating range of 194-671 microns (447-1550 GHz). The SPIRE detectors are arrays of feedhorn-coupled bolometers cooled to 0.3 K. The photometer has a field of view of 4' x 8', observed simultaneously in the three spectral bands. Its main operating mode is scan-mapping, whereby the field of view is scanned across the sky to achieve full spatial sampling and to cover large areas if desired. The spectrometer has an approximately circular field of view with a diameter of 2.6'. The spectral resolution can be adjusted between 1.2 and 25 GHz by changing the stroke length of the FTS scan mirror. Its main operating mode involves a fixed telescope pointing with multiple scans of the FTS mirror to acquire spectral data. For extended source measurements, multiple position offsets are implemented by means of an internal beam steering mirror to achieve the desired spatial sampling and by rastering of the telescope pointing to map areas larger than the field of view. The SPIRE instrument consists of a cold focal plane unit located inside the Herschel cryostat and warm electronics units, located on the spacecraft Service Module, for instrument control and data handling. Science data are transmitted to Earth with no on-board data compression, and processed by automatic pipelines to produce calibrated science products. The in-flight performance of the instrument matches or exceeds predictions based on pre-launch testing and modelling: the photometer sensitivity is comparable to or slightly better than estimated pre-launch, and the spectrometer sensitivity is also better by a factor of 1.5-2.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: SoftwareRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                2018
                9 July 2018
                : 13
                : 7
                : e0199815
                Affiliations
                [1 ] Department of Physics and Astronomy, University of Sussex, Brighton, United Kingdom
                [2 ] Division of Medical Sciences, University of Dundee, Dundee, United Kingdom
                Cincinnati Children’s Hospital Medical Center, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0001-8393-8544
                Article
                PONE-D-17-17010
                10.1371/journal.pone.0199815
                6037350
                29985939
                2c79bba6-bbbc-4f42-af7d-723c38561bf3
                © 2018 Hurley et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 3 May 2017
                : 14 June 2018
                Page count
                Figures: 3, Tables: 1, Pages: 15
                Funding
                Funded by: Science and Technology Facilities Council (GB)
                Award ID: ST/L000652/1
                Award Recipient :
                PDH was funded by the Higher Education Innovation Funding ( http://www.hefce.ac.uk/ke/heif/). SO acknowledges support from the Science and Technology Facilities Council (grant number ST/L000652/1).
                Categories
                Research Article
                Physical Sciences
                Astronomical Sciences
                Celestial Objects
                Galaxies
                People and Places
                Population Groupings
                Ethnicities
                European People
                Danish People
                Physical Sciences
                Mathematics
                Applied Mathematics
                Algorithms
                Research and Analysis Methods
                Simulation and Modeling
                Algorithms
                Physical Sciences
                Astronomical Sciences
                Astronomy
                Astronomical Instruments
                Telescopes
                Engineering and Technology
                Equipment
                Optical Equipment
                Telescopes
                Medicine and Health Sciences
                Clinical Genetics
                Genetic Diseases
                Autosomal Recessive Diseases
                Cystic Fibrosis
                Biology and Life Sciences
                Developmental Biology
                Fibrosis
                Cystic Fibrosis
                Medicine and Health Sciences
                Pulmonology
                Cystic Fibrosis
                Biology and Life Sciences
                Physiology
                Physiological Parameters
                Body Weight
                Body Mass Index
                Medicine and Health Sciences
                Physiology
                Physiological Parameters
                Body Weight
                Body Mass Index
                Computer and Information Sciences
                Computer Applications
                Catalogs
                Research and Analysis Methods
                Database and Informatics Methods
                Health Informatics
                Disease Registries
                Custom metadata
                The data used in this research are from the European Cystic Fibrosis Society Patient Registry. The data can not be made publicly available as they contain potentially identifying or sensitive patient information and consent forms signed by patients only govern certain uses of the data and place additional restrictions. For those wanting access to the same data used in this study, it is available from the ECFSPR for researchers who meet the criteria for access to confidential data. To request access, contact the Executive Coordinator via email: ecfs-pr@ 123456uzleuven.be . For more details on guidelines, see https://www.ecfs.eu/projects/efcs-patient-registry/guidelines. Our software to both generate mock datasets based on the the ECFSPR and carry out record linkage can be found at https://github.com/pdh21/problink.

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