Supporting interoperability of genetic data with LOINC

Electronic reporting of genetic testing results is increasing, but they are often represented in diverse formats and naming conventions. Logical Observation Identifiers Names and Codes (LOINC) is a vocabulary standard that provides universal identifiers for laboratory tests and clinical observations. In genetics, LOINC provides codes to improve interoperability in the midst of reporting style transition, including codes for cytogenetic or mutation analysis tests, specific chromosomal alteration or mutation testing, and fully structured discrete genetic test reporting. LOINC terms follow the recommendations and nomenclature of other standards such as the Human Genome Organization Gene Nomenclature Committee’s terminology for gene names. In addition to the narrative text they report now, we recommend that laboratories always report as discrete variables chromosome analysis results, genetic variation(s) found, and genetic variation(s) tested for. By adopting and implementing data standards like LOINC, information systems can help care providers and researchers unlock the potential of genetic information for delivering more personalized care

Implementing a mobile diagnostic unit to increase access to imaging and laboratory services in western Kenya.

Access to basic imaging and laboratory services remains a major challenge in rural, resource-limited settings in sub-Saharan Africa. In 2016, the Academic Model Providing Access to Healthcare programme in western Kenya implemented a mobile diagnostic unit (MDU) outfitted with a generator-powered X-ray machine and basic laboratory tests to address the lack of these services at rural, low-resource, public health facilities. The objective of this paper is to describe the design, implementation, preliminary impact and operational challenges of the MDU in western Kenya. Since implementing the MDU at seven rural health facilities serving a catchment of over half a million people, over 4500 chest radiographs have been performed, with one or more abnormalities detected in approximately 30% of radiographs. We observed favorable feedback and uptake of MDU services by healthcare workers and patients. However, various operational challenges in the design and construction of the MDU and the transmission and reporting of radiographs in remote areas were encountered. Our experience supports the feasibility of deploying an MDU to increase access to basic radiology and laboratory services in rural, resource-limited settings

Fundamental parameters, integrated RGB mass loss and dust production in the Galactic globular cluster 47 Tucanae

Fundamental parameters and time-evolution of mass loss are investigated for post-main-sequence stars in the Galactic globular cluster 47 Tucanae (NGC 104). This is accomplished by fitting spectral energy distributions (SEDs) to existing optical and infrared photometry and spectroscopy, to produce a true Hertzsprung--Russell diagram. We confirm the cluster's distance as 4611 (+213, -200) pc and age as 12 +/- 1 Gyr. Horizontal branch models appear to confirm that no more RGB mass loss occurs in 47 Tuc than in the more-metal-poor omega Centauri, though difficulties arise due to inconsistencies between the models. Using our SEDs, we identify those stars which exhibit infrared excess, finding excess only among the brightest giants: dusty mass loss begins at a luminosity of ~ 1000 Lsun, becoming ubiquitous above 2000 Lsun. Recent claims of dust production around lower-luminosity giants cannot be reproduced, despite using the same archival Spitzer imagery.Comment: 22 pages, 17 figures, accepted ApJ

Preparing a collection of radiology examinations for distribution and retrieval

OBJECTIVE: Clinical documents made available for secondary use play an increasingly important role in discovery of clinical knowledge, development of research methods, and education. An important step in facilitating secondary use of clinical document collections is easy access to descriptions and samples that represent the content of the collections. This paper presents an approach to developing a collection of radiology examinations, including both the images and radiologist narrative reports, and making them publicly available in a searchable database. MATERIALS AND METHODS: The authors collected 3996 radiology reports from the Indiana Network for Patient Care and 8121 associated images from the hospitals' picture archiving systems. The images and reports were de-identified automatically and then the automatic de-identification was manually verified. The authors coded the key findings of the reports and empirically assessed the benefits of manual coding on retrieval. RESULTS: The automatic de-identification of the narrative was aggressive and achieved 100% precision at the cost of rendering a few findings uninterpretable. Automatic de-identification of images was not quite as perfect. Images for two of 3996 patients (0.05%) showed protected health information. Manual encoding of findings improved retrieval precision. CONCLUSION: Stringent de-identification methods can remove all identifiers from text radiology reports. DICOM de-identification of images does not remove all identifying information and needs special attention to images scanned from film. Adding manual coding to the radiologist narrative reports significantly improved relevancy of the retrieved clinical documents. The de-identified Indiana chest X-ray collection is available for searching and downloading from the National Library of Medicine (http://openi.nlm.nih.gov/)

Discovery of long-period variable stars in the very-metal-poor globular cluster M15

We present a search for long-period variable (LPV) stars among giant branch stars in M15 which, at [Fe/H] ~ -2.3, is one of the most metal-poor Galactic globular clusters. We use multi-colour optical photometry from the 0.6-m Keele Thornton and 2-m Liverpool Telescopes. Variability of delta-V ~ 0.15 mag is detected in K757 and K825 over unusually-long timescales of nearly a year, making them the most metal-poor LPVs found in a Galactic globular cluster. K825 is placed on the long secondary period sequence, identified for metal-rich LPVs, though no primary period is detectable. We discuss this variability in the context of dust production and stellar evolution at low metallicity, using additional spectra from the 6.5-m Magellan (Las Campanas) telescope. A lack of dust production, despite the presence of gaseous mass loss raises questions about the production of dust and the intra-cluster medium of this cluster.Comment: 13 pages, 9 figures, accepted by MNRA

RR Lyrae variables in M32 and the disk of M31

We observed two fields near M32 with the Advanced Camera for Surveys/High Resolution Channel (ACS/HRC) on board the Hubble Space Telescope (HST). The main field, F1, is 1.8 arcmin from the center of M32; the second field, F2, constrains the M31 background, and is 5.4 arcmin distant. Each field was observed for 16-orbits in each of the F435W (narrow B) and F555W (narrow V) filters. The duration of the observations allowed RR Lyrae stars and other short-period variables to be detected. A population of RR Lyrae stars determined to belong to M32 would prove the existence of an ancient population in that galaxy, a subject of some debate. We detected 17 RR Lyrae variables in F1 and 14 in F2. A 1-sigma upper limit of 6 RR Lyrae variables belonging to M32 is inferred from these two fields alone. Use of our two ACS/WFC parallel fields provides better constraints on the M31 background, however, and implies that $7_{-3}^{+4}$ (68 % confidence interval) RR Lyrae variables in F1 belong to M32. We have therefore found evidence for an ancient population in M32. It seems to be nearly indistinguishable from the ancient population of M31. The RR Lyrae stars in the F1 and F2 fields have indistinguishable mean V-band magnitudes, mean periods, distributions in the Bailey diagram and ratios of RRc to RR(tot) types. However, the color distributions in the two fields are different, with a population of red RRab variables in F1 not seen in F2. We suggest that these might be identified with the detected M32 RR Lyrae population, but the small number of stars rules out a definitive claim.Comment: 19 pages, 18 figures, accepted Ap

Risk of Adverse Gastrointestinal Events from Inhaled Corticosteroids

Previous studies suggest a risk of gastrointestinal events in patients prescribed oral corticosteroids, but gastrointestinal events have not commonly been documented in patients prescribed inhaled corticosteroids. We explored whether patients prescribed inhaled corticosteroids are at risk of adverse gastrointestinal effects