A semantic interoperability approach to support integration of gene expression and clinical data in breast cancer

[Abstract] Introduction. The introduction of omics data and advances in technologies involved in clinical treatment has led to a broad range of approaches to represent clinical information. Within this context, patient stratification across health institutions due to omic profiling presents a complex scenario to carry out multi-center clinical trials. Methods. This paper presents a standards-based approach to ensure semantic integration required to facilitate the analysis of clinico-genomic clinical trials. To ensure interoperability across different institutions, we have developed a Semantic Interoperability Layer (SIL) to facilitate homogeneous access to clinical and genetic information, based on different well-established biomedical standards and following International Health (IHE) recommendations. Results. The SIL has shown suitability for integrating biomedical knowledge and technologies to match the latest clinical advances in healthcare and the use of genomic information. This genomic data integration in the SIL has been tested with a diagnostic classifier tool that takes advantage of harmonized multi-center clinico-genomic data for training statistical predictive models. Conclusions. The SIL has been adopted in national and international research initiatives, such as the EURECA-EU research project and the CIMED collaborative Spanish project, where the proposed solution has been applied and evaluated by clinical experts focused on clinico-genomic studies.Instituto de Salud Carlos III, PI13/02020Instituto de Salud Carlos III, PI13/0028

The NIKA instrument: results and perspectives towards a permanent KID based camera for the Pico Veleta observatory

The New IRAM KIDs Array (NIKA) is a pathfinder instrument devoted to millimetric astronomy. In 2009 it was the first multiplexed KID camera on the sky; currently it is installed at the focal plane of the IRAM 30-meters telescope at Pico Veleta (Spain). We present preliminary data from the last observational run and the ongoing developments devoted to the next NIKA-2 kilopixels camera, to be commissioned in 2015. We also report on the latest laboratory measurements, and recent improvements in detector cosmetics and read-out electronics. Furthermore, we describe a new acquisition strategy allowing us to improve the photometric accuracy, and the related automatic tuning procedure.Comment: 24th International Symposium on Space Terahertz Technology, ISSTT 2013, April 8 to 10, 2013, Groningen, the Netherland

Latest NIKA results and the NIKA-2 project

NIKA (New IRAM KID Arrays) is a dual-band imaging instrument installed at the IRAM (Institut de RadioAstronomie Millimetrique) 30-meter telescope at Pico Veleta (Spain). Two distinct Kinetic Inductance Detectors (KID) focal planes allow the camera to simultaneously image a field-of-view of about 2 arc-min in the bands 125 to 175 GHz (150 GHz) and 200 to 280 GHz (240 GHz). The sensitivity and stability achieved during the last commissioning Run in June 2013 allows opening the instrument to general observers. We report here the latest results, in particular in terms of sensitivity, now comparable to the state-of-the-art Transition Edge Sensors (TES) bolometers, relative and absolute photometry. We describe briefly the next generation NIKA-2 instrument, selected by IRAM to occupy, from 2015, the continuum imager/polarimeter slot at the 30-m telescope.Comment: Proceedings of Low Temperature Detectors 15 (LTD-15), Pasadena, June 201

NIKA2: a mm camera for cluster cosmology

Galaxy clusters constitute a major cosmological probe. However, Planck 2015 results have shown a weak tension between CMB-derived and cluster-derived cosmological parameters. This tension might be due to poor knowledge of the cluster mass and observable relationship. As for now, arcmin resolution Sunyaev-Zeldovich (SZ) observations ({\it e.g.} SPT, ACT and Planck) only allowed detailed studies of the intra cluster medium for low redshift clusters ($z0.5$) high resolution and high sensitivity SZ observations are needed. With both a wide field of view (6.5 arcmin) and a high angular resolution (17.7 and 11.2 arcsec at 150 and 260 GHz), the NIKA2 camera installed at the IRAM 30-m telescope (Pico Veleta, Spain) is particularly well adapted for these observations. The NIKA2 SZ observation program will map a large sample of clusters (50) at redshifts between 0.5 and 0.9. As a pilot study for NIKA2, several clusters of galaxies have been observed with the pathfinder, NIKA, at the IRAM 30-m telescope to cover the various configurations and observation conditions expected for NIKA2.

ESMO Clinical Research Observatory (ECRO): improving the efficiency of clinical research through rationalisation of bureaucracy

During the last years, there has been a dramatic increase in the administrative and bureaucratic burden associated with cli

Mapping gene associations in human mitochondria using clinical disease phenotypes

Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no standardized catalog exists of the associated clinical phenotypes. Such a catalog would be useful to develop methods to analyze human phenotypic data, to determine genotype-phenotype relations among many genes and diseases, and to support the clinical diagnosis of mitochondrial disorders. Here we establish a clinical phenotype catalog of 174 mitochondrial disease genes and study associations of diseases and genes. Phenotypic features such as clinical signs and symptoms were manually annotated from full-text medical articles and classified based on the hierarchical MeSH ontology. This classification of phenotypic features of each gene allowed for the comparison of diseases between different genes. In turn, we were then able to measure the phenotypic associations of disease genes for which we calculated a quantitative value that is based on their shared phenotypic features. The results showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, proving the usefulness of phenotype similarity values in disease gene network analysis. We then constructed a functional network of mitochondrial genes and discovered a higher connectivity for non-disease than for disease genes, and a tendency of disease genes to interact with each other. Utilizing these differences, we propose 168 candidate genes that resemble the characteristic interaction patterns of mitochondrial disease genes. Through their network associations, the candidates are further prioritized for the study of specific disorders such as optic neuropathies and Parkinson disease. Most mitochondrial disease phenotypes involve several clinical categories including neurologic, metabolic, and gastrointestinal disorders, which might indicate the effects of gene defects within the mitochondrial system. The accompanying knowledgebase (http://www.mitophenome.org/) supports the study of clinical diseases and associated genes

A Novel, Single Algorithm Approach to Predict Acenocoumarol Dose Based on CYP2C9 and VKORC1 Allele Variants

The identification of CYP2C9 and VKORC1 genes has strongly stimulated the research on pharmacogenetics of coumarins in the last decade. We assessed the combined influence of CYP2C9 *2 and *3, and VKORC1 c.-1639G>A, 497C>G, and 1173C>T variants, on acenocoumarol dosage using a novel algorithm approach, in 193 outpatients who had achieved stable anticoagulation. We constructed an “acenocoumarol-dose genotype score” (AGS, maximum score = 100) based on the number of alleles associated with higher acenocoumarol dosage carried by each subject for each polymorphism. The mean AGS was higher in the high-dose (>28mg/week) compared with the low-dose (<7mg/week) group (mean(SEM) of 84.1±3.4 vs. 62.2±4.8, P = 0.008). An AGS>70 was associated with an increased odds ratio (OR) of requiring high acenocoumarol dosage (OR: 3.347; 95%CI: 1.112–10.075; P = 0.032). In summary, although more research is necessary in other patient cohorts, and this algorithm should be replicated in an independent sample, our data suggest that the AGS algorithm could be used to help discriminating patients requiring high acenocoumarol doses to achieve stable anti-coagulation

Differential branching fraction and angular analysis of the decay B0→K∗0μ+μ−

The angular distribution and differential branching fraction of the decay B 0→ K ∗0 μ + μ − are studied using a data sample, collected by the LHCb experiment in pp collisions at s√=7 TeV, corresponding to an integrated luminosity of 1.0 fb−1. Several angular observables are measured in bins of the dimuon invariant mass squared, q 2. A first measurement of the zero-crossing point of the forward-backward asymmetry of the dimuon system is also presented. The zero-crossing point is measured to be q20=4.9±0.9GeV2/c4 , where the uncertainty is the sum of statistical and systematic uncertainties. The results are consistent with the Standard Model predictions

Improving the Timing of Insulin Administration in Adult Acute Care Patients

Background: The correct timing of insulin administration in diabetic patients admitted to the hospital is important for the prevention of transient and serious glycemic deviations that could lead to negative patient outcomes. In November 2021, a South Florida Hospital identified an area of opportunity for quality improvement related to the process of subcutaneous insulin administration. In addition to bar code scanning, manual verification of the insulin dose by the primary nurse and another nurse was required prior to administration. Patients were experiencing delays in the timing of their insulin dose and nurses were reporting frustration with the process. Methods: The project followed the Plan-Do-Study-Act (PDSA) cycle for performance improvement. Results: The change in medication administration workflow resulted in achievement of administering insulin within 30 minutes of the scheduled time. Ninety percent of the nurses surveyed reported improvement in their workflow when giving subcutaneous insulin to their patients (n=112). Conclusion: Interdisciplinary collaboration, innovation in education of the nursing staff, monitoring adherence to the process, and sustaining engagement among stakeholders contributed to the success of this initiative, resulting in improved workflow in subcutaneous insulin administration. Keywords: Bar code medication administration, insulin, safety, quality improvemen