19 research outputs found

    Privacy-Preserving Exploration of Genetic Cohorts with i2b2 At Lausanne University Hospital

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    Re-use of patients’ health records can provide tremendous benefits for clinical research. One of the first essential steps for many research studies, such as clinical trials or population health studies, is to effectively identify, from electronic health record systems, groups of well-characterized patients who meet specific inclusion and exclusion criteria. This procedure is called cohort exploration. Yet, when researchers need to compile specific cohorts of patients, privacy issues represent one of the major obstacles to accessing patients’ data, especially when sensitive data, such as genomic data, are involved. Because of this, cohort exploration could become extremely difficult and time-consuming. In this joint paper between the Ecole Polytechnique F ´ ed´ erale de Lausanne (EPFL) and the Lausanne University Hospital ´ (CHUV), we address the challenge of designing and deploying an efficient privacy-preserving explorer for genetic cohorts. Our solution is built on top of i2b2 (informatics for integrating biology and the bedside), the state-of-the-art open-source framework for cohort exploration, and exploits on cutting-edge privacy-enhancing technologies (PETs) such as homomorphic encryption and differential privacy. To the best of our knowledge, our proposed solution is the first of its kind to be successfully deployed in a real operational environment within a hospital. Especially, it has been tested as one of the services of the clinical research data-warehouse of CHUV. Solutions involving homomorphic encryption are often believed to be costly and still immature for use in operational environments. In this paper, we prove the opposite by describing how actually, for specific use cases, this kind of PETs can be very efficient enablers

    Protecting Privacy and Security of Genomic Data in i2b2 with Homomorphic Encryption and Differential Privacy

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    Re-use of patients’ health records can provide tremendous benefits for clinical research. Yet, when researchers need to access sensitive/identifying data, such as genomic data, in order to compile cohorts of well-characterized patients for specific studies, privacy and security concerns represent major obstacles that make such a procedure extremely difficult if not impossible. In this paper, we address the challenge of designing and deploying in a real operational setting an efficient privacy-preserving explorer for genetic cohorts. Our solution is built on top of the i2b2 (Informatics for Integrating Biology and the Bedside) framework and leverages cutting-edge privacy-enhancing technologies such as homomorphic encryption and differential privacy. Solutions involving homomorphic encryption are often believed to be costly and immature for use in operational environments. Here, we show that, for specific applications, homomorphic encryption is actually a very efficient enabler. Indeed, our solution outperforms prior work by enabling a researcher to securely compute simple statistics on more than 3,000 encrypted genetic variants simultaneously for a cohort of 5,000 individuals in less than 5 seconds with commodity hardware. To the best of our knowledge, our privacy-preserving solution is the first to also be successfully deployed and tested in a operation setting (Lausanne University Hospital)

    Intradecadal variations in length of day: Coherence with models of the Earth's core dynamics

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    We confirm the presence of interannual oscillations of period about 5.9 and 8.5 years in the Earth’s length of day (LOD), better visible after subtracting the atmospheric contribution. Continental water mass redistribution and oceanic angular momentum contribute to a lesser extent, and are furthermore mostly compensated by sea level variations. We show, using a continuous wavelet transform analysis of synthetic oscillators embeddedinto a random correlated noise, the limits of isolating damped signals presenting nearby periods in time series of limited duration. In particular, we emphasize the possibility that a previously documented 7.3-year oscillation could be an artefact associated with the restricted available time span covered by LOD data. Finally, we perform a wavelet coherence analysis between geodetically observed LOD changes and their prediction from geomagnetically inferred core flow models. It confirms an origin from the fluid outer core for the two signals around 5.9 and 8.5 years. A convincing coherence is also found around 3.5 and 5 years, which may reveal signatures of higher harmonics of torsional modes or of quasi-geostrophic magneto-Coriolis modes

    Estimation of the Free Core Nutation parameters from SG data : sensitivity study and comparative analysis using linearized least-squares and Bayesian methods

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    The Free Core Nutation (FCN) is investigated with the help of its resonance effect on the tidal amplitudes in Superconducting Gravimeter (SG) records of the GGP network. The FCN resonance parameters are combined in a resonance equation involving the Earth's interior parameters. The sensitivity of the FCN parameters to the diurnal tidal waves demonstrates that the quality factor of the FCN is strongly dependent on the accuracy of the imaginary part estimates of the gravimetric factors close to the resonance. The weak amplitude of Psi(1) tidal wave on the Earth, which is the closest in frequency to the FCN, in addition to errors in ocean loading correction, explains the poor determination of the quality factor Q from surface gravimetric data. The inversion of tidal gravimetric factors leads to estimates of the period, Q and resonance strength of the FCN. We show that. by inverting log(Q) instead of Q the results using the least-squares method optimized using the Levenberg-Marquardt algorithm are in agreement with the Bayesian probabilistic results and agree with the results obtained from VLBI nutation data. Finally, a combined inversion of 7 GGP European SG data is performed giving T = 428 +/- 3 days and 7762 < Q < 31,989 (90% C.I.). An experimental estimate of the internal pressure Love number is also proposed

    Lifespans of passenger cars in Europe: empirical modelling of fleet turnover dynamics

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    Cars have a high share of global transport-related CO2 emissions. To model the market diffusion of new energy carriers and powertrains like electric vehicles, fleet turnover models are commonly used. A decisive influence factor for the substitution dynamics of such transformations is the survival rate of the national car fleet of a country. It represents the likelihood of a car reaching a certain lifespan. Due to a lack of data, current methods to estimate such survival probabilities neglect the imports and exports of used cars. Existing studies are limited to countries with a predominant market of new cars, compared to low numbers of imported and exported used cars. In this study, we resolve this marked simplification and propose a new method to estimate survival probabilities for countries with a high number of imported and exported used cars. Empirical data on the car stock, on inflows of new and used cars, and on outflows of exported and scrapped cars are gathered from 71 national statistics offices. Survival rates of the car fleets of 31 European countries are derived, for which we find a pronounced regional variability. Average lifespans of cars vary from 8.0 to 35.1 years, with a mean of 18.1 years in Western and 28.4 years in Eastern European countries, revealing the high impact of cross-border flows of cars. The study also shows that survival rate estimates can be improved significantly even in the absence of reliable data if a combination of a Weibull and a Gaussian distribution is used. It is likely that the predictive power of existing models (regarding the future environmental impact of car fleets) could be improved significantly if these findings were considered accordingly. The findings of this study can directly be included in fleet turnover and policy assessment models. They also enable the analysis of economic and environmental spillover effects from the imports and exports of used cars between countries.ISSN:1867-0717ISSN:1866-888

    Non-linear oceanic tides observed by superconducting gravimeters in Europe

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    International audienceWe have analyzed data from nine superconducting gravimeters in Western Europe and detected the contribution of non-linear ocean tides in the quarter-diurnal and sixth-diurnal frequency bands. Despite their small amplitudes, a few nanogals (10-11 m s-2), we have compared the tidal loading observations with the loading effects inferred from several non-linear ocean tide models over the North-West European continental shelf and found that they are coherent with the recent models. We also confirmed our results with tide gauge data and Topex/Poseidon altimetric data. We have also shown that the differences between the ocean tidal models are significantly larger than the accuracy of recent superconducting gravimeters. Therefore, we suggest that gravity measurements can be used as an independent validation tool for non-linear ocean tidal models, complementary to tide gauge and bottom pressure records

    III. AUGMENTATION OF MACROPHAGE COMPLEMENT RECEPTOR FUNCTION IN VITRO C3b Receptors That Promote Phagocytosis Migrate within the Plane of the Macrophage Plasma Membrane*

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    The process of immunologically mediated phagocytosis can be divided into three steps: (a) attachment of a ligand-coated particle to specific receptors on the phagocytic cell&apos;s plasma membrane; (b) generation and transmission of a phagocytic signal by receptor-ligand engagement; and (c) the ingestion process per se (1). Depending upon the receptor engaged and the physiologic state of the phagocytic cell, the process may or may not proceed to completion. For example, engagement of macrophage Fc receptors by particle-bound IgG virtually always leads to particle ingestion (2-5). In contrast, engagement of macrophage complement receptors by particle-bound C3b, which always mediates efficient particle binding (2-8), promotes particle ingestion only by macrophages that have been physiologically altered (5-8). Recent studies by Michl et al. (9, 10) suggest that for a receptor to promote particle ingestion, it must be able to move within the plane of the cell&apos;s plasma membrane. The Fc receptors of both resident and thioglycollate-elicited mouse peritoneal macrophages mediate both attachment and ingestion of IgG-coated particles (2, 3, 6). The C3b receptor of resident macrophages mediates only attachment of C3b-coate
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