Stratosphere-troposphere exchange from the Lagrangian perspective: a case study and method sensitivities

International audienceAn important part of extra-tropical stratosphere-to-troposphere transport occurs in association with baroclinic wave breaking and cut-off decay at the tropopause. In the last decade many studies have attempted to estimate stratosphere-troposphere exchange (STE) in such synoptic events with various methods, and more recently efforts have been made to inter-compare these methods. These inter-comparisons show large variations between estimates from different methods. This large uncertainty points to a need to thoroughly evaluate such methods, assess the realism of the resulting STE estimates and determine the sensitivities to intrinsic parameters of the methods. The present study focuses on a trajectory-based Lagrangian method which has been applied in the past to climatological studies. This method is applied here to the quantification of STE in the context of a typical baroclinic wave breaking event. The analysis sheds light on (i) the complex three-dimensional temporal and spatial structures that are associated with the rapid inflow of stratospheric air into the troposphere, (ii) the variation of STE mass flux with the choice of the dynamical tropopause definition within 1.5 to 5 PVU, (iii) the sensitivity of the results to resolution, and in particular the minimum spatial resolution of 1°×1° required to reasonably capture STE fluxes in this wave breaking event, (iv) the effective removal of spurious exchange events using a threshold residence time larger than 8 h

Stratosphere-troposphere exchange from the Lagrangian perspective: a case study and method sensitivities

International audienceAn important part of extra-tropical stratosphere-to-troposphere transport occurs in association with baroclinic wave breaking and cut-off decay at the tropopause. In the last decade many studies have attempted to estimate stratosphere-troposphere exchange (STE) in such synoptic events with various methods, and more recently efforts have been put on inter-comparing these methods. However, large uncertainties remain on the sensitivities to methods intrinsic parameters, and on the best measure for STE with regard to end effects on chemistry. The goal of the present study is to address these two fundamental issues in the context of the application of a trajectory-based Lagrangian method, which has been applied in the past to climatological studies and has also been involved in inter-comparison studies, to a typical baroclinic wave breaking event. The analysis sheds light on (i) the fine mesoscale temporal and spatial structures that are associated with episodic, rapid inflows of stratospheric air into the troposphere; (ii) the spatial resolution of 1°×1° required to reasonably capture STE fluxes in such a wave breaking event; (iii) the effective removal of spurious exchange events using a threshold residence time; (iv) the relevance of residence time distributions for capturing the effective chemical forcing of STE; (v) the large differences in the temporal evolution and geographical distribution of STE fluxes across the 2 and the 4 potential vorticity unit iso-surface definitions of the tropopause

A Prototype System for Measuring Microwave Frequency Reflections from the Breast

Microwave imaging of the breast is of interest for monitoring breast health, and approaches to active microwave imaging include tomography and radar-based methods. While the literature contains a growing body of work related to microwave breast imaging, there are only a few prototype systems that have been used to collect data from humans. In this paper, a prototype system for monostatic radar-based imaging that has been used in an initial study measuring reflections from volunteers is discussed. The performance of the system is explored by examining the mechanical positioning of sensor, as well as microwave measurement sensitivity. To gain insight into the measurement of reflected signals, simulations and measurements of a simple phantom are compared and discussed in relation to system sensitivity. Finally, a successful scan of a volunteer is described

Edge-weighting of gene expression graphs

In recent years, considerable research efforts have been directed to micro-array technologies and their role in providing simultaneous information on expression profiles for thousands of genes. These data, when subjected to clustering and classification procedures, can assist in identifying patterns and providing insight on biological processes. To understand the properties of complex gene expression datasets, graphical representations can be used. Intuitively, the data can be represented in terms of a bipartite graph, with weighted edges corresponding to gene-sample node couples in the dataset. Biologically meaningful subgraphs can be sought, but performance can be influenced both by the search algorithm, and, by the graph-weighting scheme and both merit rigorous investigation. In this paper, we focus on edge-weighting schemes for bipartite graphical representation of gene expression. Two novel methods are presented: the first is based on empirical evidence; the second on a geometric distribution. The schemes are compared for several real datasets, assessing efficiency of performance based on four essential properties: robustness to noise and missing values, discrimination, parameter influence on scheme efficiency and reusability. Recommendations and limitations are briefly discussed

Determination of eddy-diffusivity in the lowermost stratosphere

We present a 2D-advection-diffusion model that simulates the main transport pathways influencing tracer distributions in the lowermost stratosphere (LMS). The model describes slow diabatic descent of aged stratospheric air, vertical (cross-isentropic) and horizontal (along isentropes) diffusion within the LMS and across the tropopause using equivalent latitude and potential temperature coordinates. Eddy diffusion coefficients parameterize the integral effect of dynamical processes leading to small scale turbulence and mixing. They were specified by matching model simulations to observed CO distributions. Interestingly, the model suggests mixing across isentropes to be more important than horizontal mixing across surfaces of constant equivalent latitude, shining new light on the interplay between various transport mechanisms in the LMS. The model achieves a good description of the small scale tracer features at the tropopause with squared correlation coefficients R2 = 0.72…0.94

Comparison of In-Person and Online Recordings in the Clinical Teleassessment of Speech Production: A Pilot Study.

In certain circumstances, speech and language therapy is proposed in telepractice as a practical alternative to in-person services. However, little is known about the minimum quality requirements of recordings in the teleassessment of motor speech disorders (MSD) utilizing validated tools. The aim here is to examine the comparability of offline analyses based on speech samples acquired from three sources: (1) in-person recordings with high quality material, serving as the baseline/gold standard; (2) in-person recordings with standard equipment; (3) online recordings from videoconferencing. Speech samples were recorded simultaneously from these three sources in fifteen neurotypical speakers performing a screening battery of MSD and analyzed by three speech and language therapists. Intersource and interrater agreements were estimated with intraclass correlation coefficients on seventeen perceptual and acoustic parameters. While the interrater agreement was excellent for most speech parameters, especially on high quality in-person recordings, it decreased in online recordings. The intersource agreement was excellent for speech rate and mean fundamental frequency measures when comparing high quality in-person recordings to the other conditions. The intersource agreement was poor for voice parameters, but also for perceptual measures of intelligibility and articulation. Clinicians who plan to teleassess MSD should adapt their recording setting to the parameters they want to reliably interpret

Between data providers and concerned citizens: Exploring participation in precision public health in Switzerland.

This empirical article explores the dynamics of exchange and reciprocity between cohorters, that is, study organizers, and cohortees, that is, study participants. Drawing on literature on bioeconomy and valuation, we analyze cohortees' expectations in return for the "clinical labor" they perform in the pilot phase of a Swiss precision public health study. Based on an ethnography of this cohort and data from seven focus groups with cohortees (n = 37), we identified four positions: (1) the good citizen participant, (2) the critical participant, (3) the concerned participant, and (4) the self-oriented participant. These reveal that cohortees' participation, still framed in altruistic terms, nevertheless engages expectations about reciprocal obligations of the state and science in terms of public health, confirming the deep entanglement of gift-based, financial, and moral economies of participation. The different values emerging from these expectations-robust scientific evidence about environmental exposure and a socially oriented public health-provide rich indications about stake making which might matter for the future of precision public health

On the lack of robustness of hydrologic models regarding water balance simulation: a diagnostic approach applied to three models of increasing complexity on 20 mountainous catchments

This paper investigates the robustness of rainfall–runoff models when their parameters are transferred in time. More specifically, we propose an approach to diagnose their ability to simulate water balance on periods with different hydroclimatic characteristics. The testing procedure consists in a series of parameter calibrations over 10 yr periods and the systematic analysis of mean flow volume errors on long records. This procedure was applied to three conceptual models of increasing structural complexity over 20 mountainous catchments in southern France. The results showed that robustness problems are common. Errors on 10 yr mean flow volume were significant for all calibration periods and model structures. Various graphical and numerical tools were used to investigate these errors and unexpectedly strong similarities were found in the temporal evolutions of these volume errors. We indeed showed that relative changes in simulated mean flow between 10 yr periods can remain similar, regardless of the calibration period or the conceptual model used. Surprisingly, using longer records for parameters optimisation or using a semi-distributed 19-parameter daily model instead of a simple 1-parameter annual formula did not provide significant improvements regarding these simulation errors on flow volumes. While the actual causes for these robustness problems can be manifold and are difficult to identify in each case, this work highlights that the transferability of water balance adjustments made during calibration can be poor, with potentially huge impacts in the case of studies in non-stationary conditions

A simple framework for modelling the photochemical response to solar spectral irradiance variability in the stratosphere

The stratosphere is thought to play a central role in the atmospheric response to solar irradiance variability. Recent observations suggest that the spectral solar irradiance (SSI) variability involves significant time-dependent spectral variations, with variable degrees of correlation between wavelengths, and new reconstructions are being developed. In this paper, we propose a simplified modelling framework to characterise the effect of short term SSI variability on stratospheric ozone. We focus on the pure photochemical effect, for it is the best constrained one. The photochemical effect is characterised using an ensemble simulation approach with multiple linear regression analysis. A photochemical column model is used with interactive photolysis for this purpose. Regression models and their coefficients provide a characterisation of the stratospheric ozone response to SSI variability and will allow future inter-comparisons between different SSI reconstructions. As a first step in this study, and to allow comparison with past studies, we take the representation of SSI variability from the Lean (1997) solar minimum and maximum spectra. First, solar maximum-minimum response is analysed for all chemical families and partitioning ratios, and is compared with past studies. The ozone response peaks at 0.18 ppmv (approximately 3%) at 37 km altitude. Second, ensemble simulations are regressed following two linear models. In the simplest case, an adjusted coefficient of determination <span style="border-top: 1px solid #000; color: #000;">R</span><sup>2</sup> larger than 0.97 is found throughout the stratosphere using two predictors, namely the previous day's ozone perturbation and the current day's solar irradiance perturbation. A better accuracy (<span style="border-top: 1px solid #000; color: #000;">R</span><sup>2</sup> larger than 0.9992) is achieved with an additional predictor, the previous day's solar irradiance perturbation. The regression models also provide simple parameterisations of the ozone perturbation due to SSI variability. Their skills as proxy models are evaluated independently against the photochemistry column model. The bias and RMS error of the best regression model are found smaller than 1% and 15% of the ozone response, respectively. Sensitivities to initial conditions and to magnitude of the SSI variability are also discussed

Arena3D: visualizing time-driven phenotypic differences in biological systems

<p>Abstract</p> <p>Background</p> <p>Elucidating the genotype-phenotype connection is one of the big challenges of modern molecular biology. To fully understand this connection, it is necessary to consider the underlying networks and the time factor. In this context of data deluge and heterogeneous information, visualization plays an essential role in interpreting complex and dynamic topologies. Thus, software that is able to bring the network, phenotypic and temporal information together is needed. Arena3D has been previously introduced as a tool that facilitates link discovery between processes. It uses a layered display to separate different levels of information while emphasizing the connections between them. We present novel developments of the tool for the visualization and analysis of dynamic genotype-phenotype landscapes.</p> <p>Results</p> <p>Version 2.0 introduces novel features that allow handling time course data in a phenotypic context. Gene expression levels or other measures can be loaded and visualized at different time points and phenotypic comparison is facilitated through clustering and correlation display or highlighting of impacting changes through time. Similarity scoring allows the identification of global patterns in dynamic heterogeneous data. In this paper we demonstrate the utility of the tool on two distinct biological problems of different scales. First, we analyze a medium scale dataset that looks at perturbation effects of the pluripotency regulator Nanog in murine embryonic stem cells. Dynamic cluster analysis suggests alternative indirect links between Nanog and other proteins in the core stem cell network. Moreover, recurrent correlations from the epigenetic to the translational level are identified. Second, we investigate a large scale dataset consisting of genome-wide knockdown screens for human genes essential in the mitotic process. Here, a potential new role for the gene <it>lsm14a </it>in cytokinesis is suggested. We also show how phenotypic patterning allows for extensive comparison and identification of high impact knockdown targets.</p> <p>Conclusions</p> <p>We present a new visualization approach for perturbation screens with multiple phenotypic outcomes. The novel functionality implemented in Arena3D enables effective understanding and comparison of temporal patterns within morphological layers, to help with the system-wide analysis of dynamic processes. Arena3D is available free of charge for academics as a downloadable standalone application from: <url>http://arena3d.org/</url>.</p