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 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

Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps

Background For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. Results We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. Conclusions Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html

Discovertebral (Andersson) lesions of the spine in ankylosing spondylitis revisited

A well-known complication in patients with ankylosing spondylitis (AS) is the development of localised vertebral or discovertebral lesions of the spine, which was first described by Andersson in 1937. Since then, many different terms are used in literature to refer to these localised lesions of the spine, including the eponym ‘Andersson lesion’ (AL). The use of different terms reflects an ongoing debate on the exact aetiology of the AL. In the current study, we performed an extensive review of the literature in order to align communication on aetiology, diagnosis and management between treating physicians. AL may result from inflammation or (stress-) fractures of the complete ankylosed spine. There is no evidence for an infectious origin. Regardless of the exact aetiology, a final common pathway exists, in which mechanical stresses prevent the lesion from fusion and provoke the development of pseudarthrosis. The diagnosis of AL is established on conventional radiography, but computed tomography and magnetic resonance imaging both provide additional information. There is no indication for a diagnostic biopsy. Surgical instrumentation and fusion is considered the principle management in symptomatic AL that fails to resolve from a conservative treatment. We advise to use the term Andersson lesion for these spinal lesions in patients with AS