Diagnostics of the tropical tropopause layer from in-situ observations and CCM data

A suite of diagnostics is applied to in-situ aircraft measurements and one Chemistry-Climate Model (CCM) data to characterize the vertical structure of the Tropical Tropopause Layer (TTL). The diagnostics are based on vertical tracer profiles and relative vertical tracer gradients, using tropopause-referenced coordinates, and tracer-tracer relationships in the tropical Upper Troposphere/Lower Stratosphere (UT/LS). Observations were obtained during four tropical campaigns performed from 1999 to 2006 with the research aircraft Geophysica and have been compared to the output of the ECHAM5/MESSy CCM. The model vertical resolution in the TTL (~500 m) allows for appropriate comparison with high-resolution aircraft observations and the diagnostics used highlight common TTL features between the model and the observational data. The analysis of the vertical profiles of water vapour, ozone, and nitrous oxide, in both the observations and the model, shows that concentration mixing ratios exhibit a strong gradient change across the tropical tropopause, due to the role of this latter as a transport barrier and that transition between the tropospheric and stratospheric regimes occurs within a finite layer. The use of relative vertical ozone and carbon monoxide gradients, in addition to the vertical profiles, helps to highlight the region where this transition occurs and allows to give an estimate of its thickness. The analysis of the CO-O3 and H2O-O3 scatter plots and of the Probability Distribution Function (PDF) of the H2O-O3 pair completes this picture as it allows to better distinguish tropospheric and stratospheric regimes that can be identified by their different chemical composition. The joint analysis and comparison of observed and modelled data allows to state that the model can represent the background TTL structure and its seasonal variability rather accurately. The model estimate of the thickness of the interface region between tropospheric and stratospheric regimes agrees well with average values inferred from observations. On the other hand, the measurements can be influenced by regional scale variability, local transport processes as well as deep convection, that can not be captured by the model

The quasi-biennial oscillation in a warmer climate: sensitivity to different gravity wave parameterizations

In order to simulate the quasi-biennial oscillation (QBO) with a realistic period and amplitude, general circulation models commonly include parameterizations of small scale gravity waves (GW). In this work, we explore how different GW parameterization setups determine the response of QBO properties to a warmer climate. Atmosphere-only experiments in both present day and warmer climate serve as testbed to analyze the effect of four different GW parameterization setups, active in the tropics. Having tuned the GW parameterizations to produce a realistic QBO in present day climate, we analyze changes of QBO properties in the warmer climate. The QBO period decreases in two parameterization setups by similar to 30 %, while the QBO period remains unchanged in the remaining two parameterization setups. In all parameterization setups, the QBO amplitude in the warmer climate weakens below 10 hPa but shows different behaviour above 10 hPa. We show that changes in QBO amplitude and changes in QBO period are inconsistent among experiments. In the chosen experimental design, the inconsistent future change in QBO properties among the suite of experiments depends solely on the choice of the GW parameterization setup

Diagnostics of the tropical tropopause layer from in-situ observations and CCM data

A suite of diagnostics is applied to in-situ aircraft measurements and one Chemistry-Climate Model (CCM) data to characterize the vertical structure of the Tropical Tropopause Layer (TTL). The diagnostics are based on the vertical tracers profiles, relative vertical tracers gradients, and tracer-tracer relationships in the tropical Upper Troposphere/Lower Stratosphere (UT/LS), using tropopause coordinates. Observations come from the four tropical campaigns performed from 1998 to 2006 with the research aircraft Geophysica and have been directly compared to the output of the ECHAM5/MESSy CCM. The model vertical resolution in the TTL allows for appropriate comparison with high-resolution aircraft observations and the diagnostics used highlight common TTL features between the model and the observational data. The analysis of the vertical profiles of water vapour, ozone, and nitrous oxide, in both the observations and the model, shows that concentration mixing ratios exhibit a strong gradient change across the tropical tropopause, due to the role of this latter as a transport barrier and that transition between the tropospheric and stratospheric regimes occurs within a finite layer. The use of relative vertical ozone gradients, in addition to the vertical profiles, helps to highlight the region where this transition occurs and allows to give an estimate of its thickness. The analysis of the CO-O3 and H2O-O3 scatter plots and of the Probability Distribution Function (PDF) of the H2O-O3 pair completes this picture as it allows to better distinguish tropospheric and stratospheric regimes that can be identified, first, by their differing chemical composition. The joint analysis and comparison of observed and modelled data allows us to evaluate the capability of the model in reproducing the observed vertical structure of the TTL and its variability, and also to assess whether observations from particular regions on a monthly timescale can be representative of the fine scale mean structure of the Tropical Tropopause Layer

The Stratospheric Pathway of La Niña

A Northern Hemisphere (NH) polar stratospheric pathway for La Nina events is established during wintertime based on reanalysis data for the 1958-2012 period. A robust polar stratospheric response is observed in the NH during strong La Nina events, characterized by a significantly stronger and cooler polar vortex. Significant wind anomalies reach the surface, and a robust impact on the North Atlantic-European (NAE) region is observed. A dynamical analysis reveals that the stronger polar stratospheric winds during La Nina winters are due to reduced upward planetary wave activity into the stratosphere. This finding is the result of destructive interference between the climatological and the anomalous La Nina tropospheric stationary eddies over the Pacific-North American region. In addition, the lack of a robust stratospheric signature during La Nina winters reported in previous studies is investigated. It is found that this is related to the lower threshold used to detect the events, which signature is consequently more prone to be obscured by the influence of other sources of variability. In particular, the occurrence of stratospheric sudden warmings (SSWs), partly linked to the phase of the quasi-biennial oscillation, modulates the observed stratospheric signal. In the case of La Nina winters defined by a lower threshold, a robust stratospheric cooling is found only in the absence of SSWs. Therefore, these results highlight the importance of using a relatively restrictive threshold to define La Nina events in order to obtain a robust surface response in the NAE region through the stratosphere

Tropospheric pathways of the late-winter ENSO teleconnection to Europe

The late-winter signal associated with the El Niño-Southern Oscillation (ENSO) over the European continent is unsettled. Two main anomalous patterns of sea-level pressure (SLP) can be identified: a “wave-like” pattern with two opposite-signed anomalies over Europe, and a pattern showing a single anomaly (“semi-isolated”). In this work, potential paths of the tropospheric ENSO teleconnection to Europe and their role in favoring a more wave-like or semi-isolated pattern are explored. Outputs from historical runs of two versions of the MPI-ESM coupled model, which simulate these two types of patterns, are examined. A novel ray-tracing approach that accounts for zonal asymmetries in the background flow is used to test potential propagation paths in these simulations and in observations; three source regions are considered: the tropical Pacific, the North America/North Atlantic, and the tropical Atlantic. The semi-isolated pattern is suggested to be related to the well-known Rossby wave train emanating from the tropical Pacific, either via a split over northern North America or via reflection due to inhomogeneities in the background flow. The wave-like pattern, in turn, appears to be related to a secondary wave train emerging from the tropical Atlantic. The competition between these two pathways contributes to determining the actual surface response.B.M. and J.G.-S. were supported by the “Contratos Predoctorales para la Formación de Doctores” (BES-2016-076431) and “Ramón y Cajal” (RYC-2016-21181) programmes, respectively. Tercio Ambrizzi was supported by the National Institute of Science and Technology for Climate Change Phase 2 under CNPq Grant 465501/2014-1, 301397/2019-8; FAPESP Grants 2014/50848-9 and 2017/09659-6. This study also received funding from the Spanish ATLANTE project (PID2019-110234RB-C21). We acknowledge the World Climate research Programme’s Working Group on Coupled Modelling, which is responsible for CMIP. Technical support at BSC (Computational Earth Sciences group) is sincerely acknowledged. We also thank the two anonymous reviewers for their valuable insights.Peer ReviewedPostprint (published version

Tropospheric pathways of the late-winter ENSO teleconnection to Europe

The late-winter signal associated with the El Niño-Southern Oscillation (ENSO) over the European continent is unsettled. Two main anomalous patterns of sea-level pressure (SLP) can be identified: a "wave-like" pattern with two opposite-signed anomalies over Europe, and a pattern showing a single anomaly ("semi-isolated"). In this work, potential paths of the tropospheric ENSO teleconnection to Europe and their role in favoring a more wave-like or semi-isolated pattern are explored. Outputs from historical runs of two versions of the MPI-ESM coupled model, which simulate these two types of patterns, are examined. A novel ray-tracing approach that accounts for zonal asymmetries in the background flow is used to test potential propagation paths in these simulations and in observations; three source regions are considered: the tropical Pacific, the North America/North Atlantic, and the tropical Atlantic. The semi-isolated pattern is suggested to be related to the well-known Rossby wave train emanating from the tropical Pacific, either via a split over northern North America or via reflection due to inhomogeneities in the background flow. The wave-like pattern, in turn, appears to be related to a secondary wave train emerging from the tropical Atlantic. The competition between these two pathways contributes to determining the actual surface response

Hospitalization for pneumonia is associated with decreased 1-year survival in patients with type 2 diabetes results from a prospective cohort study

Diabetes mellitus is a frequent comorbid conditions among patients with pneumonia living in the community. The aim of our study is to evaluate the impact of hospitalization for pneumonia on early (30 day) and late mortality (1 year) in patients with type 2 diabetes mellitus. Prospective comparative cohort study of 203 patients with type 2 diabetes hospitalized for pneumonia versus 206 patients with diabetes hospitalized for other noninfectious causes from January 2012 to December 2013 at Policlinico Umberto I (Rome). Enrolled patients were followed up to discharge and up to 1 year after initial hospital admission or death. Overall, 203 patients with type 2 diabetes admitted to hospital for pneumonia were compared to 206 patients with type 2 diabetes admitted for other causes (39.3% decompensated diabetes, 21.4% cerebrovascular diseases, 9.2% renal failure, 8.3% acute myocardial infarction, and 21.8% other causes). Compared to control patients, those admitted for pneumonia showed a higher 30-day (10.8% vs 1%, P<0.001) and 1-year mortality rate (30.3% vs 16.8%, P<0.001). Compared to survivors, nonsurvivor patients with pneumonia had a higher incidence of moderate to severe chronic kidney disease, hemodialysis, and malnutrition were more likely to present with a mental status deterioration, and had a higher number of cardiovascular events during the follow-up period. Cox regression analysis found age, Charlson comorbidity index, pH<7.35 at admission, hemodialysis, and hospitalization for pneumonia as variables independently associated with mortality. Hospitalization for pneumonia is associated with decreased 1-year survival in patients with type 2 diabetes, and appears to be a major determinant of long-term outcome in these patients

STAble: A novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow

Background: De novo assembly of RNA-seq data allows the study of transcriptome in absence of a reference genome either if data is obtained from a single organism or from a mixed sample as in metatranscriptomics studies. Given the high number of sequences obtained from NGS approaches, a critical step in any analysis workflow is the assembly of reads to reconstruct transcripts thus reducing the complexity of the analysis. Despite many available tools show a good sensitivity, there is a high percentage of false positives due to the high number of assemblies considered and it is likely that the high frequency of false positive is underestimated by currently used benchmarks. The reconstruction of not existing transcripts may false the biological interpretation of results as - for example - may overestimate the identification of "novel" transcripts. Moreover, benchmarks performed are usually based on RNA-seq data from annotated genomes and assembled transcripts are compared to annotations and genomes to identify putative good and wrong reconstructions, but these tests alone may lead to accept a particular type of false positive as true, as better described below. Results: Here we present a novel methodology of de novo assembly, implemented in a software named STAble (Short-reads Transcriptome Assembler). The novel concept of this assembler is that the whole reads are used to determine possible alignments instead of using smaller k-mers, with the aim of reducing the number of chimeras produced. Furthermore, we applied a new set of benchmarks based on simulated data to better define the performance of assembly method and carefully identifying true reconstructions. STAble was also used to build a prototype workflow to analyse metatranscriptomics data in connection to a steady state metabolic modelling algorithm. This algorithm was used to produce high quality metabolic interpretations of small gene expression sets obtained from already published RNA-seq data that we assembled with STAble. Conclusions: The presented results, albeit preliminary, clearly suggest that with this approach is possible to identify informative reactions not directly revealed by raw transcriptomic data