Intercomparison of stratospheric chemistry models under polar vortex conditions

Several stratospheric chemistry modules from box, 2-D or 3-D models, have been intercompared. The intercomparison was focused on the ozone loss and associated reactive species under the conditions found in the cold, wintertime Arctic and Antarctic vortices. Comparisons of both gas phase and heterogeneous chemistry modules show excellent agreement between the models under constrained conditions for photolysis and the microphysics of polar stratospheric clouds. While the mean integral ozone loss ranges from 4-80% for different 30-50 days long air parcel trajectories, the mean scatter of model results around these values is only about +/-1.5%. In a case study, where the models employed their standard photolysis and microphysical schemes, the variation around the mean percentage ozone loss increases to about +/-7%. This increased scatter of model results is mainly due to the different treatment of the PSC microphysics and heterogeneous chemistry in the models, whereby the most unrealistic assumptions about PSC processes consequently lead to the least representative ozone chemistry. Furthermore, for this case study the model results for the ozone mixing ratios at different altitudes were compared with a measured ozone profile to investigate the extent to which models reproduce the stratospheric ozone losses. It was found that mainly in the height range of strong ozone depletion all models underestimate the ozone loss by about a factor of two. This finding corroborates earlier studies and implies a general deficiency in our understanding of the stratospheric ozone loss chemistry rather than a specific problem related to a particular model simulation

Revision and Update of the Consensus Definitions of Invasive Fungal Disease From the European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium.

BACKGROUND: Invasive fungal diseases (IFDs) remain important causes of morbidity and mortality. The consensus definitions of the Infectious Diseases Group of the European Organization for Research and Treatment of Cancer and the Mycoses Study Group have been of immense value to researchers who conduct clinical trials of antifungals, assess diagnostic tests, and undertake epidemiologic studies. However, their utility has not extended beyond patients with cancer or recipients of stem cell or solid organ transplants. With newer diagnostic techniques available, it was clear that an update of these definitions was essential. METHODS: To achieve this, 10 working groups looked closely at imaging, laboratory diagnosis, and special populations at risk of IFD. A final version of the manuscript was agreed upon after the groups' findings were presented at a scientific symposium and after a 3-month period for public comment. There were several rounds of discussion before a final version of the manuscript was approved. RESULTS: There is no change in the classifications of "proven," "probable," and "possible" IFD, although the definition of "probable" has been expanded and the scope of the category "possible" has been diminished. The category of proven IFD can apply to any patient, regardless of whether the patient is immunocompromised. The probable and possible categories are proposed for immunocompromised patients only, except for endemic mycoses. CONCLUSIONS: These updated definitions of IFDs should prove applicable in clinical, diagnostic, and epidemiologic research of a broader range of patients at high-risk

ICON-ART 1.0 - a new online-coupled model system from the global to regional scale

We present the first stage of a new online-coupled global to regional scale modelling framework for the simulation of the spatiotemporal evolution of aerosols and trace gases. The underlying meteorological model is the new nonhydrostatic model system ICON (ICOsahedral Nonhydrostatic) which allows a local grid refinement with two-way interactions between the grids. We develop the extension ART (Aerosol and Reactive Trace gases) with the goal to simulate interactions between trace substances and the state of the atmosphere. Within this paper, we present the basic equations and give an overview of the physical parameterizations as well as numerical methods we use. First applications of the new model system for trace gases, monodisperse particles and polydisperse particles are shown. The simulated distribution of two very short-lived substances, Bromoform (CHBr3) and Dibrommethane (CH2Br2) reflecting the fast upward transport shows a good agreement with observations and previous model studies. Also, the shape of the simulated tropical profiles is well reproduced. As an example for the treatment of monodisperse particles we present the simulated ash plume of the Eyjafjallajökull eruption in April 2010. Here, a novel approach for the source function is applied. The pattern of the simulated distribution of volcanic ash particles shows an agreement with previous studies. As an example for the treatment of a polydisperse aerosol, where number densities and mass concentrations are accounted for, we simulated the annual emissions of sea salt. We obtain a total emission flux of 26.0 Pg yr-1 and an emission flux of particles with diameter less than 10 my m of 7.36 Pg yr-1

ICON-ART 1.0 - A new online-coupled model system from the global to regional scale

We present the first stage of a new online-coupled global to regional-scale modeling framework for the simulation of the spatiotemporal evolution of aerosols and trace gases. The underlying meteorological model is the new nonhydrostatic model system ICON (ICOsahedral Nonhydrostatic) which allows a local grid refinement with two-way interactions between the grids. We develop the extension ART (Aerosol and Reactive Trace gases) with the goal of simulating interactions between trace substances and the state of the atmosphere. Within this paper, we present the basic equations and give an overview of the physical parameterizations as well as numerical methods we use. First applications of the new model system for trace gases, monodisperse particles and polydisperse particles are shown. The simulated distribution of two very short-lived substances (VSLS), bromoform (CHBr3) and dibromomethane (CH2Br2) reflecting the fast upward transport shows a good agreement with observations and previous model studies. Also, the shape of the simulated tropical profiles is well reproduced. As an example for the treatment of monodisperse particles we present the simulated ash plume of the Eyjafjallajökull eruption in April 2010. Here, a novel approach for the source function is applied. The pattern of the simulated distribution of volcanic ash particles shows a good agreement with previous studies. As an example for the treatment of a polydisperse aerosol, where number densities and mass concentrations are accounted for, we simulated the annual emissions of sea salt. We obtain a total emission flux of 26.0 Pg yr-1 and an emission flux of particles with diameter less than 10 μm of 7.36 Pg yr-1

Small but crucial : the novel small heat shock protein Hsp21 mediates stress adaptation and virulence in Candida albicans

Peer reviewedPublisher PD

Psychological process from hospitalization to death among uninformed terminal liver cancer patients in Japan

BACKGROUND: Although the attitude among doctors toward disclosing a cancer diagnosis is becoming more positive, informing patients of their disease has not yet become a common practice in Japan. We examined the psychological process, from hospitalization until death, among uninformed terminal cancer patients in Japan, and developed a psychological model. METHODS: Terminal cancer patients hospitalized during the recruiting period voluntarily participated in in-depth interviews. The data were analyzed by grounded theory. RESULTS: Of the 87 uninformed participants at the time of hospitalization, 67% (N = 59) died without being informed of their diagnosis. All were male, 51–66 years of age, and all experienced five psychological stages: anxiety and puzzlement, suspicion and denial, certainty, preparation, and acceptance. At the end of each stage, obvious and severe feelings were observed, which were called "gates." During the final acceptance stage, patients spent a peaceful time with family, even talking about their dreams with family members. CONCLUSION: Unlike in other studies, the uninformed patients in this study accepted death peacefully, with no exceptional cases. Despite several limitations, this study showed that almost 70% of the uninformed terminal cancer patients at hospitalization died without being informed, suggesting an urgent need for culturally specific and effective terminal care services for cancer patients in Japan

Contribution of CgPDR1-Regulated Genes in Enhanced Virulence of Azole-Resistant Candida glabrata

In Candida glabrata, the transcription factor CgPdr1 is involved in resistance to azole antifungals via upregulation of ATP binding cassette (ABC)-transporter genes including at least CgCDR1, CgCDR2 and CgSNQ2. A high diversity of GOF (gain-of-function) mutations in CgPDR1 exists for the upregulation of ABC-transporters. These mutations enhance C. glabrata virulence in animal models, thus indicating that CgPDR1 might regulate the expression of yet unidentified virulence factors. We hypothesized that CgPdr1-dependent virulence factor(s) should be commonly regulated by all GOF mutations in CgPDR1. As deduced from transcript profiling with microarrays, a high number of genes (up to 385) were differentially regulated by a selected number (7) of GOF mutations expressed in the same genetic background. Surprisingly, the transcriptional profiles resulting from expression of GOF mutations showed minimal overlap in co-regulated genes. Only two genes, CgCDR1 and PUP1 (for PDR1 upregulated and encoding a mitochondrial protein), were commonly upregulated by all tested GOFs. While both genes mediated azole resistance, although to different extents, their deletions in an azole-resistant isolate led to a reduction of virulence and decreased tissue burden as compared to clinical parents. As expected from their role in C. glabrata virulence, the two genes were expressed as well in vitro and in vivo. The individual overexpression of these two genes in a CgPDR1-independent manner could partially restore phenotypes obtained in clinical isolates. These data therefore demonstrate that at least these two CgPDR1-dependent and -upregulated genes contribute to the enhanced virulence of C. glabrata that acquired azole resistance

An emission module for ICON-ART 2.0: implementation and simulations of acetone

We present a recently developed emission module for the ICON (ICOsahedral Non-hydrostatic)-ART (Aerosols and Reactive Trace gases) modelling framework. The emission module processes external flux data sets and increments the tracer volume mixing ratios in the boundary layer accordingly. The performance of the emission module is illustrated with simulations of acetone, using a simplified chemical depletion mechanism based on a reaction with OH and photolysis only. In our model setup, we calculate a tropospheric acetone lifetime of 33 days, which is in good agreement with the literature. We compare our results with ground-based as well as with airborne IAGOS-CARIBIC measurements in the upper troposphere and lowermost stratosphere (UTLS) in terms of phase and amplitude of the annual cycle. In all our ICON-ART simulations the general seasonal variability is well represented but uncertainties remain concerning the magnitude of the acetone mixing ratio in the UTLS region. In addition, the module for online calculations of biogenic emissions (MEGAN2.1) is implemented in ICON-ART and can replace the offline biogenic emission data sets. In a sensitivity study we show how different parametrisations of the leaf area index (LAI) change the emission fluxes calculated by MEGAN2.1 and demonstrate the importance of an adequate treatment of the LAI within MEGAN2.1. We conclude that the emission module performs well with offline and online emission fluxes and allows the simulation of the annual cycles of emissions-dominated substances

Observed and simulated time evolution of HCl, ClONO2, and HF total column abundances

Time series of total column abundances of hydrogen chloride (HCl), chlorine nitrate (ClONO2), and hydrogen fluoride (HF) were determined from ground-based Fourier transform infrared (FTIR) spectra recorded at 17 sites belonging to the Network for the Detection of Atmospheric Composition Change (NDACC) and located between 80.05°N and 77.82°S. By providing such a near-global overview on ground-based measurements of the two major stratospheric chlorine reservoir species, HCl and ClONO2, the present study is able to confirm the decrease of the atmospheric inorganic chlorine abundance during the last few years. This decrease is expected following the 1987 Montreal Protocol and its amendments and adjustments, where restrictions and a subsequent phase-out of the prominent anthropogenic chlorine source gases (solvents, chlorofluorocarbons) were agreed upon to enable a stabilisation and recovery of the stratospheric ozone layer. The atmospheric fluorine content is expected to be influenced by the Montreal Protocol, too, because most of the banned anthropogenic gases also represent important fluorine sources. But many of the substitutes to the banned gases also contain fluorine so that the HF total column abundance is expected to have continued to increase during the last few years. The measurements are compared with calculations from five different models: the two-dimensional Bremen model, the two chemistry-transport models KASIMA and SLIMCAT, and the two chemistry-climate models EMAC and SOCOL. Thereby, the ability of the models to reproduce the absolute total column amounts, the seasonal cycles, and the temporal evolution found in the FTIR measurements is investigated and inter-compared. This is especially interesting because the models have different architectures. The overall agreement between the measurements and models for the total column abundances and the seasonal cycles is good. Linear trends of HCl, ClONO2, and HF are calculated from both measurement and model time series data, with a focus on the time range 2000–2009. This period is chosen because from most of the measurement sites taking part in this study, data are available during these years. The precision of the trends is estimated with the bootstrap resampling method. The sensitivity of the trend results with respect to the fitting function, the time of year chosen and time series length is investigated, as well as a bias due to the irregular sampling of the measurements. The measurements and model results investigated here agree qualitatively on a decrease of the chlorine species by around 1%yr-1. The models simulate an increase of HF of around 1%yr-1. This also agrees well with most of the measurements, but some of the FTIR series in the Northern Hemisphere show a stabilisation or even a decrease in the last few years. In general, for all three gases, the measured trends vary more strongly with latitude and hemisphere than the modelled trends. Relative to the FTIR measurements, the models tend to underestimate the decreasing chlorine trends and to overestimate the fluorine increase in the Northern Hemisphere. At most sites, the models simulate a stronger decrease of ClONO2 than of HCl. In the FTIR measurements, this difference between the trends of HCl and ClONO2 depends strongly on latitude, especially in the Northern Hemisphere.Peer reviewe