The impact of mixing across the polar vortex edge on Match ozone loss estimates

The Match method for quantification of polar chemical ozone loss is investigated mainly with respect to the impact of mixing across the vortex edge onto this estimate. We show for the winter 2002/03 that significant mixing across the vortex edge occurred and was accurately modeled by the Chemical Lagrangian Model of the Stratosphere. Observations of inert tracers and ozone in-situ from HAGAR on the Geophysica aircraft and sondes and also remote from MIPAS on ENVISAT were reproduced well. The model even reproduced a small vortex remnant that was isolated until June 2003 and was observed in-situ by a balloon-borne whole air sampler. We use this CLaMS simulation to quantify the impact of cross vortex edge mixing on the results of the Match method. It is shown that a time integration of the determined vortex average ozone loss rates as performed in Match results in larger ozone loss than the polar vortex average ozone loss in CLaMS. Also, the determination of the Match ozone loss rates can be influenced by mixing. This is especially important below 430 K, where ozone outside the vortex is lower than inside and the vortex boundary is not a strong transport barrier. This effect and further sampling effects cause an offset between vortex average ozone loss rates derived from Match and deduced from CLaMS with an even sampling for the entire vortex. Both, the time-integration of ozone loss and the determination of ozone loss rates for Match are evaluated using the winter 2002/03 CLaMS simulation. These impacts can explain the differences between CLaMS and Match column ozone loss. While the investigated effects somewhat reduce the apparent discrepancy in January ozone loss rates, a discrepancy between simulations and Match remains. However, its contribution to the accumulated ozone loss over the winter is not large

Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry

BACKGROUND: Three-dimensional (3D) imaging mass spectrometry (MS) is an analytical chemistry technique for the 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D-imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives for understanding the spatial organization of biological processes, and has growing potential to be introduced into routine use in both biology and medicine. Owing to the sheer quantity of data generated, the visualization, analysis, and interpretation of 3D imaging MS data remain a significant challenge. Bioinformatics research in this field is hampered by the lack of publicly available benchmark datasets needed to evaluate and compare algorithms. FINDINGS: High-quality 3D imaging MS datasets from different biological systems at several labs were acquired, supplied with overview images and scripts demonstrating how to read them, and deposited into MetaboLights, an open repository for metabolomics data. 3D imaging MS data were collected from five samples using two types of 3D imaging MS. 3D matrix-assisted laser desorption/ionization imaging (MALDI) MS data were collected from murine pancreas, murine kidney, human oral squamous cell carcinoma, and interacting microbial colonies cultured in Petri dishes. 3D desorption electrospray ionization (DESI) imaging MS data were collected from a human colorectal adenocarcinoma. CONCLUSIONS: With the aim to stimulate computational research in the field of computational 3D imaging MS, selected high-quality 3D imaging MS datasets are provided that could be used by algorithm developers as benchmark datasets

Stakeholder perspectives from 15 countries in Africa on barriers in snakebite envenoming research and the potential role of research hubs

Snakebite envenoming is a debilitating neglected tropical disease disproportionately affecting the rural poor in low and middle-income countries in the tropics and sub-tropics. Critical questions and gaps in public health and policy need to be addressed if major progress is to be made towards reducing the negative impact of snakebite, particularly in the World Health Organisation (WHO) Africa region. We engaged key stakeholders to identify barriers to evidence-based snakebite decision making and to explore how development of research and policy hubs could help to overcome these barriers. We conducted an electronic survey among 73 stakeholders from ministries of health, health facilities, academia and non-governmental organizations from 15 countries in the WHO Africa region. The primary barriers to snakebite research and subsequent policy translation were limited funds, lack of relevant data, and lack of interest from policy makers. Adequate funding commitment, strong political will, building expert networks and a demand for scientific evidence were all considered potential factors that could facilitate snakebite research. Participants rated availability of antivenoms, research skills training and disease surveillance as key research priorities. All participants indicated interest in the development of research and policy hubs and 78% indicated their organization would be willing to actively participate. In conclusion, our survey affirms that relevant stakeholders in the field of snakebite perceive research and policy hubs as a promising development, which could help overcome the barriers to pursuing the WHO goals and targets for reducing the burden of snakebite

Mixing and chemical ozone loss during and after the Antarctic polar vortex major warming in September 2002

The 3D version of the Chemical Lagrangian Model of the Stratosphere (CLAMS) is used to study the transport of CH4 and 03 in the Antarctic stratosphere between I September and 30 November 2002, that is, over the time period when unprecedented major stratospheric warming in late September split the polar vortex into two parts. The isentropic and cross-isentropic velocities in CLAMS are derived from ECMWF winds and heating/cooling rates calculated with a radiation module. The irreversible part of transport, that is, mixing, is driven by the local horizontal strain and vertical shear rates with mixing parameters deduced from in situ observations.The CH4 distribution after the vortex split shows a completely different behavior above and below 600 K. Above this potential temperature level, until the beginning of November, a significant part of vortex air is transported into the midlatitudes up to 40 degrees S. The lifetime of the vortex remnants formed after the vortex split decreases with the altitude with values of about 3 and 6 weeks at 900 and 700 K, respectively.Despite this enormous dynamical disturbance of the vortex, the intact part between 400 and 600 K that "survived" the major warming was strongly isolated from the extravortex air until the end of November. According to CLAMS simulations, the air masses within this part of the vortex did not experience any significant dilution with the midlatitude air.By transporting ozone in CLAMS as a passive tracer, the chemical ozone loss was estimated from the difference between the observed [Polar Ozone and Aerosol Measurement III (POAM 111) and Halogen Occultation Experiment (HALOE)] and simulated ozone profiles. Starting from I September, up to 2.0 ppmv O-3 around 480 K and about 70 Dobson units between 450 and 550 K were destroyed until the vortex was split. After the major warming, no additional ozone loss can be derived, but in the intact vortex part between 450 and 550 K, the accumulated ozone loss was "frozen in" until the end of November

How permeable is the edge of the Arctic vortex: Model studies of winter 1999-2000

The edge of the Arctic vortex constitutes a strong barrier to transport; however, the extent of isolation of the vortex air as a function of altitude and season is relatively poorly quantified. In this study, by examining the transport of midlatitude air parcels across the vortex edge into the vortex, we analyze the permeability of the vortex edge. With the three-dimensional version of CLaMS (Chemical Lagrangian Model of the Stratosphere) we explore the dilution of the vortex air due to mixing in winter 1999-2000. An artificial, passive tracer was initialized on 1 December 1999 inside the polar vortex with a value of 100% and with a value of zero outside the polar vortex. Using several different definitions of the vortex edge, the resulting intrusions of midlatitude air into the vortex show the same mean features. This demonstrates that the diagnosed dilution does not strongly depend on the details of the definition of the vortex edge. At about the end of March 2000, the vertical structure of the vortex consisted of well-isolated, pure vortex layers around 500 K and 750 K, with some more diluted layers in between and at the vortex bottom. The influence of wave activity on the evolution of the intrusion layers is studied. The divergence of the Eliassen-Palm flux shows such a high variability during the whole period that it is not possible to assess a direct causality of certain intrusion layers and some specific patterns. Some characteristics of the vortex edge, in particular the shape of the gradient of potential vorticity (PV), can influence the dilution of the vortex. In cases without a distinct maximum in the PV gradient, the defined "vortex edge'' may vary substantially from day to day. The comparison of some properties of the vortex (wind speed, PV field, area of the vortex, the maximum of the PV gradient) of undisturbed versus diluted layers and the variation in time of the intrusions were analyzed. All observed intrusions begin in conditions of weak PV gradient, indicating that the value of the maximum of the PV gradient may be used as a quantitative measure of the permeability of the vortex edge