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In 2019–2020, Australia experienced its largest wildfire season on record. Smoke covered hundreds of square kilometers across the southeastern coast and reached the site of the COALA-2020 (Characterizing Organics and Aerosol Loading over Australia) field campaign in New South Wales. Using a subset of nighttime observations made by a proton-transfer-reaction time-of-flight mass spectrometer (PTR-ToF-MS), we calculate emission ratios (ERs) and factors (EFs) for 15 volatile organic compounds (VOCs). We restrict our analysis to VOCs with sufficiently long lifetimes to be minimally impacted by oxidation over the ∼ 8 h between when the smoke was emitted and when it arrived at the field site. We use oxidized VOC to VOC ratios to assess the total amount of radical oxidation: maleic anhydride / furan to assess OH oxidation, and (cis-2-butenediol + furanone) / furan to assess NO3 oxidation. We examine time series of O3 and NO2 given their closely linked chemistry with wildfire plumes and observe their trends during the smoke event. Then we compare ERs calculated from the freshest portion of the plume to ERs calculated using the entire nighttime period. Finding good agreement between the two, we are able to extend our analysis to VOCs measured in more chemically aged portions of the plume. Our analysis provides ERs and EFs for six compounds not previously reported for temperate forests in Australia: acrolein (a compound with significant health impacts), methyl propanoate, methyl methacrylate, maleic anhydride, benzaldehyde, and creosol. We compare our results with two studies in similar Australian biomes, and two studies focused on US temperate forests. We find over half of our EFs are within a factor of 2.5 relative to those presented in Australian biome studies, with nearly all within a factor of 5, indicating reasonable agreement. For US-focused studies, we find similar results with over half our EFs within a factor of 2.5, and nearly all within a factor of 5, again indicating reasonably good agreement. This suggests that comprehensive field measurements of biomass burning VOC emissions in other regions may be applicable to Australian temperate forests. Finally, we quantify the magnitude attributable to the primary compounds contributing to OH reactivity from this plume, finding results comparable to several US-based wildfire and laboratory studies.

The accumulation of gases into our atmosphere is a growing global concern that requires considerable quantification of the emission rates to mitigate the accumulation of gases in the atmosphere, especially the greenhouse gases (GHGs). In agriculture there are many sources of GHGs that require attention in order to develop practical mitigation strategies. Measuring these GHG sources often relies on highly technical instrumentation originally designed for applications outside of the emissions research in agriculture. Although the open-path laser (OPL) and open-path Fourier transform infrared (OP-FTIR) spectroscopic techniques are used in agricultural research currently, insight into their contributing error to emissions research has not been the focus of these studies. The objective of this study was to assess the applicability and performance (accuracy and precision) of OPL and OP-FTIR spectroscopic techniques for measuring gas mole fractions from agricultural sources. We measured the mole fractions of trace gases methane (CH4), nitrous oxide (N2O), and ammonia (NH3), downwind of point and area sources with a known release rate. The mole fractions measured by OP-FTIR and OPL were also input into models of atmospheric dispersion (WindTrax) allowing the calculation of fluxes. Trace gas release recoveries with WindTrax were examined by comparing the ratio of estimated and known fluxes. The OP-FTIR provided the best performance regarding stability of drift in stable conditions. The CH4 OPL accurately detected the low background (free-air) level of CH4; however, the NH3 OPL was unable to detect the background values ppbv. The dispersion modelling using WindTrax coupled with open-path measurements can be a useful tool to calculate trace gas fluxes from the well-defined source area.

Intro: Dengue epidemics can rapidly increase demand in healthcare services across many endemic settings. However, there remains a lack of tools which can rapidly inform patient management and can be used at the point of care. Digital clinical decision-support systems (CDSSs) allow for efficient organisation of care as well as improve the quality of patient management. It is important that these tools are designed for the end-user and with the healthcare setting in mind to increase adoption and usability. Methods: We adopted a ground-up human-centred design approach to design a digital CDSS system for dengue management in Vietnam (D-CASS). A multidisciplinary team of data scientists, clinicians and social scientists were involved in a series of activities designed to map clinical processes, essential tasks and decision-making priorities which were crucial in the management of dengue at our hospital setting. Frontend development was undertaken by a specialist UX designer with regular feedback from the research team and clinical end-users. Findings: Based on our previous work, the desired features for the CDSS identified were: i) patient organisation, ii) availability of guidelines and calculators with easy access, iii) display of results and iv) inference models for dengue diagnosis on admission AUCROC 0.86 (IQR, 0.84—0.86) and further risk stratification for hospitalised patients based on possible complications AUCROC 0.83 (CI, 0.76—0.85). A web-based reactive framework suitable for display on computers and tablets was produced. Priority was placed on usability and modularity so that the system can be repurposed. Conclusion: Dengue Clinical Decision Support Application (D-CASS) is a bespoke and rapidly scalable CDSS produced following clinical pathways, clinician's needs, and usability in mind. Further work will focus on prospective evaluation and iterative improvement of the CDSS including (i) end-user testing and (ii) prospective model performance. If successful, the CDSS will be implemented and deployed to evaluate its clinical utility.

Abstract Background The Wolbachia incompatible insect technique (IIT) shows promise as a method for eliminating populations of invasive mosquitoes such as Aedes aegypti (Linnaeus) (Diptera: Culicidae) and reducing the incidence of vector-borne diseases such as dengue, chikungunya and Zika. Successful implementation of this biological control strategy relies on high-fidelity separation of male from female insects in mass production systems for inundative release into landscapes. Processes for sex-separating mosquitoes are typically error-prone and laborious, and IIT programmes run the risk of releasing Wolbachia-infected females and replacing wild mosquito populations. Results We introduce a simple Markov population process model for studying mosquito populations subjected to a Wolbachia-IIT programme which exhibit an unstable equilibrium threshold. The model is used to study, in silico, scenarios that are likely to yield a successful elimination result. Our results suggest that elimination is best achieved by releasing males at rates that adapt to the ever-decreasing wild population, thus reducing the risk of releasing Wolbachia-infected females while reducing costs. Conclusions While very high-fidelity sex separation is required to avoid establishment, release programmes tend to be robust to the release of a small number of Wolbachia-infected females. These findings will inform and enhance the next generation of Wolbachia-IIT population control strategies that are already showing great promise in field trials.

In this study, we present ground-based measurements of column-averaged dry-air mole fractions (DMFs) of CO2 (or XCO2) taken in a semiarid region of Australia with an EM27/SUN portable spectrometer equipped with an automated clamshell cover. We compared these measurements to space-based XCO2 retrievals from the Greenhouse Gases Observing Satellite (GOSAT). Side-by-side measurements of EM27/SUN with the Total Carbon Column Observing Network (TCCON) instrument at the University of Wollongong were conducted in 2015–2016 to derive an XCO2 scaling factor of 0.9954 relative to TCCON. Although we found a slight drift of 0.13 % over 3 months in the calibration curve of the EM27/SUN vs. TCCON XCO2, the alignment of the EM27/SUN proved stable enough for a 2-week campaign, keeping the retrieved Xair values, another measure of stability, to within 0.5 % and the modulation efficiency to within 2 %. From the measurements in Alice Springs, we confirm a small bias of around 2 ppm in the GOSAT M-gain to H-gain XCO2 retrievals, as reported by the NIES GOSAT validation team. Based on the reported random errors from GOSAT, we estimate the required duration of a future campaign in order to better understand the estimated bias between the EM27/SUN and GOSAT. The dataset from the Alice Springs measurements is accessible at https://doi.org/10.4225/48/5b21f16ce69bc (Velazco et al., 2018).

Quantitative understanding of the sources and sinks of greenhouse gases is essential for predicting greenhouse-gas–climate feedback processes and their impacts on climate variability and change. Australia plays a significant role in driving variability in global carbon cycling, but the budgets of carbon gases in Australia remain highly uncertain. Here, shipborne Fourier transform infrared spectrometer measurements collected around Australia are used together with a global chemical transport model (GEOS-Chem) to analyse the variability of three direct and indirect carbon greenhouse gases: carbon dioxide (CO2), methane (CH4) and carbon monoxide (CO). Using these measurements, we provide an updated distribution of these gases. From the model, we quantify their sources and sinks, and we exploit the benefits of multi-species analysis to explore co-variations to constrain relevant processes. We find that for all three gases, the eastern Australian coast is largely influenced by local anthropogenic sources, while the southern, western and northern coasts are characterised by a mixture of anthropogenic and natural sources. Comparing coincident and co-located enhancements in the three carbon gases highlighted several common sources from the Australian continent. We found evidence for 17 events with similar enhancement patterns indicative of co-emission and calculated enhancement ratios and modelled source contributions for each event. We found that anthropogenic co-enhancement events are common along the eastern coast, while co-enhancement events in the tropics primarily derive from biomass burning sources. While the GEOS-Chem model generally reproduced the timing of co-enhancement events, it was less able to reproduce the magnitude of enhancements. We used these differences to identify underestimated, overestimated and missing processes in the model. We found model overestimates of CH4 from coal burning and underestimates of all three gases from biomass burning. We identified missing sources from fossil fuel, biofuel, oil, gas, coal, livestock, biomass burning and the biosphere in the model, pointing to the need to further develop and evaluate greenhouse-gas emission inventories for the Australian continent.

Among the more than 20 ground-based FTIR (Fourier transform infrared) stations currently operating around the globe, only a few have provided formaldehyde (HCHO) total column time series until now. Although several independent studies have shown that the FTIR measurements can provide formaldehyde total columns with good precision, the spatial coverage has not been optimal for providing good diagnostics for satellite or model validation. Furthermore, these past studies used different retrieval settings, and biases as large as 50 % can be observed in the HCHO total columns depending on these retrieval choices, which is also a weakness for validation studies combining data from different ground-based stations.For the present work, the HCHO retrieval settings have been optimized based on experience gained from past studies and have been applied consistently at the 21 participating stations. Most of them are either part of the Network for the Detection of Atmospheric Composition Change (NDACC) or under consideration for membership. We provide the harmonized settings and a characterization of the HCHO FTIR products. Depending on the station, the total systematic and random uncertainties of an individual HCHO total column measurement lie between 12 % and 27 % and between 1 and 11×1014 molec cm−2, respectively. The median values among all stations are 13 % and 2.9×1014 molec cm−2 for the total systematic and random uncertainties.This unprecedented harmonized formaldehyde data set from 21 ground-based FTIR stations is presented and its comparison with a global chemistry transport model shows consistency in absolute values as well as in seasonal cycles. The network covers very different concentration levels of formaldehyde, from very clean levels at the limit of detection (few 1013 molec cm−2) to highly polluted levels (7×1016 molec cm−2). Because the measurements can be made at any time during daylight, the diurnal cycle can be observed and is found to be significant at many stations. These HCHO time series, some of them starting in the 1990s, are crucial for past and present satellite validation and will be extended in the coming years for the next generation of satellite missions.

We characterised trace gas emissions from Australian temperate forest fires through a mixture of open-path Fourier transform infrared (OP-FTIR) measurements and selective ion flow tube mass spectrometry (SIFT-MS) and White cell FTIR analysis of grab samples. We report emission factors for a total of 25 trace gas species measured in smoke from nine prescribed fires. We find significant dependence on modified combustion efficiency (MCE) for some species, although regional differences indicate that the use of MCE as a proxy may be limited. We also find that the fire-integrated MCE values derived from our in situ on-the-ground open-path measurements are not significantly different from those reported for airborne measurements of smoke from fires in the same ecosystem. We then compare our average emission factors to those measured for temperate forest fires elsewhere (North America) and for fires in another dominant Australian ecosystem (savanna) and find significant differences in both cases. Indeed, we find that although the emission factors of some species agree within 20 %, including those of hydrogen cyanide, ethene, methanol, formaldehyde and 1,3-butadiene, others, such as acetic acid, ethanol, monoterpenes, ammonia, acetonitrile and pyrrole, differ by a factor of 2 or more. This indicates that the use of ecosystem-specific emission factors is warranted for applications involving emissions from Australian forest fires.

The SAFIRED (Savannah Fires in the Early Dry Season) campaign took place from 29 May until 30 June 2014 at the Australian Tropical Atmospheric Research Station (ATARS) in the Northern Territory, Australia. The purpose of this campaign was to investigate emissions from fires in the early dry season in northern Australia. Measurements were made of biomass burning aerosols, volatile organic compounds, polycyclic aromatic carbons, greenhouse gases, radon, speciated atmospheric mercury and trace metals. Aspects of the biomass burning aerosol emissions investigated included; emission factors of various species, physical and chemical aerosol properties, aerosol aging, micronutrient supply to the ocean, nucleation, and aerosol water uptake. Over the course of the month-long campaign, biomass burning signals were prevalent and emissions from several large single burning events were observed at ATARS.Biomass burning emissions dominated the gas and aerosol concentrations in this region. Dry season fires are extremely frequent and widespread across the northern region of Australia, which suggests that the measured aerosol and gaseous emissions at ATARS are likely representative of signals across the entire region of north Australia. Air mass forward trajectories show that these biomass burning emissions are carried north-west over the Timor Sea and could influence the atmosphere over Indonesia and the tropical atmosphere over the Indian Ocean. Here we present characteristics of the biomass burning observed at the sampling site and provide an overview of the more specific outcomes of the SAFIRED campaign.

The Measurements of Urban, Marine and Biogenic Air (MUMBA) campaign took place in Wollongong, New South Wales (a small coastal city approximately 80 km south of Sydney, Australia) from 21 December 2012 to 15 February 2013. Like many Australian cities, Wollongong is surrounded by dense eucalyptus forest, so the urban airshed is heavily influenced by biogenic emissions. Instruments were deployed during MUMBA to measure the gaseous and aerosol composition of the atmosphere with the aim of providing a detailed characterisation of the complex environment of the ocean–forest–urban interface that could be used to test the skill of atmospheric models. The gases measured included ozone, oxides of nitrogen, carbon monoxide, carbon dioxide, methane and many of the most abundant volatile organic compounds. The aerosol characterisation included total particle counts above 3 nm, total cloud condensation nuclei counts, mass concentration, number concentration size distribution, aerosol chemical analyses and elemental analysis.The campaign captured varied meteorological conditions, including two extreme heat events, providing a potentially valuable test for models of future air quality in a warmer climate. There was also an episode when the site sampled clean marine air for many hours, providing a useful additional measure of the background concentrations of these trace gases within this poorly sampled region of the globe. In this paper we describe the campaign, the meteorology and the resulting observations of atmospheric composition in general terms in order to equip the reader with a sufficient understanding of the Wollongong regional influences to use the MUMBA datasets as a case study for testing a chemical transport model. The data are available from PANGAEA (http://doi.pangaea.de/10.1594/PANGAEA.871982).

The Measurements of Pollution in the Troposphere (MOPITT) satellite instrument provides the longest continuous dataset of carbon monoxide (CO) from space. We perform the first validation of MOPITT version 6 retrievals using total column CO measurements from ground-based remote-sensing Fourier transform infrared spectrometers (FTSs). Validation uses data recorded at 14 stations, that span a wide range of latitudes (80° N to 78° S), in the Network for the Detection of Atmospheric Composition Change (NDACC). MOPITT measurements are spatially co-located with each station, and different vertical sensitivities between instruments are accounted for by using MOPITT averaging kernels (AKs). All three MOPITT retrieval types are analyzed: thermal infrared (TIR-only), joint thermal and near infrared (TIR–NIR), and near infrared (NIR-only). Generally, MOPITT measurements overestimate CO relative to FTS measurements, but the bias is typically less than 10 %. Mean bias is 2.4 % for TIR-only, 5.1 % for TIR–NIR, and 6.5 % for NIR-only. The TIR–NIR and NIR-only products consistently produce a larger bias and lower correlation than the TIR-only. Validation performance of MOPITT for TIR-only and TIR–NIR retrievals over land or water scenes is equivalent. The four MOPITT detector element pixels are validated separately to account for their different uncertainty characteristics. Pixel 1 produces the highest standard deviation and lowest correlation for all three MOPITT products. However, for TIR-only and TIR–NIR, the error-weighted average that includes all four pixels often provides the best correlation, indicating compensating pixel biases and well-captured error characteristics. We find that MOPITT bias does not depend on latitude but rather is influenced by the proximity to rapidly changing atmospheric CO. MOPITT bias drift has been bound geographically to within ±0.5 % yr−1 or lower at almost all locations.

There is a lack of knowledge of how biomass burning aerosols in the tropics age, including those in the fire-prone Northern Territory in Australia. This paper reports chemical characterization of fresh and aged aerosols monitored during the 1-month-long SAFIRED (Savannah Fires in the Early Dry Season) field study, with an emphasis on the chemical signature and aging of organic aerosols. The campaign took place in June 2014 during the early dry season when the surface measurement site, the Australian Tropical Atmospheric Research Station (ATARS), located in the Northern Territory, was heavily influenced by thousands of wild and prescribed bushfires. ATARS was equipped with a wide suite of instrumentation for gaseous and aerosol characterization. A compact time-of-flight aerosol mass spectrometer was deployed to monitor aerosol chemical composition. Approximately 90 % of submicron non-refractory mass was composed of organic material. Ozone enhancement in biomass burning plumes indicated increased air mass photochemistry. The diversity in biomass burning emissions was illustrated through variability in chemical signature (e.g. wide range in f44, from 0.06 to 0.18) for five intense fire events. The background particulate loading was characterized using positive matrix factorization (PMF). A PMF-resolved BBOA (biomass burning organic aerosol) factor comprised 24 % of the submicron non-refractory organic aerosol mass, confirming the significance of fire sources. A dominant PMF factor, OOA (oxygenated organic aerosol), made up 47 % of the sampled aerosol, illustrating the importance of aerosol aging in the Northern Territory. Biogenic isoprene-derived organic aerosol factor was the third significant fraction of the background aerosol (28 %).

Changes of atmospheric methane total columns (CH4) since 2005 have been evaluated using Fourier transform infrared (FTIR) solar observations carried out at 10 ground-based sites, affiliated to the Network for Detection of Atmospheric Composition Change (NDACC). From this, we find an increase of atmospheric methane total columns of 0.31 ± 0.03 % year−1 (2σ level of uncertainty) for the 2005–2014 period. Comparisons with in situ methane measurements at both local and global scales show good agreement. We used the GEOS-Chem chemical transport model tagged simulation, which accounts for the contribution of each emission source and one sink in the total methane, simulated over 2005–2012. After regridding according to NDACC vertical layering using a conservative regridding scheme and smoothing by convolving with respective FTIR seasonal averaging kernels, the GEOS-Chem simulation shows an increase of atmospheric methane total columns of 0.35 ± 0.03 % year−1 between 2005 and 2012, which is in agreement with NDACC measurements over the same time period (0.30 ± 0.04 % year−1, averaged over 10 stations). Analysis of the GEOS-Chem-tagged simulation allows us to quantify the contribution of each tracer to the global methane change since 2005. We find that natural sources such as wetlands and biomass burning contribute to the interannual variability of methane. However, anthropogenic emissions, such as coal mining, and gas and oil transport and exploration, which are mainly emitted in the Northern Hemisphere and act as secondary contributors to the global budget of methane, have played a major role in the increase of atmospheric methane observed since 2005. Based on the GEOS-Chem-tagged simulation, we discuss possible cause(s) for the increase of methane since 2005, which is still unexplained.

Marine nitrogen fixation is co-limited by the supply of iron (Fe) and phosphorus in large regions of the global ocean. The deposition of soluble aerosol Fe can initiate nitrogen fixation and trigger toxic algal blooms in nitrate-poor tropical waters. We present dry season soluble Fe data from the Savannah Fires in the Early Dry Season (SAFIRED) campaign in northern Australia that reflects coincident dust and biomass burning sources of soluble aerosol Fe. The mean soluble and total aerosol Fe concentrations were 40 and 500 ng m−3 respectively. Our results show that while biomass burning species may not be a direct source of soluble Fe, biomass burning may substantially enhance the solubility of mineral dust. We observed fractional Fe solubility up to 12 % in mixed aerosols. Thus, Fe in dust may be more soluble in the tropics compared to higher latitudes due to higher concentrations of biomass-burning-derived reactive organic species in the atmosphere. In addition, biomass-burning-derived particles can act as a surface for aerosol Fe to bind during atmospheric transport and subsequently be released to the ocean upon deposition. As the aerosol loading is dominated by biomass burning emissions over the tropical waters in the dry season, additions of biomass-burning-derived soluble Fe could have harmful consequences for initiating nitrogen-fixing toxic algal blooms. Future research is required to quantify biomass-burning-derived particle sources of soluble Fe over tropical waters.

This paper studies the seasonal variation of surface and column CO at three different sites (Paris, Jungfraujoch and Wollongong), with an emphasis on establishing a link between the CO vertical distribution and the nature of CO emission sources. We find the first evidence of a time lag between surface and free tropospheric CO seasonal variations in the Northern Hemisphere. The CO seasonal variability obtained from the total columns and free tropospheric partial columns shows a maximum around March–April and a minimum around September–October in the Northern Hemisphere (Paris and Jungfraujoch). In the Southern Hemisphere (Wollongong) this seasonal variability is shifted by about 6 months. Satellite observations by the IASI–MetOp (Infrared Atmospheric Sounding Interferometer) and MOPITT (Measurements Of Pollution In The Troposphere) instruments confirm this seasonality. Ground-based FTIR (Fourier transform infrared) measurements provide useful complementary information due to good sensitivity in the boundary layer. In situ surface measurements of CO volume mixing ratios at the Paris and Jungfraujoch sites reveal a time lag of the near-surface seasonal variability of about 2 months with respect to the total column variability at the same sites. The chemical transport model GEOS-Chem (Goddard Earth Observing System chemical transport model) is employed to interpret our observations. GEOS-Chem sensitivity runs identify the emission sources influencing the seasonal variation of CO. At both Paris and Jungfraujoch, the surface seasonality is mainly driven by anthropogenic emissions, while the total column seasonality is also controlled by air masses transported from distant sources. At Wollongong, where the CO seasonality is mainly affected by biomass burning, no time shift is observed between surface measurements and total column data.

Formic acid (HCOOH) is one of the most abundant volatile organic compounds in the atmosphere. It is a major contributor to rain acidity in remote areas. There are, however, large uncertainties on the sources and sinks of HCOOH and therefore HCOOH is misrepresented by global chemistry-transport models. This work presents global distributions from 2008 to 2014 as derived from the measurements of the Infrared Atmospheric Sounding Interferometer (IASI), based on conversion factors between brightness temperature differences and representative retrieved total columns over seven regions: Northern Africa, southern Africa, Amazonia, Atlantic, Australia, Pacific, and Russia. The dependence of the measured HCOOH signal on the thermal contrast is taken into account in the conversion method. This conversion presents errors lower than 20 % for total columns ranging between 0.5 and 1 × 1016 molec cm−2 but reaches higher values, up to 78 %, for columns that are lower than 0.3 × 1016 molec cm−2. Signatures from biomass burning events are highlighted, such as in the Southern Hemisphere and in Russia, as well as biogenic emission sources, e.g., over the eastern USA. A comparison between 2008 and 2014 with ground-based Fourier transform infrared spectroscopy (FTIR) measurements obtained at four locations (Maido and Saint-Denis at La Réunion, Jungfraujoch, and Wollongong) is shown. Although IASI columns are found to correlate well with FTIR data, a large bias (> 100 %) is found over the two sites at La Réunion. A better agreement is found at Wollongong with a negligible bias. The comparison also highlights the difficulty of retrieving total columns from IASI measurements over mountainous regions such as Jungfraujoch. A comparison of the retrieved columns with the global chemistry-transport model IMAGESv2 is also presented, showing good representation of the seasonal and interannual cycles over America, Australia, Asia, and Siberia. A global model underestimation of the distribution and a misrepresentation of the seasonal cycle over India are also found. A small positive trend in the IASI columns is observed over Australia, Amazonia, and India over the 2008–2014 period (from 0.7 to 1.5 % year−1), while a decrease of ∼ 0.8 % year−1 is measured over Siberia.

The biogenic emissions of isoprene and monoterpenes are one of the main drivers of atmospheric photochemistry, including oxidant and secondary organic aerosol production. In this paper, the emission rates of isoprene and monoterpenes from Australian vegetation are investigated for the first time using the Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGANv2.1); the CSIRO chemical transport model; and atmospheric observations of isoprene, monoterpenes and isoprene oxidation products (methacrolein and methyl vinyl ketone). Observations from four field campaigns during three different seasons are used, covering urban, coastal suburban and inland forest areas. The observed concentrations of isoprene and monoterpenes were of a broadly similar magnitude, which may indicate that southeast Australia holds an unusual position where neither chemical species dominates. The model results overestimate the observed atmospheric concentrations of isoprene (up to a factor of 6) and underestimate the monoterpene concentrations (up to a factor of 4). This may occur because the emission rates currently used in MEGANv2.1 for Australia are drawn mainly from young eucalypt trees (

We present global distributions of C2H2 and hydrogen cyanide (HCN) total columns derived from the Infrared Atmospheric Sounding Interferometer (IASI) for the years 2008–2010. These distributions are obtained with a fast method allowing to retrieve C2H2 abundance globally with a 5 % precision and HCN abundance in the tropical (subtropical) belt with a 10 % (25 %) precision. IASI data are compared for validation purposes with ground-based Fourier transform infrared (FTIR) spectrometer measurements at four selected stations. We show that there is an overall agreement between the ground-based and space measurements with correlation coefficients for daily mean measurements ranging from 0.28 to 0.81, depending on the site. Global C2H2 and subtropical HCN abundances retrieved from IASI spectra show the expected seasonality linked to variations in the anthropogenic emissions and seasonal biomass burning activity, as well as exceptional events, and are in good agreement with previous spaceborne studies. Total columns simulated by the Model for Ozone and Related Chemical Tracers, version 4 (MOZART-4) are compared to the ground-based FTIR measurements at the four selected stations. The model is able to capture the seasonality in the two species in most of the cases, with correlation coefficients for daily mean measurements ranging from 0.50 to 0.86, depending on the site. IASI measurements are also compared to the distributions from MOZART-4. Seasonal cycles observed from satellite data are reasonably well reproduced by the model with correlation coefficients ranging from −0.31 to 0.93 for C2H2 daily means, and from 0.09 to 0.86 for HCN daily means, depending on the considered region. However, the anthropogenic (biomass burning) emissions used in the model seem to be overestimated (underestimated), and a negative global mean bias of 1 % (16 %) of the model relative to the satellite observations was found for C2H2 (HCN).

We investigate the impact of biogenic emissions on carbon monoxide (CO) and formaldehyde (HCHO) in the Southern Hemisphere (SH), with simulations using two different biogenic emission inventories for isoprene and monoterpenes. Results from four atmospheric chemistry models are compared to continuous long-term ground-based CO and HCHO column measurements at the SH Network for the Detection of Atmospheric Composition Change (NDACC) sites, the satellite measurement of tropospheric CO columns from the Measurement of Pollution in the Troposphere (MOPITT), and in situ surface CO measurements from across the SH, representing a subset of the National Oceanic and Atmospheric Administration's Global Monitoring Division (NOAA GMD) network. Simulated mean model CO using the Model of Emissions of Gases and Aerosols from Nature (v2.1) computed in the frame work of the Land Community Model (CLM-MEGANv2.1) inventory is in better agreement with both column and surface observations than simulations adopting the emission inventory generated from the LPJ-GUESS dynamical vegetation model framework, which markedly underestimate measured column and surface CO at most sites. Differences in biogenic emissions cause large differences in CO in the source regions which propagate to the remote SH. Significant inter-model differences exist in modelled column and surface CO, and secondary production of CO dominates these inter-model differences, due mainly to differences in the models' oxidation schemes for volatile organic compounds, predominantly isoprene oxidation. While biogenic emissions are a significant factor in modelling SH CO, inter-model differences pose an additional challenge to constrain these emissions. Corresponding comparisons of HCHO columns at two SH mid-latitude sites reveal that all models significantly underestimate the observed values by approximately a factor of 2. There is a much smaller impact on HCHO of the significantly different biogenic emissions in remote regions, compared to the source regions. Decreased biogenic emissions cause decreased CO export to remote regions, which leads to increased OH; this in turn results in increased HCHO production through methane oxidation. In agreement with earlier studies, we corroborate that significant HCHO sources are likely missing in the models in the remote SH.

We investigate Arctic tropospheric composition using ground-based Fourier transform infrared (FTIR) solar absorption spectra, recorded at the Polar Environment Atmospheric Research Laboratory (PEARL, Eureka, Nunavut, Canada, 80°05' N, 86°42' W) and at Thule (Greenland, 76°53' N, −68°74' W) from 2008 to 2012. The target species, carbon monoxide (CO), hydrogen cyanide (HCN), ethane (C2H6), acetylene (C2H2), formic acid (HCOOH), and formaldehyde (H2CO) are emitted by biomass burning and can be transported from mid-latitudes to the Arctic. By detecting simultaneous enhancements of three biomass burning tracers (HCN, CO, and C2H6), ten and eight fire events are identified at Eureka and Thule, respectively, within the 5-year FTIR time series. Analyses of Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model back-trajectories coupled with Moderate Resolution Imaging Spectroradiometer (MODIS) fire hotspot data, Stochastic Time-Inverted Lagrangian Transport (STILT) model footprints, and Ozone Monitoring Instrument (OMI) UV aerosol index maps, are used to attribute burning source regions and travel time durations of the plumes. By taking into account the effect of aging of the smoke plumes, measured FTIR enhancement ratios were corrected to obtain emission ratios and equivalent emission factors. The means of emission factors for extratropical forest estimated with the two FTIR data sets are 0.40 ± 0.21 g kg−1 for HCN, 1.24 ± 0.71 g kg−1 for C2H6, 0.34 ± 0.21 g kg−1 for C2H2, and 2.92 ± 1.30 g kg−1 for HCOOH. The emission factor for CH3OH estimated at Eureka is 3.44 ± 1.68 g kg−1. To improve our knowledge concerning the dynamical and chemical processes associated with Arctic pollution from fires, the two sets of FTIR measurements were compared to the Model for OZone And Related chemical Tracers, version 4 (MOZART-4). Seasonal cycles and day-to-day variabilities were compared to assess the ability of the model to reproduce emissions from fires and their transport. Good agreement in winter confirms that transport is well implemented in the model. For C2H6, however, the lower wintertime concentration estimated by the model as compared to the FTIR observations highlights an underestimation of its emission. Results show that modeled and measured total columns are correlated (linear correlation coefficient r > 0.6 for all gases except for H2CO at Eureka and HCOOH at Thule), but suggest a general underestimation of the concentrations in the model for all seven tropospheric species in the high Arctic.

Savanna fires contribute approximately 40–50% of total global annual biomass burning carbon emissions. Recent comparisons of emission factors from different savanna regions have highlighted the need for a regional approach to emission factor development, and better assessment of the drivers of the temporal and spatial variation in emission factors. This paper describes the results of open-path Fourier transform infrared (OP-FTIR) spectroscopic field measurements at 21 fires occurring in the tropical savannas of the Northern~Territory, Australia, within different vegetation assemblages and at different stages of the dry season. Spectra of infrared light passing through a long (22–70 m) open-path through ground-level smoke released from these fires were collected using an infrared lamp and a field-portable FTIR system. The IR spectra were used to retrieve the mole fractions of 14 different gases present within the smoke, and these measurements used to calculate the emission ratios and emission factors of the various gases emitted by the burning. Only a handful of previous emission factor measures are available specifically for the tropical savannas of Australia and here we present the first reported emission factors for methanol, acetic acid, and formic acid for this biome. Given the relatively large sample size, it was possible to study the potential causes of the within-biome variation of the derived emission factors. We find that the emission factors vary substantially between different savanna vegetation assemblages; with a majority of this variation being mirrored by variations in the modified combustion efficiency (MCE) of different vegetation classes. We conclude that a significant majority of the variation in the emission factor for trace gases can be explained by MCE, irrespective of vegetation class, as illustrated by variations in the calculated methane emission factor for different vegetation classes using data sub-set by different combustion efficiencies. Therefore, the selection of emission factors for emissions modelling purposes need not necessarily require detailed fuel type information, if data on MCE (e.g. from future spaceborne total column measurements) or a correlated variable were available. From measurements at 21 fires, we recommend the following emission factors for Australian tropical savanna fires (in grams of gas emitted per kilogram of dry fuel burned), which are our mean measured values: 1674 ± 56 g kg−1 of carbon dioxide; 87 ± 33 g kg−1 of carbon monoxide; 2.1 ± 1.2 g kg−1 of methane; 0.11 ± 0.04 g kg−1 of acetylene; 0.49 ± 0.22 g kg−1 of ethylene; 0.08 ± 0.05 g kg−1 of ethane; 1.57 ± 0.44 g kg−1 of formaldehyde; 1.06 ± 0.87 g kg−1 of methanol; 1.54 ± 0.64 g kg−1 of acetic acid; 0.16 ± 0.07 g kg−1 of formic acid; 0.53 ± 0.31 g kg−1 of hydrogen cyanide; and 0.70 ± 0.36 g kg−1 of ammonia. In a companion paper, similar techniques are used to characterise the emissions from Australian temperate forest fires.

Biomass burning releases trace gases and aerosol particles that significantly affect the composition and chemistry of the atmosphere. Australia contributes approximately 8% of gross global carbon emissions from biomass burning, yet there are few previous measurements of emissions from Australian forest fires available in the literature. This paper describes the results of field measurements of trace gases emitted during hazard reduction burns in Australian temperate forests using open-path Fourier transform infrared spectroscopy. In a companion paper, similar techniques are used to characterise the emissions from hazard reduction burns in the savanna regions of the Northern Territory. Details of the experimental methods are explained, including both the measurement set-up and the analysis techniques employed. The advantages and disadvantages of different ways to estimate whole-fire emission factors are discussed and a measurement uncertainty budget is developed. Emission factors for Australian temperate forest fires are measured locally for the first time for many trace gases. Where ecosystem-relevant data are required, we recommend the following emission factors for Australian temperate forest fires (in grams of gas emitted per kilogram of dry fuel burned) which are our mean measured values: 1620 ± 160 g kg−1 of carbon dioxide; 120 ± 20 g kg−1 of carbon monoxide; 3.6 ± 1.1 g kg−1 of methane; 1.3 ± 0.3 g kg−1 of ethylene; 1.7 ± 0.4 g kg−1 of formaldehyde; 2.4 ± 1.2 g kg−1 of methanol; 3.8 ± 1.3 g kg−1 of acetic acid; 0.4 ± 0.2 g kg−1 of formic acid; 1.6 ± 0.6 g kg−1 of ammonia; 0.15 ± 0.09 g kg−1 of nitrous oxide and 0.5 ± 0.2 g kg−1 of ethane.

Abstract Impaired secretion of an essential blood coagulation factor fibrinogen leads to hepatic fibrinogen storage disease (HFSD), characterized by the presence of fibrinogen-positive inclusion bodies and hypofibrinogenemia. However, the molecular mechanisms underlying the biogenesis of fibrinogen in the endoplasmic reticulum (ER) remain unexplored. Here we uncover a key role of SEL1L-HRD1 complex of ER-associated degradation (ERAD) in the formation of aberrant inclusion bodies, and the biogenesis of nascent fibrinogen protein complex in hepatocytes. Acute or chronic deficiency of SEL1L-HRD1 ERAD in the hepatocytes leads to the formation of hepatocellular inclusion bodies. Proteomics studies followed by biochemical assays reveal fibrinogen as a major component of the inclusion bodies. Mechanistically, we show that the degradation of misfolded endogenous fibrinogen Aα, Bβ, and γ chains by SEL1L-HRD1 ERAD is indispensable for the formation of a functional fibrinogen complex in the ER. Providing clinical relevance of these findings, SEL1L-HRD1 ERAD indeed degrades and thereby attenuates the pathogenicity of two disease-causing fibrinogen γ mutants. Together, this study demonstrates an essential role of SEL1L-HRD1 ERAD in fibrinogen biogenesis and provides insight into the pathogenesis of protein-misfolding diseases.

We report trace-gas emission factors from three pine-understory prescribed fires in South Carolina, US measured during the fall of 2011. The fires were more intense than many prescribed burns because the fuels included mature pine stands not subjected to prescribed fire in decades that were lit following an extended drought. Emission factors were measured with a fixed open-path Fourier transform infrared (OP-FTIR) system that was deployed on the fire control lines. We compare these emission factors to those measured with a roving, point sampling, land-based FTIR and an airborne FTIR deployed on the same fires. We also compare to emission factors measured by a similar OP-FTIR system deployed on savanna fires in Africa. The data suggest that the method used to sample smoke can strongly influence the relative abundance of the emissions that are observed. The majority of fire emissions were lofted in the convection column and were sampled by the airborne FTIR. The roving, ground-based, point sampling FTIR measured the contribution of individual residual smoldering combustion fuel elements scattered throughout the burn site. The OP-FTIR provided a ~ 30 m path-integrated sample of emissions transported to the fixed path via complex ground-level circulation. The OP-FTIR typically probed two distinct combustion regimes, "flaming-like" (immediately after adjacent ignition and before the adjacent plume achieved significant vertical development) and "smoldering-like." These two regimes are denoted "early" and "late", respectively. The path-integrated sample of the ground-level smoke layer adjacent to the fire from the OP-FTIR provided our best estimate of fire-line exposure to smoke for wildland fire personnel. We provide a table of estimated fire-line exposures for numerous known air toxics based on synthesizing results from several studies. Our data suggest that peak exposures are more likely to challenge permissible exposure limits for wildland fire personnel than shift-average (8 h) exposures.

Carbon monoxide (CO) is retrieved daily and globally from space-borne IASI radiance spectra using the Fast Optimal Retrievals on Layers for IASI (FORLI) software developed at the Université Libre de Bruxelles (ULB). The IASI CO total column product for 2008 from the most recent FORLI retrieval version (20100815) is evaluated using correlative CO profile products retrieved from ground-based solar absorption Fourier transform infrared (FTIR) observations at the following FTIR spectrometer sites from the Network for the Detection of Atmospheric Composition Change (NDACC): Ny-Ålesund, Kiruna, Bremen, Jungfraujoch, Izaña and Wollongong. In order to have good statistics for the comparisons, we included all IASI data from the same day, within a 100 km radius around the ground-based stations. The individual ground-based data were adjusted to the lowest altitude of the co-located IASI CO profiles. To account for the different vertical resolutions and sensitivities of the ground-based and satellite measurements, the averaging kernels associated with the various retrieved products have been used to properly smooth coincident data products. It has been found that the IASI CO total column products compare well on average with the co-located ground-based FTIR total columns at the selected NDACC sites and that there is no significant bias for the mean values at all stations.

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.

This paper presents a validation study of SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY) carbon monoxide (CO) total column measurements from the Iterative Maximum Likelihood Method (IMLM) algorithm using ground-based spectrometer observations from twenty surface stations for the five year time period of 2003–2007. Overall we find a good agreement between SCIAMACHY and ground-based observations for both mean values as well as seasonal variations. For high-latitude Northern Hemisphere stations absolute differences between SCIAMACHY and ground-based measurements are close to or fall within the SCIAMACHY CO 2σ precision of 0.2 × 1018 molecules/cm2 (∼10%) indicating that SCIAMACHY can observe CO accurately at high Northern Hemisphere latitudes. For Northern Hemisphere mid-latitude stations the validation is complicated due to the vicinity of emission sources for almost all stations, leading to higher ground-based measurements compared to SCIAMACHY CO within its typical sampling area of 8° × 8°. Comparisons with Northern Hemisphere mountain stations are hampered by elevation effects. After accounting for these effects, the validation provides satisfactory results. At Southern Hemisphere mid- to high latitudes SCIAMACHY is systematically lower than the ground-based measurements for 2003 and 2004, but for 2005 and later years the differences between SCIAMACHY and ground-based measurements fall within the SCIAMACHY precision. The 2003–2004 bias is consistent with previously reported results although its origin remains under investigation. No other systematic spatial or temporal biases could be identified based on the validation presented in this paper. Validation results are robust with regard to the choices of the instrument-noise error filter, sampling area, and time averaging required for the validation of SCIAMACHY CO total column measurements. Finally, our results show that the spatial coverage of the ground-based measurements available for the validation of the 2003–2007 SCIAMACHY CO columns is sub-optimal for validation purposes, and that the recent and ongoing expansion of the ground-based network by carefully selecting new locations may be very beneficial for SCIAMACHY CO and other satellite trace gas measurements validation efforts.

In this paper we describe a new method for estimating trace gas emissions from large vegetation fires using satellite measurements of aerosol optical depth (AOD) at 550 nm, combined with an atmospheric chemical transport model. The method uses a threshold value to screen out normal levels of AOD that may be caused by raised dust, sea salt aerosols or diffuse smoke transported from distant fires. Using this method we infer an estimated total emission of 15±5 Tg of carbon monoxide, 0.05±0.02 Tg of hydrogen cyanide, 0.11±0.03 Tg of ammonia, 0.25±0.07 Tg of formaldehyde, 0.03±0.01 of acetylene, 0.10±0.03 Tg of ethylene, 0.03±0.01 Tg of ethane, 0.21±0.06 Tg of formic acid and 0.28±0.09 Tg of methanol released to the atmosphere from the Canberra fires of 2003. An assessment of the uncertainties in the new method is made and we show that our estimate agrees (within expected uncertainties) with estimates made using current conventional methods of multiplying together factors for the area burned, fuel load, the combustion efficiency and the emission factor for carbon monoxide. A simpler estimate derived directly from the satellite AOD measurements is also shown to be in agreement with conventional estimates, suggesting that the method may, under certain meteorological conditions, be applied without the complication of using a chemical transport model. The new method is suitable for estimating emissions from distinct large fire episodes and although it has some significant uncertainties, these are largely independent of the uncertainties inherent in conventional techniques. Thus we conclude that the new method is a useful additional tool for characterising emissions from vegetation fires.

The LuxS protein, encoded by luxS, is required for the production of autoinducer 2 (AI-2) in Streptococcus pneumoniae. The AI-2 molecule serves as a quorum sensing signal, and thus regulates cellular processes such as carbohydrate utilisation and biofilm formation, as well as impacting virulence. The role of luxS in S. pneumoniae biology and lifestyle has been predominantly assessed in the laboratory strain D39. However, as biofilm formation, which is regulated by luxS, is critical for the ability of S. pneumoniae to cause otitis media, we investigated the role of luxS in a middle ear isolate, strain 947. Our results identified luxS to have a role in prevention of S. pneumoniae transition from colonisation of the nasopharynx to the ear, and in facilitating adherence to host epithelial cells.

Cholesterol is highly abundant within all human body cells and modulates critical cellular functions related to cellular plasticity, metabolism, and survival. The cholesterol-binding toxin pneumolysin represents an essential virulence factor of Streptococcus pneumoniae in establishing pneumonia and other pneumococcal infections. Thus, cholesterol scavenging of pneumolysin is a promising strategy to reduce S. pneumoniae induced lung damage. There may also be a second cholesterol-dependent mechanism whereby pneumococcal infection and the presence of pneumolysin increase hepatic sterol biosynthesis. Here we investigated a library of polymer particles varying in size and composition that allow for the cellular delivery of cholesterol and their effects on cell survival mechanisms following pneumolysin exposure. Intracellular delivery of cholesterol by nanocarriers composed of Eudragit E100–PLGA rescued pneumolysin-induced alterations of lipid homeostasis and enhanced cell survival irrespective of neutralization of pneumolysin.

ABSTRACT Streptococcus pneumoniae is a Gram-Positive pathogen that is a major causative agent of pneumonia, otitis media, sepsis and meningitis across the world. The World Health Organization estimates that globally over 500,000 children are killed each year by this pathogen. Vaccines offer the best protection against S. pneumoniae infections. The current polysaccharide conjugate vaccines have been very effective in reducing rates of invasive pneumococcal disease caused by vaccine type strains. However, the effectiveness of these vaccines have been somewhat diminished by the increasing numbers of cases of invasive disease caused by non-vaccine type strains, a phenomenon known as serotype replacement. Since, there are currently at least 98 known serotypes of S. pneumoniae, it may become cumbersome and expensive to add many additional serotypes to the current 13-valent vaccine, to circumvent the effect of serotype replacement. Hence, alternative serotype independent strategies, such as vaccination with highly cross-reactive pneumococcal protein antigens, should continue to be investigated to address this problem. This chapter provides a comprehensive discussion of pneumococcal vaccines past and present, protein antigens that are currently under investigation as vaccine candidates, and other alternatives, such as the pneumococcal whole cell vaccine, that may be successful in reducing current rates of disease caused by S. pneumoniae.

Shiga toxin-producing E. coli (STEC) produces Stx1 and/or Stx2, and Subtilase cytotoxin (SubAB). Since these toxins may be present simultaneously during STEC infections, the purpose of this work was to study the co-action of Stx2 and SubAB. Stx2 + SubAB was assayed in vitro on monocultures and cocultures of human glomerular endothelial cells (HGEC) with a human proximal tubular epithelial cell line (HK-2) and in vivo in mice after weaning. The effects in vitro of both toxins, co-incubated and individually, were similar, showing that Stx2 and SubAB contribute similarly to renal cell damage. However, in vivo, co-injection of toxins lethal doses reduced the survival time of mice by 24 h and mice also suffered a strong decrease in the body weight associated with a lowered food intake. Co-injected mice also exhibited more severe histological renal alterations and a worsening in renal function that was not as evident in mice treated with each toxin separately. Furthermore, co-treatment induced numerous erythrocyte morphological alterations and an increase of free hemoglobin. This work shows, for the first time, the in vivo effects of Stx2 and SubAB acting together and provides valuable information about their contribution to the damage caused in STEC infections.