43 results on '"Sarah Moller"'
Search Results
2. Effect of direct-acting antivirals on the titers of human pegivirus 1 during treatment of chronic hepatitis C patients
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Ulrik Fahnøe, Lone Wulff Madsen, Peer Brehm Christensen, Christina Søhoel Sølund, Sarah Mollerup, Mette Pinholt, Nina Weis, Anne Øvrehus, and Jens Bukh
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human pegivirus ,HPgV-1 ,hepatitis C virus ,HCV ,coinfection ,direct-acting antivirals ,Microbiology ,QR1-502 - Abstract
ABSTRACT Coinfections with human pegivirus 1 (HPgV-1) are common in chronic hepatitis C virus (HCV) patients. However, little is known about whether HPgV-1 is affected by direct-acting antivirals during HCV treatment. Metagenomic analysis and reverse transcriptase-quantitative PCR (RT-qPCR) were performed on RNA from the plasma of 88 selected chronic HCV patients undergoing medical treatment. Twenty (23%) of these HCV patients had HPgV-1 coinfections and were followed by RT-qPCR during treatment and follow-up to investigate HPgV-1 RNA titers. Recovered sequences could be assembled to complete HPgV-1 genomes, and most formed a genotype 2 subclade. All HPgV-1 viral genomic regions were under negative purifying selection. Glecaprevir/pibrentasvir treatment in five patients did not consistently lower the genome titers of HPgV-1. In contrast, a one log10 drop of HPgV-1 titers at week 2 was observed in 10 patients during treatment with sofosbuvir-containing regimens, sustained to the end of treatment (EOT) and in two cases decreasing to below the detection limit of the assay. For the five patients treated with ledipasvir/sofosbuvir with the inclusion of pegylated interferon, titers decreased to below the detection limit at week 2 and remained undetectable to EOT. Subsequently, the HPgV-1 titer rebounded to pretreatment levels for all patients. In conclusion, we found that HCV treatment regimens that included the polymerase inhibitor sofosbuvir resulted in decreases in HPgV-1 titers, and the addition of pegylated interferon increased the effect on patients with coinfections. This points to the high specificity of protease and NS5A inhibitors toward HCV and the more broad-spectrum activity of sofosbuvir and especially pegylated interferon.IMPORTANCEHuman pegivirus 1 coinfections are common in hepatitis C virus (HCV) patients, persisting for years. However, little is known about how pegivirus coinfections are affected by treatment with pangenotypic direct-acting antivirals (DAAs) against HCV. We identified human pegivirus by metagenomic analysis of chronic HCV patients undergoing protease, NS5A, and polymerase inhibitor treatment, in some patients with the addition of pegylated interferon, and followed viral kinetics of both viruses to investigate treatment effects. Only during HCV DAA treatment regimens that included the more broad-spectrum drug sofosbuvir could we detect a consistent decline in pegivirus titers that, however, rebounded to pretreatment levels after treatment cessation. The addition of pegylated interferon gave the highest effect with pegivirus titers decreasing to below the assay detection limit, but without clearance. These results reveal the limited effect of frontline HCV drugs on the closest related human virus, but sofosbuvir appeared to have the potential to be repurposed for other viral diseases.
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- 2024
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3. Impacts of bromine and iodine chemistry on tropospheric OH and HO2: comparing observations with box and global model perspectives
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Peter Edwards, Stewart Vaughan, Alastair C. Lewis, Daniel Stone, Mathew J. Evans, Sarah Moller, James D. Lee, Dwayne E. Heard, Lisa K. Whalley, Tomás Sherwen, Katie A. Read, Trevor Ingham, and Lucy J. Carpenter
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Atmospheric Science ,Bromine ,Ozone ,010504 meteorology & atmospheric sciences ,Chemistry ,Radical ,Photodissociation ,chemistry.chemical_element ,010501 environmental sciences ,Atmospheric sciences ,01 natural sciences ,Tropospheric ozone depletion events ,Troposphere ,Cape verde ,chemistry.chemical_compound ,13. Climate action ,Climatology ,Halogen ,0105 earth and related environmental sciences - Abstract
The chemistry of the halogen species bromine and iodine has a range of impacts on tropospheric composition, and can affect oxidising capacity in a number of ways. However, recent studies disagree on the overall sign of the impacts of halogens on the oxidising capacity of the troposphere. We present simulations of OH and HO2 radicals for comparison with observations made in the remote tropical ocean boundary layer during the Seasonal Oxidant Study at the Cape Verde Atmospheric Observatory in 2009. We use both a constrained box model, using detailed chemistry derived from the Master Chemical Mechanism (v3.2), and the three-dimensional global chemistry transport model GEOS-Chem. Both model approaches reproduce the diurnal trends in OH and HO2. Absolute observed concentrations are well reproduced by the box model but are overpredicted by the global model, potentially owing to incomplete consideration of oceanic sourced radical sinks. The two models, however, differ in the impacts of halogen chemistry. In the box model, halogen chemistry acts to increase OH concentrations (by 9.8 % at midday at the Cape Verde Atmospheric Observatory), while the global model exhibits a small increase in OH at the Cape Verde Atmospheric Observatory (by 0.6 % at midday) but overall shows a decrease in the global annual mass-weighted mean OH of 4.5 %. These differences reflect the variety of timescales through which the halogens impact the chemical system. On short timescales, photolysis of HOBr and HOI, produced by reactions of HO2 with BrO and IO, respectively, increases the OH concentration. On longer timescales, halogen-catalysed ozone destruction cycles lead to lower primary production of OH radicals through ozone photolysis, and thus to lower OH concentrations. The global model includes more of the longer timescale responses than the constrained box model, and overall the global impact of the longer timescale response (reduced primary production due to lower O3 concentrations) overwhelms the shorter timescale response (enhanced cycling from HO2 to OH), and thus the global OH concentration decreases. The Earth system contains many such responses on a large range of timescales. This work highlights the care that needs to be taken to understand the full impact of any one process on the system as a whole.
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- 2018
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4. A trend analysis approach for air quality network data
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David C. Carslaw, Polly E. Lang, and Sarah Moller
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Pollutant ,Atmospheric Science ,Air pollutant concentrations ,Network data ,lcsh:QC851-999 ,Regression ,Trend analysis ,lcsh:Environmental pollution ,Statistics ,lcsh:TD172-193.5 ,Leverage (statistics) ,Environmental science ,lcsh:Meteorology. Climatology ,Air quality index ,NOx ,General Environmental Science - Abstract
Trend analysis of air pollutant concentrations becomes problematic when applied to data from air quality monitoring networks containing time series of differing lengths. The average trend from such data can be misleading due to biases in the monitoring network. For example, if new monitoring sites located in more polluted locations are added to a network, the introduction of these time series can leverage the trend upwards. A method for resolving this problem was developed, using rolling window regression to recursively calculate the change in pollutant concentration as a function of time, which can be used as a proxy for the true trend. The efficacy of the method was established by conducting simulations with known trends. The rolling change trend was shown to more accurately reflect the true trend than simply averaging the time series. Application of the technique to estimate trends in NOx, NO2 and NO2/NOx concentrations at London roadside monitoring sites over the period 2000–2017 revealed clear differences from the simple average. In particular, a significant monotonic downward trend in NOx concentration was observed, in stark contrast to the average trend, which suggested little change in NOx concentration had occurred over the same period. By accurately representing trends using time series of different lengths, this method has the benefit of being able to describe changes in air quality for locations and time periods with otherwise insufficient data. Keywords: Air quality, Monitoring network, Trend analysis, Bias, Rolling regression
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- 2019
5. Supplementary material to 'Demystifying academics to enhance university–business collaborations in environmental science'
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John K. Hillier, Geoffrey Saville, Mike J. Smith, Alister J. Scott, Emma K. Raven, Jonathan Gascoigne, Louise Slater, Nevil Quinn, Andreas Tsanakas, Claire Souch, Gregor C. Leckebusch, Neil Macdonald, Jennifer Loxton, Rebecca Wilebore, Alexandra Collins, Colin MacKechnie, Jaqui Tweddle, Alice M. Milner, Sarah Moller, MacKenzie Dove, Harry Langford, and Jim Craig
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- 2018
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6. Properties and evolution of biomass burning organic aerosol from Canadian boreal forest fires
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Paul I. Palmer, Matthew D. Jolleys, James D. Lee, Sarah Moller, Hugh Coe, Gordon McFiggans, P. Di Carlo, Sebastian O'Shea, Eleonora Aruffo, Stephane Bauguitte, M. Le Breton, Carl J. Percival, Jonathan Taylor, and Martin Gallagher
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biomass burning ,Atmospheric Science ,aerosol ,oxidation ,combustion fire ,Atmospheric sciences ,Combustion ,atmospheric plume ,lcsh:Chemistry ,Troposphere ,boreal forest ,NOx ,Smouldering ,aerosol composition ,Taiga ,15. Life on land ,lcsh:QC1-999 ,Plume ,Aerosol ,Dilution ,troposphere ,lcsh:QD1-999 ,13. Climate action ,Climatology ,Environmental science ,lcsh:Physics - Abstract
Airborne measurements of biomass burning organic aerosol (BBOA) from boreal forest fires reveal highly contrasting properties for plumes of different ages. These measurements, performed using an Aerodyne Research Inc. compact time-of-flight aerosol mass spectrometer (C-ToF-AMS) during the BORTAS (quantifying the impact of BOReal forest fires on Tropospheric oxidants over the Atlantic using Aircraft and Satellites) experiment in the summer of 2011, have been used to derive normalised excess organic aerosol (OA) mass concentrations (ΔOA / ΔCO), with higher average ratios observed closer to source (0.190±0.010) than in the far-field (0.097±0.002). The difference in ΔOA / ΔCO between fresh and aged plumes is influenced by a change in dominant combustion conditions throughout the campaign. Measurements at source comprised 3 plume interceptions during a single research flight and sampled largely smouldering fires. Twenty-three interceptions were made across four flights in the far-field, with plumes originating from fires occurring earlier in the campaign when fire activity had been more intense, creating an underlying contrast in emissions prior to any transformations associated with aging. Changing combustion conditions also affect the vertical distribution of biomass burning emissions, as aged plumes from more flaming-dominated fires are injected to higher altitudes of up to 6000 m. Proportional contributions of the mass-to-charge ratio (m/z) 60 and 44 peaks in the AMS mass spectra to the total OA mass (denoted f60 and f44) are used as tracers for primary and oxidised BBOA, respectively. f44 is lower on average in near-field plumes than those sampled in the far-field, in accordance with longer aging times as plumes are transported a greater distance from source. However, high levels of ΔO3 / ΔCO and −log(NOx / NOy) close to source indicate that emissions can be subject to very rapid oxidation over short timescales. Conversely, the lofting of plumes into the upper troposphere can lead to the retention of source profiles after transportation over extensive temporal and spatial scales, with f60 also higher on average in aged plumes. Evolution of OA composition with aging is comparable to observations of BB tracers in previous studies, revealing a consistent progression from f60 to f44. The elevated levels of oxygenation in aged plumes, and their association with lower average ΔOA / ΔCO, are consistent with OA loss through evaporation during aging due to a combination of dilution and chemical processing, while differences in combustion conditions throughout the campaign also have a significant influence on BBOA production and composition.
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- 2015
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7. Supplementary material to 'Analysis of the distributions of hourly NO2 concentrations contributing to annual average NO2 concentrations across the European monitoring network between 2000 and 2014'
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Christopher S. Malley, Erika von Schneidemesser, Sarah Moller, Christine F. Braban, W. Kevin Hicks, and Mathew R. Heal
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- 2017
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8. Analysis of the distributions of hourly NO2 concentrations contributing to annual average NO2 concentrations across the European monitoring network between 2000 and 2014
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Christopher S. Malley, Erika von Schneidemesser, Sarah Moller, Christine F. Braban, W. Kevin Hicks, and Mathew R. Heal
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Exposure to nitrogen dioxide (NO2) is associated with negative human health effects, both for short-term peak concentrations and from long-term exposure to a wider range of NO2 concentrations. For the latter, the European Union has established an air quality limit value of 40 µg m−3 as an annual average. However, factors such as proximity and strength of local emissions, atmospheric chemistry and meteorological conditions means that there is substantial variation in the hourly NO2 concentrations contributing to an annual average concentration. The aim of this analysis was to quantify the nature of this variation at thousands of monitoring sites across Europe through the calculation of a standard set of chemical climatology statistics. Specifically, at each monitoring site that satisfied data capture criteria for inclusion in this analysis, annual NO2 concentrations, as well as the percentage contribution from each month, hour of the day, and hourly NO2 concentrations divided into 5 µg m−3 bins were calculated. Across Europe, 2010–2014 average annual NO2 concentrations (NO2AA) exceeded the annual NO2 limit value at 8 % of > 2500 monitoring sites. The application of this chemical climatology approach showed that sites with distinct monthly, hour of day, and hourly NO2 concentration bin contributions to NO2AA were not grouped in specific regions of Europe, and within relatively small geographic regions there were sites with similar NO2AA, but with differences in these contributions. Specifically, at sites with highest NO2AA, there were generally similar contributions from across the year, but there were also differences in the contribution of peak vs moderate hourly NO2 concentrations to NO2AA, and from different hours across the day. Trends between 2000 and 2014 for 259 sites indicate that, in general, the contribution to NO2AA from winter months has increased, as has the contribution from the rush-hour periods of the day, while the contribution from peak hourly NO2 concentrations has decreased. The variety of monthly, hour of day and hourly NO2 contribution bin contributions to NO2AA, across cities, countries and regions of Europe indicate that within relatively small geographic areas different interactions between emissions, atmospheric chemistry and meteorology produce variation in NO2AA and the conditions that produce it. Therefore, measures implemented to reduce NO2AA in one location may not be as effective in others. The development of strategies to reduce NO2AA for an area should consider i) the variation in monthly, hour of day and hourly NO2 concentration bin contributions to NO2AA within that area, and ii) how specific mitigation actions will affect variability in hourly NO2 concentrations.
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- 2017
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9. Ozone photochemistry in boreal biomass burning plumes
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Sarah Moller, Stephane Bauguitte, Roland Leigh, P. Di Carlo, David E. Oram, James R. Hopkins, Shalini Punjabi, James D. Lee, Jonathan Taylor, Eleonora Aruffo, A. C. Lewis, James Allan, Andrew R. Rickard, G. Forster, Paul I. Palmer, Hugh Coe, and Mark Parrington
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Atmospheric Science ,Ozone ,Planetary boundary layer ,ozone ,forest fire ,pollution ,Atmospheric sciences ,power-plant plumes ,induced fluorescence instrument ,lcsh:Chemistry ,Troposphere ,chemistry.chemical_compound ,atmospheric composition ,Relative humidity ,Tropospheric ozone ,tropospheric ozone ,Chemistry ,boundary-layer ,volatile organic-compounds ,fast-response ,high northern latitudes ,lcsh:QC1-999 ,Aerosol ,Plume ,black carbon measurements ,nitrogen-oxides ,lcsh:QD1-999 ,Boreal ,lcsh:Physics - Abstract
We present an analysis of ozone (O3) photochemistry observed by aircraft measurements of boreal biomass burning plumes over eastern Canada in the summer of 2011. Measurements of O3 and a number of key chemical species associated with O3 photochemistry, including non-methane hydrocarbons (NMHCs), nitrogen oxides (NOx) and total nitrogen containing species (NOy), were made from the UK FAAM BAe-146 research aircraft as part of the "quantifying the impact of BOReal forest fires on Tropospheric oxidants over the Atlantic using Aircraft and Satellites" (BORTAS) experiment between 12 July and 3 August 2011. The location and timing of the aircraft measurements put BORTAS into a unique position to sample biomass burning plumes from the same source region in Northwestern Ontario with a range of ages. We found that O3 mixing ratios measured in biomass burning plumes were indistinguishable from non-plume measurements, but evaluating them in relationship to measurements of carbon monoxide (CO), total alkyl nitrates (ΣAN) and the surrogate species NOz (= NOy-NOx) revealed that the potential for O3 production increased with plume age. We used NMHC ratios to estimate photochemical ages of the observed biomass burning plumes between 0 and 10 days. The BORTAS measurements provided a wide dynamic range of O3 production in the sampled biomass burning plumes with ΔO3/ΔCO enhancement ratios increasing from 0.020 ± 0.008 ppbv ppbv−1 in plumes with photochemical ages less than 2 days to 0.55 ± 0.29 ppbv ppbv−1 in plumes with photochemical ages greater than 5 days. We found that the main contributing factor to the variability in the ΔO3/ΔCO enhancement ratio was ΔCO in plumes with photochemical ages less than 4 days, and that was a transition to ΔO3 becoming the main contributing factor in plumes with ages greater than 4 days. In comparing O3 mixing ratios with components of the NOy budget, we observed that plumes with ages between 2 and 4 days were characterised by high aerosol loading, relative humidity greater than 40%, and low ozone production efficiency (OPE) of 7.7 ± 3.5 ppbv ppbv−1 relative to ΣAN and 1.6 ± 0.9 ppbv ppbv−1 relative to NOz. In plumes with ages greater than 4 days, OPE increased to 472 ± 28 ppbv ppbv−1 relative to ΣAN and 155 ± 5 ppbv ppbv−1 relative to NOz. From the BORTAS measurements we estimated that aged plumes with low aerosol loading were close to being in photostationary steady state and O3 production in younger plumes was inhibited by high aerosol loading and greater production of ΣAN relative to O3. The BORTAS measurements of O3 photochemistry in boreal biomass burning plumes were found to be consistent with previous summertime aircraft measurements made over the same region during the Arctic Research of the Composition of the Troposphere (ARCTAS-B) in 2008 and Atmospheric Boundary Layer Experiment (ABLE 3B) in 1990.
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- 2013
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10. Quantifying the impact of BOReal forest fires on Tropospheric oxidants over the Atlantic using Aircraft and Satellites (BORTAS) experiment: design, execution and science overview
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Stephane Bauguitte, D. L. Waugh, Paul I. Palmer, K. M. Rotermund, Keith Tereszchuk, G. Forster, A. da Silva, M. Le Breton, Eleonora Aruffo, Sebastian O'Shea, R. Trigwell, Camille Pagniello, Ruth Purvis, E. Barrett, Michael E. Jenkin, D. Kindred, Mark D. Gibson, Debora Griffin, J. E. Franklin, J. Kliever, L. J. Bailey, Thomas J. Duck, Sarah Moller, Kimberly Strong, M. Maurice, James R. Hopkins, P. Di Carlo, Kaley A. Walker, Carl J. Percival, Stephan Matthiesen, Stephen J. Andrews, Peter F. Bernath, J. C. Young, Kevin Strawbridge, Detlev Helmig, Jason Hopper, Jeffrey R. Pierce, James D. Lee, David W. Tarasick, David Moore, K. R. Curry, Robert Owen, Andrew R. Rickard, David E. Oram, Lucy Chisholm, Cynthia H. Whaley, A. C. Lewis, S. Pawson, John Remedios, K. M. Sakamoto, L. Dan, Shalini Punjabi, Jonathan Taylor, Mark Parrington, and Dan Weaver
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Atmospheric Science ,Ozone ,010504 meteorology & atmospheric sciences ,010501 environmental sciences ,Atmospheric sciences ,01 natural sciences ,7. Clean energy ,Troposphere ,lcsh:Chemistry ,chemistry.chemical_compound ,0105 earth and related environmental sciences ,geography ,geography.geographical_feature_category ,Taiga ,Particulates ,lcsh:QC1-999 ,Aerosol ,Volcano ,chemistry ,Boreal ,lcsh:QD1-999 ,13. Climate action ,Environmental science ,Satellite ,lcsh:Physics - Abstract
We describe the design and execution of the BORTAS (Quantifying the impact of BOReal forest fires on Tropospheric oxidants using Aircraft and Satellites) experiment, which has the overarching objective of understanding the chemical aging of airmasses that contain the emission products from seasonal boreal wildfires and how these airmasses subsequently impact downwind atmospheric composition. The central focus of the experiment was a two-week deployment of the UK BAe-146-301 Atmospheric Research Aircraft (ARA) over eastern Canada. The planned July 2010 deployment of the ARA was postponed by 12 months because of activities related to the dispersal of material emitted by the Eyjafjallajökull volcano. However, most other planned model and measurement activities, including ground-based measurements at the Dalhousie University Ground Station (DGS), enhanced ozonesonde launches, and measurements at the Pico Atmospheric Observatory in the Azores, went ahead and constituted phase A of the experiment. Phase B of BORTAS in July 2011 included the same measurements, but included the ARA, special satellite observations and a more comprehensive measurement suite at the DGS. The high-frequency aircraft data provided a comprehensive snapshot of the pyrogenic plumes from wildfires. The coordinated ground-based and sonde data provided detailed but spatially-limited information that put the aircraft data into context of the longer burning season. We coordinated aircraft vertical profiles and overpasses of the NASA Tropospheric Emission Spectrometer and the Canadian Atmospheric Chemistry Experiment. These space-borne data, while less precise than other data, helped to relate the two-week measurement campaign to larger geographical and longer temporal scales. We interpret these data using a range of chemistry models: from a near-explicit gas-phase chemical mechanism, which tests out understanding of the underlying chemical mechanism, to regional and global 3-D models of atmospheric transport and lumped chemistry, which helps to assess the performance of the simplified chemical mechanism and effectively act as intermediaries between different measurement types. We also present an overview of some of the new science that has originated from this project from the mission planning and execution to the analysis of the ground-based, aircraft, and space-borne data.
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- 2013
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11. The influence of biomass burning on the global distribution of selected non-methane organic compounds
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Alastair C. Lewis, Sarah Moller, Andrew R. Rickard, Stephen J. Andrews, Paul I. Palmer, Mathew J. Evans, Shalini Punjabi, Lucy J. Carpenter, Mark Parrington, James D. Lee, James R. Hopkins, Katie A. Read, and Ruth Purvis
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Atmospheric Science ,Chemical transport model ,IMPACT ,FOREST-FIRE PLUMES ,SMOKE ,TRACE GASES ,Biomass ,Methane ,lcsh:Chemistry ,Atmosphere ,chemistry.chemical_compound ,Benzene ,Air quality index ,EMISSIONS ,Pollutant ,lcsh:QC1-999 ,Trace gas ,MODEL ,CO ,CANADA ,lcsh:QD1-999 ,chemistry ,Environmental chemistry ,HYDROCARBONS ,lcsh:Physics ,COMPREHENSIVE LABORATORY MEASUREMENTS - Abstract
Forests fires are a significant source of chemicals to the atmosphere including numerous non-methane organic compounds (NMOCs). We report airborne measurement of hydrocarbons, acetone and methanol from >500 whole air samples collected over Eastern Canada, including interceptions of several different boreal biomass burning plumes. From these and concurrent measurements of carbon monoxide (CO) we derive fire emission ratios for 29 different organic species relative to the emission of CO. These range from 8.9 ± 3.2 ppt ppb−1 CO for methanol to 0.007 ± 0.004 ppt ppb−1 CO for cyclopentane. The ratios are in good to excellent agreement with literature values. Using the GEOS-Chem global 3-D chemical transport model (CTM) we show the influence of biomass burning on the global distributions of benzene, toluene, ethene and propene (species which are controlled for air quality purposes and sometimes used as indicative tracers of anthropogenic activity). Using our observationally derived emission ratios and the GEOS-Chem CTM, we show that biomass burning can be the largest fractional contributor to observed benzene, toluene, ethene and propene levels in many global locations. The widespread biomass burning contribution to atmospheric benzene, a heavily regulated air pollutant, suggests that pragmatic approaches are needed when setting air quality targets as tailpipe and solvent emissions decline in developed countries. We subsequently determine the extent to which the 28 global-status World Meteorological Organisation – Global Atmosphere Watch stations worldwide are influenced by biomass burning sourced benzene, toluene, ethene and propene as compared to their exposure to anthropogenic emissions.
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- 2013
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12. Urban case studies : general discussion
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Ruth Purvis, Neil M. Donahue, Zhe Tian, Andreas Wahner, Andreas N. Skouloudis, Xavier Querol, Tim P. Murrells, Zongbo Shi, Astrid Kiendler-Scharr, Timothy J. Wallington, Tzer Ren Ho, Franz M. Geiger, Urs Baltensperger, Spyros N. Pandis, Aurélie Charron, André S. H. Prévôt, María Cruz Minguillón, Nivedita K. Kumar, Costas Sioutas, C. N. Hewitt, Athanasia Vlachou, Markus Kalberer, Gary Fuller, Matthew Hort, Thomas Karl, William H. Brune, Francis D. Pope, Jose L. Jimenez, Dominik van Pinxteren, Simone M. Pieber, William J. Bloss, Martin M. Shafer, Alison S. Tomlin, E.J.S. Mitchell, Christian Ehlers, Claudia Mohr, Louisa Kramer, Sarah Moller, James D. Lee, Rob MacKenzie, Paul S. Monks, Gordon McFiggans, Rachel Dunmore, Brian C. McDonald, Dwayne E. Heard, David C. Carslaw, Roy M. Harrison, Eben S. Cross, Department of Chemistry, King‘s College London, University of Birmingham, Laboratoire Transports et Environnement (IFSTTAR/AME/LTE), and Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Université de Lyon
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Aerosols ,[SPI.OTHER]Engineering Sciences [physics]/Other ,010504 meteorology & atmospheric sciences ,010501 environmental sciences ,01 natural sciences ,Mass Spectrometry ,TRAFFIC EMISSIONS ,Air Pollution ,POLLUTION ATMOSPHERIQUE ,Environmental science ,Nitrogen Oxides ,Particulate Matter ,[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie ,Cities ,URBAN ATMOSPHERE ,Physical and Theoretical Chemistry ,EMISSION ,ATMOSPHERIC CHEMISTRY ,MILIEU URBAIN ,0105 earth and related environmental sciences - Abstract
Urban case studies: general discussion
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- 2016
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13. Energy and ozone fluxes over sea ice
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Sarah Moller, Alexander T. Archibald, James D. Lee, Lucy J. Carpenter, Howard K. Roscoe, Helen M. Atkinson, Carl J. Percival, Rachel W. Obbard, Michael Flynn, Dudley E. Shallcross, James Dorsey, Jennifer B. A. Muller, and Martin Gallagher
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Atmospheric Science ,geography ,Ozone ,geography.geographical_feature_category ,010504 meteorology & atmospheric sciences ,Radiative cooling ,Eddy covariance ,010501 environmental sciences ,Atmospheric sciences ,01 natural sciences ,Atmosphere ,chemistry.chemical_compound ,Flux (metallurgy) ,chemistry ,Heat flux ,13. Climate action ,Climatology ,Sea ice ,Surface layer ,0105 earth and related environmental sciences ,General Environmental Science - Abstract
We present surface layer measurements made over Hudson Bay sea ice during February/March 2008 from the COBRA (Impact of combined iodine and bromine release on the Arctic atmosphere) experiment which formed part of the International OASIS (Ocean-Atmosphere-Sea Ice-Snowpack) IPY programme. All components of the local surface energy balance were measured and it was defined by net radiative cooling throughout most of the day, mainly balanced by the conductive heat flux from the warmer sea water to the cooler sea ice at the surface, and a small net radiative warming for a few hours after midday. Unique ground-level ozone fluxes were measured by eddy covariance and deposition velocities ranged from +0.5 mm s(-1) (deposition) to -1.5 mm s(-1) (emission). Ozone profile measurements suggested ozone flux divergence within the surface layer. The observed bi-directional fluxes and flux divergence with height reveal the complexity of surface ozone fluxes in the Arctic spring time surface layer, and show that ozone exchange with the sea ice surface is best probed using the eddy covariance method alongside frequent or continuous profile measurements. In this study, the local in-situ ozone-halogen photochemistry was identified as weakly controlling the measured ozone flux, whereas horizontal advection and vertical mixing were considered more important in influencing fluxes. Under these conditions, several measurement sites would be desirable in order to quantify the contribution of advection to the local surface exchange. (C) 2011 Elsevier Ltd. All rights reserved.
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- 2012
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14. The impact of local surface changes in Borneo on atmospheric composition at wider spatial scales: coastal processes, land-use change and air quality
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Ute Skiba, S. E. Yong, Glenn Carver, Noorsaadah Abdul Rahman, Pawel K. Misztal, Thomas P. Kurosu, Mohd Radzi Abas, B. Gostlow, Andrew Robinson, Kelly Chance, Alistair J. Manning, M. P. Barkley, Mohd Shahrul Mohd Nadzir, Justin Sentian, Eiko Nemitz, S. Ong, M. J. Ashfold, Siew-Moi Phang, James D. Lee, Huan Eng Ung, James Dorsey, Paul Young, Alexander T. Archibald, Graham P. Mills, Leong Kok Peng, Hannah Newton, C. N. Hewitt, Thomas A. M. Pugh, L. M. O'Brien, A. R. MacKenzie, David Fowler, Azizan Abu Samah, S. B. Langford, Sarah Moller, Kirsti Ashworth, Nicola Warwick, Siegfried Gonzi, Paul I. Palmer, John A. Pyle, David E. Oram, R. C. Pike, and Neil R. P. Harris
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Air pollution ,Atmospheric model ,Arecaceae ,medicine.disease_cause ,Atmospheric sciences ,General Biochemistry, Genetics and Molecular Biology ,Trees ,Troposphere ,chemistry.chemical_compound ,Hemiterpenes ,Ozone ,Borneo ,Air Pollution ,Formaldehyde ,Pentanes ,Tropical climate ,Butadienes ,medicine ,Computer Simulation ,Land use, land-use change and forestry ,Tropospheric ozone ,Air quality index ,Stratosphere ,Tropical Climate ,Volatile Organic Compounds ,Atmosphere ,Ecology ,Malaysia ,Agriculture ,Articles ,Bromine ,chemistry ,Environmental science ,Nitrogen Oxides ,General Agricultural and Biological Sciences ,Oxidation-Reduction ,Carbanilides - Abstract
We present results from the OP3 campaign in Sabah during 2008 that allow us to study the impact of local emission changes over Borneo on atmospheric composition at the regional and wider scale. OP3 constituent data provide an important constraint on model performance. Treatment of boundary layer processes is highlighted as an important area of model uncertainty. Model studies of land-use change confirm earlier work, indicating that further changes to intensive oil palm agriculture in South East Asia, and the tropics in general, could have important impacts on air quality, with the biggest factor being the concomitant changes in NO x emissions. With the model scenarios used here, local increases in ozone of around 50 per cent could occur. We also report measurements of short-lived brominated compounds around Sabah suggesting that oceanic (and, especially, coastal) emission sources dominate locally. The concentration of bromine in short-lived halocarbons measured at the surface during OP3 amounted to about 7 ppt, setting an upper limit on the amount of these species that can reach the lower stratosphere.
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- 2011
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15. Quantifying the magnitude of a missing hydroxyl radical source in a tropical rainforest
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Andrew Goddard, K. L. Furneaux, James R. Hopkins, Lisa K. Whalley, Mathew J. Evans, James D. Lee, Peter Edwards, Sarah Moller, A. Karunaharan, Paul S. Monks, Trevor Ingham, C. E. Jones, Alastair C. Lewis, Daniel Stone, and Dwayne E. Heard
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Hydrology ,Atmospheric Science ,Photodissociation ,Humidity ,lcsh:QC1-999 ,Methane ,lcsh:Chemistry ,Troposphere ,chemistry.chemical_compound ,lcsh:QD1-999 ,chemistry ,Environmental chemistry ,Hydroxyl radical ,lcsh:Physics ,Isoprene ,Tropical rainforest - Abstract
The lifetime of methane is controlled to a very large extent by the abundance of the OH radical. The tropics are a key region for methane removal, with oxidation in the lower tropical troposphere dominating the global methane removal budget (Bloss et al., 2005). In tropical forested environments where biogenic VOC emissions are high and NOx concentrations are low, OH concentrations are assumed to be low due to rapid reactions with sink species such as isoprene. New, simultaneous measurements of OH concentrations and OH reactivity, k'OH, in a Borneo rainforest are reported and show much higher OH than predicted, with mean peak concentrations of ~2.5×106 molecule cm−3 (10 min average) observed around solar noon. Whilst j(O1D) and humidity were high, low O3 concentrations limited the OH production from O3 photolysis. Measured OH reactivity was very high, peaking at a diurnal average of 29.1±8.5 s−1, corresponding to an OH lifetime of only 34 ms. To maintain the observed OH concentration given the measured OH reactivity requires a rate of OH production approximately 10 times greater than calculated using all measured OH sources. A test of our current understanding of the chemistry within a tropical rainforest was made using a detailed zero-dimensional model to compare with measurements. The model over-predicted the observed HO2 concentrations and significantly under-predicted OH concentrations. Inclusion of an additional OH source formed as a recycled product of OH initiated isoprene oxidation improved the modelled OH agreement but only served to worsen the HO2 model/measurement agreement. To replicate levels of both OH and HO2, a process that recycles HO2 to OH is required; equivalent to the OH recycling effect of 0.74 ppbv of NO. This recycling step increases OH concentrations by 88 % at noon and has wide implications, leading to much higher predicted OH over tropical forests, with a concomitant reduction in the CH4 lifetime and increase in the rate of VOC degradation.
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- 2011
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16. Seasonal characteristics of tropical marine boundary layer air measured at the Cape Verde Atmospheric Observatory
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Conny Müller, Udo Frieß, Jens Tschritter, Trevor Ingham, Stewart Vaughan, Alfred Wiedensohler, Steve R. Arnold, John M. C. Plane, Denis Pöhler, Mathew J. Evans, A. Karunaharan, Thomas Müller, H. Lopez, Zoe L. Fleming, Eric P. Achterberg, Matthew D. Patey, N. Niedermeier, Roland Leigh, Konrad Müller, Hartmut Herrmann, Alastair C. Lewis, Lisa K. Whalley, Hilke Oetjen, Douglas W.R. Wallace, Bernd Heinold, Elena Kozlova, Ina Tegen, Sarah Moller, Martin Heimann, Katie A. Read, Robert Holla, Michael J. Pilling, K. Wadinga Fomba, Ruth Purvis, James R. Hopkins, Daniel Stone, James D. Lee, L. M. Mendes, Anoop S. Mahajan, B. Faria, Dwayne E. Heard, D. van Pinxteren, Lucy J. Carpenter, Paul S. Monks, and Alistair J. Manning
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Cape verde ,Atmospheric Science ,Deposition (aerosol physics) ,Environmental Chemistry ,Mineral dust ,Particulates ,Atmospheric sciences ,Air quality index ,Air mass ,Trace gas ,Aerosol - Abstract
Observations of the tropical atmosphere are fundamental to the understanding of global changes in air quality, atmospheric oxidation capacity and climate, yet the tropics are under-populated with long-term measurements. The first three years (October 2006–September 2009) of meteorological, trace gas and particulate data from the global WMO/Global Atmospheric Watch (GAW) Cape Verde Atmospheric Observatory Humberto Duarte Fonseca (CVAO; 16° 51′ N, 24° 52′ W) are presented, along with a characterisation of the origin and pathways of air masses arriving at the station using the NAME dispersion model and simulations of dust deposition using the COSMO-MUSCAT dust model. The observations show a strong influence from Saharan dust in winter with a maximum in super-micron aerosol and particulate iron and aluminium. The dust model results match the magnitude and daily variations of dust events, but in the region of the CVAO underestimate the measured aerosol optical thickness (AOT) because of contributions from other aerosol. The NAME model also captured the dust events, giving confidence in its ability to correctly identify air mass origins and pathways in this region. Dissolution experiments on collected dust samples showed a strong correlation between soluble Fe and Al and measured solubilities were lower at high atmospheric dust concentrations. Fine mode aerosol at the CVAO contains a significant fraction of non-sea salt components including dicarboxylic acids, methanesulfonic acid and aliphatic amines, all believed to be of oceanic origin. A marine influence is also apparent in the year-round presence of iodine and bromine monoxide (IO and BrO), with IO suggested to be confined mainly to the surface few hundred metres but BrO well mixed in the boundary layer. Enhanced CO2 and CH4 and depleted oxygen concentrations are markers for air-sea exchange over the nearby northwest African coastal upwelling area. Long-range transport results in generally higher levels of O3 and anthropogenic non-methane hydrocarbons (NMHC) in air originating from North America. Ozone/CO ratios were highest (up to 0.42) in relatively fresh European air masses. In air heavily influenced by Saharan dust the O3/CO ratio was as low as 0.13, possibly indicating O3 uptake to dust. Nitrogen oxides (NOx and NOy) show generally higher concentrations in winter when air mass origins are predominantly from Africa. High photochemical activity at the site is shown by maximum spring/summer concentrations of OH and HO2 of 9 × 106 molecule cm−3 and 6 × 108 molecule cm−3, respectively. After the primary photolysis source, the most important controls on the HOx budget in this region are IO and BrO chemistry, the abundance of HCHO, and uptake of HOx to aerosol.
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- 2010
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17. NOx and O3 above a tropical rainforest: an analysis with a global and box model
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Sarah Moller, Pawel K. Misztal, C. N. Hewitt, James D. Lee, R. C. Pike, Ben Langford, Paul Young, Claire E. Reeves, D. J. Stewart, Glenn Carver, Nicola Warwick, Xin Yang, and John A. Pyle
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Troposphere ,Atmospheric Science ,Boundary layer ,Meteorology ,Chemistry ,Advection ,Rainforest ,Atmospheric sciences ,Deposition (chemistry) ,Mixing (physics) ,Tropical rainforest ,Dilution - Abstract
A cross-platform field campaign, OP3, was conducted in the state of Sabah in Malaysian Borneo between April and July of 2008. Among the suite of observations recorded, the campaign included measurements of NOx and O3 – crucial outputs of any model chemistry mechanism. We describe the measurements of these species made from both the ground site and aircraft. We then use the output from two resolutions of the chemistry transport model p-TOMCAT to illustrate the ability of a global model chemical mechanism to capture the chemistry at the rainforest site. The basic model performance is good for NOx and poor for ozone. A box model containing the same chemical mechanism is used to explore the results of the global model in more depth and make comparisons between the two. Without some parameterization of the nighttime boundary layer – free troposphere mixing (i.e. the use of a dilution parameter), the box model does not reproduce the observations, pointing to the importance of adequately representing physical processes for comparisons with surface measurements. We conclude with a discussion of box model budget calculations of chemical reaction fluxes, deposition and mixing, and compare these results to output from p-TOMCAT. These show the same chemical mechanism behaves similarly in both models, but that emissions and advection play particularly strong roles in influencing the comparison to surface measurements.
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- 2010
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18. Measurements of nitrogen oxides from Hudson Bay: Implications for NOx release from snow and ice covered surfaces
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Howard K. Roscoe, Alastair C. Lewis, Hilke Oetjen, Roisin Commane, Anoop S. Mahajan, James R. Hopkins, Sarah Moller, Trevor Ingham, John M. C. Plane, James D. Lee, Peter Edwards, Dwayne E. Heard, and Lucy J. Carpenter
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Atmospheric Science ,geography ,geography.geographical_feature_category ,010504 meteorology & atmospheric sciences ,010501 environmental sciences ,15. Life on land ,Snowpack ,Snow ,Atmospheric sciences ,01 natural sciences ,Latitude ,chemistry.chemical_compound ,chemistry ,13. Climate action ,Mixing ratio ,Sea ice ,Nitrogen dioxide ,Physical geography ,NOx ,Air mass ,0105 earth and related environmental sciences ,General Environmental Science - Abstract
Measurements of NO and NO2 were made at a surface site (55.28 degrees N, 77.77 degrees W) near Kuujjuarapik, Canada during February and March 2008. NOx mixing ratios ranged from near zero to 350 pptv with emission from snow believed to be the dominant source. The amount of NOx was observed to be dependent on the terrain over which the airmass has passed before reaching the measurement site. The 24 h average NOx emission rates necessary to reproduce observations were calculated using a zero-dimensional box model giving rates ranging from 6.9 x 10(8) molecule cm(-2) s(-1) to 1.2 x 10(9) molecule cm(-2) s(-1) for trajectories over land and from 3.8 x 10(8) molecule cm(-2) s(-1) to 6.6 x 10(8) molecule cm(-2) s(-1) for trajectories over sea ice. These emissions are higher than those suggested by previous studies and indicate the importance of lower latitude snowpack emissions. The difference in emission rate for the two types of snow cover shows the importance of snow depth and underlying surface type for the emission potential of snow-covered areas. (C) 2010 Elsevier Ltd. All rights reserved.
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- 2010
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19. Modelling chemistry in the nocturnal boundary layer above tropical rainforest and a generalised effective nocturnal ozone deposition velocity for sub-ppbv NOx conditions
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C. Nicholas Hewitt, James D. Lee, A. Robert MacKenzie, Eiko Nemitz, Douglas Lowe, Carole Helfter, Thomas A. M. Pugh, James Ryder, and Sarah Moller
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Atmospheric Science ,Daytime ,Ozone ,Meteorology ,Planetary boundary layer ,Nocturnal ,QD Chemistry ,Atmospheric sciences ,Atmosphere ,chemistry.chemical_compound ,chemistry ,Atmospheric chemistry ,Environmental Chemistry ,Nitrogen oxide ,S Agriculture (General) ,NOx ,GE Environmental Sciences - Abstract
Measurements of atmospheric composition have been made over a remote rainforest landscape. A box model has previously been demonstrated to model the observed daytime chemistry well. However the box model is unable to explain the nocturnal measurements of relatively high [NO] and [O3], but relatively low observed [NO2]. It is shown that a one-dimensional (1-D) column model with simple O3 -NOx chemistry and a simple representation of vertical transport is able to explain the observed nocturnal concentrations and predict the likely vertical profiles of these species in the nocturnal boundary layer (NBL). Concentrations of tracers carried over from the end of the night can affect the atmospheric chemistry of the following day. To ascertain the anomaly introduced by using the box model to represent the NBL, vertically-averaged NBL concentrations at the end of the night are compared between the 1-D model and the box model. It is found that, under low to medium [NOx] conditions (NOx 1 ppbv), the effect on the chemistry due to the vertical distribution of the species means no box model can adequately represent chemistry in the NBL without modifying reaction rate constants.
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- 2010
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20. Overview: oxidant and particle photochemical processes above a south-east Asian tropical rainforest (the OP3 project): introduction, rationale, location characteristics and tools
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Paul I. Palmer, Eiko Nemitz, Ben Langford, Dwayne E. Heard, P. DiCarlo, Hilke Oetjen, M. Irwin, David Fowler, Paul S. Monks, Nicola Carslaw, Trevor Ingham, R. C. Pike, A. Karunaharan, James Dorsey, Roisin Commane, Claire E. Reeves, V. Nicolas-Perea, Graham P. Mills, Glenn Carver, Alastair C. Lewis, Alex Guenther, C. N. Hewitt, Martin Gallagher, Anoop S. Mahajan, S. F. Lim, Pawel K. Misztal, Carole Helfter, K. L. Furneaux, David E. Oram, M. P. Barkley, John M. C. Plane, S. Malpass, Fay Davies, Mathew J. Evans, James R. Hopkins, Gavin Phillips, Brian Davison, James D. Lee, D. J. Stewart, Daniel Stone, Hugh Coe, Gordon McFiggans, A. R. MacKenzie, John A. Pyle, Nick A. Chappell, Peter Edwards, Sarah Moller, Niall Robinson, C. Di Marco, Chris G. Collier, Lisa K. Whalley, Thomas A. M. Pugh, S. M. MacDonald, Xiaobo Yin, and Chris Jones
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Canopy ,Atmospheric Science ,Reactive nitrogen ,TRACE GASES ,Eddy covariance ,MONSOON MULTIDISCIPLINARY ANALYSIS ,Rainforest ,FLUX MEASUREMENTS ,VOLATILE ORGANIC-COMPOUNDS ,Photochemistry ,lcsh:QC1-999 ,Trace gas ,EDDY-COVARIANCE ,COMPOUND EMISSIONS ,Atmosphere ,lcsh:Chemistry ,lcsh:QD1-999 ,TROPOSPHERIC NITROGEN-DIOXIDE ,Climatology ,Atmospheric chemistry ,ISOPRENE EMISSIONS ,MASTER CHEMICAL MECHANISM ,lcsh:Physics ,Tropical rainforest ,MCM V3 PART - Abstract
In April–July 2008, intensive measurements were made of atmospheric composition and chemistry in Sabah, Malaysia, as part of the "Oxidant and particle photochemical processes above a South-East Asian tropical rainforest" (OP3) project. Fluxes and concentrations of trace gases and particles were made from and above the rainforest canopy at the Bukit Atur Global Atmosphere Watch station and at the nearby Sabahmas oil palm plantation, using both ground-based and airborne measurements. Here, the measurement and modelling strategies used, the characteristics of the sites and an overview of data obtained are described. Composition measurements show that the rainforest site was not significantly impacted by anthropogenic pollution, and this is confirmed by satellite retrievals of NO2 and HCHO. The dominant modulators of atmospheric chemistry at the rainforest site were therefore emissions of BVOCs and soil emissions of reactive nitrogen oxides. At the observed BVOC:NOx volume mixing ratio (~100 pptv/pptv), current chemical models suggest that daytime maximum OH concentrations should be ca. 105 radicals cm−3, but observed OH concentrations were an order of magnitude greater than this. We confirm, therefore, previous measurements that suggest that an unexplained source of OH must exist above tropical rainforest and we continue to interrogate the data to find explanations for this.
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- 2010
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21. Aircraft observations of the lower troposphere above a megacity: alkyl nitrate and ozone chemistry
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Jennifer B. A. Muller, Eleonora Aruffo, Shalini Punjabi, G. Forster, Hannah Walker, Daniel Stone, James R. Hopkins, Franco Giammaria, Claire E. Reeves, Michael Le Breton, Sarah Moller, Marcella Busilacchio, Cesare Dari-Salisburgo, Trevor Ingham, James D. Lee, Dwayne E. Heard, Fabio Biancofiore, Stephane Bauguitte, Stewart Vaughan, Rod Jones, Debbie O'Sullivan, Carl J. Percival, and Piero Di Carlo
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chemistry.chemical_classification ,Atmospheric Science ,Ozone ,Tropospheric chemistry ,Ozone production ,Urban pollution ,Plume ,Troposphere ,Atmosphere ,chemistry.chemical_compound ,chemistry ,Nitrate ,Environmental chemistry ,Nitrogen oxide ,Alkyl ,NOx ,General Environmental Science - Abstract
Within the framework of the RONOCO (ROle of Nighttime chemistry in controlling the Oxidising Capacity of the atmOsphere) campaign a daytime flight over the metropolitan area of London were carried out to study the nitrogen oxide chemistry and its role in the production and loss of ozone (O3) and alkyl and multifunctional nitrate (ΣANs). The FAAM BAe-146 aircraft, used for these observations, was equipped with instruments to measure the most relevant compounds that control the lower troposphere chemistry, including O3, NO, NO2, NO3, N2O5, HNO3, peroxy nitrates (ΣPNs), ΣANs, OH, and HO2. In the London's flight a strong ozone titration process was observed when flying above Reading (downwind of London) and when intercepting the London plume. The coupled cycles of NOx and HOx can have different terminations forming ΣPNs, ΣANs, HNO3 or peroxides (H2O2, ROOH) altering the O3 production. In the observations reported here, we found that a strong ozone titration (ΔO3 = −16 ppb), due to a rapid increase of NOx (ΔNOx = 27 ppb), corresponds also to a high increase of ΣANs concentrations (ΔΣANs = 3 ppb), and quite stable concentrations of HNO3 and ΣPNs. Unexpectedly, compared with other megacities, the production of ΣANs is similar to that of Ox (O3 + NO2), suggesting that in the London plume, at least during these observations, the formation of ΣANs effectively removes active NOx and hence reduces the amount of O3 production. In fact, we found that the ratio between the ozone production and the alkyl nitrates production (observed) approximate the unity; on the contrary the calculated ratio is 7. In order to explain this discrepancy, we made sensitivity tests changing the alkyl nitrates branching ratio for some VOCs and we investigated the impact of the unmeasured VOCs during the flight, founding that the calculated ratio decreases from 7 to 2 and that, in this condition, the major contribution to the ΣANs production is given by Alkanes. Observations and analysis reported here suggest that in the London plume the high NOx emissions and the chemistry of some VOCs (mainly Alkanes) produce high concentrations of ΣANs competing against the local ozone production.
- Published
- 2014
22. spa Typing of Methicillin-Resistant Staphylococcus aureus Based on Whole-Genome Sequencing: the Impact of the Assembler
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Sarah Mollerup, Peder Worning, Andreas Petersen, and Mette Damkjær Bartels
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MRSA ,WGS ,Sanger ,spa typing ,assembly ,SKESA ,Microbiology ,QR1-502 - Abstract
ABSTRACT Sequencing of the spa gene of methicillin-resistant Staphylococcus aureus (MRSA) is used for assigning spa types to e.g., detect transmission and control outbreaks. Traditionally, spa typing is performed by Sanger sequencing but has in recent years been replaced by whole-genome sequencing (WGS) in some laboratories. Spa typing by WGS involves de novo assembly of millions of short sequencing reads into larger contiguous sequences, from which the spa type is then determined. The choice of assembly program therefore potentially impacts the spa typing result. In this study, WGS of 1,754 MRSA isolates was followed by de novo assembly using the assembly programs SPAdes (with two different sets of parameters) and SKESA. The spa types were assigned and compared to the spa types obtained by Sanger sequencing, regarding the latter as the correct spa types. SPAdes with the two different settings resulted in assembly of the correct spa type for 84.8% and 97.6% of the isolates, respectively, while SKESA assembled the correct spa type in 98.6% of cases. The misassembled spa types were generally two spa repeats shorter than the correct spa type and mainly included spa types with repetition of the same repeats. WGS-based spa typing is thus very accurate compared to Sanger sequencing, when the best assembly program for this purpose is used. IMPORTANCE spa typing of methicillin-resistant Staphylococcus aureus (MRSA) is widely used by clinicians, infection control workers, and researchers both in local outbreak investigations and as an easy way to communicate and compare MRSA types between laboratories and countries. Traditionally, spa types are determined by Sanger sequencing, but in recent years a whole-genome sequencing (WGS)-based approach has become increasingly used. In this study, we compared spa typing by WGS using different methods for assembling the genome from short sequencing reads and compared to Sanger sequencing as the gold standard. We find substantial differences in correct assembly of spa types between the assembly methods. Our findings are therefore important for the quality of WGS based spa typing data being exchanged by clinical microbiology laboratories.
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- 2022
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23. OH reactivity in a South East Asian Tropical rainforest during the Oxidant and Particle Photochemical Processes (OP3) project
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A. C. Lewis, Trevor Ingham, K. L. Furneaux, James R. Hopkins, Dwayne E. Heard, Chris Jones, Peter Edwards, James D. Lee, Sarah Moller, Daniel Stone, Mathew J. Evans, and Lisa K. Whalley
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chemistry.chemical_classification ,Atmospheric Science ,010504 meteorology & atmospheric sciences ,Photodissociation ,010501 environmental sciences ,Photochemistry ,Peroxide ,7. Clean energy ,01 natural sciences ,lcsh:QC1-999 ,lcsh:Chemistry ,chemistry.chemical_compound ,chemistry ,lcsh:QD1-999 ,13. Climate action ,Molecule ,Compounds of carbon ,Hydroxyl radical ,South east asian ,NOx ,Isoprene ,lcsh:Physics ,0105 earth and related environmental sciences - Abstract
OH (hydroxyl radical) reactivity, the inverse of the chemical lifetime of the hydroxyl radical, was measured for 12 days in April 2008 within a tropical rainforest on Borneo as part of the OP3 (Oxidant and Particle Photochemical Processes) project. The maximum observed value was 83.8 ± 26.0 s−1 with the campaign averaged noontime maximum being 29.1 ± 8.5 s−1. The maximum OH reactivity calculated using the diurnally averaged concentrations of observed sinks was ~ 18 s−1, significantly less than the observations, consistent with other studies in similar environments. OH reactivity was dominated by reaction with isoprene (~ 30%). Numerical simulations of isoprene oxidation using the Master Chemical Mechanism (v3.2) in a highly simplified physical and chemical environment show that the steady state OH reactivity is a linear function of the OH reactivity due to isoprene alone, with a maximum multiplier, to account for the OH reactivity of the isoprene oxidation products, being equal to the number of isoprene OH attackable bonds (10). Thus the emission of isoprene constitutes a significantly larger emission of reactivity than is offered by the primary reaction with isoprene alone, with significant scope for the secondary oxidation products of isoprene to constitute the observed missing OH reactivity. A physically and chemically more sophisticated simulation (including physical loss, photolysis, and other oxidants) showed that the calculated OH reactivity is reduced by the removal of the OH attackable bonds by other oxidants and photolysis, and by physical loss (mixing and deposition). The calculated OH reactivity is increased by peroxide cycling, and by the OH concentration itself. Notable in these calculations is that the accumulated OH reactivity from isoprene, defined as the total OH reactivity of an emitted isoprene molecule and all of its oxidation products, is significantly larger than the reactivity due to isoprene itself and critically depends on the chemical and physical lifetimes of intermediate species. When constrained to the observed diurnally averaged concentrations of primary VOCs (volatile organic compounds), O3, NOx and other parameters, the model underestimated the observed diurnal mean OH reactivity by 30%. However, it was found that (1) the short lifetimes of isoprene and OH, compared to those of the isoprene oxidation products, lead to a large variability in their concentrations and so significant variation in the calculated OH reactivity; (2) uncertainties in the OH chemistry in these high isoprene environments can lead to an underestimate of the OH reactivity; (3) the physical loss of species that react with OH plays a significant role in the calculated OH reactivity; and (4) a missing primary source of reactive carbon would have to be emitted at a rate equivalent to 50% that of isoprene to account for the missing OH sink. Although the presence of unmeasured primary emitted VOCs contributing to the measured OH reactivity is likely, evidence that these primary species account for a significant fraction of the unmeasured reactivity is not found. Thus the development of techniques for the measurement of secondary multifunctional carbon compounds is needed to close the OH reactivity budget.
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- 2013
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24. Aircraft based four-channel thermal dissociation laser induced fluorescence instrument for simultaneous measurements of NO2, total peroxy nitrate, total alkyl nitrate, and HNO3
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P. Di Carlo, Sarah Moller, Guido Visconti, Eleonora Aruffo, Stephane Bauguitte, Franco Giammaria, James D. Lee, Roderic L. Jones, Cesare Dari-Salisburgo, Fabio Biancofiore, Bin Ouyang, G. Forster, Claire E. Reeves, and Marcella Busilacchio
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chemistry.chemical_classification ,Atmospheric Science ,010504 meteorology & atmospheric sciences ,Spectrometer ,Analytical chemistry ,010501 environmental sciences ,Laser ,01 natural sciences ,Dissociation (chemistry) ,law.invention ,chemistry.chemical_compound ,Nitrate ,chemistry ,13. Climate action ,law ,Nitric acid ,Nitrogen dioxide ,Laser-induced fluorescence ,Alkyl ,0105 earth and related environmental sciences - Abstract
A four-channel thermal dissociation laser induced fluorescence (TD-LIF) instrument has been developed for simultaneous measurements of nitrogen dioxide (NO2), total peroxy nitrate (∑PNs), total alkyl nitrate (∑ANs) and nitric acid (HNO3). NO2 is measured directly by LIF at 532 nm, whereas organic nitrates and nitric acid are thermally dissociated at distinct temperatures in the inlet to form NO2, which is then measured by LIF. The concentrations of each dissociated species are derived by the differences in measured NO2 relative to the reference colder inlet channel. The TD-LIF was adapted to fly on board the UK Facility for Airborne Atmospheric Measurements (FAAM) BAe 146-301 atmospheric research aircraft in summer 2010, and to date has successfully flown in five field campaigns. This paper reports novel improvements in the TD-LIF instrumentations including: (1) the use of a single wavelength laser, which makes the system compact and relatively cheap; (2) the use of a single beam laser that allows easy alignment and optical stability against the vibrational aircraft environment and (3) the optical assembly of four detection cells that allow simultaneous and fast (time resolution up to 0.1 s) measurements of NO2, ∑PNs, ∑ANs and HNO3. Laboratory-generated mixtures of PNs, ANs and HNO3 in zero air are converted into NO2 and used to fix the dissociation temperatures of each heated inlet, to test the selectivity of the instrument and potential interferences due to recombination reactions of the dissociated products. The effectiveness of the TD-LIF was demonstrated during the RONOCO aircraft campaign (summer 2010). A chemiluminescence system that was measuring NO2 and a broadband cavity enhanced absorption spectrometer (BBCEAS) that was measuring one of the PNs (N2O5) were installed on the same aircraft during the campaign. The in-flight intercomparison of the new TD-LIF with the chemiluminescence system for NO2 measurements and the intercomparison between ∑PNs measured by the TD-LIF and N2O5 by the BBCEAS are used to assess the performance of the TD-LIF.
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- 2012
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25. The influence of boreal forest fires on the global distribution of non-methane hydrocarbons
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Lucy J. Carpenter, Katie A. Read, Andrew R. Rickard, J. D. Lee, A. C. Lewis, Stephen J. Andrews, Shalini Punjabi, James R. Hopkins, Mark Parrington, Matthew Evans, Paul I. Palmer, and Sarah Moller
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chemistry.chemical_compound ,chemistry ,Global distribution ,Taiga ,Environmental science ,Atmospheric sciences ,Methane - Abstract
Boreal forest fires are a significant source of chemicals to the atmosphere including numerous non-methane hydrocarbons (NMHCs). We report airborne measurements of NMHCs, acetone and methanol from > 500 whole air samples collected over Eastern Canada, including interception of several different boreal biomass burning plumes. From these and concurrent measurements of carbon monoxide (CO) we derive fire emission ratios for 29 different species relative to the emission of CO. These range from 8.9 ± 3.2 ppt ppb−1 CO for methanol to 0.007 ± 0.004 ppt ppb−1 CO for cyclopentane. The ratios are in good to excellent agreement with recent literature values. Using the GEOS-Chem global 3-D chemical transport model (CTM) we show the influence of biomass burning on the global distributions of benzene, toluene, ethene and propene (species considered generally as indicative tracers of anthropogenic activity). Using our derived emission ratios and the GEOS-Chem CTM, we show that biomass burning can be the largest fractional contributor to observed benzene, toluene, ethene and propene in many global locations. The widespread biomass burning contribution to atmospheric benzene, a heavily regulated air pollutant, suggests that pragmatic approaches are needed when setting air quality targets as tailpipe and solvent emissions continue to decline. We subsequently determine the extent to which the 28 Global WMO-GAW stations worldwide are influenced by biomass burning sourced benzene, toluene, ethene and propene when compared to their exposure to anthropogenic emissions.
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- 2012
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26. Observations of total peroxy nitrates and total alkyl nitrates during the OP3 campaign: isoprene nitrate chemistry above a south-east Asian tropical rain forest
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Franco Giammaria, P. Di Carlo, James D. Lee, Mathew J. Evans, C. N. Hewitt, James R. Hopkins, A. R. MacKenzie, Sarah Moller, Fabio Biancofiore, Eleonora Aruffo, Cesare Dari-Salisburgo, and Chris Jones
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chemistry.chemical_classification ,chemistry.chemical_compound ,Nitrate ,chemistry ,Diurnal cycle ,Climatology ,Yield (chemistry) ,Nitrogen dioxide ,Tropospheric ozone ,Atmospheric sciences ,Alkyl ,Isoprene ,Aerosol - Abstract
Measurements of total peroxy nitrates (ΣRO2NO2, ΣPNs), total alkyl nitrates (ΣRONO2, ΣANs) and nitrogen dioxide (NO2) were made above the surface of a Malaysian tropical rain forest in Borneo, using a laser-induced fluorescence instrument developed at the University of L'Aquila (Italy). This new instrument uses the direct excitation of NO2 at 532 nm in order to measure its concentrations detecting by the NO2 fluorescence at wavelengths longer than 610 nm. ΣPNs and ΣANs are indirectly measured after their thermal dissociation into NO2. Observations showed enhanced levels of NO2 during nighttime, an increase of ΣPNs during the afternoon and almost no evident diurnal cycle of ΣANs. The diurnal maximums of 200 pptv for ΣPNs and ΣANs are well below the peaks reported in other forest sites. A box model constrained with measured species, reproduces well the observed ΣPNs, but overestimates ΣANs concentrations. The reason of this model-observation discrepancy could be a wrong parameterization in the isoprene nitrates (INs) chemistry mechanism. Sensitivity tests show that: (1) reducing the yield of INs from the reaction of peroxy nitrates with NO to almost the lowest values reported in literature (5%), (2) reducing the INs recycling to 70% and (3) keeping the INs dry deposition at 4 cm s−1, improve the agreement between modelled and measured ΣANs of 20% on average. These results imply that in the tropical rain forest, even if ΣPNs and ΣANs concentrations are lower than those observed in other North American forests, the yield and dry deposition of INs are similar. Another comparable result is that in the INs oxidation its recycling dominates with only a 30% release of NO2, which has implications on tropospheric ozone production and aerosol budget.
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- 2012
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27. Hydrogen oxide photochemistry in the northern Canadian spring time boundary layer
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Mathew J. Evans, John M. C. Plane, Anoop S. Mahajan, James D. Lee, Daniel Stone, James Dorsey, Roland Leigh, Lucy J. Carpenter, Peter Edwards, Dwayne E. Heard, James R. Hopkins, Hilke Oetjen, Sarah Moller, Trevor Ingham, and Roisin Commane
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Atmospheric Science ,Daytime ,Ozone ,Hydrogen ,Formaldehyde ,Soil Science ,chemistry.chemical_element ,Aquatic Science ,Oceanography ,Atmospheric sciences ,chemistry.chemical_compound ,Geochemistry and Petrology ,Oxidizing agent ,Earth and Planetary Sciences (miscellaneous) ,Earth-Surface Processes ,Water Science and Technology ,Ecology ,Photodissociation ,Paleontology ,Forestry ,Geophysics ,chemistry ,Space and Planetary Science ,Halogen ,Environmental science ,Bay - Abstract
[1] Measurements of OH and HO2 concentrations were made at the surface of the eastern coast of the Hudson Bay during the COBRA campaign from February 18th to March 8th 2008. Diurnally averaged OH and HO2 concentrations peaked at 1.16 (±1.02) × 106 molecule cm−3 and 1.42 (±0.64) × 108 molecule cm−3 respectively. A box-model, constrained to supporting observations, is used to access the radical budget in this cold, northerly environment. Formaldehyde (HCHO) photolysis is found to be the dominant daytime radical source, providing 74% of the observed HOx. A considerable (>80% of the total source) surface HCHO source is required to reconcile the model and observed HCHO concentrations. Model simulations also suggest significant roles for the heterogeneous loss of HO2 and for halogen chemistry in the cycling of HO2 to OH. The formation of HO2NO2 is identified as an important radical reservoir, reducing HOx concentrations during the day and enhancing them at night. This impacts both local oxidizing capacity and reduces local ozone production by approximately 30%. The sensitivity of the local chemistry to uncertainties in these processes is explored. The majority of these processes are not currently represented in global chemistry models.
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- 2011
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28. Nitrogen management is essential to prevent tropical oil palm plantations from causing ground-level ozone pollution
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A. R. MacKenzie, Mathew J. Evans, D. J. Stewart, S. F. Lim, Jambery Siong, Gavin Phillips, Pawel K. Misztal, Alastair C. Lewis, James Ryder, John A. Pyle, C. Di Marco, Martin Gallagher, C. E. Jones, James R. Hopkins, P. Di Carlo, Ben Langford, C. N. Hewitt, Sarah Moller, James Dorsey, Susan M. Owen, James D. Lee, Claire E. Reeves, David Fowler, David E. Oram, James B. McQuaid, Thomas A. M. Pugh, Eiko Nemitz, Paul S. Monks, and Ute Skiba
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Time Factors ,Aircraft ,Nitrogen ,Nitrogen Dioxide ,Rainforest ,Arecaceae ,Palm Oil ,Nitric Oxide ,Elaeis guineensis ,Hemiterpenes ,Ozone ,Air Pollution ,Pentanes ,Tropical climate ,Butadienes ,Plant Oils ,Peracetic Acid ,Air quality index ,Tropical Climate ,Multidisciplinary ,Geography ,biology ,Tropical agriculture ,Agroforestry ,business.industry ,Agriculture ,biology.organism_classification ,Biofuel ,Physical Sciences ,Monoterpenes ,Environmental science ,business - Abstract
More than half the world's rainforest has been lost to agriculture since the Industrial Revolution. Among the most widespread tropical crops is oil palm ( Elaeis guineensis ): global production now exceeds 35 million tonnes per year. In Malaysia, for example, 13% of land area is now oil palm plantation, compared with 1% in 1974. There are enormous pressures to increase palm oil production for food, domestic products, and, especially, biofuels. Greater use of palm oil for biofuel production is predicated on the assumption that palm oil is an “environmentally friendly” fuel feedstock. Here we show, using measurements and models, that oil palm plantations in Malaysia directly emit more oxides of nitrogen and volatile organic compounds than rainforest. These compounds lead to the production of ground-level ozone (O 3 ), an air pollutant that damages human health, plants, and materials, reduces crop productivity, and has effects on the Earth's climate. Our measurements show that, at present, O 3 concentrations do not differ significantly over rainforest and adjacent oil palm plantation landscapes. However, our model calculations predict that if concentrations of oxides of nitrogen in Borneo are allowed to reach those currently seen over rural North America and Europe, ground-level O 3 concentrations will reach 100 parts per billion (10 9 ) volume (ppbv) and exceed levels known to be harmful to human health. Our study provides an early warning of the urgent need to develop policies that manage nitrogen emissions if the detrimental effects of palm oil production on air quality and climate are to be avoided.
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- 2010
29. Intra-annual cycles of NMVOC in the tropical marine boundary layer and their use for interpreting seasonal variability in CO
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Lucy J. Carpenter, L. Mendes, Katie A. Read, Sarah Moller, James D. Lee, and Alastair C. Lewis
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Atmospheric Science ,Planetary boundary layer ,Soil Science ,Aquatic Science ,Oceanography ,Atmospheric sciences ,Methane ,Cape verde ,chemistry.chemical_compound ,Geochemistry and Petrology ,Earth and Planetary Sciences (miscellaneous) ,medicine ,Earth-Surface Processes ,Water Science and Technology ,Ecology ,Paleontology ,Forestry ,Monoxide ,Seasonality ,medicine.disease ,Geophysics ,chemistry ,Space and Planetary Science ,Climatology ,Environmental science ,Hydroxyl radical ,Methanol ,Carbon monoxide - Abstract
[1] Carbon monoxide and nonmethane volatile organic compounds (NMVOC) have been measured for the first time on a continuous basis in the tropical marine boundary layer of the Atlantic Ocean. CO and ethane, which have similar lifetimes with respect to OH degradation, vary intra-annually with the sinusoidal variability expected due to a primary hydroxyl radical (OH) sink, but with CO showing a smaller cycle amplitude. The ethane measurements were used to derive the seasonal variation in the nominal OH concentration (n[OH]) experienced along the air mass trajectories arriving at Cape Verde. The n[OH] represents the variability in both the true OH concentration and any intra-annual changes in ethane emissions, and was subsequently used to simulate the seasonal cycle of CO, allowing identification of potentially differing sources and sinks from those of ethane. Deviation of the observed CO from the n[OH] fit indicated that summer sources of CO are approximately 60% (30–68%) higher than winter, assuming values of ±8% and ±49% seasonal variability, respectively, in fossil fuel and biomass burning emissions of CO and ethane, and including −29% uncertainty due to the losses of ethane through reaction with chlorine atoms. The evidence suggests that secondary production of CO from the oxidation of methane (CH4) and NMVOC and in particular from methanol, acetone and acetaldehyde may be dominant summer CO sources in this region.
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- 2009
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30. Year-round measurements of nitrogen oxides and ozone in the tropical North Atlantic marine boundary layer
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Lucy J. Carpenter, Alastair C. Lewis, Sarah Moller, James D. Lee, L. Mendes, and Katie A. Read
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Atmospheric Science ,Ozone ,Ecology ,Planetary boundary layer ,Paleontology ,Soil Science ,Forestry ,Aquatic Science ,Oceanography ,Cape verde ,Troposphere ,chemistry.chemical_compound ,Geophysics ,chemistry ,Space and Planetary Science ,Geochemistry and Petrology ,Climatology ,Earth and Planetary Sciences (miscellaneous) ,Mixing ratio ,Environmental science ,Nitrogen dioxide ,Nitrogen oxide ,NOx ,Earth-Surface Processes ,Water Science and Technology - Abstract
[1] A highly sensitive chemiluminescence instrument has been deployed to measure nitric oxide (NO) and nitrogen dioxide (NO 2 ) at the Cape Verde Atmospheric Observatory in the remote tropical North Atlantic marine boundary layer (MBL). Using two different methods, the instrument was assessed to have a detection limit of around 1.8 parts per trillion by volume (pptv) for NO and 5.5 pptv for NO 2 for hour-long integration periods. The overall accuracy was estimated at ∼18% for NO and 30% for NO 2 . Measurements of NO, NO 2 , and ozone (0 3 ) over a period of 12 months in 2007 show very low levels of NO x (typically
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- 2009
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31. Extensive halogen-mediated ozone destruction over the tropical Atlantic Ocean
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Bruno V. E. Faria, Michael J. Pilling, Mathew J. Evans, John M. C. Plane, Lucy J. Carpenter, Dwayne E. Heard, Alfonso Saiz-Lopez, Sarah Moller, Hilke Oetjen, James D. Lee, L. Mendes, Anoop S. Mahajan, James R. Hopkins, Alastair C. Lewis, James B. McQuaid, and Katie A. Read
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Ozone ,Meteorology ,Iodine oxide ,Marine Biology ,Tropical Atlantic ,Atmospheric sciences ,Tropospheric ozone depletion events ,Cape verde ,chemistry.chemical_compound ,Halogens ,Seawater ,Tropospheric ozone ,Atlantic Ocean ,Tropical Climate ,Multidisciplinary ,Geography ,Atmosphere ,Temperature ,Eukaryota ,Trace gas ,Africa, Western ,chemistry ,Atmospheric chemistry ,Seasons ,Methane - Abstract
Increasing tropospheric ozone levels over the past 150 years have led to a significant climate perturbation; the prediction of future trends in tropospheric ozone will require a full understanding of both its precursor emissions and its destruction processes. A large proportion of tropospheric ozone loss occurs in the tropical marine boundary layer and is thought to be driven primarily by high ozone photolysis rates in the presence of high concentrations of water vapour. A further reduction in the tropospheric ozone burden through bromine and iodine emitted from open-ocean marine sources has been postulated by numerical models, but thus far has not been verified by observations. Here we report eight months of spectroscopic measurements at the Cape Verde Observatory indicative of the ubiquitous daytime presence of bromine monoxide and iodine monoxide in the tropical marine boundary layer. A year-round data set of co-located in situ surface trace gas measurements made in conjunction with low-level aircraft observations shows that the mean daily observed ozone loss is approximately 50 per cent greater than that simulated by a global chemistry model using a classical photochemistry scheme that excludes halogen chemistry. We perform box model calculations that indicate that the observed halogen concentrations induce the extra ozone loss required for the models to match observations. Our results show that halogen chemistry has a significant and extensive influence on photochemical ozone loss in the tropical Atlantic Ocean boundary layer. The omission of halogen sources and their chemistry in atmospheric models may lead to significant errors in calculations of global ozone budgets, tropospheric oxidizing capacity and methane oxidation rates, both historically and in the future.
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- 2008
32. No Effect of Lactobacillus rhamnosus GG on Eradication of Colonization by Vancomycin-Resistant Enterococcus faecium or Microbiome Diversity in Hospitalized Adult Patients
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Ingrid Maria Cecilia Rubin, Sarah Mollerup, Christa Broholm, Signe Boye Knudsen, Adam Baker, Morten Helms, Mona Katrine Alberthe Holm, Thomas Kallemose, Henrik Westh, Jenny Dahl Knudsen, Mette Pinholt, and Andreas Munk Petersen
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vancomycin-resistant Enterococcus faecium ,gut microbiome ,Lactobacillus rhamnosus ,probiotics ,Microbiology ,QR1-502 - Abstract
ABSTRACT The purpose of this trial was to evaluate the efficacy of a 4-week supplementation of Lactobacillus rhamnosus GG (LGG) in eliminating the gastrointestinal carrier state of vancomycin-resistant Enterococcus faecium (VREfm) in hospitalized adults. The primary outcome of the study was the number of patients with cleared VREfm colonization after the 4-week intervention. Secondary outcomes were clearance of VREfm colonization at weeks 8, 16, and 24, number of VREfm infections (isolated from nonintestinal foci), and changes in fecal microbiome diversity after the intervention. The trial was a multicenter, randomized, double-blind, placebo-controlled trial in hospitalized adult VREfm carriers. Patients were enrolled and randomized to receive 60 billion CFU of LGG daily or placebo for 4 weeks. For a subgroup of patients, rectal swabs for VREfm were collected also at 8, 16, and 24 weeks and analyzed using shotgun metagenomics. Patients ingesting a minimum of 50% of the probiotic during the 4-week intervention were included in subsequent outcome analyses (48 of 81 patients). Twelve of 21 patients in the LGG group (57%) compared to 15 of 27 patients in the placebo group (56%) cleared their VREfm carriage. Eighteen patients completed the entire 24-week intervention with the same minimum compliancy. Of these, almost 90% in both groups cleared their VREfm carriage. We found a statistically significant difference between VREfm clearers and nonclearers regarding metronidazole and vancomycin usage as well as length of hospitalization after inclusion. The microbiome analyses revealed no significant difference in alpha diversity between the LGG and the placebo group. Beta diversity differed between the groups and the different time points. This study did not show an effect of LGG in eradication of VREfm after a 4-week intervention. IMPORTANCE Whereas other studies exploring the effect of L. rhamnosus in clearing VREfm from the intestine included children and adults, with a wider age range, our study consisted of a geriatric patient cohort. The natural clearance of VREfm in this study was almost 60% after 4 weeks, thus much higher than described previously. Also, this study characterizes the microbiome of VREfm patients in detail. This article showed no effect of the probiotic L. rhamnosus in clearing VREfm from the intestine of patients.
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- 2022
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33. Bacteraemia caused by Lactobacillus rhamnosus given as a probiotic in a patient with a central venous catheter: a WGS case report
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Ingrid Maria Cecilia Rubin, Lea Stevnsborg, Sarah Mollerup, Andreas Munk Petersen, and Mette Pinholt
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Infectious and parasitic diseases ,RC109-216 ,Public aspects of medicine ,RA1-1270 - Abstract
Summary: Introduction: Lactobacilli, especially Lactobacillus (L.) rhamnosus, are common and well-documented components of commercial probiotics [1]. Whole genome sequencing (WGS) is often used to compare bacterial genomes and their relatedness. In outbreak situations, it is used to investigate the transmission of pathogenic bacteria. WGS has also been used to determine safety in probiotics, by looking at potential virulence factors and resistance genes. Case presentation: This case report describes a 56-year old multi-traumatised, immunocompetent woman who was given L. rhamnosus GG as a probiotic, and later developed a blood stream infection with L. rhamnosus GG.The patient was fed by a nasogastric tube, and she also had a central venous catheter for parenteral feeding. When the patient developed diarrhoea after long-term hospitalisation, she was given L. rhamnosus GG, as a probiotic, which was standard care on the ward where she was hospitalised. In this case report we describe the use of WGS to demonstrate that a patient fed with L. rhamnosus GG as a probiotic, developed a blood stream infection with the same strain. Conclusion: In this case WGS was applied to show the relatedness of a probiotic and a pathogenic strain of L. rhamnosus GG. This case emphasises the need for caution when administering probiotics to patients with indwelling catheters. The patient was immunocompetent and she cleared the infection without the need for antibiotics.
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- 2022
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34. Corrigendum to 'Overview: oxidant and particle photochemical processes above a south-east Asian tropical rainforest (the OP3 project): introduction, rationale, location characteristics and tools' published in Atmos. Chem. Phys., 10, 169–199, 2010
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K. L. Furneaux, M. P. Barkley, Pawel K. Misztal, Paul S. Monks, C. Di Marco, Graham P. Mills, James R. Hopkins, John M. C. Plane, C. N. Hewitt, S. F. Lim, Xin Yang, P. DiCarlo, A. R. MacKenzie, Paul I. Palmer, Niall Robinson, V. Nicolas-Perea, Hugh Coe, Claire E. Reeves, Mathew J. Evans, M. Irwin, G. J. Phillips, Gordon McFiggans, Anoop S. Mahajan, S. M. MacDonald, Roisin Commane, A. Karunaharan, Chris Jones, Brian Davison, Chris G. Collier, Peter Edwards, James Dorsey, Alex Guenther, D. J. Stewart, Dwayne E. Heard, James D. Lee, A. C. Lewis, Sarah Moller, Daniel Stone, David Fowler, Nick A. Chappell, Lisa K. Whalley, Thomas A. M. Pugh, Hilke Oetjen, John A. Pyle, Nicola Carslaw, Fay Davies, Eiko Nemitz, Glenn Carver, R. C. Pike, Carole Helfter, David E. Oram, S. Malpass, Trevor Ingham, Martin Gallagher, and Ben Langford
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Hydrology ,Atmospheric Science ,Philosophy ,South east asian ,Humanities - Abstract
Author(s): Hewitt, CN; Lee, JD; MacKenzie, AR; Barkley, MP; Carslaw, N; Carver, GD; Chappell, NA; Coe, H; Collier, C; Commane, R; Davies, F; Davison, B; DiCarlo, P; Di Marco, CF; Dorsey, JR; Edwards, PM; Evans, MJ; Fowler, D; Furneaux, KL; Gallagher, M; Guenther, A; Heard, DE; Helfter, C; Hopkins, J; Ingham, T; Irwin, M; Jones, C; Karunaharan, A; Langford, B; Lewis, AC; Lim, SF; MacDonald, SM; Mahajan, AS; Malpass, S; McFiggans, G; Mills, G; Misztal, P; Moller, S; Monks, PS; Nemitz, E; Nicolas-Perea, V; Oetjen, H; Oram, DE; Palmer, PI; Phillips, GJ; Pike, R; Plane, JMC; Pugh, T; Pyle, JA; Reeves, CE; Robinson, NH; Stewart, D; Stone, D; Whalley, LK; Yang, X
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- 2010
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35. Cancer associated fibroblasts (CAFs) are activated in cutaneous basal cell carcinoma and in the peritumoural skin
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Silje Haukali Omland, Erika Elgstrand Wettergren, Sarah Mollerup, Maria Asplund, Tobias Mourier, Anders Johannes Hansen, and Robert Gniadecki
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background Cutaneous basal cell carcinoma (BCC) is the commonest cancer worldwide. BCC is locally invasive and the surrounding stromal microenvironment is pivotal for tumourigenesis. Cancer associated fibroblasts (CAFs) in the microenvironment are essential for tumour growth in a variety of neoplasms but their role in BCC is poorly understood. Methods Material included facial BCC and control skin from the peritumoural area and from the buttocks. With next-generation sequencing (NGS) we compared mRNA expression between BCC and peritumoural skin. qRT-PCR, immunohistochemical and immunofluorescent staining were performed to validate the NGS results and to investigate CAF-related cyto-and chemokines. Results NGS revealed upregulation of 65 genes in BCC coding for extracellular matrix components pointing at CAF-related matrix remodeling. qRT-PCR showed increased mRNA expression of CAF markers FAP-α, PDGFR-β and prolyl-4-hydroxylase in BCC. Peritumoural skin (but not buttock skin) also exhibited high expression of PDGFR-β and prolyl-4-hydroxylase but not FAP-α. We found a similar pattern for the CAF-associated chemokines CCL17, CCL18, CCL22, CCL25, CXCL12 and IL6 with high expression in BCC and peritumoural skin but absence in buttock skin. Immunofluorescence revealed correlation between FAP-α and PDGFR-β and CXCL12 and CCL17. Conclusion Matrix remodeling is the most prominent molecular feature of BCC. CAFs are present within BCC stroma and associated with increased expression of chemokines involved in tumour progression and immunosuppression (CXCL12, CCL17). Fibroblasts from chronically sun-exposed skin near tumours show gene expression patterns resembling that of CAFs, indicating that stromal fibroblasts in cancer-free surgical BCC margins exhibit a tumour promoting phenotype.
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- 2017
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36. Metagenomic analysis of viruses in toilet waste from long distance flights-A new procedure for global infectious disease surveillance.
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Mathis Hjort Hjelmsø, Sarah Mollerup, Randi Holm Jensen, Carlotta Pietroni, Oksana Lukjancenko, Anna Charlotte Schultz, Frank M Aarestrup, and Anders Johannes Hansen
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Medicine ,Science - Abstract
Human viral pathogens are a major public health threat. Reliable information that accurately describes and characterizes the global occurrence and transmission of human viruses is essential to support national and global priority setting, public health actions, and treatment decisions. However, large areas of the globe are currently without surveillance due to limited health care infrastructure and lack of international cooperation. We propose a novel surveillance strategy, using metagenomic analysis of toilet material from international air flights as a method for worldwide viral disease surveillance. The aim of this study was to design, implement, and evaluate a method for viral analysis of airplane toilet waste enabling simultaneous detection and quantification of a wide range of human viral pathogens. Toilet waste from 19 international airplanes was analyzed for viral content, using viral capture probes followed by high-throughput sequencing. Numerous human pathogens were detected including enteric and respiratory viruses. Several geographic trends were observed with samples originating from South Asia having significantly higher viral species richness as well as higher abundances of salivirus A, aichivirus A and enterovirus B, compared to samples originating from North Asia and North America. In addition, certain city specific trends were observed, including high numbers of rotaviruses in airplanes departing from Islamabad. Based on this study we believe that central sampling and analysis at international airports could be a useful supplement for global viral surveillance, valuable for outbreak detection and for guiding public health resources.
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- 2019
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37. High diversity of picornaviruses in rats from different continents revealed by deep sequencing
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Thomas Arn Hansen, Sarah Mollerup, Nam-phuong Nguyen, Nicole E White, Megan Coghlan, David E Alquezar-Planas, Tejal Joshi, Randi Holm Jensen, Helena Fridholm, Kristín Rós Kjartansdóttir, Tobias Mourier, Tandy Warnow, Graham J Belsham, Michael Bunce, Eske Willerslev, Lars Peter Nielsen, Lasse Vinner, and Anders Johannes Hansen
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cardiovirus ,metagenomics ,picornavirus ,Rattus norvegicus ,sequencing ,viral discovery ,Infectious and parasitic diseases ,RC109-216 ,Microbiology ,QR1-502 - Abstract
Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler’s encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.
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- 2016
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38. Cutavirus in Cutaneous Malignant Melanoma
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Sarah Mollerup, Helena Fridholm, Lasse Vinner, Kristín Rós Kjartansdóttir, Jens Friis-Nielsen, Maria Asplund, Jose A.R. Herrera, Torben Steiniche, Tobias Mourier, Søren Brunak, Eske Willerslev, Jose M.G. Izarzugaza, Anders J. Hansen, and Lars P. Nielsen
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Cutavirus ,bufavirus ,viruses ,cancer ,malignant melanoma ,protoparvovirus ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
A novel human protoparvovirus related to human bufavirus and preliminarily named cutavirus has been discovered. We detected cutavirus in a sample of cutaneous malignant melanoma by using viral enrichment and high-throughput sequencing. The role of cutaviruses in cutaneous cancers remains to be investigated.
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- 2017
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39. Correction to: Cancer associated fibroblasts (CAFs) are activated in cutaneous basal cell carcinoma and in the peritumoural skin
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Silje Haukali Omland, Erika Elgstrand Wettergren, Sarah Mollerup, Maria Asplund, Tobias Mourier, Anders Johannes Hansen, and Robert Gniadecki
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract After publication of the original article [1] it was identified that order of the author list had been presented incorrectly. The author Robert Gniadecki’s surname was also incorrect in the original article.
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- 2018
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40. Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery.
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Randi Holm Jensen, Sarah Mollerup, Tobias Mourier, Thomas Arn Hansen, Helena Fridholm, Lars Peter Nielsen, Eske Willerslev, Anders Johannes Hansen, and Lasse Vinner
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Medicine ,Science - Abstract
Viral infections cause many different diseases stemming both from well-characterized viral pathogens but also from emerging viruses, and the search for novel viruses continues to be of great importance. High-throughput sequencing is an important technology for this purpose. However, viral nucleic acids often constitute a minute proportion of the total genetic material in a sample from infected tissue. Techniques to enrich viral targets in high-throughput sequencing have been reported, but the sensitivity of such methods is not well established. This study compares different library preparation techniques targeting both DNA and RNA with and without virion enrichment. By optimizing the selection of intact virus particles, both by physical and enzymatic approaches, we assessed the effectiveness of the specific enrichment of viral sequences as compared to non-enriched sample preparations by selectively looking for and counting read sequences obtained from shotgun sequencing. Using shotgun sequencing of total DNA or RNA, viral targets were detected at concentrations corresponding to the predicted level, providing a foundation for estimating the effectiveness of virion enrichment. Virion enrichment typically produced a 1000-fold increase in the proportion of DNA virus sequences. For RNA virions the gain was less pronounced with a maximum 13-fold increase. This enrichment varied between the different sample concentrations, with no clear trend. Despite that less sequencing was required to identify target sequences, it was not evident from our data that a lower detection level was achieved by virion enrichment compared to shotgun sequencing.
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- 2015
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41. Simulating atmospheric composition over a South-East Asian tropical rainforest: Performance of a chemistry box model
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Dwayne E. Heard, Graham P. Mills, K. L. Furneaux, A. R. MacKenzie, A. Karunaharan, Sarah Moller, James R. Hopkins, C. N. Hewitt, C. E. Jones, Ben Langford, James D. Lee, Pawel K. Misztal, Paul S. Monks, Lisa K. Whalley, Thomas A. M. Pugh, and Peter Edwards
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Atmospheric Science ,Chemistry ,Planetary boundary layer ,Methacrolein ,Rainforest ,lcsh:QC1-999 ,lcsh:Chemistry ,Reaction rate ,chemistry.chemical_compound ,Flux (metallurgy) ,Deposition (aerosol physics) ,lcsh:QD1-999 ,Environmental chemistry ,Hydroxyl radical ,lcsh:Physics ,Isoprene - Abstract
Atmospheric composition and chemistry above tropical rainforests is currently not well established, particularly for south-east Asia. In order to examine our understanding of chemical processes in this region, the performance of a box model of atmospheric boundary layer chemistry is tested against measurements made at the top of the rainforest canopy near Danum Valley, Malaysian Borneo. Multi-variate optimisation against ambient concentration measurements was used to estimate average canopy-scale emissions for isoprene, total monoterpenes and nitric oxide. The excellent agreement between estimated values and measured fluxes of isoprene and total monoterpenes provides confidence in the overall modelling strategy, and suggests that this method may be applied where measured fluxes are not available, assuming that the local chemistry and mixing are adequately understood. The largest contributors to the optimisation cost function at the point of best-fit are OH (29%), NO (22%) and total peroxy radicals (27%). Several factors affect the modelled VOC chemistry. In particular concentrations of methacrolein (MACR) and methyl-vinyl ketone (MVK) are substantially overestimated, and the hydroxyl radical (OH) concentration is substantially underestimated; as has been seen before in tropical rainforest studies. It is shown that inclusion of dry deposition of MACR and MVK and wet deposition of species with high Henry's Law values substantially improves the fit of these oxidised species, whilst also substantially decreasing the OH sink. Increasing OH production arbitrarily, through a simple OH recycling mechanism , adversely affects the model fit for volatile organic compounds (VOCs). Given the constraints on isoprene flux provided by measurements, a substantial decrease in the rate of reaction of VOCs with OH is the only remaining option to explain the measurement/model discrepancy for OH. A reduction in the isoprene+OH rate constant of 50%, in conjunction with increased deposition of intermediates and some modest OH recycling, is able to produce both isoprene and OH concentrations within error of those measured. Whilst we cannot rule out an important role for missing chemistry, particularly in areas of higher isoprene flux, this study demonstrates that the inadequacies apparent in box and global model studies of tropical VOC chemistry may be more strongly influenced by representation of detailed physical and micrometeorological effects than errors in the chemical scheme.
42. Reactive Halogens in the Marine Boundary Layer (RHaMBLe): The tropical North Atlantic experiments
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A. M. Hollingsworth, Alexander A. P. Pszenny, Anoop S. Mahajan, Gordon McFiggans, K. L. Furneaux, Thomas Müller, Roderic L. Jones, Michael J. Lawler, James R. Hopkins, Dwayne E. Heard, Alastair C. Lewis, Hartmut Herrmann, E. Fuentes, Eric S. Saltzman, M. Irwin, William C. Keene, Dickon Young, James D. Lee, B. D. Finley, A. K. Benton, Andrew Goddard, Sarah Moller, Jacqueline F. Hamilton, Alex R. Baker, John Methven, S. Lehmann, Lisa K. Whalley, Stephen M. Ball, N. Niedermeier, Lucy J. Carpenter, Nicholas Good, Trevor Ingham, Simon O'Doherty, James Allan, John M. C. Plane, Rolf Sander, Hilke Oetjen, Roisin Commane, Michael S. Long, Katie A. Read, Alfonso Saiz-Lopez, A. Wiedensohler, K. Müller, R. von Glasow, C. E. Jones, and Mathew J. Evans
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iodine chemistry ,Atmospheric Science ,Marine boundary layer ,010504 meteorology & atmospheric sciences ,bromine ,doas measurements ,nonmethane hydrocarbons ,010501 environmental sciences ,01 natural sciences ,lcsh:Chemistry ,Troposphere ,Physical Sciences and Mathematics ,ozone destruction ,14. Life underwater ,indian-ocean ,mace head ,0105 earth and related environmental sciences ,sea-salt aerosol ,eastern atlantic ,lcsh:QC1-999 ,Indian ocean ,Oceanography ,lcsh:QD1-999 ,troposphere ,13. Climate action ,lcsh:Physics ,Geology - Abstract
The NERC UK SOLAS-funded Reactive Halogens in the Marine Boundary Layer (RHaMBLe) programme comprised three field experiments. This manuscript presents an overview of the measurements made within the two simultaneous remote experiments conducted in the tropical North Atlantic in May and June 2007. Measurements were made from two mobile and one ground-based platforms. The heavily instrumented cruise D319 on the RRS Discovery from Lisbon, Portugal to São Vicente, Cape Verde and back to Falmouth, UK was used to characterise the spatial distribution of boundary layer components likely to play a role in reactive halogen chemistry. Measurements onboard the ARSF Dornier aircraft were used to allow the observations to be interpreted in the context of their vertical distribution and to confirm the interpretation of atmospheric structure in the vicinity of the Cape Verde islands. Long-term ground-based measurements at the Cape Verde Atmospheric Observatory (CVAO) on São Vicente were supplemented by long-term measurements of reactive halogen species and characterisation of additional trace gas and aerosol species during the intensive experimental period. This paper presents a summary of the measurements made within the RHaMBLe remote experiments and discusses them in their meteorological and chemical context as determined from these three platforms and from additional meteorological analyses. Air always arrived at the CVAO from the North East with a range of air mass origins (European, Atlantic and North American continental). Trace gases were present at stable and fairly low concentrations with the exception of a slight increase in some anthropogenic components in air of North American origin, though NOx mixing ratios during this period remained below 20 pptv (note the non-IUPAC adoption in this manuscript of pptv and ppbv, equivalent to pmol mol−1 and nmol mol−1 to reflect common practice). Consistency with these air mass classifications is observed in the time series of soluble gas and aerosol composition measurements, with additional identification of periods of slightly elevated dust concentrations consistent with the trajectories passing over the African continent. The CVAO is shown to be broadly representative of the wider North Atlantic marine boundary layer; measurements of NO, O3 and black carbon from the ship are consistent with a clean Northern Hemisphere marine background. Aerosol composition measurements do not indicate elevated organic material associated with clean marine air. Closer to the African coast, black carbon and NO levels start to increase, indicating greater anthropogenic influence. Lower ozone in this region is possibly associated with the increased levels of measured halocarbons, associated with the nutrient rich waters of the Mauritanian upwelling. Bromide and chloride deficits in coarse mode aerosol at both the CVAO and on D319 and the continuous abundance of inorganic gaseous halogen species at CVAO indicate significant reactive cycling of halogens. Aircraft measurements of O3 and CO show that surface measurements are representative of the entire boundary layer in the vicinity both in diurnal variability and absolute levels. Above the inversion layer similar diurnal behaviour in O3 and CO is observed at lower mixing ratios in the air that had originated from south of Cape Verde, possibly from within the ITCZ. ECMWF calculations on two days indicate very different boundary layer depths and aircraft flights over the ship replicate this, giving confidence in the calculated boundary layer depth.
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43. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers
- Author
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Jens Friis-Nielsen, Kristín Rós Kjartansdóttir, Sarah Mollerup, Maria Asplund, Tobias Mourier, Randi Holm Jensen, Thomas Arn Hansen, Alba Rey-Iglesia, Stine Raith Richter, Ida Broman Nielsen, David E. Alquezar-Planas, Pernille V. S. Olsen, Lasse Vinner, Helena Fridholm, Lars Peter Nielsen, Eske Willerslev, Thomas Sicheritz-Pontén, Ole Lund, Anders Johannes Hansen, Jose M. G. Izarzugaza, and Søren Brunak
- Subjects
sequence clustering ,taxonomic characterisation ,novel sequence identification ,next generation sequencing ,cancer causing viruses ,oncoviruses ,assay contamination ,Microbiology ,QR1-502 - Abstract
Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32 non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified inhabitants of the healthy tissue flora as well as experimental contaminants. Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified.
- Published
- 2016
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