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Pollen are hygroscopic; therefore, they have the potential to act as cloud condensation nuclei (CCN) in the atmosphere. This could have uncertain implications for cloud processes and climate as well as plant biodiversity and human health. Previous studies have investigated the hygroscopic swelling of pollen, linked to CCN activity by the κ-Köhler theory, using methods that follow observed mass increase by electrodynamic balance (EDB) or vapour sorption analyser. This study uses an acoustic levitator to levitate pollen grains in the true aerosol phase and uses a macroscope to image the pollen to investigate hygroscopic behaviour when relative humidity (RH) is changed. Two pollen species were studied in this work: Lilium orientalis (oriental lily) and Populus deltoides (eastern cottonwood). Both species were successfully levitated; however, the smaller Populus deltoides showed greater instability throughout experiments. The quality of images taken by the macroscope, and thus calculations of pollen area and aspect ratio, varied significantly and were sensitive to lighting conditions as well as to levitated pollen grain movement and orientation. Experiments with surface-fixed pollen grains were also conducted. They showed evidence that pollen hygroscopic swelling could be observed by the macroscope. The produced results were comparable with previously reported mass increase values. Although less accurate than methods that measure mass changes, the acoustic levitator and macroscope set-up offer an attractive alternative by virtue of being commercial, off-the-shelf, low-cost, and versatile techniques. A key advantage of this method is that it is possible to visually observe particle shape dynamics under varying environmental conditions.

Icelandic dust can impact the radiative budget in high-latitude regions directly by affecting light absorption and scattering and indirectly by changing the surface albedo after dust deposition. This tends to produce a positive radiative forcing. However, the limited knowledge of the spectral optical properties of Icelandic dust prevents an accurate assessment of these radiative effects. Here, the spectral single scattering albedo (SSA) and the complex refractive index (m=n-ik) of Icelandic dust from five major emission hotspots were retrieved between 370–950 nm using online measurements of size distribution and spectral absorption (βabs) and scattering (βsca) coefficients of particles suspended in a large-scale atmospheric simulation chamber. The SSA(λ) estimated from the measured βabs and βsca increased from 0.90–0.94 at 370 nm to 0.94–0.96 at 950 nm in Icelandic dust from the different hotspots, which falls within the range of mineral dust from northern Africa and eastern Asia. The spectral complex refractive index was retrieved by minimizing the differences between the measured βabs and βsca and those computed using the Mie theory for spherical and internally homogeneous particles, using the size distribution data as input. The real part of the complex refractive index (n(λ)) was found to be 1.60–1.61 in the different samples and be independent of wavelength. The imaginary part (k(λ)) was almost constant with wavelength and was found to be around 0.004 at 370 nm and 0.002–0.003 at 950 nm. The estimated complex refractive index was close to the initial estimates based on the mineralogical composition, also suggesting that the high magnetite content observed in Icelandic dust may contribute to its high absorption capacity in the shortwave part of the spectrum. The k(λ) values retrieved for Icelandic dust are at the upper end of the reported range for low-latitude dust (e.g., from the Sahel). Furthermore, Icelandic dust tends to be more absorbing towards the near-infrared. In Icelandic dust, k(λ) between 660–950 nm was 2–8 times higher than most of the dust samples sourced in northern Africa and eastern Asia. This suggests that Icelandic dust may have a stronger positive direct radiative forcing on climate that has not been accounted for in climate predictions.

In forests, the residence time of air – the inverse of first-order exchange rates – influences in-canopy chemistry and the exchanges of momentum, energy, and mass with the surrounding atmosphere. Accurate estimates are needed for chemical investigations of reactive trace species, such as volatile organic compounds, some of whose chemical lifetimes are on the order of average residence times. However, very few observational residence-time estimates have been reported. Little is known about even the basic statistics of real-world residence times or how they are influenced by meteorological variables such as turbulence or atmospheric stability. Here, we report opportunistic investigations of residence time of air in a free-air carbon dioxide enrichment (FACE) facility in a mature, broadleaf deciduous forest with canopy height of hc≈25 m. Using nearly 50 million FACE observations, we find that median daytime residence times in the tree crowns range from around 70 s when the trees are in leaf to just over 34 s when they are not. Residence times increase with increasing atmospheric stability, as does the spread around their central value. Residence times scale approximately with the reciprocal of the friction velocity, u∗. During some calm evenings in the growing season, we observe distinctly different behaviour: pooled air being sporadically and unpredictably vented – evidenced by sustained increases in CO2 concentration – when intermittent turbulence penetrates the canopy. In these conditions, the concept of a residence time is less clearly defined. Parameterisations available in the literature underestimate turbulent exchange in the upper half of forest crowns and overestimate the frequency of long residence times. Robust parameterisations of residence times (or, equivalently, fractions of emissions escaping the canopy) may be generated from inverse-gamma distributions, with the parameters 1.4≤α≤1.8 and β=hc/u∗ estimated from widely measured flow variables. In this case, the mean value for τ becomes formally defined as τ‾=β/(α-1). For species released in the canopy during the daytime, chemical transformations are unlikely unless the reaction timescale is on the order of a few minutes or less.

Forest environments contain a wide variety of airborne biological particles (bioaerosols), including pollen, fungal spores, bacteria, viruses, plant detritus, and soil particles. Forest bioaerosol plays a number of important roles related to plant and livestock health, human disease and allergenicity, and forest and wider ecology and are thought to influence biosphere–atmosphere interactions via warm and cold cloud formation. Despite the importance of bioaerosols, there are few measurements of forest aerosol, and there is a lack of understanding of how climate change will affect forest bioaerosol in the future. We installed low-cost optical particle counters (OPCs) to measure particles in the size range between 1 and 10 µm (PM10–PM1) for a period of 2 months in autumn 2018 at the Birmingham Institute of Forest Research (BIFoR) free-air carbon dioxide enrichment (FACE) facility. In the paper, we propose that the PM10–PM1 (particulate matter) metric is a good proxy for bioaerosols because of the bioaerosol representative size range, the location of the study site (a woodland in a rural location), the field measurement taking place during the season of peak fungal activity, and the low hygroscopicity of the particles measured. The BIFoR FACE facility fumigates three 700 m2 areas of the forest with an additional 150 ppm CO2 above ambient levels with minimal impacts on other potential environmental drivers such as temperature, humidity, and wind. This experimental set-up enabled us to investigate the effect of environmental variables, including elevated CO2 (eCO2), on bioaerosol proxy concentrations and to evaluate the performance of the low-cost OPCs in a forested environment. Operating the low-cost OPCs during autumn 2018, we aimed to capture predominantly the fungal bioaerosol season. Across the experimental duration, the OPCs captured both temporal and spatial variation in bioaerosol concentrations. Aerosol concentrations were affected by changing temperatures and wind speeds but, contrary to our initial hypothesis, not by relative humidity. We detected no effect of the eCO2 treatment on total bioaerosol concentrations, but a potential suppression of high-concentration bioaerosol events was detected under eCO2. In-canopy atmospheric dispersion modelling indicates that the median spore dispersion distance is sufficiently small that there is little mixing between treatment and control experiments. Our data demonstrate the suitability of low-cost OPCs, interpreted with due caution, for use in forests and so opens the possibility of forest bioaerosol monitoring in a wider range of habitats to a wider range of researchers at a modest cost.

Iceland is a highly active source of natural dust. Icelandic dust has the potential to directly affect the climate via dust–radiation interaction and indirectly via dust–cloud interaction, the snow/ice albedo effect and impacts on biogeochemical cycles. The impacts of Icelandic dust depend on its mineralogical and chemical composition. However, a lack of data has prevented an accurate assessment of the role of Icelandic dust in the Earth system. Here, we collected surface sediment samples from five major Icelandic dust hotspots. Dust aerosols were generated and suspended in atmospheric chambers, and PM10 and PM20 fractions were collected for further analysis. We found that the dust samples primarily consist of amorphous basaltic materials ranging from 8 wt % (from the Hagavatn hotspot) to 60 wt %–90 wt % (other hotspots). Samples had relatively high total Fe content (10 wt %–13 wt %). Sequential extraction of Fe to determine its chemical form shows that dithionite Fe (Fe oxides such as hematite and goethite) and ascorbate Fe (amorphous Fe) contribute respectively 1 %–6 % and 0.3 %–1.4 % to the total Fe in Icelandic dust. The magnetite fraction is 7 %–15 % of total Fe and 1 %–2 wt % of PM10, which is orders of magnitude higher than in mineral dust from northern Africa. Nevertheless, about 80 %–90% of the Fe is contained in pyroxene and amorphous glass. The initial Fe solubility (ammonium acetate extraction at pH 4.7) is from 0.08 % to 0.6 %, which is comparable to low-latitude dust such as that from northern Africa. The Fe solubility at low pH (i.e. pH 2) is significantly higher than typical low-latitude dust (up to 30 % at pH 2 after 72 h). Our results revealed the fundamental differences in composition and mineralogy of Icelandic dust from low-latitude dust. We attribute these differences to the low degree of chemical weathering, the basaltic composition of the parent sediments and glacial processes. Icelandic dust contributes to the atmospheric deposition of soluble Fe and can impact primary productivity in the North Atlantic Ocean. The distinct chemical and mineralogical composition, particularly the high magnetite content (1 wt %–2 wt %), indicates a potentially significant impact of Icelandic dust on the radiation balance in the subpolar and polar regions.

A recent study demonstrated that diesel particles in urban air undergo evaporative shrinkage when advected to a cleaner atmosphere (Harrison et al., 2016). We explore, in a structured and systematic way, the sensitivity of nucleation-mode diesel particles (diameter < 30 nm) to changes in particle composition, saturation vapour pressure, and the mass accommodation coefficient. We use a multicomponent aerosol microphysics model based on surrogate molecule (C16−C32 n-alkane) volatilities. For standard atmospheric conditions (298 K, 1013.25 hPa), and over timescales (ca. 100 s) relevant for dispersion on the neighbourhood scale (up to 1 km), the choice of a particular vapour pressure dataset changes the range of compounds that are appreciably volatile by two to six carbon numbers. The nucleation-mode peak diameter, after 100 s of model runtime, is sensitive to the vapour pressure parameterisations for particles with compositions centred on surrogate molecules between C22H46 and C24H50. The vapour pressure range, derived from published data, is between 9.23 × 10−3 and 8.94 × 10−6 Pa for C22H46 and between 2.26 × 10−3 and 2.46 × 10−7 Pa for C24H50. Therefore, the vapour pressures of components in this range are critical for the modelling of nucleation-mode aerosol dynamics on the neighbourhood scale and need to be better constrained. Laboratory studies have shown this carbon number fraction to derive predominantly from engine lubricating oil. The accuracy of vapour pressure data for other (more and less volatile) components from laboratory experiments is less critical. The influence of a core of non-volatile material is also considered; non-volatile core fractions of more than 5 % are inconsistent with the field measurements that we test the model against. We consider mass accommodation coefficient values less than unity and find that model runs with more volatile vapour pressure parameterisations and lower accommodation coefficients are similar to runs with less volatile vapour pressure parameterisations and higher accommodation coefficients. The new findings of this study may also be used to identify semi-volatile organic compound (SVOC) compositions that play dominating roles in the evaporative shrinkage of the nucleation mode observed in field measurements (Dall'Osto et al., 2011).

Airborne particles and vapours, like many other environmental samples including water, soils and sediments, contain complex mixtures of hydrocarbons, often deriving from crude oil either before or after fractionation into fuels, lubricants and feedstocks. Comprehensive 2D gas chromatography time-of-flight mass spectrometry (GC × GC-ToF-MS), offers a very powerful technique that separates and identifies many compounds in complicated hydrocarbon mixtures. However, quantification and identification of individual constituents at high ionization energies would require hundreds of expensive (when available) standards for calibration. Although the precise chemical structure of hydrocarbons does matter for their environmental impact and fate, strong similarities can be expected for compounds having very similar chemical structures and carbon numbers. There is, therefore, a clear benefit in an analytical technique which is specific enough to separate different classes of compounds and to distinguish homologous series while avoiding the need to handle each isomer individually. Varying EI (electron impact) ionization mass spectrometry significantly enhances the identification of individual isomers and homologous compound groups, which we refer to as isomer sets. Advances are reported in mapping and quantifying isomer sets of hydrocarbons (≥ C12) in diesel fuel, lubricating oil and diesel exhaust emissions. By using this analysis we report mass closures of ca. 90 and 75 % for diesel fuel and lubricating oil, and identify 85 and 75 % of the total ion current for gas- and particulate-phase diesel exhaust emissions.

Highly non-linear dynamical systems, such as those found in atmospheric chemistry, necessitate hierarchical approaches to both experiment and modelling in order to ultimately identify and achieve fundamental process-understanding in the full open system. Atmospheric simulation chambers comprise an intermediate in complexity, between a classical laboratory experiment and the full, ambient system. As such, they can generate large volumes of difficult-to-interpret data. Here we describe and implement a chemometric dimension reduction methodology for the deconvolution and interpretation of complex gas- and particle-phase composition spectra. The methodology comprises principal component analysis (PCA), hierarchical cluster analysis (HCA) and positive least-squares discriminant analysis (PLS-DA). These methods are, for the first time, applied to simultaneous gas- and particle-phase composition data obtained from a comprehensive series of environmental simulation chamber experiments focused on biogenic volatile organic compound (BVOC) photooxidation and associated secondary organic aerosol (SOA) formation. We primarily investigated the biogenic SOA precursors isoprene, α-pinene, limonene, myrcene, linalool and β-caryophyllene. The chemometric analysis is used to classify the oxidation systems and resultant SOA according to the controlling chemistry and the products formed. Results show that "model" biogenic oxidative systems can be successfully separated and classified according to their oxidation products. Furthermore, a holistic view of results obtained across both the gas- and particle-phases shows the different SOA formation chemistry, initiating in the gas-phase, proceeding to govern the differences between the various BVOC SOA compositions. The results obtained are used to describe the particle composition in the context of the oxidised gas-phase matrix. An extension of the technique, which incorporates into the statistical models data from anthropogenic (i.e. toluene) oxidation and "more realistic" plant mesocosm systems, demonstrates that such an ensemble of chemometric mapping has the potential to be used for the classification of more complex spectra of unknown origin. More specifically, the addition of mesocosm data from fig and birch tree experiments shows that isoprene and monoterpene emitting sources, respectively, can be mapped onto the statistical model structure and their positional vectors can provide insight into their biological sources and controlling oxidative chemistry. The potential to extend the methodology to the analysis of ambient air is discussed using results obtained from a zero-dimensional box model incorporating mechanistic data obtained from the Master Chemical Mechanism (MCMv3.2). Such an extension to analysing ambient air would prove a powerful asset in assisting with the identification of SOA sources and the elucidation of the underlying chemical mechanisms involved.

Concentrations and fluxes of seven volatile organic compounds (VOCs) were measured between August and December 2012 at a rooftop site in central London as part of the ClearfLo project (Clean Air for London). VOC concentrations were quantified using a proton transfer reaction mass spectrometer (PTR-MS) and fluxes were calculated using a virtual disjunct eddy covariance technique. The median VOC fluxes, including aromatics, oxygenated compounds and isoprene, ranged from 0.07 to 0.33 mg m−2 h−1. Median mixing ratios were 7.3 ppb for methanol and < 1 ppb for the other compounds. Strong relationships were observed between the fluxes and concentrations of some VOCs with traffic density and between the fluxes and concentrations of isoprene and oxygenated compounds with photosynthetically active radiation (PAR) and temperature. An estimated 50–90 % of the fluxes of aromatic VOCs were attributable to traffic activity, which showed little seasonal variation, suggesting that boundary layer effects or possibly advected pollution may be the primary causes of increased concentrations of aromatics in winter. Isoprene, methanol and acetaldehyde fluxes and concentrations in August and September showed high correlations with PAR and temperature, when fluxes and concentrations were largest suggesting that biogenic sources contributed to their fluxes. Modelled biogenic isoprene fluxes from urban vegetation using the Guenther et al. (1995) algorithm agreed well with measured fluxes in August and September. Comparisons of estimated annual benzene emissions from both the London and the National Atmospheric Emissions Inventories agreed well with measured benzene fluxes. Flux footprint analysis indicated emission sources were localised and that boundary layer dynamics and source strengths were responsible for temporal and spatial VOC flux and concentration variability during the measurement period.

Silver birch (Betula pendula) and three Southeast Asian tropical plant species (Ficus cyathistipula, Ficus benjamina and Caryota millis) from the pantropical fig and palm genera were grown in a purpose-built and environment-controlled whole-tree chamber. The volatile organic compounds emitted from these trees were characterised and fed into a linked photochemical reaction chamber where they underwent photo-oxidation under a range of controlled conditions (relative humidity or RH ~65–89%, volatile organic compound-to-NOx or VOC / NOx ~3–9 and NOx ~2 ppbV). Both the gas phase and the aerosol phase of the reaction chamber were monitored in detail using a comprehensive suite of on-line and off-line chemical and physical measurement techniques. Silver birch was found to be a high monoterpene and sesquiterpene but low isoprene emitter, and its emissions were observed to produce measurable amounts of secondary organic aerosol (SOA) via both nucleation and condensation onto pre-existing seed aerosol (YSOA 26–39%). In contrast, all three tropical species were found to be high isoprene emitters with trace emissions of monoterpenes and sesquiterpenes. In tropical plant experiments without seed aerosol there was no measurable SOA nucleation, but aerosol mass was shown to increase when seed aerosol was present. Although principally isoprene emitting, the aerosol mass produced from tropical fig was mostly consistent (i.e. in 78 out of 120 aerosol mass calculations using plausible parameter sets of various precursor specific yields) with condensation of photo-oxidation products of the minor volatile organic compounds (VOCs) co-emitted; no significant aerosol yield from condensation of isoprene oxidation products was required in the interpretations of the experimental results. This finding is in line with previous reports of organic aerosol loadings consistent with production from minor biogenic VOCs co-emitted with isoprene in principally isoprene-emitting landscapes in Southeast Asia. Moreover, in general the amount of aerosol mass produced from the emissions of the principally isoprene-emitting plants was less than would be expected from published single-VOC experiments, if co-emitted species were solely responsible for the final SOA mass. Interpretation of the results obtained from the fig data sets leaves room for a potential role for isoprene in inhibiting SOA formation under certain ambient atmospheric conditions, although instrumental and experimental constraints impose a level of caution in the interpretation of the results. Concomitant gas- and aerosol-phase composition measurements also provide a detailed overview of numerous key oxidation mechanisms at work within the systems studied, and their combined analysis provides insight into the nature of the SOA formed.

A systematic, semi-automatic method for imaging the cards from the widely used Campbell–Stokes sunshine recorder is described. We show how the application of inexpensive commercial equipment and practices can simply and robustly build an archive of high-quality card images and manipulate them into a form suitable for easy further analysis. Rectified and registered digital images are produced, with the card's midday marker in the middle of the longest side, and with a temporal scaling of 150 pixels per hour. The method improves on previous, mostly manual, analyses by simplifying and automating steps into a process capable of handling thousands of cards in a practical timescale. A prototype method of extraction of data from this archive is then tested by comparison with records from a co-located pyrheliometer at a resolution of the order of minutes. The comparison demonstrates that the Campbell–Stokes recorder archive contains a time series of downwelling solar-irradiance-related data with similar characteristics to that of benchmark pyrheliometer data from the Baseline Surface Radiation Network. A universal transfer function for card burn to direct downwelling short-wave radiation is still some way off and is the subject of ongoing research. Until such time as a universal transfer function is available, specific functions for extracting data in particular circumstances offer a useful way forward. The new image-capture method offers a practical way to exploit the worldwide sets of long-term Campbell–Stokes recorder data to create a time series of solar irradiance and atmospheric aerosol loading metrics reaching back over 100 yr from the present day.

ABSTRACT Knowledge about sex‐specific difference in life‐history traits—like growth, mortality, or behavior—is of key importance for management and conservation as these parameters are essential for predictive modeling of population sustainability. We applied a newly developed molecular sex identification method, in combination with a SNP (single nucleotide polymorphism) panel for inferring the population of origin, for more than 300 large Atlantic bluefin tuna (ABFT) collected over several years from newly reclaimed feeding grounds in the Northeast Atlantic. The vast majority (95%) of individuals were genetically assigned to the eastern Atlantic population, which migrates between spawning grounds in the Mediterranean and feeding grounds in the Northeast Atlantic. We found a consistent pattern of a male bias among the eastern Atlantic individuals, with a 4‐year mean of 63% males (59%–65%). Males were most prominent within the smallest ( 250 cm) length classes, while the sex ratio was close to 1:1 for intermediate sizes (230–250 cm). The results from this new, widely applicable, and noninvasive approach suggests differential occupancy or migration timing of ABFT males and females, which cannot be explained alone by sex‐specific differences in growth. Our findings are corroborated by previous traditional studies of sex ratios in dead ABFT from the Atlantic, the Mediterranean, and the Gulf of Mexico. In concert with observed differences in growth and mortality rates between the sexes, these findings should be recognized in order to sustainably manage the resource, maintain productivity, and conserve diversity within the species.

A Lagrangian model of photochemistry and mixing is described (CiTTyCAT, stemming from the Cambridge Tropospheric Trajectory model of Chemistry And Transport), which is suitable for transport and chemistry studies throughout the troposphere. Over the last five years, the model has been developed in parallel at several different institutions and here those developments have been incorporated into one "community" model and documented for the first time. The key photochemical developments include a new scheme for biogenic volatile organic compounds and updated emissions schemes. The key physical development is to evolve composition following an ensemble of trajectories within neighbouring air-masses, including a simple scheme for mixing between them via an evolving "background profile", both within the boundary layer and free troposphere. The model runs along trajectories pre-calculated using winds and temperature from meteorological analyses. In addition, boundary layer height and precipitation rates, output from the analysis model, are interpolated to trajectory points and used as inputs to the mixing and wet deposition schemes. The model is most suitable in regimes when the effects of small-scale turbulent mixing are slow relative to advection by the resolved winds so that coherent air-masses form with distinct composition and strong gradients between them. Such air-masses can persist for many days while stretching, folding and thinning. Lagrangian models offer a useful framework for picking apart the processes of air-mass evolution over inter-continental distances, without being hindered by the numerical diffusion inherent to global Eulerian models. The model, including different box and trajectory modes, is described and some output for each of the modes is presented for evaluation. The model is available for download from a Subversion-controlled repository by contacting the corresponding authors.

This paper reports the first direct eddy covariance fluxes of reactive biogenic volatile organic compounds (BVOCs) from oil palms to the atmosphere using proton-transfer-reaction mass spectrometry (PTR-MS), measured at a plantation in Malaysian Borneo. At midday, net isoprene flux constituted the largest fraction (84 %) of all emitted BVOCs measured, at up to 30 mg m−2 h−1 over 12 days. By contrast, the sum of its oxidation products methyl vinyl ketone (MVK) and methacrolein (MACR) exhibited clear deposition of 1 mg m−2 h−1, with a small average canopy resistance of 230 s m−1. Approximately 15 % of the resolved BVOC flux from oil palm trees could be attributed to floral emissions, which are thought to be the largest reported biogenic source of estragole and possibly also toluene. Although on average the midday volume mixing ratio of estragole exceeded that of toluene by almost a factor of two, the corresponding fluxes of these two compounds were nearly the same, amounting to 0.81 and 0.76 mg m−2 h−1, respectively. By fitting the canopy temperature and PAR response of the MEGAN emissions algorithm for isoprene and other emitted BVOCs a basal emission rate of isoprene of 7.8 mg m−2 h−1 was derived. We parameterise fluxes of depositing compounds using a resistance approach using direct canopy measurements of deposition. Consistent with Karl et al. (2010), we also propose that it is important to include deposition in flux models, especially for secondary oxidation products, in order to improve flux predictions.

Biogenic volatile organic compounds (BVOCs) such as isoprene constitute a large proportion of the global atmospheric oxidant sink. Their reactions in the atmosphere contribute to processes such as ozone production and secondary organic aerosol formation. However, over the tropical rainforest, where 50 % of the global emissions of BVOCs are believed to occur, atmospheric chemistry models have been unable to simulate concurrently the measured daytime concentration of isoprene and that of its principal oxidant, hydroxyl (OH). One reason for this model-measurement discrepancy may be incomplete mixing of isoprene within the convective boundary layer, leading to patchiness or segregation in isoprene and OH mixing ratios and average concentrations that appear to be incompatible with each other. One way of capturing this effect in models of atmospheric chemistry is to use a reduced effective rate constant for their reaction. Recent studies comparing atmospheric chemistry global/box models with field measurements have suggested that this effective rate reduction may be as large as 50 %; which is at the upper limit of that calculated using large eddy simulation models. To date there has only been one field campaign worldwide that has reported co-located measurements of isoprene and OH at the necessary temporal resolution to calculate the segregation of these compounds. However many campaigns have recorded sufficiently high resolution isoprene measurements to capture the small-scale fluctuations in its concentration. Assuming uniform distributions of other OH production and loss processes, we use a box model of atmospheric chemistry, constrained by the spectrum of isoprene concentrations measured, as a virtual instrument, to estimate the variability in OH at a point and hence, to estimate the segregation intensity of isoprene and OH from high-frequency isoprene time series. The method successfully reproduces the only directly observed segregation, using measurements made in a deciduous forest in Germany. The effective rate constant reduction for the reaction of isoprene and OH over a South-East Asian rainforest is calculated to be typically

As part of the OP3 field study of rainforest atmospheric chemistry, above-canopy fluxes of isoprene, monoterpenes and oxygenated volatile organic compounds were made by virtual disjunct eddy covariance from a South-East Asian tropical rainforest in Malaysia. Approximately 500 hours of flux data were collected over 48 days in April–May and June–July 2008. Isoprene was the dominant non-methane hydrocarbon emitted from the forest, accounting for 80% (as carbon) of the measured emission of reactive carbon fluxes. Total monoterpene emissions accounted for 18% of the measured reactive carbon flux. There was no evidence for nocturnal monoterpene emissions and during the day their flux rate was dependent on both light and temperature. The oxygenated compounds, including methanol, acetone and acetaldehyde, contributed less than 2% of the total measured reactive carbon flux. The sum of the VOC fluxes measured represents a 0.4% loss of daytime assimilated carbon by the canopy, but atmospheric chemistry box modelling suggests that most (90%) of this reactive carbon is returned back to the canopy by wet and dry deposition following chemical transformation. The emission rates of isoprene and monoterpenes, normalised to 30 °C and 1000 μmol m−2 s−1 PAR, were 1.6 mg m−2 h−1 and 0.46mg m−2 h−1 respectively, which was 4 and 1.8 times lower respectively than the default value for tropical forests in the widely-used MEGAN model of biogenic VOC emissions. This highlights the need for more direct canopy-scale flux measurements of VOCs from the world's tropical forests.

A new modelling tool for the investigation of large-scale behaviour of cirrus clouds has been developed. This combines two existing models, the TOMCAT/SLIMCAT chemistry transport model (nupdate library version 0.80, script mpc346_l) and cirrus parameterisation of Ren and MacKenzie (LACM implementation not versioned). The development process employed a subset of best-practice software engineering and quality assurance processes, selected to be viable for small-scale projects whilst maintaining the same traceability objectives. The application of the software engineering and quality control processes during the development has been shown to be not a great overhead, and their use has been of benefit to the developers as well as the end users of the results. We provide a step-by-step guide to the implementation of traceability tailored to the production of geo-scientific research software, as distinct from commercial and operational software. Our recommendations include: maintaining a living "requirements list"; explicit consideration of unit, integration and acceptance testing; and automated revision/configuration control, including control of analysis tool scripts and programs. Initial testing of the resulting model against satellite and in-situ measurements has been promising. The model produces representative results for both spatial distribution of the frequency of occurrence of cirrus ice, and the drying of air as it moves across the tropical tropopause. The model is now ready for more rigorous quantitative testing, but will require the addition of a vertical wind velocity downscaling scheme to better represent extra-tropical continental cirrus.

A multi-platform field measurement campaign involving aircraft and balloons took place over West Africa between 26 July and 25 August 2006, in the frame of the concomitant AMMA Special Observing Period and SCOUT-O3 African tropical activities. Specifically aiming at sampling the upper troposphere and lower stratosphere, the high-altitude research aircraft M55 Geophysica was deployed in Ouagadougou (12.3° N, 1.7° W), Burkina Faso, in conjunction with the German D-20 Falcon, while a series of stratospheric balloons and sonde flights were conducted from Niamey (13.5° N, 2.0° E), Niger. Altogether, these measurements were intended to provide experimental evidence for a better understanding of large scale transport, assessing the effect of lightning on NOx production, and studying the impact of intense mesoscale convective systems on water, aerosol, dust and chemical species in the upper troposphere and lower stratosphere. The M55 Geophysica carried out five local and four transfer flights between southern Europe and the Sahel and back, while eight stratospheric balloons and twenty-nine sondes were flown from Niamey. These experiments allowed a characterization of the tropopause and lower stratosphere of the region. The paper provides an overview of SCOUT-AMMA campaign activities together with a description of the meteorology of the African monsoon and the situation prevailing during the flights and a brief summary of the observations accomplished.

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.

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.

An aircraft measurement campaign involving the Russian high-altitude aircraft M55 Geophysica and the German DLR Falcon was conducted in Darwin, Australia in November and December 2005 as part of the European integrated project SCOUT-O3. The overall objectives of the campaign were to study the transport of trace gases through the tropical tropopause layer (TTL), mechanisms of dehydration close to the tropopause, and the role of deep convection in these processes. In this paper a detailed roadmap of the campaign is presented, including rationales for each flight, and an analysis of the local and large-scale meteorological context in which they were embedded. The campaign took place during the pre-monsoon season which is characterized by a pronounced diurnal evolution of deep convection including a mesoscale system over the Tiwi Islands north of Darwin known as "Hector". This allowed studying in detail the role of deep convection in structuring the tropical tropopause region, in situ sampling convective overshoots above storm anvils, and probing the structure of anvils and cirrus clouds by Lidar and a suite of in situ instruments onboard the two aircraft. The large-scale flow during the first half of the campaign was such that local flights, away from convection, sampled air masses downstream of the "cold trap" region over Indonesia. Abundant cirrus clouds enabled the study of active dehydration, in particular during two TTL survey flights. The campaign period also encompassed a Rossby wave breaking event transporting stratospheric air to the tropical middle troposphere and an equatorial Kelvin wave modulating tropopause temperatures and hence the conditions for dehydration.

During the APE-THESEO mission in the Indian Ocean the Myasishchev Design Bureau stratospheric research aircraft M55 Geophysica performed a flight over and within the inner core region of tropical cyclone Davina. Measurements of total water, water vapour, temperature, aerosol backscattering, ozone and tracers were made and are discussed here in comparison with the averages of those quantities acquired during the campaign time frame. Temperature anomalies in the tropical tropopause layer (TTL), warmer than average in the lower part and colder than average in the upper TTL were observed. Ozone was strongly reduced compared to its average value, and thick cirrus decks were present up to the cold point, sometimes topped by a layer of very dry air. Evidence for meridional transport of trace gases in the stratosphere above the cyclone was observed and perturbed water distribution in the TTL was documented. The paper discuss possible processes of dehydration induced by the cirrus forming above the cyclone, and change in the chemical tracer and water distribution in the lower stratosphere 400–430 K due to meridional transport from the mid-latitudes and link with Davina. Moreover it compares the data prior and after the cyclone passage to discuss its actual impact on the atmospheric chemistry and thermodynamics.

We have developed a Lagrangian air-parcel cirrus model (LACM), to diagnose the processes controlling water in the tropical tropopause layer (TTL). LACM applies parameterised microphysics to air parcel trajectories. The parameterisation includes the homogeneous freezing of aerosol droplets, the growth/sublimation of ice particles, and sedimentation of ice particles, so capturing the main dehydration mechanism for air in the TTL. Rehydration is also considered by resetting the water vapour mixing ratio in an air parcel to the value at the point in the 4-D analysis/forecast data used to generate the trajectories, but only when certain conditions, indicative of convection, are satisfied. The conditions act to restrict rehydration of the Lagrangian air parcels to regions where convective transport of water vapour from below is significant, at least to the extent that the analysis/forecast captures this process. The inclusion of hydration and dehydration mechanisms in LACM results in total water fields near tropical convection that have more of the "stripy" character of satellite observations of high cloud, than do either the ECMWF analysis or trajectories without microphysics. The mixing ratios of total water in the TTL, measured by a high-altitude aircraft over Brazil (during the TROCCINOX campaign), have been reconstructed by LACM using trajectories generated from ECMWF analysis. Two other Lagrangian reconstructions are also tested: linear interpolation of ECMWF analysed specific humidity onto the aircraft flight track, and instantaneous dehydration to the saturation vapour pressure over ice along trajectories. The reconstructed total water mixing ratios along aircraft flight tracks are compared with observations from the FISH total water hygrometer. Process-oriented analysis shows that modelled cirrus cloud events are responsible for dehydrating the air parcels coming from lower levels, resulting in total water mixing ratios as low as 2 μmol/mol. Without adding water back to some of the trajectories, the LACM and instantaneous-dehydration reconstructions have a dry bias. The interpolated-ECMWF reconstruction does not suffer this dry bias, because convection in the ECMWF model moistens air parcels dramatically, by pumping moist air upwards. This indicates that the ECMWF model captures the gross features of the rehydration of air in the TTL by convection. Overall, the ECMWF models captures well the exponential decrease in total water mixing ratio with height above 250 hPa, so that all the reconstruction techniques capture more than 75% of the standard deviation in the measured total water mixing ratios over the depth of the TTL. By picking up the main contributing processes to dehydration and rehydration in the TTL, LACM reconstructs total water mixing ratios at the top of the TTL, close to the cold point, that are always in substantially better agreement with observations than instantaneous-dehydration reconstructions, and better than the ECMWF analysis for regions of high relative humidity and cloud.

Abstract Comorbid proteinopathies are observed in many neurodegenerative disorders including Alzheimer’s disease (AD), increase with age, and influence clinical outcomes, yet the mechanisms remain ill-defined. Here, we show that reduction of progranulin (PGRN), a lysosomal protein associated with TDP-43 proteinopathy, also increases tau inclusions, causes concomitant accumulation of α-synuclein and worsens mortality and disinhibited behaviors in tauopathy mice. The increased inclusions paradoxically protect against spatial memory deficit and hippocampal neurodegeneration. PGRN reduction in male tauopathy attenuates activity of β-glucocerebrosidase (GCase), a protein previously associated with synucleinopathy, while increasing glucosylceramide (GlcCer)-positive tau inclusions. In neuronal culture, GCase inhibition enhances tau aggregation induced by AD-tau. Furthermore, purified GlcCer directly promotes tau aggregation in vitro. Neurofibrillary tangles in human tauopathies are also GlcCer-immunoreactive. Thus, in addition to TDP-43, PGRN regulates tau- and synucleinopathies via GCase and GlcCer. A lysosomal PGRN–GCase pathway may be a common therapeutic target for age-related comorbid proteinopathies.

Abstract Tauopathies encompass a group of neurodegenerative disorders characterised by diverse tau amyloid fibril structures. The persistence of polymorphism across tauopathies suggests that distinct pathological conditions dictate the adopted polymorph for each disease. However, the extent to which intrinsic structural tendencies of tau amyloid cores contribute to fibril polymorphism remains uncertain. Using a combination of experimental approaches, we here identify a new amyloidogenic motif, PAM4 (Polymorphic Amyloid Motif of Repeat 4), as a significant contributor to tau polymorphism. Calculation of per-residue contributions to the stability of the fibril cores of different pathologic tau structures suggests that PAM4 plays a central role in preserving structural integrity across amyloid polymorphs. Consistent with this, cryo-EM structural analysis of fibrils formed from a synthetic PAM4 peptide shows that the sequence adopts alternative structures that closely correspond to distinct disease-associated tau strains. Furthermore, in-cell experiments revealed that PAM4 deletion hampers the cellular seeding efficiency of tau aggregates extracted from Alzheimer’s disease, corticobasal degeneration, and progressive supranuclear palsy patients, underscoring PAM4’s pivotal role in these tauopathies. Together, our results highlight the importance of the intrinsic structural propensity of amyloid core segments to determine the structure of tau in cells, and in propagating amyloid structures in disease.

Mountain wave polar stratospheric clouds (PSCs) were detected on 8 February 2003 above the Scandinavian Mountains by in-situ instruments onboard the M55 Geophysica aircraft. PSC particle composition, backscatter and chlorine activation for this case are studied with a recently developed non-equilibrium microphysical box model for liquid aerosol. Results from the microphysical model, run on quasi-lagrangian trajectories, show that the PSC observed was composed of supercooled ternary (H2O/HNO3/H2SO4) solution (STS) particles, which are out of equilibrium with the gas phase. The measured condensed nitric acid and aerosol backscatter of the PSC can well be simulated with the model. Up to 0.15 ppbv Cl2 can be released by the PSC within 2 h, showing the propensity of these small-scale clouds for chlorine activation. Equilibrium calculations – of the sort commonly used in large scale chemistry transport models – overestimate the measured condensed nitrate by up to a factor of 3, and overestimates chlorine activation by 10%, in this mountain wave cloud.

In-situ measurements of ozone and water vapour, in the Antarctic lower stratosphere, were made as part of the APE-GAIA mission in September and October 1999. The measurements show a distinct difference above and below the 415K isentrope. Above 415K, the chemically perturbed region of low ozone and water vapour is clearly evident. Below 415K, but still above the tropopause, no sharp meridional gradients in ozone and water vapour were observed. The observations are consistent with analyses of potential vorticity from the European Centre for Medium Range Weather Forecasting, which show smaller radial gradients at 380K than at 450K potential temperature. Ozone loss in the chemically perturbed region above 415K averages 5ppbv per day for mid-September to mid-October. Apparent ozone loss rates in the sub-vortex region are greater, at 7ppbv per day. The data support, therefore, the existence of a sub-vortex region in which meridional transport is more efficient than in the vortex above. The low ozone mixing ratios in the sub-vortex region may be due to in-situ chemical destruction of ozone or transport of ozone-poor air out of the bottom of the vortex. The aircraft data we use cannot distinguish between these two processes. Key words. Meteorology and atmospheric dynamics polar meteorology) – Atmospheric composition and structure (middle atmosphere–composition and chemistry)

A Lagrangian trajectory model used to simulate photochemistry has been extended to include a simple parameterisation of primary and secondary aerosol particles. The model uses emission inventories of primary particles for the UK from the NAEI (National Atmospheric Emissions Inventory for the UK), and for Europe from the TNO (Institute of Environmental Sciences, Energy Research and Process Innovation, the Netherlands) respectively, to transport tracers representing PM10. One biogenic and two anthropogenic organic compounds were chosen as surrogates to model the formation of condensable material suitable for the production of secondary organic aerosol (SOA). The SOA is added to the primary PM10 and compared to measured PM10 at one urban and two rural UK receptor sites. The results show an average under-prediction by factors of 4.5 and 8.9 in the urban and rural cases respectively. The model is also used to simulate production of two secondary inorganic species, H2SO4 and HNO3, which are assumed, as a limiting case, to be present in the particle phase. The relationships between modelled and measured total PM10 improved with the addition of secondary inorganic compounds, and the overall model under-prediction factors are reduced to 3.5 and 3.9 in the urban and rural cases respectively. Nevertheless, our conclusion is that current emissions and chemistry do not appear to provide sufficient information to model PM10 well (i.e. to within a factor of two). There is a need for further process studies to inform global climate modelling that includes climate forcing by aerosol.

We present a condensed-mass advection based model (MADVEC) designed to simulate the condensation/evaporation of liquid polar stratospheric cloud (PSC) particles. A (Eulerian-in-radius) discretization scheme is used, making the model suitable for use in global or mesoscale chemistry and transport models (CTMs). The mass advection equations are solved using an adaption of the weighted average flux (WAF) scheme. We validate the numerical scheme using an analytical solution for multicomponent aerosols. The physics of the model are tested using a test case designed by Meilinger et al. (1995). The results from this test corroborate the composition gradients across the size distribution under rapid cooling conditions that were reported in earlier studies.

BackgroundFrontotemporal lobar degeneration (FTLD) is a leading cause of dementia in individuals aged

Key Clinical Message Recurrent depression with psychotic features is an atypical presentation of neurosyphilis. This case emphasizes the polymorphic clinical presentation of neurosyphilis and how it mimics affective disorders with psychotic symptoms.

Abstract TAR DNA-binding protein 43 (TDP-43) and Fused in Sarcoma/Translocated in Sarcoma (FUS) are ribonucleoproteins associated with pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Under physiological conditions, TDP-43 and FUS are predominantly localized in the nucleus, where they participate in transcriptional regulation, RNA splicing and metabolism. In disease, however, they are typically mislocalized to the cytoplasm where they form aggregated inclusions. A number of shared cellular pathways have been identified that contribute to TDP-43 and FUS toxicity in neurodegeneration. In the present study, we report a novel pathogenic mechanism shared by these two proteins. We found that pathological FUS co-aggregates with a ribosomal protein, the Receptor for Activated C-Kinase 1 (RACK1), in the cytoplasm of spinal cord motor neurons of ALS, as previously reported for pathological TDP-43. In HEK293T cells transiently transfected with TDP-43 or FUS mutant lacking a functional nuclear localization signal (NLS; TDP-43ΔNLS and FUSΔNLS), cytoplasmic TDP-43 and FUS induced co-aggregation with endogenous RACK1. These co-aggregates sequestered the translational machinery through interaction with the polyribosome, accompanied by a significant reduction of global protein translation. RACK1 knockdown decreased cytoplasmic aggregation of TDP-43ΔNLS or FUSΔNLS and alleviated associated global translational suppression. Surprisingly, RACK1 knockdown also led to partial nuclear localization of TDP-43ΔNLS and FUSΔNLS in some transfected cells, despite the absence of NLS. In vivo, RACK1 knockdown alleviated retinal neuronal degeneration in transgenic Drosophila melanogaster expressing hTDP-43WT or hTDP-43Q331K and improved motor function of hTDP-43WT flies, with no observed adverse effects on neuronal health in control knockdown flies. In conclusion, our results revealed a novel shared mechanism of pathogenesis for misfolded aggregates of TDP-43 and FUS mediated by interference with protein translation in a RACK1-dependent manner. We provide proof-of-concept evidence for targeting RACK1 as a potential therapeutic approach for TDP-43 or FUS proteinopathy associated with ALS and FTLD.

Cytochrome P450 enzymes (P450s) play a critical role in drug metabolism, with the CYP3A subfamily being responsible for the biotransformation of over 50% of marked drugs. While CYP3A enzymes are known for their extensive catalytic versatility, one intriguing and less understood function is the ability to mediate carbon–carbon (C–C) bond cleavage. These uncommon reactions can lead to unusual metabolites and potentially influence drug safety and efficacy. This review focuses on examining examples of C–C bond cleavage catalyzed by CYP3A, exploring the mechanisms, physiological significance, and implications for drug metabolism. Additionally, examples of CYP3A-mediated ring expansion via C–C bond cleavages are included in this review. This work will enhance our understanding of CYP3A-catalyzed C–C bond cleavages and their mechanisms by carefully examining and analyzing these case studies. It may also guide future research in drug metabolism and drug design, improving drug safety and efficacy in clinical practice.

Abstract Background Anal sac adenocarcinoma (ASACA) in dogs is a malignant perianal tumour that often metastasizes to the iliosacral lymph nodes. Additionally, this tumour can be associated with hypercalcemia of malignancy. To date, no study has looked at the association between increased blood calcium levels and suspected or confirmed lymph node metastasis as a primary objective. Objective The objective of this study was to determine if increased total serum calcium level is associated with iliosacral lymph node metastasis in dogs diagnosed with ASACA. Methods Medical records of a single referral hospital were searched to identify dogs examined between 2011 and 2021 that had a diagnosis of ASACA via cytology or histopathology. Only dogs that had serum total calcium recorded and abdominal ultrasound were included in the study. All images were reviewed by a board‐certified radiologist blinded to any patient identifiers. Results Of the 58 dogs, 33% (19/58) had total hypercalcaemia, and of these, 68% had confirmed or suspected iliosacral lymph node metastasis. Total hypercalcaemia was significantly associated with confirmed or suspected iliosacral lymph node metastasis (p < 0.01). However, 46% (11/24) of dogs with confirmed or suspected iliosacral lymph node metastasis were normocalcaemic. Conclusions Based on these results, it is suggested that while the presence of total hypercalcaemia may increase the likelihood of concurrent lymph node metastasis, total hypercalcaemia alone cannot be used as a screening tool for lymph node metastasis. Dogs diagnosed with ASACA should undergo full staging regardless of total serum calcium values.

No abstract available.

Background: Anal sac adenocarcinoma (ASACA) in dogs is a malignant perianal tumour that often metastasizes to the iliosacral lymph nodes. Additionally, this tumour can be associated with hypercalcemia of malignancy. To date, no study has looked at the association between increased blood calcium levels and suspected or confirmed lymph node metastasis as a primary objective. Objective: The objective of this study was to determine if increased total serum calcium level is associated with iliosacral lymph node metastasis in dogs diagnosed with ASACA. Methods: Medical records of a single referral hospital were searched to identify dogs examined between 2011 and 2021 that had a diagnosis of ASACA via cytology or histopathology. Only dogs that had serum total calcium recorded and abdominal ultrasound were included in the study. All images were reviewed by a board‐certified radiologist blinded to any patient identifiers. Results: Of the 58 dogs, 33% (19/58) had total hypercalcaemia, and of these, 68% had confirmed or suspected iliosacral lymph node metastasis. Total hypercalcaemia was significantly associated with confirmed or suspected iliosacral lymph node metastasis (p < 0.01). However, 46% (11/24) of dogs with confirmed or suspected iliosacral lymph node metastasis were normocalcaemic. Conclusions: Based on these results, it is suggested that while the presence of total hypercalcaemia may increase the likelihood of concurrent lymph node metastasis, total hypercalcaemia alone cannot be used as a screening tool for lymph node metastasis. Dogs diagnosed with ASACA should undergo full staging regardless of total serum calcium values. [ABSTRACT FROM AUTHOR]