Sources of water-soluble Brown Carbon at a South-Eastern European Site

Atmospheric brown carbon (BrC) is a highly uncertain, but potentially important contributor to light absorption in the atmosphere. Laboratory and field studies have shown that BrC can be produced from multiple sources, including primary emissions from fossil fuel combustion and biomass burning (BB), as well as secondary formation through a number of reaction pathways. It is currently thought that the dominant source of atmospheric BrC is primary emissions from BB, but relatively few studies demonstrate this in environments with complex source profiles. A field campaign was conducted during a month-long wintertime period in 2020 on the campus of the University of Peloponnese in the southwest of Patras, Greece which represents an urban site. During this time, ambient filter samples (a total of 35 filters) were collected from which the water-soluble BrC was determined using a semi-automated system similar to Hecobian et al. (2010), where absorption was measured over a 1 m path length. To measure the BrC, a UV-Vis Spectrophotometer was coupled to a Liquid Waveguide Capillary Cell and the light absorption intensity was recorded at 365 and 700 nm. The latter was used as a reference wavelength. We found that the average BrC absorption in Patras at a wavelength of 365 nm was 8.5 ± 3.9 Mm-1 suggesting that there was significant BrC in the organic aerosol during this period. Attribution of sources of BrC was done using simultaneous chemical composition data observations (primarily organic carbon, black carbon, and nitrate) combined with Positive Matrix Factorization analysis. This analysis showed that in addition to the important role of biomass burning (a contribution of about 20%) and other combustion emissions (also close to 20%), oxidized organic aerosol (approximately 40%) is also a significant contributor to BrC in the study area. Reference Hecobian, A., Zhang, X., Zheng, M., Frank, N., Edgerton, E.S., Weber, R.J., 2010. Water-soluble organic aerosol material and the light-absorption characteristics of aqueous extracts measured over the Southeastern United States. Atmos. Chem. Phys. 10, 5965–5977. https://doi.org/10.5194/acp-10-5965-201

Sources and processes that control the submicron organic aerosol composition in an urban Mediterranean environment (Athens): a high temporal-resolution chemical composition measurement study

Submicron aerosol chemical composition was studied during a year-long period (26 July 2016–31 July 2017) and two wintertime intensive campaigns (18 December 2013–21 February 2014 and 23 December 2015–17 February 2016), at a central site in Athens, Greece, using an Aerosol Chemical Speciation Monitor (ACSM). Concurrent measurements included a particle-into-liquid sampler (PILS-IC), a scanning mobility particle sizer (SMPS), an AE-33 Aethalometer, and ion chromatography analysis on 24 or 12&thinsp;h filter samples. The aim of the study was to characterize the seasonal variability of the main submicron aerosol constituents and decipher the sources of organic aerosol (OA). Organics were found to contribute almost half of the submicron mass, with 30&thinsp;min resolution concentrations during wintertime reaching up to 200&thinsp;µg&thinsp;m−3. During winter (all three campaigns combined), primary sources contributed about 33&thinsp;% of the organic fraction, and comprised biomass burning (10&thinsp;%), fossil fuel combustion (13&thinsp;%), and cooking (10&thinsp;%), while the remaining 67&thinsp;% was attributed to secondary aerosol. The semi-volatile component of the oxidized organic aerosol (SV-OOA; 22&thinsp;%) was found to be clearly linked to combustion sources, in particular biomass burning; part of the very oxidized, low-volatility component (LV-OOA; 44&thinsp;%) could also be attributed to the oxidation of emissions from these primary combustion sources. These results, based on the combined contribution of biomass burning organic aerosol (BBOA) and SV-OOA, indicate the importance of increased biomass burning in the urban environment of Athens as a result of the economic recession. During summer, when concentrations of fine aerosols are considerably lower, more than 80&thinsp;% of the organic fraction is attributed to secondary aerosol (SV-OOA 31&thinsp;% and LV-OOA 53&thinsp;%). In contrast to winter, SV-OOA appears to result from a well-mixed type of aerosol that is linked to fast photochemical processes and the oxidation of primary traffic and biogenic emissions. Finally, LV-OOA presents a more regional character in summer, owing to the oxidation of OA over the period of a few days.</p

Oxidative Potential of Atmospheric Particles at an Eastern Mediterranean Site

Aerosol oxidative potential (OP; the inherent ability of ambient particles to generate reactive oxygen species in vivo) may be linked to the health effects of population exposure to aerosol and is a metric of their toxicity. The goal of this work was to quantify the water-soluble OP of particles in an urban area in Patras, Greece and to investigate its links with source emissions or components of this particulate matter (PM). A field campaign was conducted during a monthlong wintertime period in 2020 (January 10 to February 13) on the campus of the University of Peloponnese in the southwest of Patras. During this time, ambient filter samples (a total of 35 filters) were collected. To measure the water-soluble OP we used a semiautomated system similar to Fang et al. (2015) based on the dithiothreitol (DTT) assay. The accuracy of our system was validated by measuring the DTT activity of 11 phenanthrequinone (PQN) solutions on both our system and the identical semi-automated validated system at the National Observatory of Athens (NOA). These two sets of analysed DTT activities (current vs. NOA system) were significantly correlated (R2=0.99) with a slope of 1.15 ± 0.04 and an intercept close to zero. We found that the average water-soluble OP in Patras was 1.5 ± 0.3 nmol min-1 m-3, ranging from 0.7 to 2 nmol min-1 m-3. The OP measured in Patras during the campaign is higher than reported values from similar wintertime studies in other urban areas such as Athens (Paraskevopoulou et al., 2019). The average watersoluble OP during a summer study for Patras was significantly lower and equal to 0.18 ± 0.02 nmol min-1 m- 3. Taking into account the average PM1 mass concentrations for these two periods (summer: 6 μg m-3 and winter: 23 μg m-3) it is clear that the increase in OP was two times the increase in PM mass making the wintertime aerosol more toxic. Additionally, the water-soluble brown carbon (BrC) was determined using an offline semi-automated system, where absorption was measured over a 1 m path length. The average BrC absorption in Patras at a wavelength of 365 nm was 8.6 ± 3.9 Mm-1 suggesting that there was significant BrC in the organic aerosol during this period. The coefficients of determination, R2, in Table 1 are used as a metric of the potential relationships between the various carbonaceous aerosol components and the DTT activity. The results suggest that the OP is not dominated by a single source or component, but that there are multiple components contributing to it during the study period. Interestingly, the highest correlation coefficient (R2 = 0.46) was found between the OP and Brown Carbon. This is consistent with recently published results for an urban site in Atlanta where the oxidative potential measured with the DTT method also had stronger correlations with BrC during the winter (Gao et al., 2020)

Genomic characteristics and clinical effect of the emergent SARS-CoV-2 B.1.1.7 lineage in London, UK: a whole-genome sequencing and hospital-based cohort study

BACKGROUND: Emergence of variants with specific mutations in key epitopes in the spike protein of SARS-CoV-2 raises concerns pertinent to mass vaccination campaigns and use of monoclonal antibodies. We aimed to describe the emergence of the B.1.1.7 variant of concern (VOC), including virological characteristics and clinical severity in contemporaneous patients with and without the variant. METHODS: In this cohort study, samples positive for SARS-CoV-2 on PCR that were collected from Nov 9, 2020, for patients acutely admitted to one of two hospitals on or before Dec 20, 2020, in London, UK, were sequenced and analysed for the presence of VOC-defining mutations. We fitted Poisson regression models to investigate the association between B.1.1.7 infection and severe disease (defined as point 6 or higher on the WHO ordinal scale within 14 days of symptoms or positive test) and death within 28 days of a positive test and did supplementary genomic analyses in a cohort of chronically shedding patients and in a cohort of remdesivir-treated patients. Viral load was compared by proxy, using PCR cycle threshold values and sequencing read depths. FINDINGS: Of 496 patients with samples positive for SARS-CoV-2 on PCR and who met inclusion criteria, 341 had samples that could be sequenced. 198 (58%) of 341 had B.1.1.7 infection and 143 (42%) had non-B.1.1.7 infection. We found no evidence of an association between severe disease and death and lineage (B.1.1.7 vs non-B.1.1.7) in unadjusted analyses (prevalence ratio [PR] 0·97 [95% CI 0·72-1·31]), or in analyses adjusted for hospital, sex, age, comorbidities, and ethnicity (adjusted PR 1·02 [0·76-1·38]). We detected no B.1.1.7 VOC-defining mutations in 123 chronically shedding immunocompromised patients or in 32 remdesivir-treated patients. Viral load by proxy was higher in B.1.1.7 samples than in non-B.1.1.7 samples, as measured by cycle threshold value (mean 28·8 [SD 4·7] vs 32·0 [4·8]; p=0·0085) and genomic read depth (1280 [1004] vs 831 [682]; p=0·0011). INTERPRETATION: Emerging evidence exists of increased transmissibility of B.1.1.7, and we found increased virus load by proxy for B.1.1.7 in our data. We did not identify an association of the variant with severe disease in this hospitalised cohort. FUNDING: University College London Hospitals NHS Trust, University College London/University College London Hospitals NIHR Biomedical Research Centre, Engineering and Physical Sciences Research Council

Serum microRNA array analysis identifies miR-140-3p, miR-33b-3p and miR-671-3p as potential osteoarthritis biomarkers involved in metabolic processes.

Background: MicroRNAs (miRNAs) in circulation have emerged as promising biomarkers. In this study, we aimed to identify a circulating miRNA signature for osteoarthritis (OA) patients and in combination with bioinformatics analysis to evaluate the utility of selected differentially expressed miRNAs in the serum as potential OA biomarkers. Methods: Serum samples were collected from 12 primary OA patients, and 12 healthy individuals were screened using the Agilent Human miRNA Microarray platform interrogating 2549 miRNAs. Receiver Operating Characteristic (ROC) curves were constructed to evaluate the diagnostic performance of the deregulated miRNAs. Expression levels of selected miRNAs were validated by quantitative real-time PCR (qRT-PCR) in all serum and in articular cartilage samples from OA patients (n = 12) and healthy individuals (n = 7). Bioinformatics analysis was used to investigate the involved pathways and target genes for the above miRNAs. Results: We identified 279 differentially expressed miRNAs in the serum of OA patients compared to controls. Two hundred and five miRNAs (73.5%) were upregulated and 74 (26.5%) downregulated. ROC analysis revealed that 77 miRNAs had area under the curve (AUC) > 0.8 and p < 0.05. Bioinformatics analysis in the 77 miRNAs revealed that their target genes were involved in multiple signaling pathways associated with OA, among which FoxO, mTOR, Wnt, pI3K/akt, TGF-β signaling pathways, ECM-receptor interaction, and fatty acid biosynthesis. qRT-PCR validation in seven selected out of the 77 miRNAs revealed 3 significantly downregulated miRNAs (hsa-miR-33b-3p, hsa-miR-671-3p, and hsa-miR-140-3p) in the serum of OA patients, which were in silico predicted to be enriched in pathways involved in metabolic processes. Target-gene analysis of hsa-miR-140-3p, hsa-miR-33b-3p, and hsa-miR-671-3p revealed that InsR and IGFR1 were common targets of all three miRNAs, highlighting their involvement in regulation of metabolic processes that contribute to OA pathology. Hsa-miR-140-3p and hsa-miR-671-3p expression levels were consistently downregulated in articular cartilage of OA patients compared to healthy individuals. Conclusions: A serum miRNA signature was established for the first time using high density resolution miR-arrays in OA patients. We identified a three-miRNA signature, hsa-miR-140-3p, hsa-miR-671-3p, and hsa-miR-33b-3p, in the serum of OA patients, predicted to regulate metabolic processes, which could serve as a potential biomarker for the evaluation of OA risk and progression.Peer reviewedFinal Published versio

Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains

Background: The degree of heterotypic immunity induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains is a major determinant of the spread of emerging variants and the success of vaccination campaigns, but remains incompletely understood. Methods: We examined the immunogenicity of SARS-CoV-2 variant B.1.1.7 (Alpha) that arose in the United Kingdom and spread globally. We determined titres of spike glycoprotein-binding antibodies and authentic virus neutralising antibodies induced by B.1.1.7 infection to infer homotypic and heterotypic immunity. Results: Antibodies elicited by B.1.1.7 infection exhibited significantly reduced recognition and neutralisation of parental strains or of the South Africa variant B.1.351 (Beta) than of the infecting variant. The drop in cross-reactivity was significantly more pronounced following B.1.1.7 than parental strain infection. Conclusions: The results indicate that heterotypic immunity induced by SARS-CoV-2 variants is asymmetric

Multi-year chemical composition of the fine-aerosol fraction in Athens, Greece, with emphasis on the contribution of residential heating in wintertime

In an attempt to take effective action towards mitigating pollution episodes in Athens, precise knowledge of PM2.5 composition and its sources is a prerequisite. Thus, a 2-year chemical composition dataset from aerosol samples collected in an urban background site in central Athens from December 2013 to March 2016 has been obtained and a positive matrix factorization (PMF) was applied in order to identify and apportion fine aerosols to their sources. A total of 850 aerosol samples were collected on a 12 to 24&thinsp;h basis and analyzed for major ions, trace elements, and organic and elemental carbon, allowing us to further assess the impact of residential heating as a source of air pollution over Athens.The ionic and carbonaceous components were found to constitute the major fraction of the PM2.5 aerosol mass. The annual contribution of the ion mass (IM), particulate organic mass (POM), dust, elemental carbon (EC), and sea salt (SS) was calculated at 31&thinsp;%, 38&thinsp;%, 18&thinsp;%, 8&thinsp;%, and 3&thinsp;%, respectively, and exhibited considerable seasonal variation. In winter, the share of IM was estimated down to 23&thinsp;%, with POM&thinsp;+ EC being the dominant component accounting for 52&thinsp;% of the PM2.5 mass, while in summer, IM (42&thinsp;%) and carbonaceous aerosols (41&thinsp;%) contributed almost equally.Results from samples collected on a 12&thinsp;h basis (day and night) during the three intensive winter campaigns indicated the impact of heating on the levels of a series of compounds. Indeed, PM2.5, EC, POM, NO3−, C2O42−, non sea salt (nss) K+ and selected trace metals including Cd and Pb were increased by up to a factor of 4 in the night compared to the day, highlighting the importance of heating on air quality in Athens. Furthermore, in order to better characterize wintertime aerosol sources and quantify the impact of biomass burning on PM2.5 levels, source apportionment was performed. The data can be interpreted on the basis of six sources, namely biomass burning (31&thinsp;%), vehicular emissions (19&thinsp;%), heavy oil combustion (7&thinsp;%), regional secondary (21&thinsp;%), marine aerosols (9&thinsp;%), and dust particles (8&thinsp;%). Regarding night-to-day patterns their contributions shifted from 19&thinsp;%, 19&thinsp;%, 8&thinsp;%, 31&thinsp;%, 12&thinsp;%, and 10&thinsp;% of the PM2.5 mass during day to 39&thinsp;%, 19&thinsp;%, 6&thinsp;%, 14&thinsp;%, 7&thinsp;%, and 7&thinsp;% during the night, underlining the significance of biomass burning as the main contributor to fine particle levels during nighttime in winter.</p

Triticum timopheevii s.l. (‘new glume wheat’) finds in regions of southern and eastern Europe across space and time

Triticum timopheevii sensu lato (‘new glume wheat’, NGW) was first recognised as a distinct prehistoric cereal crop through work on archaeobotanical finds from Neolithic and Bronze Age sites in northern Greece. This was later followed by its identification in archaeobotanical assemblages from other parts of Europe. This paper provides an overview of the currently known archaeobotanical finds of Timopheev’s wheat in southeastern and eastern Europe and observes their temporal span and spatial distribution. To date, there are 89 prehistoric sites with these finds, located in different parts of the study region and dated from the Neolithic to the very late Iron Age. Their latest recorded presence in the region is in the last centuries BCE. For assemblages from the site as a whole containing at least 30 grain and/or chaff remains of Timopheev’s wheat, we take a brief look at the overall relative proportions of Triticum monococcum (einkorn), T. dicoccum (emmer) and T. timopheevii s.l. (Timopheev’s wheat), the three most common glume wheats in our study region in prehistory. We highlight several sites where the overall proportions of Timopheev’s wheat might be taken to suggest it was a minor component of a mixed crop (maslin), or an unmonitored inclusion in einkorn or emmer fields. At the same sites, however, there are also discrete contexts where this wheat is strongly predominant, pointing to its cultivation as a pure crop. We therefore emphasise the need to evaluate the relative representation of Timopheev’s wheat at the level of individual samples or contexts before making inferences on its cultivation status. We also encourage re-examination of prehistoric and historic cereal assemblages for its remains

Advances in Property-Based Testing for αProlog

$\alpha$Check is a light-weight property-based testing tool built on top of $\alpha$Prolog, a logic programming language based on nominal logic. $\alpha$Prolog is particularly suited to the validation of the meta-theory of formal systems, for example correctness of compiler translations involving name-binding, alpha-equivalence and capture-avoiding substitution. In this paper we describe an alternative to the negation elimination algorithm underlying $\alpha$Check that substantially improves its effectiveness. To substantiate this claim we compare the checker performances w.r.t. two of its main competitors in the logical framework niche, namely the QuickCheck/Nitpick combination offered by Isabelle/HOL and the random testing facility in PLT-Redex.Comment: To appear, Tests and Proofs 2016; includes appendix with details not in the conference versio