Introduction to Special Issue - In-depth study of air pollution sources and processes within Beijing and its surrounding region (APHH-2 Beijing)

Abstract. The Atmospheric Pollution and Human Health in a Chinese Megacity (APHH-Beijing) programme is an international collaborative project focusing on understanding the sources, processes and health effects of air pollution in the Beijing megacity. APHH-Beijing brings together leading China and UK research groups, state-of-the-art infrastructure and air quality models to work on four research themes: (1) sources and emissions of air pollutants; (2) atmospheric processes affecting urban air pollution; (3) air pollution exposure and health impacts; and (4) interventions and solutions. Themes 1 and 2 are closely integrated and support Theme 3, while Themes 1-3 provide scientific data for Theme 4 to develop cost-effective air pollution mitigation solutions. This paper provides an introduction to (i) the rationale of the APHH-Beijing programme, and (ii) the measurement and modelling activities performed as part of it. In addition, this paper introduces the meteorology and air quality conditions during two joint intensive field campaigns - a core integration activity in APHH-Beijing. The coordinated campaigns provided observations of the atmospheric chemistry and physics at two sites: (i) the Institute of Atmospheric Physics in central Beijing, and (ii) Pinggu in rural Beijing during 10 November – 10 December 2016 (winter) and 21 May- 22 June 2017 (summer). The campaigns were complemented by numerical modelling and automatic air quality and low-cost sensor observations in the Beijing megacity. In summary, the paper provides background information on the APHH-Beijing programme, and sets the scene for more focussed papers addressing specific aspects, processes and effects of air pollution in Beijing

A Calanais myth and an alignment of the east stone-row with both the rising of the Pleiades and crossovers of Venus at sunrise on the summer solstices

Acknowledgements My thanks to Stefan Sagrott of Historic Environment Scotland for his help in obtaining Patrick Ashmore’s data and to David Forrest, School of Geographical and Earth Sciences, University of Glasgow, for providing a copy of David Tait’s map of Calanais.Peer reviewedPublisher PD

Evaluating the sensitivity of radical chemistry and ozone formation to ambient VOCs and NOxin Beijing

Measurements of OH, HO2, complex RO2 (alkene-and aromatic-related RO2) and total RO2 radicals taken during the integrated Study of AIR Pollution PROcesses in Beijing (AIRPRO) campaign in central Beijing in the summer of 2017, alongside observations of OH reactivity, are presented. The concentrations of radicals were elevated, with OH reaching up to 2:8 × 107 molecule cm-3, HO2 peaking at 1 × 109 molecule cm-3 and the total RO2 concentration reaching 5:5×109 molecule cm-3. OH reactivity (k.OH/) peaked at 89 s-1 during the night, with a minimum during the afternoon of 22s-1 on average. An experimental budget analysis, in which the rates of production and destruction of the radicals are compared, highlighted that although the sources and sinks of OH were balanced under high NO concentrations, the OH sinks exceeded the known sources (by 15 ppbvh-1) under the very low NO conditions (< 0:5ppbv) experienced in the afternoons, demonstrating a missing OH source consistent with previous studies under high volatile organic compound (VOC) emissions and low NO loadings. Under the highest NO mixing ratios (104 ppbv), the HO2 production rate exceeded the rate of destruction by 50ppbvh-1, whilst the rate of destruction of total RO2 exceeded the production by the same rate, indicating that the net propagation rate of RO2 to HO2 may be substantially slower than assumed. If just 10 % of the RO2 radicals propagate to HO2 upon reaction with NO, the HO2 and RO2 budgets could be closed at high NO, but at low NO this lower RO2 to HO2 propagation rate revealed a missing RO2 sink that was similar in magnitude to the missing OH source. A detailed box model that incorporated the latest Master Chemical Mechanism (MCM3.3.1) reproduced the observed OH concentrations well but over-predicted the observed HO2 under low concentrations of NO (< 1ppbv) and under-predicted RO2 (both the complex RO2 fraction and other RO2 types which we classify as simple RO2) most significantly at the highest NO concentrations. The model also under-predicted the observed k.OH/consistently by 10s-1 across all NOx levels, highlighting that the good agreement for OH was fortuitous due to a cancellation of missing OH source and sink terms in its budget. Including heterogeneous loss of HO2 to aerosol surfaces did reduce the modelled HO2 concentrations in line with the observations but only at NO mixing ratios < 0:3ppbv. The inclusion of Cl atoms, formed from the photolysis of nitryl chloride, enhanced the modelled RO2 concentration on several mornings when the Cl atom concentration was calculated to exceed 1 × 104 atoms cm-3 and could reconcile the modelled and measured RO2 concentrations at these times. However, on other mornings, when the Cl atom concentration was lower, large under-predictions in total RO2 remained. Furthermore, the inclusion of Cl atom chemistry did not enhance the modelled RO2 beyond the first few hours after sunrise and so was unable to resolve the modelled under-prediction in RO2 observed at other times of the day. Model scenarios, in which missing VOC reactivity was included as an additional reaction that converted OH to RO2, highlighted that the modelled OH, HO2 and RO2 concentrations were sensitive to the choice of RO2 product. The level of modelled to measured agreement for HO2 and RO2 (both complex and simple) could be improved if the missing OH reactivity formed a larger RO2 species that was able to undergo reaction with NO, followed by isomerisation reactions reforming other RO2 species, before eventually generating HO2. In this work an a-pinene-derived RO2 species was used as an example. In this simulation, consistent with the experimental budget analysis, the model underestimated the observed OH, indicating a missing OH source. The model uncertainty, with regards to the types of RO2 species present and the radicals they form upon reaction with NO (HO2 directly or another RO2 species), leads to over an order of magnitude less O3 production calculated from the predicted peroxy radicals than calculated from the observed peroxy radicals at the highest NO concentrations. This demonstrates the rate at which the larger RO2 species propagate to HO2, to another RO2 or indeed to OH needs to be understood to accurately simulate the rate of ozone production in environments such as Beijing, where large multifunctional VOCs are likely present

Impact of HO2 aerosol uptake on radical levels and O3 production during summertime in Beijing

The impact of heterogeneous uptake of HO2 on aerosol surfaces on radical concentrations and the O3 production regime in Beijing in summertime was investigated. The uptake coefficient of HO2 onto aerosol surfaces, γHO2 , was calculated for the AIRPRO campaign in Beijing, in summer 2017, as a function of measured aerosol soluble copper concentration, [Cu2+]eff, aerosol liquid water content, [ALWC], and particulate matter concentration, [PM]. An average γHO2 across the entire campaign of 0.070 ± 0.035 was calculated, with values ranging from 0.002 to 0.15, and found to be significantly lower than the value of γHO2 = 0.2, commonly used in modelling studies. Using the calculated γHO2 values for the summer AIRPRO campaign, OH, HO2 and RO2 radical concentrations were modelled using a box model incorporating the Master Chemical Mechanism (v3.3.1), with and without the addition of γHO2 , and compared to the measured radical concentrations. The rate of destruction analysis showed the dominant HO2 loss pathway to be HO2 + NO for all NO concentrations across the summer Beijing campaign, with HO2 uptake contributing < 0.3 % to the total loss of HO2 on average. This result for Beijing summertime would suggest that under most conditions encountered, HO2 uptake onto aerosol surfaces is not important to consider when investigating increasing O3 production with decreasing [PM] across the North China Plain. At low [NO], however, i.e. < 0.1 ppb, which was often encountered in the afternoons, up to 29 % of modelled HO2 loss was due to HO2 uptake on aerosols when calculated γHO2 was included, even with the much lower γHO2 values compared to γHO2 = 0.2, a result which agrees with the aerosol-inhibited O3 regime recently proposed by Ivatt et al. (2022). As such it can be concluded that in cleaner environments, away from polluted urban centres where HO2 loss chemistry is not dominated by NO but where aerosol surface area is high still, changes in PM concentration and hence aerosol surface area could still have a significant effect on both overall HO2 concentration and the O3 production regime. Using modelled radical concentrations, the absolute O3 sensitivity to NOx and volatile organic compounds (VOCs) showed that, on average across the summer AIRPRO campaign, the O3 production regime remained VOC-limited, with the exception of a few days in the afternoon when the NO mixing ratio dropped low enough for the O3 regime to shift towards being NOx -limited. The O3 sensitivity to VOCs, the dominant regime during the summer AIRPRO campaign, was observed to decrease and shift towards a NOx -sensitive regime both when NO mixing ratio decreased and with the addition of aerosol uptake. This suggests that if [NOx ] continues to decrease in the future, ozone reduction policies focussing solely on NOx reductions may not be as efficient as expected if [PM] and, hence, HO2 uptake to aerosol surfaces continue to decrease. The addition of aerosol uptake into the model, for both the γHO2 calculated from measured data and when using a fixed value of γHO2 = 0.2, did not have a significant effect on the overall O3 production regime across the campaign. While not important for this campaign, aerosol uptake could be important for areas of lower NO concentration that are already in a NOx -sensitive regime

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Rare variants in NR2F2 cause congenital heart defects in humans

Congenital heart defects (CHDs) are the most common birth defect worldwide and are a leading cause of neonatal mortality. Nonsyndromic atrioventricular septal defects (AVSDs) are an important subtype of CHDs for which the genetic architecture is poorly understood. We performed exome sequencing in 13 parent-offspring trios and 112 unrelated individuals with nonsyndromic AVSDs and identified five rare missense variants (two of which arose de novo) in the highly conserved gene NR2F2, a very significant enrichment (p = 7.7 × 10?7) compared to 5,194 control subjects. We identified three additional CHD-affected families with other variants in NR2F2 including a de novo balanced chromosomal translocation, a de novo substitution disrupting a splice donor site, and a 3 bp duplication that cosegregated in a multiplex family. NR2F2 encodes a pleiotropic developmental transcription factor, and decreased dosage of NR2F2 in mice has been shown to result in abnormal development of atrioventricular septa. Via luciferase assays, we showed that all six coding sequence variants observed in individuals significantly alter the activity of NR2F2 on target promoters

Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing.

Congenital heart defects (CHDs) have a neonatal incidence of 0.8-1% (refs. 1,2). Despite abundant examples of monogenic CHD in humans and mice, CHD has a low absolute sibling recurrence risk (∼2.7%), suggesting a considerable role for de novo mutations (DNMs) and/or incomplete penetrance. De novo protein-truncating variants (PTVs) have been shown to be enriched among the 10% of 'syndromic' patients with extra-cardiac manifestations. We exome sequenced 1,891 probands, including both syndromic CHD (S-CHD, n = 610) and nonsyndromic CHD (NS-CHD, n = 1,281). In S-CHD, we confirmed a significant enrichment of de novo PTVs but not inherited PTVs in known CHD-associated genes, consistent with recent findings. Conversely, in NS-CHD we observed significant enrichment of PTVs inherited from unaffected parents in CHD-associated genes. We identified three genome-wide significant S-CHD disorders caused by DNMs in CHD4, CDK13 and PRKD1. Our study finds evidence for distinct genetic architectures underlying the low sibling recurrence risk in S-CHD and NS-CHD