Mapping Patterns and Trends in the Spatial Availability of Alcohol Using Low-Level Geographic Data: A Case Study in England 2003–2013

Much literature examines the relationship between the spatial availability of alcohol and alcohol-related harm. This study aims to address an important gap in this evidence by using detailed outlet data to examine recent temporal trends in the sociodemographic distribution of spatial availability for different types of alcohol outlet in England. Descriptive analysis of measures of alcohol outlet density and proximity using extremely high resolution market research data stratified by outlet type and quintiles of area-level deprivation from 2003, 2007, 2010 and 2013 was undertaken and hierarchical linear growth models fitted to explore the significance of socioeconomic differences. We find that overall availability of alcohol changed very little from 2003 to 2013 (density +1.6%), but this conceals conflicting trends by outlet type and area-level deprivation. Mean on-trade density has decreased substantially (−2.2 outlets within 1 km (Inter-Quartile Range (IQR) −3–0), although access to restaurants has increased (+1.0 outlets (IQR 0–1)), while off-trade access has risen substantially (+2.4 outlets (IQR 0–3)). Availability is highest in the most deprived areas (p < 0.0001) although these areas have also seen the greatest falls in on-trade outlet availability (p < 0.0001). This study underlines the importance of using detailed, low-level geographic data to understand patterns and trends in the spatial availability of alcohol. There are significant variations in these trends by outlet type and deprivation level which may have important implications for health inequalities and public health policy

Changes in physical activity and sedentary behaviours from before to during the COVID-19 pandemic lockdown:A systematic review

Objective: In March 2020, several countries banned unnecessary outdoor activities during COVID-19, commonly called ‘lockdowns. These lockdowns have the potential to impact associated levels of physical activity and sedentary behaviour. Given the numerous health outcomes associated with physical activity and sedentary behaviour, the aim of this review was to summarise literature that investigated differences in physical activity and sedentary behaviour before vs during the COVID-19 lockdown. Design, data sources and eligibility criteria: Electronic databases were searched from November 2019 to October 2020 using terms and synonyms relating to physical activity, sedentary behaviour and COVID-19. The coprimary outcomes were changes in physical activity and/or sedentary behaviour captured via device-based measures or self-report tools. Risk of bias was measured using the Newcastle-Ottawa Scale. Results: Sixty six articles met the inclusion criteria and were included in the review (total n=86 981). Changes in physical activity were reported in 64 studies, with the majority of studies reporting decreases in physical activity and increases in sedentary behaviours during their respective lockdowns across several populations, including children and patients with a variety of medical conditions. Conclusion: Given the numerous physical and mental benefits of increased physical activity and decreased sedentary behaviour, public health strategies should include the creation and implementation of interventions that promote safe physical activity and reduce sedentary behaviour should other lockdowns occur

Field measurements of trace gases and aerosols emitted by peat fires in Central Kalimantan, Indonesia, during the 2015 El Niño

Peat fires in Southeast Asia have become a major annual source of trace gases and particles to the regional-global atmosphere. The assessment of their influence on atmospheric chemistry, climate, air quality, and health has been uncertain partly due to a lack of field measurements of the smoke characteristics. During the strong 2015 El Niño event we deployed a mobile smoke sampling team in the Indonesian province of Central Kalimantan on the island of Borneo and made the first, or rare, field measurements of trace gases, aerosol optical properties, and aerosol mass emissions for authentic peat fires burning at various depths in different peat types. This paper reports the trace gas and aerosol measurements obtained by Fourier transform infrared spectroscopy, whole air sampling, photoacoustic extinctiometers (405 and 870 nm), and a small subset of the data from analyses of particulate filters. The trace gas measurements provide emission factors (EFs; grams of a compound per kilogram biomass burned) for up to ∼ 90 gases, including CO2, CO, CH4, non-methane hydrocarbons up to C10, 15 oxygenated organic compounds, NH3, HCN, NOx, OCS, HCl, etc. The modified combustion efficiency (MCE) of the smoke sources ranged from 0.693 to 0.835 with an average of 0.772 ± 0.053 (n = 35), indicating essentially pure smoldering combustion, and the emissions were not initially strongly lofted. The major trace gas emissions by mass (EF as g kg-1) were carbon dioxide (1564 ± 77), carbon monoxide (291 ± 49), methane (9.51 ± 4.74), hydrogen cyanide (5.75 ± 1.60), acetic acid (3.89 ± 1.65), ammonia (2.86 ± 1.00), methanol (2.14 ± 1.22), ethane (1.52 ± 0.66), dihydrogen (1.22 ± 1.01), propylene (1.07 ± 0.53), propane (0.989 ± 0.644), ethylene (0.961 ± 0.528), benzene (0.954 ± 0.394), formaldehyde (0.867 ± 0.479), hydroxyacetone (0.860 ± 0.433), furan (0.772 ± 0.035), acetaldehyde (0.697 ± 0.460), and acetone (0.691 ± 0.356). These field data support significant revision of the EFs for CO2 (g-8 %), CH4 (g-55 %), NH3 (g-86 %), CO (+39 %), and other gases compared with widely used recommendations for tropical peat fires based on a lab study of a single sample published in 2003. BTEX compounds (benzene, toluene, ethylbenzene, xylenes) are important air toxics and aerosol precursors and were emitted in total at 1.5 ± 0.6 g kg-1. Formaldehyde is probably the air toxic gas most likely to cause local exposures that exceed recommended levels. The field results from Kalimantan were in reasonable agreement with recent lab measurements of smoldering Kalimantan peat for overlap species, lending importance to the lab finding that burning peat produces large emissions of acetamide, acrolein, methylglyoxal, etc., which were not measurable in the field with the deployed equipment and implying value in continued similar efforts. The aerosol optical data measured include EFs for the scattering and absorption coefficients (EF Bscat and EF Babs, m2 kg-1 fuel burned) and the single scattering albedo (SSA) at 870 and 405 nm, as well as the absorption Ångström exponents (AAE). By coupling the absorption and co-located trace gas and filter data we estimated black carbon (BC) EFs (g kg-1) and the mass absorption coefficient (MAC, m2 g-1) for the bulk organic carbon (OC) due to brown carbon (BrC). Consistent with the minimal flaming, the emissions of BC were negligible (0.0055 ± 0.0016 g kg-1). Aerosol absorption at 405 nm was ∼ 52 times larger than at 870 nm and BrC contributed ∼ 96 % of the absorption at 405 nm. Average AAE was 4.97 ± 0.65 (range, 4.29-6.23). The average SSA at 405 nm (0.974 ± 0.016) was marginally lower than the average SSA at 870 nm (0.998 ± 0.001). These data facilitate modeling climate-relevant aerosol optical properties across much of the UV/visible spectrum and the high AAE and lower SSA at 405 nm demonstrate the dominance of absorption by the organic aerosol. Comparing the Babs at 405 nm to the simultaneously measured OC mass on filters suggests a low MAC (∼ 0.1) for the bulk OC, as expected for the low BC/OC ratio in the aerosol. The importance of pyrolysis (at lower MCE), as opposed to glowing (at higher MCE), in producing BrC is seen in the increase of AAE with lower MCE (r2 = 0.65)

ANDES: Statistical tools for the ANalyses of DEep Sequencing

<p>Abstract</p> <p>Background</p> <p>The advancements in DNA sequencing technologies have allowed researchers to progress from the analyses of a single organism towards the deep sequencing of a sample of organisms. With sufficient sequencing depth, it is now possible to detect subtle variations between members of the same species, or between mixed species with shared biomarkers, such as the 16S rRNA gene. However, traditional sequencing analyses of samples from largely homogeneous populations are often still based on multiple sequence alignments (MSA), where each sequence is placed along a separate row and similarities between aligned bases can be followed down each column. While this visual format is intuitive for a small set of aligned sequences, the representation quickly becomes cumbersome as sequencing depths cover loci hundreds or thousands of reads deep.</p> <p>Findings</p> <p>We have developed ANDES, a software library and a suite of applications, written in Perl and R, for the statistical ANalyses of DEep Sequencing. The fundamental data structure underlying ANDES is the position profile, which contains the nucleotide distributions for each genomic position resultant from a multiple sequence alignment (MSA). Tools include the root mean square deviation (RMSD) plot, which allows for the visual comparison of multiple samples on a position-by-position basis, and the computation of base conversion frequencies (transition/transversion rates), variation (Shannon entropy), inter-sample clustering and visualization (dendrogram and multidimensional scaling (MDS) plot), threshold-driven consensus sequence generation and polymorphism detection, and the estimation of empirically determined sequencing quality values.</p> <p>Conclusions</p> <p>As new sequencing technologies evolve, deep sequencing will become increasingly cost-efficient and the inter and intra-sample comparisons of largely homogeneous sequences will become more common. We have provided a software package and demonstrated its application on various empirically-derived datasets. Investigators may download the software from Sourceforge at <url>https://sourceforge.net/projects/andestools</url>.</p

A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses

ABSTRACT Several biosafety level 3 and/or 4 (BSL-3/4) pathogens are high-consequence, single-stranded RNA viruses, and their genomes, when introduced into permissive cells, are infectious. Moreover, many of these viruses are select agents (SAs), and their genomes are also considered SAs. For this reason, cDNAs and/or their derivatives must be tested to ensure the absence of infectious virus and/or viral RNA before transfer out of the BSL-3/4 and/or SA laboratory. This tremendously limits the capacity to conduct viral genomic research, particularly the application of next-generation sequencing (NGS). Here, we present a sequence-independent method to rapidly amplify viral genomic RNA while simultaneously abolishing both viral and genomic RNA infectivity across multiple single-stranded positive-sense RNA (ssRNA+) virus families. The process generates barcoded DNA amplicons that range in length from 300 to 1,000 bp, which cannot be used to rescue a virus and are stable to transport at room temperature. Our barcoding approach allows for up to 288 barcoded samples to be pooled into a single library and run across various NGS platforms without potential reconstitution of the viral genome. Our data demonstrate that this approach provides full-length genomic sequence information not only from high-titer virion preparations but it can also recover specific viral sequence from samples with limited starting material in the background of cellular RNA, and it can be used to identify pathogens from unknown samples. In summary, we describe a rapid, universal standard operating procedure that generates high-quality NGS libraries free of infectious virus and infectious viral RNA. IMPORTANCE This report establishes and validates a standard operating procedure (SOP) for select agents (SAs) and other biosafety level 3 and/or 4 (BSL-3/4) RNA viruses to rapidly generate noninfectious, barcoded cDNA amenable for next-generation sequencing (NGS). This eliminates the burden of testing all processed samples derived from high-consequence pathogens prior to transfer from high-containment laboratories to lower-containment facilities for sequencing. Our established protocol can be scaled up for high-throughput sequencing of hundreds of samples simultaneously, which can dramatically reduce the cost and effort required for NGS library construction. NGS data from this SOP can provide complete genome coverage from viral stocks and can also detect virus-specific reads from limited starting material. Our data suggest that the procedure can be implemented and easily validated by institutional biosafety committees across research laboratories

Evaluating the effects of six alcohol-related message frames on emotions and intentions: The neglected role of disgust

A total of 120 18- to 56-year-olds, divided into six groups containing equal numbers of men and women, were shown a textual message and associated photograph featuring alcohol-related behaviour. Subsequently, questions were answered about intentions to reduce consumption, to drink moderately and how positive and negative the messages made participants feel. Loss-framed messages, in particular those featuring health-related disgust, were the most effective for increasing intentions to reduce alcohol intake. In conclusion, studies have over-focused on fear-loss frames, neglecting the utility of disgust-loss frames in health messages. This study suggests that disgust-loss frames deserve equivalent attention