New SOA Treatments Within the Energy Exascale Earth System Model (E3SM): Strong Production and Sinks Govern Atmospheric SOA Distributions and Radiative Forcing

Secondary organic aerosols (SOA) are large contributors to fine particle mass loading and number concentration and interact with clouds and radiation. Several processes affect the formation, chemical transformation, and removal of SOA in the atmosphere. For computational efficiency, global models use simplified SOA treatments, which often do not capture the dynamics of SOA formation. Here we test more complex SOA treatments within the global Energy Exascale Earth System Model (E3SM) to investigate how simulated SOA spatial distributions respond to some of the important but uncertain processes affecting SOA formation, removal, and lifetime. We evaluate model predictions with a suite of surface, aircraft, and satellite observations that span the globe and the full troposphere. Simulations indicate that both a strong production (achieved here by multigenerational aging of SOA precursors that includes moderate functionalization) and a strong sink of SOA (especially in the middle upper troposphere, achieved here by adding particle-phase photolysis) are needed to reproduce the vertical distribution of organic aerosol (OA) measured during several aircraft field campaigns; without this sink, the simulated middle upper tropospheric OA is too large. Our results show that variations in SOA chemistry formulations change SOA wet removal lifetime by a factor of 3 due to changes in horizontal and vertical distributions of SOA. In all the SOA chemistry formulations tested here, an efficient chemical sink, that is, particle-phase photolysis, was needed to reproduce the aircraft measurements of OA at high altitudes. Globally, SOA removal rates by photolysis are equal to the wet removal sink, and photolysis decreases SOA lifetimes from 10 to ~3 days. A recent review of multiple field studies found no increase in net OA formation over and downwind biomass burning regions, so we also tested an alternative, empirical SOA treatment that increases primary organic aerosol (POA) emissions near source region and converts POA to SOA with an aging time scale of 1 day. Although this empirical treatment performs surprisingly well in simulating OA loadings near the surface, it overestimates OA loadings in the middle and upper troposphere compared to aircraft measurements, likely due to strong convective transport to high altitudes where wet removal is weak. The default improved model formulation (multigenerational aging with moderate fragmentation and photolysis) performs much better than the empirical treatment in these regions. Differences in SOA treatments greatly affect the SOA direct radiative effect, which ranges from -0.65 (moderate fragmentation and photolysis) to -2 W m-2 (moderate fragmentation without photolysis). Notably, most SOA formulations predict similar global indirect forcing of SOA calculated as the difference in cloud forcing between present-day and preindustrial simulations. © 2020. The Authors

Incongruous consultation behaviour: results from a UK-wide population survey

<p>Abstract</p> <p>Background</p> <p>Symptom characteristics are strong drivers of care seeking. Despite this, incongruous consultation behaviour occurs and has implications for both individuals and health-care services. The aim of this study was to determine how frequently incongruous consultation behaviour occurs, to examine whether it is more common for certain types of symptoms and to identify the factors associated with being an incongruous consulter.</p> <p>Methods</p> <p>An age and sex stratified random sample of 8,000 adults was drawn from twenty UK general practices. A postal questionnaire was used to collect detailed information on the presence and characteristics of 25 physical and psychological symptoms, actions taken to manage the symptoms, general health, attitudes to symptom management and demographic/socio-economic details. Two types of incongruous consultation behaviour were examined: i) consultation with a GP for symptoms self-rated as low impact and ii) no consultation with a GP for symptoms self-rated as high impact.</p> <p>Results</p> <p>A fifth of all symptoms experienced resulted in consultation behaviour which was incongruous based on respondents' own rating of the symptoms' impact. Low impact consultations were not common, although symptoms indicative of a potentially serious condition resulted in a higher proportion of low impact consultations. High impact non-consultations were more common, although there was no clear pattern in the type of associated symptoms. Just under half of those experiencing symptoms in the previous two weeks were categorised as an incongruous consulter (low impact consulter: 8.3%, high impact non-consulter: 37.1%). Employment status, having a chronic condition, poor health, and feeling that reassurance or advice from a health professional is important were associated with being a low impact consulter. Younger age, employment status, being an ex-smoker, poor health and feeling that not wasting the GPs time is important were associated with being a high impact non-consulter.</p> <p>Conclusions</p> <p>This is one of the first studies to examine incongruous consultation behaviour for a range of symptoms. High impact non-consultations were common and may have important health implications, particularly for symptoms indicative of serious disease. More research is now needed to examine incongruous consultation behaviour and its impact on both the public's health and health service use.</p

Site identification in high-throughput RNA-protein interaction data

Motivation: Post-transcriptional and co-transcriptional regulation is a crucial link between genotype and phenotype. The central players are the RNA-binding proteins, and experimental technologies [such as cross-linking with immunoprecipitation-(CLIP-) and RIP-seq] for probing their activities have advanced rapidly over the course of the past decade. Statistically robust, flexible computational methods for binding site identification from high-throughput immunoprecipitation assays are largely lacking however.Results: We introduce a method for site identification which provides four key advantages over previous methods: (i) it can be applied on all variations of CLIP and RIP-seq technologies, (ii) it accurately models the underlying read-count distributions, (iii) it allows external covariates, such as transcript abundance (which we demonstrate is highly correlated with read count) to inform the site identification process and (iv) it allows for direct comparison of site usage across cell types or conditions. © The Author 2012. Published by Oxford University Press. All rights reserved

Caribbean Corals in Crisis: Record Thermal Stress, Bleaching, and Mortality in 2005

BACKGROUND The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. METHODOLOGY/PRINCIPAL FINDINGS Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. CONCLUSIONS/SIGNIFICANCE Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.This work was partially supported by salaries from the NOAA Coral Reef Conservation Program to the NOAA Coral Reef Conservation Program authors. NOAA provided funding to Caribbean ReefCheck investigators to undertake surveys of bleaching and mortality. Otherwise, no funding from outside authors' institutions was necessary for the undertaking of this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Evaluating stratospheric ozone and water vapour changes in CMIP6 models from 1850 to 2100

Stratospheric ozone and water vapour are key components of the Earth system, and past and future changes to both have important impacts on global and regional climate. Here, we evaluate long-term changes in these species from the pre-industrial period (1850) to the end of the 21st century in Coupled Model Intercomparison Project phase 6 (CMIP6) models under a range of future emissions scenarios. There is good agreement between the CMIP multi-model mean and observations for total column ozone (TCO), although there is substantial variation between the individual CMIP6 models. For the CMIP6 multi-model mean, global mean TCO has increased from ∼300 DU in 1850 to ∼ 305 DU in 1960, before rapidly declining in the 1970s and 1980s following the use and emission of halogenated ozone-depleting substances (ODSs). TCO is projected to return to 1960s values by the middle of the 21st century under the SSP2-4.5, SSP3-7.0, SSP4-3.4, SSP4-6.0, and SSP5-8.5 scenarios, and under the SSP3-7.0 and SSP5-8.5 scenarios TCO values are projected to be ∼ 10 DU higher than the 1960s values by 2100. However, under the SSP1-1.9 and SSP1-1.6 scenarios, TCO is not projected to return to the 1960s values despite reductions in halogenated ODSs due to decreases in tropospheric ozone mixing ratios. This global pattern is similar to regional patterns, except in the tropics where TCO under most scenarios is not projected to return to 1960s values, either through reductions in tropospheric ozone under SSP1-1.9 and SSP1-2.6, or through reductions in lower stratospheric ozone resulting from an acceleration of the Brewer-Dobson circulation under other Shared Socioeconomic Pathways (SSPs). In contrast to TCO, there is poorer agreement between the CMIP6 multi-model mean and observed lower stratospheric water vapour mixing ratios, with the CMIP6 multi-model mean underestimating observed water vapour mixing ratios by ∼ 0.5 ppmv at 70 hPa. CMIP6 multi-model mean stratospheric water vapour mixing ratios in the tropical lower stratosphere have increased by ∼ 0.5 ppmv from the pre-industrial to the present-day period and are projected to increase further by the end of the 21st century. The largest increases (∼ 2 ppmv) are simulated under the future scenarios with the highest assumed forcing pathway (e.g. SSP5-8.5). Tropical lower stratospheric water vapour, and to a lesser extent TCO, shows large variations following explosive volcanic eruptions. © Author(s) 2021

A solution scan of societal options to reduce transmission and spread of respiratory viruses: SARS-CoV-2 as a case study.

Societal biosecurity - measures built into everyday society to minimize risks from pests and diseases - is an important aspect of managing epidemics and pandemics. We aimed to identify societal options for reducing the transmission and spread of respiratory viruses. We used SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) as a case study to meet the immediate need to manage the COVID-19 pandemic and eventually transition to more normal societal conditions, and to catalog options for managing similar pandemics in the future. We used a 'solution scanning' approach. We read the literature; consulted psychology, public health, medical, and solution scanning experts; crowd-sourced options using social media; and collated comments on a preprint. Here, we present a list of 519 possible measures to reduce SARS-CoV-2 transmission and spread. We provide a long list of options for policymakers and businesses to consider when designing biosecurity plans to combat SARS-CoV-2 and similar pathogens in the future. We also developed an online application to help with this process. We encourage testing of actions, documentation of outcomes, revisions to the current list, and the addition of further options

Direct Bacterial Killing In Vitro by Recombinant Nod2 Is Compromised by Crohn's Disease-Associated Mutations

Background: A homeostatic relationship with the intestinal microflora is increasingly appreciated as essential for human health and wellbeing. Mutations in the leucine-rich repeat (LRR) domain of Nod2, a bacterial recognition protein, are associated with development of the inflammatory bowel disorder, Crohn’s disease. We investigated the molecular mechanisms underlying disruption of intestinal symbiosis in patients carrying Nod2 mutations. Methodology/Principal Findings: In this study, using purified recombinant LRR domains, we demonstrate that Nod2 is a direct antimicrobial agent and this activity is generally deficient in proteins carrying Crohn’s-associated mutations. Wildtype, but not Crohn’s-associated, Nod2 LRR domains directly interacted with bacteria in vitro, altered their metabolism and disrupted the integrity of the plasma membrane. Antibiotic activity was also expressed by the LRR domains of Nod1 and other pattern recognition receptors suggesting that the LRR domain is a conserved anti-microbial motif supporting innate cellular immunity. Conclusions/Significance: The lack of anti-bacterial activity demonstrated with Crohn’s-associated Nod2 mutations in vitro, supports the hypothesis that a deficiency in direct bacterial killing contributes to the association of Nod2 polymorphism