Estimates of tropical bromoform emissions using an inversion method

Abstract. Bromine plays an important role in ozone chemistry in both the troposphere and stratosphere. When measured by mass, bromoform (CHBr3) is thought to be the largest organic source of bromine to the atmosphere. While seaweed and phytoplankton are known to be dominant sources, the size and the geographical distribution of CHBr3 emissions remains uncertain. Particularly little is known about emissions from the Maritime Continent, which have usually been assumed to be large, and which appear to be especially likely to reach the stratosphere. In this study we aim to reduce this uncertainty by combining the first multi-annual set of CHBr3 measurements from this region, and an inversion process, to investigate systematically the distribution and magnitude of CHBr3 emissions. The novelty of our approach lies in the application of the inversion method to CHBr3. We find that local measurements of a short-lived gas like CHBr3 can be used to constrain emissions from only a relatively small, sub-regional domain. We then obtain detailed estimates of CHBr3 emissions within this area, which appear to be relatively insensitive to the assumptions inherent in the inversion process. We extrapolate this information to produce estimated emissions for the entire tropics (defined as 20° S–20° N) of 225 Gg CHBr3 yr−1. The ocean in the area we base our extrapolations upon is typically somewhat shallower, and more biologically productive, than the tropical average. Despite this, our tropical estimate is lower than most other recent studies, and suggests that CHBr3 emissions in the coastline-rich Maritime Continent may not be stronger than emissions in other parts of the tropics. M. Ashfold thanks the Natural Environment Research Council (NERC) for a research studentship, and is grateful for support through the ERC ACCI project (project number 267760). N. Harris is supported by a NERC Advanced Research Fellowship. This work was supported through the EU SHIVA project, through the NERC OP3 project, and NERC grants NE/F020341/1 and NE/J006246/1. We also acknowledge the Department of Energy and Climate Change for their support in the development of InTEM (contract GA0201). For field site support we thank S.-M. Phang, A. A. Samah and M. S. M. Nadzir of Universiti Malaya, S. Ong and H. E. Ung of Global Satria, Maznorizan Mohamad, L. K. Peng and S. E. Yong of the Malaysian Meteorological Department, the Sabah Foundation, the Danum Valley Field Centre and the Royal Society. This paper constitutes publication no. 613 of the Royal Society South East Asia Rainforest Research Programme.This is the final published version. It first appeared at http://www.atmos-chem-phys.net/14/979/2014/acp-14-979-2014.html

An in vivo platform to select and evolve aggregation-resistant proteins

Protein biopharmaceuticals are highly successful, but their utility is compromised by their propensity to aggregate during manufacture and storage. As aggregation can be triggered by non-native states, whose population is not necessarily related to thermodynamic stability, prediction of poorly-behaving biologics is difficult, and searching for sequences with desired properties is labour-intensive and time-consuming. Here we show that an assay in the periplasm of E. coli linking aggregation directly to antibiotic resistance acts as a sensor for the innate (un-accelerated) aggregation of antibody fragments. Using this assay as a directed evolution screen, we demonstrate the generation of aggregation resistant scFv sequences when reformatted as IgGs. This powerful tool can thus screen and evolve ‘manufacturable’ biopharmaceuticals early in industrial development. By comparing the mutational profiles of three different immunoglobulin scaffolds, we show the applicability of this method to investigate protein aggregation mechanisms important to both industrial manufacture and amyloid disease

Long-term halocarbon observations from a coastal and an inland site in Sabah, Malaysian Borneo

Abstract. Short-lived halocarbons are believed to have important sources in the tropics, where rapid vertical transport could provide a significant source to the stratosphere. In this study, quasi-continuous measurements of short-lived halocarbons are reported for two tropical sites in Sabah (Malaysian Borneo), one coastal and one inland (rainforest). We present the observations for C2Cl4, CHBr3, CH2Br2* (actually ~80% CH2Br2 and ~20% CHBrCl2) and CH3I from November 2008 to January 2010 made using our μDirac gas chromatographs with electron capture detection (GC-ECD). We focus on the first 15 months of observations, showing over one annual cycle for each compound and therefore adding significantly to the few limited-duration observational studies that have been conducted thus far in southeast Asia. The main feature in the C2Cl4 behaviour at both sites is its annual cycle, with the winter months being influenced by northerly flow with higher concentrations, typical of the Northern Hemisphere, and with the summer months influenced by southerly flow and lower concentrations representative of the Southern Hemisphere. No such clear annual cycle is seen for CHBr3, CH2Br2* or CH3I. The baseline values for CHBr3 and CH2Br2* are similar at the coastal (overall median: CHBr3 1.7 ppt, CH2Br2* 1.4 ppt) and inland sites (CHBr3 1.6 ppt, CH2Br2* 1.1 ppt), but periods with elevated values are seen at the coast (overall 95th percentile: CHBr3 4.4 ppt, CH2Br2ast 1.9 ppt), presumably resulting from the stronger influence of coastal emissions. Overall median bromine values from [CHBr3 × 3] + [CH2Br2* × 2] are 8.0 ppt at the coast and 6.8 ppt inland. The median values reported here are largely consistent with other limited tropical data and imply that southeast Asia generally is not, as has been suggested, a hot spot for emissions of these compounds. These baseline values are consistent with the most recent emissions found for southeast Asia using the p-TOMCAT (Toulouse Off-line Model of Chemistry And Transport) model. CH3I, which is only observed at the coastal site, is the shortest-lived compound measured in this study, and the observed atmospheric variations reflect this, with high variability throughout the study period. This work was supported by a NERC consortium grant to the OP3 team, by NCAS, by the European Commission through the SCOUT-O3 project (505390-GOCE-CF2004) and by NERC western Pacific grant number NE/F020341/1 and NERC CAST grant number NE/J006246/1. L. M. O’Brien and M. J. Ashfold thank NERC for research studentships. A. D. Robinson acknowledges NERC for their support through small grant project NE/D008085/1. N. R. P. Harris is supported by a NERC Advanced Research Fellowship. We thank the Sabah Foundation, Danum Valley Field Centre and the Royal Society (Glen Reynolds) for field site support. The research leading to these results has received funding from the European Union’s Seventh Framework Programme FP7/2007–2013 under grant agreement no. 226224 – SHIVA. We thank David Oram and Stephen Humphrey at UEA for their assistance in checking the calibration of our Aculife cylinder in May 2009. This is paper number 626 of the Royal Society’s South East Asian Rainforest Research Programme.This is the final published version. It first appeared at http://www.atmos-chem-phys.net/14/8369/2014/acp-14-8369-2014.html

Biodiversity Loss and the Taxonomic Bottleneck: Emerging Biodiversity Science

Human domination of the Earth has resulted in dramatic changes to global and local patterns of biodiversity. Biodiversity is critical to human sustainability because it drives the ecosystem services that provide the core of our life-support system. As we, the human species, are the primary factor leading to the decline in biodiversity, we need detailed information about the biodiversity and species composition of specific locations in order to understand how different species contribute to ecosystem services and how humans can sustainably conserve and manage biodiversity. Taxonomy and ecology, two fundamental sciences that generate the knowledge about biodiversity, are associated with a number of limitations that prevent them from providing the information needed to fully understand the relevance of biodiversity in its entirety for human sustainability: (1) biodiversity conservation strategies that tend to be overly focused on research and policy on a global scale with little impact on local biodiversity; (2) the small knowledge base of extant global biodiversity; (3) a lack of much-needed site-specific data on the species composition of communities in human-dominated landscapes, which hinders ecosystem management and biodiversity conservation; (4) biodiversity studies with a lack of taxonomic precision; (5) a lack of taxonomic expertise and trained taxonomists; (6) a taxonomic bottleneck in biodiversity inventory and assessment; and (7) neglect of taxonomic resources and a lack of taxonomic service infrastructure for biodiversity science. These limitations are directly related to contemporary trends in research, conservation strategies, environmental stewardship, environmental education, sustainable development, and local site-specific conservation. Today’s biological knowledge is built on the known global biodiversity, which represents barely 20% of what is currently extant (commonly accepted estimate of 10 million species) on planet Earth. Much remains unexplored and unknown, particularly in hotspots regions of Africa, South Eastern Asia, and South and Central America, including many developing or underdeveloped countries, where localized biodiversity is scarcely studied or described. ‘‘Backyard biodiversity’’, defined as local biodiversity near human habitation, refers to the natural resources and capital for ecosystem services at the grassroots level, which urgently needs to be explored, documented, and conserved as it is the backbone of sustainable economic development in these countries. Beginning with early identification and documentation of local flora and fauna, taxonomy has documented global biodiversity and natural history based on the collection of ‘‘backyard biodiversity’’ specimens worldwide. However, this branch of science suffered a continuous decline in the latter half of the twentieth century, and has now reached a point of potential demise. At present there are very few professional taxonomists and trained local parataxonomists worldwide, while the need for, and demands on, taxonomic services by conservation and resource management communities are rapidly increasing. Systematic collections, the material basis of biodiversity information, have been neglected and abandoned, particularly at institutions of higher learning. Considering the rapid increase in the human population and urbanization, human sustainability requires new conceptual and practical approaches to refocusing and energizing the study of the biodiversity that is the core of natural resources for sustainable development and biotic capital for sustaining our life-support system. In this paper we aim to document and extrapolate the essence of biodiversity, discuss the state and nature of taxonomic demise, the trends of recent biodiversity studies, and suggest reasonable approaches to a biodiversity science to facilitate the expansion of global biodiversity knowledge and to create useful data on backyard biodiversity worldwide towards human sustainability

X-ray Absorption and Reflection in Active Galactic Nuclei

X-ray spectroscopy offers an opportunity to study the complex mixture of emitting and absorbing components in the circumnuclear regions of active galactic nuclei, and to learn about the accretion process that fuels AGN and the feedback of material to their host galaxies. We describe the spectral signatures that may be studied and review the X-ray spectra and spectral variability of active galaxies, concentrating on progress from recent Chandra, XMM-Newton and Suzaku data for local type 1 AGN. We describe the evidence for absorption covering a wide range of column densities, ionization and dynamics, and discuss the growing evidence for partial-covering absorption from data at energies > 10 keV. Such absorption can also explain the observed X-ray spectral curvature and variability in AGN at lower energies and is likely an important factor in shaping the observed properties of this class of source. Consideration of self-consistent models for local AGN indicates that X-ray spectra likely comprise a combination of absorption and reflection effects from material originating within a few light days of the black hole as well as on larger scales. It is likely that AGN X-ray spectra may be strongly affected by the presence of disk-wind outflows that are expected in systems with high accretion rates, and we describe models that attempt to predict the effects of radiative transfer through such winds, and discuss the prospects for new data to test and address these ideas.Comment: Accepted for publication in the Astronomy and Astrophysics Review. 58 pages, 9 figures. V2 has fixed an error in footnote

Taxonomic Distinctness of Demersal Fishes of the California Current: Moving Beyond Simple Measures of Diversity for Marine Ecosystem-Based Management

BACKGROUND: Large-scale patterns or trends in species diversity have long interested ecologists. The classic pattern is for diversity (e.g., species richness) to decrease with increasing latitude. Taxonomic distinctness is a diversity measure based on the relatedness of the species within a sample. Here we examined patterns of taxonomic distinctness in relation to latitude (ca. 32-48 degrees N) and depth (ca. 50-1220 m) for demersal fishes on the continental shelf and slope of the US Pacific coast. METHODOLOGY/PRINCIPAL FINDINGS: Both average taxonomic distinctness (AvTD) and variation in taxonomic distinctness (VarTD) changed with latitude and depth. AvTD was highest at approximately 500 m and lowest at around 200 m bottom depth. Latitudinal trends in AvTD were somewhat weaker and were depth-specific. AvTD increased with latitude on the shelf (50-150 m) but tended to decrease with latitude at deeper depths. Variation in taxonomic distinctness (VarTD) was highest around 300 m. As with AvTD, latitudinal trends in VarTD were depth-specific. On the shelf (50-150 m), VarTD increased with latitude, while in deeper areas the patterns were more complex. Closer inspection of the data showed that the number and distribution of species within the class Chondrichthyes were the primary drivers of the overall patterns seen in AvTD and VarTD, while the relatedness and distribution of species in the order Scorpaeniformes appeared to cause the relatively low observed values of AvTD at around 200 m. CONCLUSIONS/SIGNIFICANCE: These trends contrast to some extent the patterns seen in earlier studies for species richness and evenness in demersal fishes along this coast and add to our understanding of diversity of the demersal fishes of the California Current

Prospective validation of the RAPID clinical risk prediction score in adult patients with pleural infection: the PILOT study

BACKGROUND: Over 30% of adult patients with pleural infection either die and/or require surgery. There is no robust means of predicting at baseline presentation which patients will suffer a poor clinical outcome. A validated risk prediction score would allow early identification of high-risk patients, potentially directing more aggressive treatment thereafter. OBJECTIVES: To prospectively assess a previously described risk score (RAPID - Renal (urea), Age, fluid Purulence, Infection source, Dietary (albumin)) in adults with pleural infection. METHODS: Prospective observational cohort study recruiting patients undergoing treatment for pleural infection. RAPID score and risk category were calculated at baseline presentation. The primary outcome was mortality at 3 months; secondary outcomes were mortality at 12 months, length of hospital stay, need for thoracic surgery, failure of medical treatment, and lung function at 3 months. RESULTS: Mortality data were available in 542 of 546 (99.3%) patients recruited. Overall mortality was 10% (54/542) at 3 months and 19% (102/542) at 12 months. The RAPID risk category predicted mortality at 3 months; low-risk (RAPID score 0-2) mortality 5/222 (2.3%, 95%CI 0.9 to 5.7), medium-risk (RAPID score 3-4) mortality 21/228 (9.2%, 95%CI 6.0 to 13.7), and high-risk (RAPID score 5-7) mortality 27/92 (29.3%, 95%CI 21.0 to 39.2). C-statistics for the score at 3 and 12 months were 0.78 (95%CI 0.71 to 0.83) and 0.77 (95%CI 0.72 to 0.82) respectively. CONCLUSIONS: The RAPID score stratifies adults with pleural infection according to increasing risk of mortality and should inform future research directed at improving outcomes in this patient population

"I don't eat a hamburger and large chips every day!" A qualitative study of the impact of public health messages about obesity on obese adults

BackgroundWe are a society that is fixated on the health consequences of \u27being fat\u27. Public health agencies play an important role in \u27alerting\u27 people about the risks that obesity poses both to individuals and to the broader society. Quantitative studies suggest people comprehend the physical health risks involved but underestimate their own risk because they do not recognise that they are obese.MethodsThis qualitative study seeks to expand on existing research by exploring obese individuals\u27 perceptions of public health messages about risk, how they apply these messages to themselves and how their personal and social contexts and experiences may influence these perceptions. The study uses in depth interviews with a community sample of 142 obese individuals. A constant comparative method was employed to analyse the data.ResultsPersonal and contextual factors influenced the ways in which individuals interpreted and applied public health messages, including their own health and wellbeing and perceptions of stigma. Individuals felt that messages were overly focused on the physical rather than emotional health consequences of obesity. Many described feeling stigmatised and blamed by the simplicity of messages and the lack of realistic solutions. Participants described the need for messages that convey the risks associated with obesity while minimising possible stigmatisation of obese individuals. This included ensuring that messages recognise the complexity of obesity and focus on encouraging healthy behaviours for individuals of all sizes.ConclusionThis study is the first step in exploring the ways in which we understand how public health messages about obesity resonate with obese individuals in Australia. However, much more research - both qualitative and quantitative - is needed to enhance understanding of the impact of obesity messages on individuals