The calibration of read-out-streak photometry in the XMM-Newton Optical Monitor and the construction of a bright-source catalogue

The dynamic range of the XMM-Newton Optical Monitor (XMM-OM) is limited at the bright end by coincidence loss, the superposition of multiple photons in the individual frames recorded from its micro-channel-plate (MCP) intensified charge-coupled device (CCD) detector. One way to overcome this limitation is to use photons that arrive during the frame transfer of the CCD, forming vertical read-out streaks for bright sources. We calibrate these read-out streaks for photometry of bright sources observed with XMM-OM. The bright source limit for read-out streak photometry is set by the recharge time of the MCPs. For XMM-OM we find that the MCP recharge time is 0.55 ms. We determine that the effective bright limits for read-out streak photometry with XMM-OM are approximately 1.5 magnitudes brighter than the bright source limits for normal aperture photometry in full-frame images. This translates into bright-source limits in Vega magnitudes of UVW2=7.1, UVM2=8.0, UVW1=9.4, U=10.5, B=11.5, V=10.2 and White=12.5 for data taken early in the mission. The limits brighten by up to 0.2 magnitudes, depending on filter, over the course of the mission as the detector ages. The method is demonstrated by deriving UVW1 photometry for the symbiotic nova RR Telescopii, and the new photometry is used to constrain the e-folding time of its decaying UV emission. Using the read-out streak method, we obtain photometry for 50 per cent of the missing UV source measurements in version 2.1 of the XMM-Newton Serendipitous UV Source Survey (XMM-SUSS 2.1) catalogue

Is metal theft committed by organized crime groups, and why does it matter?

Using the example of metal theft in the United Kingdom, this study used mixed methods to evaluate the accuracy of police estimates of the involvement of organised crime groups (OCGs) in crime. Police estimate that 20-30% of metal theft is committed by OCGs, but this study found that only 0.5% of metal thieves had previous convictions for offences related to OCGs, that only 1.3% were linked to OCGs by intelligence information, that metal thieves typically offended close to their homes and that almost no metal thefts involved sophisticated offence methods. It appears that police may over-estimate the involvement of OCGs in some types of crime. The reasons for and consequences of this over-estimation are discussed

Exhaled Breath Isoprene Rises During Hypoglycemia in Type 1 Diabetes.

Work was supported by the NIHR Cambridge Biomedical Research Centre including salary support for SN. Hormonal assays were performed by Keith Burling and colleagues in the NIHR Cambridge Biomedical Research Centre Core Biochemical Assay Laboratory. Clamp studies were performed in the Cambridge NIHR/ Wellcome Trust Clinical Research Facility.This is the author accepted manuscript. The final version is available from the American Diabetes Association via http://dx.doi.org/10.2337/dc16-046

Coral restoration - A systematic review of current methods, successes, failures and future directions.

Coral reef ecosystems have suffered an unprecedented loss of habitat-forming hard corals in recent decades. While marine conservation has historically focused on passive habitat protection, demand for and interest in active restoration has been growing in recent decades. However, a disconnect between coral restoration practitioners, coral reef managers and scientists has resulted in a disjointed field where it is difficult to gain an overview of existing knowledge. To address this, we aimed to synthesise the available knowledge in a comprehensive global review of coral restoration methods, incorporating data from the peer-reviewed scientific literature, complemented with grey literature and through a survey of coral restoration practitioners. We found that coral restoration case studies are dominated by short-term projects, with 60% of all projects reporting less than 18 months of monitoring of the restored sites. Similarly, most projects are relatively small in spatial scale, with a median size of restored area of 100 m2. A diverse range of species are represented in the dataset, with 229 different species from 72 coral genera. Overall, coral restoration projects focused primarily on fast-growing branching corals (59% of studies), and report survival between 60 and 70%. To date, the relatively young field of coral restoration has been plagued by similar 'growing pains' as ecological restoration in other ecosystems. These include 1) a lack of clear and achievable objectives, 2) a lack of appropriate and standardised monitoring and reporting and, 3) poorly designed projects in relation to stated objectives. Mitigating these will be crucial to successfully scale up projects, and to retain public trust in restoration as a tool for resilience based management. Finally, while it is clear that practitioners have developed effective methods to successfully grow corals at small scales, it is critical not to view restoration as a replacement for meaningful action on climate change

Integrated groundwater management: An overview of concepts and challenges

Managing water is a grand challenge problem and has become one of humanity’s foremost priorities. Surface water resources are typically societally managed and relatively well understood; groundwater resources, however, are often hidden and more difficult to conceptualize. Replenishment rates of groundwater cannot match past and current rates of depletion in many parts of the world. In addition, declining quality of the remaining groundwater commonly cannot support all agricultural, industrial and urban demands and ecosystem functioning, especially in the developed world. In the developing world, it can fail to even meet essential human needs. The issue is: how do we manage this crucial resource in an acceptable way, one that considers the sustainability of the resource for future generations and the socioeconomic and environmental impacts? In many cases this means restoring aquifers of concern to some sustainable equilibrium over a negotiated period of time, and seeking opportunities for better managing groundwater conjunctively with surface water and other resource uses. However, there are many, often-interrelated, dimensions to managing groundwater effectively. Effective groundwater management is underpinned by sound science (biophysical and social) that actively engages the wider community and relevant stakeholders in the decision making process. Generally, an integrated approach will mean “thinking beyond the aquifer”, a view which considers the wider context of surface water links, catchment management and cross-sectoral issues with economics, energy, climate, agriculture and the environment. The aim of the book is to document for the first time the dimensions and requirements of sound integrated groundwater management (IGM). The primary focus is on groundwater management within its system, but integrates linkages beyond the aquifer. The book provides an encompassing synthesis for researchers, practitioners and water resource managers on the concepts and tools required for defensible IGM, including how IGM can be applied to achieve more sustainable socioeconomic and environmental outcomes, and key challenges of IGM. The book is divided into five parts: integration overview and problem settings; governance; socioeconomics; biophysical aspects; and modelling and decision support. However, IGM is integrated by definition, thus these divisions should be considered a convenience for presenting the topics rather than hard and fast demarcations of the topic area

Evaluation of the impact of a school gardening intervention on children's fruit and vegetable intake: a randomised controlled trial.

Background: Current academic literature suggests that school gardening programmes can provide an interactive environment with the potential to change children’s fruit and vegetable intake. This is the first cluster randomised controlled trial (RCT) designed to evaluate whether a school gardening programme can have an effect on children’s fruit and vegetable intake. Methods: The trial included children from 23 schools; these schools were randomised into two groups, one to receive the Royal Horticultural Society (RHS)-led intervention and the other to receive the less involved Teacher-led intervention. A 24-hour food diary (CADET) was used to collect baseline and follow-up dietary intake 18 months apart. Questionnaires were also administered to evaluate the intervention implementation. Results: A total of 641 children completed the trial with a mean age of 8.1 years (95% CI: 8.0, 8.4). The unadjusted results from multilevel regression analysis revealed that for combined daily fruit and vegetable intake the Teacher-led group had a higher daily mean change of 8 g (95% CI: −19, 36) compared to the RHS-led group -32 g (95% CI: −60, −3). However, after adjusting for possible confounders this difference was not significant (intervention effect: −40 g, 95% CI: −88, 1; p = 0.06). The adjusted analysis of process measures identified that if schools improved their gardening score by 3 levels (a measure of school gardening involvement - the scale has 6 levels from 0 ‘no garden’ to 5 ‘community involvement’), irrespective of group allocation, children had, on average, a daily increase of 81 g of fruit and vegetable intake (95% CI: 0, 163; p = 0.05) compared to schools that had no change in gardening score. Conclusions: This study is the first cluster randomised controlled trial designed to evaluate a school gardening intervention. The results have found very little evidence to support the claims that school gardening alone can improve children’s daily fruit and vegetable intake. However, when a gardening intervention is implemented at a high level within the school it may improve children’s daily fruit and vegetable intake by a portion. Improving children’s fruit and vegetable intake remains a challenging task

Attenuation of acute lung inflammation induced by cigarette smoke in CXCR3 knockout mice

Background: CD8+ T cells may participate in cigarette smoke (CS) induced-lung inflammation in mice. CXCL10/IP-10 (IFNγ-inducible protein 10) and CXCL9/Mig (monokine induced by IFN-$\gamma$) are up-regulated in CS-induced lung injury and may attract T-cell recruitment to the lung. These chemokines together with CXCL11/ITAC (IFN-inducible T-cell alpha chemoattractant) are ligands for the chemokine receptor CXCR3 which is preferentially expressed chiefly in activated CD8+ T cells. The purpose of this investigation was to study the contribution of CXCR3 to acute lung inflammation induced by CS using CXCR3 knockout (KO) mice. Methods: Mice (n = 8 per group) were placed in a closed plastic box connected to a smoke generator and were exposed whole body to the tobacco smoke of five cigarettes four times a day for three days. Lung pathological changes, expression of inflammatory mediators in bronchoalveolar lavage (BAL) fluid and lungs at mRNA and protein levels, and lung infiltration of CD8+ T cells were compared between CXCR3-/- mice and wild type (WT) mice. Results: Compared with the WT littermates, CXCR3 KO mice showed less CS-induced lung inflammation as evidenced by less infiltration of inflammatory cells in airways and lung tissue, particularly fewer CD8+ T cells, lower levels of IFNγ and CXCR3 ligands (particularly CXCL10). Conclusion: Our findings show that CXCR3 is important in promoting CD8+ T cell recruitment and in initiating IFNγ and CXCL10 release following CS exposure. CXCR3 may represent a promising therapeutic target for acute lung inflammation induced by CS

Serum methylarginines and spirometry-measured lung function in older adults

Rationale: Methylarginines are endogenous nitric oxide synthase inhibitors that have been implicated in animal models of lung disease but have not previously been examined for their association with spirometric measures of lung function in humans. Objectives: This study measured serum concentrations of asymmetric and symmetric dimethylarginine in a representative sample of older community-dwelling adults and determined their association with spirometric lung function measures. Methods: Data on clinical, lifestyle, and demographic characteristics, methylated arginines, and L-arginine (measured using LC-MS/MS) were collected from a population-based sample of older Australian adults from the Hunter Community Study. The five key lung function measures included as outcomes were Forced Expiratory Volume in 1 second, Forced Vital Capacity, Forced Expiratory Volume in 1 second to Forced Vital Capacity ratio, Percent Predicted Forced Expiratory Volume in 1 second, and Percent Predicted Forced Vital Capacity. Measurements and Main Results: In adjusted analyses there were statistically significant independent associations between a) higher asymmetric dimethylarginine, lower Forced Expiratory Volume in 1 second and lower Forced Vital Capacity; and b) lower L-arginine/asymmetric dimethylarginine ratio, lower Forced Expiratory Volume in 1 second, lower Percent Predicted Forced Expiratory Volume in 1 second and lower Percent Predicted Forced Vital Capacity. By contrast, no significant associations were observed between symmetric dimethylarginine and lung function. Conclusions: After adjusting for clinical, demographic, biochemical, and pharmacological confounders, higher serum asymmetric dimethylarginine was independently associated with a reduction in key measures of lung function. Further research is needed to determine if methylarginines predict the decline in lung function

Estimation of the solubility parameters of model plant surfaces and agrochemicals: a valuable tool for understanding plant surface interactions

Background Most aerial plant parts are covered with a hydrophobic lipid-rich cuticle, which is the interface between the plant organs and the surrounding environment. Plant surfaces may have a high degree of hydrophobicity because of the combined effects of surface chemistry and roughness. The physical and chemical complexity of the plant cuticle limits the development of models that explain its internal structure and interactions with surface-applied agrochemicals. In this article we introduce a thermodynamic method for estimating the solubilities of model plant surface constituents and relating them to the effects of agrochemicals. Results Following the van Krevelen and Hoftyzer method, we calculated the solubility parameters of three model plant species and eight compounds that differ in hydrophobicity and polarity. In addition, intact tissues were examined by scanning electron microscopy and the surface free energy, polarity, solubility parameter and work of adhesion of each were calculated from contact angle measurements of three liquids with different polarities. By comparing the affinities between plant surface constituents and agrochemicals derived from (a) theoretical calculations and (b) contact angle measurements we were able to distinguish the physical effect of surface roughness from the effect of the chemical nature of the epicuticular waxes. A solubility parameter model for plant surfaces is proposed on the basis of an increasing gradient from the cuticular surface towards the underlying cell wall. Conclusions The procedure enabled us to predict the interactions among agrochemicals, plant surfaces, and cuticular and cell wall components, and promises to be a useful tool for improving our understanding of biological surface interactions

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The gain represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The loss represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is Codon Disappearance, where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the Unassigned Codon mechanism, the loss occurs first, whereas in the Ambiguous Intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. Codon disappearance is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense to sense reassignments cannot be explained by codon disappearance. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the Unassigned Codon and Ambiguous Intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.Comment: 53 pages (45 pages, including 4 figures + 8 pages of supplementary information). To appear in J.Mol.Evo