Spatio-temporal bivariate statistical models for atmospheric trace-gas inversion

Atmospheric trace-gas inversion refers to any technique used to predict spatial and temporal fluxes using mole-fraction measurements and atmospheric simulations obtained from computer models. Studies to date are most often of a data-assimilation flavour, which implicitly consider univariate statistical models with the flux as the variate of interest. This univariate approach typically assumes that the flux field is either a spatially correlated Gaussian process or a spatially uncorrelated non-Gaussian process with prior expectation fixed using flux inventories (e.g., NAEI or EDGAR in Europe). Here, we extend this approach in three ways. First, we develop a bivariate model for the mole-fraction field and the flux field. The bivariate approach allows optimal prediction of both the flux field and the mole-fraction field, and it leads to significant computational savings over the univariate approach. Second, we employ a lognormal spatial process for the flux field that captures both the lognormal characteristics of the flux field (when appropriate) and its spatial dependence. Third, we propose a new, geostatistical approach to incorporate the flux inventories in our updates, such that the posterior spatial distribution of the flux field is predominantly data-driven. The approach is illustrated on a case study of methane (CH$_4$) emissions in the United Kingdom and Ireland.Comment: 39 pages, 8 figure

Plasma proteome profiling of freshwater and seawater life stages of rainbow trout (Oncorhynchus mykiss)

The sea-run phenotype of rainbow trout (Oncorhynchus mykiss), like other anadromous salmonids, present a juvenile stage fully adapted to life in freshwater known as parr. Development in freshwater is followed by the smolt stage, where preadaptations needed for seawater life are developed making fish ready to migrate to the ocean, after which event they become post-smolts. While these three life stages have been studied using a variety of approaches, proteomics has never been used for such purpose. The present study characterised the blood plasma proteome of parr, smolt and post-smolt rainbow trout using a gel electrophoresis liquid chromatography tandem mass spectrometry approach alone or in combination with low-abundant protein enrichment technology (combinatorial peptide ligand library). In total, 1,822 proteins were quantified, 17.95% of them being detected only in plasma post enrichment. Across all life stages, the most abundant proteins were ankyrin-2, DNA primase large subunit, actin, serum albumin, apolipoproteins, hemoglobin subunits, hemopexin-like proteins and complement C3. When comparing the different life stages, 17 proteins involved in mechanisms to cope with hyperosmotic stress and retinal changes, as well as the downregulation of nonessential processes in smolts, were significantly different between parr and smolt samples. On the other hand, 11 proteins related to increased growth in post-smolts, and also related to coping with hyperosmotic stress and to retinal changes, were significantly different between smolt and post-smolt samples. Overall, this study presents a series of proteins with the potential to complement current seawater-readiness assessment tests in rainbow trout, which can be measured non-lethally in an easily accessible biofluid. Furthermore, this study represents a first in-depth characterisation of the rainbow trout blood plasma proteome, having considered three life stages of the fish and used both fractionation alone or in combination with enrichment methods to increase protein detection

Local observables for entanglement witnesses

We present an explicit construction of entanglement witnesses for depolarized states in arbitrary finite dimension. For infinite dimension we generalize the construction to twin-beams perturbed by Gaussian noises in the phase and in the amplitude of the field. We show that entanglement detection for all these families of states requires only three local measurements. The explicit form of the corresponding set of local observables (quorom) needed for entanglement witness is derived.Comment: minor corrections, title change

High Prevalence of the Amphibian Chytrid Fungus (\u3cem\u3eBatrachochytrium dendrobatidis\u3c/em\u3e) across Multiple Taxa and Localities in the Highlands of Ethiopia

Surveys of the potentially lethal amphibian chytrid fungus (Batrachochytrium dendrobatidis - Bd) in Africa are patchy, especially in some regions of high species endemicity. We present results of the first Bd surveys of wild amphibians in Ethiopia, for two upland regions on either side of the Rift Valley: the Bale Mountains and the Kaffa region. Surveys were opportunistic so that robust interpretation of the data is limited. Utilizing diagnostic qPCR assays, 51 out of 120 frogs (14 species in 10 genera) tested positive for Bd at altitudes of 1,620–3,225 m, across all genera and species, and all but two localities. Prevalence was not significantly different between the two regions or two years (2008, 2009) sampled. Prevalence and parasite load was higher in species with aquatic tadpoles than those with terrestrial early life-history stages, but these differences were not significant. Impacts of Bd infection were not investigated, but no dead or dying frogs were found. This is the first report of Bd in Ethiopia, a country in which approximately 40% of its more than 60 species are endemic. Declines have occurred in some frog species in some localities in Ethiopia, and although habitat degradation is a likely cause in at least some places, further studies of Bd in Ethiopia are required to understand if it is a threat

Improved FTIR retrieval strategy for HCFC-22 (CHClF₂), comparisons with in situ and satellite datasets with the support of models, and determination of its long-term trend above Jungfraujoch

Hydrochlorofluorocarbons (HCFCs) are the first, but temporary, substitution products for the strong ozone-depleting chlorofluorocarbons (CFCs). HCFC consumption and production are currently regulated under the Montreal Protocol on Substances that Deplete the Ozone Layer and their emissions have started to stabilize or even decrease. As HCFC-22 (CHClF2) is by far the most abundant HCFC in today\u27s atmosphere, it is crucial to continue to monitor the evolution of its atmospheric concentration. In this study, we describe an improved HCFC-22 retrieval strategy from ground-based high-resolution Fourier transform infrared (FTIR) solar spectra recorded at the high-altitude scientific station of Jungfraujoch, the Swiss Alps, 3580 m a.m.s.l. (above mean sea level). This new strategy distinguishes tropospheric and lower-stratospheric partial columns. Comparisons with independent datasets, such as the Advanced Global Atmospheric Gases Experiment (AGAGE) and the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS), supported by models, such as the Belgian Assimilation System for Chemical ObErvation (BASCOE) and the Whole Atmosphere Community Climate Model (WACCM), demonstrate the validity of our tropospheric and lower-stratospheric long-term time series. A trend analysis on the datasets used here, now spanning 30 years, confirms the last decade\u27s decline in the HCFC-22 growth rate. This updated retrieval strategy can be adapted for other ozone-depleting substances (ODSs), such as CFC-12. Measuring or retrieving ODS atmospheric concentrations is essential for scrutinizing the fulfilment of the globally ratified Montreal Protocol

Endoplasmic reticulum stress as a key mechanism in stunted growth of seawater rainbow trout (Oncorhynchus mykiss)

Background Rainbow trout (Oncorhynchus mykiss) is a salmonid species with a complex life-history. Wild populations are naturally divided into freshwater residents and sea-run migrants. Migrants undergo an energy-demanding adaptation for life in seawater, known as smoltification, while freshwater residents display these changes in an attenuated magnitude and rate. Despite this, in seawater rainbow trout farming all fish are transferred to seawater. Under these circumstances, weeks after seawater transfer, a significant portion of the fish die (around 10%) or experience growth stunting (GS; around 10%), which represents an important profitability and welfare issue. The underlying causes leading to GS in seawater-transferred rainbow trout remain unknown. In this study, we aimed at characterising the GS phenotype in seawater-transferred rainbow trout using untargeted and targeted approaches. To this end, the liver proteome (LC-MS/MS) and lipidome (LC-MS) of GS and fast-growing phenotypes were profiled to identify molecules and processes that are characteristic of the GS phenotype. Moreover, the transcription, abundance or activity of key proteins and hormones related to osmoregulation (Gill Na+, K + –ATPase activity), growth (plasma IGF-I, and liver igf1, igfbp1b, ghr1 and ctsl) and stress (plasma cortisol) were measured using targeted approaches. Results No differences in Gill Na+, K + –ATPase activity and plasma cortisol were detected between the two groups. However, a significant downregulation in plasma IGF-I and liver igf1 transcription pointed at this growth factor as an important pathomechanism for GS. Changes in the liver proteome revealed reactive-oxygen-species-mediated endoplasmic reticulum stress as a key mechanism underlying the GS phenotype. From the lipidomic analysis, key observations include a reduction in triacylglycerols and elevated amounts of cardiolipins, a characteristic lipid class associated with oxidative stress, in GS phenotype. Conclusion While the triggers to the activation of endoplasmic reticulum stress are still unknown, data from this study point towards a nutritional deficiency as an underlying driver of this phenotype

Aspects of bovine herpesvirus-1 infection in dairy and beef herds in the Republic of Ireland

<p>Abstract</p> <p>Background</p> <p>Infection with bovine herpesvirus-1 (BHV-1) causes a wide range of disease manifestations, including respiratory disease and abortion, with world-wide distribution. The primary objective of the present study was to describe aspects of BHV-1 infection and control on Irish farms, including herd-level seroprevalence (based on pooled sera) and vaccine usage.</p> <p>Methods</p> <p>The characteristics of a diagnostic indirect BHV-1 antibody ELISA test when used on serum pools were evaluated using laboratory replicates for use in the seroprevalence study. The output from this indirect ELISA was expressed as a percentage positivity (PP) value. A proposed cut off (PCO) PP was applied in a cross-sectional study of a stratified random sample of 1,175 Irish dairy and beef cattle herds in 2009, using serum pools, to estimate herd seroprevalence. The study was observational, based primarily on the analysis of existing samples, and only aggregated results were reported. For these reasons, ethical approval was not required. Bulk milk samples from a subset of 111 dairy herds were analysed using the same ELISA. Information regarding vaccine usage was determined in a telephone survey.</p> <p>Results</p> <p>A PCO PP of 7.88% was determined to give 97.1% sensitivity and 100% specificity relative to the use of the ELISA on individual sera giving maximization of the prevalence independent Youden's index, on receiver operating characteristics analysis of replicate results. The herd-level BHV-1 seroprevalence was 74.9% (95% CI - 69.9%-79.8%), with no significant difference between dairy and beef herds. 95.5% agreement in herd classification was found between bulk milk and serum pools. Only 1.8 percent of farmers used BHV-1 marker vaccine, 80% of which was live while 75% of vaccinated herds were dairy.</p> <p>A significant association was found between herd size (quartiles) and seroprevalence (quartiles).</p> <p>Conclusions</p> <p>The results from this study indicate BHV-1 infection is endemic, although BHV-1 vaccines are rarely used, in the cattle population in Ireland.</p

Characterising the application of the “progressive overload” principle of exercise training within cardiac rehabilitation: A United Kingdom-based community programme

Background: Recent concerns have cast doubt over the effectiveness of cardiac rehabilitation [CR] programmes for improving cardiorespiratory fitness [CRF] in patients with a history of cardiac disease in the United Kingdom [UK]. We aimed to characterise the weekly progression of exercise training dose over an 8-week Phase III CR programme as we felt this may be partly responsible for the lack of improvement in CRF reported in previous studies. Design: Observational study. Methods: We evaluated a community-based Phase III CR programme in the UK. During each training session, patients wore an Apple Watch and the weekly progression of exercise training dose/load was quantified. The analysis was based on 332 individual training sessions. Exercise intensity [% heart rate reserve] during the cardiovascular [CV] exercise training component [%HRR-CV], CV training duration; estimated changes in cardiorespiratory fitness [change in estimated metabolic equivalents (METs)]; session rating of perceived exertion [sRPE], sRPE training load [sRPE-TL], and exercise training impulse [TRIMP] were evaluated. Results: Thirty cardiac patients [83% male; age [SD] 67.0 [10.0] years; body mass index [SD] 28.3 [4.6] kg∙m-2] were recruited to an 8-week programme [16 sessions in total]. Bayesian repeated-measures ANOVA indicated anecdotal evidence for the alternative hypothesis for changes in %HRR-CV (BF10 = 0.61), sRPE (BF10 = 1.1), and change in estimated METs (BF10 = 1.2) during CR. Conversely, Bayesian repeated-measures ANOVA showed extreme evidence for changes in CV training duration (BF10 = 2.438e+26), TRIMP (BF10 = 71436), and sRPE-TL (BF10 = 779570). Conclusion: The key exercise training principle of progressive overload was only partially applied. Increases observed in exercise dose were due to increases in the duration of CV training, rather than combined with increases in exercise intensity [%HRR-CV and sRPE]. Accordingly, allied health professionals must ensure that exercise intensity is more consistently progressed to optimise the exercise stimulus and improvements in CRF and patient outcomes

Speaking and Listening with the Eyes: Gaze Signaling during Dyadic Interactions

Cognitive scientists have long been interested in the role that eye gaze plays in social interactions. Previous research suggests that gaze acts as a signaling mechanism and can be used to control turn-taking behaviour. However, early research on this topic employed methods of analysis that aggregated gaze information across an entire trial (or trials), which masks any temporal dynamics that may exist in social interactions. More recently, attempts have been made to understand the temporal characteristics of social gaze but little research has been conducted in a natural setting with two interacting participants. The present study combines a temporally sensitive analysis technique with modern eye tracking technology to 1) validate the overall results from earlier aggregated analyses and 2) provide insight into the specific moment-to-moment temporal characteristics of turn-taking behaviour in a natural setting. Dyads played two social guessing games (20 Questions and Heads Up) while their eyes were tracked. Our general results are in line with past aggregated data, and using cross-correlational analysis on the specific gaze and speech signals of both participants we found that 1) speakers end their turn with direct gaze at the listener and 2) the listener in turn begins to speak with averted gaze. Convergent with theoretical models of social interaction, our data suggest that eye gaze can be used to signal both the end and the beginning of a speaking turn during a social interaction. The present study offers insight into the temporal dynamics of live dyadic interactions and also provides a new method of analysis for eye gaze data when temporal relationships are of interest

Comparing nuclear power trajectories in Germany and the UK: from ‘regimes' to ‘democracies’ in sociotechnical transitions and Discontinuities

This paper focuses on arguably the single most striking contrast in contemporary major energy politics in Europe (and even the developed world as a whole): the starkly differing civil nuclear policies of Germany and the UK. Germany is seeking entirely to phase out nuclear power by 2022. Yet the UK advocates a ‘nuclear renaissance’, promoting the most ambitious new nuclear construction programme in Western Europe.Here,this paper poses a simple yet quite fundamental question: what are the particular divergent conditions most strongly implicated in the contrasting developments in these two countries. With nuclear playing such an iconic role in historical discussions over technological continuity and transformation, answering this may assist in wider understandings of sociotechnical incumbency and discontinuity in the burgeoning field of‘sustainability transitions’. To this end, an ‘abductive’ approach is taken: deploying nine potentially relevant criteria for understanding the different directions pursued in Germany and the UK. Together constituted by 30 parameters spanning literatures related to socio-technical regimes in general as well as nuclear technology in particular, the criteria are divided into those that are ‘internal’ and ‘external’ to the ‘focal regime configuration’ of nuclear power and associated ‘challenger technologies’ like renewables. It is ‘internal’ criteria that are emphasised in conventional sociotechnical regime theory, with ‘external’ criteria relatively less well explored. Asking under each criterion whether attempted discontinuation of nuclear power would be more likely in Germany or the UK, a clear picture emerges. ‘Internal’ criteria suggest attempted nuclear discontinuation should be more likely in the UK than in Germany– the reverse of what is occurring. ‘External’ criteria are more aligned with observed dynamics –especially those relating to military nuclear commitments and broader ‘qualities of democracy’. Despite many differences of framing concerning exactly what constitutes ‘democracy’, a rich political science literature on this point is unanimous in characterising Germany more positively than the UK. Although based only on a single case,a potentially important question is nonetheless raised as to whether sociotechnical regime theory might usefully give greater attention to the general importance of various aspects of democracy in constituting conditions for significant technological discontinuities and transformations. If so, the policy implications are significant. A number of important areas are identified for future research, including the roles of diverse understandings and specific aspects of democracy and the particular relevance of military nuclear commitments– whose under-discussion in civil nuclear policy literatures raises its own questions of democratic accountability