Operationalising a metric of nitrogen impacts on biodiversity for the UK response to a data request from the Coordination Centre for Effects

As a signatory party to the Convention on Long Range Transboundary Air Pollution (CLRTAP), the UK has been requested to provide biodiversity metrics for use in assessing impacts of atmospheric nitrogen (N) pollution. Models of soil and vegetation responses to N pollution can predict changes in habitat suitability for many plant and lichen species. Metrics are required to relate changes in a set of species to biodiversity targets. In a previous study, the suitability of the habitat for a set of positive indicator-species was found to be the measure, out of potential outputs from models currently applicable to the UK, which was most clearly related to the assessment methods of habitat specialists at the Statutory Nature Conservation Bodies (SNCBs). This report describes the calculation of values for a metric, based on this principle, for a set of example habitats under different N pollution scenarios. The examples are mainly from Natura-2000 sites, and are defined at EUNIS Level 3 (e.g. F4.1 Wet heath). Values for the biodiversity metric were shown to be greater on all sites in the “Background” scenario than in the scenario with greater N and S pollution, illustrating a positive response of biodiversity to reduced pollution. Results of the study were submitted in response to the ‘Call for Data 2012-14’ by the CLTRAP Co-ordination Centre for Effects (CCE), and presented at the 24th CCE Workshop in April 2014. Metrics calculated on a similar basis were also presented by the Netherlands, Switzerland and Denmark. Such metrics indicate biodiversity status more accurately than other types of metric such as Simpson index or similarity to a reference community, so it was decided to adopt habitat-suitability for positive indicator-species as a common basis for a biodiversity metric in this context. Further work is needed to determine the typical range of metric values in different habitats, and threshold values for damage and recovery. Requirements are likely to be specified in detail in the next CCE Call for Data. The current study shows that a biodiversity metric based on habitat-suitability for positive indicator-species is a useful and responsive method for summarising outputs of models of air pollution impacts on ecosystems

Plant functional type affects nitrogen use efficiency in high-Arctic tundra

To unravel the potential effects of climate warming on soil N availability in a high Arctic tundra ecosystem we studied temperature effects on soil mineralization, and N uptake from different soil depths (−3, −10 and −30 cm) by tundra plants. Uptake was assessed using 15N tracer injected directly into mineral soil as 15NH4Cl solution to specifically mimic altered N availability from enhanced mineralization. Net N mineralization rates were very low, suggesting that N is strongly limiting in this system. There was no apparent temperature effect (−2 °C, 5 °C, 10 °C) on mineralization, but net nitrification was strongly limited by temperature – under the −2 °C treatment no nitrification occurred. As a consequence of ongoing mineralization and limited nitrification under freezing conditions, mineral NH4 may accumulate during the winter season and be available for plant uptake without risk of loss via View the MathML sourceNO3− leaching immediately after snowmelt. Nitrogen uptake niches were clearly stratified by depth. Graminoids (Carex misandra and Luzula arctica) were most effective at taking up N from deep soil horizons, and recovery in graminoid biomass after one year was independent of 15N injection depth. Recovery of N by the dwarf shrub Salix polaris was significantly higher following shallow application (−3 cm) compared to deeper treatments (−10 and −30 cm). Lichens and mosses also showed a decline in N uptake with application depth, and very little N was recovered by lichens and mosses even from −3 cm, in contrast to the strong uptake that has been observed in mosses when N is applied to the vegetation surface. The ability of graminoids to access nutrients from deeper mineral soil may give them an advantage over mosses and dwarf shrubs in warmer high Arctic tundra in acquiring limited available nutrient resources

A scalable analytical framework for spatio-temporal analysis of neighborhood change: A sequence analysis approach

© Springer Nature Switzerland AG 2020. Spatio-temporal changes reflect the complexity and evolution of demographic and socio-economic processes. Changes in the spatial distribution of population and consumer demand at urban and rural areas are expected to trigger changes in future housing and infrastructure needs. This paper presents a scalable analytical framework for understanding spatio-temporal population change, using a sequence analysis approach. This paper uses gridded cell Census data for Great Britain from 1971 to 2011 with 10-year intervals, creating neighborhood typologies for each Census year. These typologies are then used to analyze transitions of grid cells between different types of neighborhoods and define representative trajectories of neighborhood change. The results reveal seven prevalent trajectories of neighborhood change across Great Britain, identifying neighborhoods which have experienced stable, upward and downward pathways through the national socioeconomic hierarchy over the last four decades

Generalizations of entanglement based on coherent states and convex sets

Unentangled pure states on a bipartite system are exactly the coherent states with respect to the group of local transformations. What aspects of the study of entanglement are applicable to generalized coherent states? Conversely, what can be learned about entanglement from the well-studied theory of coherent states? With these questions in mind, we characterize unentangled pure states as extremal states when considered as linear functionals on the local Lie algebra. As a result, a relativized notion of purity emerges, showing that there is a close relationship between purity, coherence and (non-)entanglement. To a large extent, these concepts can be defined and studied in the even more general setting of convex cones of states. Based on the idea that entanglement is relative, we suggest considering these notions in the context of partially ordered families of Lie algebras or convex cones, such as those that arise naturally for multipartite systems. The study of entanglement includes notions of local operations and, for information-theoretic purposes, entanglement measures and ways of scaling systems to enable asymptotic developments. We propose ways in which these may be generalized to the Lie-algebraic setting, and to a lesser extent to the convex-cones setting. One of our original motivations for this program is to understand the role of entanglement-like concepts in condensed matter. We discuss how our work provides tools for analyzing the correlations involved in quantum phase transitions and other aspects of condensed-matter systems.Comment: 37 page

Managing for nitrogen, the lesser of two evils. A response to Maes et al.

Letter to the Editor

Niche models for British plants and lichens obtained using an ensemble approach

Site-occupancy models that predict habitat suitability for plant species in relation to measurable environmental factors can be useful for conservation planning. Such models can be derived from large-scale presence–absence datasets on the basis of environmental observations or, where only floristic data are available, using plant trait values averaged across a plot. However, the estimated modelled relationship between species presence and environmental variables depends on the type of statistical model adopted and hence can introduce additional uncertainty. Authors used an ensemble-modelling approach to constrain and quantify the uncertainty because of the choice of statistical model, applying generalised linear models (GLM), generalised additive models (GAM), and multivariate adaptive regression splines (MARS). Niche models were derived for over 1000 species of vascular plants, bryophytes and lichens, representing a large proportion of the British flora and many species occurring in continental Europe. Each model predicts habitat suitability for a species in response to climate variables and trait-based scores (evaluated excluding the species being modelled) for soil pH, fertility, wetness and canopy height. An R package containing the fitted models for each species is presented which allows the user to predict the habitat suitability of a given set of conditions for a particular species. Further functions within the package are included so that these habitat suitability scores can be plotted in relation to individual explanatory variables. A simple case study shows how the R package (MultiMOVE) can be used quickly and efficiently to answer questions of scientific interest, specifically whether climate change will counteract any benefits of sheep-grazing for a particular plant community. The package itself is freely available via http://doi.org/10.5285/94ae1a5a-2a28-4315-8d4b-35ae964fc3b9

The diversity, evolution and ecology of Salmonella in venomous snakes

BACKGROUND: Reptile-associated Salmonella bacteria are a major, but often neglected cause of both gastrointestinal and bloodstream infection in humans globally. The diversity of Salmonella enterica has not yet been determined in venomous snakes, however other ectothermic animals have been reported to carry a broad range of Salmonella bacteria. We investigated the prevalence and diversity of Salmonella in a collection of venomous snakes and non-venomous reptiles. METHODOLOGY/PRINCIPLE FINDINGS: We used a combination of selective enrichment techniques to establish a unique dataset of reptilian isolates to study Salmonella enterica species-level evolution and ecology and used whole-genome sequencing to investigate the relatedness of phylogenetic groups. We observed that 91% of venomous snakes carried Salmonella, and found that a diverse range of serovars (n = 58) were carried by reptiles. The Salmonella serovars belonged to four of the six Salmonella enterica subspecies: diarizonae, enterica, houtanae and salamae. Subspecies enterica isolates were distributed among two distinct phylogenetic clusters, previously described as clade A (52%) and clade B (48%). We identified metabolic differences between S. diarizonae, S. enterica clade A and clade B involving growth on lactose, tartaric acid, dulcitol, myo-inositol and allantoin. SIGNIFICANCE: We present the first whole genome-based comparative study of the Salmonella bacteria that colonise venomous and non-venomous reptiles and shed new light on Salmonella evolution. Venomous snakes examined in this study carried a broad range of Salmonella, including serovars which have been associated with disease in humans such as S. Enteritidis. The findings raise the possibility that venomous snakes could be a reservoir for Salmonella serovars associated with human salmonellosis

Administrative Coding in Electronic Health Care Record-Based Research of NAFLD: An Expert Panel Consensus Statement

cited By 0Background and Aims Electronic health record (EHR)-based research allows the capture of large amounts of data, which is necessary in NAFLD, where the risk of clinical liver outcomes is generally low. The lack of consensus on which International Classification of Diseases (ICD) codes should be used as exposures and outcomes limits comparability and generalizability of results across studies. We aimed to establish consensus among a panel of experts on ICD codes that could become the reference standard and provide guidance around common methodological issues. Approach and Results Researchers with an interest in EHR-based NAFLD research were invited to collectively define which administrative codes are most appropriate for documenting exposures and outcomes. We used a modified Delphi approach to reach consensus on several commonly encountered methodological challenges in the field. After two rounds of revision, a high level of agreement (>67%) was reached on all items considered. Full consensus was achieved on a comprehensive list of administrative codes to be considered for inclusion and exclusion criteria in defining exposures and outcomes in EHR-based NAFLD research. We also provide suggestions on how to approach commonly encountered methodological issues and identify areas for future research. Conclusions This expert panel consensus statement can help harmonize and improve generalizability of EHR-based NAFLD research.Peer reviewe

Modelling impacts of atmospheric deposition and temperature on long-term DOC trends

It is increasingly recognised that widespread and substantial increases in Dissolved organic carbon (DOC) concentrations in remote surface, and soil, waters in recent decades are linked to declining acid deposition. Effects of rising pH and declining ionic strength on DOC solubility have been proposed as potential dominant mechanisms. However, since DOC in these systems is derived mainly from recently-fixed carbon, and since organic matter decomposition rates are considered sensitive to temperature, uncertainty persists over the extent to which other drivers that could influence DOC production. Such potential drivers include fertilization by nitrogen (N) and global warming. We therefore ran the dynamic soil chemistry model MADOC for a range of UK soils, for which time series data are available, to consider the likely relative importance of decreased deposition of sulphate and chloride, accumulation of reactive N, and higher temperatures, on soil DOC production in different soils. Modelled patterns of DOC change generally agreed favourably with measurements collated over 10-20 years, but differed markedly between sites. While the acidifying effect of sulphur deposition appeared to be the predominant control on the observed soil water DOC trends in all the soils considered other than a blanket peat, the model suggested that over the long term, the effects of nitrogen deposition on N-limited soils may have been sufficient to raise the “acid recovery DOC baseline” significantly. In contrast, reductions in non-marine chloride deposition and effects of long term warming appeared to have been relatively unimportant. The suggestion that future DOC concentrations might exceed preindustrial levels as a consequence of nitrogen pollution has important implications for drinking water catchment management and the setting and pursuit of appropriate restoration targets, but findings still require validation from reliable centennial-scale proxy records, such as those being developed using palaeolimnological techniques

Thick-film technology for ultra high vacuum interfaces of micro-structured traps

We adopt thick-film technology to produce ultra high vacuum compatible interfaces for electrical signals. These interfaces permit voltages of hundreds of Volts and currents of several Amperes and allow for very compact vacuum setups, useful in quantum optics in general, and especially for quantum information and quantum simulations using miniaturized traps for ions or neutral atoms. Such printed circuits can also be useful as pure in-vacuum devices. We demonstrate a specific interface, which provides eleven current feedthroughs, more than 70 dc feedthroughs and a feedthrough for radio frequencies. We achieve a pressure in the low 1e-11mbar range and demonstrate the full functionality of the interface by trapping chains of cold ytterbium ions, which requires all of the signals mentioned above being present. In addition, a versatile multi-channel device for supplying precise time-dependent voltages has been developed.Comment: 8 pages, 7 figures added references to recent literature about microwave anipulated ions and fast shuttlin