Isca, v1.0: a framework for the global modelling of the atmospheres of Earth and other planets at varying levels of complexity

This is the final version of the article. Available from EGU via the DOI in this record.The accepted author manuscript, published in Geoscientific Model Development Discussions, is in ORE: http://hdl.handle.net/10871/31579Isca is a framework for the idealized modelling of the global circulation of planetary atmospheres at varying levels of complexity and realism. The framework is an outgrowth of models from the Geophysical Fluid Dynamics Laboratory in Princeton, USA, designed for Earth's atmosphere, but it may readily be extended into other planetary regimes. Various forcing and radiation options are available, from dry, time invariant, Newtonian thermal relaxation to moist dynamics with radiative transfer. Options are available in the dry thermal relaxation scheme to account for the effects of obliquity and eccentricity (and so seasonality), different atmospheric optical depths and a surface mixed layer. An idealized grey radiation scheme, a two-band scheme, and a multiband scheme are also available, all with simple moist effects and astronomically based solar forcing. At the complex end of the spectrum the framework provides a direct connection to comprehensive atmospheric general circulation models. For Earth modelling, options include an aquaplanet and configurable continental outlines and topography. Continents may be defined by changing albedo, heat capacity, and evaporative parameters and/or by using a simple bucket hydrology model. Oceanic Q fluxes may be added to reproduce specified sea surface temperatures, with arbitrary continental distributions. Planetary atmospheres may be configured by changing planetary size and mass, solar forcing, atmospheric mass, radiation, and other parameters. Examples are given of various Earth configurations as well as a giant planet simulation, a slowly rotating terrestrial planet simulation, and tidally locked and other orbitally resonant exoplanet simulations. The underlying model is written in Fortran and may largely be configured with Python scripts. Python scripts are also used to run the model on different architectures, to archive the output, and for diagnostics, graphics, and post-processing. All of these features are publicly available in a Git-based repository.This work was funded by the Leverhulme Trust, NERC (grant NE/M006123/1), the Royal Society (Wolfson Foundation), EPSRC, the Newton Fund (CSSP project), and the Marie Curie Foundation

Isca, v1.0: a framework for the global modelling of the atmospheres of Earth and other planets at varying levels of complexity

This is the final version of the article. Available from EGU via the DOI in this record.The accepted author manuscript, published in Geoscientific Model Development Discussions, is in ORE: http://hdl.handle.net/10871/31579Isca is a framework for the idealized modelling of the global circulation of planetary atmospheres at varying levels of complexity and realism. The framework is an outgrowth of models from the Geophysical Fluid Dynamics Laboratory in Princeton, USA, designed for Earth's atmosphere, but it may readily be extended into other planetary regimes. Various forcing and radiation options are available, from dry, time invariant, Newtonian thermal relaxation to moist dynamics with radiative transfer. Options are available in the dry thermal relaxation scheme to account for the effects of obliquity and eccentricity (and so seasonality), different atmospheric optical depths and a surface mixed layer. An idealized grey radiation scheme, a two-band scheme, and a multiband scheme are also available, all with simple moist effects and astronomically based solar forcing. At the complex end of the spectrum the framework provides a direct connection to comprehensive atmospheric general circulation models. For Earth modelling, options include an aquaplanet and configurable continental outlines and topography. Continents may be defined by changing albedo, heat capacity, and evaporative parameters and/or by using a simple bucket hydrology model. Oceanic Q fluxes may be added to reproduce specified sea surface temperatures, with arbitrary continental distributions. Planetary atmospheres may be configured by changing planetary size and mass, solar forcing, atmospheric mass, radiation, and other parameters. Examples are given of various Earth configurations as well as a giant planet simulation, a slowly rotating terrestrial planet simulation, and tidally locked and other orbitally resonant exoplanet simulations. The underlying model is written in Fortran and may largely be configured with Python scripts. Python scripts are also used to run the model on different architectures, to archive the output, and for diagnostics, graphics, and post-processing. All of these features are publicly available in a Git-based repository.This work was funded by the Leverhulme Trust, NERC (grant NE/M006123/1), the Royal Society (Wolfson Foundation), EPSRC, the Newton Fund (CSSP project), and the Marie Curie Foundation

Exploring the measurement of markedness and its relationship with other linguistic variables

Antonym pair members can be differentiated by each word's markedness-that distinction attributable to the presence or absence of features at morphological or semantic levels. Morphologically marked words incorporate their unmarked counterpart with additional morphs (e.g., "unlucky" vs. "lucky"); properties used to determine semantically marked words (e.g., "short" vs. "long") are less clearly defined. Despite extensive theoretical scrutiny, the lexical properties of markedness have received scant empirical study. The current paper employs an antonym sequencing approach to measure markedness: establishing markedness probabilities for individual words and evaluating their relationship with other lexical properties (e.g., length, frequency, valence). Regression analyses reveal that markedness probability is, as predicted, related to affixation and also strongly related to valence. Our results support the suggestion that antonym sequence is reflected in discourse, and further analysis demonstrates that markedness probabilities, derived from the antonym sequencing task, reflect the ordering of antonyms within natural language. In line with the Pollyanna Hypothesis, we argue that markedness is closely related to valence; language users demonstrate a tendency to present words evaluated positively ahead of those evaluated negatively if given the choice. Future research should consider the relationship of markedness and valence, and the influence of contextual information in determining which member of an antonym pair is marked or unmarked within discourse

Labrador retrievers under primary veterinary care in the UK: demography, mortality and disorders

Abstract Background Labrador retrievers are reportedly predisposed to many disorders but accurate prevalence information relating to the general population are lacking. This study aimed to describe demography, mortality and commonly recorded diseases in Labrador retrievers under UK veterinary care. Methods The VetCompass™ programme collects electronic patient record data on dogs attending UK primary-care veterinary practices. Demographic analysis covered all33,320 Labrador retrievers in the VetCompass™ database under veterinary care during 2013 while disorder and mortality data were extracted from a random sample of 2074 (6.2%) of these dogs. Results Of the Labrador retrievers with information available, 15,427 (46.4%) were female and 15,252 (53.6%) were male. Females were more likely to be neutered than males (59.7% versus 54.8%, P <  0.001). The overall mean adult bodyweight was 33.0 kg (SD 6.1). Adult males were heavier (35.2 kg, SD 5.9 kg) than adult females (30.4 kg, SD 5.2 kg) (P <  0.001). The median longevity of Labrador retrievers overall was 12.0 years (IQR 9.9–13.8, range 0.0–16.0). The most common recorded colours were black (44.6%), yellow (27.8%) and liver/chocolate (reported from hereon as chocolate) (23.8%). The median longevity of non-chocolate coloured dogs (n = 139, 12.1 years, IQR 10.2–13.9, range 0.0–16.0) was longer than for chocolate coloured animals (n = 34, 10.7 years, IQR 9.0–12.4, range 3.8–15.5) (P = 0.028). Of a random sample of 2074 (6.2%) Labrador retrievers under care in 2013 that had full disorder data extracted, 1277 (61.6%) had at least one disorder recorded. The total number of dogs who died at any date during the study was 176. The most prevalent disorders recorded were otitis externa (n = 215, prevalence 10.4%, 95% CI: 9.1–11.8), overweight/obesity (183, 8.8%, 95% CI: 7.6–10.1) and degenerative joint disease (115, 5.5%, 95% CI: 4.6–6.6). Overweight/obesity was not statistically significantly associated with neutering in females (8.3% of entire versus 12.5% of neutered, P = 0.065) but was associated with neutering in males (4.1% of entire versus 11.4% of neutered, P < 0.001). The prevalence of otitis externa in black dogs was 12.8%, in yellow dogs it was 17.0% but, in chocolate dogs, it rose to 23.4% (P < 0.001). Similarly, the prevalence of pyo-traumatic dermatitis in black dogs was 1.1%, in yellow dogs it was 1.6% but in chocolate dogs it rose to 4.0% (P = 0.011). Conclusions The current study assists prioritisation of health issues within Labrador retrievers. The most common disorders were overweight/obesity, otitis externa and degenerative joint disease. Males were significantly heavier females. These results can alert prospective owners to potential health issues and inform breed-specific wellness checks

An Incomplete TCA Cycle Increases Survival of Salmonella Typhimurium during Infection of Resting and Activated Murine Macrophages

In comparison to the comprehensive analyses performed on virulence gene expression, regulation and action, the intracellular metabolism of Salmonella during infection is a relatively under-studied area. We investigated the role of the tricarboxylic acid (TCA) cycle in the intracellular replication of Salmonella Typhimurium in resting and activated macrophages, epithelial cells, and during infection of mice.We constructed deletion mutations of 5 TCA cycle genes in S. Typhimurium including gltA, mdh, sdhCDAB, sucAB, and sucCD. We found that the mutants exhibited increased net intracellular replication in resting and activated murine macrophages compared to the wild-type. In contrast, an epithelial cell infection model showed that the S. Typhimurium ΔsucCD and ΔgltA strains had reduced net intracellular replication compared to the wild-type. The glyoxylate shunt was not responsible for the net increased replication of the TCA cycle mutants within resting macrophages. We also confirmed that, in a murine infection model, the S. Typhimurium ΔsucAB and ΔsucCD strains are attenuated for virulence.Our results suggest that disruption of the TCA cycle increases the ability of S. Typhimurium to survive within resting and activated murine macrophages. In contrast, epithelial cells are non-phagocytic cells and unlike macrophages cannot mount an oxidative and nitrosative defence response against pathogens; our results show that in HeLa cells the S. Typhimurium TCA cycle mutant strains show reduced or no change in intracellular levels compared to the wild-type. The attenuation of the S. Typhimurium ΔsucAB and ΔsucCD mutants in mice, compared to their increased net intracellular replication in resting and activated macrophages suggest that Salmonella may encounter environments within the host where a complete TCA cycle is advantageous

A virtual reality extended neuropsychological assessment for topographical disorientation: a feasibility study

<p>Abstract</p> <p>Background</p> <p>Topographical disorientation represents one of the main consequences of brain injury. Up to now several methodological approaches have been used in the assessment of the brain injured patient's navigational abilities showing a moderate correlation with the impairments observed in everyday contexts.</p> <p>Methods</p> <p>We propose a combination of standardized neuropsychological tests and a more situated virtual reality-based assessment for the evaluation of spatial orientation in brain injured patients.</p> <p>Results</p> <p>When tested with this virtual reality integrated procedure patients showed performance and execution times congruent with their neuropsychological evaluation. When compared to a control group, patients revealed significantly slower times and greater errors in solving virtual reality based spatial tasks.</p> <p>Conclusion</p> <p>The use of virtual reality, when combined with classical neuropsychological tests, can provide an effective tool for the study of topographical disorientation.</p

A transcription factor contributes to pathogenesis and virulence in streptococcus pneumoniae

To date, the role of transcription factors (TFs) in the progression of disease for many pathogens is yet to be studied in detail. This is probably due to transient, and generally low expression levels of TFs, which are the central components controlling the expression of many genes during the course of infection. However, a small change in the expression or specificity of a TF can radically alter gene expression. In this study, we combined a number of quality-based selection strategies including structural prediction of modulated genes, gene ontology and network analysis, to predict the regulatory mechanisms underlying pathogenesis of Streptococcus pneumoniae (the pneumococcus). We have identified two TFs (SP_0676 and SP_0927 [SmrC]) that might control tissue-specific gene expression during pneumococcal translocation from the nasopharynx to lungs, to blood and then to brain of mice. Targeted mutagenesis and mouse models of infection confirmed the role of SP_0927 in pathogenesis and virulence, and suggests that SP_0676 might be essential to pneumococcal viability. These findings provide fundamental new insights into virulence gene expression and regulation during pathogenesis.Layla K. Mahdi, Esmaeil Ebrahimie, David L. Adelson, James C. Paton, Abiodun D. Ogunniy

Comparison of sterols and fatty acids in two species of Ganoderma

<p>Abstract</p> <p>Background</p> <p>Two species of <it>Ganoderma, G. sinense </it>and <it>G. lucidum</it>, are used as <it>Lingzhi </it>in China. Howerver, the content of triterpenoids and polysaccharides, main actives compounds, are significant different, though the extracts of both <it>G. lucidum </it>and <it>G. sinense </it>have antitumoral proliferation effect. It is suspected that other compounds contribute to their antitumoral activity. Sterols and fatty acids have obvious bioactivity. Therefore, determination and comparison of sterols and fatty acids is helpful to elucidate the active components of <it>Lingzhi</it>.</p> <p>Results</p> <p>Ergosterol, a specific component of fungal cell membrane, was rich in <it>G. lucidum </it>and <it>G. sinense</it>. But its content in <it>G. lucidum </it>(median content 705.0 μg·g^-1, range 189.1-1453.3 μg·g^-1, n = 19) was much higher than that in <it>G. sinense </it>(median content 80.1 μg·g^-1, range 16.0-409.8 μg·g^-1, n = 13). Hierarchical clustering analysis based on the content of ergosterol showed that 32 tested samples of <it>Ganoderma </it>were grouped into two main clusters, <it>G. lucidum </it>and <it>G. sinense</it>. Hierarchical clustering analysis based on the contents of ten fatty acids showed that two species of <it>Ganoderma </it>had no significant difference though two groups were also obtained. The similarity of two species of <it>Ganoderma </it>in fatty acids may be related to their antitumoral proliferation effect.</p> <p>Conclusions</p> <p>The content of ergosterol is much higher in <it>G. lucidum </it>than in <it>G. sinense</it>. Palmitic acid, linoleic acid, oleic acid, stearic acid are main fatty acids in <it>Ganoderma </it>and their content had no significant difference between <it>G. lucidum </it>and <it>G. sinense</it>, which may contribute to their antitumoral proliferation effect.</p

Integrative care for the management of low back pain: use of a clinical care pathway

<p>Abstract</p> <p>Background</p> <p>For the treatment of chronic back pain, it has been theorized that integrative care plans can lead to better outcomes than those achieved by monodisciplinary care alone, especially when using a collaborative, interdisciplinary, and non-hierarchical team approach. This paper describes the use of a care pathway designed to guide treatment by an integrative group of providers within a randomized controlled trial.</p> <p>Methods</p> <p>A clinical care pathway was used by a multidisciplinary group of providers, which included acupuncturists, chiropractors, cognitive behavioral therapists, exercise therapists, massage therapists and primary care physicians. Treatment recommendations were based on an evidence-informed practice model, and reached by group consensus. Research study participants were empowered to select one of the treatment recommendations proposed by the integrative group. Common principles and benchmarks were established to guide treatment management throughout the study.</p> <p>Results</p> <p>Thirteen providers representing 5 healthcare professions collaborated to provide integrative care to study participants. On average, 3 to 4 treatment plans, each consisting of 2 to 3 modalities, were recommended to study participants. Exercise, massage, and acupuncture were both most commonly recommended by the team and selected by study participants. Changes to care commonly incorporated cognitive behavioral therapy into treatment plans.</p> <p>Conclusion</p> <p>This clinical care pathway was a useful tool for the consistent application of evidence-based care for low back pain in the context of an integrative setting.</p> <p>Trial registration</p> <p>ClinicalTrials.gov NCT00567333</p

Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family

Abstract Background Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence. Results We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae. Conclusions A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae.Apple genome research at FEM is supported by the research office of the Provincia autonoma di Trento. DJS and ELG acknowledge a grant from the East Malling Trust. Fragaria genomics at EMR is funded by the BBSRC. JMB is supported by a grant by Plant & Food Research's Excellence Programme. Apple genomics at Plant & Food Research is partially supported by the New Zealand Foundation for Research Science and Technology project C06X0812 "Exploiting Opportunities from Horticultural Genomics". Research conducted at IRTA was partly funded by the CONSOLIDER-INGENIO 2010 Program (CSD2007-00036) and project INIA-RTA2007-00063-00-00, both from the Spanish Ministry of Science and Innovation. RosCOS development at OSU/MSU was funded by the National Research Initiative Competitive Grant 2005-35300-15454 of USDA's National Institute of Food and Agriculture.Peer Reviewe