DNAContentViewer a BioJS component to visualise GC/AT Content

Summary: Compositional GC/AT content of DNA sequences is a useful feature in genome analysis. GC/AT content provides useful information about evolution, structure and function of genomes, giving clues about their biological function and organisation. We have developed DNAContentViewer, a BioJS component for visualisation of compositional GC/AT content in raw sequences. DNAContentViewer has been integrated in the BioJS project as part of the BioJS registry of components. DNAContentViewer requires a simple configuration and installation. Its design allows potential interactions with other components via predefined events

Bioaccumulation surveillance in Milford Haven Waterway

Biomonitoring of contaminants (metals, organotins, PAHs, PCBs) was carried out along the Milford Haven Waterway (MHW) and at a reference site in the Tywi Estuary during 2007-2008. The species used as bioindicators encompass a variety of uptake routes - Fucus vesiculosus (dissolved contaminants); Littorina littorea (grazer); Mytilus edulis and Cerastoderma edule (suspension feeders); and Nereis diversicolor (omnivore which often reflects contaminants in sediment). Differences in feeding strategy and habitat preference have subtle implications for bioaccumulation trends though, with few exceptions, contaminant body burdens in Milford Haven (MH) were higher than those at the Tywi reference site, reflecting inputs. Elevated concentrations of metals were occasionally observed at individual MH sites, whilst As and Se (molluscs and seaweed) were, for much of MHW, consistently at the higher end of the UK range. However, for the majority of metals, distributions in MH biota were not exceptional by UK standards. Several metal-species combinations indicated increases in bioavailability at upstream sites, which may reflect the influence of geogenic or other land-based sources – perhaps enhanced by lower salinity (greater proportions of more bioavailable forms). TBT levels in MH mussels were below OSPAR toxicity thresholds and in the Tywi were close to zero. Phenyltins were not accumulated appreciably in Mytilus, whereas some Nereis populations may have been subjected to localized (historical) sources. PAHs in Nereis tended to be evenly distributed across most sites, but with somewhat higher values at Dale for acenaphthene, fluoranthene, pyrene, benzo(a)anthracene and chrysene; naphthalenes tended to be enriched further upstream in the mid-upper Haven (a pattern seen in mussels for most PAHs). Whilst concentrations in MH mussels were mostly above reference site and OSPAR backgrounds, it is unlikely that ecotoxicological guidelines would be exceeded. PCBs in mussels were between upper and lower OSPAR guidelines and were unusual in their distribution in that highest levels occurred at the mouth of MH. Condition indices (CI) of bivalves (mussels and cockles) were highest at the Tywi reference site and at the seaward end of MH, decreasing upstream along the Waterway. There were a number of significant (negative) relationships between CI and body burdens and multivariate analysis indicated that a combination of contaminants could influence the pattern in condition (and sub-lethal responses such as MT and TOSC) across sites. Cause and effect needs to be tested more rigorously in future assessments

A feasibility study of signed consent for the collection of patient identifiable information for a national paediatric clinical audit database

Objectives: To investigate the feasibility of obtaining signed consent for submission of patient identifiable data to a national clinical audit database and to identify factors influencing the consent process and its success. Design: Feasibility study. Setting: Seven paediatric intensive care units in England. Participants: Parents/guardians of patients, or patients aged 12-16 years old, approached consecutively over three months for signed consent for submission of patient identifiable data to the national clinical audit database the Paediatric Intensive Care Audit Network (PICANet). Main outcome measures: The numbers and proportions of admissions for which signed consent was given, refused, or not obtained (form not returned or form partially completed but not signed), by age, sex, level of deprivation, ethnicity (South Asian or not), paediatric index of mortality score, length of hospital stay (days in paediatric intensive care). Results: One unit did not start and one did not fully implement the protocol, so analysis excluded these two units. Consent was obtained for 182 of 422 admissions (43%) (range by unit 9% to 84%). Most (101/182; 55%) consents were taken by staff nurses. One refusal (0.2%) was received. Consent rates were significantly better for children who were more severely ill on admission and for hospital stays of six days or more, and significantly poorer for children aged 10-14 years. Long hospital stays and children aged 10-14 years remained significant in a stepwise regression model of the factors that were significant in the univariate model. Conclusion: Systematically obtaining individual signed consent for sharing patient identifiable information with an externally located clinical audit database is difficult. Obtaining such consent is unlikely to be successful unless additional resources are specifically allocated to training, staff time, and administrative support

Symmetries of Abelian Orbifolds

Using the Polya Enumeration Theorem, we count with particular attention to C^3/Gamma up to C^6/Gamma, abelian orbifolds in various dimensions which are invariant under cycles of the permutation group S_D. This produces a collection of multiplicative sequences, one for each cycle in the Cycle Index of the permutation group. A multiplicative sequence is controlled by its values on prime numbers and their pure powers. Therefore, we pay particular attention to orbifolds of the form C^D/Gamma where the order of Gamma is p^alpha. We propose a generalization of these sequences for any D and any p.Comment: 75 pages, 13 figures, 30 table

Extension in the western Ross Sea region-links between Adare Basin and Victoria Land Basin

Spreading in the Adare Basin off north-western Ross Sea (43–26 Ma) and extension in the Victoria Land Basin (VLB, > 36 Ma) are used to constrain the pole of rotation for the Adare Basin, providing a rifting model for the region for the past 45 Ma. The offset from Northern Basin to VLB at about 74°S coincides with the linear Polar-3 magnetic anomaly, inferred to be caused by a major 48 - 34 Ma igneous intrusion. The style of extension apparently changed at about 34 Ma, with the end of intrusion at the Polar-3 anomaly, a change from highly asymmetric extension in Adare Basin, and the onset of major subsidence on the flanks of VLB. Ductile lower crustal and lithospheric flow is proposed as the cause of the inferred thick crust underlying southern Adare Basin, and a result of the constraining of extension to the adjacent contiguous Northern Basin

Are "EIT Waves" Fast-Mode MHD Waves?

We examine the nature of large-scale, coronal, propagating wave fronts (``EIT waves'') and find they are incongruous with solutions using fast-mode MHD plane-wave theory. Specifically, we consider the following properties: non-dispersive single pulse manifestions, observed velocities below the local Alfven speed, and different pulses which travel at any number of constant velocities, rather than at the ``predicted'' fast-mode speed. We discuss the possibility of a soliton-like explanation for these phenomena, and show how it is consistent with the above-mentioned aspects.Comment: to be published in the Astrophysical Journa

Deceleration and Dispersion of Large-scale Coronal Bright Fronts

One of the most dramatic manifestations of solar activity are large-scale coronal bright fronts (CBFs) observed in extreme ultraviolet (EUV) images of the solar atmosphere. To date, the energetics and kinematics of CBFs remain poorly understood, due to the low image cadence and sensitivity of previous EUV imagers and the limited methods used to extract the features. In this paper, the trajectory and morphology of CBFs was determined in order to investigate the varying properties of a sample of CBFs, including their kinematics and pulse shape, dispersion, and dissipation. We have developed a semi-automatic intensity profiling technique to extract the morphology and accurate positions of CBFs in 2.5-10 min cadence images from STEREO/EUVI. The technique was applied to sequences of 171A and 195A images from STEREO/EUVI in order to measure the wave properties of four separate CBF events. Following launch at velocities of ~240-450kms^{-1} each of the four events studied showed significant negative acceleration ranging from ~ -290 to -60ms^{-2}. The CBF spatial and temporal widths were found to increase from ~50 Mm to ~200 Mm and ~100 s to ~1500 s respectively, suggesting that they are dispersive in nature. The variation in position-angle averaged pulse-integrated intensity with propagation shows no clear trend across the four events studied. These results are most consistent with CBFs being dispersive magnetoacoustic waves.Comment: 15 pages, 18 figure

Modelling environmental factors correlated with podoconiosis: a geospatial study of non-filarial elephantiasis

Introduction The precise trigger of podoconiosis — endemic non-filarial elephantiasis of the lower legs — is unknown. Epidemiological and ecological studies have linked the disease with barefoot exposure to red clay soils of volcanic origin. Histopathology investigations have demonstrated that silicon, aluminium, magnesium and iron are present in the lower limb lymph node macrophages of both patients and non-patients living barefoot on these clays. We studied the spatial variation (variations across an area) in podoconiosis prevalence and the associated environmental factors with a goal to better understanding the pathogenesis of podoconiosis. Methods Fieldwork was conducted from June 2011 to February 2013 in 12 kebeles (administrative units) in northern Ethiopia. Geo-located prevalence data and soil samples were collected and analysed along with secondary geological, topographic, meteorological and elevation data. Soil data were analysed for chemical composition, mineralogy and particle size, and were interpolated to provide spatially continuous information. Exploratory, spatial, univariate and multivariate regression analyses of podoconiosis prevalence were conducted in relation to primary (soil) and secondary (elevation, precipitation, and geology) covariates. Results Podoconiosis distribution showed spatial correlation with variation in elevation and precipitation. Exploratory analysis identified that phyllosilicate minerals, particularly clay (smectite and kaolinite) and mica groups, quartz (crystalline silica), iron oxide, and zirconium were associated with podoconiosis prevalence. The final multivariate model showed that the quantities of smectite (RR = 2.76, 95% CI: 1.35, 5.73; p = 0.007), quartz (RR = 1.16, 95% CI: 1.06, 1.26; p = 0.001) and mica (RR = 1.09, 95% CI: 1.05, 1.13; p < 0.001) in the soil had positive associations with podoconiosis prevalence. Conclusions More quantities of smectite, mica and quartz within the soil were associated with podoconiosis prevalence. Together with previous work indicating that these minerals may influence water absorption, potentiate infection and be toxic to human cells, the present findings suggest that these particles may play a role in the pathogenesis of podoconiosis and acute adenolymphangitis, a common cause of morbidity in podoconiosis patients

Podoconiosis in East and West Gojam Zones, Northern Ethiopia

Background: Podoconiosis is a neglected tropical disease (NTD) that is prevalent in red clay soil-covered highlands of tropical Africa, Central and South America, and northern India. It is estimated that up to one million cases exist in Ethiopia. This study aimed to estimate the prevalence of podoconiosis in East and West Gojam Zones of Amhara Region in northern Ethiopia. Methodology/Principal Findings: A cross-sectional household survey was conducted in Debre Eliyas and Dembecha woredas (districts) in East and West Gojam Zones, respectively. The survey covered all 17,553 households in 20 kebeles (administrative subunits) randomly selected from the two woredas. A detailed structured interview was conducted on 1,704 cases of podoconiosis identified in the survey. Results: The prevalence of podoconiosis in the population aged 15 years and above was found to be 3.3% (95% CI, 3.2% to 3.6%). 87% of cases were in the economically active age group (15–64 years). On average, patients sought treatment five years after the start of the leg swelling. Most subjects had second (42.7%) or third (36.1%) clinical stage disease, 97.9% had mossy lesions, and 53% had open wounds. On average, patients had five episodes of acute adenolymphangitis (ALA) per year and spent a total of 90 days per year with ALA. The median age of first use of shoes and socks were 22 and 23 years, respectively. More men than women owned more than one pair of shoes (61.1% vs. 50.5%; x2 = 11.6 p = 0.001). At the time of interview, 23.6% of the respondents were barefoot, of whom about two-thirds were women. Conclusions: This study showed high prevalence of podoconiosis and associated morbidities such as ALA, mossy lesions and open wounds in northern Ethiopia. Predominance of cases at early clinical stage of podoconiosis indicates the potential for reversing the swelling and calls for disease prevention interventions

Particle abundance in a thermal plasma: quantum kinetics vs. Boltzmann equation

We study the abundance of a particle species in a thermalized plasma by introducing a quantum kinetic description based on the non-equilibrium effective action. A stochastic interpretation of quantum kinetics in terms of a Langevin equation emerges naturally. We consider a particle species that is stable in the vacuum and interacts with \emph{heavier} particles that constitute a thermal bath in equilibrium and define of a fully renormalized single particle distribution function. The distribution function thermalizes on a time scale determined by the \emph{quasiparticle} relaxation rate. The equilibrium distribution function depends on the full spectral density and features off-shell contributions to the particle abundance. A model of a bosonic field $\Phi$ in interaction with two \emph{heavier} bosonic fields is studied. We find substantial departures from the Bose-Einstein result both in the high temperature and the low temperature but high momentum region. In the latter the abundance is exponentially suppressed but larger than the Bose-Einstein result. We obtain the Boltzmann equation in renormalized perturbation theory and highlight the origin of the differences. We argue that the corrections to the abundance of cold dark matter candidates are observationally negligible and that recombination erases any possible spectral distortions of the CMB. However we expect that the enhancement at high temperature may be important for baryogenesis.Comment: 39 pages, 11 figures. Clarifying remarks. To appear in Physical Review