Vorticity in the solar photosphere

Aims. We use magnetic and non-magnetic 3D numerical simulations of solar granulation and G-band radiative diagnostics from the resulting models to analyse the generation of small-scale vortex motions in the solar photosphere.
Methods. Radiative MHD simulations of magnetoconvection are used to produce photospheric models. Our starting point is a non-magnetic model of solar convection, where we introduce a uniform magnetic field and follow the evolution of the field in the simulated photosphere. We find two different types of photospheric vortices, and provide a link between the vorticity generation and the presence of the intergranular magnetic field. A detailed analysis of the vorticity equation, combined with the G-band radiative diagnostics, allows us to identify the sources and observational signatures of photospheric vorticity in the simulated photosphere.
Results. Two different types of photospheric vorticity, magnetic and non-magnetic, are generated in the domain. Non-magnetic vortices are generated by the baroclinic motions of the plasma in the photosphere, while magnetic vortices are produced by the magnetic tension in the intergranular magnetic flux concentrations. The two types of vortices have different shapes. We find that the vorticity is generated more efficiently in the magnetised model. Simulated G-band images show a direct connection between magnetic vortices and rotary motions of photospheric bright points, and suggest that there may be a connection between the magnetic bright point rotation and small-scale swirl motions observed higher in the atmosphere.

Accuracy of Death Certificates in COPD: Analysis from the TORCH Trial

The Towards a Revolution in COPD Health (TORCH) trial was an international clinical trial of chronic obstructive pulmonary disease (COPD) patients where cause of death was assigned by an independent committee. Comparison of death certificate data and adjudicated cause of death allows a unique opportunity to determine death certificate accuracy and frequency of COPD listing on death certificates of COPD patients. In this analysis, the authors determine the concordance between adjudicated cause of death and primary and secondary cause of death from death certificates. In 317 (80%) of informative deaths, the primary or secondary cause of death from certificates agreed with adjudicated cause of death. Only 229 (58%) of death certificates in these COPD patients listed COPD on the certificate. COPD was not listed on the death certificate in 21% of deaths adjudicated to be caused by COPD exacerbation. Compared with pulmonary causes, the listing of COPD on certificates occurred with less frequency than cardiovascular, cancer and other categories of death. The combined primary and secondary listing on death certificates has good concordance with actual cause of death. COPD is under-reported on death certificates, and this under-reporting is more frequent when the primary cause of death is not pulmonary.

Microarray-based classifiers and prognosis models identify subgroups with distinct clinical outcomes and high risk of AML transformation of myelodysplastic syndrome

The diagnosis of myelodysplastic syndrome (MDS) currently relies primarily on the morphologic assessment of the patient's bone marrow and peripheral blood cells. Moreover, prognostic scoring systems rely on observer-dependent assessments of blast percentage and dysplasia. Gene expression profiling could enhance current diagnostic and prognostic systems by providing a set of standardized, objective gene signatures. Within the Microarray Innovations in LEukemia study, a diagnostic classification model was investigated to distinguish the distinct subclasses of pediatric and adult leukemia, as well as MDS. Overall, the accuracy of the diagnostic classification model for subtyping leukemia was approximately 93%, but this was not reflected for the MDS samples giving only approximately 50% accuracy. Discordant samples of MDS were classified either into acute myeloid leukemia (AML) or

A Novel Multilocus Sequence Typing Scheme for the Opportunistic Pathogen Propionibacterium acnes and Characterisation of Type I Cell Surface-Associated Antigens.

We have developed a novel Multilocus Sequence Typing Scheme (MLST) and database (http://pubmlst.org/pacnes/) for Propionibacterium acnes based on the analysis of seven core housekeeping genes. The scheme, which was validated against previously described antibody, single locus and Random Amplification of Polymorphic DNA (RAPD) typing methods, displayed excellent resolution and differentiated 123 isolates into 37 sequence types (ST). An overall clonal population structure was detected with six eBURST groups representing the major clades I, II and III, along with two singletons. Two highly successful and global clonal lineages, ST6 (type IA) and ST10 (type IB1), representing 65% of this current MLST isolate collection were identified. The ST6 clone and closely related single locus variants (SLV), which comprise a large clonal complex CC6, dominated isolates from patients with acne, and were also significantly associated with ophthalmic infections. Our data therefore supports an association between acne and P. acnes strains from the type IA cluster and highlights the role of a widely disseminated clonal genotype in this condition. Characterisation of type I cell surface-associated antigens that are not detected in ST10 or strains of type II and III identified two dermatan-sulphate-binding proteins with putative phase/antigenic variation signatures. We propose that the expression of these proteins by type IA organisms contributes to their role in the pathophysiology of acne and helps explain the recurrent nature of the disease. The MLST scheme and database described in this study should provide a valuable platform for future epidemiological and evolutionary studies of P. acnes.

High-velocity features: A ubiquitous property of Type Ia supernovae

Evidence of high-velocity features (HVFs) such as those seen in the near-maximum spectra of some Type Ia supernovae (SNe Ia; e. g., SN 2000cx) has been searched for in the available SN Ia spectra observed earlier than 1 week before B maximum. Recent observational efforts have doubled the number of SNe Ia with very early spectra. Remarkably, all SNe Ia with early data ( seven in our Research Training Network sample and 10 from other programs) show signs of such features, to a greater or lesser degree, in Ca II IR and some also in the Si II lambda 6355 line. HVFs may be interpreted as abundance or density enhancements. Abundance enhancements would imply an outer region dominated by Si and Ca. Density enhancements may result from the sweeping up of circumstellar material (CSM) by the highest velocity SN ejecta. In this scenario, the high incidence of HVFs suggests that a thick disk and/or a high-density companion wind surrounds the exploding white dwarf, as may be the case in single degenerate systems. Large-scale angular fluctuations in the radial density and abundance distribution may also be responsible: this could originate in the explosion and would suggest a deflagration as the more likely explosion mechanism. CSM interaction and surface fluctuations may coexist, possibly leaving different signatures on the spectrum. In some SNe, the HVFs are narrowly confined in velocity, suggesting the ejection of blobs of burned material.

Implications for Powering Biomarker Discovery Studies

This study examined variations in gene expression between FFPE blocks within tumors of individual patients. Microarray data were used to measure tumor heterogeneity within and between patients and disease states. Data were used to determine the number of samples needed to power biomarker discovery studies. Bias and variation in gene expression were assessed at the intrapatient and interpatient levels and between adenocarcinoma and squamous samples. A mixed-model analysis of variance was fitted to gene expression data and model signatures to assess the statistical significance of observed variations within and between samples and disease states. Sample size analysis, adjusted for sample heterogeneity, was used to determine the number of samples required to support biomarker discovery studies. Variation in gene expression was observed between blocks taken from a single patient. However, this variation was considerably less than differences between histological characteristics. This degree of block-to-block variation still permits biomarker discovery using either macrodissected tumors or whole FFPE sections, provided that intratumor heterogeneity is taken into account. Failure to consider intratumor heterogeneity may result in underpowered biomarker studies that may result in either the generation of longer gene signatures or the inability to identify a viable biomarker. Moreover, the results of this study indicate that a single biopsy sample is suitable for applying a biomarker in nonsmall-cell lung cancer. © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology.

Comparison of passive millimeter-wave and IR imagery in a nautical environment

Results are presented from a trial in which a real-time passive millimetre-wave camera was mounted on a landing craft. The vessel was operated on rivers in the UK, and imagery of surrounding terrain, structures, obstacles and other vessels was obtained. An IR camera was also used, and the differences in signatures of various features are discussed. Opportunities for image fusion are highlighted.

Carbon Isotopic Fractionation of CFCs during Abiotic and Biotic Degradation

Carbon stable isotope ((13)C) fractionation in chlorofluorocarbon (CFC) compounds arising from abiotic (chemical) degradation using zero-valent iron (ZVI) and biotic (landfill gas attenuation) processes is investigated. Batch tests (at 25 °C) for CFC-113 and CFC-11 using ZVI show quantitative degradation of CFC-113 to HCFC-123a and CFC-1113 following pseudo-first-order kinetics corresponding to a half-life (t(1/2)) of 20.5 h, and a ZVI surface-area normalized rate constant (k(SA)) of -(9.8 ± 0.5) × 10(-5) L m(-2) h(-1). CFC-11 degraded to trace HCFC-21 and HCFC-31 following pseudo-first-order kinetics corresponding to t(1/2) = 17.3 h and k(SA) = -(1.2 ± 0.5) × 10(-4) L m(-2) h(-1). Significant kinetic isotope effects of e(‰) = -5.0 ± 0.3 (CFC-113) and -17.8 ± 4.8 (CFC-11) were observed. Compound-specific carbon isotope analyses also have been used here to characterize source signatures of CFC gases (HCFC-22, CFC-12, HFC-134a, HCFC-142b, CFC-114, CFC-11, CFC-113) for urban (UAA), rural/remote (RAA), and landfill (LAA) ambient air samples, as well as in situ surface flux chamber (FLUX; NO FLUX) and landfill gas (LFG) samples at the Dargan Road site, Northern Ireland. The latter values reflect biotic degradation and isotopic fractionation in LFG production, and local atmospheric impact of landfill emissions through the cover. Isotopic fractionations of ?(13)C ~ -13‰ (HCFC-22), ?(13)C ~ -35‰ (CFC-12) and ?(13)C ~ -15‰ (CFC-11) were observed for LFG in comparison to characteristic solvent source signatures, with the magnitude of the isotopic effect for CFC-11 apparently similar to the kinetic isotope effect for (abiotic) ZVI degradation.

Geophysical and geochemical survey of a large marine pockmark on the Malin Shelf, Ireland

Marine pockmarks are a specific type of seabed geological setting resembling craters or pits and are considered seabed surface expressions of fluid flow in the subsurface. A large composite pockmark on the Malin Shelf, off the northern coast of Ireland was surveyed and ground truthed to assess its activity and investigate fluid related processes in the subsurface. Geophysical (including acoustic and electromagnetic) data confirmed the subsurface presence of signatures typical of fluids within the sediment. Shallow seismic profiling revealed a large shallow gas pocket and typical gas related indicators such as acoustic blanking and enhanced reflectors present underneath and around the large pockmark. Sulphate profiles indicate that gas from the shallow reservoir has been migrating upwards, at least recently. However, there are no chimney structures observed in the sub-bottom data and the migration pathways are not apparent. Electromagnetic data show slightly elevated electrical conductivity on the edges of the pockmarks and a drop below regional levels within the confines of the pockmark, suggesting changes in physical properties of the sediment. Nuclear Magnetic Resonance (NMR) experiments were employed to characterize the organic component of sediments from selected depths. Very strong microbial signatures were evident in all NMR spectra but microbes outside the pockmark appear to be much more active than inside. These observations coincide with spikes in conductivity and the lateral gas bearing body suggesting that there is an increase in microbial activity and biomass when gas is present.

Observations of Sausage Modes in Magnetic Pores

We present here evidence for the observation of the magnetohydrodynamic (MHD) sausage modes in magnetic pores in the solar photosphere. Further evidence for the omnipresent nature of acoustic global modes is also found. The empirical decomposition method of wave analysis is used to identify the oscillations detected through a 4170 Å "blue continuum" filter observed with the Rapid Oscillations in the Solar Atmosphere (ROSA) instrument. Out of phase, periodic behavior in pore size and intensity is used as an indicator of the presence of magnetoacoustic sausage oscillations. Multiple signatures of the magnetoacoustic sausage mode are found in a number of pores. The periods range from as short as 30 s up to 450 s. A number of the magnetoacoustic sausage mode oscillations found have periods of 3 and 5 minutes, similar to the acoustic global modes of the solar interior. It is proposed that these global oscillations could be the driver of the sausage-type magnetoacoustic MHD wave modes in pores.

Circulating and synovial antibody profiling of juvenile arthritis patients by nucleic acid programmable protein arrays.

Introduction Juvenile idiopathic arthritis (JIA) is a heterogeneous disease characterized by chronic joint inflammation of unknown cause in children. JIA is an autoimmune disease and small numbers of auto-antibodies have been reported in JIA patients. The identification of antibody markers could improve the existing clinical management of patients. Methods A pilot study was performed on the application of a high-throughput platform, nucleic acid programmable protein arrays (NAPPA), to assess the levels of antibodies present in the systemic circulation and synovial joint of a small cohort of juvenile arthritis patients. Plasma and synovial fluid from ten JIA patients was screened for antibodies against 768 proteins on NAPPA. Results Quantitative reproducibility of NAPPA was demonstrated with >0.95 intra- and inter- array correlations. A strong correlation was also observed for the levels of antibodies between plasma and synovial fluid across the study cohort (r=0.96). Differences in the levels of 18 antibodies were revealed between sample types across all patients. Patients were segregated into two clinical subtypes with distinct antibody signatures by unsupervised hierarchical cluster analysis. Conclusions NAPPA provides a high-throughput quantitatively reproducible platform to screen for disease specific autoantibodies at the proteome level on a microscope slide. The strong correlation between the circulating antibody levels and those of the inflamed joint represents a novel finding and provides confidence to use plasma for discovery of autoantibodies in JIA, thus circumventing the challenges associated with joint aspiration. We expect that autoantibody profiling of JIA patients on NAPPA could yield antibody markers that can act as criteria to stratify patients, predict outcomes and understand disease etiology at the molecular level.

Special Needs Education, eLearning and the Reflective ePortfolio: Implications for Developing and Assessing Competence in Pre-Service Education.

This paper reports on the use of an eportfolio for assessing aspects of a Post-Graduate pre-service teacher education programme specifically in the context of special needs education in Northern Ireland. Participants were challenged to develop their individual eportfolios by selecting and presenting evidence for assessment drawn from diverse sources. The rationale for using eportfolios for assessment purposes was to offer students the opportunity to demonstrate competencies by documenting and reflecting upon academic and pedagogical learning during a one year Post Graduate Certificate of Education (PGCE) programme.

Detection of Mixing Dynamics During Pumping of a Flooded Coal Mine

In complex hydrogeological environments the effective management of groundwater quality problems by pump-and-treat operations can be most confidently achieved if the mixing dynamics induced within the aquifer by pumping are well understood. The utility of isotopic environmental tracers (C-, H-, O-, S-stable isotopic analyses and age indicators—14C, 3H) for this purpose is illustrated by the analysis of a pumping test in an abstraction borehole drilled into flooded, abandoned coal mineworkings at Deerplay (Lancashire, UK). Interpretation of the isotope data was undertaken conjunctively with that of major ion hydrochemistry, and interpreted in the context of the particular hydraulic setting of flooded mineworkings to identify the sources and mixing of water qualities in the groundwater system. Initial pumping showed breakdown of initial water quality stratification in the borehole, and gave evidence for distinctive isotopic signatures (d34S(SO4) ~= -1.6‰, d18O(SO4) ~= +15‰) associated with primary oxidation of pyrite in the zone of water table fluctuation—the first time this phenomenon has been successfully characterized by these isotopes in a flooded mine system. The overall aim of the test pumping—to replace an uncontrolled outflow from a mine entrance in an inconvenient location with a pumped discharge on a site where treatment could be provided—was swiftly achieved. Environmental tracing data illustrated the benefits of pumping as little as possible to attain this aim, as higher rates of pumping induced in-mixing of poorer quality waters from more distant old workings, and/or renewed pyrite oxidation in the shallow subsurface.

Degradation of carbon disulphide (CS2) in soils and groundwater from a CS2 -contaminated site

This study is the first investigation of biodegradation of carbon disulphide (CS₂) in soil that provides estimates of degradation rates and identifies intermediate degradation products and carbon isotope signatures of degradation. Microcosm studies were undertaken under anaerobic conditions using soil and groundwater recovered from CS₂-contaminated sites. Proposed degradation mechanisms were validated using equilibrium speciation modelling of concentrations and carbon isotope ratios. A first-order degradation rate constant of 1.25 × 10-2 h-1 was obtained for biological degradation with soil. Carbonyl sulphide (COS) and hydrogen sulphide (H₂S) were found to be intermediates of degradation, but did not accumulate in vials. A 13C/12C enrichment factor of -7.5 ± 0.8 ‰ was obtained for degradation within microcosms with both soil and groundwater whereas a 13C/12C enrichment factor of -23.0 ± 2.1 ‰ was obtained for degradation with site groundwater alone. It can be concluded that biological degradation of both CS2-contaminated soil and groundwater is likely to occur in the field suggesting that natural attenuation may be an appropriate remedial tool at some sites. The presence of biodegradation by-products including COS and H₂S indicates that biodegradation of CS₂ is occurring and stable carbon isotopes are a promising tool to quantify CS₂ degradation.

Genome-wide profiling of methylation identifies novel targets with aberrant hyper-methylation and reduced expression in low-risk myelodysplastic syndromes

Gene expression profiling signatures may be used to classify the subtypes of Myelodysplastic syndrome (MDS) patients. However, there are few reports on the global methylation status in MDS. The integration of genome-wide epigenetic regulatory marks with gene expression levels would provide additional information regarding the biological differences between MDS and healthy controls. Gene expression and methylation status were measured using high-density microarrays. A total of 552 differentially methylated CpG loci were identified as being present in low-risk MDS; hypermethylated genes were more frequent than hypomethylated genes. In addition, mRNA expression profiling identified 1005 genes that significantly differed between low-risk MDS and the control group. Integrative analysis of the epigenetic and expression profiles revealed that 66.7% of the hypermethylated genes were underexpressed in low-risk MDS cases. Gene network analysis revealed molecular mechanisms associated with the low-risk MDS group, including altered apoptosis pathways. The two key apoptotic genes BCL2 and ETS1 were identified as silenced genes. In addition, the immune response and micro RNA biogenesis were affected by the hypermethylation and underexpression of IL27RA and DICER1. Our integrative analysis revealed that aberrant epigenetic regulation is a hallmark of low-risk MDS patients and could have a central role in these diseases.