Hydrodynamic simulations of shell convection in stellar cores

Shell convection driven by nuclear burning in a stellar core is a common hydrodynamic event in the evolution of many types of stars. We encounter and simulate this convection (i) in the helium core of a low-mass red giant during core helium flash leading to a dredge-down of protons across an entropy barrier, (ii) in a carbon-oxygen core of an intermediate-mass star during core carbon flash, and (iii) in the oxygen and carbon burning shell above the silicon-sulfur rich core of a massive star prior to supernova explosion. Our results, which were obtained with the hydrodynamics code HERAKLES, suggest that both entropy gradients and entropy barriers are less important for stellar structure than commonly assumed. Our simulations further reveal a new dynamic mixing process operating below the base of shell convection zones.Comment: 8 pages, 3 figures .. submitted to a proceedings of conference about "Red Giants as Probes of the Structure and Evolution of the Milky Way" which has taken place between 15-17 November 2010 in Rom

The Evershed Effect with SOT/Hinode

The Solar Optical Telescope onboard Hinode revealed the fine-scale structure of the Evershed flow and its relation to the filamentary structures of the sunspot penumbra. The Evershed flow is confined in narrow channels with nearly horizontal magnetic fields, embedded in a deep layer of the penumbral atmosphere. It is a dynamic phenomenon with flow velocity close to the photospheric sound speed. Individual flow channels are associated with tiny upflows of hot gas (sources) at the inner end and downflows (sinks) at the outer end. SOT/Hinode also discovered ``twisting'' motions of penumbral filaments, which may be attributed to the convective nature of the Evershed flow. The Evershed effect may be understood as a natural consequence of thermal convection under a strong, inclined magnetic field. Current penumbral models are discussed in the lights of these new Hinode observations.Comment: To appear in "Magnetic Coupling between the Interior and the Atmosphere of the Sun", eds. S.S. Hasan and R.J. Rutten, Astrophysics and Space Science Proceedings, Springer-Verlag, Heidelberg, Berlin, 200

Downward pumping of magnetic flux as the cause of filamentary structures in sunspot penumbrae

The structure of a sunspot is determined by the local interaction between magnetic fields and convection near the Sun's surface. The dark central umbra is surrounded by a filamentary penumbra, whose complicated fine structure has only recently been revealed by high-resolution observations. The penumbral magnetic field has an intricate and unexpected interlocking-comb structure and some field lines, with associated outflows of gas, dive back down below the solar surface at the outer edge of the spot. These field lines might be expected to float quickly back to the surface because of magnetic buoyancy, but they remain submerged. Here we show that the field lines are kept submerged outside the spot by turbulent, compressible convection, which is dominated by strong, coherent, descending plumes. Moreover, this downward pumping of magnetic flux explains the origin of the interlocking-comb structure of the penumbral magnetic field, and the behaviour of other magnetic features near the sunspot

Theoretical Models of Sunspot Structure and Dynamics

Recent progress in theoretical modeling of a sunspot is reviewed. The observed properties of umbral dots are well reproduced by realistic simulations of magnetoconvection in a vertical, monolithic magnetic field. To understand the penumbra, it is useful to distinguish between the inner penumbra, dominated by bright filaments containing slender dark cores, and the outer penumbra, made up of dark and bright filaments of comparable width with corresponding magnetic fields differing in inclination by some 30 degrees and strong Evershed flows in the dark filaments along nearly horizontal or downward-plunging magnetic fields. The role of magnetic flux pumping in submerging magnetic flux in the outer penumbra is examined through numerical experiments, and different geometric models of the penumbral magnetic field are discussed in the light of high-resolution observations. Recent, realistic numerical MHD simulations of an entire sunspot have succeeded in reproducing the salient features of the convective pattern in the umbra and the inner penumbra. The siphon-flow mechanism still provides the best explanation of the Evershed flow, particularly in the outer penumbra where it often consists of cool, supersonic downflows.Comment: To appear in "Magnetic Coupling between the Interior and the Atmosphere of the Sun", eds. S.S. Hasan and R.J. Rutten, Astrophysics and Space Science Proceedings, Springer-Verlag, Heidelberg, Berlin, 200

Mercury sources to Lake Ozette and Lake Dickey : highly contaminated remote coastal lakes, Washington State, USA

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Water, Air, & Soil Pollution 208 (2009): 275-286, doi:10.1007/s11270-009-0165-y.Mercury concentrations in largemouth bass and mercury accumulation rates in age-dated sediment cores were examined at Lake Ozette and Lake Dickey in Washington State. Goals of the study were to compare concentrations in fish tissues at the two lakes with lakes in a larger statewide dataset and evaluate factors influencing lake loading at Ozette and Dickey, which may include: catchment disturbances, coastal mercury cycling, and the role of trans-Pacific Asian mercury. Mercury fish tissue concentrations at the lakes were among the highest recorded in Washington State. Wet deposition and historical atmospheric monitoring from the area show no indication of enhanced deposition from Asian sources or coastal atmospheric processes. Sediment core records from the lakes displayed rapidly increasing sedimentation rates coinciding with commercial logging. The unusually high mercury flux rates and mercury tissue concentrations recorded at Lake Ozette and Lake Dickey appear to be associated with logging within the catchments

Annotation analysis for testing drug safety signals using unstructured clinical notes

BackgroundThe electronic surveillance for adverse drug events is largely based upon the analysis of coded data from reporting systems. Yet, the vast majority of electronic health data lies embedded within the free text of clinical notes and is not gathered into centralized repositories. With the increasing access to large volumes of electronic medical data-in particular the clinical notes-it may be possible to computationally encode and to test drug safety signals in an active manner.ResultsWe describe the application of simple annotation tools on clinical text and the mining of the resulting annotations to compute the risk of getting a myocardial infarction for patients with rheumatoid arthritis that take Vioxx. Our analysis clearly reveals elevated risks for myocardial infarction in rheumatoid arthritis patients taking Vioxx (odds ratio 2.06) before 2005.ConclusionsOur results show that it is possible to apply annotation analysis methods for testing hypotheses about drug safety using electronic medical records

Bordetella pertussis Autotransporter Vag8 Binds Human C1 Esterase Inhibitor and Confers Serum Resistance

Bordetella pertussis employs numerous strategies to evade the immune system, including the ability to resist killing via complement. Previously we have shown that B. pertussis binds a complement regulatory protein, C1 esterase inhibitor (C1inh) to its surface in a Bvg-regulated manner (i.e. during its virulence phase), but the B. pertussis factor was not identified. Here we set out to identify the B. pertussis C1inh-binding factor. Using a serum overlay assay, we found that this factor migrates at approximately 100 kDa on an SDS-PAGE gel. To identify this factor, we isolated proteins of approximately 100 kDa from wild type strain BP338 and from BP347, an isogenic Bvg mutant that does not bind C1inh. Using mass spectrometry and bioinformatics, we identified the autotransporter protein Vag8 as the putative C1inh binding protein. To prove that Vag8 binds C1inh, vag8 was disrupted in two different B. pertussis strains, namely BP338 and 18–323, and the mutants were tested for their ability to bind C1inh in a surface-binding assay. Neither mutant strain was capable of binding C1inh, whereas a complemented strain successfully bound C1inh. In addition, the passenger domain of Vag8 was expressed and purified as a histidine-tagged fusion protein and tested for C1inh-binding in an ELISA assay. Whereas the purified Vag8 passenger bound C1inh, the passenger domain of BrkA (a related autotransporter protein) failed to do so. Finally, serum assays were conducted to compare wild type and vag8 mutants. We determined that vag8 mutants from both strains were more susceptible to killing compared to their isogenic wild type counterparts. In conclusion, we have discovered a novel role for the previously uncharacterized protein Vag8 in the immune evasion of B. pertussis. Vag8 binds C1inh to the surface of the bacterium and confers serum resistance

Common marmoset (Callithrix jacchus) personality, subjective well-being, hair cortisol level and AVPR1a, OPRM1, and DAT genotypes

We studied personality, subjective well-being, and hair cortisol level, in common marmosets Callithrix jacchus, a small, cooperatively breeding New World monkey, by examining their associations with one another and genotypes. Subjects were 68 males and 9 females that lived in the RIKEN Center for Life Science Technologies. Personality and subjective well-being were assessed by keeper ratings on two questionnaires, hair samples were obtained to assay cortisol level and buccal swabs were used to assess AVPR1a, OPRM1 and DAT genotypes. Three personality domains—Dominance, Sociability, and Neuroticism—were identified. Consistent with findings in other species, Sociability and Neuroticism were related to higher and lower subjective well-being, respectively. Sociability was also associated with higher hair cortisol levels. The personality domains and hair cortisol levels were heritable and associated with genotypes: the short form of AVPR1a was associated with lower Neuroticism and the AA genotype of the A111T SNP of OPRM1 was related to lower Dominance, lower Neuroticism, and higher hair cortisol level. Some genetic associations were not in directions that one would expect given findings in other species. These findings provide insights into the proximate and ultimate bases of personality in common marmosets, other primates and humans

Socio-demographic and AIDS-related factors associated with tuberculosis stigma in southern Thailand: a quantitative, cross-sectional study of stigma among patients with TB and healthy community members

<p>Abstract</p> <p>Background</p> <p>Tuberculosis (TB) remains one of the most important infectious diseases worldwide. A comprehensive approach towards disease control that addresses social factors including stigma is now advocated. Patients with TB report fears of isolation and rejection that may lead to delays in seeking care and could affect treatment adherence. Qualitative studies have identified socio-demographic, TB knowledge, and clinical determinants of TB stigma, but only one prior study has quantified these associations using formally developed and validated stigma scales. The purpose of this study was to measure TB stigma and identify factors associated with TB stigma among patients and healthy community members.</p> <p>Methods</p> <p>A cross-sectional study was performed in southern Thailand among two different groups of participants: 480 patients with TB and 300 healthy community members. Data were collected on socio-demographic characteristics, TB knowledge, and clinical factors. Scales measuring perceived TB stigma, experienced/felt TB stigma, and perceived AIDS stigma were administered to patients with TB. Community members responded to a community TB stigma and community AIDS stigma scale, which contained the same items as the perceived stigma scales given to patients. Stigma scores could range from zero to 30, 33, or 36 depending on the scale. Three separate multivariable linear regressions were performed among patients with TB (perceived and experience/felt stigma) and community members (community stigma) to determine which factors were associated with higher mean TB stigma scores.</p> <p>Results</p> <p>Only low level of education, belief that TB increases the chance of getting AIDS, and AIDS stigma were associated with higher TB stigma scores in all three analyses. Co-infection with HIV was associated with higher TB stigma among patients. All differences in mean stigma scores between index and referent levels of each factor were less than two points, except for incorrectly believing that TB increases the chance of getting AIDS (mean difference of 2.16; 95% CI: 1.38, 2.94) and knowing someone who died from TB (mean difference of 2.59; 95% CI: 0.96, 4.22).</p> <p>Conclusion</p> <p>These results suggest that approaches addressing the dual TB/HIV epidemic may be needed to combat TB stigma and that simply correcting misconceptions about TB may have limited effects.</p

Oral cholera vaccine use in Zanzibar: socioeconomic and behavioural features affecting demand and acceptance

Cholera remains a serious public health problem in low-income countries despite efforts in the past to promote oral rehydration therapy as major treatment. In 2007, the majority of worldwide cases (94%) and deaths (99%) were reported from Africa. To improve cholera control efforts in addition to maintaining and improving existing water supply, sanitation and hygiene behaviour measures, the World Health Organization has recently started to consider the use of vaccines as an additional public health tool. To assess this new approach in endemic settings, a project was launched in Zanzibar to vaccinate 50,000 individuals living in communities at high risk of cholera with an oral two-dose vaccine (Dukoral). Immunisation programmes in low-income countries have suffered a reduced coverage or were even brought to a halt because of an ignorance of local realities. To ensure the success of vaccination campaigns, implementers have to consider community-held perceptions and behaviours regarding the infectious disease and the vaccine of interest. The main aim of this study is to provide advice to the Ministry of Health and Social Welfare of Zanzibar regarding routine introduction of an oral cholera vaccine from a socioeconomic and behavioural perspective as part of a long-term development for a sustained cholera prevention strategy. Qualitative and quantitative methods of health social science research will be applied on four stakeholder levels before and after the mass vaccination campaign. Rapid assessment individual interviews and focus groups will be used to describe cholera- and vaccine-related views of policy makers, health care professionals and community representatives. The cultural epidemiological approach will be employed on the individual household resident level in a repeated cross-sectional design to estimate determinants of anticipated and actual oral cholera vaccine acceptance. The study presented here is designed to inform about people's perceptions regarding cholera and about socioeconomic and behavioural factors determining anticipated and actual oral cholera vaccine acceptance in Zanzibar. Its pre- and post-intervention design using a mixed-methods approach on different stakeholder levels in communities at high risk of cholera outbreaks will ensure the collection of locally valid data relevant for public health action and planning