A qualitative study exploring awareness and attitudes towards tuberculosis in migrant populations in a Metropolitan District Council in the North of England

Background: The majority of tuberculosis (TB) cases in the UK occur among people born in high-burden countries (73%), and are concentrated in large urban centres. This study explores migrants' attitudes and beliefs towards TB in an English District where the incidence is higher than the UK average. Methods: Community engagement workers ran 26 focus groups using a standardized questionnaire. Purposeful sampling was used to obtain a cross-section of migrant communities. The summary reports were analysed using thematic analysis. Results: Most groups did not see TB as a current issue in their community and associated it either with the past or with their country of birth. It appeared to be rarely discussed in their communities and generally not noted as being associated with stigma. Conclusions: This study revealed a change in social attitudes to TB in migrant groups to those reported in previous literature. Stigma had considerably less effect than expected. However, the evidence revealed that these high-risk groups made the erroneous assumption that, by moving to a low incidence country, they were no longer at risk of the disease. TB services need to respond by revising the information that they provide to take into account the risk perception of these populations

OH emission from warm and dense gas in the Orion Bar PDR

As part of a far-infrared (FIR) spectral scan with Herschel/PACS, we present the first detection of the hydroxyl radical (OH) towards the Orion Bar photodissociation region (PDR). Five OH rotational Lambda-doublets involving energy levels out to E_u/k~511 K have been detected (at ~65, ~79, ~84, ~119 and ~163um). The total intensity of the OH lines is I(OH)~5x10^-4 erg s^-1 cm^-2 sr^-1. The observed emission of rotationally excited OH lines is extended and correlates well with the high-J CO and CH^+ J=3-2 line emission (but apparently not with water vapour), pointing towards a common origin. Nonlocal, non-LTE radiative transfer models including excitation by the ambient FIR radiation field suggest that OH arises in a small filling factor component of warm (Tk~160-220 K) and dense (n_H~10^{6-7} cm^-3) gas with source-averaged OH column densities of ~10^15 cm^-2. High density and temperature photochemical models predict such enhanced OH columns at low depths (A_V<1) and small spatial scales (~10^15 cm), where OH formation is driven by gas-phase endothermic reactions of atomic oxygen with molecular hydrogen. We interpret the extended OH emission as coming from unresolved structures exposed to far-ultraviolet (FUV) radiation near the Bar edge (photoevaporating clumps or filaments) and not from the lower density "interclump" medium. Photodissociation leads to OH/H2O abundance ratios (>1) much higher than those expected in equally warm regions without enhanced FUV radiation fields.Comment: Accepted for publication in A&A Letters. Figure B.2. is bitmapped to lower resolutio

CCBuilder:An interactive web-based tool for building, designing and assessing coiled-coil protein assemblies

Motivation: The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo . Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models. Results: We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover &gt;96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures. Availability and implementation: CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder

Spatial distribution of far-infrared rotationally excited CH⁺ and OH emission lines in the Orion Bar photodissociation region

Context. The methylidyne cation (CH+) and hydroxyl (OH) are key molecules in the warm interstellar chemistry, but their formation and excitation mechanisms are not well understood. Their abundance and excitation are predicted to be enhanced by the presence of vibrationally excited H2 or hot gas (~500−1000 K) in photodissociation regions (PDRs) with high incident far-ultraviolet (FUV) radiation field. The excitation may also originate in dense gas (>105 cm-3) followed by nonreactive collisions with H2, H, and electrons. Previous observations of the Orion Bar suggest that the rotationally excited CH+ and OH correlate with the excited CO, which is a tracer of dense and warm gas, and that formation pumping contributes to CH+ excitation.Aims. Our goal is to examine the spatial distribution of the rotationally excited CH+ and OH emission lines in the Orion Bar to establish their physical origin and main formation and excitation mechanisms.Methods. We present spatially sampled maps of the CH+ J = 3–2 transition at 119.8 μm and the OH Λ doublet at 84 μm in the Orion Bar over an area of 110″× 110″ with Herschel/PACS. We compare the spatial distribution of these molecules with those of their chemical precursors, C+ , O and H2, and tracers of warm and dense gas (high- J CO). We assess the spatial variation of the CH+ J = 2–1 velocity-resolved line profile at 1669 GHz with Herschel/HIFI spectrometer observations.Results. The OH and especially CH+ lines correlate well with the high-J CO emission and delineate the warm and dense molecular region at the edge of the Bar. While notably similar, the differences in the CH+ and OH morphologies indicate that CH+ formation and excitation are strongly related to the observed vibrationally excited H2. This, together with the observed broad CH+ line widths, indicates that formation pumping contributes to the excitation of this reactive molecular ion. Interestingly, the peak of the rotationally excited OH 84 μm emission coincides with a bright young object, proplyd 244–440, which shows that OH can be an excellent tracer of UV-irradiated dense gas.Conclusions. The spatial distribution of CH+ and OH revealed in our maps is consistent with previous modeling studies. Both formation pumping and nonreactive collisions in a UV-irradiated dense gas are important CH+ J = 3–2 excitation processes. The excitation of the OH Λ doublet at 84 μm is mainly sensitive to the temperature and density

HI Narrow Self-Absorption in Dark Clouds: Correlations with Molecular Gas and Implications for Cloud Evolution and Star Formation

We present the results of a comparative study of HI narrow self-absorption (HINSA), OH, 13CO, and C18O in five dark clouds. The HINSA follows the distribution of the emission of the carbon monoxide isotopologues, and has a characteristic size close to that of 13CO. This confirms that the HINSA is produced by cold HI which is well mixed with molecular gas in well-shielded regions. The ratio of the atomic hydrogen density to total proton density for these sources is 5 to 27 x 10^{-4}. Using cloud temperatures and the density of HI, we set an upper limit to the cosmic ray ionization rate of 10^{-16} s^{-1}. Comparison of observed and modeled fractional HI abundances indicates ages for these clouds to be 10^{6.5} to 10^{7} yr. The low values of the HI density we have determined make it certain that the time scale for evolution from an atomic to an almost entirely molecular phase, must be a minimum of several million years. This clearly sets a lower limit to the overall time scale for star formation and the lifetime of molecular clouds

Herschel observations of the hydroxyl radical (OH) in young stellar objects

Water in Star-forming regions with Herschel (WISH) is a Herschel Key Program investigating the water chemistry in young stellar objects (YSOs) during protostellar evolution. Hydroxyl (OH) is one of the reactants in the chemical network most closely linked to the formation and destruction of H2O. High-temperature chemistry connects OH and H2O through the OH + H2 H2O + H reactions. Formation of H2O from OH is efficient in the high-temperature regime found in shocks and the innermost part of protostellar envelopes. Moreover, in the presence of UV photons, OH can be produced from the photo-dissociation of H2O. High-resolution spectroscopy of the OH 163.12 micron triplet towards HH 46 and NGC 1333 IRAS 2A was carried out with the Heterodyne Instrument for the Far Infrared (HIFI) on board Herschel. The low- and intermediate-mass YSOs HH 46, TMR 1, IRAS 15398-3359, DK Cha, NGC 7129 FIRS 2, and NGC 1333 IRAS 2A were observed with the Photodetector Array Camera and Spectrometer (PACS) in four transitions of OH and two [OI] lines. The OH transitions at 79, 84, 119, and 163 micron and [OI] emission at 63 and 145 micron were detected with PACS towards the class I low-mass YSOs as well as the intermediate-mass and class I Herbig Ae sources. No OH emission was detected from the class 0 YSO NGC 1333 IRAS 2A, though the 119 micron was detected in absorption. With HIFI, the 163.12 micron was not detected from HH 46 and only tentatively detected from NGC 1333 IRAS 2A. The combination of the PACS and HIFI results for HH 46 constrains the line width (FWHM > 11 km/s) and indicates that the OH emission likely originates from shocked gas. This scenario is supported by trends of the OH flux increasing with the [OI] flux and the bolometric luminosity. Similar OH line ratios for most sources suggest that OH has comparable excitation temperatures despite the different physical properties of the sources.Comment: Accepted for publication in Astronomy and Astrophysics (Herschel special issue