Paired-end read length lower bounds for genome re-sequencing

International audienceNext-generation sequencing technology is enabling massive production of high-quality paired-end reads. Many platforms (Illumina Genome Analyzer, Applied Biosystems SOLID, Helicos HeliScope) are currently able to produce "ultra-short" paired reads of lengths starting at 25 nt. An analysis by Whiteford et al. [1] on sequencing using unpaired reads shows that ultra-short reads theoretically allow whole genome re-sequencing and de novo assembly of only small eukaryotic genomes. By conducting an analysis extending Whiteford et al. results, we investigate to what extent genome re-sequencing is feasible with ultra-short paired reads. We obtain theoretical read length lower bounds for re-sequencing that are also applicable to paired-end de novo assembly

Two buses and a short walk: the place of geography in recovery

Purpose – As UK substance misuse policy has increasingly focused on the concept of recovery, policymakers, service providers and service users have found “recovery capital” a useful concept to understand the barriers to and facilitators of recovery from substance misuse. There is a rich strand of research that considers the composition of recovery capital in terms of the relevance of resources such as access to mutual aid, familial support and friendship networks, stable housing, structured psychosocial support and education, training and employment. However, such general accounts have tended not to engage with the potential spatial element of recovery capital; that is, how location contributes to the acquisition and management of recovery capital. The purpose of this paper is to add nuance to more generalised accounts through a critical interrogation, exploration and analysis of the role of geography in recovery. Design/methodology/approach – The paper draws on in-depth interviews with service users and service providers in a predominantly rural county in the south-west of England. Findings – The ability to build and sustain recovery capital is shown to be marked by a complex web of social and spatial inclusions/exclusions. Originality/value – This paper makes three important contributions to prevailing understandings of recovery capital. First, it shows how narratives of recovery are intimately tied to perceptions and experiences of place. Second, it reveals some of the important challenges and complex dilemmas that local drug and alcohol commissioners face in designing and delivering recovery-orientated treatment systems. Third, and finally, it argues that there is a pressing need for a more nuanced appreciation of the social and spatial dynamics of recovery capital

The CMV early enhancer/chicken β actin (CAG) promoter can be used to drive transgene expression during the differentiation of murine embryonic stem cells into vascular progenitors

<p>Abstract</p> <p>Background</p> <p>Mouse embryonic stem cells cultured <it>in vitro </it>have the ability to differentiate into cells of the three germ layers as well as germ cells. The differentiation mimics early developmental events, including vasculogenesis and early angiogenesis and several differentiation systems are being used to identify factors that are important during the formation of the vascular system. Embryonic stem cells are difficult to transfect, while downregulation of promoter activity upon selection of stable transfectants has been reported, rendering the study of proteins by overexpression difficult.</p> <p>Results</p> <p>CCE mouse embryonic stem cells were differentiated on collagen type IV for 4–5 days, Flk1⁺mesodermal cells were sorted and replated either on collagen type IV in the presence of VEGFA to give rise to endothelial cells and smooth muscle cells or in collagen type I gels for the formation of vascular tubes. The activity of the CMV and β-actin promoters was downregulated during selection of stable transfectants and during differentiation to the Flk1 stage, while the CMV immediate enhancer/β-actin promoter in the pCAGIPuro-GFP vector led to 100% of stably transfected undifferentiated and differentiated cells expressing GFP. To further test this system we expressed syndecan-2 and -4 in these cells and demonstrated high levels of transgene expression in both undifferentiated cells and cells differentiated to the Flk1 stage.</p> <p>Conclusion</p> <p>Vectors containing the CAG promoter offer a valuable tool for the long term expression of transgenes during stem cell differentiation towards mesoderm, while the CMV and β-actin promoters lead to very poor transgene expression during this process.</p

Recombination Rate Coefficients for KLL Di-electronic Satellite Lines of Fe XXV and Ni XXVII

The unified method for total electron-ion recombination is extended to study the dielectronic satellite (DES) lines. These lines, formed from radiative decay of autoionizing states, are highly sensitive temperature diagnostics of astrophysical and laboratory plasma sources. The computation of the unified recombination rates is based on the relativistic Breit-Pauli R-matrix method and close coupling approximation. Extending the theoretical formulation developed earlier we present recombination rate coefficients for the 22 satellite lines of KLL complexes of helium-like Fe XXV and Ni XXVII. The isolated resonance approximation, commonly used throughout plasma modeling, treats these resonances essentially as bound features except for dielectronic capture into, and autoionization out of, these levels. A line profile or cross section shape is often assumed. On the other hand, by including the coupling between the autoionizing and continuum channels, the unified method gives the intrinsic spectrum of DES lines which includes not only the energies and strengths, but also the natural line or cross section shapes. A formulation is presented to derive autoionization rates from unified resonance strengths and enable correspondence with the isolated resonance approximation. While the rates compare very well with existing rates for the strong lines to <20%, the differences for weaker DES lines are larger. We also illustrate the application of the present results to the analysis of K ALPHA complexes observed in high-temperature X-ray emission spectra of Fe XXV and Ni XXVII. There are considerable differences with previous results in the total KLL intensity for Fe XXV at temperatures below the temperature of maximum abundance in coronal equilibrium. (Abbreviated Abstract)Comment: 21 pages, 5 figures, to appear in Physica Script

Updated Atomic Data and Calculations for X-ray Spectroscopy

We describe the latest release of AtomDB, version 2.0.2, a database of atomic data and a plasma modeling code with a focus on X-ray astronomy. This release includes several major updates to the fundamental atomic structure and process data held within AtomDB, incorporating new ionization balance data, state-selective recombination data, and updated collisional excitation data for many ions, including the iron L-shell ions from Fe$^{+16}$ to Fe$^{+23}$ and all of the hydrogen- and helium-like sequences. We also describe some of the effects that these changes have on calculated emission and diagnostic line ratios, such as changes in the temperature implied by the He-like G-ratios of up to a factor of 2.Comment: Submitted to ApJ, 12 pages, 9 figure

Atomic data from the IRON Project. I. Electron-impact scattering of Fe17+ using <I>R</I>-matrix theory with intermediate coupling

We present results for electron-impact excitation of F-like Fe calculated using R-matrix theory where an intermediate-coupling frame transformation (ICFT) is used to obtain level-resolved collision strengths. Two such calculations are performed, the first expands the target using 2s2 2p5, 2s 2p6, 2s2 2p4 3l, 2s 2p5 3l, and 2p6 3l configurations while the second calculation includes the 2s2 2p4 4l, 2s 2p5 4l, and 2p6 4l configurations as well. The effect of the additional structure in the latter calculation on the n=3 resonances is explored and compared with previous calculations. We find strong resonant enhancement of the effective collision strengths to the 2s2 2p4 3s levels. A comparison with a Chandra X-ray observation of Capella shows that the n=4 R-matrix calculation leads to good agreement with observation</p

Spatial variations in snowpack chemistry and isotopic composition of NO3- along a nitrogen deposition gradient in West Greenland

Snowpack chemistry, nitrate stable isotopes and net deposition fluxes for the largest ice-free region in Greenland were investigated to determine whether there are spatial gradients from the ice sheet margin to the coast linked to a gradient in precipitation. Late-season snowpack was sampled in March 2011 at 8 locations within 3 lake catchments in each of 3 regions (ice sheet margin in the east, central area near Kelly Ville and the coastal zone to the west). At the coast, snowpack accumulation averaged 181 mm snow water equivalent (SWE), compared with 36 mm SWE by the ice sheet. Coastal snowpack showed significantly greater concentrations of marine salts (Na+, Cl−, other major cations), ammonium (regional means 1.4–2.7 µmol L−1), total and non-sea salt sulfate (total 1.8–7.7, non-sea salt 1.0–1.8 µmol L−1) than the two inland regions. Nitrate (1.5–2.4 µmol L−1) showed significantly lower concentrations at the coast. Despite lower concentrations, higher precipitation at the coast results in a strong deposition gradient for NO3− as well as NH4+ and non-sea salt sulfate (nss-SO42−) increasing from the inland regions to the coast (lowest at Kelly Ville 6, 4 and 3; highest at coast 9, 17 and 11 mol ha−1 yr−1 of NO3−, NH4+ and nss-SO42− respectively). The δ(15N) of snowpack NO3− shows a significant decrease from the ice sheet margin (−7.5 ‰) to the coast (−11.3 ‰). We attribute the spatial gradient of δ(15N) in SW Greenland to post-deposition processing rather than differing sources because of (1) the climatic gradient from ice sheet margin to coast, (2) within-catchment isotopic differences between terrestrial snowpack and lake-ice snowpack, and (3) similarities between fresh snow (rather than accumulated snowpack) at Kelly Ville and the coast. Hence the δ(15N) of coastal snowpack is most representative of snowfall in SW Greenland, but after deposition the effects of photolysis, volatilization and sublimation lead to enrichment of the remaining snowpack with the greatest effect in inland areas of low precipitation and high sublimation losses

Remunerating private psychiatrists for participating in case conferences

BACKGROUND: On 1 November 2000, a series of new item numbers was added to the Medicare Benefits Schedule, which allowed for case conferences between physicians (including psychiatrists) and other multidisciplinary providers. On 1 November 2002, an additional set of numbers was added, designed especially for use by psychiatrists. This paper reports the findings of an evaluation of these item numbers. RESULTS: The uptake of the item numbers in the three years post their introduction was low to moderate at best. Eighty nine psychiatrists rendered 479 case conferences at a cost to the Health Insurance Commission of $70,584. Psychiatrists who have used the item numbers are generally positive about them, as are consumers. Psychiatrists who have not used them have generally not done so because of a lack of knowledge, rather than direct opposition. The use of the item numbers is increasing over time, perhaps as psychiatrists become more aware of their existence and of their utility in maximising quality of care. CONCLUSION: The case conferencing item numbers have potential, but as yet this potential is not being realised. Some small changes to the conditions associated with the use of the item numbers could assist their uptake

Decolonising the curriculum is an ongoing and collective effort: Responding to Townsend (2020) and Gibson and Farias (2020)

This paper responds to Townsend (2020), and Gibson and Farias (2020), who were invited to write commentaries regarding Simaan’s (2020) ‘Decolonising occupational science education through learning activities based on a study from the Global South’. My reply acknowledges work done by scholars in the Global North and South, both in and outside occupational science, that critiques Western-centric hegemony in academia. It recognises the multiple aspects of decolonial work in occupational science education, and its collective and continuous nature. I argue that my objective of stimulating reflections and discussion about decolonising occupational science education and knowledge has been achieved by this collective effort to extend this discourse. Future reflections, research, and activism in this area are of paramount importance if we are to truly decolonise occupational science

Ionization state, excited populations and emission of impurities in dynamic finite density plasmas: I. The generalized collisional-radiative model for light elements

The paper presents an integrated view of the population structure and its role in establishing the ionization state of light elements in dynamic, finite density, laboratory and astrophysical plasmas. There are four main issues, the generalized collisional-radiative picture for metastables in dynamic plasmas with Maxwellian free electrons and its particularizing to light elements, the methods of bundling and projection for manipulating the population equations, the systematic production/use of state selective fundamental collision data in the metastable resolved picture to all levels for collisonal-radiative modelling and the delivery of appropriate derived coefficients for experiment analysis. The ions of carbon, oxygen and neon are used in illustration. The practical implementation of the methods described here is part of the ADAS Project