Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

BackgroundSingle-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve.ResultsWe introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods.ConclusionsSlingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression

Simulations of the Mg II k and Ca II 8542 lines from an AlfvÉn Wave-heated Flare Chromosphere

We use radiation hydrodynamic simulations to examine two models of solar flare chromospheric heating: Alfven wave dissipation and electron beam collisional losses. Both mechanisms are capable of strong chro- ´ mospheric heating, and we show that the distinctive atmospheric evolution in the mid-to-upper chromosphere results in Mg ii k-line emission that should be observably different between wave-heated and beam-heated simulations. We also present Ca ii 8542Å profiles which are formed slightly deeper in the chromosphere. The Mg ii k-line profiles from our wave-heated simulation are quite different from those from a beam-heated model and are more consistent with IRIS observations. The predicted differences between the Ca ii 8542Å in the two models are small. We conclude that careful observational and theoretical study of lines formed in the mid-toupper chromosphere holds genuine promise for distinguishing between competing models for chromospheric heating in flares

EPUAP classification system for pressure ulcers: European reliability study

‘The definitive version is available at www3.interscience.wiley.com .' Copyright Blackwell PublishingPeer reviewe

"Aye, but it were wasted on thee": Cricket, British Asians, ethnic identities, and the 'magical recovery of community'

People in sport tend to possess rather jaded perceptions of its colour-blindness and thus, they are reluctant to confront the fact that, quite often racism is endemic. Yorkshire cricket in particular, has faced frequent accusations from minority ethnic communities of inveterate and institutionalised racism and territorial defensiveness. Drawing upon semi-structured interviews conducted with amateur white and British Asian cricketers, this paper examines the construction of regional identities in Yorkshire at a time when traditional myths and invented traditions of Yorkshire and 'Yorkshireness' are being deconstructed. This is conceptualised through a reading of John Clarke's 'magical recovery of community'. Although cricket has been multiracial for decades, I argue that some people's position as insiders is more straightforward than others. I present evidence to suggest that, regardless of being committed to Yorkshire and their 'Yorkshireness', white Yorkshire people may never fully accept British Asians as 'one of us'. Ideologically and practically, white Yorkshire people are engaged in constructing British Asians as anathema to Yorkshire culture. The paper concludes by advocating that, for sports cultures to be truly egalitarian, the ideology of sport itself has to change. True equality will only ever be achieved within a deracialised discourse that not only accepts difference, but embraces it

Alfvénic wave heating of the upper chromosphere in flares

We have developed a numerical model of flare heating due to the dissipation of Alfv\'enic waves propagating from the corona to the chromosphere. With this model, we present an investigation of the key parameters of these waves on the energy transport, heating, and subsequent dynamics. For sufficiently high frequencies and perpendicular wave numbers, the waves dissipate significantly in the upper chromosphere, strongly heating it to flare temperatures. This heating can then drive strong chromospheric evaporation, bringing hot and dense plasma to the corona. We therefore find three important conclusions: (1) Alfv\'enic waves, propagating from the corona to the chromosphere, are capable of heating the upper chromosphere and the corona, (2) the atmospheric response to heating due to the dissipation of Alfv\'enic waves can be strikingly similar to heating by an electron beam, and (3) this heating can produce explosive evaporation.Comment: Accepted to ApJ

Temporary storage or permanent removal? The division of nitrogen between biotic assimilation and denitrification in stormwater biofiltration systems

The long-term efficacy of stormwater treatment systems requires continuous pollutant removal without substantial re-release. Hence, the division of incoming pollutants between temporary and permanent removal pathways is fundamental. This is pertinent to nitrogen, a critical water body pollutant, which on a broad level may be assimilated by plants or microbes and temporarily stored, or transformed by bacteria to gaseous forms and permanently lost via denitrification. Biofiltration systems have demonstrated effective removal of nitrogen from urban stormwater runoff, but to date studies have been limited to a 'black-box' approach. The lack of understanding on internal nitrogen processes constrains future design and threatens the reliability of long-term system performance. While nitrogen processes have been thoroughly studied in other environments, including wastewater treatment wetlands, biofiltration systems differ fundamentally in design and the composition and hydrology of stormwater inflows, with intermittent inundation and prolonged dry periods. Two mesocosm experiments were conducted to investigate biofilter nitrogen processes using the stable isotope tracer 15NO3(-) (nitrate) over the course of one inflow event. The immediate partitioning of 15NO3(-) between biotic assimilation and denitrification were investigated for a range of different inflow concentrations and plant species. Assimilation was the primary fate for NO3(-) under typical stormwater concentrations (∼1-2 mg N/L), contributing an average 89-99% of 15NO3(-) processing in biofilter columns containing the most effective plant species, while only 0-3% was denitrified and 0-8% remained in the pore water. Denitrification played a greater role for columns containing less effective species, processing up to 8% of 15NO3(-), and increased further with nitrate loading. This study uniquely applied isotope tracing to biofiltration systems and revealed the dominance of assimilation in stormwater biofilters. The findings raise important questions about nitrogen release upon plant senescence, seasonally and in the long term, which have implications on the management and design of biofiltration systems.Emily G. I. Payne, Tim D. Fletcher, Douglas G. Russell, Michael R. Grace, Timothy R. Cavagnaro, Victor Evrard, Ana Deletic, Belinda E. Hatt, Perran L. M. Coo

Training teachers in classroom management to improve mental health in primary school children: the STARS cluster RCT

This is the final version. Available from NIHR Journals Library via the DOI in this record.Background Poor mental health in childhood is common, persistent and associated with a range of adverse outcomes that include persistent psychopathology, as well as risk-taking behaviour, criminality and educational failure, all of which may also compromise health. There is a growing policy focus on children’s mental health and the role of schools in particular in addressing this. Objectives To evaluate whether or not the Incredible Years® (IY) Teacher Classroom Management (TCM) training improved children’s mental health, behaviour, educational attainment and enjoyment of school, improved teachers’ mental health and relationship with work, and was cost-effective in relation to potential improvements. Design A two-arm, pragmatic, parallel-group, superiority, cluster randomised controlled trial. Setting A total of 80 UK schools (clusters) were recruited in three distinct cohorts between 2012 and 2014 and randomised to TCM (intervention) or teaching as usual [(TAU) control] with follow-ups at 9, 18 and 30 months. Schools and teachers were not masked to allocation. Participants Eighty schools (n = 2075 children) were randomised: 40 (n = 1037 children) to TCM and 40 (n = 1038 children) to TAU. Interventions TCM was delivered to teachers in six whole-day sessions, spread over 6 months. The explicit goals of TCM are to enhance classroom management skills and improve teacher–student relationships. Main outcome measures The primary planned outcome was the teacher-reported Strengths and Difficulties Questionnaire Total Difficulties (SDQ-TD) score. Random-effects linear regression and marginal logistic regression models using generalized estimating equations were used to analyse outcomes. Results The intervention reduced the SDQ-TD score at 9 months [adjusted mean difference (AMD) –1.0, 95% confidence interval (CI) –1.9 to –0.1; p = 0.03] but there was little evidence of effects at 18 months (AMD –0.1, 95% CI –1.5 to 1.2; p = 0.85) and 30 months (AMD –0.7, 95% CI –1.9 to 0.4; p = 0.23). Planned subgroup analyses suggested that TCM is more effective than TAU for children with poor mental health. Cost-effectiveness analysis using the SDQ-TD suggested that the probability of TCM being cost-effective compared with TAU was associated with some uncertainty (range of 40% to 80% depending on the willingness to pay for a unit improvement in SDQ-TD score). In terms of quality-adjusted life-years (QALYs), there was evidence to suggest that TCM was cost-effective compared with TAU at the National Institute for Health and Care Excellence thresholds of £20,000–30,000 per QALY at 9- and 18-month follow-up, but not at 30-month follow-up. There was evidence of reduced disruptive behaviour (p = 0.04) and reductions in inattention and overactivity (p = 0.02) at the 30-month follow-up. Despite no main effect on educational attainment, subgroup analysis indicated that the intervention’s effect differed between those who did and those who did not have poor mental health for both literacy (interaction p = 0.04) and numeracy (interaction p = 0.03). Independent blind observations and qualitative feedback from teachers suggested that teachers’ behaviour in the classroom changed as a result of attending TCM training. Limitations Teachers were not masked to allocation and attrition was marked for parent-reported data. Conclusions Our findings provide tentative evidence that TCM may be an effective universal child mental health intervention in the short term, particularly for primary school children who are identified as struggling, and it may be a cost-effective intervention in the short term. Future work Further research should explore TCM as a whole-school approach by training all school staff and should evaluate the impact of TCM on academic progress in a more thorough and systematic manner.National Institute for Health Research (NIHR