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

Realist trials and the testing of context-mechanism-outcome configurations: a response to Van Belle et al.

BACKGROUND: Van Belle et al. argue that our attempt to pursue realist evaluation via a randomised trial will be fruitless because we misunderstand realist ontology (confusing intervention mechanisms with intervention activities and with statistical mediation analyses) and because RCTs cannot comprehensively examine how and why outcome patterns are caused by mechanisms triggered in specific contexts. METHODS: Through further consideration of our trial methods, we explain more fully how we believe complex social interventions work and what realist evaluation should aim to do within a trial. RESULTS: Like other realists, those undertaking realist trials assume that: social interventions provide resources which local actors may draw on in actions that can trigger mechanisms; these mechanisms may interact with contextual factors to generate outcomes; and data in the 'empirical' realm can be used to test hypotheses about mechanisms in the 'real' realm. Whether or not there is sufficient contextual diversity to test such hypotheses is a contingent not a necessary feature of trials. Previous exemplars of realist evaluation have compared empirical data from intervention and control groups to test hypotheses about real mechanisms. There is no inevitable reason why randomised trials should not also be able to do so. Random allocation merely ensures the comparability of such groups without necessarily causing evaluation to lapse from a realist into a 'positivist' or 'post-positivist' paradigm. CONCLUSIONS: Realist trials are ontologically and epistemologically plausible. Further work is required to assess whether they are feasible and useful but such work should not be halted on spurious philosophical grounds

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

The three stages of building and testing mid-level theories in a realist RCT: a theoretical and methodological case-example.

BACKGROUND: Randomised controlled trials (RCTs) of social interventions are often criticised as failing to open the 'black box' whereby they only address questions about 'what works' without explaining the underlying processes of implementation and mechanisms of action, and how these vary by contextual characteristics of person and place. Realist RCTs are proposed as an approach to evaluation science that addresses these gaps while preserving the strengths of RCTs in providing evidence with strong internal validity in estimating effects. METHODS: In the context of growing interest in designing and conducting realist trials, there is an urgent need to offer a worked example to provide guidance on how such an approach might be practically taken forward. The aim of this paper is to outline a three-staged theoretical and methodological process of undertaking a realist RCT using the example of the evaluation of a whole-school restorative intervention aiming to reduce aggression and bullying in English secondary schools. DISCUSSION: First, informed by the findings of our initial pilot trial and sociological theory, we elaborate our theory of change and specific a priori hypotheses about how intervention mechanisms interact with context to produce outcomes. Second, we describe how we will use emerging findings from the integral process evaluation within the RCT to refine, and add to, these a priori hypotheses before the collection of quantitative, follow-up data. Third, we will test our hypotheses using a combination of process and outcome data via quantitative analyses of effect mediation (examining mechanisms) and moderation (examining contextual contingencies). The results are then used to refine and further develop the theory of change. CONCLUSION: The aim of the realist RCT approach is thus not merely to assess whether the intervention is effective or not, but to develop empirically informed mid-range theory through a three-stage process. There are important implications for those involved with reporting and reviewing RCTs, including the use of new, iterative protocols. TRIAL REGISTRATION: Current Controlled Trials ISRCTN10751359 (Registered 11 March 2014)

Adsorbents for the sequestration of the Pimelea toxin, simplexin

Pimelea poisoning affects cattle grazing arid rangelands of Australia, has no known remedy and significant outbreaks can cost the industry $50 million per annum. Poisoning is attributable to consumption of native Pimelea plants containing the toxin simplexin. Charcoal, bentonite and other adsorbents are currently used by the livestock industry to mitigate the effects of mycotoxins. The efficacy of such adsorbents to mitigate Pimelea poisoning warrants investigation. Through a series of in vitro experiments, different adsorbents were evaluated for their effectiveness to bind simplexin using a simple single concentration, dispersive adsorbent rapid screening method. Initial experiments were conducted in a rumen fluid based medium, with increasing quantities of each adsorbent: sodium bentonite (Trufeed®, Sibelco Australia), biochar (Nutralick®Australia) and Elitox® (Impextraco, Belgium). Data showed the unbound concentration of simplexin decreased with increasing quantities of each adsorbent tested. Sodium bentonite performed best, removing ~95% simplexin at 12 mg/mL. A second experiment using a single amount of adsorbent included two additional adsorbents: calcium bentonite (Bentonite Resources, Australia) and a synthetic adsorbent (Waters, USA). The concentration of simplexin remaining in the solution after 1 h, the amount able to be desorbed off the adsorbent-toxin matrix with replacement fresh fluid, and the amount remaining bound to the adsorbent were measured. All samples containing an adsorbent were statistically different compared to the blank (p < 0.05), indicating some binding activity. Future work will explore the binding mechanisms and behaviour of the toxin-adsorbent complex in the lower gastrointestinal tract

Role of β-adrenergic receptors in the oral activity of zinc-α2-glycoprotein (ZAG)

Zinc-a2-glycoprotein (ZAG) is an adipokine with the potential as a therapeutic agent in the treatment of obesity and type 2 diabetes. In this study we show that human ZAG, which is a 41-kDa protein, when administered to ob/ob mice at 50 µg/d-1 orally in the drinking water produced a progressive loss of body weight (5 g after 8 d treatment), together with a 0.5 C increase in rectal temperature and a 40% reduction in urinary excretion of glucose. There was also a 33% reduction in the area under the curve during an oral glucose tolerance test and an increased sensitivity to insulin. These results were similar to those after iv administration of ZAG. However, tryptic digestion was shown to inactivate ZAG. There was no evidence of human ZAG in the serum but a 2-fold elevation of murine ZAG, which was also observed in target tissues such as white adipose tissue. To determine whether the effect was due to interaction of the human ZAG with the ß-adrenergic (ß-AR) in the gastrointestinal tract before digestion, ZAG was coadministered to ob/ob mice together with propanolol (40 mg/kg-1), a nonspecific ß-AR antagonist. The effect of ZAG on body weight, rectal temperature, urinary glucose excretion, improvement in glucose disposal, and increased insulin sensitivity were attenuated by propanolol, as was the increase in murine ZAG in the serum. These results suggest that oral administration of ZAG increases serum levels through interaction with a ß-AR in the upper gastrointestinal tract, and gene expression studies showed this to be in the esophagus

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets

Clustering of genes and/or samples is a common task in gene expression analysis. The goals in clustering can vary, but an important scenario is that of finding biologically meaningful subtypes within the samples. This is an application that is particularly appropriate when there are large numbers of samples, as in many human disease studies. With the increasing popularity of single-cell transcriptome sequencing (RNA-Seq), many more controlled experiments on model organisms are similarly creating large gene expression datasets with the goal of detecting previously unknown heterogeneity within cells. It is common in the detection of novel subtypes to run many clustering algorithms, as well as rely on subsampling and ensemble methods to improve robustness. We introduce a Bioconductor R package, clusterExperiment, that implements a general and flexible strategy we entitle Resampling-based Sequential Ensemble Clustering (RSEC). RSEC enables the user to easily create multiple, competing clusterings of the data based on different techniques and associated tuning parameters, including easy integration of resampling and sequential clustering, and then provides methods for consolidating the multiple clusterings into a final consensus clustering. The package is modular and allows the user to separately apply the individual components of the RSEC procedure, i.e., apply multiple clustering algorithms, create a consensus clustering or choose tuning parameters, and merge clusters. Additionally, clusterExperiment provides a variety of visualization tools for the clustering process, as well as methods for the identification of possible cluster signatures or biomarkers. The R package clusterExperiment is publicly available through the Bioconductor Project, with a detailed manual (vignette) as well as well documented help pages for each function.</div