Branch-recombinant Gaussian processes for analysis of perturbations in biological time series.

MOTIVATION: A common class of behaviour encountered in the biological sciences involves branching and recombination. During branching, a statistical process bifurcates resulting in two or more potentially correlated processes that may undergo further branching; the contrary is true during recombination, where two or more statistical processes converge. A key objective is to identify the time of this bifurcation (branch or recombination time) from time series measurements, e.g. by comparing a control time series with perturbed time series. Gaussian processes (GPs) represent an ideal framework for such analysis, allowing for nonlinear regression that includes a rigorous treatment of uncertainty. Currently, however, GP models only exist for two-branch systems. Here, we highlight how arbitrarily complex branching processes can be built using the correct composition of covariance functions within a GP framework, thus outlining a general framework for the treatment of branching and recombination in the form of branch-recombinant Gaussian processes (B-RGPs). RESULTS: We first benchmark the performance of B-RGPs compared to a variety of existing regression approaches, and demonstrate robustness to model misspecification. B-RGPs are then used to investigate the branching patterns of Arabidopsis thaliana gene expression following inoculation with the hemibotrophic bacteria, Pseudomonas syringae DC3000, and a disarmed mutant strain, hrpA. By grouping genes according to the number of branches, we could naturally separate out genes involved in basal immune response from those subverted by the virulent strain, and show enrichment for targets of pathogen protein effectors. Finally, we identify two early branching genes WRKY11 and WRKY17, and show that genes that branched at similar times to WRKY11/17 were enriched for W-box binding motifs, and overrepresented for genes differentially expressed in WRKY11/17 knockouts, suggesting that branch time could be used for identifying direct and indirect binding targets of key transcription factors. AVAILABILITY AND IMPLEMENTATION: https://github.com/cap76/BranchingGPs. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

The kinetics of surfactant desorption at the air–solution interface

The kinetics of desorption of the anionic surfactant sodium dodecylbenzene sulfonate at the air–solution interface have been studied using neutron reflectivity (NR). The experimental arrangement incorporates a novel flow cell in which the subphase can be exchanged (diluted) using a laminar flow whilst the surface region remains unaltered. The kinetics of the desorption is relatively slow and occurs over many tens of minutes compared with the dilution timescale of approximately 10–30 minutes. A detailed mathematical model, in which the rate of the desorption is determined by transport through a near-surface diffusion layer into a diluted bulk solution below, is developed and provides a good description of the timedependent adsorption data.\ud \ud A key parameter of the model is the ratio of the depth of the diffusion layer, Hc , to the depth of the fluid, Hf, and we find that this is related to the reduced Péclet number, Pe*, for the system, via Hc/Hf, = C/Pe* 1/ 2 . Although from a highly idealised experimental arrangement, the results provide an important insight into the ‘rinse mechanism’, which is applicable to a wide variety of domestic and industrial circumstances

The use of segmented regression in analysing interrupted time series studies : an example in pre-hospital ambulance care

Peer reviewedPublisher PD

Probing the mechanism for hydrogel-based stasis induction in human pluripotent stem cells : is the chemical functionality of the hydrogel important?

It is well-known that pluripotent human embryonic stem cells (hPSC) can differentiate into any cell type. Recently, we reported that hPSC colonies enter stasis when immersed in an extremely soft hydrogel comprising hydroxyl-functional block copolymer worms (I. Canton, N. J. Warren, A. Chahal, K. Amps, A. Wood, R. Weightman, E. Wang, H. Moore and S. P. Armes, ACS Centr. Sci., 2016, 2, 65–74). The gel modulus and chemical structure of this synthetic hydrogel are similar to that of natural mucins, which are implicated in the mechanism of diapause for mammalian embryos. Does stasis induction occur merely because of the very soft nature of such hydrogels or does chemical functionality also play a role? Herein, we address this key question by designing a new hydrogel of comparable softness in which the PGMA stabilizer chains are replaced with non-hydroxylated poly(ethylene glycol) [PEG]. Immunolabeling studies confirm that hPSC colonies immersed in such PEG-based hydrogels do not enter stasis but instead proliferate (and differentiate if no adhesion substrate is present). However, pluripotency is retained if an appropriate adhesion substrate is provided. Thus, the chemical functionality of the hydrogel clearly plays a decisive role in the stasis induction mechanism

Tracking nuclear motion in single-molecule magnets using femtosecond X-ray absorption spectroscopy

The development of new data storage solutions is crucial for emerging digital technologies. Recently, all-optical magnetic switching has been achieved in dielectrics, proving to be faster than traditional methods. Despite this, single-molecule magnets (SMMs), which are an important class of magnetic materials due to their nanometre size, remain underexplored for ultrafast photomagnetic switching. Herein, we report femtosecond time-resolved K-edge X-ray absorption spectroscopy (TR-XAS) on a Mn(III)-based trinuclear SMM. Exploiting the elemental specificity of XAS, we directly track nuclear dynamics around the metal ions and show that the ultrafast dynamics upon excitation of a crystal-field transition are dominated by a magnetically active Jahn-Teller mode. Our results, supported by simulations, reveal minute bond length changes from 0.01 to 0.05 \uc5 demonstrating the sensitivity of the method. These geometrical changes are discussed in terms of magneto-structural relationships and consequently our results illustrate the importance of TR-XAS for the emerging area of ultrafast molecular magnetism

'It was nothing that you would think was anything': Qualitative analysis of appraisal and help seeking preceding brain cancer diagnosis.

BACKGROUND: The patient's interpretation of the events and decisions leading up to consultation with a healthcare professional for symptoms of brain cancer is under researched. The aim of this study was to document responses to noticing the changes preceding a diagnosis of brain cancer and living with them, focusing on appraisal of changes and the decision to seek (and re-seek) help, with attention to the psychological processes underpinning the appraisal and help-seeking intervals. METHOD: In this qualitative study set in Eastern and NW England, in-depth interviews with adult patients recently diagnosed with primary brain cancer and their family members were analysed thematically, using the Model of Pathways to Treatment as a conceptual framework. RESULTS: 39 adult patients were interviewed. Regarding the appraisal interval, cognitive heuristics were found to underpin explanations of changes/symptoms. The subtlety and normality of changes often suggested nothing serious was wrong. Common explanations included stress or being busy at work, or age and these did not seem to warrant a visit to a doctor. Explanations and the decision to seek help were made within the social context, with friends, family and work colleagues contributing to appraisal and help-seeking decisions. Regarding the help-seeking interval, barriers to seeking help reflected components of Social Cognitive Theory, and included having other priorities, outcome expectations (e.g. 'feeling silly', not sure much can be done about it, not wanting to waste doctors' time) and accessibility of a preferred healthcare professional. CONCLUSION: Application of psychological theory facilitated understanding of the influences on cognition and behaviour. The study highlights implications for theory, awareness campaigns and potential opportunities promoting more timely help-seeking.the brain tumour charit

Evaluation of variants in the selectin genes in age-related macular degeneration

<p>Abstract</p> <p>Background</p> <p>Age-related macular degeneration (AMD) is a common disease of the elderly that leads to loss of the central visual field due to atrophic or neovascular events. Evidence from human eyes and animal models suggests an important role for macrophages and endothelial cell activation in the pathogenesis of AMD. We sought to determine whether common ancestral variants in genes encoding the selectin family of proteins are associated with AMD.</p> <p>Methods</p> <p>Expression of E-selectin, L-selectin and P-selectin was examined in choroid and retina by quantitative PCR and immunofluorescence. Samples from patients with AMD (n = 341) and controls (n = 400) were genotyped at a total of 34 SNPs in the <it>SELE</it>, <it>SELL </it>and <it>SELP </it>genes. Allele and genotype frequencies at these SNPs were compared between AMD patients and controls as well as between subtypes of AMD (dry, geographic atrophy, and wet) and controls.</p> <p>Results</p> <p>High expression of all three selectin genes was observed in the choroid as compared to the retina. Some selectin labeling of retinal microglia, drusen cores and the choroidal vasculature was observed. In the genetic screen of AMD versus controls, no positive associations were observed for <it>SELE </it>or <it>SELL</it>. One SNP in <it>SELP </it>(rs3917751) produced p-values < 0.05 (uncorrected for multiple measures). In the subtype analyses, 6 SNPs (one in <it>SELE</it>, two in <it>SELL</it>, and three in <it>SELP</it>) produced p-values < 0.05. However, when adjusted for multiple measures with a Bonferroni correction, only one SNP in <it>SELP </it>(rs3917751) produced a statistically significant p-value (p = 0.0029).</p> <p>Conclusions</p> <p>This genetic screen did not detect any SNPs that were highly associated with AMD affection status overall. However, subtype analysis showed that a single SNP located within an intron of <it>SELP </it>(rs3917751) is statistically associated with dry AMD in our cohort. Future studies with additional cohorts and functional assays will clarify the biological significance of this discovery. Based on our findings, it is unlikely that common ancestral variants in the other selectin genes (<it>SELE </it>and <it>SELL</it>) are risk factors for AMD. Finally, it remains possible that sporadic or rare mutations in <it>SELE</it>, <it>SELL</it>, or <it>SELP </it>have a role in the pathogenesis of AMD.</p

One size fits all? Mixed methods evaluation of the impact of 100% single room accommodation on staff and patient experience, safety and costs

BACKGROUND AND OBJECTIVES: There is little strong evidence relating to the impact of single-room accommodation on healthcare quality and safety. We explore the impact of all single rooms on staff and patient experience; safety outcomes; and costs.METHODS: Mixed methods pre/post 'move' comparison within four nested case study wards in a single acute hospital with 100% single rooms; quasi-experimental before-and-after study with two control hospitals; analysis of capital and operational costs associated with single rooms.RESULTS: Two-thirds of patients expressed a preference for single rooms with comfort and control outweighing any disadvantages (sense of isolation) felt by some. Patients appreciated privacy, confidentiality and flexibility for visitors afforded by single rooms. Staff perceived improvements (patient comfort and confidentiality), but single rooms were worse for visibility, surveillance, teamwork, monitoring and keeping patients safe. Staff walking distances increased significantly post move. A temporary increase of falls and medication errors in one ward was likely to be associated with the need to adjust work patterns rather than associated with single rooms per se. We found no evidence that single rooms reduced infection rates. Building an all single-room hospital can cost 5% more with higher housekeeping and cleaning costs but the difference is marginal over time.CONCLUSIONS: Staff needed to adapt their working practices significantly and felt unprepared for new ways of working with potentially significant implications for the nature of teamwork in the longer term. Staff preference remained for a mix of single rooms and bays. Patients preferred single rooms.<br/