Energy spectrum of turbulent fluctuations in boundary driven reduced magnetohydrodynamics

The nonlinear dynamics of a bundle of magnetic flux ropes driven by stationary fluid motions at their endpoints is studied, by performing numerical simulations of the magnetohydrodynamic (MHD) equations. The development of MHD turbulence is shown, where the system reaches a state that is characterized by the ratio between the Alfven time (the time for incompressible MHD waves to travel along the field lines) and the convective time scale of the driving motions. This ratio of time scales determines the energy spectra and the relaxation toward different regimes ranging from weak to strong turbulence. A connection is made with phenomenological theories for the energy spectra in MHD turbulence.Comment: Published in Physics of Plasma

Circadian deep sequencing reveals stress-response genes that adopt robust rhythmic expression during aging

Disruption of the circadian clock, which directs rhythmic expression of numerous output genes, accelerates aging. To enquire how the circadian system protects aging organisms, here we compare circadian transcriptomes in heads of young and old Drosophila melanogaster. The core clock and most output genes remained robustly rhythmic in old flies, while others lost rhythmicity with age, resulting in constitutive over- or under-expression. Unexpectedly, we identify a subset of genes that adopted increased or de novo rhythmicity during aging, enriched for stress-response functions. These genes, termed late-life cyclers, were also rhythmically induced in young flies by constant exposure to exogenous oxidative stress, and this upregulation is CLOCK-dependent. We also identify age-onset rhythmicity in several putative primary piRNA transcripts overlapping antisense transposons. Our results suggest that, as organisms age, the circadian system shifts greater regulatory priority to the mitigation of accumulating cellular stress

Equilibrium Sampling From Nonequilibrium Dynamics

We present some applications of an Interacting Particle System (IPS) methodology to the field of Molecular Dynamics. This IPS method allows several simulations of a switched random process to keep closer to equilibrium at each time, thanks to a selection mechanism based on the relative virtual work induced on the system. It is therefore an efficient improvement of usual non-equilibrium simulations, which can be used to compute canonical averages, free energy differences, and typical transitions paths

PROPEL: implementation of an evidence based pelvic floor muscle training intervention for women with pelvic organ prolapse: a realist evaluation and outcomes study protocol

Abstract Background Pelvic Organ Prolapse (POP) is estimated to affect 41%–50% of women aged over 40. Findings from the multi-centre randomised controlled “Pelvic Organ Prolapse PhysiotherapY” (POPPY) trial showed that individualised pelvic floor muscle training (PFMT) was effective in reducing symptoms of prolapse, improved quality of life and showed clear potential to be cost-effective. However, provision of PFMT for prolapse continues to vary across the UK, with limited numbers of women’s health physiotherapists specialising in its delivery. Implementation of this robust evidence from the POPPY trial will require attention to different models of delivery (e.g. staff skill mix) to fit with differing care environments. Methods A Realist Evaluation (RE) of implementation and outcomes of PFMT delivery in contrasting NHS settings will be conducted using multiple case study sites. Involving substantial local stakeholder engagement will permit a detailed exploration of how local sites make decisions on how to deliver PFMT and how these lead to service change. The RE will track how implementation is working; identify what influences outcomes; and, guided by the RE-AIM framework, will collect robust outcomes data. This will require mixed methods data collection and analysis. Qualitative data will be collected at four time-points across each site to understand local contexts and decisions regarding options for intervention delivery and to monitor implementation, uptake, adherence and outcomes. Patient outcome data will be collected at baseline, six months and one year follow-up for 120 women. Primary outcome will be the Pelvic Organ Prolapse Symptom Score (POP-SS). An economic evaluation will assess the costs and benefits associated with different delivery models taking account of further health care resource use by the women. Cost data will be combined with the primary outcome in a cost effectiveness analysis, and the EQ-5D-5L data in a cost utility analysis for each of the different models of delivery. Discussion Study of the implementation of varying models of service delivery of PFMT across contrasting sites combined with outcomes data and a cost effectiveness analysis will provide insight into the implementation and value of different models of PFMT service delivery and the cost benefits to the NHS in the longer term

Genome landscapes and bacteriophage codon usage

Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns of codon usage across 74 diverse bacteriophages that infect E. coli, P. aeruginosa and L. lactis as their primary host. We introduce the concept of a `genome landscape,' which helps reveal non-trivial, long-range patterns in codon usage across a genome. We develop a series of randomization tests that allow us to interrogate the significance of one aspect of codon usage, such a GC content, while controlling for another aspect, such as adaptation to host-preferred codons. We find that 33 phage genomes exhibit highly non-random patterns in their GC3-content, use of host-preferred codons, or both. We show that the head and tail proteins of these phages exhibit significant bias towards host-preferred codons, relative to the non-structural phage proteins. Our results support the hypothesis of translational selection on viral genes for host-preferred codons, over a broad range of bacteriophages.Comment: 9 Color Figures, 5 Tables, 53 Reference

Measuring cognition and function in the preclinical stage of Alzheimer\u27s disease

© 2018 The Authors The Alzheimer\u27s Association\u27s Research Roundtable met in November 2016 to explore how best to measure changes in cognition and function in the preclinical stage of Alzheimer\u27s disease. This review will cover the tools and instruments currently available to identify populations for prevention trials, and measure subtle disease progression in the earliest stages of Alzheimer\u27s disease, and will include discussions of suitable cognitive, behavioral, functional, composite, and biological endpoints for prevention trials. Current prevention trials are reviewed including TOMMOROW, Alzheimer\u27s Prevention Initiative Autosomal Dominant Alzheimer\u27s Disease Trial, the Alzheimer\u27s Prevention Initiative Generation Study, and the Anti-Amyloid Treatment in Asymptomatic Alzheimer\u27s to compare current approaches and tools that are being developed

Predicting aflatoxin content in peanuts using ambient temperature, soil temperature and soil moisture content during pod development

Higher than acceptable aflatoxin levels in peanut kernels (Arachis hypogaea L.) and related products is a worldwide food safety concern. Strict regulatory standards by major importers of peanuts limit the marketability of peanuts for many developing tropical countries including Zambia. The incidence of preharvest aflatoxins is strongly linked to soil and weather conditions during pod-development. This study aimed to formulate statistical models to predict total aflatoxin content in peanut kernels using selected environmental factors during pod development. Field experiments were conducted for two years during which the peanut crop was exposed to 84 combinations of ambient temperature, soil temperature and soil moisture content measured during the last 30 days of pod development. These data were used to formulate regression models to predict total aflatoxin content in peanut kernels. Simple linear regression models had R2 values of 0.30 for maximum ambient temperature, 0.24 for soil temperature and 0.38 for soil moisture content. Combining soil moisture content and soil temperature in a multivariate regression model could explain 54% of the variation in total aflatoxin content while a combination of soil moisture content and maximum ambient temperature could only explain 46% of the variation in total aflatoxin content

Metalevel algorithms for variant satisfiability

Variant satisfiability is a theory-generic algorithm to decide quantifier-free satisfiability in an initial algebra when its corresponding theory has the finite variant property and its constructors satisfy a compactness condition. This paper: (i) gives a precise definition of several meta-level sub-algorithms needed for variant satisfiability; (ii) proves them correct; and (iii) presents a reflective implementation in Maude 2.7 of variant satisfiability using these sub-algorithms.NSF CNS 13-19109Ope

Hands help hearing: Facilitatory audiotactile interaction at low sound-intensity levels

Auditory and vibrotactile stimuli share similar temporal patterns. A psychophysical experiment was performed to test whether this similarity would lead into an intermodal bias in perception of sound intensity. Nine normal-hearing subjects performed a loudness-matching task of faint tones, adjusting the probe tone to sound equally loud as a reference tone. The task was performed both when the subjects were touching and when they were not touching a tube that vibrated simultaneously with the probe tone. The subjects chose on average 12% lower intensities (p<0.01) for the probe tone when they touched the tube, suggesting facilitatory interaction between auditory and tactile senses in normal-hearing subjects.Peer reviewe