Endogenous pararetrovirus sequences associated with 24 nt small RNAs at the centromeres of Fritillaria imperialis L. (Liliaceae), a species with a giant genome

Funded by: Leonardo da Vinci programme, Marie Curie programme, Natural Environment Research Council. Grant Number: NE/G01724/1, Czech Science Foundation. Grant Number: P501/13/10057S

Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway

We are grateful for the FP7 Marie Curie IEF (Lu Ma), the FP7 Marie Curie ITN INTERCROSSING (Andrea Hatlen), the Czech Science Foundation (501/12/G090, Ales Kovarik), China Scholarship Council (Wencai Wang), and NERC (NE/ G01724/1, Laura Kelly, Ilia Leitch, Andrew Leitch). The Illumina sequencing of Fritillaria was funded by NERC (NE/G01724/1) and generated by the Centre of Genomic Research in the University of Liverpool, UK. This research utilised Queen Mary's MidPlus computational facilities, supported by QMUL Research-IT and funded by EPSRC grant EP/K000128/1. We thank an anonymous referee for a rigorous, insightful and helpful revie

Model study of tropospheric trace species distributions during PEM-West A

A three-dimensional mesoscale transport/photochemical model is used to study the transport and photochemical transformation of trace species over eastern Asia and western Pacific for the period from September 20 to October 6, 1991, of the Pacific Exploratory Mission-West A experiment. The influence of emissions from the continental boundary layer that was evident in the observed trace species distributions in the lower troposphere over the ocean is well simulated by the model. In the upper troposphere, species such as O3, NOy (total reactive nitrogen species), and SO2 which have a significant source in the stratosphere are also simulated well in the model, suggesting that the upper tropospheric abundances of these species are strongly influenced by stratospheric fluxes and upper tropospheric sources. In the case of SO2 the stratospheric flux is identified to be mostly from the Mount Pinatubo eruption. Concentrations in the upper troposphere for species such as CO and hydrocarbons, which are emitted in the continental boundary layer and have a sink in the troposphere, are significantly underestimated by the model. Two factors have been identified to contribute significantly to the underestimate: one is emissions upwind of the model domain (eastern Asia and western Pacific); the other is that vertical transport is underestimated in the model. Model results are also grouped by back trajectories to study the contrast between compositions of marine and continental air masses. The model-calculated altitude profiles of trace species in continental and marine air masses are found to be qualitatively consistent with observations. However, the difference in the median values of trace species between continental air and marine air is about twice as large for the observed values as for model results. This suggests that the model underestimates the outflow fluxes of trace species from the Asian continent and the Pacific rim countries to the ocean. Observed altitude profiles for species like CO and hydrocarbons show a negative gradient in continental air and a positive gradient in marine air. A mechanism which may be responsible for the altitude gradients is proposed

Endomicroscopic and transcriptomic analysis of impaired barrier function and malabsorption in environmental enteropathy

Introduction: Environmental enteropathy (EE) is associated with growth failure, micronutrient malabsorption and impaired responses to oral vaccines. We set out to define cellular mechanisms of impaired barrier function in EE and explore protective mechanisms. Methods: We studied 49 adults with environmental enteropathy in Lusaka, Zambia using confocal laser endomicroscopy (CLE); histology, immunohistochemistry and mRNA sequencing of small intestinal biopsies; and correlated these with plasma lipopolysaccharide (LPS) and a zinc uptake test. Results: CLE images (median 134 for each study) showed virtually ubiquitous small intestinal damage. Epithelial defects, imaged by histology and claudin 4 immunostaining, were predominantly seen at the tips of villi and corresponded with leakage imaged in vivo by CLE. In multivariate analysis, circulating log-transformed LPS was correlated with cell shedding events (β = 0.83; P = 0.035) and with serum glucagon-like peptide-2 (β = -0.13; P = 0.007). Zinc uptake from a test dose of 25mg was attenuated in 30/47 (64%) individuals and in multivariate analysis was reduced by HIV, but positively correlated with GLP-2 (β = 2.72; P = 0.03). There was a U-shaped relationship between circulating LPS and villus surface area. Transcriptomic analysis identified 23 differentially expressed genes in severe enteropathy, including protective peptides and proteins. Conclusions: Confocal endomicroscopy, claudin 4 immunostaining and histology identify epithelial defects which are probably sites of bacterial translocation, in the presence of which increased epithelial surface area increases the burden of translocation. GLP 2 and other protective peptides may play an important role in mucosal protection in EE

Exploring the context of sedentary behaviour in older adults (what, where, why, when and with whom)

BACKGROUND: Older adults are the most sedentary segment of the population. Little information is available about the context of sedentary behaviour to inform guidelines and intervention. There is a dearth of information about when, where to intervene and which specific behaviours intervention should target. The aim of this exploratory study was to obtain objective information about what older adults do when sedentary, where and when they are sedentary and in what social context. METHODS: The study was a cross-sectional data collection. Older adults (Mean age = 73.25, SD ± 5.48, median = 72, IQR = 11) volunteers wore activPAL monitors and a Vicon Revue timelapse camera between 1 and 7 days. Periods of sedentary behaviour were identified using the activPAL and the context extracted from the pictures taken during these periods. Analysis of context was conducted using the Sedentary Behaviour International Taxonomy classification system. RESULTS: In total, 52 days from 36 participants were available for analysis. Participants spent 70.1 % of sedentary time at home, 56.9 % of sedentary time on their own and 46.8 % occurred in the afternoon. Seated social activities were infrequent (6.9 % of sedentary bouts) but prolonged (18 % of sedentary time). Participants appeared to frequently have vacant sitting time (41 % of non-screen sedentary time) and screen sitting was prevalent (36 % of total sedentary time). CONCLUSIONS: This study provides valuable information to inform future interventions to reduce sedentary behaviour. Interventions should consider targeting the home environment and focus on the afternoon sitting time, though this needs confirmation in a larger study. Tackling social isolation may also be a target to reduce sedentary time

Estimation in a multiplicative mixed model involving a genetic relationship matrix

Genetic models partitioning additive and non-additive genetic effects for populations tested in replicated multi-environment trials (METs) in a plant breeding program have recently been presented in the literature. For these data, the variance model involves the direct product of a large numerator relationship matrix A, and a complex structure for the genotype by environment interaction effects, generally of a factor analytic (FA) form. With MET data, we expect a high correlation in genotype rankings between environments, leading to non-positive definite covariance matrices. Estimation methods for reduced rank models have been derived for the FA formulation with independent genotypes, and we employ these estimation methods for the more complex case involving the numerator relationship matrix. We examine the performance of differing genetic models for MET data with an embedded pedigree structure, and consider the magnitude of the non-additive variance. The capacity of existing software packages to fit these complex models is largely due to the use of the sparse matrix methodology and the average information algorithm. Here, we present an extension to the standard formulation necessary for estimation with a factor analytic structure across multiple environments

Developing a Method to Test the Validity of 24 Hour Time Use Diaries Using Wearable Cameras: A Feasibility Pilot

Self-report time use diaries collect a continuous sequenced record of daily activities but the validity of the data they produce is uncertain. This study tests the feasibility of using wearable cameras to generate, through image prompted interview, reconstructed 'near-objective' data to assess their validity. 16 volunteers completed the Harmonised European Time Use Survey (HETUS) diary and used an Autographer wearable camera (recording images at approximately 15 second intervals) for the waking hours of the same 24-hour period. Participants then completed an interview in which visual images were used as prompts to reconstruct a record of activities for comparison with the diary record. 14 participants complied with the full collection protocol. We compared time use and number of discrete activities from the diary and camera records (using 10 classifications of activity). In terms of aggregate totals of daily time use we found no significant difference between the diary and camera data. In terms of number of discrete activities, participants reported a mean of 19.2 activities per day in the diaries, while image prompted interviews revealed 41.1 activities per day. The visualisations of the individual activity sequences reveal some potentially important differences between the two record types, which will be explored at the next project stage. This study demonstrates the feasibility of using wearable cameras to reconstruct time use through image prompted interview in order to test the concurrent validity of 24-hour activity time-use budgets. In future we need a suitably powered study to assess the validity and reliability of 24-hour time use diaries

Dependence of the 0.7 anomaly on the curvature of the potential barrier in quantum wires

. Ninety-eight one-dimensional channels defined using split gates fabricated on a GaAs/AlGaAs heterostructure are measured during one cooldown at 1.4 K. The devices are arranged in an array on a single chip and are individually addressed using a multiplexing technique. The anomalous conductance feature known as the "0.7 structure" is studied using statistical techniques. The ensemble of data shows that the 0.7 anomaly becomes more pronounced and occurs at lower values as the curvature of the potential barrier in the transport direction decreases. This corresponds to an increase in the effective length of the device. The 0.7 anomaly is not strongly influenced by other properties of the conductance related to density. The curvature of the potential barrier appears to be the primary factor governing the shape of the 0.7 structure at a given T and B.his work was supported by Engineering and Physical Sciences Research Council Grant No. EP/I014268/1

Adolescents with Obstructive Sleep Apnea Adhere Poorly to Positive Airway Pressure (PAP), but PAP Users Show Improved Attention and School Performance

Background: Obstructive Sleep Apnea (OSA) is associated with medical and neurobehavioral morbidity across the lifespan. Positive airway pressure (PAP) treatment has demonstrated efficacy in treating OSA and has been shown to improve daytime functioning in adults, but treatment adherence can be problematic. There are nearly no published studies examining functional outcomes such as academic functioning in adolescents treated with PAP. This study was conducted as an initial step towards determining whether PAP treatment improves daytime functioning among adolescents with OSA. Methods: Self-reported academic grades, self- and parent-reported academic quality of life, and objectively-measured attention were assessed before and after PAP was clinically initiated in a sample of 13 obese adolescents with OSA, as well as 15 untreated obese Controls without OSA. Based on adherence data, the treated group was divided into PAP Users (n = 6) and Non-Adherent participants (n = 7). Results: Though demographically similar, the three groups significantly differed in how their academic performance and attention scores changed from baseline to follow-up. Non-Adherent participants showed worsening functioning over time, while PAP Users showed stable or improved functioning, similar to controls. Conclusion: Although many adolescents prescribed PAP for OSA are non-adherent to the treatment, those who adhere t