Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma

Background

The human microbiome plays a significant role in maintaining normal physiology. Changes in its composition have been associated with bowel disease, metabolic disorders and atherosclerosis. Sequences of microbial origin have been observed within small RNA sequencing data obtained from blood samples. The aim of this study was to characterise the microbiome from which these sequences are derived.

Abundant non-human small RNA sequences were identified in plasma and plasma exosomal samples. Assembly of these short sequences into longer contigs was the pivotal novel step in ascertaining their origin by BLAST searches. Most reads mapped to rRNA sequences. The taxonomic profiles of the microbes detected were very consistent between individuals but distinct from microbiomes reported at other sites. The majority of bacterial reads were from the phylum Proteobacteria, whilst for 5 of 6 individuals over 90% of the more abundant fungal reads were from the phylum Ascomycota; of these over 90% were from the order Hypocreales. Many contigs were from plants, presumably of dietary origin.  In addition, extremely abundant small RNAs derived from human Y RNAs were detected.

A characteristic profile of a subset of the human microbiome can be obtained by sequencing small RNAs present in the blood. The source and functions of these molecules remain to be determined, but the specific profiles are likely to reflect health status. The potential to provide biomarkers of diet and for the diagnosis and prognosis of human disease is immense.

The Sexual Offences (NI) Order 2008 implications for nurses

This article outlines the changes to the definition of sexual offences in Northern Ireland following the implementation of the Sexual offences Northern Ireland Order 2008 in 2009, and its implications for nurses working with sexually active children in a range of clinical settings. The paper outlines the key changes for practice and addresses the needs of children in three different age groups with emphasis on children aged 13-15 years, and reviews mandatory reporting, the differences between the rights of children to consent and confidentiality, developmental sexual experimentation and sexual health promotion. It reviews related policy and guidance and makes clear the differences between sexual abuse and exploitation, and experimentation. It seeks to advise the Safeguarding Committee of the Department of Health Northern Ireland on how best to support nurses working with sexually active children and when this activity should be discussed with line managers and safeguarding specialists or referred to the safeguarding authorities.

Automatic extraction of Reduced order models from CFD simulations for building energy modeling

Thermal comfort is defined as “that condition of mind which expresses satisfaction with the thermal environment’ [1] [2]. Field studies have been completed in order to establish the governing conditions for thermal comfort [3]. These studies showed that the internal climate of a room was the strongest factor in establishing thermal comfort. Direct manipulation of the internal climate is necessary to retain an acceptable level of thermal comfort. In order for Building Energy Management Systems (BEMS) strategies to be efficiently utilised it is necessary to have the ability to predict the effect that activating a heating/cooling source (radiators, windows and doors) will have on the room. The numerical modelling of the domain can be challenging due to necessity to capture temperature stratification and/or different heat sources (radiators, computers and human beings). Computational Fluid Dynamic (CFD) models are usually utilised for this function because they provide the level of details required. Although they provide the necessary level of accuracy these models tend to be highly computationally expensive especially when transient behaviour needs to be analysed. Consequently they cannot be integrated in BEMS. This paper presents and describes validation of a CFD-ROM method for real-time simulations of building thermal performance. The CFD-ROM method involves the automatic extraction and solution of reduced order models (ROMs) from validated CFD simulations. The test case used in this work is a room of the Environmental Research Institute (ERI) Building at the University College Cork (UCC). ROMs have shown that they are sufficiently accurate with a total error of less than 1% and successfully retain a satisfactory representation of the phenomena modelled. The number of zones in a ROM defines the size and complexity of that ROM. It has been observed that ROMs with a higher number of zones produce more accurate results. As each ROM has a time to solution of less than 20 seconds they can be integrated into the BEMS of a building which opens the potential to real time physics based building energy modelling.

REDUCED ORDER MODELLING OF THE THERMAL BEHAVIOUR OF AN OFFICE SPACE

Reduced Order Models (ROMs) have proven to be a valid and efficient approach to model the thermal behaviour of building zones. The main issues associated with the use of zonal/lumped models are how to (1) divide the domain (lumps) and (2) evaluate the pa- rameters which characterise the lump-to-lump exchange of energy and momentum. The object of this research is to develop a methodology for the generation of ROMs from CFD models. The lumps of the ROM and their average property values are automatically ex- tracted from the CFD models through user defined constraints. This methodology has been applied to validated CFD models of a zone of the Environmental Research Insti- tute (ERI) Building in University College Cork (UCC). The ROM predicts temperature distribution in the domain with an average error lower than 2%. It is computationally efficient with an execution time of 3.45 seconds. Future steps in this research will be the development of the procedure to automatically extract the parameters which define lump-to-lump energy and momentum exchange. At the moment these parameters are evaluated through the minimisation of a cost function. The ROMs will also be utilised to predict the transient thermal behaviour of the building zone.

A Lagrangian approach for modeling road collisions using second-order models of traffic flow

In [M. Herty, A. Klein, S. Moutari, V. Schleper, and G. Steinaur, IMA J. Appl. Math., 78(5), 1087–1108, 2013] and [M. Herty and V. Schleper, ZAMM J. Appl. Math. Mech., 91, 763–776, 2011], a macroscopic approach, derived from fluid-dynamics models, has been introduced to infer traffic conditions prone to road traffic collisions along highways’ sections. In these studies, the governing equations are coupled within an Eulerian framework, which assumes fixed interfaces between the models. A coupling in Lagrangian coordinates would enable us to get rid of this (not very realistic) assumption. In this paper, we investigate the well-posedness and the suitability of the coupling of the governing equations within the Lagrangian framework. Further, we illustrate some features of the proposed approach through some numerical simulations.

Kernel-based local order estimation of nonlinear nonparametric systems

We consider the local order estimation of nonlinear autoregressive systems with exogenous inputs (NARX), which may have different local dimensions at different points. By minimizing the kernel-based local information criterion introduced in this paper, the strongly consistent estimates for the local orders of the NARX system at points of interest are obtained. The modification of the criterion and a simple procedure of searching the minimum of the criterion, are also discussed. The theoretical results derived here are tested by simulation examples.

Expertly validated models and phylogenetically-controlled analysis suggests responses to climate change are related to species traits in the Order Lagomorpha

Climate change during the last five decades has impacted significantly on natural ecosystems and the rate of current climate change is of great concern among conservation biologists. Species Distribution Models (SDMs) have been used widely to project changes in species’ bioclimatic envelopes under future climate scenarios. Here, we aimed to advance this technique by assessing future changes in the bioclimatic envelopes of an entire mammalian order, the Lagomorpha, using a novel framework for model validation based jointly on subjective expert evaluation and objective model evaluation statistics. SDMs were built using climatic, topographical and habitat variables for all 87 lagomorph species under past and current climate scenarios. Expert evaluation and Kappa values were used to validate past and current models and only those deemed ‘modellable’ within our framework were projected under future climate scenarios (58 species). Phylogenetically-controlled regressions were used to test whether species traits correlated with predicted responses to climate change. Climate change is likely to impact more than two-thirds of lagomorph species, with leporids (rabbits, hares and jackrabbits) likely to undertake poleward shifts with little overall change in range extent, whilst pikas are likely to show extreme shifts to higher altitudes associated with marked range declines, including the likely extinction of Kozlov’s Pika (Ochotona koslowi). Smaller-bodied species were more likely to exhibit range contractions and elevational increases, but showing little poleward movement, and fecund species were more likely to shift latitudinally and elevationally. Our results suggest that species traits may be important indicators of future climate change and we believe multi-species approaches, as demonstrated here, are likely to lead to more effective mitigation measures and conservation management. We strongly advocate studies minimising data gaps in our knowledge of the Order, specifically collecting more specimens for biodiversity archives and targeting data deficient geographic regions.

Biogeography, macroecology and species’ traits mediate competitive interactions in the order Lagomorpha

1. In addition to abiotic determinants, biotic factors, including competitive, interspecific interactions, limit species’ distributions. Environmental changes in human disturbance, land use and climate are predicted to have widespread impacts on interactions between species, especially in the order Lagomorpha due to the higher latitudes and more extreme environmental conditions they occupy.
2. We reviewed the published literature on interspecific interactions in the order Lagomorpha, and compared the biogeography, macroecology, phylogeny and traits of species known to interact with those of species with no reported interactions, to investigate how projected future environmental change may affect interactions and potentially alter species’ distributions.
3. Thirty-three lagomorph species have competitive interactions reported in the literature; the majority involve hares (Lepus sp.) or the eastern cottontail rabbit (Sylvilagus floridanus). Key regions for interactions are located between 30-50°N of the Equator, and include eastern Asia (southern Russia on the border of Mongolia) and North America (north western USA).
4. Closely related, large-bodied, similarly sized species occurring in regions of human-modified, typically agricultural landscapes, or at high elevations are significantly more likely to have reported competitive interactions than other lagomorph species.
5. We identify species’ traits associated with competitive interactions, and highlight some potential impacts that future environmental change may have on interspecific interactions. Our approach using bibliometric and biological data is widely applicable, and with relatively straightforward methodologies, can provide insights into interactions between species.
6. Our results have implications for predicting species’ responses to global change, and we advise that capturing, parameterizing and incorporating interspecific interactions into analyses (for example, species distribution modelling) may be more important than suggested by the literature.

High-order harmonic generation from controlled plasma mirrors

Ultrashort, high contrast laser pulses when focused to high intensity and reflected from a steep solid density 'plasma mirror (PM)' contain coherent XUV radiation in the form of high-order harmonics. The emission can either be due to the relativistically driven oscillating PM (ROM) [1] or due to Coherent wake emission (CWE) [2]. Selective control over the mechanisms and the characteristics of these harmonics and understanding the physics is crucial for the development of intense attosecond light sources. © 2013 IEEE.

Blind Characterisation of Sensors with Second-Order Dynamic Response

Compensation for the dynamic response of a temperature sensor usually involves the estimation of its input on the basis of the measured output and model parameters. In the case of temperature measurement, the sensor dynamic response is strongly dependent on the measurement environment and fluid velocity. Estimation of time-varying sensor model parameters therefore requires continuous textit{in situ} identification. This can be achieved by employing two sensors with different dynamic properties, and exploiting structural redundancy to deduce the sensor models from the resulting data streams. Most existing approaches to this problem assume first-order sensor dynamics. In practice, however second-order models are more reflective of the dynamics of real temperature sensors, particularly when they are encased in a protective sheath. As such, this paper presents a novel difference equation approach to solving the blind identification problem for sensors with second-order models. The approach is based on estimating an auxiliary ARX model whose parameters are related to the desired sensor model parameters through a set of coupled non-linear algebraic equations. The ARX model can be estimated using conventional system identification techniques and the non-linear equations can be solved analytically to yield estimates of the sensor models. Simulation results are presented to demonstrate the efficiency of the proposed approach under various input and parameter conditions.

Local order and frustration in the geometrically frustrated spinels Cd1-xZnxV2O4

Orbitally degenerate frustrated spinels, Cd1-xZnxV2O4, with 0 <= x <= 1 were investigated using elastic and inelastic neutron scattering techniques. In the end members with x=0 and 1, a tetragonal distortion (c < a) has been observed upon cooling mediated by a Jahn-Teller distortion that gives rise to orbital ordering. This leads to the formation of spin chains in the ab-plane that upon further cooling, Neel ordering is established due to interchain coupling. In the doped compositions, however, the bulk susceptibility, chi, shows that the macroscopic transitions to cooperative orbital ordering and long-range antiferromagnetic ordering are suppressed. However, the inelastic neutron scattering measurements suggest that the dynamic spin correlations at low temperatures have similar one-dimensional characteristics as those observed in the pure samples. The pair density function analysis of neutron diffraction data shows that the local atomic structure does not become random with doping but rather consists of two distinct environments corresponding to ZnV2O4 and CdV2O4. This indicates that short-range orbital ordering is present which leads to the one-dimensional character of the spin correlations even in the low temperature cubic phase of the doped compositions.