Echolocation detections and digital video surveys provide reliable estimates of the relative density of harbour porpoises

Acknowledgements We would like to thank Erik Rexstad and Rob Williams for useful reviews of this manuscript. The collection of visual and acoustic data was funded by the UK Department of Energy & Climate Change, the Scottish Government, Collaborative Offshore Wind Research into the Environment (COWRIE) and Oil & Gas UK. Digital aerial surveys were funded by Moray Offshore Renewables Ltd and additional funding for analysis of the combined datasets was provided by Marine Scotland. Collaboration between the University of Aberdeen and Marine Scotland was supported by MarCRF. We thank colleagues at the University of Aberdeen, Moray First Marine, NERI, Hi-Def Aerial Surveying Ltd and Ravenair for essential support in the field, particularly Tim Barton, Bill Ruck, Rasmus Nielson and Dave Rutter. Thanks also to Andy Webb, David Borchers, Len Thomas, Kelly McLeod, David L. Miller, Dinara Sadykova and Thomas Cornulier for advice on survey design and statistical approache. Data Accessibility Data are available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.cf04gPeer reviewedPublisher PD

Power scalable TEM(oo) CW Nd: YAG laser with thermal lens compensation

We present finite-element analyzes and experimental results to validate our approach for building high-power single-mode Nd:YAG lasers. We show that the thermooptical and thermomechanical properties of a slab laser can be controlled. This is essential for the use of the proposed unstable resonator. We include demonstration of an efficient subscale laser operating at 20 W TEM00.D. Mudge, M. Ostermeyer, P. J. Veitch, J. Munch, B. Middlemiss, D. J. Ottaway and M. W. Hamilto

Compensation of Strong Thermal Lensing in High Optical Power Cavities

In an experiment to simulate the conditions in high optical power advanced gravitational wave detectors such as Advanced LIGO, we show that strong thermal lenses form in accordance with predictions and that they can be compensated using an intra-cavity compensation plate heated on its cylindrical surface. We show that high finesse ~1400 can be achieved in cavities with internal compensation plates, and that the cavity mode structure can be maintained by thermal compensation. It is also shown that the measurements allow a direct measurement of substrate optical absorption in the test mass and the compensation plate.Comment: 8 page

Mobility deficit – Rehabilitate, an opportunity for functionality

There are many pathological conditions that cause mobility deficits and that ultimately influence someone’s autonomy.Aims: to evaluate patients with mobility deficits functional status; to implement a Rehabilitation Nursing intervention plan; to monitor health gains through mobility deficits rehabilitation.Conclusion: Early intervention and the implementation of a nursing rehabilitation intervention plan results in health gains (direct or indirect), decreases the risk of developing Pressure Ulcers (PU) and the risk of developing a situation of immobility that affects patients’ autonomy and quality of life

A consensus statement on the renal monitoring of Australian patients receiving tenofovir based antiviral therapy for HIV/HBV infection

A number of antiviral agents used against Human Immunodeficiency Virus (HIV) infection and hepatitis B virus (HBV) mono or co-infection have been associated with real nephrotoxicity (including tenofovir disoproxil fumarate (TDF), atazanavir, indinavir and lopinavir) or apparent changes in renal function (e.g. cobicistat, ritonavir, rilpivirine and dolutegravir). Patients with HIV are at higher risk of acute and chronic renal dysfunction, so baseline assessment and ongoing monitoring of renal function is an important part of routine management of patients with HIV. Given the paucity of evidence in this area, we sought to establish a consensus view on how routine monitoring could be performed in Australian patients on ART regimens, especially those involving TDF. A group of nephrologists and prescribers (an HIV physician and a hepatologist) were assembled by Gilead to discuss practical and reasonable renal management strategies for patients particularly those on TDF-based combination regimens (in the case of those with HIV-infection) or on TDF-monotherapy (in the case of HBV-mono infection). The group considered which investigations should be performed as part of routine practice, their frequency, and when specialist renal referral is warranted. The algorithm presented suggests testing for serum creatinine along with plasma phosphate and an assessment of urinary protein (rather than albumin) and glucose. Here we advocate baseline tests of renal function at initiation of therapy. If creatinine excretion inhibitors (e.g. cobicistat or rilpivirine) are used as part of the ART regimen, we suggest creatinine is rechecked at 4 weeks and this value used as the new baseline. Repeat testing is suggested at 3-monthly intervals for a year and then at least yearly thereafter if no abnormalities are detected. In patients with abnormal baseline results, renal function assessment should be performed at least 6 monthly. In HBV mono-infected patients advocate that a similar testing protocol may be logical.Stephen G Holt, David M Gracey, Miriam T Levy, David W Mudge, Ashley B Irish, Rowan G Walker, Richard Baer, Jacob Sevastos, Riaz Abbas and Mark A Boy

The Interface Region Imaging Spectrograph (IRIS)

The Interface Region Imaging Spectrograph (IRIS) small explorer spacecraft provides simultaneous spectra and images of the photosphere, chromosphere, transition region, and corona with 0.33-0.4 arcsec spatial resolution, 2 s temporal resolution and 1 km/s velocity resolution over a field-of-view of up to 175 arcsec x 175 arcsec. IRIS was launched into a Sun-synchronous orbit on 27 June 2013 using a Pegasus-XL rocket and consists of a 19-cm UV telescope that feeds a slit-based dual-bandpass imaging spectrograph. IRIS obtains spectra in passbands from 1332-1358, 1389-1407 and 2783-2834 Angstrom including bright spectral lines formed in the chromosphere (Mg II h 2803 Angstrom and Mg II k 2796 Angstrom) and transition region (C II 1334/1335 Angstrom and Si IV 1394/1403 Angstrom). Slit-jaw images in four different passbands (C II 1330, Si IV 1400, Mg II k 2796 and Mg II wing 2830 Angstrom) can be taken simultaneously with spectral rasters that sample regions up to 130 arcsec x 175 arcsec at a variety of spatial samplings (from 0.33 arcsec and up). IRIS is sensitive to emission from plasma at temperatures between 5000 K and 10 MK and will advance our understanding of the flow of mass and energy through an interface region, formed by the chromosphere and transition region, between the photosphere and corona. This highly structured and dynamic region not only acts as the conduit of all mass and energy feeding into the corona and solar wind, it also requires an order of magnitude more energy to heat than the corona and solar wind combined. The IRIS investigation includes a strong numerical modeling component based on advanced radiative-MHD codes to facilitate interpretation of observations of this complex region. Approximately eight Gbytes of data (after compression) are acquired by IRIS each day and made available for unrestricted use within a few days of the observation.Comment: 53 pages, 15 figure

Investigation of guided wave propagation in pipes fully- and partially-embedded in concrete

The application of long-range guided-wave testing to pipes embedded in concrete results in unpredictable test-ranges. The influence of the circumferential extent of the embedding-concrete around a steel pipe on the guided wave propagation is investigated. An analytical model is used to study the axisymmetric fully embedded pipe case, while explicit finite-element and semi-analytical finite-element simulations are utilised to investigate a partially embedded pipe. Model predictions and simulations are compared with full-scale guided-wave tests. The transmission-loss of the T(0,1)-mode in an 8 in. steel pipe fully embedded over an axial length of 0.4 m is found to be in the range of 32–36 dB while it reduces by a factor of 5 when only 50% of the circumference is embedded. The transmission-loss in a fully embedded pipe is mainly due to attenuation in the embedded section while in a partially embedded pipe it depend strongly on the extent of mode-conversion at entry to the embedded-section; low loss modes with energy concentrated in the region of the circumference not-covered with concrete have been identified. The results show that in a fully embedded pipe, inspection beyond a short distance will not be possible, whereas when the concrete is debonded over a fraction of the pipe circumference, inspection of substantially longer lengths may be possible

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Abstract Background Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome. Results Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable – estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation. Conclusions Analysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation

Early Cenozoic denudation of central west Britain in response to transient and permanent uplift above a mantle plume

Upwelling mantle plumes beneath continental crust are predicted to produce difficult to quantify, modest uplift and denudation. The contribution of permanent and transient components to the uplift is also difficult to distinguish. A pulse of denudation in Britain in the Early Paleogene has been linked, although with some controversy, with the arrival of the proto-Iceland mantle plume. In this contribution we show that combining apatite and zircon (U-Th-Sm)/He and apatite fission track analyses from central west Britain with numerical modeling clearly identifies a pulse of early Cenozoic denudation. The data indicate that rock uplift and denudation were centered on the northern East Irish Sea Basin and 1.0–2.4 km of rocks were removed during the latest Cretaceous-early Paleogene. Uplift and erosion appears to have started a few million years before the earliest magmatism in the region. The regional denudation pattern mirrors the distribution of low-density magmatic rocks that has been imaged in the deep crust. However, the injection of the underplating melt is not enough to account for the total denudation. An additional regional uplift of at least 300 m is required, which is consistent with a transient thermal effect from the hot mantle plume. The rapid exhumation event ceased by ~40 Ma and the data do not require significant Neogene exhumation