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

Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size.

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families.Thiswork was supported by the Natural Environment ResearchCouncil (grant no. NE/G017 24/1), the Czech Science Fou nda-tion (grant no. P501/12/G090), the AVCR (grant no.RVO:60077344) and a Beatriu de Pinos postdoctoral fellowshipto J.P. (grant no. 2011-A-00292; Catalan Government-E.U. 7thF.P.)

Crude incidence in two-phase designs in the presence of competing risks.

BackgroundIn many studies, some information might not be available for the whole cohort, some covariates, or even the outcome, might be ascertained in selected subsamples. These studies are part of a broad category termed two-phase studies. Common examples include the nested case-control and the case-cohort designs. For two-phase studies, appropriate weighted survival estimates have been derived; however, no estimator of cumulative incidence accounting for competing events has been proposed. This is relevant in the presence of multiple types of events, where estimation of event type specific quantities are needed for evaluating outcome.MethodsWe develop a non parametric estimator of the cumulative incidence function of events accounting for possible competing events. It handles a general sampling design by weights derived from the sampling probabilities. The variance is derived from the influence function of the subdistribution hazard.ResultsThe proposed method shows good performance in simulations. It is applied to estimate the crude incidence of relapse in childhood acute lymphoblastic leukemia in groups defined by a genotype not available for everyone in a cohort of nearly 2000 patients, where death due to toxicity acted as a competing event. In a second example the aim was to estimate engagement in care of a cohort of HIV patients in resource limited setting, where for some patients the outcome itself was missing due to lost to follow-up. A sampling based approach was used to identify outcome in a subsample of lost patients and to obtain a valid estimate of connection to care.ConclusionsA valid estimator for cumulative incidence of events accounting for competing risks under a general sampling design from an infinite target population is derived

Increase in the flock prevalence of lameness in ewes is associated with a reduction in farmers using evidence-based management of prompt treatment : a longitudinal observational study of 154 English sheep flocks 2013–2015

Since 2006, farmers in England have received new recommendations on best practice to manage lameness in sheep through a range of knowledge exchange activities. The adoption of each recommendation varied, but in 2013 approximately 50% of farmers reported treating all lame sheep within 3 days of onset of lameness (prompt treatment), 41% did not practice routine foot trimming, 50% culled sheep that had been lame and 14% vaccinated against footrot; all recommended best practices. The aim of this study was to investigate the prevalence of lameness in ewes in England from 2013 to 2015 and to identify changes in practice to manage lameness between 2013 and 2015 and the population attributable fraction for these managements. A longitudinal study with a cohort of 154 English sheep farmers was run for three years, farmers completed questionnaires on lameness in their flock for the previous 12 months in 2013, 2014 and 2015. The geometric mean prevalence of lameness in ewes was 4.1% in 2015, significantly higher than 3.3% and 3.2% for the same 128 farmers who provided data in both 2013 and 2014. Between 2013 and 2015 there was a significant reduction in farmers practising prompt treatment (50.6%–28.6%) but an increase in not practising routine foot trimming (40.9%–79.2%), culling sheep that had been lame (49.4%–81.8%), and vaccinating against footrot (14.3%–29.2%). Not practising prompt treatment, ≥5% of sheep feet bleeding during routine foot trimming, vaccinating ewes for 5 years, not treating lame sheep promptly, ≥5% of sheep feet bleeding during routine foot trimming, and mixing of flocks were 34.5%, 25.3%, 2.9% and 2.4%. In 2013, when 50% of farmers used prompt treatment, the PAF for not using prompt treatment was only 13.3%. We conclude that the change in practice by these farmers towards flock-level managements and a reduction in individual prompt treatment of lame sheep negatively impacted the prevalence of lameness in sheep. This change occurred despite the evidence that prompt treatment of lame sheep is highly effective at reducing the prevalence of lameness in sheep flocks and is an example of cognitive dissonance

Methods for the analysis of ordinal response data in medical image quality assessment.

The assessment of image quality in medical imaging often requires observers to rate images for some metric or detectability task. These subjective results are used in optimisation, radiation dose reduction or system comparison studies and may be compared to objective measures from a computer vision algorithm performing the same task. One popular scoring approach is to use a Likert scale, then assign consecutive numbers to the categories. The mean of these response values is then taken and used for comparison with the objective or second subjective response. Agreement is often assessed using correlation coefficients. We highlight a number of weaknesses in this common approach, including inappropriate analyses of ordinal data, and the inability to properly account for correlations caused by repeated images or observers. We suggest alternative data collection and analysis techniques such as amendments to the scale and multilevel proportional odds models. We detail the suitability of each approach depending upon the data structure and demonstrate each method using a medical imaging example. Whilst others have raised some of these issues, we evaluated the entire study from data collection to analysis, suggested sources for software and further reading, and provided a checklist plus flowchart, for use with any ordinal data. We hope that raised awareness of the limitations of the current approaches will encourage greater method consideration and the utilisation of a more appropriate analysis. More accurate comparisons between measures in medical imaging will lead to a more robust contribution to the imaging literature and ultimately improved patient care

Biomass-modulated fire dynamics during the last glacial-interglacial transition at the central pyrenees (Spain)

Understanding long-term fire ecology is essential for current day interpretation of ecosystem fire responses. However palaeoecology of fire is still poorly understood, especially at high-altitude mountain environments, despite the fact that these are fire-sensitive ecosystems and their resilience might be affected by changing fire regimes. We reconstruct wildfire occurrence since the Lateglacial (14.7. cal. ka BP) to the Mid-Holocene (6. cal. ka BP) and investigate the climate-fuel-fire relationships in a sedimentary sequence located at the treeline in the Central Spanish Pyrenees. Pollen, macro- and micro-charcoal were analysed for the identification of fire events (FE) in order to detect vegetation post-fire response and to define biomass-fire interactions. mean fire intervals (mfi) reduced since the Lateglacial, peaking at 9-7.7. cal. ka BP while from 7.7 to 6. cal. ka BP no fire is recorded. We hypothesise that Early Holocene maximum summer insolation, as climate forcing, and mesophyte forest expansion, as a fuel-creating factor, were responsible for accelerating fire occurrence in the Central Pyrenees treeline. We also found that fire had long-lasting negative effects on most of the treeline plant communities and that forest contraction from 7.7. cal. ka BP is likely linked to the ecosystem's threshold response to high fire frequencies.This research has been funded by the projects DINAMO (CGL2009-07992) (funding EGPF — grant ref. BES-2010-038593 and MSC), DINAMO2 (CGL2012-33063), ARAFIRE (2012 GA LC 064), GRACCIE-CONSOLIDER (CSD2007-00067). GGR was funded by the Juan de la Cierva Program (grant ref. JCI2009-04345) and JAE-Doc CSIC Program, LLM was supported by a postdoctoral MINT fellowship funded by the Institute for the Environment (Brunel University), AMC is a Ramón y Cajal fellow (ref: RYC-2008-02431), APS holds a grant funded by the Aragon Government (ref. 17030G/5423/480072/14003) and JAE holds a grant funded by the Basque Country Government (BFI-2010-5)

Historical legacies of river pollution reconstructed from fish scales

Many rivers have been impacted by heavy metal pollution in the past but the long-term legacies on biodiversity are difficult to estimate. The River Ulla (NW Spain) was impacted by tailings from a copper mine during the 1970-1980s but absence of baseline values and lack of subsequent monitoring have prevented a full impact assessment. We used archived fish scales of Atlantic salmon to reconstruct levels of historical copper pollution and its effects on salmon fitness. Copper bioaccumulation significantly increased over baseline values during the operation of the mine, reaching sublethal levels for salmon survival. Juvenile growth and relative population abundance decreased during mining, but no such effects were observed in a neighbouring river unaffected by mining. Our results indicate that historical copper exposure has probably compromised the fitness of this Atlantic salmon population to the present day, and that fish scales are suitable biomarkers of past river pollution

Growth patterns in early childhood: Better trajectories in Afro-Ecuadorians independent of sex and socioeconomic factors.

The first years of life are the most dynamic period for childhood growth. There are limited data available on growth patterns of infants and children living in rural Latin America. The aim of this study was to describe the growth patterns from birth to 5years in children living in a rural District of tropical coastal Ecuador using data from a birth cohort of 2404 neonates. We hypothesize that there would be growth differences according to ethnicity and sex. Evaluations were conducted at birth or until 2weeks of age and at 7, 13, 24, 36 and 60months during clinic and home visits. Individual growth trajectories for weight-for-age, height-for-age and weight/height-for-age Z-scores were estimated using multilevel models. Girls were lighter and shorter than boys at birth. However, Afro-Ecuadorian children (versus mestizo or indigenous) were longer/taller and heavier throughout the first 5years of life and had greater mean trajectories for HAZ and WAZ independent of sex and socioeconomic factors. Our data indicate that ethnicity is a determinant of growth trajectories during the first 5years of life independent of socioeconomic factors in a birth cohort conducted in a rural region of Latin America

The incidence function model as a tool for landscape ecological impact assessments

Landscape-scale approaches to assessing the impact of land-use change on species' persistence are necessary because species depend on processes acting at varying scales, yet existing approaches to ecological impact assessment tend only to be site-based. A further major criticism of current ecological impact assessments is that they tend to be qualitative. Here we develop methods that apply the Incidence Function Model (IFM) in real urban planning contexts, by generating repeatable and comparable quantitative measures of ecological impacts. To demonstrate the methods for a case study (Nottingham, UK), we estimated landscape-scale measures of species' persistence that indicate metapopulation viability. We based these on Nottingham’s landscape when urban developments were recently proposed, then adjust the land cover to include the proposed developments, and also for two projected landscapes where 10% and 20% of the original natural or semi-natural land cover is lost. We find that the IFM shows promise as a tool for quantitative landscape-scale ecological impact assessment, depending on the size of the impact. We detected minimal differences in the species' viability measures between the original and post-development landscapes. This suggests that for small (around 2%) cumulative losses of natural/ semi-natural space, current site-based approaches are sufficient. However, when the cumulative effect of continued development was modelled by increasing the losses of natural/semi-natural land cover to 10–20% of existing cover, the impact on many of the species studied was more substantial. This indicates that a landscape-scale approach is necessary for larger, prolonged and cumulative habitat losses

Information professionals and copyright literacy: a multinational study

Purpose: The purpose of this paper is to present findings from a multinational survey on copyright literacy of specialists from libraries and other cultural institutions. Design/methodology/approach: This paper is based on a multinational survey of copyright literacy competencies of Library and Information Science (LIS) professionals and those who work in the cultural heritage sector (archives and museums), conducted in 13 countries, namely Bulgaria (BG), Croatia (CR), Finland (FI), France (FR), Hungary (HU), Lithuania (LT), Mexico (MX), Norway (NO), Portugal (PT), Romania (RO), Turkey (TR), UK and USA in the period July 2013-March 2015. An online survey instrument was developed in order to collect data from professionals regarding their familiarity with, knowledge and awareness of, and opinions on copyright-related issues. Findings: Findings of this study highlight gaps in existing knowledge of copyright, and information about the level of copyright literacy of LIS and cultural sector professionals. Also attitudes toward copyright learning content in academic education and continuing professional development training programs are investigated. Originality/value: This study aimed to address a gap in the literature by encompassing specialists from the cultural institutions in an international comparative context. The paper offers guidance for further understanding of copyright in a wider framework of digital and information literacy; and for the implementation of copyright policy, and the establishment of copyright advisor positions in cultural institutions. The recommendations support a revision of academic and continuing education programs learning curriculum and methods