Models of Type Theory Based on Moore Paths

This paper introduces a new family of models of intensional Martin-Löf type theory. We use constructive ordered algebra in toposes. Identity types in the models are given by a notion of Moore path. By considering a particular gros topos, we show that there is such a model that is non-truncated, i.e. contains non-trivial structure at all dimensions. In other words, in this model a type in a nested sequence of identity types can contain more than one element, no matter how great the degree of nesting. Although inspired by existing non-truncated models of type theory based on simplicial and cubical sets, the notion of model presented here is notable for avoiding any form of Kan filling condition in the semantics of types.Orton was supported by a PhD studentship from the UK EPSRC funded by grants EP/L504920/1 and EP/M506485/1

GLEAM v3 : satellite-based land evaporation and root-zone soil moisture

The Global Land Evaporation Amsterdam Model (GLEAM) is a set of algorithms dedicated to the estimation of terrestrial evaporation and root-zone soil moisture from satellite data. Ever since its development in 2011, the model has been regularly revised, aiming at the optimal incorporation of new satellite-observed geophysical variables, and improving the representation of physical processes. In this study, the next version of this model (v3) is presented. Key changes relative to the previous version include (1) a revised formulation of the evaporative stress, (2) an optimized drainage algorithm, and (3) a new soil moisture data assimilation system. GLEAM v3 is used to produce three new data sets of terrestrial evaporation and root-zone soil moisture, including a 36-year data set spanning 1980-2015, referred to as v3a (based on satellite-observed soil moisture, vegetation optical depth and snow-water equivalent, reanalysis air temperature and radiation, and a multi-source precipitation product), and two satellite-based data sets. The latter share most of their forcing, except for the vegetation optical depth and soil moisture, which are based on observations from different passive and active C-and L-band microwave sensors (European Space Agency Climate Change Initiative, ESA CCI) for the v3b data set (spanning 2003-2015) and observations from the Soil Moisture and Ocean Salinity (SMOS) satellite in the v3c data set (spanning 2011-2015). Here, these three data sets are described in detail, compared against analogous data sets generated using the previous version of GLEAM (v2), and validated against measurements from 91 eddy-covariance towers and 2325 soil moisture sensors across a broad range of ecosystems. Results indicate that the quality of the v3 soil moisture is consistently better than the one from v2: average correlations against in situ surface soil moisture measurements increase from 0.61 to 0.64 in the case of the v3a data set and the representation of soil moisture in the second layer improves as well, with correlations increasing from 0.47 to 0.53. Similar improvements are observed for the v3b and c data sets. Despite regional differences, the quality of the evaporation fluxes remains overall similar to the one obtained using the previous version of GLEAM, with average correlations against eddy-covariance measurements ranging between 0.78 and 0.81 for the different data sets. These global data sets of terrestrial evaporation and root-zone soil moisture are now openly available at www.GLEAM.eu and may be used for large-scale hydrological applications, climate studies, or research on land-atmosphere feedbacks

Aerial photography collected with a multirotor drone reveals impact of Eurasian beaver reintroduction on ecosystem structure

doi: 10.1139/juvs-2015-0005Copyright © 2015 Canadian Science PublishingBeavers are often described as ecological engineers with an ability to modify the structure and flow of fluvial systems and create complex wetland environments with dams, ponds and canals. Consequently, beaver activity has implications for a wide range of environmental ecosystem services including biodiversity, flood risk mitigation, water quality and sustainable drinking water provision. With the current debate surrounding the reintroduction of beavers into the United Kingdom, it is critical to be able to monitor the impact of beavers upon the environment. This study presents the first proof of concept results showing how a lightweight hexacopter fitted with a simple digital camera can be used to derive orthophoto and digital surface model (DSM) data products at a site where beavers have recently been reintroduced. Early results indicate that analysis of the fine-scale (0.01 m) orthophoto and DSM can be used to identify impacts on the ecosystem structure including the extent of dams and associated ponds, and changes in vegetation structure due to beaver tree felling activity. Unmanned aerial vehicle data acquisition offers an effective toolkit for regular repeat monitoring at fine spatial resolution which is a critical attribute for monitoring rapidly-changing and difficult to access beaver-impacted ecosystems

Breeding value estimation with incomplete marker data

International audienc

Bayesian estimation of dispersion parameters with a reduced animal model including polygenic and QTL effects

International audienc

Assessing the contribution of breeds to genetic diversity in conservation schemes

The quantitative assessment of genetic diversity within and between populations is important for decision making in genetic conservation plans. In this paper we define the genetic diversity of a set of populations, S, as the maximum genetic variance that can be obtained in a random mating population that is bred from the set of populations S. First we calculated the relative contribution of populations to a core set of populations in which the overlap of genetic diversity was minimised. This implies that the mean kinship in the core set should be minimal. The above definition of diversity differs from Weitzman diversity in that it attempts to conserve the founder population (and thus minimises the loss of alleles), whereas Weitzman diversity favours the conservation of many inbred lines. The former is preferred in species where inbred lines suffer from inbreeding depression. The application of the method is illustrated by an example involving 45 Dutch poultry breeds. The calculations used were easy to implement and not computer intensive. The method gave a ranking of breeds according to their contributions to genetic diversity. Losses in genetic diversity ranged from 2.1% to 4.5% for different subsets relative to the entire set of breeds, while the loss of founder genome equivalents ranged from 22.9% to 39.3%

Not identifying with postnatal depression: A qualitative study of womens postnatal symptoms of distress and need for support

Introduction: Diagnoses and symptoms of postnatal mental health problems are associated with adverse outcomes for women and their families. Current classification and assessment of postnatal mental health problems may not adequately address the range or combination of emotional distress experienced by mothers. This study aims to explore symptoms of mental health problems reported by new mothers and their experiences of being assessed for these.Methods: In-depth interviews with 17 women in southeast England with a baby under 1-year old who experienced a postnatal mental health problem. Data were analyzed using inductive thematic analysis.Results: Women described a lack of identification with the concept of postnatal depression and felt that other forms of emotional distress were not recognized by the healthcare system. Women felt that support seeking for postnatal mental health problems needed to be normalized and that support should be available whether or not women were diagnosed. Assessment needs to be well timed and caringly implemented.Discussion: Identification and recognition of symptoms and disorders other than postnatal depression need to be improved. Awareness of multiple types of distress needs to be raised both for women experiencing such distress, and for healthcare professionals, to enable them to support women at this time. Different approaches to assessment that include the range of symptoms reported should be piloted

Large scale variation in DNA copy number in chicken breeds

Background Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species. Here we describe a genome-wide CNV study using array comparative genomic hybridization (aCGH) in a wide variety of chicken breeds. Results We identified 3,154 CNVs, grouped into 1,556 CNV regions (CNVRs). Thirty percent of the CNVs were detected in at least 2 individuals. The average size of the CNVs detected was 46.3 kb with the largest CNV, located on GGAZ, being 4.3 Mb. Approximately 75% of the CNVs are copy number losses relatively to the Red Jungle Fowl reference genome. The genome coverage of CNVRs in this study is 60 Mb, which represents almost 5.4% of the chicken genome. In particular large gene families such as the keratin gene family and the MHC show extensive CNV. Conclusions A relative large group of the CNVs are line-specific, several of which were previously shown to be related to the causative mutation for a number of phenotypic variants. The chance that inter-specific CNVs fall into CNVRs detected in chicken is related to the evolutionary distance between the species. Our results provide a valuable resource for the study of genetic and phenotypic variation in this phenotypically diverse species

Making a splash with water repellency

A 'splash' is usually heard when a solid body enters water at large velocity. This phenomena originates from the formation of an air cavity resulting from the complex transient dynamics of the free interface during the impact. The classical picture of impacts on free surfaces relies solely on fluid inertia, arguing that surface properties and viscous effects are negligible at sufficiently large velocities. In strong contrast to this large-scale hydrodynamic viewpoint, we demonstrate in this study that the wettability of the impacting body is a key factor in determining the degree of splashing. This unexpected result is illustrated in Fig.1: a large cavity is evident for an impacting hydrophobic sphere (1.b), contrasting with the hydrophilic sphere's impact under the very same conditions (1.a). This unforeseen fact is furthermore embodied in the dependence of the threshold velocity for air entrainment on the contact angle of the impacting body, as well as on the ratio between the surface tension and fluid viscosity, thereby defining a critical capillary velocity. As a paradigm, we show that superhydrophobic impacters make a big 'splash' for any impact velocity. This novel understanding provides a new perspective for impacts on free surfaces, and reveals that modifications of the detailed nature of the surface -- involving physico-chemical aspects at the nanometric scales -- provide an efficient and versatile strategy for controlling the water entry of solid bodies at high velocity.Comment: accepted for publication in Nature Physic

Regional regulation of transcription in the chicken genome

<p>Abstract</p> <p>Background</p> <p>Over the past years, the relationship between gene transcription and chromosomal location has been studied in a number of different vertebrate genomes. Regional differences in gene expression have been found in several different species. The chicken genome, as the closest sequenced genome relative to mammals, is an important resource for investigating regional effects on transcription in birds and studying the regional dynamics of chromosome evolution by comparative analysis.</p> <p>Results</p> <p>We used gene expression data to survey eight chicken tissues and create transcriptome maps for all chicken chromosomes. The results reveal the presence of two distinct types of chromosomal regions characterized by clusters of highly or lowly expressed genes. Furthermore, these regions correlate highly with a number of genome characteristics. Regions with clusters of highly expressed genes have higher gene densities, shorter genes, shorter average intron and higher GC content compared to regions with clusters of lowly expressed genes. A comparative analysis between the chicken and human transcriptome maps constructed using similar panels of tissues suggests that the regions with clusters of highly expressed genes are relatively conserved between the two genomes.</p> <p>Conclusions</p> <p>Our results revealed the presence of a higher order organization of the chicken genome that affects gene expression, confirming similar observations in other species. These results will aid in the further understanding of the regional dynamics of chromosome evolution.</p> <p>The microarray data used in this analysis have been submitted to NCBI GEO database under accession number GSE17108. The reviewer access link is: <url>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=tjwjpscyceqawjk&acc=GSE17108</url></p