The landscape ecological impact of afforestation on the British uplands and some initiatives to restore native woodland cover

The majority of forest cover in the British Uplands had been lost by the beginning of the Nineteenth Century, because of felling followed by overgrazing by sheep and deer. The situation remained unchanged until a government policy of afforestation, mainly by exotic conifers, after the First World War up to the present day. This paper analyses the distribution of these predominantly coniferous plantations, and shows how they occupy specific parts of upland landscapes in different zones throughout Britain. Whilst some landscapes are dominated by these new forests, elsewhere the blocks of trees are more localised. Although these forests virtually eliminate native ground vegetation, except in rides and unplanted land, the major negative impacts are at the landscape level. For example, drainage systems are altered and ancient cultural landscape patterns are destroyed. These impacts are summarised and possible ways of amelioration are discussed. By contrast, in recent years, a series of projects have been set up to restore native forest cover, as opposed to the extensive plantations of exotic species. Accordingly, the paper then provides three examples of such initiatives designed to restore native forests to otherwise bare landscapes, as well as setting them into a policy context. Whilst such projects cover a limited proportion of the British Uplands they nevertheless restore forest to landscapes at a local level

Identification of genetic variants associated with Huntington's disease progression: a genome-wide association study

Background Huntington's disease is caused by a CAG repeat expansion in the huntingtin gene, HTT. Age at onset has been used as a quantitative phenotype in genetic analysis looking for Huntington's disease modifiers, but is hard to define and not always available. Therefore, we aimed to generate a novel measure of disease progression and to identify genetic markers associated with this progression measure. Methods We generated a progression score on the basis of principal component analysis of prospectively acquired longitudinal changes in motor, cognitive, and imaging measures in the 218 indivduals in the TRACK-HD cohort of Huntington's disease gene mutation carriers (data collected 2008–11). We generated a parallel progression score using data from 1773 previously genotyped participants from the European Huntington's Disease Network REGISTRY study of Huntington's disease mutation carriers (data collected 2003–13). We did a genome-wide association analyses in terms of progression for 216 TRACK-HD participants and 1773 REGISTRY participants, then a meta-analysis of these results was undertaken. Findings Longitudinal motor, cognitive, and imaging scores were correlated with each other in TRACK-HD participants, justifying use of a single, cross-domain measure of disease progression in both studies. The TRACK-HD and REGISTRY progression measures were correlated with each other (r=0·674), and with age at onset (TRACK-HD, r=0·315; REGISTRY, r=0·234). The meta-analysis of progression in TRACK-HD and REGISTRY gave a genome-wide significant signal (p=1·12 × 10−10) on chromosome 5 spanning three genes: MSH3, DHFR, and MTRNR2L2. The genes in this locus were associated with progression in TRACK-HD (MSH3 p=2·94 × 10−8 DHFR p=8·37 × 10−7 MTRNR2L2 p=2·15 × 10−9) and to a lesser extent in REGISTRY (MSH3 p=9·36 × 10−4 DHFR p=8·45 × 10−4 MTRNR2L2 p=1·20 × 10−3). The lead single nucleotide polymorphism (SNP) in TRACK-HD (rs557874766) was genome-wide significant in the meta-analysis (p=1·58 × 10−8), and encodes an aminoacid change (Pro67Ala) in MSH3. In TRACK-HD, each copy of the minor allele at this SNP was associated with a 0·4 units per year (95% CI 0·16–0·66) reduction in the rate of change of the Unified Huntington's Disease Rating Scale (UHDRS) Total Motor Score, and a reduction of 0·12 units per year (95% CI 0·06–0·18) in the rate of change of UHDRS Total Functional Capacity score. These associations remained significant after adjusting for age of onset. Interpretation The multidomain progression measure in TRACK-HD was associated with a functional variant that was genome-wide significant in our meta-analysis. The association in only 216 participants implies that the progression measure is a sensitive reflection of disease burden, that the effect size at this locus is large, or both. Knockout of Msh3 reduces somatic expansion in Huntington's disease mouse models, suggesting this mechanism as an area for future therapeutic investigation

CSIRO Land and Water

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Hierarchical neural networks for reducing systematic prediction errors

Abstract not available

Estimating genetic parameters of digital behavior traits and their relationship with production traits in purebred pigs

Abstract Background With the introduction of digital phenotyping and high-throughput data, traits that were previously difficult or impossible to measure directly have become easily accessible, offering the opportunity to enhance the efficiency and rate of genetic gain in animal production. It is of interest to assess how behavioral traits are indirectly related to the production traits during the performance testing period. The aim of this study was to assess the quality of behavior data extracted from day-wise video recordings and estimate the genetic parameters of behavior traits and their phenotypic and genetic correlations with production traits in pigs. Behavior was recorded for 70 days after on-test at about 10 weeks of age and ended at off-test for 2008 female purebred pigs, totaling 119,812 day-wise records. Behavior traits included time spent eating, drinking, laterally lying, sternally lying, sitting, standing, and meters of distance traveled. A quality control procedure was created for algorithm training and adjustment, standardizing recording hours, removing culled animals, and filtering unrealistic records. Results Production traits included average daily gain (ADG), back fat thickness (BF), and loin depth (LD). Single-trait linear models were used to estimate heritabilities of the behavior traits and two-trait linear models were used to estimate genetic correlations between behavior and production traits. The results indicated that all behavior traits are heritable, with heritability estimates ranging from 0.19 to 0.57, and showed low-to-moderate phenotypic and genetic correlations with production traits. Two-trait linear models were also used to compare traits at different intervals of the recording period. To analyze the redundancies in behavior data during the recording period, the averages of various recording time intervals for the behavior and production traits were compared. Overall, the average of the 55- to 68-day recording interval had the strongest phenotypic and genetic correlation estimates with the production traits. Conclusions Digital phenotyping is a new and low-cost method to record behavior phenotypes, but thorough data cleaning procedures are needed. Evaluating behavioral traits at different time intervals offers a deeper insight into their changes throughout the growth periods and their relationship with production traits, which may be recorded at a less frequent basis

The Landscape Ecological Impact of Afforestation on the British Uplands and Some Initiatives to Restore Native Woodland Cover

The majority of forest cover in the British Uplands had been lost by the beginning of the Nineteenth Century, because of felling followed by overgrazing by sheep and deer. The situation remained unchanged until a government policy of afforestation, mainly by exotic conifers, after the First World War up to the present day. This paper analyses the distribution of these predominantly coniferous plantations, and shows how they occupy specific parts of upland landscapes in different zones throughout Britain Whilst some landscapes are dominated by these new forests, elsewhere the blocks of trees are more localised. Although these forests virtually eliminate native ground vegetation, except in rides and unplanted land, the major negative impacts are at the landscape level. For example, drainage systems are altered and ancient cultural landscape patterns are destroyed. These impacts are summarised and possible ways of amelioration are discussed. By contrast, in recent years, a series of projects have been set up to restore native forest cover, as opposed to the extensive plantations of exotic species. Accordingly, the paper then provides three examples of such initiatives designed to restore native forests to otherwise bare landscapes, as well as setting them into a policy context. Whilst such projects cover a limited proportion of the British Uplands they nevertheless restore forest to landscapes at a local level

Cervical cancers associated with human papillomavirus types 16, 18 and 45 are diagnosed in younger women than cancers associated with other types: A cross-sectional observational study in Wales and Scotland (UK)

Background: Most cervical cancers are attributable to infection with one of fourteen types of human papillomavirus (HPV), but HPV types differ in oncogenic potential. Characterisation of cancers associated with specific HPV types is required to predict the likely impact of current prophylactic vaccines and the potential benefits of vaccine formulations including additional HPV types. Objective: The study aimed to correlate HPV type with histology and age at diagnosis, in Invasive Cervical Cancers (ICCs) from two of the devolved countries of the UK (Wales and Scotland). Study design: Centralised histopathology review and rigorously standardised HPV-DNA typing were applied to 592 ICC diagnosed 2001-2006. HPV status was analysed in relation to histology and age at diagnosis. Results: HPV infection was confirmed in 535/592 cases. Among the 497 tumours infected with single HPV types, the three most common types were HPV16 (62% 95%CI: 57.6-66.1), HPV18 (18.9% 95%CI: 15.7-22.6) and HPV45 (5.4% 95%CI: 3.7-7.8). HPV16 or 18 were present in 80.9% of HPV positive cases. Women with tumours associated with HPV types 16, 18 and 45 were on average 10.5 years younger at diagnosis than women with tumours associated with other HPV types. Conclusions: Prophylactic vaccines targeting HPV16 and 18 could potentially prevent up to 80.9% of ICC in the populations investigated. Cancers associated with HPV16, 18 and 45 were diagnosed at younger ages, supporting the hypothesis of faster progression than for tumours caused by other HPV types

Cervical cancers associated with human papillomavirus types 16, 18 and 45 are diagnosed in younger women than cancers associated with other types: A cross-sectional observational study in Wales and Scotland (UK)

Background: Most cervical cancers are attributable to infection with one of fourteen types of human papillomavirus (HPV), but HPV types differ in oncogenic potential. Characterisation of cancers associated with specific HPV types is required to predict the likely impact of current prophylactic vaccines and the potential benefits of vaccine formulations including additional HPV types. Objective: The study aimed to correlate HPV type with histology and age at diagnosis, in Invasive Cervical Cancers (ICCs) from two of the devolved countries of the UK (Wales and Scotland). Study design: Centralised histopathology review and rigorously standardised HPV-DNA typing were applied to 592 ICC diagnosed 2001-2006. HPV status was analysed in relation to histology and age at diagnosis. Results: HPV infection was confirmed in 535/592 cases. Among the 497 tumours infected with single HPV types, the three most common types were HPV16 (62% 95%CI: 57.6-66.1), HPV18 (18.9% 95%CI: 15.7-22.6) and HPV45 (5.4% 95%CI: 3.7-7.8). HPV16 or 18 were present in 80.9% of HPV positive cases. Women with tumours associated with HPV types 16, 18 and 45 were on average 10.5 years younger at diagnosis than women with tumours associated with other HPV types. Conclusions: Prophylactic vaccines targeting HPV16 and 18 could potentially prevent up to 80.9% of ICC in the populations investigated. Cancers associated with HPV16, 18 and 45 were diagnosed at younger ages, supporting the hypothesis of faster progression than for tumours caused by other HPV types