West Antarctic ice loss influenced by internal climate variability and anthropogenic forcing

Recent ice loss from the West Antarctic Ice Sheet has been caused by ocean melting of ice shelves in the Amundsen Sea. Eastward wind anomalies at the shelf break enhance the import of warm Circumpolar Deep Water onto the Amundsen Sea continental shelf, which creates transient melting anomalies with an approximately decadal period. No anthropogenic influence on this process has been established. Here, we combine observations and climate model simulations to suggest that increased greenhouse gas forcing caused shelf-break winds to transition from mean easterlies in the 1920s to the near-zero mean zonal winds of the present day. Strong internal climate variability, primarily linked to the tropical Pacific, is superimposed on this forced trend. We infer that the Amundsen Sea experienced decadal ocean ariability throughout the twentieth century, with warm anomalies gradually becoming more prevalent, offering a credible explanation for the ongoing ice loss. Existing climate model projections show that strong future greenhouse gas forcing creates persistent mean westerly shelf-break winds by 2100, suggesting a further enhancement of warm ocean anomalies. These wind changes are weaker under a scenario in which greenhouse gas concentrations are stabilized

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

The 6dF Galaxy Survey: peculiar velocity field and cosmography

We derive peculiar velocities for the 6dF Galaxy Survey (6dFGS) and describe the velocity field of the nearby ($z<0.055$) southern hemisphere. The survey comprises 8885 galaxies for which we have previously reported Fundamental Plane data. We obtain peculiar velocity probability distributions for the redshift space positions of each of these galaxies using a Bayesian approach. Accounting for selection bias, we find that the logarithmic distance uncertainty is 0.11 dex, corresponding to $26\%$ in linear distance. We use adaptive kernel smoothing to map the observed 6dFGS velocity field out to $cz \sim 16,000$ \kms, and compare this to the predicted velocity fields from the PSCz Survey and the 2MASS Redshift Survey. We find a better fit to the PSCz prediction, although the reduced $\chi^2$ for the whole sample is approximately unity for both comparisons. This means that, within the observational uncertainties due to redshift independent distance errors, observed galaxy velocities and those predicted by the linear approximation from the density field agree. However, we find peculiar velocities that are systematically more positive than model predictions in the direction of the Shapley and Vela superclusters, and systematically more negative than model predictions in the direction of the Pisces-Cetus Supercluster, suggesting contributions from volumes not covered by the models.Comment: 22 pages, 14 figures, accepted for publication in MNRAS. Table 1 is available in its entirety as an ancillary file. Fully interactive 3D versions of Figures 11 and 12 are also available as ancillary files. A version of this paper with the 3D versions of Figs. 11 and 12 embedded within the pdf can also be accessed from http://www.6dfgs.net/vfield/veldata.pd

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1

Abdominal aortic aneurysm (AAA) is a common cause of morbidity and mortality and has a significant heritability. We carried out a genome-wide association discovery study of 1866 patients with AAA and 5435 controls and replication of promising signals (lead SNP with a p value &lt; 1 × 10-5) in 2871 additional cases and 32,687 controls and performed further follow-up in 1491 AAA and 11,060 controls. In the discovery study, nine loci demonstrated association with AAA (p &lt; 1 × 10-5). In the replication sample, the lead SNP at one of these loci, rs1466535, located within intron 1 of low-density-lipoprotein receptor-related protein 1 (LRP1) demonstrated significant association (p = 0.0042). We confirmed the association of rs1466535 and AAA in our follow-up study (p = 0.035). In a combined analysis (6228 AAA and 49182 controls), rs1466535 had a consistent effect size and direction in all sample sets (combined p = 4.52 × 10-10, odds ratio 1.15 [1.10-1.21]). No associations were seen for either rs1466535 or the 12q13.3 locus in independent association studies of coronary artery disease, blood pressure, diabetes, or hyperlipidaemia, suggesting that this locus is specific to AAA. Gene-expression studies demonstrated a trend toward increased LRP1 expression for the rs1466535 CC genotype in arterial tissues; there was a significant (p = 0.029) 1.19-fold (1.04-1.36) increase in LRP1 expression in CC homozygotes compared to TT homozygotes in aortic adventitia. Functional studies demonstrated that rs1466535 might alter a SREBP-1 binding site and influence enhancer activity at the locus. In conclusion, this study has identified a biologically plausible genetic variant associated specifically with AAA, and we suggest that this variant has a possible functional role in LRP1 expression

Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.

OBJECTIVE: Proinsulin is a precursor of mature insulin and C-peptide. Higher circulating proinsulin levels are associated with impaired β-cell function, raised glucose levels, insulin resistance, and type 2 diabetes (T2D). Studies of the insulin processing pathway could provide new insights about T2D pathophysiology. RESEARCH DESIGN AND METHODS: We have conducted a meta-analysis of genome-wide association tests of ∼2.5 million genotyped or imputed single nucleotide polymorphisms (SNPs) and fasting proinsulin levels in 10,701 nondiabetic adults of European ancestry, with follow-up of 23 loci in up to 16,378 individuals, using additive genetic models adjusted for age, sex, fasting insulin, and study-specific covariates. RESULTS: Nine SNPs at eight loci were associated with proinsulin levels (P < 5 × 10(-8)). Two loci (LARP6 and SGSM2) have not been previously related to metabolic traits, one (MADD) has been associated with fasting glucose, one (PCSK1) has been implicated in obesity, and four (TCF7L2, SLC30A8, VPS13C/C2CD4A/B, and ARAP1, formerly CENTD2) increase T2D risk. The proinsulin-raising allele of ARAP1 was associated with a lower fasting glucose (P = 1.7 × 10(-4)), improved β-cell function (P = 1.1 × 10(-5)), and lower risk of T2D (odds ratio 0.88; P = 7.8 × 10(-6)). Notably, PCSK1 encodes the protein prohormone convertase 1/3, the first enzyme in the insulin processing pathway. A genotype score composed of the nine proinsulin-raising alleles was not associated with coronary disease in two large case-control datasets. CONCLUSIONS: We have identified nine genetic variants associated with fasting proinsulin. Our findings illuminate the biology underlying glucose homeostasis and T2D development in humans and argue against a direct role of proinsulin in coronary artery disease pathogenesis

Semantic labelling to aid navigation in prosthetic vision

Current and near-term implantable prosthetic vision systems offer the potential to restore some visual function, but suffer from limited resolution and dynamic range of induced visual percepts. This can make navigating complex environments difficult for users. Using semantic labelling techniques, we demonstrate that a computer system can aid in obstacle avoidance, and localizing distant objects. Our system automatically classifies each pixel in a natural image into a semantic class, then produces an image from the induced visual percepts that highlights certain classes. This technique allows the user to clearly perceive the location of different types of objects in their field of view, and can be adapted for a range of navigation tasks

Dietary niche differentiation of five sympatric species of Platycephalidae

The dietary composition and partitioning of food resources between five sympatric species of Platycephalidae inhabiting the coastal waters of New South Wales, Australia was investigated. Samples were collected monthly between March and November 2007 onboard commercial ocean prawn trawlers based in the ports of Yamba and Newcastle. Monthly percentage weight contribution of 12 prey categories was analysed to determine if diet was influenced by the variables: species, location, depth, size and maturity. Of the 959 stomachs from the five species examined, 28–54% contained prey. All Platycephalid species primarily consumed teleosts, however the diversity of prey and the proportion each prey type contributed to the overall diet varied substantially between species. Platycephalus caeruleopunctatus, P. longispinis, P. richardsoni and Ambiserrula jugosa were generalist carnivores and consumed prey from a wide variety of phyla including teleosts, crustaceans, polychaetes, molluscs and echinoderms. In contrast, Ratabulus diversidens were primarily piscivorous. Partitioning of prey resources between species was more evident in waters at Yamba than at Newcastle. Differences in diet between locations were considered a result of differential prey exploitation rather than shifts in the suite of prey consumed. Dietary composition was observed to be influenced by size, maturity status and depth however these differences were not observed for all species.13 page(s

Utility and efficiency of multi-mesh gill nets and trammel nets for sampling assemblages and populations of estuarine fish

Two replicate multi-mesh gill and trammel nets, each comprising five 30 m long panels made from different-sized mesh (38, 54, 70, 90 and 100 mm stretched mesh openings) were fished in a south-east Australian barrier estuary over seven nights to evaluate their potential as sampling gears for fishery-independent surveys of estuarine fish assemblages. There were no differences in composition and structure of assemblages, mean abundance, or diversity of catches between the two types of net. The composition and structure of catches differed between mesh sizes, with the panels made from 38 and 54 mm mesh retaining significantly more fish and species than the larger-sized meshes. The two smallest mesh sizes were important for capturing sub-adults and juveniles of some species. Based on a greater precision of catch per unit effort (CPUE) estimates, less sampling effort and greater ease of use, the multi-mesh gill net was a better sampling unit than the trammel net for assessments of estuarine fish populations

Sampling estuarine fish using multi-mesh gill nets: Effects of panel length and soak and setting times

Experiments on the effects of soak (1, 3 and 6 h) and setting times (18:00, 22:00 and 3:00 h), and panel length (20, 50, 120 m) on catches of fish in multi-mesh (38, 54 and 89 mm) gill nets were done in a south-east Australian estuary to develop an optimal, representative and standardized sampling methodology for future fishery-independent surveys of estuarine icthyofauna. Univariate analysis revealed that while the longest soak times and panels often caught significantly more numbers and species of fish, there were no differences between short and intermediate soak times. Further, where differences between soak time and panel length treatments were detected, fish were often being caught in the same relative proportions. Standardized catch-per-unit-of-effort (CPUE) (numbers of fish caught 20 m of net h) decreased significantly with increasing soak time, but there were no differences in CPUE between different panel lengths for the total numbers of fish and key species caught. Multivariate analyses failed to detect any differences in fish assemblages between soak times and panel lengths for 38 and 89 mm mesh. However, inconsistent and species-specific differences in the abundances of common species accounted for differences in assemblage structure for the 54 mm mesh. Similarly, while the size ranges of most species of economic importance were comparable between different panel lengths and soak times, there were inconsistent differences in the proportions of fish captured across size classes for some species. Setting time had no effect on the mean numbers of fish or species caught, structure of assemblages or size-ranges of most species investigated. Based on these results, the use of 20-m panels soaked for 1 h at any time during the night was considered optimal for future surveys. The benefits of this uniform sampling methodology are discussed in terms of increased replication, reduced costs and the potential for lower fish mortality