Model metadata report for the GSI3D model of the superficial geology of the ground seaward of the Drigg Low Level Waste Repository Site, West Cumbria

This report describes the GSI3D model of the superficial geology of the ground seaward of the Drigg Low Level Waste Repository site, West Cumbria. This geological model is based on the GSI3D geophysical model described in IR/12/071: Callaghan, E, Kearsey, T, Finlayson, A and Auton, C.A. 2012. Model metadata repport for the GSI3D model of shallow geophysical surveys of the ground seaward of the Drigg Low Level Waste Repository Site, West Cumbria. British Geological Survey Internal Report, IR/12/071. 16pp. The geophysical model was built to show resistivity characteristics of Quaternary sequences overlying sandstone bedrock and was commissioned by the National Nuclear Laboratory (NNL) for Low Level Waste Repository Ltd (LLWR) and is Commercial in Confidence. The superficial geological model is not Commercial in Confidence

Relating in situ hydraulic conductivity, particle size and relative density of superficial deposits in a heterogeneous catchment

Estimating the permeability of superficial deposits is fundamental to many aspects of catchment science, but can be problematic where insufficient in situ measurements are available from pumping tests in piezometers. Consequently, common practice is to estimate permeability from the material description or, where available, particlesize distribution using a formula such as Hazen. In this study, we examine the relationships between particlesize, relativedensity and hydraulicconductivity in superficial deposits in Morayshire, Northern Scotland: a heterogeneous environment typical of many catchments subject to previous glaciations. The superficial deposits comprise glaciofluvial sands and gravels, glacial tills and moraines, raised marine sediments, and blown sands. Thirty-eight sites were investigated: hydraulicconductivity measurements were made using repeated Guelph permeameter measurements, cone resistance was measured in situ with a Panda dynamic cone penetrometer; material descriptions were made in accordance with BS5930:1999; and disturbed samples were taken for particlesize analysis. Overall hydraulicconductivity (K) varied from 0.001 m/d to >40 m/d; glacial till had the lowest K (median 0.027 m/d) and glacial moraine the highest K (median 30 m/d). However, within each geological unit there was great variability in measured hydraulicconductivity values. Multiple linear regression of the data indicated that log d10 and relativedensity (indicated by cone resistance or BS5930:1999 soil state description) were independent predictors of log K and together gave a relationship with an R2 of 0.80. Material description using the largest fraction (e.g. sand or gravel) had little predictive power. Therefore, in heterogeneous catchments, the permeability of superficial deposits is most strongly related to the finest fraction (d10) and relativedensity of the material. In situ Guelph permeameter measurements at outcrops with good geological characterisation provide an easy and reliable method of determining the permeability of particular units of superficial deposits

Physical properties and micromorphology of till deposits from Talla Earth Observatory, Southern Uplands, Scotland

This factual report describes the 2007 field program at BGS’ Talla Earth Observatory, in the Scottish Southern Uplands, UK. The work involved 12 trial pits with logging of pit walls, soil sampling for particle size analysis and undisturbed sampling for thin sections and micromorphological analysis of a till and a hard pan in moranic deposits. The tills of the Langholm Till Formation (of McMillan & Merritt, 2012) are technically ‘coarse soils’ from a BS5930:1999 ground engineering perspective; typically very dense/hard, very wellgraded silty sandy gravels with a matrix dominated by silt and sand. In thin section the till sandmatrix-supported gravel clasts show a preferred alignment orientated suggesting a micro-fabric indicative of a subglacially deposited till. Clast lithology includes sandstone, siltstone and mudstone, and are consistent with the local bedrock lithology. Cobbles and boulders are often ‘very strong’ from a geotechnical perspective, but may have weaker ‘rotten’ crust in valley floor settings. The work provides new data on the geotechnical properties of Scottish tills and enhances our understanding of the physical and hydrological properties of commonly encountered Quaternary deposits that occur in the Talla Burn and nearby upland catchments

The relationship of soil and woodland cover on soil hydraulic conductivity at a hillslope scale and local flood management in the Scottish Borders

An important criteria in Natural Flood Management (NFM) is understanding and improving the surface soil permeability (or field, saturated hydraulic conductivity, Kfs; Talsma, 1987) of natural ground surfaces with the view of increasing rainfall infiltration and storage capacity (Marshall et al., 2009). At the local scale infiltrability and soil hydraulic conductivity (Ks) are key soil properties as they activate surface and near-surface flow paths that influence runoff generation (Elsenbeer, 2001; Bonell et al., 2010)

Groundwater, flooding and hydrological functioning in the Findhorn floodplain, Scotland

A large floodplain of the River Findhorn, northeast Scotland, was investigated using hydrogeological and hydrochemical methods (including residence time indicators) to characterise groundwater/surface-water coupling and groundwater flooding. The study demonstrated widespread stratification within the floodplain: shallow (30 mm). Persistent groundwater flooding occurs within topographical lows and also in the discharge zone where it is largely managed with a series of drains constructed in the 19th century. The significant and complex role of groundwater in floodplains, demonstrated by this study, highlights the importance of fully considering groundwater in flood management schemes

Genome-wide association study identifies nine novel loci for 2D:4D finger ratio, a putative retrospective biomarker of testosterone exposure in utero

The ratio of the length of the index finger to that of the ring finger (2D:4D) is sexually dimorphic and is commonly used as a non-invasive biomarker of prenatal androgen exposure. Most association studies of 2D:4D ratio with a diverse range of sexspecific traits have typically involved small sample sizes and have been difficult to replicate, raising questions around the utility and precise meaning of the measure. In the largest genome-wide association meta-analysis of 2D:4D ratio to date (N=15 661, with replication N=75 821), we identified 11 loci (9 novel) explaining 3.8% of the variance in mean 2D:4D ratio. We also found weak evidence for association (b=0.06; P=0.02) between 2D:4D ratio and sensitivity to testosterone [length of the CAG microsatellite repeat in the androgen receptor (AR) gene] in females only. Furthermore, genetic variants associated with (adult) testosterone levels and/or sex hormone-binding globulin were not associated with 2D:4D ratio in our sample. Although we were unable to find strong evidence from our genetic study to support the hypothesis that 2D:4D ratio is a direct biomarker of prenatal exposure to androgens in healthy individuals, our findings do not explicitly exclude this possibility, and pathways involving testosterone may become apparent as the size of the discovery sample increases further. Our findings provide new insight into the underlying biology shaping 2D:4D variation in the general population

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

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

The Quaternary geology of the Solway

This report describes results of a resurvey of the Quaternary landforms and deposits in the cross-border area of eastern Dumfries and Galloway and northern Cumbria, around the inner Solway Firth. The work was carried out under the BGS Geology and Landscape (Scotland) programme and predecessor programmes, by a multidisciplinary team of geologists and Quaternary specialists. The Solway Project was initiated in 1998 to resurvey the Quaternary geology of the Solway lowlands. Field Survey was undertaken between 1998 and 2000, and two special 1:50 000 sheets (Solway West and Solway East) depicting superficial deposits and simplified bedrock were published in 2005 and 2006 respectively. Prior to this survey, published Geological Survey maps of the district were based on surveys carried out in the 1880s (Dumfriesshire) and the 1920s (Cumbria), when understanding of both the Quaternary and bedrock geology was limited. It was acknowledged by the BGS that there was a requirement for up-to-date geological data for a range of applications