Application of discrete fracture networks (DFN) in the stability analysis of Delabole Slate Quarry, Cornwall, UK

This is the author accepted manuscript. The final version is available from ARMA.50th US Rock Mechanics/Geomechanics Symposium, Houston, USA, 26-29 June 2016The failure mechanism of rock slopes is mainly controlled by the strength and orientation of discontinuities within the rock mass. A realistic representation of the joint network within the rock mass is therefore an essential component of stability analysis of rock structures (e.g. rock slopes, tunnels etc.). Discontinuity persistence and connectivity are significant parameters which control the stability of rock slopes. A small percentage of rock bridges on the discontinuity surface can significantly increase its strength and prevent slope failure. Discontinuities within the rock mass are rarely fully connected. In practice, however, discontinuities are often assumed fully persistent due to the difficulties both in mapping and simulation of non-persistence. Discrete fracture networks (DFN) provide a rigorous and convenient tool for the simulation of joint systems within a rock mass. Utilizing statistical methods, DFNs consider the stochastic nature of some key parameters (e.g. persistence and orientation) within numerical models. Discrete fracture network engineering is increasingly used due to recent developments in discontinuity data acquisition techniques (e.g. ground-based digital photogrammetry and laser scanning). Recent development in geomechanical modelling codes and increased computing power have also allowed to either import DFN’s into models or to generate DFN’s within the numerical modelling code itself (e.g. 3DEC). This paper describes the use of photogrammetry at the Delabole slate quarry in Cornwall, UK for remotely acquiring key discontinuity parameter data (orientation, intensity and length) and its subsequent use in developing statistically validated discrete fracture network parameters. The 3D distinct element code, 3DEC, is used for the DFN generation and subsequent stability analysis. Several realizations of the 3DEC-DFN models are run to investigate the stochastic nature of discontinuities within the quarry and their potential influence on the stability of the pit. Finally the simulation results are used to determine the slope instability mechanisms and determine the most likely areas of potential instability

Polygenic burden has broader impact on health, cognition, and socioeconomic outcomes than most rare and high-risk copy number variants

Copy number variants (CNVs) are associated with syndromic and severe neurological and psychiatric disorders (SNPDs), such as intellectual disability, epilepsy, schizophrenia, and bipolar disorder. Although considered high-impact, CNVs are also observed in the general population. This presents a diagnostic challenge in evaluating their clinical significance. To estimate the phenotypic differences between CNV carriers and non-carriers regarding general health and well-being, we compared the impact of SNPD-associated CNVs on health, cognition, and socioeconomic phenotypes to the impact of three genome-wide polygenic risk score (PRS) in two Finnish cohorts (FINRISK, n = 23,053 and NFBC1966, n = 4895). The focus was on CNV carriers and PRS extremes who do not have an SNPD diagnosis. We identified high-risk CNVs (DECIPHER CNVs, risk gene deletions, or large [\u3e1 Mb] CNVs) in 744 study participants (2.66%), 36 (4.8%) of whom had a diagnosed SNPD. In the remaining 708 unaffected carriers, we observed lower educational attainment (EA; OR = 0.77 [95% CI 0.66-0.89]) and lower household income (OR = 0.77 [0.66-0.89]). Income-associated CNVs also lowered household income (OR = 0.50 [0.38-0.66]), and CNVs with medical consequences lowered subjective health (OR = 0.48 [0.32-0.72]). The impact of PRSs was broader. At the lowest extreme of PRS for EA, we observed lower EA (OR = 0.31 [0.26-0.37]), lower-income (OR = 0.66 [0.57-0.77]), lower subjective health (OR = 0.72 [0.61-0.83]), and increased mortality (Cox\u27s HR = 1.55 [1.21-1.98]). PRS for intelligence had a similar impact, whereas PRS for schizophrenia did not affect these traits. We conclude that the majority of working-age individuals carrying high-risk CNVs without SNPD diagnosis have a modest impact on morbidity and mortality, as well as the limited impact on income and educational attainment, compared to individuals at the extreme end of common genetic variation. Our findings highlight that the contribution of traditional high-risk variants such as CNVs should be analyzed in a broader genetic context, rather than evaluated in isolation

The alignment of galaxy spin with the shear field in observations

Tidal torque theory suggests that galaxies gain angular momentum in the linear stage of structure formation. Such a theory predicts alignments between the spin of haloes and tidal shear field. However, non-linear evolution and angular momentum acquisition may alter this prediction significantly. In this paper, we use a reconstruction of the cosmic shear field from observed peculiar velocities combined with spin axes extracted from galaxies within $115\, \mathrm{Mpc}$ ($\sim8000 \, {\mathrm {km}}{\mathrm s}^{-1}$) from 2MRS catalog, to test whether or not galaxies appear aligned with principal axes of shear field. Although linear reconstructions of the tidal field have looked at similar issues, this is the first such study to examine galaxy alignments with velocity-shear field. Ellipticals in the 2MRS sample, show a statistically significant alignment with two of the principal axes of the shear field. In general, elliptical galaxies have their short axis aligned with the axis of greatest compression and perpendicular to the axis of slowest compression. Spiral galaxies show no signal. Such an alignment is significantly strengthened when considering only those galaxies that are used in velocity field reconstruction. When examining such a subsample, a weak alignment with the axis of greatest compression emerges for spiral galaxies as well. This result indicates that although velocity field reconstructions still rely on fairly noisy and sparse data, the underlying alignment with shear field is strong enough to be visible even when small numbers of galaxies are considered - especially if those galaxies are used as constraints in the reconstruction.Comment: 9 pages, 3 figures, accepted in MNRA

Proceedings of a Symposium: Pollution Control of Industrial Wastewaters

inclusion in Reports by an authorized administrator o

Recovering 3D structural properties of galaxies from SDSS-like photometry

Because of the 3D nature of galaxies, an algorithm for constructing spatial density distribution models of galaxies on the basis of galaxy images has many advantages over surface density distribution approximations. We present a method for deriving spatial structure and overall parameters of galaxies from images and estimate its accuracy and derived parameter degeneracies on a sample of idealised model galaxies. The test galaxies consist of a disc-like component and a spheroidal component with varying proportions and properties. Both components are assumed to be axially symmetric and coplanar. We simulate these test galaxies as if observed in the SDSS project through ugriz filters, thus gaining a set of realistically imperfect images of galaxies with known intrinsic properties. These artificial SDSS galaxies were thereafter remodelled by approximating the surface brightness distribution with a 2D projection of a bulge+disc spatial distribution model and the restored parameters were compared to the initial ones. Down to the r-band limiting magnitude 18, errors of the restored integral luminosities and colour indices remain within 0.05 mag and errors of the luminosities of individual components within 0.2 mag. Accuracy of the restored bulge-to-disc ratios (B/D) is within 40% in most cases, and becomes worse for galaxies with low B/D, but the general balance between bulges and discs is not shifted systematically. Assuming that the intrinsic disc axial ratio is < 0.3, the inclination angles can be estimated with errors < 5deg for most of the galaxies with B/D < 2 and with errors < 15deg up to B/D = 6. Errors of the recovered sizes of the galactic components are below 10% in most cases. In general, models of disc components are more accurate than models of spheroidal components for geometrical reasons.Comment: 15 pages, 13 figures, accepted for publication in RA

Antibodies to infliximab and adalimumab in patients with rheumatoid arthritis in clinical remission:a cross-sectional study

Objective. To investigate if antibodies towards biological TNF-α inhibitors (anti-TNFi Abs) are present in patients with rheumatoid arthritis (RA) in clinical remission and to relate any anti-TNFi Abs to circulating level of TNF-α inhibitor (TNFi). Methods. Patients with RA, treated with infliximab or adalimumab, and in clinical remission (DAS28(CRP) < 2.6) were included from 6 out-patient clinics. In blood samples, presence of anti-TNFi Abs was determined by radioimmunoassay, and concentration of bioactive TNFi was measured by a cell-based reporter gene assay. Results. Anti-TNFi Abs were present in 8/44 patients (18%) treated with infliximab and 1/49 patients (2%) treated with adalimumab (p=0.012). In the former group, anti-TNFi Abs corresponded with low levels of TNFi (p=0.048). Anti-TNFi Ab-positive patients had shorter disease duration at initiation of TNFi therapy (p=0.023) but were similar for the rest of the compared parameters. Conclusions. In RA patients in clinical remission, anti-TNFi Abs occur frequently in patients treated with infliximab, while they occur rarely in patients treated with adalimumab. Presence of anti-infliximab Abs is accompanied by low or undetectable levels of infliximab. These data suggest that continued infliximab treatment may be redundant in a proportion of RA patients treated with infliximab and in clinical remission

Quantifying the Impact of Rare and Ultra-rare Coding Variation across the Phenotypic Spectrum

There is a limited understanding about the impact of rare protein-truncating variants across multiple phenotypes. We explore the impact of this class of variants on 13 quantitative traits and 10 diseases using whole-exome sequencing data from 100,296 individuals. Protein-truncating variants in genes intolerant to this class of mutations increased risk of autism, schizophrenia, bipolar disorder, intellectual disability, and ADHD. In individuals without these disorders, there was an association with shorter height, lower education, increased hospitalization, and reduced age at enrollment. Gene sets implicated from GWASs did not show a significant protein-truncating variants burden beyond what was captured by established Mendelian genes. In conclusion, we provide a thorough investigation of the impact of rare deleterious coding variants on complex traits, suggesting widespread pleiotropic risk.Peer reviewe

Polygenic burden has broader impact on health, cognition, and socioeconomic outcomes than most rare and high-risk copy number variants

Copy number variants (CNVs) are associated with syndromic and severe neurological and psychiatric disorders (SNPDs), such as intellectual disability, epilepsy, schizophrenia, and bipolar disorder. Although considered high-impact, CNVs are also observed in the general population. This presents a diagnostic challenge in evaluating their clinical significance. To estimate the phenotypic differences between CNV carriers and non-carriers regarding general health and well-being, we compared the impact of SNPD-associated CNVs on health, cognition, and socioeconomic phenotypes to the impact of three genome-wide polygenic risk score (PRS) in two Finnish cohorts (FINRISK, n = 23,053 and NFBC1966, n = 4895). The focus was on CNV carriers and PRS extremes who do not have an SNPD diagnosis. We identified high-risk CNVs (DECIPHER CNVs, risk gene deletions, or large [>1 Mb] CNVs) in 744 study participants (2.66%), 36 (4.8%) of whom had a diagnosed SNPD. In the remaining 708 unaffected carriers, we observed lower educational attainment (EA; OR = 0.77 [95% CI 0.66-0.89]) and lower household income (OR = 0.77 [0.66-0.89]). Income-associated CNVs also lowered household income (OR = 0.50 [0.38-0.66]), and CNVs with medical consequences lowered subjective health (OR = 0.48 [0.32-0.72]). The impact of PRSs was broader. At the lowest extreme of PRS for EA, we observed lower EA (OR = 0.31 [0.26-0.37]), lower-income (OR = 0.66 [0.57-0.77]), lower subjective health (OR = 0.72 [0.61-0.83]), and increased mortality (Cox's HR = 1.55 [1.21-1.98]). PRS for intelligence had a similar impact, whereas PRS for schizophrenia did not affect these traits. We conclude that the majority of working-age individuals carrying high-risk CNVs without SNPD diagnosis have a modest impact on morbidity and mortality, as well as the limited impact on income and educational attainment, compared to individuals at the extreme end of common genetic variation. Our findings highlight that the contribution of traditional high-risk variants such as CNVs should be analyzed in a broader genetic context, rather than evaluated in isolation.Peer reviewe