Use of seasonal trend decomposition to understand groundwater behaviour in the Permo-Triassic Sandstone aquifer, Eden Valley, UK

The daily groundwater level (GWL) response in the Permo-Triassic Sandstone aquifers in the Eden Valley, England (UK), has been studied using the seasonal trend decomposition by LOESS (STL) technique. The hydrographs from 18 boreholes in the Permo-Triassic Sandstone were decomposed into three components: seasonality, general trend and remainder. The decomposition was analysed first visually, then using tools involving a variance ratio, time-series hierarchical clustering and correlation analysis. Differences and similarities in decomposition pattern were explained using the physical and hydrogeological information associated with each borehole. The Penrith Sandstone exhibits vertical and horizontal heterogeneity, whereas the more homogeneous St Bees Sandstone groundwater hydrographs characterize a well-identified seasonality; however, exceptions can be identified. A stronger trend component is obtained in the silicified parts of the northern Penrith Sandstone, while the southern Penrith, containing Brockram (breccias) Formation, shows a greater relative variability of the seasonal component. Other boreholes drilled as shallow/deep pairs show differences in responses, revealing the potential vertical heterogeneities within the Penrith Sandstone. The differences in bedrock characteristics between and within the Penrith and St Bees Sandstone formations appear to influence the GWL response. The de-seasonalized and de-trended GWL time series were then used to characterize the response, for example in terms of memory effect (autocorrelation analysis). By applying the STL method, it is possible to analyse GWL hydrographs leading to better conceptual understanding of the groundwater flow. Thus, variation in groundwater response can be used to gain insight into the aquifer physical properties and understand differences in groundwater behaviour

3D geological models and their hydrogeological applications : supporting urban development : a case study in Glasgow-Clyde, UK

Urban planners and developers in some parts of the United Kingdom can now access geodata in an easy-to-retrieve and understandable format. 3D attributed geological framework models and associated GIS outputs, developed by the British Geological Survey (BGS), provide a predictive tool for planning site investigations for some of the UK's largest regeneration projects in the Thames and Clyde River catchments. Using the 3D models, planners can get a 3D preview of properties of the subsurface using virtual cross-section and borehole tools in visualisation software, allowing critical decisions to be made before any expensive site investigation takes place, and potentially saving time and money. 3D models can integrate artificial and superficial deposits and bedrock geology, and can be used for recognition of major resources (such as water, thermal and sand and gravel), for example in buried valleys, groundwater modelling and assessing impacts of underground mining. A preliminary groundwater recharge and flow model for a pilot area in Glasgow has been developed using the 3D geological models as a framework. This paper focuses on the River Clyde and the Glasgow conurbation, and the BGS's Clyde Urban Super-Project (CUSP) in particular, which supports major regeneration projects in and around the City of Glasgow in the West of Scotland

Metamodel-assisted analysis of an integrated model composition: an example using linked surface water-groundwater models

Integrated modelling is a promising approach to simulate processes operating within complex environmental systems. It is possible, however, that this integration may lead to computationally expensive compositions. In order to retain the process fidelity without loss of accuracy, the use of Kriging metamodels is proposed to perform Monte Carlo simulation and sensitivity analysis, in lieu of compositions developed using the model linking standard OpenMI. Results from the Monte Carlo simulation showed that the metamodels were in a good agreement with the original responses. However, metamodels provided a less accurate approximation of the original output distribution for the composition which involved a stronger non-linear behaviour. The fast runtimes of the metamodels allowed for increased computational budgets leading to an accurate screening of the important parameters for an Elementary Effects Test. Overall, Kriging metamodels provided significant computational savings without compromising the quality of the outcomes, even using small training data sets

Unveiling Dust-enshrouded Star Formation in the Early Universe: a Sub-mm Survey of the Hubble Deep Field

The advent of sensitive sub-mm array cameras now allows a proper census of dust-enshrouded massive star-formation in very distant galaxies, previously hidden activity to which even the faintest optical images are insensitive. We present the deepest sub-mm survey of the sky to date, taken with the SCUBA camera on the James Clerk Maxwell Telescope and centred on the Hubble Deep Field. The high source density found in this image implies that the survey is confusion-limited below a flux density of 2 mJy. However, within the central 80 arcsec radius independent analyses yield 5 reproducible sources with S(850um) > 2 mJy which simulations indicate can be ascribed to individual galaxies. We give positions and flux densities for these, and furthermore show using multi-frequency photometric data that the brightest sources in our map lie at redshifts z~3. These results lead to integral source counts which are completely inconsistent with a no-evolution model, and imply that massive star-formation activity continues at redshifts > 2. The combined brightness of the 5 most secure sources in our map is sufficient to account for 30 - 50% of the previously unresolved sub-mm background, and we estimate statistically that the entire background is resolved at about the 0.3 mJy level. Finally we discuss possible optical identifications and redshift estimates for the brightest sources. One source appears to be associated with an extreme starburst galaxy at z~1, whilst the remaining four appear to lie in the redshift range 2 < z < 4. This implies a star-formation density over this redshift range that is at least five times higher than that inferred from the ultraviolet output of HDF galaxies.Comment: 19 pages, 6 figures (to appear as a Nature Article

A Submillimetre Survey of the Hubble Deep Field: Unveiling Dust-Enshrouded Star Formation in the Early Universe

The advent of sensitive sub-mm array cameras now allows a proper census of dust-enshrouded massive star-formation in very distant galaxies, previously hidden activity to which even the deepest optical images are insensitive. We present the deepest sub-mm survey, taken with the SCUBA camera on the James Clerk Maxwell Telescope (JCMT) and centred on the Hubble Deep Field (HDF). The high source density on this image implies that the survey is confusion-limited below a flux density of 2 mJy. However within the central 80 arcsec radius independent analyses yield 5 reproducible sources with S(850um) > 2 mJy which simulations indicate can be ascribed to individual galaxies. These data lead to integral source counts which are completely inconsistent with a no evolution model, whilst the combined brightness of the 5 most secure sources in our map is sufficient to account for 30-50% of the previously unresolved sub-mm background, and statistically the entire background is resolved at about the 0.3 mJy level. Four of the five brightest sources appear to be associated with galaxies which lie in the redshift range 2 < z < 4. With the caveat that this is a small sample of sources detected in a small survey area, these submm data imply a star-formation density over this redshift range that is at least five times higher than that inferred from the rest-frame ultraviolet output of HDF galaxies.Comment: to appear in the proceedings of `The Birth of Galaxies', Xth Rencontres de Blois, 4 pages, 1 postscript figure, uses blois.sty (included

Effect of body composition methodology on heritability estimation of body fatness

Heritability estimates of human body fatness vary widely and the contribution of body composition methodology to this variability is unknown. The effect of body composition methodology on estimations of genetic and environmental contributions to body fatness variation was examined in 78 adult male and female monozygotic twin pairs reared apart or together. Body composition was assessed by six methods - body mass index (BMI), dual energy x-ray absorptiometry (DXA), underwater weighing (UWW), total body water (TBW), bioelectric impedance (BIA), and skinfold thickness. Body fatness was expressed as percent body fat, fat mass, and fat mass/height2 to assess the effect of body fatness expression on heritability estimates. Model-fitting multivariate analyses were used to assess the genetic and environmental components of variance. Mean BMI was 24.5 kg/m2 (range of 17.8-43.4 kg/m2). There was a significant effect of body composition methodology (p<0.001) on heritability estimates, with UWW giving the highest estimate (69%) and BIA giving the lowest estimate (47%) for fat mass/height2. Expression of body fatness as percent body fat resulted in significantly higher heritability estimates (on average 10.3% higher) compared to expression as fat mass/height2 (p=0.015). DXA and TBW methods expressing body fatness as fat mass/height2 gave the least biased heritability assessments, based on the small contribution of specific genetic factors to their genetic variance. A model combining DXA and TBW methods resulted in a relatively low FM/ht2 heritability estimate of 60%, and significant contributions of common and unique environmental factors (22% and 18%, respectively). The body fatness heritability estimate of 60% indicates a smaller contribution of genetic variance to total variance than many previous studies using less powerful research designs have indicated. The results also highlight the importance of environmental factors and possibly genotype by environmental interactions in the etiology of weight gain and the obesity epidemic.R01 AR046124 - NIAMS NIH HHS; R01 MH065322 - NIMH NIH HHS; T32 HL069772 - NHLBI NIH HHS; R21 DK078867 - NIDDK NIH HHS; R37 DA018673 - NIDA NIH HHS; R01 DK076092 - NIDDK NIH HHS; R01 DK079003 - NIDDK NIH HHS; F32 DK009747 - NIDDK NIH HHS; R01 DA018673 - NIDA NIH HH

The spatial effect of protein deuteration on nitroxide spin-label relaxation:implications for EPR distance measurement

This work was supported by a Wellcome Trust Senior Fellowship (095062) to T.O.-H. The Authors would also like to acknowledge funding from The MRC – United Kingdom, Grant G1100021.Pulsed electron-electron double resonance (PELDOR) coupled with site-directed spin labeling is a powerful technique for the elucidation of protein or nucleic acid, macromolecular structure and interactions. The intrinsic high sensitivity of electron paramagnetic resonance enables measurement on small quantities of bio-macromolecules, however short relaxation times impose a limit on the sensitivity and size of distances that can be measured using this technique. The persistence of the electron spin-echo, in the PELDOR experiment, is one of the most crucial limitations to distance measurement. At a temperature of around 50 K one of the predominant factors affecting persistence of an echo, and as such, the sensitivity and measurable distance between spin labels, is the electron spin echo dephasing time (Tm). It has become normal practice to use deuterated solvents to extend Tm and recently it has been demonstrated that deuteration of the underlying protein significantly extends Tm. Here we examine the spatial effect of segmental deuteration of the underlying protein, and also explore the concentration and temperature dependence of highly deuterated systems.Publisher PDFPeer reviewe

Massively parallel cis-regulatory analysis in the mammalian central nervous system

Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies in functionally interpreting these data. To address this issue, massively parallel reporter assays (MPRAs) have emerged, in which barcoded reporter libraries are introduced into cells, and the resulting barcoded transcripts are quantified by next-generation sequencing. Thus far, MPRAs have been largely restricted to assaying short CREs in a limited repertoire of cultured cell types. Here, we present two advances that extend the biological relevance and applicability of MPRAs. First, we adapt exome capture technology to instead capture candidate CREs, thereby tiling across the targeted regions and markedly increasing the length of CREs that can be readily assayed. Second, we package the library into adeno-associated virus (AAV), thereby allowing delivery to target organs in vivo. As a proof of concept, we introduce a capture library of about 46,000 constructs, corresponding to roughly 3500 DNase I hypersensitive (DHS) sites, into the mouse retina by ex vivo plasmid electroporation and into the mouse cerebral cortex by in vivo AAV injection. We demonstrate tissue-specific cis-regulatory activity of DHSs and provide examples of high-resolution truncation mutation analysis for multiplex parsing of CREs. Our approach should enable massively parallel functional analysis of a wide range of CREs in any organ or species that can be infected by AAV, such as nonhuman primates and human stem cell-derived organoids

Mapping and simplifying construction project delivery

The nature of project complexity within construction engineering projects has been the subject of study with growing interest, especially since the Engineering and Physical Sciences Research Council (EPSRC) Networks- Engineering and Physical Sciences Research Council was set-up in 2003. Yet, it could be argued in research terms, that project complexity has been neglected both in terms of conceptualising it and in terms of empirical study. Given the supposed severity of project complexity and the obvious failings of the industry’s approach towards project delivery, it is reasonable to assume that such an issue would provide a focus for research to improve practice. The main issues appraised are structural complexity, uncertainty, organisational complexity and technological complexity. As established from the reviewed literature, one of the hindrances to project performance within the construction industry is project complexity, which mainly emerges during the construction and design process

The draft genome and transcriptome of Cannabis sativa

Background: Cannabis sativa has been cultivated throughout human history as a source of fiber, oil and food, and for its medicinal and intoxicating properties. Selective breeding has produced cannabis plants for specific uses, including high-potency marijuana strains and hemp cultivars for fiber and seed production. The molecular biology underlying cannabinoid biosynthesis and other traits of interest is largely unexplored. Results: We sequenced genomic DNA and RNA from the marijuana strain Purple Kush using shortread approaches. We report a draft haploid genome sequence of 534 Mb and a transcriptome of 30,000 genes. Comparison of the transcriptome of Purple Kush with that of the hemp cultivar 'Finola' revealed that many genes encoding proteins involved in cannabinoid and precursor pathways are more highly expressed in Purple Kush than in 'Finola'. The exclusive occurrence of \u3949-tetrahydrocannabinolic acid synthase in the Purple Kush transcriptome, and its replacement by cannabidiolic acid synthase in 'Finola', may explain why the psychoactive cannabinoid \u3949-tetrahydrocannabinol (THC) is produced in marijuana but not in hemp. Resequencing the hemp cultivars 'Finola' and 'USO-31' showed little difference in gene copy numbers of cannabinoid pathway enzymes. However, single nucleotide variant analysis uncovered a relatively high level of variation among four cannabis types, and supported a separation of marijuana and hemp. Conclusions: The availability of the Cannabis sativa genome enables the study of a multifunctional plant that occupies a unique role in human culture. Its availability will aid the development of therapeutic marijuana strains with tailored cannabinoid profiles and provide a basis for the breeding of hemp with improved agronomic characteristics.Peer reviewed: YesNRC publication: Ye