The Glasgow (Scotland) geotechnical GIS: a desk study tool

Desk study is an essential part of all civil engineering project ground investigations. It is usually a collation and review of existing data and information about a site and, in some cases, the surrounding area, and carried out at an early stage of the ground investigation to inform and guide the ground investigation. It should provide suitable data and information to assess the ground conditions and the implications for the proposed engineering design. A similar approach can be taken to inform local, regional or national government with regard to development and the redevelopment of urban areas where ground investigation data and information are available. This paper describes a spatially defined geotechnical information system (GIS) designed to provide geological, geotechnical and geoenvironmental data and information for Glasgow City Council (Scotland). The system contains three main parts: the geology (bedrock, Quaternary and artificial deposits and the thickness and depth of these deposits); the data are presented as various summary graphs illustrating the variation of various parameters as well as a geotechnical and geoenvironmental database; and tools specifically developed to present the data. As undermining is a hazard in part of Glasgow, a dataset showing the distribution of mining is included. Further interpretation of the characteristics of the geological units has produced an engineering geological classification which may be used to provide rapid assessment of the engineering geological conditions

The Critical Importance of Rhodoliths in the Life Cycle Completion of Both Macro- and Microalgae, and as Holobionts for the Establishment and Maintenance of Marine Biodiversity

Rhodoliths are the main hard substrata for the attachment of benthic macroalgae in the NW Gulf of Mexico rubble habitats that are associated with salt domes, unique deep bank habitats at ~50–90 m depth on the continental shelf offshore Louisiana and Texas. With the advent of additional sequencing technologies, methodologies for biodiversity assessments are now rapidly shifting to DNA metabarcoding, i.e., High Throughput Sequencing (HTS) of environmental DNA mixtures with standardized molecular markers, such as 16S V4, for rapid, cost-effective biodiversity measurement. We newly tested 16S V4 metabarcoding on endolithic portions of mesophtic rhodoliths exhibiting low phototroph colonization that revealed a hidden, cryptic algal diversity targeting spores, propagules, and unsuspected life history stages. We explored cryo-SEM as a potentially more informative method than regular SEM to minimize artifacts of sample preparation in the study of endolithic cell inclusions which brought to light a suite of microalgal stages. We were able to differentiate floridean starch from cellular inclusions. We associated the effect of anatomical growth pattern on presence or absence of cellular inclusions in biogenic rhodoliths. Analyses of combined 16S V4 metabarcodes and 16S Sanger sequences of two red algal orders, the Halymeniales and Bonnemaisoniales, increased the established record of diversity in the region. We view rhodoliths as marine biodiversity hotspots that may function as seedbanks, temporary reservoirs for life history stages of ecologically important eukaryotic microalgae, and macroalgae or as refugia for ecosystem resilience following environmental stress

What can the Gulf of Mexico and Panama tell us about education and outreach?

ABSTRACT: A series of research grants funded by the National Science Foundation involved a major component about education and outreach as it pertained to marine algal diversity. These included comprehensive studies into 1) the diversity of the deep bank marine algae in the Gulf of Mexico (NSF Biodiversity Surveys and Inventories program) and the discovery of unsuspected eukaryotic life inhabiting rhodolith forming coralline algae (NSF DEB), 2) monographic research (NSF PEET), 3) advanced tropical phycology with the integration of modern and traditional techniques in the study of tropical algae of Panama (NSF PASI), among others.info:eu-repo/semantics/publishedVersio

The contribution of geology and groundwater studies to city-scale ground source heat network strategies: a case study from Cardiff, Wales, UK

The development of integrated heat network strategies involving exploitation of the shallow subsurface requires knowledge of ground conditions at the feasibility stage, and throughout the life of the system. We describe an approach to the assessment of ground constraints and energy opportunities in data-rich urban areas. Geological and hydrogeological investigations have formed a core component of the strategy development for sustainable thermal use of the subsurface in Cardiff, UK. We present findings from a 12 month project titled ‘Ground Heat Network at a City Scale’, which was co-funded by NERC/BGS and the UK Government through the InnovateUK Energy Catalyst grant in 2015-16. The project examined the technical feasibility of extracting low grade waste heat from a shallow gravel aquifer using a cluster of open loop ground source heat pumps. Heat demand mapping was carried out separately. The ground condition assessment approach involved the following steps: (1) city-wide baseline groundwater temperature mapping in 2014 with seasonal monitoring for at least 12 months prior to heat pump installation (Patton et al 2015); (2) desk top and field-based investigation of the aquifer system to determine groundwater levels, likely flow directions, sustainable pumping yields, water chemistry, and boundary conditions; (3) creation of a 3D geological framework model with physical property testing and model attribution; (4) use steps 1-3 to develop conceptual ground models and production of maps and GIS data layers to support scenario planning, and initial heat network concept designs; (5) heat flow modelling in FEFLOW software to analyse sustainability and predict potential thermal breakthrough in higher risk areas; (6) installation of a shallow open loop GSHP research observatory with real-time monitoring of groundwater bodies to provide data for heat flow model validation and feedback for system control. In conclusion, early ground condition modelling and subsurface monitoring have provided an initial indication of ground constraints and opportunities supporting development of aquifer thermal energy systems in Cardiff. Ground models should consider the past and future anthropogenic processes that influence and modify the condition of the ground. These include heat losses from buildings, modification of the groundwater regime by artificial pumping, sewers, and other GSH schemes, and construction hazards such as buried infrastructure, old foundations, land contamination and un-exploded ordnance. This knowledge base forms the foundation for a ‘whole life’ approach for sustainable thermal use of the subsurface. Benefits of the approach include; timely and easy to understand information for land use and financial resource planning, reduced financial risk for developers and investors, clear evidence to help improve public perception of GSHP technology, and provision of independent environmental data to satisfy the needs of the regulator

Mapping HIV-1 Vaccine Induced T-Cell Responses: Bias towards Less-Conserved Regions and Potential Impact on Vaccine Efficacy in the Step Study

T cell directed HIV vaccines are based upon the induction of CD8+ T cell memory responses that would be effective in inhibiting infection and subsequent replication of an infecting HIV-1 strain, a process that requires a match or near-match between the epitope induced by vaccination and the infecting viral strain. We compared the frequency and specificity of the CTL epitope responses elicited by the replication-defective Ad5 gag/pol/nef vaccine used in the Step trial with the likelihood of encountering those epitopes among recently sequenced Clade B isolates of HIV-1. Among vaccinees with detectable 15-mer peptide pool ELISpot responses, there was a median of four (one Gag, one Nef and two Pol) CD8 epitopes per vaccinee detected by 9-mer peptide ELISpot assay. Importantly, frequency analysis of the mapped epitopes indicated that there was a significant skewing of the T cell response; variable epitopes were detected more frequently than would be expected from an unbiased sampling of the vaccine sequences. Correspondingly, the most highly conserved epitopes in Gag, Pol, and Nef (defined by presence in >80% of sequences currently in the Los Alamos database www.hiv.lanl.gov) were detected at a lower frequency than unbiased sampling, similar to the frequency reported for responses to natural infection, suggesting potential epitope masking of these responses. This may be a generic mechanism used by the virus in both contexts to escape effective T cell immune surveillance. The disappointing results of the Step trial raise the bar for future HIV vaccine candidates. This report highlights the bias towards less-conserved epitopes present in the same vaccine used in the Step trial. Development of vaccine strategies that can elicit a greater breadth of responses, and towards conserved regions of the genome in particular, are critical requirements for effective T-cell based vaccines against HIV-1

Creation of an Open-Access, Mutation-Defined Fibroblast Resource for Neurological Disease Research

Our understanding of the molecular mechanisms of many neurological disorders has been greatly enhanced by the discovery of mutations in genes linked to familial forms of these diseases. These have facilitated the generation of cell and animal models that can be used to understand the underlying molecular pathology. Recently, there has been a surge of interest in the use of patient-derived cells, due to the development of induced pluripotent stem cells and their subsequent differentiation into neurons and glia. Access to patient cell lines carrying the relevant mutations is a limiting factor for many centres wishing to pursue this research. We have therefore generated an open-access collection of fibroblast lines from patients carrying mutations linked to neurological disease. These cell lines have been deposited in the National Institute for Neurological Disorders and Stroke (NINDS) Repository at the Coriell Institute for Medical Research and can be requested by any research group for use in in vitro disease modelling. There are currently 71 mutation-defined cell lines available for request from a wide range of neurological disorders and this collection will be continually expanded. This represents a significant resource that will advance the use of patient cells as disease models by the scientific community

Creation of an Open-Access, Mutation-Defined Fibroblast Resource for Neurological Disease Research

Our understanding of the molecular mechanisms of many neurological disorders has been greatly enhanced by the discovery of mutations in genes linked to familial forms of these diseases. These have facilitated the generation of cell and animal models that can be used to understand the underlying molecular pathology. Recently, there has been a surge of interest in the use of patient-derived cells, due to the development of induced pluripotent stem cells and their subsequent differentiation into neurons and glia. Access to patient cell lines carrying the relevant mutations is a limiting factor for many centres wishing to pursue this research. We have therefore generated an open-access collection of fibroblast lines from patients carrying mutations linked to neurological disease. These cell lines have been deposited in the National Institute for Neurological Disorders and Stroke (NINDS) Repository at the Coriell Institute for Medical Research and can be requested by any research group for use in in vitro disease modelling. There are currently 71 mutation-defined cell lines available for request from a wide range of neurological disorders and this collection will be continually expanded. This represents a significant resource that will advance the use of patient cells as disease models by the scientific community

Health, education, and social care provision after diagnosis of childhood visual disability

Aim: To investigate the health, education, and social care provision for children newly diagnosed with visual disability.Method: This was a national prospective study, the British Childhood Visual Impairment and Blindness Study 2 (BCVIS2), ascertaining new diagnoses of visual impairment or severe visual impairment and blindness (SVIBL), or equivalent vi-sion. Data collection was performed by managing clinicians up to 1-year follow-up, and included health and developmental needs, and health, education, and social care provision.Results: BCVIS2 identified 784 children newly diagnosed with visual impairment/SVIBL (313 with visual impairment, 471 with SVIBL). Most children had associated systemic disorders (559 [71%], 167 [54%] with visual impairment, and 392 [84%] with SVIBL). Care from multidisciplinary teams was provided for 549 children (70%). Two-thirds (515) had not received an Education, Health, and Care Plan (EHCP). Fewer children with visual impairment had seen a specialist teacher (SVIBL 35%, visual impairment 28%, χ2p < 0.001), or had an EHCP (11% vs 7%, χ2p < 0 . 01).Interpretation: Families need additional support from managing clinicians to access recommended complex interventions such as the use of multidisciplinary teams and educational support. This need is pressing, as the population of children with visual impairment/SVIBL is expected to grow in size and complexity.This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited

Inheritance of DNA methylation level in healthy human tissues

DNA methylation (DNAm) is the covalent modification of DNA by addition of a methyl group primarily at the cytosine directly upstream of a guanine. DNAm level plays a central role in transcriptional regulation and is linked to disease. Therefore, understanding genetic and environmental influences on DNAm level in healthy tissue is an important step in the elucidation of trait and disease etiology. However, at present only a minority of easy to access human tissues and ethnicities have been investigated. Therefore, we studied DNAm level measured in five human tissues: cerebellum, frontal cortex, pons, temporal cortex and colon in either North American or South American samples. We applied a novel statistical approach to estimate the heritability attributable to genomic regions (regional heritability, ĥ²/r,g ) for DNAm level at thousands of individual DNAm sites genome-wide. In all five tissues, DNAm level was significantly associated with the local genomic region for more DNAm sites than expected by chance. Moreover, DNAm level could be predicted from the local sequence variants with an accuracy that scaled with the estimated ĥ²/r,g . Our results inform on molecular mechanisms regulating DNAm level and trait etiology in several ways. Firstly, DNAm level at DNAm sites located in genomic risk regions and measured in a tissue relevant to the disease can be influenced by the local genetic variants. Specifically, we found that genetic variation within a region associated with Fluid Intelligence was also associated with local DNAm level at the proline-rich coiled-coil 1 (PRRC1) gene in healthy temporal cortex tissue. Additionally, we replicated the finding of a Colorectal Cancer risk variant (rs4925386) associated with two DNAm sites in healthy colon tissue. More generally, we showed that DNAm sites located within a susceptibility region and measured in a relevant tissue exhibit a similar overall pattern of estimated ĥ²/r,g to DNAm sites outwith a susceptibility region. Secondly, the propensity for DNAm level to be associated with the local sequence variation differs with respect to CpG dinucleotide density and genic location. Most notably, DNAm sites located in CpG dense regions of the genome are less likely to be heritable than DNAm sites located in CpG sparse regions of the genome. Additionally, within both CpG dense and CpG sparse regions of the genome intergenic DNAm sites are more likely to be heritable than intragenic DNAm sites. Overall, our study suggests that variation in DNAm level at some DNAm sites is at least partially controlled by nuclear genetic variation. Moreover, DNAm level in healthy tissue has the potential to act as an intermediary in trait variation and etiology

The structure and operation of the BGS National Geotechnical Properties Database. Version 2

The main part of this report describes the development history, structure and content of the BGS National Geotechnical Properties Database, with a final section describing planned future developments to enhance ease of access to, and promote wider use of, the database information for a variety of applications. The National Geotechnical Properties Database primarily holds geotechnical information extracted from site investigation records provided by clients, consultants and contractors, and from field and, secondarily, from laboratory test results carried out by the British Geological Survey. Information held within the database includes locations to British National Grid Coordinates; borehole, core and in situ test data; sample data; and a range of laboratory index, mechanical properties and chemical test data on soils, rocks and water. The database tables and fields are designed to be compatible with data supplied in the Association of Geotechnical and Geoenvironmental Specialists (AGS) industry standard digital transfer format, enabling rapid addition of data electronically, in addition to manual entry of analogue legacy data. This information forms the basis for the geotechnical attribution of the 2D and 3D digital geological models and underpins BGS core and commissioned engineering geology research. It also provides an important information resource for external customers and internal/external enquiries. The role of Geotechnical Database Manager has been undertaken by Suzanne Self since 2000