DNAReplication: a database of information and resources for the eukaryotic DNA replication community

DNAReplication (at http://www.dnareplication.net) has been set up as a freely available single resource to facilitate access to information on eukaryotic DNA replication. This database summarizes organism-sorted data on replication proteins in the categories of nomenclature, biochemical properties, motifs, interactions, modifications, structure, cell localization and expression, and general comments. Replication concepts are defined and a general model of the steps in DNA replication is presented. Links to relevant websites and homepages of replication labs are provided. The site also has an interactive section where links to recent replication papers are posted and readers are provided with the facility to post comments about each paper. The interactive and links pages are modified weekly and the whole site is updated annually

Multi-proxy palaeoclimate reconstruction of the permian-triassic mass extinction event

Access to the full-text thesis is no longer available at the author's request, due to 3rd party copyright restrictions. Access removed on 28.11.2016 by CS (TIS).Metadata merged with duplicate record (http://hdl.handle.net/10026.1/2096) on 20.12.2016 by CS (TIS).The Permian/Triassic (P/Tr) boundary is widely assumed to have been a time of extreme environmental upheaval and change. In the terrestrial realm, a negative anomaly in 813C isotope values has been reported from organic carbon in Antarctica, Australia, India and Madagascar, and from marine carbonate in the Karoo Basin. However, these sections are all from southern palaeolatitudes. Analysis from the Permian-Triassic terrestrial sedimentary record of the South Urals, in Russia, comprising of many Aridisol and Vertisol horizons has revealed that, like the Southern Hemisphere, there is a dramatic change in paleosol morphology across the P/Tr boundary linked to a shift from meandering rivers to conglomeratic alluvial fans. Most of the paleosols include pedogenic carbonates at different stages of development, both above and below the P/Tr boundary. By the Triassic there is evidence of depressed water tables and increased seasonality. Analyses of the S13Qarba nd S18Ocarbsi gnatures of these pedogenic carbonates have revealed a number of negative excursions in 813Ccarabn d 5180carbin the Late Permian, including a negative excursion in the mid-Changhsingian, the first time such an event has been recorded in a terrestrial environment. Associated with this excursion are indicators of increasing extremes of climate, including pedogenic dolomite, which suggest a dramatic change in climate up to the P/Tr boundary. Equally, there is an increase in the range of precipitation, suggesting that what caused this mid-Changhsingian event also had a profound effect on the atmosphere. There is also evidence, in the form of the 818Ocaeßx, cursion, of a rise in temperaturej ust prior to the onset of the conglomeratic alluvial fan deposits, which mark the P/Tr boundary in Russia. Although in the Russian paleosols this excursion could be explained by a rise in the effect of seasonal rain or atmospheric temperature, estimates from unaltered brachiopods from the Italian Dolomites confirm that there is a rise in temperature and suggests that this is in the region of 7-8°C. These paleosols also record a dramatic rise in pCO2 in the Earliest Triassic similar to what has been recorded in stomatal records across this period suggesting a dramatic input of CO2 in to the atmosphere

Synchrotron radiation and the structure of the galaxy

The structure of the Galaxy is still largely unknown. Our only direct source of information is the radiation it emits; electromagnetic radiation at metre wavelengths being particularly important as it remains largely unabsorbed on passage through the Galaxy, allowing an unhindered view of its large-scale structure. Analysis of its distribution over the sky can provide insight into this structure. An attempt was made to investigate the properties of our Galaxy by modelling the radio synchrotron emission at 408MHz and comparing the predicted distribution with a newly available, high resolution survey of the whole sky at this frequency. A model previously employed with some success at 150MHz; was used as a basis for this work. A suite of computer programs was developed to perform the necessary calculations, and to handle and present the results and the survey data. Refinements were made to the basic model to try to reproduce the observed distribution more accurately. A model of the Galaxy emerges featuring a central bar, each end joined by an elliptical arm section. These divide to form four spiral arras which sweep out to a radius of 15kpc. In addition, a number of short 'feather' arms, branching off from the main arms, are required. The local Orion arm is one such 'feather', branching from the Perseus arm, passing 0.5kpc from the sun in the anticentre direction and ending a few kiloparsecs further on. A weak halo of emission extending several kiloparsecs out from the plane is also required. Independent confirmation of this is found from consideration of cosmic ray diffusion through the Galaxy. Finally, comparison was made between the 408MHz survey and the COS-B gamma ray distribution. The similarity between them in the plane provides information about the relationship between various components of the galactic disc

Benchmarking of three parallelized implementations of LS-Dyna on a HPC server cluster

This paper discusses the benchmarking of three parallelized implementations of the popular LS-Dyna® finite element code (Livermore Software Technology Corp.) on the STePS2 high performance computing (HPC) server cluster. SMP, MPP and SMP-MPP hybrid implementations of LS-Dyna® are benchmarked over various numbers of nodes, cpus and cpu cores. The STePS2 HPC cluster consists of a dual-cpu head node and 16 homogeneous dual-cpu compute nodes. All nodes are interconnected via an Infiniband® network fabric. All cpus are quad-core Intel Xeon 64-bit and the operating system(s) is the ROCKS cluster management software implemented through Redhat Enterprise Linux 5 (x86_64). SMP, MPP and MPP-SMP hybrid implementations of LS-Dyna were compiled for use with the HPMPI message passing interface

Devonian and Carboniferous stratigraphical correlation and interpretation in the Orcadian area, Central North Sea, Quadrants 7 - 22

This report details the stratigraphy and palaeogeography of Devonian and Carboniferous rocks of the northern sector of the UK Central North Sea (the ‘Orcadian Area’) for the 21CXRM Palaeozoic project. The work integrates the lithostratigraphic framework for the Middle Devonian to Late Carboniferous succession in the region of the Mid North Sea High developed in the first phase of the 21CXRM Palaeozoic project (Kearsey et al., 2015), with the Early Devonian to Early Carboniferous succession present in the north Central North Sea. This report describes the stratigraphical correlation of Devonian and Carboniferous strata of the Orcadian Basin and the northern extension of the Forth Approaches into the Witch Ground Graben (Quadrants 7 – 22). A lithostratigraphic framework for the region is presented, building on the work of Cameron (1993) and Marshall and Hewett (2003). For the Devonian strata, the lithostratigraphic framework developed by Marshall and Hewett (2003) is followed. Their study presented a substantial revision of the previous Devonian stratigraphy for the region, particularly related to (1) reassessment of the Devonian - Permian contact and (2) the identification of the Eday Group offshore in the Inner Moray Firth Basin. In this study, onshore outcrops, well data and seismic interpretation (cf. Arsenikos et al., 2016) verify the key elements of the framework of Marshall and Hewett (2003). In addition, well interpretations further define the extent of the stratigraphical units and form the basis of potential source and reservoir horizon palaeogeographic reconstructions for four time intervals within the Devonian succession. For example, the potential source rock of the Orcadia Formation has been interpreted to the north of the Halibut Horst and into the East Orkney Basin, significantly increasing the extent of this unit outside the Inner Moray Firth. A revised lithostratigraphic framework for the Carboniferous strata of Quadrants 14, 15, 20 and 21 is presented. This framework links the Carboniferous succession of the Orcadian Area with equivalent age strata in areas on and surrounding the Mid North Sea High (Kearsey et al., 2015). Well and seismic interpretations have been integrated to better define the extent of Carboniferous units. Regional facies variations for key time intervals in the Early Carboniferous are presented which highlight relationships between the Carboniferous basins of the Witch Ground Graben and Forth Approaches, and those of the Mid North Sea High and adjacent regions to the south. For example, fluvial channel systems have been interpreted within late Visean age coal-bearing, fluvial and lacustrine deposits of the Firth Coal Formation, that are potential feeder systems for Yoredale Formation fluvio-deltaic to marine deposits farther south. This report forms one of a series of outputs from the 21CXRM Palaeozoic project (Orcadian Area) and provides explanatory information for the associated digital datasets (spreadsheet). The Orcadian Area study follows previous work undertaken in the Mid North Sea High area of the Central North Sea (CNS area; Figure 1). Key elements of the regional petroleum geology of the Orcadian area are summarised in an accompanying synthesis report (Monaghan et al., 2016)

Norham West Mains Farm borehole : operations report

A borehole was drilled to a total depth of 501.33 m by Drilcorp Ltd at Norham West Mains Farm, near the village of Norham, Berwick upon Tweed. Work was commenced on the 27th of March 2013 and completed on 7th Obtaining cores from the Norham West Mains Farm Borehole is a major task within the TW:eed Project, which is investigating how limbed vertebrates adapted to walk on land around 360 million years ago (see June 2013. The borehole was fully cored from 10.22 m to its total depth through rocks of the Lower Carboniferous Inverclyde Group. http://www.tetrapods.org/). This was a key stage in the evolution of life on Earth and shaped the future evolution of vertebrates, including the eventual appearance of humans. The project builds on some unique new fossil finds made recently in the Scottish Borders and adjacent areas. Analysis of the borehole will provide a framework upon which this research is to be pinned. This scientific research programme is being undertaken by a consortium of organisations led by the University of Cambridge, and including the universities of Southampton and Leicester, the National Museums of Scotland and the British Geological Survey, and funded through the Natural Environment Research Council

Integrating deterministic lithostratigraphic models in stochastic realizations of subsurface heterogeneity. Impact on predictions of lithology, hydraulic heads and groundwater fluxes

Realistic representations of geological complexity are important to address several engineering and environmental challenges. The spatial distribution of properties controlling physical and geochemical processes can be effectively described by the geological structure of the subsurface. In this work, we present an approach to account for geological structure in geostatistical simulations of categorical variables. The approach is based on the extraction of information from a deterministic conceptualization of the subsurface, which is then used in the geostatistical analysis for the development of models of spatial correlation and as soft conditioning data. The approach was tested to simulate the distribution of four lithofacies in highly heterolithic Quaternary deposits. A transition probability-based stochastic model was implemented using hard borehole data and soft data extracted from a 3-D deterministic lithostratigraphic model. Simulated lithofacies distributions were also used as input in a flow model for numerical simulation of hydraulic head and groundwater flux. The outputs from these models were compared to corresponding values from models based exclusively on borehole data. Results show that soft lithostratigraphic information increases the accuracy and reduces the uncertainty of these predictions. The representation of the geological structure also allows a more precise definition of the spatial distribution of prediction uncertainty, here quantified with a metric based on Shannon information entropy. Correlations between prediction uncertainties for lithofacies, hydraulic heads and groundwater fluxes were also investigated. The results from this analysis provide useful insights about the incorporation of soft geological data into stochastic realizations of subsurface heterogeneity, and emphasize the critical importance of this type of information for reducing the uncertainty of simulations considering flux-dependent processes

Using LOOP 3D modelling to unlock the knowledge held in BGS maps

Geological 2D bedrock maps are ideally supposed to be the intersection of a 3D geological conceptual model with topography. However, often when you try to build 3D models from geological maps you find that this is not always the case. Sometimes geometries that might seemingly work on a 2D map face, do not actually project into 3D in the way the geologist imagined. This is especially true for older maps which may have been constructed before modern geological understandings like plate tectonics or sequence stratigraphy. Most geological maps are reviewed by other geologists who may have their own differing backgrounds and biases and therefore is no automatic way of assessing the geometrical accuracy of a map. The British Geological Survey (BGS) produces geological mapping at a range of scales. Our highest resolution national mapping is our 1:50,000 digital map dataset. This was compiled from BGS’s New Series 1:50 000 and 1:63 360-scale (one-inch to one-mile) paper maps with updated nomenclature, including a few 1:100 000-scale maps of Orkney and the Hebrides. As such it still uses a few maps that were surveyed before 1918 (Figure 1). Up until recently we did not have a way of assessing the geometrical accuracy of a map and determining if they need resurveying. The development of open-source implicit modelling platforms, specifically designed to work with geological map data by the LOOP project, means there is now a tool that we can use to understand the 3D geometrical accuracy of the geological map. Here in we discuss the results of the trials where we have used Map2Loop and Loop Structural to help us understand and improve our geological mapping