118 research outputs found

    Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots in the germline

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    Abstract Background Chromatin loops form a basic unit of interphase nuclear organization, with chromatin loop anchor points providing contacts between regulatory regions and promoters. However, the mutational landscape at these anchor points remains under-studied. Here, we describe the unusual patterns of somatic mutations and germline variation associated with loop anchor points and explore the underlying features influencing these patterns. Results Analyses of whole genome sequencing datasets reveal that anchor points are strongly depleted for single nucleotide variants (SNVs) in tumours. Despite low SNV rates in their genomic neighbourhood, anchor points emerge as sites of evolutionary innovation, showing enrichment for structural variant (SV) breakpoints and a peak of SNVs at focal CTCF sites within the anchor points. Both CTCF-bound and non-CTCF anchor points harbour an excess of SV breakpoints in multiple tumour types and are prone to double-strand breaks in cell lines. Common fragile sites, which are hotspots for genome instability, also show elevated numbers of intersecting loop anchor points. Recurrently disrupted anchor points are enriched for genes with functions in cell cycle transitions and regions associated with predisposition to cancer. We also discover a novel class of CTCF-bound anchor points which overlap meiotic recombination hotspots and are enriched for the core PRDM9 binding motif, suggesting that the anchor points have been foci for diversity generated during recent human evolution. Conclusions We suggest that the unusual chromatin environment at loop anchor points underlies the elevated rates of variation observed, marking them as sites of regulatory importance but also genomic fragility

    Tephrochronology

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    Tephrochronology is the use of primary, characterized tephras or cryptotephras as chronostratigraphic marker beds to connect and synchronize geological, paleoenvironmental, or archaeological sequences or events, or soils/paleosols, and, uniquely, to transfer relative or numerical ages or dates to them using stratigraphic and age information together with mineralogical and geochemical compositional data, especially from individual glass-shard analyses, obtained for the tephra/cryptotephra deposits. To function as an age-equivalent correlation and chronostratigraphic dating tool, tephrochronology may be undertaken in three steps: (i) mapping and describing tephras and determining their stratigraphic relationships, (ii) characterizing tephras or cryptotephras in the laboratory, and (iii) dating them using a wide range of geochronological methods. Tephrochronology is also an important tool in volcanology, informing studies on volcanic petrology, volcano eruption histories and hazards, and volcano-climate forcing. Although limitations and challenges remain, multidisciplinary applications of tephrochronology continue to grow markedly

    Factors influencing user acceptance of public sector big open data

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    In recent years Government departments and public/private organizations are becoming increasingly transparent with their data to establish the whole new paradigm of big open data. Increasing research interest arises from the claimed usability of big open data in improving public sector reforms, facilitating innovation, improving supplier and distribution networks and creating resilient supply chains that help improve the efficiency of public services. Despite the advantages of big open data for supply chain and operations management, there is severe shortage of empirical analyses in this field, especially with regards to its acceptance. To address this gap, in this paper we use an extended Technology Acceptance Model (TAM) to empirically examine the factors affecting users’ behavioural intentions towards public sector big open data. We outline the importance of our model for operations and supply chain managers, the limitations of the study, and future research directions

    Elastomeric Construction Adhesives: Influence of Solvent Retention on Strength

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    Solvent retention for a styrene-butadiene elastomeric construction adhesive was determined by gas-liquid chromatography and compared to shear strength development during a 5-month cure period at ambient temperature. Both low (hexanes) ahd high boiling (toluene) solvents were found to be present and strength development was directly related to solvent losses

    Preparation and Structure of Dimethyl α-Conidendrin-8-methyl Sulfonate

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    Coalinga Chrysotile: A Short Fibre, Amphibole Free, Chrysotile: Part V - Lack of Amphibole Asbestos Contamination

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    A Distributed computing workflow for modelling environmental flows in complex terrain

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    Numerical modelling of extreme environmental flows such as flash floods, avalanches and mudflows can be used to understand fundamental processes, predict outcomes and assess the loss potential of future events. These extreme flows can produce complicated and dynamic free surfaces as a result of interactions with the terrain and built environment. In order to resolve these features that may affect flows, high resolution, accurate terrain models are required. However, terrain models can be difficult and costly to acquire, and often lack detail of important flow steering structures such as bridges or debris. To overcome these issues we have developed a photogrammetry workflow for reconstructing high spatial resolution three dimensional terrain models. The workflow utilises parallel and distributed computing to provide inexpensive terrain models that can then be used in numerical simulations of environmental flows. A section of Quebrada San Lazaro within the city of Arequipa, Peru is used as a case study to demonstrate the construction and usage of the terrain models and applicability of the workflow for a flash flood scenario.12 page(s
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