Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Hydrodynamic Loads Induced By Earthquakes

This paper was prepared for presentation at the Fourth Annual Offshore Technology Conference held in Houston, Tex., May 1-3, 1972 .When bottom mounted structures of large displacement are immersed in the sea. earthquake induced hydrodynamic loads may become important design factors. Specifically, as the earth oscillates, a bottom mounted structure is forced to describe time dependent motion in an otherwise still fluid. As a result, hydrodynamic loads in addition to the inertial loads of the structure itself are induced. In this paper, a theoretical approach to the calculation of these hydrodynamic loads is outlined and numerical results are presented for several submerged configurations . Practical geometries considered include a submerged 011 storage tank configuration and a conical configuration as has been proposed for offshore drilling rig designs for deployment in the Arctic. Also, computations were carried out for a sphere and vertical circular cylinder and various comparisons with classical results are made. Numerical results for these submerged structures are presented in the form of a dimensionless hydrodynamic load parameter or added mass coefficient. Results corresponding to a number of different water depths are presented to show the rather sizable effect of the relative water depth on the hydrodynamic force. It is shown that for typical earthquake frequencies, the effect of the free water surf ace is to reduce the hydrodynamic loads in comparison to the corresponding infinite depth values . Experimental results obtained by vibration testing are presented for a submerged sphere and a vertical circular cylinder. These results show excellent agreement with the theoretical results

The Albian-Cenomanian boundary at Eggardon Hill, Dorset (England) : an anomaly resolved?

Re-examination of the classic exposures of the Eggardon Grit (topmost Upper Greensand Formation) at Eggardon Hill, Dorset shows that the upper part of this unit has a more complex stratigraphy than has been previously recognised. The Eggardon Grit Member, as described herein, is capped by a hardground and associated conglomerate, and is entirely of Late Albian age. The hardground is probably the lateral equivalent of the Small Cove Hardground, which marks the top of the Upper Greensand succession in southeast Devon. The conglomerate is overlain by a thin sandy limestone containing Early Cenomanian ammonites. This limestone is almost certainly the horizon of the Early Cenomanian ammonite fauna that has previously been attributed to the top of the Eggardon Grit. The limestone is regarded as a thin lateral equivalent of the Beer Head Limestone Formation (formerly Cenomanian Limestone) exposed on the southeast Devon coast. The fauna of the limestone at Eggardon suggests that it is probably the age equivalent to the two lowest subdivisions of the Beer Head Limestone in southeast Devon, with a remanié fauna of the Pounds Pool Sandy Limestone Member combined with indigenous macrofossils of the Hooken Nodular Limestone Member. The next highest subdivision of the Beer Head Limestone in southeast Devon (Little Beach Bioclastic Limestone Member), equates with the ammonite-rich phosphatic conglomerate of the ‘Chalk Basement Bed’, which caps the Beer Head Limestone at Eggardon, and which was previously regarded as the base of the Chalk Group on Eggardon Hill. Petrographic analysis of the Eggardon Grit shows that lithologically it should more correctly be described as a sandy limestone rather than sandstone. The original stratigraphical definition of the unit should probably be modified to exclude the softer, nodular calcareous sandstones that have traditionally been included in the lower part of the member. Without the apparently clear evidence of unbroken sedimentation across the Albian–Cenomanian boundary, suggested by the previous interpretation of the Eggardon succession, it is harder to argue for this being a prevalent feature of Upper Greensand stratigraphy in southwest England. Correlation of the Eggardon succession with successions in Dorset and southeast Devon reveals a widespread regional break in sedimentation at the Albian–Cenomanian boundary. The sand-rich facies above this unconformity represent the true base of the Chalk Group, rather than the ‘Chalk Basement Bed’ of previous interpretations. Selected elements of regionally important Upper Greensand ammonite faunas previously reported from Shapwick Quarry, near Lyme Regis, and Babcombe Copse, near Newton Abbot, are newly figured herein

NStars project: The southern sample. I.

VizieR online Data Catalogue associated with article published in journal Astronomical Journal (AAS) with title \u27Contributions to the nearby stars (NStars) project: spectroscopy of stars earlier than M0 within 40 pc. The southern sample.\u27 (bibcode: 2006AJ....132..161G