Identification of HIV integration sites in infected host genomic DNA.

The integration of the Human Immunodeficiency Virus (HIV) genetic information into the host genome is fundamental for its replication and long-term persistence in the host. Isolating and characterizing the integration sites can be useful for obtaining data such as identifying the specific genomic location of integration or understanding the forces dictating HIV integration site selection. The methods outlined in this article describe a highly efficient and precise technique for identifying HIV integration sites in the host genome on a small scale using molecular cloning techniques and standard sequencing or on a massive scale using 454 pyrosequencing

Modelling split-Hopkinson pressure bar tests on quartz sand

FE modelling of a confined split Hopkinson pressure bar (SHPB) test on dry quartz sand was carried out using LS-DYNA in order to assess whether Material Model 5 could replicate experimental results, which would enable a more detailed investigation of the stress state in SHPB specimen. Quasi-static test data was used to select the material model input, and the model SHPB was set up to replicate the experimental conditions. The results show that Material Model 5 replicates the volumetric response provided as input data, but fails to predict the shear response observed in the quasi-static experiments. This was found to be due to the model treating the shear modulus as a constant rather than it increasing with strain, a feature which makes the Material Model 5 unsuitable for modelling SHPB tests on sand

Effects of strain rate and moisture content on the behaviour of sand under one-dimensional compression

The influence of strain rate and moisture content on the behaviour of a quartz sand was assessed using high-pressure quasi-static (0.001 /s) and high-strain-rate (1000 /s) experiments under uniaxial strain. Quasi-static compression to axial stresses of 800 MPa was carried out alongside split Hopkinson pressure bar (SHPB) experiments to 400 MPa, where in each case lateral deformation of the specimen was prevented using a steel test box or ring, and lateral stresses were recorded. A significant increase in constrained modulus was observed between strain rates of 0.001 /s and 1000 /s, however a consistently lower Poisson's ratio in the dynamic tests minimised changes in bulk modulus. The reduction in Poisson’s ratio suggests that the stiffening of the sand in the SHPB tests is due to additional inertial confinement rather than an inherent strain-rate dependence. In the quasi-static tests the specimens behaved less stiffly with increasing moisture content, while in the dynamic tests the addition of water had little effect on the overall stiffness, causing the quasi-static and dynamic series to diverge with increasing moisture content

Electromagnetic Interference in Measurements of Radial Stress During Split Hopkinson Pressure Bar Experiments

Split Hopkinson pressure bar experiments on soils are often carried out using a rigid steel confining ring to provide plane strain conditions, and measurements of the circumferential strain in the ring can be used to infer the radial stress on the surface of the specimen. Previous experiments have shown evidence of irregular electromagnetic interference in measurements of radial stress, which obscures the signals and impedes analysis. The development of robust constitutive models for soils in blast and impact events relies on the accurate characterisation of this behaviour, and so it is necessary to isolate and remove the source of interference. This paper uses an induction coil to identify the source of the anomalous signals, which are found to be due to induced currents in the gauge lead wires from the movement of magnetised pressure bars (martensitic stainless steel, 440C). Comparative experiments on sand and rubber specimens are used to show that the deforming soil specimen does not make a significant contribution to this activity, and recommendations are made on reducing electromagnetic interference to provide reliable radial stress measurements

Temporally and spatially resolved reflected overpressure measurements in the extreme near field

The design of blast-resistant structures and protective systems requires a firm understanding of the loadings imparted to structures by blast waves. While empirical methods can reliably predict these loadings in the far field, there is currently a lack of understanding on the pressures experienced in the very near field, where physics-based numerical modelling and semi-empirical fast-running engineering model predictions can vary by an order of magnitude. In this paper, we present the design of an experimental facility capable of providing definitive spatially and temporally resolved reflected pressure data in the extreme near field (Z<0.5 m/kg1/3 ). The Mechanisms and Characterisation of Explosions (MaCE) facility is a specific near-field evolution of the existing Characterisation of Blast Loading (CoBL) facility, which uses an array of Hopkinson pressure bars embedded in a stiff target plate. Maraging steel pressure bars and specially designed strain gauges are used to increase the measurement capacity from 600 MPa to 1800 MPa, and 33 pressure bars in a radial grid are used to improve the spatial resolution from 25 mm to 12.5 mm over the 100 mm radius measurement area. In addition, the pressure bar diameter is reduced from 10 mm to 4 mm, which greatly reduces stress wave dispersion, increasing the effective bandwidth. This enables the observation of high-frequency features in the pressure measurements, which is vital for validating the near-field transient effects predicted by numerical modelling and developing effective blast mitigation methods

Quasi-static and high-strain-rate experiments on sand under one-dimensional compression

This paper investigates the effect of strain rate on the behaviour of dry and partially - saturated sand at very high stresses, seekin g to clarify the existence of a strain - rat e dependence and how this is affected by changes in moisture content. Dynamic one - dim ensional compression tests on a fine quartz sand have been carried out to axial stresses of 4 00 MPa using a split Hopkinson pressure bar, alongside quasi - static tests to 8 00 MPa using the mac 2T multi - axial test rig at The University of Sheffiel d . Specimens were prepared at moisture contents of 0.0%, 2.5% and 5.0%, and were laterally confined using a steel ring or steel loading box to ensure one - dimensional test conditions. Lateral stresses were recorded to allow the three-dimensional stress state of the specimens to be analysed. The results show that knowledge of both the axial and radial stresses is important for understanding the response of sand at higher strain rates, where an increase in stiffness is observed axially when compared to the quasi-static results

Measuring spatial pressure distribution from explosives buried in dry Leighton Buzzard sand

Direct measurement of the intense loading produced by the detonation of a buried explosive is an extremely difficult task. Historically, high-fidelity measurement techniques have not been sufficiently robust to capture the extremely high pressures associated with such events, and researchers have relied on ‘global’ measurements such as the average loading acting over a particular area of interest. Recently, a large-scale experimental approach to the direct measurement of the spatial and temporal variation in loading resulting from an explosive event has been developed, which utilises Hopkinson pressure bars (HPBs) inserted through holes in a large target plate such that their faces lie flush with the loaded face. This article presents results from ten experiments conducted at 1/4 scale, using 17 HPBs to measure the spatial pressure distribution from explosives buried in dry Leighton Buzzard sand, a commonly available sand used in many geotechnical applications. Localised pressure measurements are used in conjunction with high speed video to provide a detailed examination of the physical processes occurring at the loaded face, as well allowing quantification of these effects. Example pressure–time and impulse–time traces are provided in full to allow researchers to use this data for validation of numerical modelling approaches

Far-field positive phase blast parameter characterisation of RDX and PETN based explosives

A significant amount of scientific effort has been dedicated to measuring and understanding the effects of explosions, leading to the development of semi-empirical methods for rapid prediction of blast load parameters. The most well-known of these, termed the Kingery and Bulmash method, makes use of polylogarithmic curves derived from a compilation of medium to large scale experimental tests performed over many decades. However, there is still no general consensus on the accuracy and validity of this approach, despite some researchers reporting consistently high levels of agreement. Further, it is still not known whether blast loading can be considered deterministic, or whether it is intrinsically variable, the extent of this variability, and the range and scales over which these variations are observed. This article critically reviews historic and contemporary blast experiments, including newly generated arena tests with RDX and PETN-based explosives, with a view to demonstrating the accuracy with which blast load parameters can be predicted using semi-empirical approaches

Structure of Fat Jets at the Tevatron and Beyond

Boosted resonances is a highly probable and enthusiastic scenario in any process probing the electroweak scale. Such objects when decaying into jets can easily blend with the cornucopia of jets from hard relative light QCD states. We review jet observables and algorithms that can contribute to the identification of highly boosted heavy jets and the possible searches that can make use of such substructure information. We also review previous studies by CDF on boosted jets and its measurements on specific jet shapes.Comment: invited review for a special "Top and flavour physics in the LHC era" issue of The European Physical Journal C, we invite comments regarding contents of the review; v2 added references and institutional preprint number