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An LTR-based quantitative PCR (qPCR) assay was modified and optimized for the quantification of total HIV-1 nucleic acids in plasma and PBMC. TaqMan qPCR primers and probes were designed against the NCBI/LANL HIV-1 compendium database by analyzing sequences used in assays for sensitive cross-clade detection of HIV-1 as reported in the literature and elucidating regions of improved cross-subtype specificity. Inosine and mixed nucleotide bases were included at polymorphic sites. Real-time RT-qPCR and qPCR were performed on plasma viral RNA and cellular lysates. A step-up amplification approach to allow binding of primers across polymorphic regions showed improved sensitivity compared to universal cycling. Unlike a lead competing laboratory-developed assay, all major HIV-1 subtypes, and a wide range of recombinants from a 127-member diversity panel were detected and accurately quantified in spiked plasmas. Semi-nested PCR increased detection sensitivity even further. The assay was able to detect down to 88 copies/mL of HIV-1 in plasma with 95% efficiency or the equivalent of a single infected cell. The PCR assay will be valuable in studies that monitor very low viral levels including residual or break through HIV-1 in patients receiving antiretroviral therapy, in HIV-1 cure, and in other research studies.

Summary Background: Antiretroviral therapy (ART) cannot cure HIV infection because of a persistent reservoir of latently infected cells. Approaches that force HIV transcription from these cells, making them susceptible to killing - termed ���kick and kill��� - have been explored as a strategy towards an HIV cure. RIVER is the first randomized trial to determine the impact of ART alone versus ART plus ���kick-and-kill��� on markers of the HIV reservoir. Methods: RIVER (Trial registration: NCT02336074) was an open-label, multicenter, 1:1 randomized controlled trial of ART-only (control) versus ART plus the histone deacetylase inhibitor vorinostat (the ���kick���) and replication-deficient viral vector vaccines encoding conserved HIV sequences ChAdV63.HIVconsv-prime, MVA.HIVconsv-boost T-cell vaccination (the ���kill���) (ART+V+V; intervention) in HIV-positive adults treated in recent HIV-infection. The primary endpoint was total HIV DNA in peripheral blood CD4+ T-cells at weeks 16 and 18 post-randomization. Secondary endpoints included safety, alternative measures of the HIV reservoir including quantitative viral outgrowth, HIV-specific T-cell frequencies, and CD8+ T-cell mediated viral inhibition. Findings: Between December 2015 and November 2017, 60 HIV-positive male participants were randomized (computer-based and stratified by time since diagnosis; 30 participants in each trial arm) and completed the study interventions, with no loss-to-follow-up. There were no intervention-related serious adverse events. Mean total HIV DNA at weeks 16 and 18 was 3.02 log10 copies HIV DNA/106 CD4+ T-cells in the control and 3.06 log10 copies HIV DNA/106 CD4+ T-cells in the intervention arm, with no statistically significant difference (mean difference of 0.04 (95%CI -0.03, 0.11) log10 total HIV DNA copies/106 CD4+ T-cells (p=0.26)). Interpretation: This ���kick-and-kill��� approach conferred no significant benefit compared to ART alone on measures of the HIV reservoir. Although this does not disprove the ���kick and kill��� strategy, for future trials significant enhancement of both ���kick��� and ���kill��� agents will be required., Medical Research Council (MR/L00528X/1).

The epidemic of acute HCV infection among HIV-infected men who have sex with men (MSM) is ongoing. Transmission of drug-resistant variants (DRVs) after HCV treatment failure could pose a major threat to the effectiveness of future therapies. We determined the baseline prevalence of pre-existing DRVs in the HCV NS3 protease gene and their effects on the addition of telaprevir (TVR) to standard pegylated interferon and ribavirin (PEG-IFN/RBV) for acute HCV infection in individuals enrolled in a multicentre randomized controlled trial (2013 and 2014). The HCV NS3 viral protease was analyzed using Sanger and next-generation sequencing (NGS) for DRVs at baseline (n = 31), and at viral breakthrough following TVR-based treatment (n = 3) or PEG-IFN/RBV alone (n = 2). Sequence analysis indicated that all individuals were infected with HCV genotype 1a. Complete (100%) concordance was seen between Sanger and NGS for high levels of mutant viral populations. The simeprevir-associated Q80K variant was present at high frequency in the German samples (7/11–64%) and infrequently in the UK samples (1/20–5%). In the three TVR-based treatment failures, V36M/l and R155K/T emerged, but not R155G which was detectable at low levels in two individuals at baseline. Failure rate at week 24 was 26.7% (with baseline DRVs) vs. 6.3% (without baseline DRVs), p = 0.17). Comparison of sequences pre- and post-therapy in 5 who failed therapy revealed the emergence of not previously described variants V193G, E176K, P189S (on TVR), and V181S in one instance each. The presence of baseline DRVs for the NS3 protease gene of HCV genotype 1a did not appear to predict treatment failure in our patient cohort. Where detected, Q80K was present at high levels (>98%), but had no effect on outcomes and remained high after failure.

An essay based on spreadsheet calculations for campaigning Roman armies. The spreadsheet is available at www.bandaarcgeophysics.co.uk/arch_intro.html . It allows the definition of army sizes, march rates and the building of camp defences before calculating over 70 parameters and metrics. Calculated camps sizes are cross-matched to extant camps allowing comparisons.This essay contains a description of the spreadsheet, some observations arising and a description of all input and output variables.

First, take Tacitus’ description of the battle site - a defile facing an open plain - and as objectively as possible search the terrain of southern Britain for matching sites. Second, compute the river flows across Britain in August; calculate the water requirements for the protagonists; use both to identify rivers capable of supplying sufficient water to the Romans and Britons. Third, calculate topographical and hydrological descriptors for 374 known Roman marching camps in Britain and use these data to predict the location of possible marching camps. Combining the three steps eliminates large areas unsuitable for a marching Roman army or battle ground, and identifies 110 possible battle sites. Apply a statistical weighting to the 110 sites and then rank them. Combining the ranked battle sites with an examination of Tacitus’ account and a consideration of political and military logic, strongly suggests Suetonius, the Roman commander, marched west after leaving an indefensible London., Poster and presentation given at 'ON BOUDICA'S TRAIL': A one-day conference, June 29th 2013, held at Warwick University

Searching for the location of Boudica's last battle using terrain analysis, hydrology, Roman marching camp data and the logistical strengths and weaknesses of the British tribal forces and the Roman legions.

A study of known Roman marching camps throughout Britain and the use of the resulting data to predict the locations of unknown marching camp locations. Marching camp data are integrated into a study of hydrology, thereby refining the predictive method.

Unexpected faults are a serious production problem in numerous, complex and compartmentalised oil and gas fields, and are often the single most important restraint on recovery. Fractal mathematics has demonstrated a surprising degree of order in many natural, apparently random systems. It has been shown that fault patterns exhibit a similar order which could be used to indicate the presence of structures missed in the original interpretation of the seismic data and to predict faults below the approximate 20 m limit of seismic resolution. The potential for greater clarity and resolution opened up by this method may greatly aid field description and reservoir production. We will discuss the development of a comprehensive fault pattern characterisation quantatively with a set of parameters arising from non-linear methods of analysis. This allows for the standardised comparison of seismic interpretations and a precise method for testing interpretations from the same dataset. We will show how fractal mathematics may give a measure of the density of the fault set, the number of faults below the limit of seismic resolution, resolve small fault clusters below the limit of seismic resolution and aid in the description and analysis of fault sets., Stolum,H-H. and Kaye,S.J.1992. Energy Exploration and Exploitation. Vol 10, Numbers 4 and 5. Special Issue, Oryx Energy Company, Focus on technology.