Locating Boosted Kerr and Schwarzschild Apparent Horizons

We describe a finite-difference method for locating apparent horizons and illustrate its capabilities on boosted Kerr and Schwarzschild black holes. Our model spacetime is given by the Kerr-Schild metric. We apply a Lorentz boost to this spacetime metric and then carry out a 3+1 decomposition. The result is a slicing of Kerr/Schwarzschild in which the black hole is propagated and Lorentz contracted. We show that our method can locate distorted apparent horizons efficiently and accurately.Comment: Submitted to Physical Review D. 12 pages and 22 figure

The Nitrile Bis-Thiol Bioconjugation Reaction

Electron-poor aryl nitriles are promising reagents for bioconjugation due to their high electrophilicity and selectivity for reaction with thiols, albeit generally in a reversible manner. A transient species has previously been observed in such reactions, involving the addition of two thiols to the nitrile functional group, forming a tetrahedral amino dithioacetal (ADTA). In this work, the reaction of heteroaryl nitriles with bis-thiols is explored in an attempt to generate stable ADTAs, which could facilitate new bioconjugation protocols. By use of a 1,2-dithiol, or the incorporation of an electrophilic trap into the aryl nitrile design, the formation of stable products is achieved. The resultant "nitrile bis-thiol" (NBT) reaction is then explored in the context of protein modification, specifically to carry out antibody conjugation. By addition of these nitriles to the reduced disulfide bond of an antibody fragment, it is shown that, depending on the reagent design, cysteine-to-lysine transfer or disulfide bridged NBT products can be generated. Both represent site-selective conjugates and are shown to be stable when challenged with glutathione under physiological conditions and upon incubation in serum. Furthermore, the NBT reaction is tested in the more challenging context of a full antibody, and all four disulfide bonds are effectively modified by these new one-carbon bridging reagents. Overall, this reaction of heteroaryl-nitriles with bis-thiols is shown to be highly efficient and versatile, of tunable reversibility, and offers enticing prospects as a new addition to the toolbox of biocompatible "click"-type reactions

Southern Ocean Overturning Compensation in an Eddy-Resolving Climate Simulation

The Southern Ocean’s Antarctic Circumpolar Current (ACC) and meridional overturning circulation (MOC) response to increasing zonal wind stress is, for the first time, analyzed in a high-resolution (0.1° ocean and 0.25° atmosphere), fully coupled global climate simulation using the Community Earth System Model. Results from a 20-yr wind perturbation experiment, where the Southern Hemisphere zonal wind stress is increased by 50% south of 30°S, show only marginal changes in the mean ACC transport through Drake Passage—an increase of 6% [136–144 Sverdrups (Sv; 1 Sv ≡ 10^6 m^3 s^(−1))] in the perturbation experiment compared with the control. However, the upper and lower circulation cells of the MOC do change. The lower cell is more affected than the upper cell with a maximum increase of 64% versus 39%, respectively. Changes in the MOC are directly linked to changes in water mass transformation from shifting surface isopycnals and sea ice melt, giving rise to changes in surface buoyancy forcing. The increase in transport of the lower cell leads to upwelling of warm and salty Circumpolar Deep Water and subsequent melting of sea ice surrounding Antarctica. The MOC is commonly supposed to be the sum of two opposing components: a wind- and transient-eddy overturning cell. Here, the transient-eddy overturning is virtually unchanged and consistent with a large-scale cancellation of localized regions of both enhancement and suppression of eddy kinetic energy along the mean path of the ACC. However, decomposing the time-mean overturning into a time- and zonal-mean component and a standing-eddy component reveals partial compensation between wind-driven and standing-eddy components of the circulation

Genome sequence of human papillomavirus type 20, strain HPV-20/Lancaster/2015

The genome sequence of human papillomavirus type 20 (HPV-20; family Papillomaviridae, genus Betapapillomavirus, species Betapapillomavirus 1, type 20) was assembled by deep sequencing from nasopharyngeal swabs. The assembled genome is 0.37% divergent over its full length from the single complete genome of HPV-20 in GenBank (U31778). We named the strain HPV-20/Lancaster/2015

Southern Ocean Overturning Compensation in an Eddy-Resolving Climate Simulation

The Southern Ocean’s Antarctic Circumpolar Current (ACC) and meridional overturning circulation (MOC) response to increasing zonal wind stress is, for the first time, analyzed in a high-resolution (0.1° ocean and 0.25° atmosphere), fully coupled global climate simulation using the Community Earth System Model. Results from a 20-yr wind perturbation experiment, where the Southern Hemisphere zonal wind stress is increased by 50% south of 30°S, show only marginal changes in the mean ACC transport through Drake Passage—an increase of 6% [136–144 Sverdrups (Sv; 1 Sv ≡ 10^6 m^3 s^(−1))] in the perturbation experiment compared with the control. However, the upper and lower circulation cells of the MOC do change. The lower cell is more affected than the upper cell with a maximum increase of 64% versus 39%, respectively. Changes in the MOC are directly linked to changes in water mass transformation from shifting surface isopycnals and sea ice melt, giving rise to changes in surface buoyancy forcing. The increase in transport of the lower cell leads to upwelling of warm and salty Circumpolar Deep Water and subsequent melting of sea ice surrounding Antarctica. The MOC is commonly supposed to be the sum of two opposing components: a wind- and transient-eddy overturning cell. Here, the transient-eddy overturning is virtually unchanged and consistent with a large-scale cancellation of localized regions of both enhancement and suppression of eddy kinetic energy along the mean path of the ACC. However, decomposing the time-mean overturning into a time- and zonal-mean component and a standing-eddy component reveals partial compensation between wind-driven and standing-eddy components of the circulation

COVID-19 risk, attitudes and behaviour study (CRAB study): A knowledge, attitudes, and practise qualitative study of COVID-19 in the Royal Navy

Introduction: Outbreaks of SARS-CoV-2 onboard maritime platforms spread rapidly and have high attack rates. The aim of the COVID-19 Risk, Attitudes and Behaviour (CRAB) study was to investigate the knowledge, attitudes, and practises in the Royal Navy in relation to COVID-19 prevention. Methods: The CRAB study was a cross-sectional survey, using a census sampling method, conducted in May and June 2021. An online questionnaire was distributed to all serving Royal Navy regular personnel using either the MyNavy application or via a QR code through email for a continuous 14 day period. The questionnaire was based on an existing validated questionnaire used for avian influenza epidemics. Questions investigated individual perceptions of COVID-19 seriousness, compliance with prevention methods, explored vaccination intention and vaccine hesitancy (unvaccinated individuals who declined or were unsure about receiving a COVID-19 vaccine). The chi-squared test of best fit was used to compare the demographic responses against the whole organisation, with p-value < 0.05 deemed significant. Odds ratios were used to investigate associations between demographic groups and responses to questions, with an odds ratio crossing 1.0 deemed non-significant. Results: The response rate was 6% (2,080/33,200), with 315 responses collated in the pilot phase and 1,765 in the main study phase. Male participants were less likely to rate COVID-19 as serious (OR 0.34; 95% CI: 0.23–0.49). BAME ethnicity (OR 2.41; 95% CI: 1.12–5.17) rated it as more serious. At the time of the study 62% of respondents had received one dose of a COVID-19 vaccine. In the 797 unvaccinated personnel, vaccine hesitancy accounted for 24.2% (193/797), of whom 136 were white males. Those who had a higher COVID-19 serious rating, the most significant factor for non-adherence to COVID-19 prevention measures in both vaccinated (OR 1.61 [95%CI: 1.20–2.17]) and vaccine-hesitant (OR 3.24 [95%CI: 1.63–6.41]) individuals was colleagues' non-adherence. The most trusted source of information on vaccines was provided by the Defence Medical Services (77.2% [1,606/2,080]). Conclusion: This study has identified reasons for COVID-19 protective measure adherence, sources of information trusted by respondents and vaccine hesitancy, in the Royal Navy. The questionnaire can be used to investigate attitudes and behaviours in future emerging infectious diseases

Methods for Bayesian inversion of seismic data

The purpose of Bayesian seismic inversion is to combine information derived from seismic data and prior geological knowledge to determine a posterior probability distribution over parameters describing the elastic and geological properties of the subsurface. Typically the subsurface is modelled by a cellular grid model containing thousands or millions of cells within which these parameters are to be determined. Thus such inversions are computationally expensive due to the size of the parameter space (being proportional to the number of grid cells) over which the posterior is to be determined. Therefore, in practice approximations to Bayesian seismic inversion must be considered. A particular, existing approximate workflow is described in this thesis: the so-called two-stage inversion method explicitly splits the inversion problem into elastic and geological inversion stages. These two stages sequentially estimate the elastic parameters given the seismic data, and then the geological parameters given the elastic parameter estimates, respectively. In this thesis a number of methodologies are developed which enhance the accuracy of this approximate workflow. To reduce computational cost, existing elastic inversion methods often incorporate only simplified prior information about the elastic parameters. Thus a method is introduced which transforms such results, obtained using prior information specified using only two-point geostatistics, into new estimates containing sophisticated multi-point geostatistical prior information. The method uses a so-called deep neural network, trained using only synthetic instances (or `examples') of these two estimates, to apply this transformation. The method is shown to improve the resolution and accuracy (by comparison to well measurements) of elastic parameter estimates determined for a real hydrocarbon reservoir. It has been shown previously that so-called mixture density network (MDN) inversion can be used to solve geological inversion analytically (and thus very rapidly and efficiently) but only under certain assumptions about the geological prior distribution. A so-called prior replacement operation is developed here, which can be used to relax these requirements. It permits the efficient MDN method to be incorporated into general stochastic geological inversion methods which are free from the restrictive assumptions. Such methods rely on the use of Markov-chain Monte-Carlo (MCMC) sampling, which estimate the posterior (over the geological parameters) by producing a correlated chain of samples from it. It is shown that this approach can yield biased estimates of the posterior. Thus an alternative method which obtains a set of non-correlated samples from the posterior is developed, avoiding the possibility of bias in the estimate. The new method was tested on a synthetic geological inversion problem; its results compared favourably to those of Gibbs sampling (a MCMC method) on the same problem, which exhibited very significant bias. The geological prior information used in seismic inversion can be derived from real images which bear similarity to the geology anticipated within the target region of the subsurface. Such so-called training images are not always available from which this information (in the form of geostatistics) may be extracted. In this case appropriate training images may be generated by geological experts. However, this process can be costly and difficult. Thus an elicitation method (based on a genetic algorithm) is developed here which obtains the appropriate geostatistics reliably and directly from a geological expert, without the need for training images. 12 experts were asked to use the algorithm (individually) to determine the appropriate geostatistics for a physical (target) geological image. The majority of the experts were able to obtain a set of geostatistics which were consistent with the true (measured) statistics of the target image

All clinically-relevant blood components transmit prion disease following a single blood transfusion: a sheep model of vCJD

Variant CJD (vCJD) is an incurable, infectious human disease, likely arising from the consumption of BSE-contaminated meat products. Whilst the epidemic appears to be waning, there is much concern that vCJD infection may be perpetuated in humans by the transfusion of contaminated blood products. Since 2004, several cases of transfusion-associated vCJD transmission have been reported and linked to blood collected from pre-clinically affected donors. Using an animal model in which the disease manifested resembles that of humans affected with vCJD, we examined which blood components used in human medicine are likely to pose the greatest risk of transmitting vCJD via transfusion. We collected two full units of blood from BSE-infected donor animals during the pre-clinical phase of infection. Using methods employed by transfusion services we prepared red cell concentrates, plasma and platelets units (including leucoreduced equivalents). Following transfusion, we showed that all components contain sufficient levels of infectivity to cause disease following only a single transfusion and also that leucoreduction did not prevent disease transmission. These data suggest that all blood components are vectors for prion disease transmission, and highlight the importance of multiple control measures to minimise the risk of human to human transmission of vCJD by blood transfusion