Modelling and in vitro testing of the HIV-1 Nef fitness landscape.

An effective vaccine is urgently required to curb the HIV-1 epidemic. We have previously described an approach to model the fitness landscape of several HIV-1 proteins, and have validated the results against experimental and clinical data. The fitness landscape may be used to identify mutation patterns harmful to virus viability, and consequently inform the design of immunogens that can target such regions for immunological control. Here we apply such an analysis and complementary experiments to HIV-1 Nef, a multifunctional protein which plays a key role in HIV-1 pathogenesis. We measured Nef-driven replication capacities as well as Nef-mediated CD4 and HLA-I down-modulation capacities of thirty-two different Nef mutants, and tested model predictions against these results. Furthermore, we evaluated the models using 448 patient-derived Nef sequences for which several Nef activities were previously measured. Model predictions correlated significantly with Nef-driven replication and CD4 down-modulation capacities, but not HLA-I down-modulation capacities, of the various Nef mutants. Similarly, in our analysis of patient-derived Nef sequences, CD4 down-modulation capacity correlated the most significantly with model predictions, suggesting that of the tested Nef functions, this is the most important in vivo. Overall, our results highlight how the fitness landscape inferred from patient-derived sequences captures, at least in part, the in vivo functional effects of mutations to Nef. However, the correlation between predictions of the fitness landscape and measured parameters of Nef function is not as accurate as the correlation observed in past studies for other proteins. This may be because of the additional complexity associated with inferring the cost of mutations on the diverse functions of Nef

P-67: Dose response antihypertensive efficacy of aliskiren (SPP 100), an orally active renin inhibitor

Aliskiren (SPP 100), an orally active renin inhibitor, has been shown to inhibit the production of angiotensin I and angiotensin II in healthy volunteers. In a pilot study, aliskiren decreased BP in hypertensive patients at daily doses of 75 and 150 mg. In this multi-centre, double-blind, active comparator trial, the dose-dependent effects of aliskiren were evaluated in 226 patients with mild to moderate hypertension. Parallel groups of randomized patients were assessed at the end of a washout period and again after a 4-week treatment period. Treatment consisted of single oral daily doses of aliskiren (37.5, 75, 150 or 300 mg) or of losartan 100 mg once daily. Daytime ambulatory systolic BP was defined as the primary variable of the study. As illustrated in the figure, a clear dose-response curve was observed for the decrease (mean +/- SEM) in daytime ambulatory systolic BP. The mean (SD) change at the end of the 4-week treatment period was -1.3 (9.5) mmHg, -5.5 (10.6) mmHg, -8.5 (10.4) mmHg, -10.5 (10.7) mmHg, and -11.1 (13.4) mmHg for 37.5, 75, 150, and 300 mg aliskiren and 100mg losartan, respectively. Statistically significant lowering occurred with 75, 150 and 300 mg of aliskiren. The daytime ambulatory systolic BP responses to aliskiren doses of 150 and 300 mg were not significantly different from that of 100 mg losartan. Similar results were shown for daytime ambulatory diastolic BP and for night-time ambulatory systolic and diastolic BP. Aliskiren was well tolerated - there was no increase in the number of adverse events with increasing doses of aliskiren, and the safety profile of aliskiren was similar to that of losartan. The results of this dose-ranging study confirm a dose-dependent reduction in BP with aliskiren in mild to moderate hypertension. Additional exploratory studies testing the efficacy and safety of this new renin inhibitor in patients with renal disease and congestive heart failure are currently underwa

On the Gerasimov-Drell-Hearn sum rule for the deuteron

The Gerasimov-Drell-Hearn sum rule is evaluated for the deuteron by explicit integration up to 550 MeV including contributions from the photodisintegration channel and from coherent and incoherent single pion production as well. The photodisintegration channel converges fast enough in this energy range and gives a large negative contribution, essentially from the $^1S_0$ resonant state near threshold. Its absolute value is about the same size as the sum of proton and neutron GDH values. It is only partially cancelled by the single pion production contribution. But the incoherent channel has not reached convergence at 550 MeV.Comment: 6 pages latex including 3 postscript figures, talk at the 15th Int. Conf. on Few-Body Problems in Physics, Groningen, Netherlands, 22-26 July 1997. To be published in Nucl. Phys.

Propagation of vacuum polarized photons in topological black hole spacetimes

The one-loop effective action for QED in curved spacetime contains equivalence principle violating interactions between the electromagnetic field and the spacetime curvature. These interactions lead to the dependence of photon velocity on the motion and polarization directions. In this paper we investigate the gravitational analogue to the electromagnetic birefringence phenomenon in the static and radiating topological black hole backgrounds, respectively. For the static topological black hole spacetimes, the velocity shift of photons is the same as the one in the Reissner-Nordstr\"om black holes. This reflects that the propagation of vacuum polarized photons is not sensitive to the asymptotic behavior and topological structure of spacetimes. For the massless topological black hole and BTZ black hole, the light cone condition keeps unchanged. In the radiating topological black hole backgrounds, the light cone condition is changed even for the radially directed photons. The velocity shifts depend on the topological structures. Due to the null fluid, the velocity shift of photons does no longer vanish at the apparent horizons as well as the event horizons. But the ``polarization sum rule'' is still valid.Comment: 18 pages, Revtex, no figure

The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

Viral immune evasion by sequence variation is a major hindrance to HIV-1 vaccine design. To address this challenge, our group has developed a computational model, rooted in physics, that aims to predict the fitness landscape of HIV-1 proteins in order to design vaccine immunogens that lead to impaired viral fitness, thus blocking viable escape routes. Here, we advance the computational models to address previous limitations, and directly test model predictions against in vitro fitness measurements of HIV-1 strains containing multiple Gag mutations. We incorporated regularization into the model fitting procedure to address finite sampling. Further, we developed a model that accounts for the specific identity of mutant amino acids (Potts model), generalizing our previous approach (Ising model) that is unable to distinguish between different mutant amino acids. Gag mutation combinations (17 pairs, 1 triple and 25 single mutations within these) predicted to be either harmful to HIV-1 viability or fitness-neutral were introduced into HIV-1 NL4-3 by site-directed mutagenesis and replication capacities of these mutants were assayed in vitro. The predicted and measured fitness of the corresponding mutants for the original Ising model (r = −0.74, p = 3.6×10−6) are strongly correlated, and this was further strengthened in the regularized Ising model (r = −0.83, p = 3.7×10−12). Performance of the Potts model (r = −0.73, p = 9.7×10−9) was similar to that of the Ising model, indicating that the binary approximation is sufficient for capturing fitness effects of common mutants at sites of low amino acid diversity. However, we show that the Potts model is expected to improve predictive power for more variable proteins. Overall, our results support the ability of the computational models to robustly predict the relative fitness of mutant viral strains, and indicate the potential value of this approach for understanding viral immune evasion, and harnessing this knowledge for immunogen design

Generalized polarizabilities and the spin-averaged amplitude in virtual Compton scattering off the nucleon

We discuss the low-energy behavior of the spin-averaged amplitude of virtual Compton scattering (VCS) off a nucleon. Based on gauge invariance, Lorentz invariance and the discrete symmetries, it is shown that to first order in the frequency of the final real photon only two generalized polarizabilities appear. Different low-energy expansion schemes are discussed and put into perspective.Comment: 13 pages, 1 postscript figure, Revtex using eps

Randomised evaluation of modified valsalva effectiveness in re-entrant tachycardias (REVERT) study

Introduction: The Valsalva manoeuvre (VM) is a recommended first-line physical treatment for patients with re-entrant supraventricular tachycardia (SVT), but is often ineffective in standard practice. A failed VM is typically followed by treatment with intravenous adenosine, which patients often find unpleasant. VM effectiveness might be improved by a modification to posture which exaggerates the manoeuvre's vagal response and reduces the need for further emergency treatment. Methods and analysis: This is a multicentre randomised controlled clinical trial in 10 UK emergency departments (EDs). It compares a standard VM with a modified VM incorporating leg elevation and a supine posture after a standardised strain in stable adult patients presenting to the ED with SVT. The primary outcome measure is return to sinus rhythm on a 12-lead ECG. Secondary outcome measures include the need for treatment with adenosine or other antiarrhythmic treatments and the time patients spend in the ED. We plan to recruit approximately 372 patients, with 80% power to demonstrate an absolute improvement in cardioversion rate of 12%. An improvement of this magnitude through the use of a modified VM would be of significant benefit to patients and healthcare providers, and justify a change to standard practice. Ethics and dissemination: The study has been approved by the South West - Exeter Research Ethics Committee (REC reference 12/SW/0281). The trial will be published in an international peer reviewed journal. Study findings will be sent to the European and International resuscitation councils to inform future revisions of arrhythmia management guidelines. Results: The trial will also be disseminated at international conferences and to patients through the Arrhythmia Alliance, a patient support charity. Registration: The study is registered with Current Controlled Trials (ISRCTN67937027) and has been adopted by the National Institute for Health Research (NIHR) Clinical Research Network

Postural modification to the standard Valsalva manoeuvre for emergency treatment of supraventricular tachycardias (REVERT): A randomised controlled trial

© 2015 Appelboam et al. Open Access article distributed under the terms of CC BY-ND-NC. Background The Valsalva manoeuvre is an internationally recommended treatment for supraventricular tachycardia, but cardioversion is rare in practice (5-20%), necessitating the use of other treatments including adenosine, which patients often find unpleasant. We assessed whether a postural modification to the Valsalva manoeuvre could improve its effectiveness. Methods We did a randomised controlled, parallel-group trial at emergency departments in England. We randomly allocated adults presenting with supraventricular tachycardia (excluding atrial fibrillation and flutter) in a 1:1 ratio to undergo a modified Valsalva manoeuvre (done semi-recumbent with supine repositioning and passive leg raise immediately after the Valsalva strain), or a standard semi-recumbent Valsalva manoeuvre. A 40 mm Hg pressure, 15 s standardised strain was used in both groups. Randomisation, stratified by centre, was done centrally and independently, with allocation with serially numbered, opaque, sealed, tamper-evident envelopes. Patients and treating clinicians were not masked to allocation. The primary outcome was return to sinus rhythm at 1 min after intervention, determined by the treating clinician and electrocardiogram and confirmed by an investigator masked to treatment allocation. This study is registered with Current Controlled Trials (ISRCTN67937027). Findings We enrolled 433 participants between Jan 11, 2013, and Dec 29, 2014. Excluding second attendance by five participants, 214 participants in each group were included in the intention-to-treat analysis. 37 (17%) of 214 participants assigned to standard Valsalva manoeuvre achieved sinus rhythm compared with 93 (43%) of 214 in the modified Valsalva manoeuvre group (adjusted odds ratio 3·7 (95% CI 2·3-5·8;