A bioinformatic approach to identify new potential resistance relevant amino acid substitutions (AAS) in HIV-1 protease (H1P)

Background: Predicting potential drug resistance mutations are important when evaluating protein-drug interactions of potential new antiviral drugs. Here we used evolutionary data from the Retroviral Aspartyl Protease (RVP) family (PF00077, 54135 sequences) to estimate plausible PI resistant-associated AAS within the H1P. Methods: Using a Hidden Markov Model (HMM) of the RVP family probabilities were extracted for each possible AAS limited to the 38 positions reported in the IAS drug resistance listing for H1P (December 2008 version). The HMM is a dynamic Bayesian network, modeling sequences of amino acids. The HMM is based on curated and representative sequences from the RVP family. Results: Theoretically 760 AAS (20 × 38) are possible for the 38 evaluated positions within the H1P. Of these, the RVP-HMM detected a total of 229 AAS (30.1%) with a probability above 1/20 (0.05). Of the 229 AAS, 51 (70%) were among the 73 AAS included in the IAS listing as PI-resistant mutations, leaving 178 AAS with P > 0.05 as evolutionary plausible. Conclusion: Based on exploration of the RVP family by HMM, 70% of the established PI-resistant associated AAS could be predicted to occur. Additional 178 AAS was identified as evolutionary plausible and potentially could allow for drug-resistance. In conclusion, we provide a probability landscape of plausible/unfavorable AAS based on inherited structure through evolution and genetic distance, which could prove useful for future drug design

The clinical utility of FDG PET/CT among solid organ transplant recipients suspected of malignancy or infection

PURPOSE: Solid organ transplant (SOT) recipients are at high risk of developing infections and malignancies. (18)F-FDG PET/CT may enable timely detection of these diseases and help to ensure early intervention. We aimed to describe the clinical utility of FDG PET/CT in consecutive, diagnostic unresolved SOT recipients transplanted from January 2004 to May 2015. METHODS: Recipients with a post-transplant FDG PET/CT performed as part of diagnostic work-up were included. Detailed chart reviews were done to extract relevant clinical information and determine the final diagnosis related to the FDG PET/CT. Based on á priori defined criteria and the final diagnosis, results from each scan were classified as true or false, and diagnostic values determined. RESULTS: Among the 1,814 recipients in the cohort, 145 had an FDG PET/CT performed; 122 under the indication of diagnostically unresolved symptoms with a suspicion of malignancy or infection. The remaining (N = 23) had an FDG PET/CT to follow-up on a known disease or to stage a known malignancy. The 122 recipients underwent a total of 133 FDG PET/CT scans performed for a suspected malignancy (66 %) or an infection (34 %). Sensitivity, specificity, and positive and negative predictive values of the FDG PET/CT in diagnosing these conditions were 97, 84, 87, and 96 %, respectively. CONCLUSION: FDG PET/CT is an accurate diagnostic tool for the work-up of diagnostic unresolved SOT recipients suspected of malignancy or infection. The high sensitivity and NPV underlines the potential usefulness of PET/CT for excluding malignancy or focal infections in this often complex clinical situation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00259-016-3564-5) contains supplementary material, which is available to authorized users

Public administration in an age of austerity:the future of the discipline

Reflecting changes in the nature of governance, some have questioned whether Public Administration is now an historical anachronism. While a legitimate debate exists between sceptics and optimists, this special issue demonstrates grounds for optimism by indicating the continuing diversity and adaptability of the field of Public Administration. In this introduction, we first sketch the variety of intellectual traditions which comprise the field of modern Public Administration. We then consider institutional challenges facing the subject given considerable pressures towards disciplinary fragmentation, and ideological challenges arising from a new distrust of public provision in the UK. Despite these challenges, Public Administration continues to provide a framework to analyse the practice of government and governance, governing institutions and traditions, and their wider sociological context. It can also directly inform policy reform - even if this endeavour can have its own pitfalls and pratfalls for the 'engaged' academic. We further suggest that, rather than lacking theoretical rigour, new approaches are developing that recognise the structural and political nature of the determinants of public administration. Finally, we highlight the richness of modern comparative work in Public Administration. Researchers can usefully look beyond the Atlantic relationship for theoretical enhancement and also consider more seriously the recursive and complex nature of international pressures on public administration

Seasonality of halogen deposition in polar snow and ice

Abstract. The atmospheric chemistry of iodine and bromine in Polar regions is of interest due to the key role of halogens in many atmospheric processes, particularly tropospheric ozone destruction. Bromine is emitted from the open ocean but is enriched above first-year sea ice during springtime bromine explosion events, whereas iodine emission is attributed to biological communities in the open ocean and hosted by sea ice. It has been previously demonstrated that bromine and iodine are present in Antarctic ice over glacial–interglacial cycles. Here we investigate seasonal variability of bromine and iodine in polar snow and ice, to evaluate their emission, transport and deposition in Antarctica and the Arctic and better understand potential links to sea ice. We find that bromine and iodine concentrations and Br enrichment (relative to sea salt content) in polar ice do vary seasonally in Arctic snow and Antarctic ice. Although seasonal variability in halogen emission sources is recorded by satellite-based observations of tropospheric halogen concentrations, seasonal patterns observed in snowpack are likely also influenced by photolysis-driven processes. Peaks of bromine concentration and Br enrichment in Arctic snow and Antarctic ice occur in spring and summer, when sunlight is present. A secondary bromine peak, observed at the end of summer, is attributed to bromine deposition at the end of the polar day. Iodine concentrations are largest in winter Antarctic ice strata, contrary to contemporary observations of summer maxima in iodine emissions. These findings support previous observations of iodine peaks in winter snow strata attributed to the absence of sunlight-driven photolytic re-mobilisation of iodine from surface snow. Further investigation is required to confirm these proposed mechanisms explaining observations of halogens in polar snow and ice, and to evaluate the extent to which halogens may be applied as sea ice proxies

A multi-disciplinary perspective on emergent and future innovations in peer review [version 1; peer review: 2 approved with reservations]

Peer review of research articles is a core part of our scholarly communication system. In spite of its importance, the status and purpose of peer review is often contested. What is its role in our modern digital research and communications infrastructure? Does it perform to the high standards with which it is generally regarded? Studies of peer review have shown that it is prone to bias and abuse in numerous dimensions, frequently unreliable, and can fail to detect even fraudulent research. With the advent of Web technologies, we are now witnessing a phase of innovation and experimentation in our approaches to peer review. These developments prompted us to examine emerging models of peer review from a range of disciplines and venues, and to ask how they might address some of the issues with our current systems of peer review. We examine the functionality of a range of social Web platforms, and compare these with the traits underlying a viable peer review system: quality control, quantified performance metrics as engagement incentives, and certification and reputation. Ideally, any new systems will demonstrate that they out-perform current models while avoiding as many of the biases of existing systems as possible. We conclude that there is considerable scope for new peer review initiatives to be developed, each with their own potential issues and advantages. We also propose a novel hybrid platform model that, at least partially, resolves many of the technical and social issues associated with peer review, and can potentially disrupt the entire scholarly communication system. Success for any such development relies on reaching a critical threshold of research community engagement with both the process and the platform, and therefore cannot be achieved without a significant change of incentives in research environments